🧬 PART TWO PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY

5 AUTOSOMAL RECIPROCAL TRANSLOCATIONS RECIPROCAL TRANSLOCATIONS ARE common, and about one or two people per 1,000 are carriers. Every counselor can expect to see translocation families. The usual form is the simple, or two-way, reciprocal translocation: Only two chromosomes, usually autosomes, are involved, with one breakpoint in each. It is this category we consider in this chapter. The special cases of translocations involving sex chromosomes, and of complex translocations, are dealt with in separate chapters. The translocation heterozygote (carrier) may have a risk to have a child who would be intellectually and physically abnormal due to a “segmental aneusomy”: that is, segments that are not euploid. Typically, the imbalance is due to a segment of one of the participating chromosomes being duplicated and a segment of the other chromosome being deleted. This confers a partial trisomy and a concomitant partial monosomy. A few translocations are associated with a high risk, as much as 20% or, very rarely, up to 50% or more, to have an abnormal child. Many translocations imply an intermediate level of risk in the region of 5%–10%. Some carriers have a low risk, 1% or less; but the woman who is a carrier, or the partner of a male carrier, may have a high miscarriage rate. Others imply, apparently, no risk to have an abnormal child, but the likelihood of miscarriage is high. Yet others, discovered fortuitously, seem to be of no reproductive significance, with carriers having no difficulties in conceiving or carrying pregnancies and having normal children. The counselor needs to distinguish these different functional categories of translocation, in order to provide each family with tailor-made advice. BIOLOGY Simple reciprocal translocations (rcp) arise when a two-way exchange of material takes place between two chromosomes. This event might, for example, occur in one gamete of a 46,N parent, who then has a child who carries this de novo translocation. Or, the translocation could have been familial, transmitted through generations, and sometimes of centuries-long duration. For example, Koskinen et al. (1993) trace a t(12;21) in western Finland back to a couple born in 1752. The process of formation follows the physical apposition of a segment of each chromosome, which may have been promoted by the presence in each segment of a similar DNA sequence. A break occurs in one arm of each chromosome, and the portions of chromosome material distal to the breakpoints switch positions. The distal portions exchanged are the translocated segments; the rest of the chromosome (which includes the centromere) is the centric segment. The rearranged chromosome is called a derivative (der) chromosome. It is identified according to which centromere it possesses, as in the der(5) and der(10) depicted in Figure 5–1. When no loss or perturbation of genetic 90  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY material occurs—in other words, the translocation is balanced—the phenotype of the heterozygote is normal, other things being equal. When one of the translocated segments is very small and comprises only the telomeric cap of a chromosome arm—and thus we suppose contains no genes—this is regarded as being, effectively, a single-segment exchange. The t(1;4) translocation shown in Figure 5–1, involving a substantial piece of chromosome 4 long arm exchanging positions with the terminal tip of a chromosome 1 long arm, exemplifies single-segment exchange. On the other hand, when both translocated segments are of substantial size, we refer to this as a double-segment1 exchange. The translocation shown in Figure 5–1 between a chromosome 5 and a chromosome 10, with breakpoints in about the mid–short arm of chromosome 5 and a little below the middle of the chromosome 10 long arm, is an example of a double-segment exchange. The translocation involving breakpoints right at, or actually within, the centromere, with Figure 5–1.  The Reciprocal Translocation. Reciprocal translocations demonstrating (above) double-segment and (below) single-segment exchange. The translocations are t(5;10)(p13;q23.3) and t(1;4)(q44;q31.3). (Cases of MA Leversha and NA Adams.) 1 There is scope for confusion in the use of these terms: Of course, all reciprocal exchanges, by definition, involve two segments. A true single-segment exchange—that is, a one-way translocation—is generally considered not to exist, in that a segment of chromosome cannot attach to an intact telomere, although there are rare exceptions to this rule. The distinction begins to break down when a translocated segment is very small (subtelomeric) but could still contain genes. Be this as it may, the terms double- and single-segment exchange, used knowledgeably, serve a practical purpose. Autosomal Reciprocal Translocations  91 an exchange of entire arms, is a particular and rare type of double-segment exchange known as a whole-arm translocation. Details of Meiotic Behavior At meiosis I in the primary gametocyte, the oöcyte or spermatocyte, the four chromosomes with segments in common come together as a foursome: a quadrivalent. In order to match homologous segments, the four chromosomes must form a cross-shaped configuration. This is most clearly seen when the chromosomes are at the pachytene stage (Figure 5–2). As meiosis progresses, the four components of the quadrivalent release their points of attachment except at the tips of the chromosome arms, and they form a ring. If attachment fails, or if one of the terminal pairings releases, a chain forms instead of a ring (Oliver-Bonet et al. 2004). With breakdown of the nuclear envelope, spindles forming at each pole of the cell can track to the equator and seek attachment to the centromeres. A cellular motor comes into play, and each chromosome travels to one or other pole. According to which spindle attaches to which centromere—and this may in part be influenced by the configuration of the ring or chain—the distribution of the four chromosomes to the two daughter gametocytes is determined. Which chromosomes go to which pole is referred to as segregation. The expression 2:2 segregation describes two chromosomes going to one daughter cell, and two to the other. In 3:1 segregation, three chromosomes go to one daughter cell, and one to the other. In 4:0 segregation, all four chromosomes go to one daughter cell, and none to the other. Modes of Segregation Within these three broad categories we can list the particular modes of segregation, according to which chromosomes actually go where. Referring to the four chromosomes of the quadrivalent as A, B, A′, and B′ (Figure 5–2), the modes of segregation are summarized as follows (Table 5–1): Figure 5–2.  Meiotic Behavior of the Reciprocal Translocation. Pachytene configuration, simplified outline. The two normal (A, B) and the two translocation (A′, B′) homologs align corresponding segments of chromatin during meiosis I.

92  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 5–3 depicts five of the possible pairs of daughter gametocytes. Other things being equal, the chromosomal combination is conserved through meiosis II, and the mature gamete forms. From one primary gametocyte, one ovum and its polar bodies, or four spermatozoa, are thus produced. Gametes from alternate segregation are normal or balanced, and the conceptions from them likewise normal or balanced, other things being equal. Conceptions from adjacent-1 gametes have a partial trisomy (duplication) of one translocated segment and partial monosomy (deletion) of the other. Adjacent-2 conceptions have a duplication of one centric segment and deletion of the other. Tertiary aneuploidies have duplication, or deletion, with respect to the combined chromosomal content of one of the derivative chromosomes. Interchange aneuploidies have a full autosomal trisomy or a full monosomy. In 4:0 segregation, there is a double trisomy or a double monosomy. Some of the gametes with these unbalanced combinations may be “viable” in the sense of being “capable of giving rise to a conceptus, which would proceed through to the birth of a child.” Mostly, in fact, they are not. Recombination at meiosis I, and asymmetric segregation at meiosis II, can complicate the story, although not often does this have a practical implication. If recombination occurs in the interstitial segment (between the centromere and the breakpoint), further unbalanced combinations are generated, most of which would not be remotely viable. This phenomenon may possibly have some relevance in preimplantation genetic testing, because testing is done at a stage where there has been little opportunity for selective pressure to have had an effect. Scriven et al. (1998) list various of these recombination possibilities, and Van Hummelen et al. (1997) diagram the process with respect to a particular translocation on which they had undertaken sperm studies (and also illustrate the interesting point that a normal/balanced gamete can be restored following recombination in adjacent-1 segregation). The most telling evidence that recombination can happen comes from the observation of a meiosis I chromosome having one normal and one derivative chromatid, and polar body analysis has enabled such an observation to be made (Munné et al. 1998a). At meiosis II, asymmetric segregation may lead to two copies of a derivative chromosome being transmitted, as noted below in the section “Meiosis II Nondisjunction.” Table 5–1.  Modes of Segregation of Reciprocal Translocations ONE DAUGHTER GAMETOCYTE WITH: OTHER DAUGHTER GAMETOCYTE WITH: SEGREGATION MODE 2:2 Segregations A and B A′ and B′ Alternate segregation A and B′ B and A′ Adjacent-1 segregation A and A′ B and B′ Adjacent-2 segregation 3:1 Segregations A B and A′ B′ 3:1 segregation with tertiary trisomy or monosomy A B and B′ A′ A′ B′ and A B 3:1 segregation with interchange trisomy or monosomy A′ B′ and B A 4:0 Segregation A B A′ B′ None 4:0 segregation with double trisomy or monosomy Autosomal Reciprocal Translocations  93 ALTERNATE SEGREGATION In 2:2 alternate segregation, looking at each centromere in turn around the quadrivalent, one centromere goes to one pole, and the next centromere goes to the other pole. In other words, each centromere goes “alternately”2 to one or the other pole. Thus, the two daughter cells come to contain, respectively, the two normal homologs in one, and the Figure 5–3.  Segregation at Meiosis. The categories of 2:2 and 3:1 segregation that may occur in gametogenesis in the translocation heterozygote. In the four 3:1 categories, only one of the two possible combinations in each category is depicted (both of each are shown in Fig. 5–4). 2 Not “alternatively,” as some publications erroneously use. 94  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY two derivative chromosomes in the other. Note that alternate segregation is essentially the only mode that leads to gametes with a complete genetic complement—one with a normal karyotype, the other with the reciprocal translocation in the balanced state. All other modes can be classified as malsegregation. ADJACENT SEGREGATION In 2:2 adjacent segregation, adjacent centromeres travel together (“adjacent” in the sense of centromeres being next to each other in their positions around the quadrivalent). There are two categories. In adjacent-1 segregation, adjacent chromosomes with unalike (nonhomologous) centromeres travel to the same daughter cell (an aide-mémoire: in adjacent-1, the daughter cells get one of each centromere). Overall, adjacent-1 is the most frequently seen mode of malsegregation in the children of translocation heterozygotes. In adjacent-2 segregation, which is rather uncommonly seen, adjacent chromosomes with like (homologous) centromeres go to the same daughter cell (another aide-mémoire: in adjacent-2, the two homologous centromeres go together). 3:1 SEGREGATION This is also referred to as 3:1 nondisjunction. Gametes with 24 chromosomes and 22 chromosomes are formed, and the conceptuses therefore have 47 or 45 chromosomes. Almost always in autosomal translocations, the 47-chromosome conceptus is the only viable one. Two categories exist: Either the two normal chromosomes of the quadrivalent plus one of the translocation chromosomes go together to one daughter cell (tertiary trisomy) or, rarely, the two translocation chromosomes and one of the normal chromosomes segregate together (interchange trisomy). Tertiary monosomy, with a 45-chromosome conceptus, is very rare. Interchange monosomy is never seen, except at preimplantation genetic testing. 4:0 SEGREGATION In autosomal translocations, 4:0 segregation has been regarded as being of academic interest only. But it may have some practical relevance in preimplantation genetic testing. Segregant Outcomes In theory, 16 possible chromosomal combinations could be produced in the gametes of the autosomal translocation heterozygote. In terms of a consideration of the risk for a liveborn child, four of these we can, for the most part, ignore (3:1 interchange monosomies and 4:0 segregants) because they are never viable. The two balanced gametes (2:2 alternate segregants) are always viable, other things being equal. Of the remaining 10 possibilities, it is common for none to be viable, with non-implantation or spontaneous abortion the inevitable outcome. If, however, a translocation heterozygote does have the potential for viable imbalance in an offspring, it is most likely that there will be only one such combination (this was the case in 99% and 100% of translocations, respectively, in the considerable experience of two groups; see Scriven et al. 1998). Usually, this sole survivable imbalance will be one that endows a partial trisomy. Infrequently two, and very rarely more than two, of the imbalances may be viable. Figure 5–4 depicts the various combinations that may be considered (using the previously discussed t(1;4) translocation as an example). In a review Autosomal Reciprocal Translocations  95 Figure 5–4.  The Range of Segregant Gametes. The full range of segregant gametes that may be produced by the translocation heterozygote, using the t(1;4) depicted in Figure 5–1 as an example. Chromosome 1 chromatin is shown open; chromosome 4 chromatin is cross-hatched.

96  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY of 1,159 translocation families, Cohen et al. (1994) found the proportions of chromosomally unbalanced offspring as follows: 71% adjacent-1, 4% adjacent-2, 22% tertiary trisomy/monosomy, and 2.5% interchange trisomy. Gametes.  It is, apparently, the norm for the heterozygote to produce gametes in which many of the possible chromosomal combinations occur, although the proportions may differ, and very substantially so, for different translocations. Oöcyte and sperm karyotyping results from nine women and 45 men, heterozygous for a translocation, are summarized in Figure 5–5. Overall, between the sexes, around a half of sperm and two-thirds of ova from translocation carriers attending a fertility clinic are chromosomally unbalanced. The great majority, if not all, of these studied individuals would have presented to the clinic because of reproductive difficulty, and so these data are rather likely to be biased in the direction of unbalanced forms compared to the whole population of translocation heterozygotes. Those with more favorable fractions might never have needed clinic help. On average, alternate and adjacent-1 segregants are the predominant types in spermatogenesis, occurring in fairly similar fractions (Figure 5–5; 44% and 31%, respectively). Adjacent-2 at 13% and 3:1 at 11% are less frequently seen,3 and barely any 4:0 segregant sperm. The spread of segregant types seems to be rather similar with men having the same translocation, such as the t(15;17)(q21;q25) seen in related individuals in Benet et al. (2005). Between different translocations, however, considerable variation occurs. Some male heterozygotes in Benet et al. had no 3:1 segregants, and one had 47%; for adjacent-2, the range is 0%–40%. In male carriers of various translocations, the widely varying proportions of gametes that have a balanced complement is seen in the material presented in Del Llano et al. (2023), as depicted in Figure 5–6. Figure 5–5.  Chromosomal Segregations in Oöcytes and Spermatocytes of Translocation Carriers. Notes: The tested populations were presumably biased toward less fortunate reproductive outcomes. The sperm data are from Benet et al. (2005); the oöcyte data (some inferentially from polar body analysis), which naturally are based on much smaller numbers (2–11 observations per woman), are from Munné et al. (1998a, b), Conn et al. (1999), Escudero et al. (2000), Durban et al. (2001). 3 The differences from the fractions in viable offspring, noted above, presumably reflects a differential survival in utero of unbalanced forms. Autosomal Reciprocal Translocations  97 The fractions in ova are derived from very few numbers, and alternate segregations per woman range from 0% to 100%; thus, the reader should not place too great a weight on the average fraction of 30% normal in Figure 5–5. The higher fraction of 3:1 segregations in ova (27%) might be, in part, an age-related effect. Conceptions. The range of segregations in day-3 embryos from balanced translocation carriers in one substantial study is shown in Figure 5–7. It would be expected that the distribution of normal and abnormal conceptions would largely follow the distributions of karyotypes in the gametes, if the fertilizing/fertilizable capacity of partially aneuploid gametes is not compromised; and indeed, this appears substantially to be the case. There is a fair degree of overlap in the data from gametes and day-3 embryos, comparing Figures 5–5 and 5–7. For female translocation heterozygotes, somewhat of an Figure 5–6.  The Range of Sperm Segregants from Translocation Carriers. Box and whisker plot showing proportions of chromosomally balanced sperm from 318 balanced translocation carriers; each dot represents the average finding from one man. Note that most observations lie within mid-range (the box), averaging 44%. Thus, most carrier men in this population produce a little under half of sperm with a balanced complement; but outliers extend from only 19%, to as many as 88% balanced forms. Source: From E Del Llano et al., Sperm meiotic segregation analysis of reciprocal translocations carriers: We have bigger FISH to fry, Int J Mol Sci 24:3664, 2023. Courtesy G Martinez, and with the permission of MDPI. Figure 5–7.  Chromosomal Segregations in Day-3 Embryos of Translocation Carriers. Notes: The segregant patterns differ according to the gender of the carrier parent. Source: From data in C Mackie Ogilvie and PN Scriven, Meiotic outcomes in reciprocal translocation carriers ascertained in 3-day human embryos, Eur J Hum Genet 10:801–806, 2002.

98  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY increase is seen in the average normal fraction for embryos (45%) versus gametes (30%), although the oöcyte numbers upon which the 30% figure is based are very small, and this difference should not be unduly weighted. For male translocation heterozygotes, for whom the numbers of gamete observations are substantial, the average normal fraction of embryos (41%) is very similar to that of gametes (44%). Thus, we might infer that balanced and unbalanced gametes have very similar fertilizing/fertilizable capacities and that little selective pressure applies, at least in the first three days of development of the partially aneuploid embryo.4 There appears to be little difference according to the gender of the translocation parent (Figure 5–8). However, a selective pressure apparently does apply in the short period from the day-3 embryo to the day-5 blastocyst, in particular with respect to 3:1 malsegregants and, in consequence, the relative fractions of alternate and adjacent segregants increase from day 3 to day 5 (Figure 5–9). Acrocentric Chromosomes. Acrocentric chromosomes participating in a reciprocal translocation might be expected to hinder normal segregation, due to the very small lengths of their short arms and thus a marked asymmetry of the quadrivalent, and more so in the direction of 3:1 malsegregation; and indeed, this is what is observed. In Verdoni et al. (2021), among 196 autosomal translocation couples, one-third involved an acrocentric, but fully half of the instances of 3:1 malsegregation were seen in these cases. Figure 5–10 shows data from Xie et al. (2022), who analyzed over 10,000 blastocysts from 2,253 translocation couples, teasing out the influence of gender and whether or not the translocation included an acrocentric chromosome. The tendency to 3:1 malsegregation in the female carrier, and more particularly so with an acrocentric-related translocation, is well illustrated. The early (day 3 to day 5) lethality of many 3:1 conceptions is noted in Figure 5–9. 4 And yet, not all studies support such a conclusion. In a study based upon 10 male rcp heterozygotes, Haapaniemi Kouru et al. (2017) made the curious observation that the proportions of unbalanced forms seen at the day-3 embryo stage (52%) were very substantially greater than the fractions at sperm analysis (21%) might have suggested. The authors conclude that sperm FISH is not a reliable indicator of PGT outcome. Figure 5–8.  Chromosomal Segregations in Day-3 Embryos of Translocation Carriers, According to the Parental Gender. Source: From J Wang et al., Analysis of meiotic segregation modes in biopsied blastocysts from preimplantation genetic testing cycles of reciprocal translocations, Mol Cytogenet 12:11, 2019, with the permission of Springer Nature. Autosomal Reciprocal Translocations  99 Figure 5–9.  Comparing Chromosomal Segregations in Day-3 and Day 5 Embryos of Translocation Carriers. Notes: Segregant categories from rcp carriers, comparing observations at day 3 embryos cf. day 5 blastocysts. The substantial fall-off of 3:1 from day 3 to day 5 leads to higher relative fractions of alternate and adjacent conceptions remaining. The difference in the Day 3 fractions cf. Figure 5-8 lies in the proportions, in the two studies, of 3:1 cases. Source: From ZN Tonyan et al., Assessment of quadrivalent characteristics influencing chromosome segregation by analyzing human preimplantation embryos from reciprocal translocation carriers, Comp Cytogenet 18:1–13, 2024. Courtesy ZN Tonyan, and with the permission of Pensoft. Figure 5–10.  The Influence of Parental Gender on Translocation Segregation, as Observed at the Blastocyst Stage. Notes: The fractions of segregation types are shown according to the gender of the translocation carrier parent, and according to the participation, or not, of an acrocentric chromosome in the rearrangement. Note that alternate segregation is slightly favored in the absence of an acrocentric, while 3:1 is markedly favored when an acrocentric is present. F = female, M = male, y axis is % of all embryos in this series. Compare the data in Figure 5–7, based upon day-3 embryos, at which earlier stage the parental gender has apparently had little influence upon 3:1 malsegregation. Source: Adapted from P Xie et al., Risk factors affecting alternate segregation in blastocysts from preimplantation genetic testing cycles of autosomal reciprocal translocations, Front Genet 13:880208, 2022. Courtesy G Lin, and with the permission of Frontiers in Genetics.

100  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Viability In Utero. Further along in pregnancy, most unbalanced combinations would produce such enormous genetic imbalance that the conceptus would be lost very early in pregnancy (occult abortion), or even fail to implant. Moderate imbalances could, following implantation, proceed to the stage of recognizable miscarriage or to later fetal death in utero. Only those conceptuses with lesser imbalances might eventually result in the birth of an abnormal child. Viability is much more likely in the case of effective single-segment imbalance, with only one segment of substantial size, as discussed above. This is of particular relevance in adjacent-1 segregation. Consider, for example, gamete (3) in Figure 5–4. The material missing from the telomeric tip of chromosome 1 long arm—the telomeric cap—is so small that its loss is, as far as we can tell, of nil or insignificant phenotypic effect. For practical purposes, we can ignore this partial monosomy. Thus, the significant imbalance reduces to a partial 4q trisomy (dup 4q31.3qter). This, as it happens, is well recognized as being a viable complement (and it is the imbalance in the children whose photograph appears in the frontispiece). On the other hand, in the double-segment exchange, the imbalance contributed by each segment must be taken into account. Thus, adjacent-1 gametes have both a partial trisomy and a partial monosomy to a significant degree and would produce a “phenotypic hybrid.” Very frequently, such a combination is nonviable. Predicting Segregant Outcomes How can we determine, for the individual translocation carrier, which segregant outcomes, if any, might lead to the birth of an abnormal child? What might be the relative roles of an inherent tendency for a particular type of segregation to occur, and of in utero selection against unbalanced forms? A useful approach is to imagine how the chromosomes come to be distributed during meiosis. Following Jalbert et al. (1980, 1988) we may draw, roughly to scale, a diagram of the presumed pachytene configuration of the quadrivalent, and then deduce which modes of segregation are likely to lead to the formation of gametes, which could then produce a viable conceptus. The following, and with reference to Figure 5–11, are the ground rules: 1. We assume that alternate segregation is (a) frequent and (b) associated with phenotypic normality. 2. The least imbalanced, least monosomic of the imbalanced gametes is the one most likely to produce a viable conceptus. 3. If the translocated segments are small in genetic content, adjacent-1 is the most likely type of malsegregation to be capable of giving rise to viable abnormal offspring (Figure 5–11a). 4. If the centric segments are small in content, adjacent-2 is the most likely segregation to give a viable abnormal outcome (Figure 5–11b). 5. If one of the whole chromosomes of the quadrivalent is small in content, typically a small derivative chromosome, 3:1 disjunction is the most likely (Figure 5–11c). 6. If the quadrivalent has characteristics of both Rules 3 and 5, or of Rules 4 and 5, then both adjacent and 3:1 segregations may give rise to viable offspring. 7. If the translocated and centric segments both have large content, no mode of segregation could produce an unbalanced gamete that would lead to a viable offspring (Figure 5–11d). Autosomal Reciprocal Translocations  101 8. If the translocated segments are both very small (subtelomeric), the chromosomes may not necessarily form a quadrivalent, and the pairs of homologs might simply join up as bivalents as if they were normal, each pair then segregating independently. Some examples to illustrate these points follow.5 ADJACENT-1 SEGREGATION, SINGLE-SEGMENT EXCHANGE Many translocations involve an effectively single-segment exchange, with the “single” translocated segment comprising a fairly small amount of chromatin (1%–2% of the haploid autosomal length, or HAL). This is the classical scenario for adjacent-1 segregation to occur, and to produce a phenotype capable of post-natal survival. The family with the t(1;4) in Figure 5–1, whose children with partial 4q trisomy are shown in the frontispiece and as discussed above, provides an example. Consider now the family whose pedigree is depicted in Figure 5–12a, in which the individuals shown as heterozygotes have the balanced translocation t(3;11)(p26;q21). A segment of chromatin consisting of almost half of the long arm of chromosome 11, and comprising 1.4% of the HAL, is translocated to the tip of chromosome 3 short arm 5 The reader wishing to study further worked examples is referred to Midro et al. (1992), who analyze in some detail a series of translocations of differing risk potentials. Figure 5–11.  Predicting Segregant Outcomes. Prediction of likely viable segregant outcomes by pachytene diagram drawing and assessment of the configuration of the quadrivalent. 102  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 5–12.  Adjacent-1 segregation. (a) Pedigree of a family in which there segregates a t(3;11)(p26;q21) having the characteristics associated with adjacent-1 malsegregation. Two independently ascertained probands have a partial 11q trisomy, and a deceased relative, who died at age 18 years in an institution for the retarded, had a similar appearance from photographs, and so very probably had the same karyotype. Filled symbol, unbalanced karyotype; half-filled symbol, balanced carrier; N in symbol = 46,N; small diamond, prenatal diagnosis; arrow, proband. (b) Partial karyotype of a translocation heterozygote (above), showing the 3;11 translocation, and a child with the unbalanced complement (below). (Case of AJ Watt.) (c) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 3 chromatin, open; chromosome 11 chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in adjacent-1 segregation; heavy arrows show the combination observed in this family.

Autosomal Reciprocal Translocations  103 (Figure 5–12b). The telomeric tip of chromosome 3 short arm, which we imagine to comprise little or no phenotypically important genetic material, has moved reciprocally across to chromosome 11. The presumed pachytene configuration during gametogenesis in the heterozygote would be as drawn in Figure 5–12c. The adjacent-1 segregant gamete with der(3) plus normal 11 (heavy arrows) produces a conceptus that has a partial 11q trisomy, since the der(3) carries the segment 11q21qter. The loss of the 3p telomeric tip in this der(3) we suppose to have no effect. Two, probably three children in the family had been born with this karyotype. No individuals are known having the other adjacent-1 combination (Figure 5–12c, light arrows), that is, the 46,+der(11) karyotype, which would endow a partial 11q monosomy. Consulting Schinzel (2001), viability for the segment 11q21qter in monosomic state is recorded in only two cases. We assume, therefore, that it has a very high lethality in utero. The scenario of a single survivable imbalanced form due to a partial trisomy from adjacent-1 segregation in a “single-segment” translocation, as in this t(3;11) example, is, as mentioned above, much the most commonly encountered circumstance in translocation families at risk for having an abnormal child. Infrequently, both the partial trisomic and the partial monosomic forms are observed in families segregating a single-segment rcp. A good example of this is given by distal 4p translocations: Both deletion and duplication for this segment are well recognized as capable of going through to live birth. Consider the translocation t(4;12)(p14;p13) described in a family study in Mortimer et al. (1980). The breakpoints of the translocation are in distal 4p and at the very tip of 12p (12pter). A number of family members over three or more generations were balanced carriers, and abnormal children had been born with typical Wolf-Hirschhorn syndrome (all dying in infancy), while others presented the syndrome of partial 4p trisomy (all surviving at least well into childhood). The presumed pachytene configuration would be as drawn in Figure 5–11a (imagining the chromosome 4 chromatin open and chromosome 12 chromatin cross-hatched). With such short translocated segments (and very long centric segments), adjacent-1 segregation is the only possibility for viable imbalance. If we ignore the tiny contribution of a duplication or deletion for telomeric 12p—in other words, if we interpret this as an effective single-segment imbalance—the situation reduces to the two possible adjacent-1 outcomes being a partial 4p trisomy and a partial 4p monosomy. Both of these are recognized entities, as noted above, and apparently both have substantial viability in utero. The abnormal karyotypes would be written 46,der(12)t(4;12)(p14;p13) and 46,der(4) t(4;12)(p14;p13). If the “other segment” can actually be proven not to contain any coding genes, the case for considering the translocation as a single-segment entity is particularly valid, with the resulting imbalances being demonstrably “pure.” Martínez-Juárez et al. (2014) allowed such a conclusion to be drawn in the case of two children born from a translocation carrier mother, 46,XX,t(2;12)(p24.2;q24.31). The 12q breakpoint was at chr12:132,960,869, and the 12q translocated segment, which comprised only 300 kb, was beyond the distalmost gene on that chromosome.6 Thus, the children’s abnormal phenotype was due purely to trisomy for the large segment chr2:1-32,745,624 6 The final nucleotide on chromosome 12, at 12qter, is number 133,275,309.

104  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY (containing very many genes). Given that the short arms of the acrocentrics contain no protein-coding genes, De Carvalho et al. (2008) could similarly conclude, in a large family segregating a t(5;15)(p13.3;p12) translocation, that the 5p deletions and duplications observed (in an extraordinary total of 21 individuals) would represent, respectively, pure partial monosomies and trisomies, from an effectively truly single-segment rearrangement. ADJACENT-1 SEGREGATION, DOUBLE-SEGMENT EXCHANGE With a double-segment translocation, an adjacent-1 imbalanced conceptus has both a partial trisomy and a partial monosomy (also called a duplication/deficiency, or deletion/duplication, abbreviated to del/dup). The combined effect of the two imbalances is typically more severe than either separately, and “the whole may be worse than the sum of the parts.” Thus, it is infrequent that the carrier of a “double-segment” exchange can ever have a chromosomally unbalanced pregnancy proceeding through to term or close to term. Multiple miscarriage is the typical observation (e.g., Figure 5–22). But occasionally, viability is observed for one, or rarely both, of the dup/del combinations, and we illustrate this with four examples following. Nucaro et al. (2008) studied a t(3;10)(p26;p12) family with affected individuals in three generations, and yet all still living and able to be examined, and their karyotypes confirmed as 46,der(3) t(3;10)(p26;p12), conveying a partial 3p monosomy and 10p trisomy. The countertype adjacent-1 karyotype was not observed, but it may well have been the cause of the several miscarriages recorded. The double-segment t(4;8)(p16.1;p23.1) depicted in Figure 5–13 has very small translocated segments: the distalmost parts of chromosome 4 and of chromosome 8 have exchanged positions.7 In this family, both of the two possible adjacent-1 segregant outcomes were observed: the index case with del(4p)/dup(8p), and his uncle with dup(4p)/del(8p). In the former, a Wolf-Hirschhorn gestalt was discernible, reflecting the del(4p) component. A similar example is seen in the family reported in Rogers et al. (1997). They provide in their paper a photograph of six siblings sitting on a sofa in 1958, one with a dup(11q)/del(4q) karyotype, two who since died presumed to have been del(11q)/(dup(4q), and one girl carrying the family balanced t(4;11) (q34.3;q23.1), who went on to have, in the next generation, a del(11q)/(dup(4q) child. In the t(4;10) family in Fan et al. (2023b), the two possible adjacent-1 del/dup combinations were seen in two siblings, still living and in fair health in their late 30s, from their t(4;10)(q33;p15.1) mother: one sibling with a gain and loss, respectively, of 19.4 Mb of 4q and 5.2 Mb of 10p, and vice versa in the other. Very small double-segment imbalances, detectable with clarity (or at all) only upon molecular karyotyping, may be associated with viability in both the del and the dup circumstance. In the t(7;12)(q36.2;p13.31) family reported in Izumi et al. (2010), the translocated segments at distal 7q and distal 12p were of sizes, respectively, of 5.53 Mb and 7.27 Mb. The 7q segment, at chr7:153,908,498-qter, carried, among others, the SHH and MNX1 genes, while some 80 genes were resident in the 12p segment, chr12:1-7,272,466. 7 This same 4;8 translocation has been observed in a small number of unrelated families, and it may be, after the t(11;22) noted below, the most frequent human reciprocal translocation. This recurrence reflects the presence in distal 4p and 8p of “olfactory-receptor clusters,” which can act as recombination-predisposing duplicons (Maas et al. 2007). Other recurrent rearrangements are the translocations t(4;18)(q35;q23) and t(8;22)(q24.13;q11.21) (Horbinski et al. 2008; Sheridan et al. 2010). But some apparent recurrences may actually reflect unrecognized identity by descent (Youings et al. 2004). Autosomal Reciprocal Translocations  105 The phenotype in the del(7q)/dup(12p) case presumably reflected the combined effects of a haploinsufficiency of the 7q loci, and triplo-excess of the 12p loci. And likewise, Iype et al. (2015) describe a five-generation kindred segregating a t(3;4)(p26.3;p16.1), in which several individuals had either del(3p)/dup(4p) or del(4p)/dup(3p)—or, to be more precise, del or dup chr3:1-2.1 Mb, and del or dup chr4:1-10.3 Mb. The der(3) comprised almost entirely 3 material, and the der(4) almost entirely 4; just the very small subtelomeric 3p and 4p segments were exchanged. Similarly to the 4p/8p story in Figure 5–13, elements of the respective 4p syndromes could be discerned in the affected individuals. In meiosis of a parent carrying a very small segment translocation such as these, Figure 5–13.  Adjacent-1 segregation, double-segment translocation with very small segments. (a) Parent with the translocation t(4;8)(p16.1;p23.1). The index case, his child, has the karyotype 46,+der(4) and so has a del(4p)/dup(8p) imbalance, and an uncle has the countertype dup(4p)/del(8p) imbalance due to the 46,+der(8) karyotype. (Case of CE Vaux.) (b) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 4 chromatin, open; chromosome 8 chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in adjacent-1 segregation. The upper combination (light arrows) would produce the dup(4p)/del(8p) imbalance, and the lower (heavy arrows) the del(4p)/dup(8p) imbalance.

106  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY it is probable that the normal and the derivative would simply pair up as would a normal bivalent, leaving the tiny nonhomologous segments at the ends unpaired. In that case, the expected segregations at meiosis would be random, with equal probability for each outcome, namely normal:balanced:(dup/del):(del/dup) in the ratio 1:1:1:1. The opportunity occasionally arises to provide direct evidence of early in utero lethality of a particular imbalanced state. In a family study of a t(8;18) (p21.3;p11.23), Cockwell et al. (1996) demonstrated on a severely malformed spontaneously aborted 11-week fetus one of the adjacent-1 conceptions, the dup(8p)/del(18p) state. This chromosomal constitution caused a double-segment imbalance, with a trisomy for 8p21.3pter and a monosomy for 18p11.23pter, giving a combined 1.2% HAL imbalance (0.8% for trisomy, 0.4% for monosomy). The countertype dup(18p)/del(8p) karyotype had produced, in this family, a child with an abnormal phenotype. Atypically, this viable form had more HAL monosomy than trisomy. Exceptionally, both translocated segments can be of substantial size and yet be survivable, if barely, to term. The outlying points in Figure 5–28 reflect such cases. The double-segment t(5;10)(p13;q23.3) exchange illustrated in Figure 5–1 provides an example, this translocation having been identified in a family following the death of a neonate with multiple malformations. The genetic abnormality comprised a deletion of 5p and a duplication of 10q, for a total imbalance of 2.5% HAL (1.1% HAL monosomy plus 1.4% HAL trisomy). These two segments are, as the reader will likely have guessed, relatively gene-sparse. ADJACENT-2 SEGREGATION This is an uncommonly observed mode of segregation in a liveborn child, typically limited to translocations in which each of the two participating chromosomes has a short arm of small genetic content, and small enough that the whole short arm can be viable in the trisomic state. In fact, most cases involve an exchange between chromosome 9 and an acrocentric, or between two acrocentrics (Duckett and Roberts 1981; Stene and Stengel-Rutkowski 1988; Chen et al. 2005c; Niida et al. 2016). The breakpoints characteristically occur in the upper long arm of one chromosome and immediately below the centromere in the long arm of the other (an acrocentric). Thus, the centric segments are small. The t(9;21)(q12;q11) illustrated in Figure 5–14 exemplifies the adjacent-2 scenario. At meiosis I, the form of the quadrivalent would be as drawn in Figure 5–11b. The “least imbalanced, least monosomic” gamete from 2:2 malsegregation is the one receiving chromosome 9 and the der(9) (heavy arrows). The conceptus will have, in consequence, a duplication of 9p (and a small amount of 9q heterochromatin) and a deletion of 21p (and a minuscule amount of subcentromeric 21q). Although comprising a substantial piece of chromatin (1.8% of HAL), 9p is qualitatively “small” in the trisomic state. Monosomy for 21p is without effect, and the 21q loss makes little if any contribution; thus the picture is practically that of a pure 9p trisomy, from an effectively single-segment imbalance. This is a known viable aneuploidy. The countertype gamete with the der(21) causes monosomy 9p and is not viable. A very similar circumstance applies with the t(4;13)(q12;q12) described in Velagaleti et al. (2001); the open and cross-hatched chromosomes in the cartoon karyotype (Figure 5–14) could be regarded, for this example, as chromosomes 4 and 13, respectively. The Autosomal Reciprocal Translocations  107 index case in this family was trisomic for all of 4p and the small segment 4cen-q12 (and monosomic for the tiny segment 13p-q12), having the karyotype 46,XY,+der(4),–13. The del(22)(q11) syndrome, so well known otherwise due to microdeletion, can also arise from a familial translocation, and this provides an example of a double-segment imbalance with adjacent-2 segregation. Imagine a t(9;22)(q12;q11.21) with the 22q breakpoint just below the DiGeorge critical region (DGCR; at chr22:19.0-20.0 Mb). Considering the cross-hatched chromosome in Figure 5–14b to be a chromosome 22, then the der(9) will lack the DGCR. A 46,+der(9),–22 child from adjacent-2 segregation (the heavy arrows) will have the 22q deletion syndrome, superadded upon a 9p trisomy. Pivnick et al. (1990) and El-Fouly et al. (1991) describe children in whom these separate-and-together dup(9p) and del(22q) phenotypes could be distinguished. Figure 5–14.  Adjacent-2 segregation. (a) Mother (above) has a reciprocal translocation t(9;21)(q12;q11), and her child (below) has the adjacent-2 karyotype 46,+der(9)t(9;21)(q12;q11). (Case of CM Morris and PH Fitzgerald.) (b) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 9 chromatin, open; chromosome 21 chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in adjacent-2 segregation; heavy arrows show the viable combination, as observed in this family.

108  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY If one of the centric segments contains loci subject to parent-of-origin imprinting, the child with an imbalanced adjacent-2 segregant may present an “imprintable syndrome” (Chapter 19) over and above the phenotype otherwise due to the imbalance. Proximal chromosome 15 is the famous segment apropos. For example, in the family reported by Abeliovich et al. (1996), the father carried a translocation due to breakpoints in the long arms of chromosomes 15 and 21, t(15;21)(q15;q22.1). Both centric segments, 15pter-q15 and 21pter-q22.1, are of quite substantial size. One child had the karyotype 46,–15,+der(21), with a proximal partial 15q monosomy and a proximal partial 21q trisomy. The phenotype was predominantly that of the Prader-Willi syndrome (PWS), reflecting the lack of a paternally contributed PWS/Angelman critical region, residing in 15q11q13; there was no clearly apparent contribution from the partial trisomy for 21pter-q22.1. The other child, with a dup(15q)/del(21q) combination, 46,+ der(15),–21, displayed a combination of features due to monosomy 21pter-q22.1 and trisomy 15pter-q15. If the carrier parent of such a 15q translocation is the mother, the other “imprintable syndrome” due to this region is seen. In Kosaki et al. (2009), as an example, the mother carrying a translocation t(15;22)(q13;q11.2) had a child with the 46,–15,+ der(22) combination presenting the clinical picture of Angelman syndrome, due to absence of a maternally originating PWS/Angelman critical region. Another child of hers had the opposite adjacent-2 imbalance, 46,–22,+der(15), and his phenotype was that of DiGeorge syndrome. Other such cases are on record (Niida et al. (2016). A double-segment case in which the two centric segments were much smaller is exemplified in Chen et al. (2005c). Here, in a 14;21 rearrangement, described as t(14;21) (q11.2;q11.2), both breakpoints were in the first sub-band below the centromere. The der(14) thus comprised almost all chromosome 21 material, with just the short arm, centromere, and a very small amount of proximal long arm being from chromosome 14; and vice versa, the der(21) consisted largely of chromosome 14 material. Three affected family members, two brothers and their aunt, carried the der(14) in unbalanced state due to adjacent-2 segregation, and they were thus trisomic for the small proximal 14q segment and monosomic for the small proximal 21q segment. The dysmorphology was quite mild, but the functional neurobehavioral phenotype was rather severe. Very similar examples are seen in Koochek et al. (2006) and Dave et al. (2009). Some adjacent-2 imbalances will be of a degree allowing survival beyond the embryonic period but no further. The karyotype shown in Figure 5–15 comes from the products of conception obtained at miscarriage from a woman who was herself a translocation carrier, 46,XX,t(13;16)(q12.3;q13). The karyotype of the cultured products, 46,XX,–13,+der(16), displays an overall HAL imbalance of 2.7%. Two previous miscarriages to this couple might have had this same karyotype. The reason so few examples of adjacent-2 segregants are seen in life is that most are of such size (e.g., gametes 5 and 6 in Figure 5–4) that they convey a lethal imbalance during early embryogenesis. Naturally, if the window of observation were to be shifted to this period of development before natural selection may have operated, more cases would reveal themselves. In a study based upon 278 day-3 embryos from 34 translocation couples, the incidence of adjacent-2 segregation products was substantial at 12%, although less than half of adjacent-1 (28%) (Ye et al. 2012). On a blastocyst study due to Nakano et al. (2022), and via microarray and NGS technology, the ratios were very similar: of 242 cases, 13% were due to adjacent-2 malsegregation, versus 30% adjacent-1. Nearly identical observations are recorded in Xie et al. (2022), from over 10,000 blastocysts; see also Figures 5–7 to 5–9. Autosomal Reciprocal Translocations  109 3:1 SEGREGATION WITH TERTIARY TRISOMY Tertiary trisomy is fairly uncommon—or to be precise, fairly uncommonly seen in a term pregnancy (3:1 is actually a quite commonly observed malsegregation at the blastocyst stage: for example, 5.4% in the survey of Xie et al. 2022). A pregnancy from 3:1 tertiary trisomy can be viable only in the setting of one of the derivative chromosomes being of small genetic content. It exists in the abnormal individual as a supernumerary chromosome, with the karyotype 47,+der. The centric segment will necessarily contain the whole short arm of the derivative chromosome, and for a pregnancy to be viable it will necessarily be of a chromosome having a small short arm; thus an acrocentric chromosome is very often implicated. Subtlety according to an influence of parental gender, and to the presence or not of an acrocentric chromosome, is set out in Figure 5–10. But almost always, complete long arms (and in fact, most complete short arms) contain too much material to allow viability further into pregnancy with a supernumerary derivative chromosome, and spontaneous abortion ensues. A rare chance to illustrate this point is given in Fritz et al. (2000), who, as mentioned above, studied archived material from an abortus, the mother carrying a subtle translocation, 46,XX,t(4;12)(q34;p13). They showed a tertiary trisomy, 47,XY,+der(4), with almost the entire chromosome 4 and the tip of 12p, present as an additional chromosome. There is, as noted below, a significant maternal-age effect in 3:1 imbalance. The Common t(11;22)(q23;q11). Curiously enough, in this, by far the most common human reciprocal translocation, practically all abnormal offspring of the heterozygote have a tertiary trisomy due to 3:1 malsegregation (Figure 5–16a). Carter et al. (2009) review the clinical features associated with this imbalance, known as Emanuel syndrome. The quadrivalent of this 11;22 translocation would have the form outlined in Figure 5–16b. The content of the smallest chromosome, the der(22), is small (respecting Figure 5–15.  Adjacent-2 Segregation with Pregnancy Loss. Adjacent-2 segregation with an imbalance lethal in early pregnancy. The mother (above) has the karyotype 46,XX,t(13;16)(q12.3;q13). Tissue from the products of conception of a spontaneous first-trimester abortion was cultured, and the chromosomal complement from these cells (below) showed the karyotype 46,XX,–13,+der(16). There is monosomy of proximal 13q for a segment of HAL 0.6%, and partial trisomy 16 for a segment of HAL 2.1%. (Case of MD Pertile.)

110  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY the requirement for the derivative to have a small short arm, acrocentric chromosome 22 easily qualifies), and its major genetic composition is accounted for by the distal 11q segment. The presence of this 47th chromosome does not necessarily impose a lethal distortion upon intrauterine development, and a pregnancy could continue through to the birth of a child with a 47,+der(22) karyotype, with trisomy for the segment 11q23qter (and for the very small segment 22pter-q11). The male t(11;22) heterozygote produces other types of unbalanced gamete as shown on sperm chromosome study, but none of these is ever viable.8 On embryo study, in fact the most frequent category of malsegregation is adjacent-1, with as high as 68% from the male heterozygote and 50% from the female, but none of these will survive; the survivable 3:1 combination accounts for only 5% of embryos (Zenagui et al. 2019). Figure 5–16.  Tertiary Trisomy and Emanuel Syndrome. (a) The common t(11;22)(q23;q11) in the heterozygous state (above) and in the typical unbalanced state, associated with Emanuel syndrome (below). (b) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 11 chromatin, open; chromosome 22 chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in a 3:1 tertiary segregation; heavy arrows show the viable trisomic combination. 8 Except in the extraordinary setting of post-zygotic rescue. Kulharya et al. (2002) report a t(11;22) carrier mother having had a child from presumed adjacent-1 segregation with 46,XY,der(22) at conception, and then mitotic loss of the der(22) in one cell and duplication of the normal 22, leading to 46,XY,der(22)/46,XY mosaicism. Autosomal Reciprocal Translocations  111 This t(11;22) is the spectacular exception to the rule that, in different families, translocations arise at different sites. The great majority of families have a “private translocation,” and many may represent the first and only case in the whole of human evolution. Apparently, few predispositions for specific rearrangement exist. Equally apparently, 11q23 and 22q11 show a remarkable predisposition, which may reflect a physical proximity between the two chromosomes during meiosis (Ashley et al. 2006). Kurahashi and Emanuel (2001) studied normal volunteers and, being able to test very large numbers of sperm, they could show that de novo t(11;22)(q23;q11) translocations must be being generated from time to time; and Ohye et al. (2010), studying eight de novo cases, showed the translocation in each to have been of paternal origin. Supernumerary Marker Chromosomes. The point is to be noted that probands in whom a supernumerary marker chromosome (SMC) is discovered are often found, on parental study, to have a derivative chromosome reflecting a tertiary trisomy (Stamberg and Thomas 1986). Braddock et al. (2000) describe a family in which an SMC due to 3:1 malsegregation had initially escaped recognition as such. In the family, a child with “atypical Down syndrome” had been karyotyped as trisomy 21. On attending a Down syndrome clinic at age 9 years, the clinical picture raised doubt, and his chromosomes were restudied. He turned out to have a tertiary trisomy for a der(21), which comprised much of chromosome 21 and a small part of distal 5p. His mother and several other relatives carried a t(5;21)(p15.1;q22.1), and a similarly abnormal aunt had the same tertiary trisomy, 47,+der(21). A rather similar account comes from Valetto et al. (2013). A young woman with a mild intellectual disability and what looked like 47,XX,+21 on classical karyotyping proved actually to have 47,XX,+der(21) due a maternal t(8;21)(q24.21;q21.1), and the imbalance precisely defined as dup chr8:128,493,142-145,054,634, dup chr21:13,045,202-22,115,024. In the family in Ouboukss et al. (2024), a child presenting with dysmorphism and psychomotor delay karyotyped initially as having a small SMC due to dup(14). Family studies revealed his mother and brother to carry a t(8;14)(p22.3;q21), and thus the SMC in the child could be seen as a dup14q/dup8p chromosome, from a tertiary trisomy of maternal origin. These stories have lessons both for cytogeneticists and for genetic counselors, although modern methodology will usually allow a “SMC” to be properly identified. 3:1 SEGREGATION WITH TERTIARY MONOSOMY If one derivative is very small, and the amount of material that is missing is “monosomically small,” the countertype 3:1 22-chromosome gamete may lead to a viable conceptus. Consider the 12;13 translocation t(12;13)(p13.32;q12.11) shown in Figure 5–17a. The large derivative chromosome is not far from being a composite of the two complete chromosomes. It is missing only subterminal 12p and pericentromeric chromosome 13. This is a “small” loss, and thus the 45,der(12) conceptus is viable (Figure 5–17b). Any initially 45-count karyotype obliges consideration that there may, in fact, be a tertiary monosomy. For example, Courtens et al. (1994) describe an infant who died at birth with, at first sight cytogenetically, monosomy 21 (45,–21). But on further study, a 45,+ der(1) from a maternal 1;21 translocation was discovered. In Nur et al. (2015), a baby with multiple abnormalities who died at age 5 months had a 45-chromosome count, with a der(18;22) comprising most of chromosomes 18 and 22. Her mother proved to carry a t(18;22)(p11.2;q11.2), enabling a diagnosis in her child of tertiary monosomy for 112  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY most of 18p and the DiGeorge critical region of 22q. Prenatal diagnosis at a subsequent pregnancy gave a normal result. Sometimes the two phenotypes of the two contributing monosomies can be separately discerned. Thus, Reddy et al. (1996) describe children with a combined DiGeorge (DGS) and Wolf-Hirschhorn (WHS) phenotype, having the karyotype 45,der(4)t(4;22)(p16.3;q11.2)mat. The large derivative chromosome comprised Figure 5–17.  Tertiary Monosomy. (a) Mother (above) has a reciprocal translocation between nos. 12 and 13, 46,t(12;13) (p13.32;q12.11). Two children (below) inherited the derivative 12, but no normal chromosome 12 or 13 from the mother, and have the karyotype 45,der(12). They are thus monosomic for the tip of 12p and pericentromeric 13 (and show only a mildly abnormal phenotype). Chorionic villus sampling in a subsequent pregnancy gave a 46,XX result; an elder sister was a balanced carrier. (Case of MD Pertile) (b) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 12 chromatin, open; chromosome 13 chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in a 3:1 tertiary segregation; heavy arrow shows the monosomic complement. Alternatively, the three large chromosomes might form a trivalent, and the tiny der(13), being unattached, might segregate at random.

Autosomal Reciprocal Translocations  113 almost all of 4 and almost all of 22q, but it lacked the WHS and DGS critical segments. Cases in which one of the deleted segments includes the Angelman region at 15q13 are reported in Wenger et al. (1997) and Torisu et al. (2004), and in which this syndrome is seen in 3:1 malsegregant children of the carrier mother. An interesting historical example, in that it provided a key observation toward the discovery of the TSC2 locus, is that of a child with 45,der(16), who had monosomy for the segment 16p13pter, and who had both tuberous sclerosis complex and polycystic kidney disease due to loss and disruption, respectively, of the adjacent TSC2 and PKD1 loci. The heterozygous 46,t(16;22) family members had polycystic kidney disease, due to the disruption of PKD1 (European Polycystic Kidney Disease Consortium 1994). Almost all conceptions with a tertiary monosomy are expected to be lethal preimplantation or in early embryogenesis. A direct demonstration of this circumstance is illustrated in the case of a 3:1 malsegregation of a maternal t(11;22) in a spontaneous abortus at seven weeks gestation with 45,der(11), which resulted in monosomy for distal 11q and monosomy for proximal 22q (Jobanputra et al. 2005). 3:1 SEGREGATION WITH INTERCHANGE TRISOMY This mode of segregation can only produce a liveborn child when a “trisomically viable chromosome” (i.e., 13, 18, or 21) participates in the translocation (Figure 5–18a). This chromosome accompanies the two translocation (interchange) elements of the quadrivalent to one daughter cell (Figure 5–18b). Interchange trisomy 21 is rare, interchange trisomies 13 and 18 are extremely rare, and interchange trisomy 9 is barely recorded (Table 5–2). Concerning other (nonviable) autosomes, interchange trisomy can be seen at PGT (Lim et al. 2008) or upon analysis of abortus material, such as the trisomy 2 in a pregnancy from a t(2;17)(q32.1;q24.3) carrier discussed in Lorda-Sánchez et al. (2005). Theoretically, uniparental disomy can be a consequence of interchange trisomy, if one of the “trisomic” chromosomes is subsequently lost post-zygotically and if this chromosome had come from the non-carrier parent. If this chromosome is one that is subject to imprinting according to parent of origin, phenotypic abnormality will be the consequence notwithstanding the apparently balanced karyotype, the same as the parent’s. Thus, for example, a 46,t(8;15) father could have a 46,t(8;15) child with Angelman syndrome, or a mother could have a child with Prader-Willi syndrome. Actual examples of this type of mechanism are extremely rare (Table 19–6). 3:1  SEGREGATION WITH INTERCHANGE MONOSOMY Autosomal monosomy is typically associated with very early arrested development of the embryo. Only with PGT does a practical relevance of interchange monosomy emerge, since there may not yet have been the chance for selection pressure to have operated. In the PGT case reported in Conn et al. (1999) noted earlier, the woman being a t(6;21) heterozygote, a transferred embryo that implanted only transiently may have had an interchange monosomy 6. Sperm capable of giving rise to interchange monosomy can certainly be produced in numbers, as Midro et al. (2006) show in a man heterozygous for a t(7;13)(q34;q13), from whom 2.8% of sperm showed interchange nullisomy 7 and 8.0% 114  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY interchange nullisomy 13; had these sperm fertilized, the corresponding interchange monosomy would have resulted. Yet to be observed is uniparental disomy following “correction” by duplication of the single normal homolog in the embryo resulting from interchange monosomy. The countertype gamete in Figure 5–18b (light arrow), for example, would be nullisomic for 21. Replication of the chromosome 21 from the other gamete could restore disomy and with a normal karyotype. Note that this would be uniparental iso-disomy, and from the other parent. Figure 5–18.  Interchange Trisomy. (a) Mother (above) has a reciprocal translocation between nos. 12 and 21; her child (below) inherited the maternal translocation chromosomes and a “free” chromosome 21. The breakpoints are 12q13.1 and 21p13; an apparent gap, comprising satellite stalk, can be discerned between the centromere of the der(21) and its 12q component. (Case of R Oertel.) (b) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 12 chromatin, open; chromosome 21 chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in 3:1 interchange segregation; heavy arrows show the trisomic combination. Autosomal Reciprocal Translocations  115 4:0 SEGREGATION A total nondisjunction of the quadrivalent complex is rare indeed. In sperm studies, only fractions of a percent of 4:0 gametes are ever seen (Benet et al. 2005). If 4:0 segregation should happen and conception follow, preimplantation lethality would, in practically all, supervene. The question may not be entirely academic, however, now that PGT has brought the 4:0 gamete out from its former place of practical irrelevance (Table 5–3). Out of interest, the reader may care to note how a hypothetical double trisomy of 18 plus 21, based on the 4:0 combination in Figure 5–4 (15) and potentially associated with some in utero survival (Reddy 1997), could come from the t(18;21) shown in Figure 5–20 below. More than One Unbalanced Segregant Type Sometimes a reciprocal translocation has characteristics associated with more than one type of malsegregation, and so each type may be seen in the family (Abeliovich et al. 1982). Consider the 11;18 translocation t(11;18)(p15;q11) shown in Figure 5–19. Table 5–2.  The Rarity of Recorded Cases of 3:1 Interchange Trisomy from a Reciprocal Translocation in a Term Pregnancy INTERCHANGE TRISOMY CASES STUDIES 13 2 Stene and Stengel-Rutkowski 1988; Midro et al. 2006 18 3 Stene and Stengel-Rutkowski 1988; Teshima et al. 1992 21 7 Prieto et al. 1980; Stene and Stengel-Rutkowski 1988; Koskinen et al. 1993; Conn et al. 1999; Dominguez et al. 2001; Girisha et al. 2010; Tug et al. 2016 9 1 Ninomiya et al. 1994 Note: Some of the trisomy diagnoses were clinical, and not karyotypically proven. The infant with interchange trisomy 9 died immediately after birth. Table 5–3.  The Rarity of 4:0 Malsegregation from Translocation Carriers at Preimplantation Genetic Testing STUDY EMBRYOS ANALYZED DAY 3 EMBRYOS WITH 4:0 DAY 5 BLASTOCYSTS WITH 4:0 Ye et al. 2012 278 day-3 4 - Wang et al. 2019 378 day-5 - 1 Tonyan et al. 2024 306 day-3 4 - Ibid. 93 day-5 - 0 Note: The numbers of translocation carriers in the three studies were 34 in Ye et al., 89 in Wang et al., and 39 in Tonyan et al.

116  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 5–19.  More than One Viable Malsegregant Form. (a) Pedigree. Filled symbols, unbalanced karyotype, as shown; half–filled symbols, heterozygote. (b) Mother and one daughter have a reciprocal translocation of chromosomes 11 and 18, t(11;18)(p15;q11) (upper). Each had one unbalanced offspring, one having 47,+ der(18) due to 3:1 tertiary trisomy (middle), and the other 46,+der(11) from adjacent-1 segregation (lower). The former had a complete trisomy 18p and the latter a partial 18q trisomy. (Case of C Ho and I Teshima.) (c) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 11 chromatin, open; chromosome 18 chromatin, cross-hatched). Heavy arrows indicate one adjacent-1 segregant movement of chromosomes, and light arrows indicate movements of chromosomes to daughter cells in a 3:1 tertiary trisomy segregation, each of which occurred in this family. Source: From RJM Gardner et al., Autosomal imbalance with a near-normal phenotype: The small effect of trisomy for the short arm of chromosome 18, Birth Defects Orig Artic Ser 14: 359–363, 1978. Autosomal Reciprocal Translocations  117 First, the translocated segments are small: 18q is known to be viable in the trisomic state, and the tip of 11p contributes a minimal/nil imbalance (thus, this is regarded as a single-segment imbalance). Accordingly, one of the adjacent-1 segregants is presumed to be viable. Second, two component chromosomes of the pachytene configuration, the der(18) and chromosome 18, are of small overall genetic content. Thus, 3:1 segregation with either tertiary trisomy or interchange trisomy is possible. In the event, the two unbalanced karyotypes in this family reflected adjacent-1 and 3:1 tertiary trisomy segregation. Rather more spectacular is the translocation illustrated in Figure 5–20. A mother had the karyotype 46,XX,t(18;21)(q22.1;q11.2): these breakpoints are toward the end of 18q and immediately below the centromere in 21q. She had a stillborn child with tertiary monosomy, a miscarriage with adjacent-1 malsegregation (and two other unkaryotyped miscarriages), and a surviving child with tertiary trisomy. These three karyotyped Figure 5–20.  Several Viable Unbalanced Forms. The karyotype is illustrated (top) of a mother carrying the translocation t(18;21) (q22.1;q11.2). She had a miscarriage due to adjacent-1 segregation, an abnormal child with a tertiary trisomy, and a stillborn child with a tertiary monosomy, as depicted in the cartoon karyotypes. An uncle with Down syndrome may have had the same adjacent-1 karyotype as in the second row, or possibly interchange trisomy 21, as depicted in the bottom row. (Case of MD Pertile.) 118  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY pregnancy outcomes were, respectively, 45,der(18), 46,der(18), and 47,+der(18). An uncle said to have had Down syndrome may have had the 46,der(18) karyotype (the der(18) includes the segment of 21 that contributes substantially to the Down syndrome phenotype), or possibly interchange trisomy with 47,+21,t(18;21). Some of the other possible imbalanced segregants could theoretically be viable, and the reader may wish to determine which ones these would be. This is due to the fact that many of these combinations have a genetically “small” imbalance. All partial trisomies and some partial monosomies for segments of chromosomes 18 and 21 can be viable as a single imbalance; and when two different imbalances occur in combination, for example, partial trisomy 21 plus partial monosomy 18, a pregnancy may still be capable of proceeding substantially along its course. Failure to Form Quadrivalent Where very small segments are involved, the imperative may lack for the coming together of the four chromosomes with segments in common, and they might simply synapse as bivalent pairs along their matching lengths and then segregate independently. In that case, a segregation ratio of 1:1:1:1 would presumably operate for normal, balanced, and the two imbalanced outcomes—clearly a high-risk circumstance. This likely applies to the general case of the subtelomeric translocation, such as the t(3;4) (p26.3;p16.1) in Iype et al. (2015) referred to above, in which the derivative chromosomes comprise almost a complete copy of the normal. The opposite, in which the der consists almost entirely of chromatin of the other chromosome, is exemplified in the t(14;15)(q12;q12) in Burke et al. (1996), in which the derivative chromosomes each comprise near to an entire chromosome 14 and chromosome 15, respectively (Figure 5–21). Different grounds for the non-formation of a quadrivalent may exist if one chromosome is a very small one. While the three other chromosomes could have come together as a trivalent, the fourth very small one might fail to be captured by the meiotic mechanism. That being so, it could then segregate at random (a variation on the theme of 3:1 segregation; see “Acrocentric Chromosomes” above). Figure 5–21.  Probable Independent Segregation. Notes: The translocation t(14;15)(q12;q12) in Burke et al. (1996). The der(14) comprises almost completely 15 chromatin, and the der(15) is almost completely of 14 chromatin. Shown are the two unbalanced gametic combinations of 14 and 15 homologs that are potentially viable, following independent segregation of the 14 and der(15), and the 15 and der(14), at meiosis I. In this family, the 14 + der(14) combination (upper) lacked the Angelman region in proximal 15q, and this was the syndromic diagnosis in their index case.

Autosomal Reciprocal Translocations  119 No Unbalanced Mode Viable Finally, for the translocation in which the quadrivalent is characterized by long translocated and long centric segments, no mode of segregation could produce a viable unbalanced outcome. We emphasize the point that many reciprocal translocations (including whole-arm translocations, see below) are in this category. Consider the family depicted in Figure 5–22, in which a 4;6 translocation t(4;6) (q25;p23) was discovered by chance at amniocentesis. The quadrivalent would have the form depicted in Figure 5–11d. It possesses none of the criteria that would allow a viable imbalance to result, by whatever mode of segregation. The translocated segments are both large (leading to double-segment imbalance); the centric segments are very large; and the content of all four chromosomes is large. Miscarriage is as far as any unbalanced conceptus could ever get, and in some such instances pregnancy loss will be the presenting complaint. The large kindred of Madan and Kleinhout (1987) graphically illustrates this circumstance: 11 carriers of a t(1;20)(p36;p11) had had two or more miscarriages and numerous normal children, but none had had an abnormal child. In some such translocations identified fortuitously—for example, at amniocentesis for maternal age—there may be little or no history of apparent reproductive difficulty. Meiotic Drive. The nature of the quadrivalent may, of itself, influence segregation. The propensity for a particular segregation outcome may reflect a particular geometry of the quadrivalent and what sort of ring or chain it forms. Quadrivalents that have translocation chromosomes with short translocated segments more usually form a ring, and have the quality of being more likely to generate adjacent-1 gametes, while those with short centric segments, more often existing as a chain, may have a predisposition to the Figure 5–22.  No Unbalanced Product Viable. (a) Pedigree of a kindred in which mother and daughter have had multiple miscarriages, each having (b) the karyotype 46,XX,t(4;6)(q25;p23). (Case of AJ Watt.) The presumed pachytene configuration during gametogenesis in the heterozygote would be as in Figure 5–11d (chromosome 4 chromatin, open; chromosome 6 chromatin, cross-hatched) and, with large centric and translocated segments, the translocation has none of the features that enable viability of any unbalanced segregant combination. 120  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY formation of adjacent-2 and 3:1 gametes (Faraut et al. 2000; Benet et al. 2005). Zhang et al. (2014) analyzed segregations at PGT, and determined that increasing asymmetry of the quadrivalent (estimated from increased ratios of the lengths of the two translocated and of the two centric segments) reduced the fraction of embryos due to alternate segregation by an average of almost one-half. This predisposition to form particular classes of segregant gamete may be considered a form of “meiotic drive.” As we have had cause to comment more than once, each translocation is entitled to its individuality and need not necessarily follow the “rules” set out earlier. Faraut et al. (2000) identified a few translocations that “should” have produced sperm with certain expected proportions of adjacent-1 and adjacent-2, but which did not. We have seen a remarkable family in which, over some 10 years of marriage, the wife had had innumerable very early miscarriages—about eight at 12–14 weeks, one at 16 weeks—and one phenotypically normal son. The husband (and the son) had the translocation t(12;20) (q15;p13). Perhaps the quadrivalent was configured in such a way that alternate segregation was very difficult to achieve, and so almost all sperm had an unbalanced complement. De Perdigo et al. (1991) report a possibly similar case, in which they propose that heterosynapsis in the quadrivalent permitted spermatogenesis to proceed, but at the cost of producing many unbalanced gametes. Observations from the PGT laboratory are further illustrating the point that translocation carriers with very poor reproductive histories may indeed reflect a very high rate of meiotic malsegregation in some individuals; note the left-hand side of the plot in Figure 5–6, showing outliers with an unfavorable ratio of normal versus unbalanced forms in sperm from translocation carriers. The patient in Conn et al. (1999) mentioned earlier, she having the karyotype 46,XX,t(6;21)(q13;q22.3), had had four miscarriages and one child with interchange trisomy 21. She came to PGT, and not one of two oöcytes and nine embryos were chromosomally normal (they were mostly 3:1, some adjacent segregations). Parental Origin and Parental Age Effect. There are more women who have been mothers (whether the children are normal or not) than there are men who have been fathers in translocation families. In their review of 1,597 children in 1,271 translocation families, Faraut et al. (2000) found the mother to be the carrier parent in 61% of the adjacent-1 children, 70% of the adjacent-2 children, and in as many as 92% of the unbalanced offspring from 3:1 segregations. This 3:1 association may reflect an actual maternal predisposition. With advancing maternal age, and after some decades of being held in meiosis I prophase, the small supernumerary chromosome may be increasingly likely to detach from the quadrivalent and then to migrate at random to one or other daughter cell, when meiosis has reactivated in that particular menstrual cycle. On the other hand, no maternal-age effect applies to adjacent-1 or adjacent-2 offspring. Here, the maternal excess may more accurately be termed a paternal deficiency, due to reduction in fertility of the male heterozygote (discussed below). No paternal-age effect is discernible in any segregation mode. Infertility We may note a distinction between pregestational (an inability to conceive) and gestational (pregnancy loss) infertility. The male translocation heterozygote is more susceptible to an effect upon fertility than the female, and apparently balanced translocations (ABTs) are seen in about 1% of men presenting with azoöspermia or severe oligospermia. The quadrivalent may be incompletely synapsed, and its close association with the X-Y bivalent may have been the factor leading to spermatogenic arrest (Figure 5–23).

Autosomal Reciprocal Translocations  121 In the analysis of reproductive outcomes in the translocation families of Faraut et al. (2000), looking at prenatal diagnoses in order to avoid bias, 61% of all fetuses came from a carrier mother versus only 39% from a carrier father; this ratio presumably reflects the relative male infertility associated with the carrier state. This infertility is generally not something that is predictable from the nature of the translocation, and indeed the same translocation may compromise fertility in only some men in the same family. Pasińska et al. (2018) (Figure 5–24) describe a family of what could be called relative infertility, in which miscarriages outnumbered live births: in the index t(7;17)(p22;p13.2) Figure 5–23.  Disrupted Synapsis at Meiosis as a Cause of Infertility. Notes: The translocation is 46,XY,t(1;21)(q11;p11). Testicular tissue was biopsied from a 27 year-old azoöspermic man. The quadrivalent which formed at meiosis is shown here immunostained with synaptonemal complex axial element protein SCP3 (red), centromeres (blue), and sites of recombination (yellow). Synapsis of homologous elements of the quadrivalent is incomplete, and the X-Y bivalent (sex body) is closely associated with the quadrivalent. Source: From M Leng et al., Abnormal synapses and recombination in an azoospermic male carrier of a reciprocal translocation t(1;21), Fertil Steril 91:1293.e17–22, 2009. Courtesy Q Shi, and with the permission of the American Society for Reproductive Medicine. Figure 5–24.  Pedigree of a Translocation Family Showing Both Affected Persons and Miscarriages. Notes: The translocation t(7;17)(p22;p13.2) is identified in intellectually affected persons with dup17p13.3 (filled symbol), and in carriers (half-filled symbol). Similarly intellectually affected persons, but not tested, are shown as greyed symbol; quite likely they had the same duplication (in which case, the connecting relatives would be obligate carriers). It is rather probable the miscarriages (small black symbols) were chromosomally imbalanced, possibly with the countertype 17p deletion. Source: From M Pasińska et al., Multiple occurrence of psychomotor retardation and recurrent miscarriages in a family with a submicroscopic reciprocal translocation t(7;17)(p22;p13.2), BMC Med Genomics 11:69, 2018. Courtesy M Pasińska, and with the permission of Springer Nature. 122  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY sibship, five miscarriages, alongside three abnormal individuals with proven or probable dup17p13.3 syndrome, very likely reflected the opposite del17p imbalance. Oögenesis is not, however, immune to the translocation obstacle, and indeed in the rcp series of Verdoni et al. (2021), women outnumbered men as the carrier in those couples whose presentation had been through recurrent pregnancy loss. Chen et al. (2005d) studied a number of “translocation couples” and compared ovarian responses between those where the male or the female partner was the heterozygote. The 28 female rcp carriers did worse than the women whose male partner was the heterozygote, as measured by estradiol levels following human chorionic gonadotrophin (HCG)9 stimulation: 23% were “very low responders” compared with 7% where the female was not the carrier. It remains true, however, that oögenesis in most female carriers is apparently unscathed. The sex difference in susceptibility is striking in the family of Paoloni-Giacobino et al. (2000b). A mother was a t(6;21)(p21.1;p13) heterozygote, and she had eight children— four sons and four daughters—and two miscarriages. The four sons, each 46,XY,t(6;21), were all married, (one three times), and none had any children. Each had severe oligospermia or oligoasthenoteratospermia, and the two having testicular biopsies manifested spermatogenic arrest at meiosis I prophase, with extensive asynapsis of several chromosomes. Two sisters were 46,XX,t(6;21), and the one who was married had had two children (and two miscarriages). The Practical Problem of the Apparently Balanced Translocation The ABT is not uncommon in the general population, about 2 to 5 per 1,000 persons. When an ABT has been discovered in the course of investigation of a child with a nonspecific picture of cognitive compromise and sometimes also some dysmorphic signs, and particularly when de novo, this raises the question: Is the translocation causative, or simply coincidental? If an ABT co-segregates faithfully with a consistent abnormal phenotype in a good number of individuals in a family, a conclusion can reasonably be drawn that the ABT is indeed the cause, and that the translocation is, in fact—at least functionally—unbalanced. A de novo case, however, cannot so readily be interpreted. The abnormal phenotype could be coincidental, unrelated to the ABT. Families such as those reported in Hussain et al. (2000) offer useful illustration: in this example, an ABT that was co-segregating with a phenotype of “varying degrees of behavioral and learning difficulties.” Presumably this translocation, a t(1;17)(p36.3;p11.2), had been de novo at some prior point, possibly with the 65-year-old grandmother of their index case. In this family, there were children and grandchildren (seven of them) to bear witness to the apparent harmful role of the translocation, notwithstanding an inability, given the methodology of the day, to show (as these authors suspected) an imbalance. With the improving technology of this century, it is usually possible to make the distinction between an actually balanced versus a truly unbalanced ABT. In a paper attesting to the international collegiality of the profession, from over 100 institutions, Redin et al. (2017) accumulated data on 248 subjects in whom a spectrum of congenital anomalies and neurobehavioral disability had been presented, and each with an apparently 9 HCG is very similar functionally to luteinizing hormone (LH). FSH and LH promote egg production and estrogen output.

Autosomal Reciprocal Translocations  123 balanced rearrangement. Most were de novo. Whole genome sequencing led to a revision of the interpretation in terms of the cytogenetic band(s) involved, in as many as 93% of karyotypes. In what way might an ABT lead to phenotypic abnormality? (1) A very small, submicroscopic deletion, but containing an important gene or genes, is one obvious candidate. (2) A more complicated submicroscopic rearrangement may happen, with losses and gains. (3) Numerous cases have been shown due to the breakpoint occurring actually within a gene, disrupting it and making it nonfunctional, thus leading to an effectively haplo insufficient state. (4) Otherwise, the genomic landscape may put an intact gene within a region of inappropriate influence: “position effect.” (5) Mosaicism with a concealed unbalanced cell line is a theoretical, and very occasionally proven, possibility. Finally (6), uniparental disomy with a functional imbalance is a rarely seen basis for abnormality in a structurally balanced rearrangement (Chapter 19). An example of gene disruption is provided in Kurahashi et al. (1998). A child with lissencephaly (a severe structural brain abnormality; Figure 14–68) had a de novo t(8;17) (p11.2;p13.3). The p13.3 breakpoint on the chromosome 17 was sited within intron 1 of the LIS gene, with the gene being split between the two derivative chromosomes, its 5′ part on the der(8) and the remainder on the der(17). The gene could not, in consequence, function, and this functional haplo insufficiency at the LIS locus affected brain development. An example of one case from the series of Redin et al. (2017) is shown in Figure 5–25. A position effect—a “disrupted long-range regulatory interaction”—may be the consequence of an inappropriate apposition of “topologically associating domains”10 (TADs) in this part of the chromosome. A well-known example of position effect is campomelic dysplasia with sex reversal due to a chromosome 17q25.1 translocation, whose breakpoint is up to a megabase away from the (intact) SOX9 locus; but the activity of this gene, within this new landscape, is nevertheless compromised (Figure 3–18) (Fonseca et al. 2013). A similar phenotype may result via either of the above two mechanisms: In the study of Redin et al. mentioned above, a number of patients with a phenotype consistent with the 5q14.3 deletion syndrome (Chapter 14) had a breakpoint within (disruption) or close to (position effect) the MEF2C locus. Loci that were definitely or plausibly the basis of phenotypic abnormality, by whichever mechanism, in the 242 cases in Redin et al. (2017) are depicted in Figure 5–26. Likewise, in the international breakpoint mapping consortium presented in Tommerup et al. (2017) and comparing NGS findings in phenotypically normal and abnormal carriers of ABTs, breakpoints in the abnormal cases are more likely to occur within known autosomal dominant genes, genes that are susceptible to loss of function, or within TADs. The case reported by Dufke et al. (2001) illustrates the possible scenario of mosaicism. An abnormal child with the same balanced t(17;22)(q24.2;q11.23) as his mother on peripheral blood analysis showed, on skin fibroblast culture, a 47,t(17;22),+der(22) karyotype. This mosaic picture may reflect there having been an interchange tertiary trisomy complement in the conceptus, with post-zygotic loss of one of the two der(22)s 10 A topologically associating domain is a segment of chromatin, the DNA of kb to Mb size, within which physical interactions can take place. A spatial folding brings enhancers into closer proximity to their client genes (which might otherwise be quite apart in linear genomic distance), thus enabling a long-range regulatory control. A 3-D genome browser enables interrogation apropos: http://promoter.bx.psu.edu/hi-c/ (Wang et al. 2018). Figure 5–25.  Two Apparently Balanced Translocations that were Not. Notes: The translocation above was initially reported as t(4;14)(p15.2;q13)dn. Black = chromosome 14, orange = chromosome 4, circles = centromeres, rectangles = telomeres. Red dot-and-dash lines = breakpoints. Array-CGH was normal, and chromosome 4 and 14 DNA is present in the correct amount. In the der(4), a short ~2.5 Mb segment of chr 14 is inserted in an opposite direction, and genes NPAS3 and AP4S1 at the two breakpoints are disrupted, and in consequence, a functional imbalance. The translocation below was initially reported as t(8;10)(q13;p13)dn. Purple = chromosome 8, green = chromosome 10. Red dot-and-dash lines = breakpoints. Two submicroscopic deleted segments, of 10p and 8q, are shown as green and purple dashed lines respectively. Following the nucleotide numbering will enable the reader to piece together the several breakages and rejoinings. Source: From C Redin et al., The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies, Nat Genet 49: 36–45, 2017. Courtesy ME Talkowski, and with the permission of Springer Nature. Autosomal Reciprocal Translocations  125 in blood-forming tissue. A similar scenario is documented in Prontera et al. (2006): A mother carrying a t(1;15)(q10;p11) had an abnormal child, in whom the same apparently balanced karyotype had been shown at prenatal diagnosis. In view of the abnormal phenotype, a stringent post-natal analysis was done, which revealed a small fraction of cells, 4% (on blood), with trisomy 15; the conclusion is thus drawn that the initial conception had been from a 3:1 malsegregation with interchange trisomy, and a mitotic “correction” thereafter resulted in loss of the additional chromosome 15 in a substantial fraction of cells, but obviously not all. In the extraordinary coincidence of a recessive mutation being on the intact homolog, a translocation breakpoint that disrupted a gene would lead to the appearance of the recessive syndrome, as Kuechler et al. (2010) exemplify in a teenage girl with gonadal failure, who received an apparently balanced t(2;8)(p21;p23.1) from her mother that removed two exons from the FSHR gene (FSH receptor gene, which is located at 2p21) and a point mutation in that same gene on her paternal chromosome 2. Figure 5–26.  Loci Affected in Apparently Balanced Translocations. Apparently balanced rearrangements subjected to analysis by whole genome sequencing, from a study of 248 cases. At the molecular level, the loci depicted were compromised, due to their residence at or near a chromosomal breakpoint. Those loci in bold are presumed to have been, by virtue of their structural/functional haploinsufficient state, definitely pathogenic; those in gray are likely pathogenic. The Venn diagram shows phenotypes associated with these several loci. ASD, autism spectrum disorder. Source: From C Redin et al., The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies, Nat Genet 49: 36–45, 2017. Courtesy ME Talkowski, and with the permission of Springer Nature.

126  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY The possibility of a coincidental genetic abnormality is to be borne in mind. Aristidou et al. (2022) reanalyzed four kindreds in which an ABT co-segregated with phenotypic abnormality. They made the case, applying whole exome sequencing, that particular Mendelian mutations, actually on another chromosome, were likely candidates to have produced the observed pathological states. Coincidences can happen. Indeed, in some of the cases studied in De Gregori et al. (2007), coincidental de novo deletions were identified at chromosomal sites other than on the translocation chromosomes. The discovery of a de novo ABT at prenatal diagnosis is a particular case, which we review in Chapter 22. Rare Complexities Double Translocation Carrier. The double two-way rcp translocation comprises, essentially, two coincidental simple rcps (Phelan et al. 1990; Yardin et al. 1997). Presumably, two separate and independently operating quadrivalents can form. Burns et al. (1986) record sperm karyotypes in a man with a double two-way rcp(5;11) (p13;q23.2),rcp(7;14)(q11.23;q24.1), whose wife had had four miscarriages, a child with cri du chat syndrome, and a normal son carrying the rcp(7;14). Only four of 23 sperm analyzed had an overall balanced complement, and the majority (13) had adjacent-1 segregants for one or the other translocation. Another five showed 3:1, and one sperm showed 4:0 segregation. Bowser-Riley et al. (1988) proposed that the risk of having an abnormal child would be approximately the sum of the figures derived separately for each rcp. They acknowledge that might be an overestimate due to nonviability of doubly imbalanced combinations, notwithstanding that each on its own might be viable. We have seen a couple, the husband having a double two-way translocation t(2;20)(p25.1;p11.23),t(4;8) (q27;p21.1), who presented following four first-trimester miscarriages, although their first pregnancy had produced a normal (but unkaryotyped) son. Of 320 theoretically possible karyotypes, only four (1.25%) would be balanced (thus raising a glimmer of hope that their first fortunate pregnancy might reflect a tendency toward a balanced combination). Following the collection of 25 eggs, of which 23 were subjected to intracytoplasmic sperm injection (ICSI) and with 18 embryos then resulting, biopsy was achieved in 15 embryos, but none had a balanced constitution. A triple two-way balanced translocation carrier is extremely rare. In one such case, Gupta et al. (2019) describe 46,XX,t(1;3)(q44;p11),t(2;14)(q11.2;q13),t(9;11)(p22;p15) in a woman presenting with infertility, herself physically and mentally normal. Carrier Couple. Since reciprocal translocation heterozygotes are not uncommon in the population, on rare occasions both members of a couple will, by chance, carry a translocation (Neu et al. 1988b). We have seen, for example, a couple who had had several miscarriages, from 5 weeks to 9 weeks gestation. The husband’s karyotype was 46,XY,t(7;11)(q22;q23) and the wife’s 46,XX,t(7;22)(p13;q11.2). Presumably, their history of miscarriage reflected at least one parent transmitting an unbalanced gamete with each pregnancy— as the reader can determine, rather many unbalanced karyotypes are possible! A normal child is possible if each contributes a normal or a balanced gamete to the same conceptus. It should, in theory, be reasonably likely in a given conception for the two contemporaneous gametes to have arisen from Autosomal Reciprocal Translocations  127 alternate segregation—as an educated guess, the chance might be about 20%—although at the time of our seeing this family, only miscarriage had occurred. A child of theirs having each parental translocation would qualify as having a “double two-way translocation.” If a translocation is in a family and a couple are related, the possibility is open that they might both be carriers. Such a scenario is illustrated in Kupchik et al. (2005), who report a consanguineous husband and wife with the same t(16;18)(p13.3;p11.2). Their child received two copies of the der(18) and one of the der(16), due to alternate segregation in one parent and adjacent-1 in the other. As the reader may determine, the end result was a duplication of distal 16p and a deletion of 18p. In Martinet et al. (2006), a first-cousin couple each carried a t(17;20)(q21.1;p11.21), and their severely malformed fetus was homozygous for the translocation. The phenotype may have been due to a recessive gene. Similar histories with respect to a Robertsonian translocation, and to an inversion, are noted in Chapter 7 and Chapter 9, respectively. Mosaicism. Almost all balanced reciprocal translocations are seen in the non-mosaic state. This reflects either that the translocation had been inherited from a carrier parent, or that the rearrangement had arisen preconceptually in one or other parental gamete. Rarely (or at least rarely recognized), a balanced translocation can be generated as a post-zygotic event, and the person is a 46,rcp/46,N mosaic (Garzo et al. 2020). Most often, the clinical presentation is due to multiple miscarriage or infertility, or in the pursuit of a family study following the discovery of a non-mosaic (balanced or unbalanced) case. In these cases, the mosaicism is necessarily, at least inferentially, somatic-gonadal. An incidentally discovered case could be somatic-gonadal, or purely somatic. The infrequency with which a mosaic rcp is recognized is attested in the analysis of Park et al. (2022), who reviewed chromosomal findings in 399 female and male rcp carriers presenting with recurrent pregnancy loss. In only one—0.25% of the whole group—was mosaicism for a rcp seen: mos 46,XX,t(11;22)(q23;q11.2)/46,XX(50%). We have seen this same mosaic translocation in 40% of cells of a man whose partner had presented with a miscarriage due to trisomy 22. (Mosaicism for an unbalanced translocation is well recorded [e.g., Choi et al. 2015], but our concern here is with the balanced state.) Unstable Familial Translocation. Tomkins (1981) documents a family in which a mother with 46,XX,t(11;22)(p11;p12) had one daughter with the same translocation and another daughter with 46,XX,t(11;15)(p11;p12), and a very few other similar cases are on record. Typically, the translocation breakpoints are at telomeres, centromeres, or in nucleolar organizing regions. There is some sequence similarity in these regions between different chromosomes, and this may set the stage for these very rare “second translocation” events (and see “Jumping Translocation,” Chapter 12). Homologous Translocation. A reciprocal translocation between each of a pair of homologs is extremely rare, and only three such cases are reported in Almeida et al. (2012), all phenotypically normal persons presenting with infertility/repeated pregnancy loss. The karyotype description has the notable observation that the homologs in the first set of brackets are the same: for example, 46,XY,t(2;2)(p23;q21.2). All heterozygotes would necessarily have been of de novo generation. Such translocations would be expected inevitably to lead to an unbalanced state in the conceptus—a 100% genetic risk—and only the possibility of gonadal mosaicism (which actually was so in the t(2;2) man in Almeida et al.) would offer the prospect of a successful pregnancy.

128  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Whole-Arm Translocation. When entire arms of chromosomes are translocated (whole-arm translocation), it is almost always so that the unbalanced segregants would be unviable, and infertility is the usual presentation (Vázquez-Cárdenas et al. 2007; Yunchun et al. 2023). Rare exceptions exist. Czakó et al. (2002) report a t(18;20) (p11.1;p11.1), in which the abnormal child of a carrier father was effectively trisomic for all of 20p and monosomic for all of 18p. GENETIC COUNSELING The counselor may have to deal with these questions: 1. Is there a risk of having an abnormal child? 2. If so, what is the magnitude of the risk? 3. What would be the abnormality, and would the child survive? 4. Could there be miscarriage? 5. What testing in pregnancy is open to us? 6. Could we avoid the risk by testing an embryo in the IVF laboratory? 7. What if the same translocation that I have is found at prenatal or preimplantation testing? 8. Anything else I should know? Does a Risk Exist of Having an Abnormal Child? If a family is ascertained through a liveborn aneuploid child, that very fact demonstrates viability for that particular aneuploid combination. It could happen again. If, on the other hand, the family was ascertained by miscarriage or infertility, or fortuitously, and there is no known family history of an abnormal child, the picture is less clear. Most likely, no aneuploid combination is viable. Alternatively, a viable imbalance may be possible, but it has not yet happened; or an imbalance could occasionally be viable, but usually it is not, and (so far) has led only to abortion. The approach here is to determine the potentially unbalanced segregant outcomes, according to the favored mode of segregation—adjacent-1, adjacent-2, or 3:1—and to check to see whether any of these is on record in a pregnancy that produced an abnormal child. Valuable sources of information include Schinzel’s (2001) catalog and sites such as Decipher, ClinGen, and the CNV morbidity map. Where a single-segment imbalance from adjacent segregation is a potential outcome in a conceptus, and if the potential imbalance comprises an aneuploidy equal to or less than one of these segments on record, viability must be assumed to be possible. If the potential imbalance comprised an aneuploidy greater than any on record, viability would be unlikely, especially if the aneuploidy is much greater. The great majority of double-segment imbalances from adjacent segregation due to a translocation, ascertained other than by a liveborn aneuploid child, would be expected to lead to lethality in utero. Nearly always, a “new” double-segment exchange presenting at the clinic will truly be new, and there will be no literature record of exactly the same thing to which the counselor may appeal. In many instances one has to make an educated guess, erring on the side of caution, whether the combination of imbalances from a derivative chromosome might, in sum, be viable. Autosomal Reciprocal Translocations  129 The Magnitude of Risk The lowest risk for a surviving abnormal child, namely zero, applies in the case of imbalances of large genetic content, in which in utero lethality would be seen as inevitable. This essentially no-risk circumstance may apply to a considerable fraction, perhaps the great majority of “translocation couples.” If, in a family, it is judged that there does exist a risk to have an abnormal child, a broad estimate of the level of risk may be derived from a consideration of these factors: the assessed imbalance of potentially viable gametes; the predicted type of segregation leading to potentially viable gametes; the mode of ascertainment of the family; and in 3:1, the sex of the transmitting parent. Most risk figures fall in a range from 0% to 30%; higher risks are rare. These percentages are expressed in terms of abnormal live births as a proportion of all live births, although there are other ways of looking at the risk: the risk for an unbalanced embryo at preimplantation diagnosis; risk at prenatal diagnosis; the risk for miscarriage. Overall, the livebirth risk is higher in cases ascertained through an abnormal child, versus those identified through other routes; in the review of Youings et al. (2004), the respective pooled figures were 19% and 3%. A precise risk estimate needs to be based on the actual cytogenetic, or molecular cytogenetic, imbalance.11 Different chromosomal segments contain, of course, different genomic information. Some segments, in the imbalanced state, impose a lesser degree of compromise on the process of embryonic development, and the pregnancy may proceed through to live birth. Other segments, although they may be shorter but carrying more “important” genes, are lethal during early pregnancy and lead to miscarriage. Different segments associated with different translocations are associated with differing outcomes (Figure 5–27). It is scarcely possible to come up with a unifying format, given that chromatin is not uniform; as Cohen et al. commented in 1994, “it would be hazardous to suggest a simple mathematical relationship between unbalance length and viability” (Cohen et al. 1994). Nonetheless, attempts have been to calculate a correlation of quantitative chromatin imbalance with risk to have a liveborn affected child. Daniel et al. (1989), Cans et al. (1993), and Cohen et al. (1994) have compared the HAL with viability in translocation families. Most (96%) viable imbalances comprise up to 2% monosomy and up to 4% trisomy, with combinations of monosomy/trisomy viable only when the additive (or multiplicative) effect of x% monosomy plus y% trisomy falls within a triangular area defined by joining the 2% and 4% points on the x and y axes of a graph (Figure 5–28). A few (4%) fall outside of this area, and these cases define the boundaries of a “surface of viable unbalances,” reflecting the effects of qualitative differences in different segments of chromatin. For routine practice in the genetic clinic, and if the counselee wishes to have a good idea of the level of risk, we suggest starting off with the unvarnished empiric data for individual chromosome segments collected by Stengel-Rutkowski and colleagues, as set out in their invaluable monograph (Stengel-Rutkowski et al. 1988), and discussed in a review and further illustrated in practice (Stene and Stengel-Rutkowski 1988; Midro et al. 1992), and to which we have already referred several times above. The figures set out in Tables 5–4, 5–8, and 5–9 for the three major categories of malsegregation are 11 Translocation breakpoints mapped using only G-banded karyotype can also be surprisingly inaccurate when compared to molecular data, differing by as much as 50Mb (Ordulu et al. 2016) and adding another layer of imprecision to risk estimation.

130  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 5–28.  Assessing Viability of Unbalanced Forms. Viability of combined duplication/deletion states, according to amount of imbalance, measured as % HAL. Most (96%) fall within the triangular area whose hypotenuse lies between 4% duplication/0% deletion and 2% deletion/0% duplication, and a few outliers define an envelope of viable imbalances. Source: From O Cohen et al. 1994, Viability thresholds for partial trisomies and monosomies. A study of 1,159 viable unbalanced reciprocal translocations, Hum Genet 93: 188–194. Courtesy O Cohen, and with the permission of Springer-Verlag. Figure 5–27.  Differing Outcomes from Different Translocations. Notes: Different translocated chromosomes have different associations with reproductive outcomes, presumably reflecting, in part at least, the number and nature of the genes within translocated segments. The gene-sparse nature of parts of chromosomes 4, 9, 18, and 21 may be a factor behind their quite substantial fractions in the survivable “unbalanced offspring” category (albeit that the very small fraction due to gene-sparse chromosome 13 might seem inconsistent; but this may simply be a matter of the numbers in this study). Colored segments indicate proportions (y axis) associated with particular reproductive outcomes, for each chromosome (x axis). Source: From A Verdoni et al., Reproductive outcomes in individuals with chromosomal reciprocal translocations, Genet Med 23:1753–1760, 2021. Courtesy SA Yatsenko, and with the permission of Elsevier and the American College of Medical Genetics and Genomics. Autosomal Reciprocal Translocations  131 (continued) Table 5–4.  Risks in the Case of Adjacent-1 Segregation, with Single-Segment Imbalance Specific Risk Figures, Based upon Empiric Data, for Having a Liveborn Aneuploid Child or a Child Stillborn or Dying as a Neonatea Because of Single-Segment Imbalance from 2:2 Adjacent-1 Segregationb TRANSLOCATED SEGMENT THAT WOULD BE IMBALANCEDc RISK % LIVEBORN S.D. + % STILLBORN, NEONATAL DEATHe 1. 1pter→1p11–p34 0 1p35 ? 1qter→q11–q22 0 q23–q32 <1.3 + 5.1 q42 13.6 5.2 2. 2pter→p11–p12 0 p13–p16 <2.5 + 15.0 p21–p23 5.7 3.9 + 14.3 2qter→q11–q23 0 q31–q32 <1.7 + 6.7 q33 20.0 8.9 q34–q35 22.9 7.1 + 11.4 3. 3pter→p13–p14 0 p21 <2.3 + 13.6 p22–p25 28.6 17.1 3qter→q12–q13.2 0 q21–q27 <1.1 4. 4pter→p11 7.7 5.2 + 38.5 p14 15.4 4.5 + 7.7 p15 28.6 12 + 7.1 4qter→q11–q13 ?0 q21–34 0.8 0.8 + 14.1 5. 5pter→p11–p12 3.3 2.3 + 13.1 p13 7.0d 2.6 + 4.0 p14 29.4 11.1 5qter→q13–q21 ? q22–q33 7.7 7.4 + 7.7 q34 25.0 7.2 6. 6pter→p11–p12 ? p21.2–24 1.3 1.3 + 11.8 6qter→q11–q16 ?0 q21–q24 20.0 17.9 q25–q26 33.3 15.7 + 33.3 7. 7pter→p11–p13 4.4 3.0 + 4.4 p15–p21 19.1 8.6 + 4.8 7qter→q11–q21 ?0 q22–q35 <0.8 + 7.9 132  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY TRANSLOCATED SEGMENT THAT WOULD BE IMBALANCEDc RISK % LIVEBORN S.D. + % STILLBORN, NEONATAL DEATHe 8. 8pter→p11–p23 9.1 3.5 p23.1 40e 12.6 +20 8qter→q11–q13 2.0 2.0 q21.2–q24.2 11.1 6.1 9. 9pter→p11.2 11.8 3.7 +9.2 p13 25 8.8 +4.2 p22 21.2 4.4 +2.4 9qter→q11–q13 0 q21–33 <0.8 + 8.3 10. 10pter→p11.1 4.7 2.6 + 4.7 p12–p14 18.8 9.7 + 18.8 10qter→q11–q21 ?0 q22–q23 <1.4 + 5.7 q24 5.9 2.6 + 9.4 q25–q26 14.0 4.9 + 12.0 11. 11pter→p11–p13 ?0 p14 <3.1 + 6.3 11qter→q13–q22 <2.6 q23 7.0 3.9 + 18.6 12. 12pter→p11.1 9.4 5.2 + 3.1 p12 9.1 8.7 + 18.2 12qter→q11–q15 0 q21–q24.3 <1.5 + 3.8 13. 13qter→q11–q33 1.6 1.1 14. 14qter→q11.1–q31 1.0 1.0 15. 15qter→q11–q15 0 q21–25 2.7 2.7 16. 16pter→p11.11 8.3 3.6 16qter→q11–q13 6.2 6 + <3.1 q21–q23 <5.4 + <5.4 17. 17pter→p13.3 18.9 3.5 + 7.1 p11.1 <2.7 17qter→q11–12 ?0 q21–23 10.0 6.7 18. 18pter→p11.1–p11.2 ? (probably high) 18qter→q11.1–q12 2.5 2.5 q21 2.9 2.8 + 6.7 q22 15.0 7.8 + 15.0 19. 19pter→p11–p13.2 ?0 19qter→q11–q12 ?0 q13.2–q13.3 11.1 6.1 Table 5–4.  Continued

Autosomal Reciprocal Translocations  133 TRANSLOCATED SEGMENT THAT WOULD BE IMBALANCEDc RISK % LIVEBORN S.D. + % STILLBORN, NEONATAL DEATHe 20. 20pter→p11.1–p11.2 20.0 8.0 20qter→q11.1 ?0 21. 21qter→q11.1–q22 13.8 6.4 22. 22qter→q11.1–q13 <2.6 aFigures are expressed as a percentage of all karyotyped liveborn infants, typically considered as a baby of >28 weeks gestation, with survival at least beyond the neonatal period. Where there are data relating to unkaryotyped stillbirths or neonatal deaths, the figures for these are indicated with a + sign in the third column under “Risk,” as a probable additional component of the overall risk, on the assumption that many, at least, of these cases would have been karyotypically abnormal. The maximum estimate of risk will thus be given by the sum of the two percentage figures. This combined figure may be an overestimate but if so, likely of small degree, and this may be the more useful figure to consider. bOne specific translocated segment is of substantial genetic content (the one shown here), and the other is judged to be of minimal content. For adjacent-1 segregation, the risk does not differ between male and female heterozygotes. For segments not listed here, no specific data are recorded in Stengel-Rutkowski et al. (1988). cSome segments are noted precisely (e.g., 1pter→1p35). Most are given as a pair of breakpoints encompassing a range (e.g., 1pter→1p11–34), extending from a maximum length of terminal-to-proximal breakpoint to a minimum length of terminal-to-distal breakpoint. Thus, 1pter→1p11–p34 refers to an imbalanced segment comprising anywhere from a maximum of 1pter→1p11 (the whole of the short arm) to a minimum of 1pter→1p34 (about one-third of the short arm). dIn one reported large family with several cases of “pure” deletion or duplication of this segment (the other segment being derived from acrocentric short arm), the risk was very high: 54% (De Carvalho et al. 2008; and see text). eWhen the combined live birth + neonatal death figure approximates 50%, this may suggest that the single-segment imbalance is fully viable in utero in either the duplicated or deleted state, with approximately equal numbers of offspring due to alternate and to adjacent-1 segregation. S.D., standard deviation; ?, Rare cases have occurred, but data too few to derive a figure; ?0, Probably no risk; <, No additional aneuploid child has been born apart from the proband, figure is estimate of upper limit of risk interval. Sources: From Stengel-Rutkowski et al. 1988, with further entries/amendments from Pollin et al. 1999 (17p13.3), Stasiewicz-Jarocka et al. 2000 and 2004 (1q42, 2q33, 16q), and Panasiuk et al. 2007 and 2009 (4p, 9p), and personal communications A Midro (8p23.1) and M Ozaki (5p14). We are unaware of any more recent such studies; perhaps there is an opportunity for updating from services with large databases, and now in the more subtle molecular age. summarized from their monograph and from additional subsequent data. It would give a false sense of precision to use decimal points; a rounded figure will suffice. The paucity of information for some chromosomes has necessitated lumping of data for considerable lengths of a chromosome arm; the risk figures derived in this way are, naturally, composites, and indicative rather than definitive. We assume that, in different families with the same translocation (Table 5–5), the genetic risks will likely be the same, regardless of what may have been the mode of ascertainment. And of course, the principle always applies: If the counselee’s family is large enough, do a segregation analysis to derive a “private” recurrence risk, as well exemplified in Šumanović-Glamuzina et al. (2017). The figure given for a segment, say, q31/q34qter—in other words, a lumped figure applying to a segment extending anywhere from q31qter to q34qter—might be given as, say, <0.8%: in other words, a very small risk. (The “less than” sign in the risk data tables is used for estimates in those translocations where no additional aneuploid child Table 5–4.  Continued 134  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY has been born apart from probands.) But this figure might have been based mostly on data from families having a q31 breakpoint. A breakpoint at q34 might happen to exclude a dosage-sensitive region of major effect within q33, and thus imbalance for the slightly smaller segment q34qter might be of considerably greater viability. The risk figure needs to be interpreted intelligently in the light of what is otherwise known from the literature and Web resources about the segments in question, and naturally from observation within the same family. The reader consulting and using these figures, imperfect though they may be, will gain a good sense of the practical principles of estimating risk. Additional data may come to hand. For example, Stasiewicz-Jarocka et al. (2004) assembled data from 65 new pedigrees involving 16q, to add to the original 35 pedigrees from Stengel-Rutkowski and colleagues, and their combined risk calculations are included in the Tables. As expected, the new data continue to be consistent with the notion that the risk for viable unbalanced offspring increases with decreasing length of the segments. In another study, the methods of Stengel-Rutkowski et al. were applied to a large pedigree segregating a double-segment t(7;13)(q34;q13). Midro and colleagues (2006) were able to predict the chance of a miscarriage or stillbirth from carriers in this family to be 13% and 30%, respectively. The high rate of selection against abnormal karyotypes, applying in particular in the latter part of pregnancy with this particular translocation, resulted in a very low presumed risk (0.3%) of the abnormal outcome of a surviving liveborn. A determination of precise genetic risk in couples in whom the translocation implies a negligible risk of having a liveborn unbalanced child, may be, for some, less important now that genome-wide NIPT can be used to detect unbalanced segregants of translocations that have at least one large segment (Flowers et al. 2020). This approach allows couples to avoid the risks of invasive testing and to receive reassurance at 10 to 12 weeks’ gestation that the pregnancy is balanced. However, invasive testing remains a high priority for translocations in which both segments are very small, as these have the highest risk of leading to a liveborn unbalanced child, and the reliability of NIPT in this setting remains under assessment (Srebniak et al. 2021). For these couples, a precise risk assessment remains useful. Table 5–5.  Recurrent Translocations TRANSLOCATION TYPICAL PHENOTYPE OF UNBALANCED STATE REFERENCES t(11;22)(q23;q11) Emanuel syndrome Carter et al. 2009 t(4;8)(p16;p23) Wolf-Hirschhorn syndrome and * Giglio et al. 2002 t(4;11)(p16.2;p15.4) * Ou et al. 2011 t(8;22)(q24.13;q11.21) * Sheridan et al. 2010 t(5;11)(p15;p15) Beckwith-Wiedemann syndrome Slavotinek et al. 1997 t(6;20)(p21;p13) * Berner et al. 2012 t(1;12)(q43;q21.1) Vascular Luukkonen et al. 2018 Notes: The phenotypes in the unbalanced state due to the asterisked translocations are relatively nonspecific, with intellectual compromise in all. In the case of the t(1;12)(q43;q21.1), the phenotype is due to locus disruption, in the apparently balanced state.

Autosomal Reciprocal Translocations  135 RISK AT THE TIME OF PREIMPLANTATION GENETIC TESTING PGT for a reciprocal translocation has been available for much of this century. Initially, it was the day-3 cleavage-stage embryo at IVF that was analyzed, but latterly it has been the day-5 blastocyst that is chosen (Chapter 23). In terms of the relative detection rates at these two timeframes, there is a small but definite increase in the normal/balanced detection rate, from 25% to 28% (Tian et al. 2022); this likely reflects a lethality of embryos with a substantial monosomic load during the day 4 to day 5–6 period. PGT requires a very different viewpoint, since in utero (in other words, post-implantation) lethality has not had the chance to operate; hence a wide range of imbalances may be seen, the great majority of which could never survive to term, and indeed, many would fail even before implantation. The numerator/denominator of the risk figure becomes the fractions of euploid and aneuploid embryos out of all created embryos. The overall figure of about one-quarter to one-third, for the fraction of day-5 embryos that are euploid, is consistently seen across a number of studies in which large numbers (thousands) of blastocysts have been analyzed (Xie et al. 2022; Oğur et al. 2023; Zhou et al.2024). A typical range of findings is shown (Table 5–6) in the smaller study of Shetty et al. (2022). In the series of Xie et al., in which over 2,000 rcp carrier couples were studied—all of whom had presented with histories of infertility, recurrent spontaneous abortion, or having had a pregnancy with a chromosomal abnormality—the segregation ratios were as follows: alternate, 46%; adjacent-1, 31%; adjacent-2, 12%; and 3:1, 30%. A proportion of these embryos may have other aneuploidies unrelated to the translocation, and more so in the case of an older mother. In the series of Zhou et al. (2024), one-fifth of blastocysts had an abnormality unrelated to the translocation. The subtleties of the range of potential imbalances here may be, to some counselees, a little beside the point: the aim is, naturally, to select a normal/balanced embryo, and whatever the abnormal ones are, they can be disregarded. What really matters, of course, is the take-home baby rate (Lledó et al. 2010). Overall, the proportion of successful pregnancies per embryo transfer, after PGT, is around one-half. In the series of Oğur et al. (2023), that figure was 43% for mothers under age 35, and 58% for those over that age; interestingly, the respective miscarriage rates, at 12% and 5%, were actually less than the general population risk.12 Xie et al. (2022) reported an overall delivery rate, per embryo transfer, of 50%. A similar livebirth figure (56%) comes from Zhou et al. (2024) in couples who had a single embryo transfer. If the chances of an embryo at PGT being normal is one-third, and the odds for a successful transfer one-half, only one in six fertilized ova will, on average, result in a baby. Tong et al. (2022b) propose that four or more embryos would need to be created in order to improve the odds of having at least one euploid embryo. The absence of any effect on the outcome due to parental gender is confirmed in Tan et al. (2025). Of the euploid embryos, essentially one-half are non-carriers of the translocation (Zhou et al. 2024). It is possible to distinguish between a carrier and a normal embryo via haplotype analysis, using genotype data generated from SNP arrays (Treff et al. 2016; Xu et al. 2017), whole genome sequencing (Zhai et al. 2022), or long-read nanopore sequencing (Madjunkova et al. 2020). While this may be an attractive option to parents who will be only too aware of the complicated reproductive implications of 12 The numbers in each age group were not large, 52 cf. 22, and so the apparently better outcomes for older mothers should not be over-interpreted. Table 5–6.  Chromosome Segregations in 65 Blastocysts of 8 Female and 8 Male Reciprocal Translocation Heterozygotes, and the Outcomes TRANSLOCATION BLASTOCYSTS BIOPSIED CHROMOSOMAL DIAGNOSES EMBRYOS TRANSFERRED OUTCOME POST TRANSFER Normal (n) Unbalanced 46,XX, t(1;6)(p36.1;q13) 4 0 (−6), (+1,−6), (+6), M 0 n/a 46,XY,t(2;17)(q31;p13) 3 1 (−2), (+2) 1 Delivery 46,XY,t(4;18)(p12;q11.2) 3 1 (−4,+8), M 1 Delivery 46,XY,t(4;21)(q25;q22) 2 0 (+4, −21), (−4,+21) 0 n/a 46,XX,t(5;8)(q31;p22) 4 2 7, S 2 Delivery 46,XX,t(5;9)(q22;p22) 7 2 (+5,−9) ×3, (−5,+9) ×2 2 Delivery 46,XX,t(6;7)(q25;q22) 5 2 (−6,+7), (−7), (−6,+7,−16) 1 Failed transfer 46,XY,t(6;11)(p21;q23) 2 1 (−6,+11) 1 Delivery 46,XX,t(7;13)(p13;q22) 6 2 (+7,−13), (+7,−13,−11), (−7,+13), M 1 Failed transfer 46,XY,t(7;17)(p22;p11) 4 2 (−17), M 1 Failed transfer 46,XX,t(8;12)(p11.2;q24.3) 5 2 (−8), (+8,−12), M 2 Delivery 46,XY,t(8;15)(q13;q24) 4 1 (+8,−15), +3, +6 1 Delivery 46,XY,t(9;22)(q34;q11) 4 3 +6 2 Delivery 46,XX,t(10;14)(p13;q24) 3 2 (−14,−22) 1 Miscarriage 46,XX,t(11;22)(q23;q11.2) 6 1 (+11,−22) ×2, (+11), (−11+22), S 1 Failed transfer 46,XY,t(14;21)(q22;q22.1) 3 0 (+3,+6), (+14, −21), (−14, +21) 0 n/a TOTALS 65 22 43 8 deliveries Notes: The + and − refer either to translocation segments, or to the whole chromosome. Thus, +2 = dup(2) or trisomy 2, and −6 = del(6) or monosomy 6. M = multiple aneuploidies; S = sex chromosome abnormality. n/a = not applicable. As well as an overall fraction of 46% of embryos imbalanced due to malsegregation of the translocation chromosomes, 17% had an unrelated sporadic aneuploidy: note that some of the imbalances listed above involve a chromosome not involved in the translocation. “Normal” includes the balanced carrier state. In half of couples, a successful pregnancy was achieved. Source: S Shetty et al., Preimplantation genetic testing for couples with balanced chromosomal rearrangements, J Reprod Infertil 23:213–223, 2022.

Autosomal Reciprocal Translocations  137 the carrier state, many couples will not have a luxury of being able to discard any euploid embryos. RISK AT THE TIME OF AMNIOCENTESIS The likelihood of detecting an abnormality is higher at prenatal diagnosis than it is at the birth of a live baby, reflecting the differential survival throughout pregnancy. Daniel et al. (1988) derived an overall figure of about 25% for carriers to have an unbalanced fetal karyotype detected at early second trimester (the time at which amniocentesis would usually be done) when ascertainment was through a previous aneuploid child, and about 5% when it was through recurrent miscarriage. The amniocentesis-time figure is at its highest, 35%, in the carrier whose risk otherwise to have an aneuploid live birth lies in the “medium” range (5%–10%) (Stengel-Rutkowski et al. 1988). To give an example from a specific chromosomal segment, Stengel-Rutkowski and colleagues record a 6% risk for an imbalance in the liveborn from translocations with a proximal 9p breakpoint, versus a 33% risk to detect an imbalance at amniocentesis. In a series of 57 pregnancies in 40 translocation couples, Barišić et al. (1996) determined an overall risk of 16% to discover an unbalanced karyotype at second-trimester amniocentesis, confirming a higher risk (32%) for couples who had previously had an abnormal child, versus a lower figure (12%) where ascertainment had been because of miscarriage. Similar data concerning chorionic villus sampling and noninvasive prenatal testing are not available. Risks According to Likely Segregation Mode ADJACENT-1 SEGREGATION, SINGLE SEGMENT Specific risk figures for individual single-segment imbalances, in terms of the outcome of an aneuploid liveborn child, are set out in Table 5–4. A notable point is the number of risk figures that are very small, less than 1%. This most likely reflects that many imbalances are almost always lethal in utero, and survival through to term is the exception. In fact, we can say that in order of frequency, there are imbalances which are (1) invariably lethal; (2) almost always lethal; (3) often lethal; and (4) the least frequent category, usually survivable. These risk figures are likely to be valid irrespective of the mode of ascertainment of the family or of the identity of the other chromosome contributing the telomeric tip, at least in the majority of translocations. By way of example, imagine that a carrier in the t(4;12)(p14;p13) family of Mortimer et al. (1980) noted above had sought advice about their own risk to have an abnormal baby. The single-segment involved is 4p14pter. According to the rules set out earlier, adjacent-1 segregation is the category that implies risk for viable imbalance in this family translocation. Consulting Table 5–4, therefore, we see that the risk for imbalance (whether deletion or duplication) is given as 15.4%. The standard deviation (± 4.5) is quite small, indicating that the estimate is based on a good number of cases. But we also pay attention to the datum “+ 7.7” with reference to previous unkaryotyped stillbirths and neonatal deaths, many of which will have been, surely, chromosomally abnormal: the dysmorphology evident in old photographs can be quite indicative (Figure 5–29). So the true figure to have an abnormal baby at term, who might or might not live, could well be 15.4 + 7.7 = 23.1%. A “private estimate” in this family had come up 138  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY with a figure of 25%, which is sufficiently close to 23.1% to provide reassurance as to its accuracy. The risk at preimplantation testing is naturally seen through a different lens. Here, the full range of malsegregation may be observed. As noted above, around one-quarter to one-third of blastocysts will be euploid, while the remainder majority are imbalanced due to malsegregation of the translocation or to an unrelated aneuploidy. ADJACENT-1 SEGREGATION, DOUBLE SEGMENT Every double-segment translocation is likely to be a unique case (or at least no other described family is known), and risk assessment is less precise. One known recurrent double-segment translocation, the t(4;8)(p16;p23), has been seen in sufficient numbers for a useful risk estimate to be derived (Table 5–5), and some other examples are listed. Of course, if the family is large enough, a private segregation analysis will provide the best estimate. If no literature data is available, and in the absence of a family study, Stengel-Rutkowski et al. (1988) otherwise recommend considering each segment separately. They propose the rule of thumb that the risk will be half that of the smaller of the two risk figures. Even this may be an overestimate. Consider the t(4;9)(p15.2;p13) family listed in Table 5–7. The smaller of the risks is that applying to 9p13, as a single-segment, and which is given at 25% (from Table 5–4); this halves to 12.5%. But from an actual family study, the empiric figure was only 3.2% (Midro et al. 2000). And in many cases, the duplication/deficiency from a double-segment imbalance will be invariably lethal in utero—a risk of 0%—notwithstanding that each segment separately is on record with viability in the single-segment state. When the translocated segments are of small content, one or possibly both of the dup/ del and del/dup combinations could be viable. Segregation may be due to the adjacent-1 format, or possibly simply an independent 1:1 segregation of each normal homolog and its derivative chromosome, as discussed above. The family history may well be informative, as illustrated in Midro et al. (2014). Two large kindreds were segregating apparently the same t(1;11)(p36.22;q12.2); and although no familial link was known between the kindreds, who both came from the same region in Poland, it would not be surprising were Figure 5–29.  Photograph of a Baby who had Died in Infancy Years Before, from a t(4p;12p) Family. Note: A retrospective diagnosis of Wolf-Hirschhorn syndrome is reasonably proposed. Source: From JG Mortimer et al., A further report on a kindred with cases of 4p trisomy and monosomy, Hum Hered 30:58–61, 1980.

Autosomal Reciprocal Translocations  139 this indeed the case. The only viable imbalanced outcome was taken to be the adjacent-1 combination, with monosomy 1p36.22→pter, and trisomy 11q12.2→qter (Figure 5–30). The no. 11 segment was not small in terms of length, but is apparently small in content, such that trisomy for most of 11q is a viable imbalance. The risk for this outcome was calculated at 6%, which is rather more than might have been drawn from Stengel-Rutkoski et al. (1988). As with the t(4;12) family above, retrospective assumptions had to be made, since all the presumed affected babies had died, with similar neural tube malformations. Carriers had an increased risk for miscarriage, 35%. Sperm studies in one heterozygote showed gametes of alternate, adjacent-1, adjacent-2, and 3:1 malsegregation, of relative fractions 40%, 38%, 5%, and 11% respectively. Table 5–7.  Risks in the Case of Adjacent-1 Segregation, with Double-Segment Imbalance TRANSLOCATION RISKc % LIVEBORN S.D. + % STILLBORN, NEONATAL DEATH t(1;2)(q42;q33) 6.8 t(1:3)(q42.3;p25) 63.6 14.5 t(1;11)(p36.22;q12.2) 6.2 3.5 <1.1 t(2;13)(p25.1;q32.3) 14.5 7.6 + 4.8 t(3;10)(p26; p12) 24.0 8.5 t(3;15)(q21.3;q26.1) ?0 + 17 t(4;5)(p15.1;p12) 1.6 t(4;8)(p16.1;p23.1) 18.8 9.7 t(4;8)(p16.3;p23.1) 41.2 11.9 t(4;9)(p15.2;p13) 3.2 3.2 + 6.5 t(4;19)(p15.32;p13.3) 3.7 3.6 + 7.4 t(7;9)(q36.2;p21.2) 30 14.5 + 10 t(7;13)(q34;q13) 0.3* + 29.0 t(12;14)(q15;q13) ?0 +?0 t(16;19)(q13;q13.3) 1.2 t(16;20)(q11.1;q12) 1.1 Notes: Empiric risk figures for having a liveborn aneuploid child, or a child stillborn or dying as a neonate,a because of double-segment imbalance from 2:2 adjacent-1 segregation, in 14 specific translocationsb *Plus another 0.2% to account for a theoretical risk for interchange trisomy 13. The considerable gap to the next risk figure, 29%, reflects the several instances in this family of unkaryotyped stillbirths and early neonatal deaths. aFigures are expressed as a percentage of all karyotyped liveborn infants, as described in the legend in Table 5–4. ?0 indicates probably no risk, albeit that the 17% risk figure above for stillbirth/neonatal death in the t(3;15)(q21.3;q26.1) indicates viability of the unbalanced state through to the end of pregnancy. bFamilies published in Kozma et al. (2004), Midro et al. (2000, 2006, 2014, 2016), Nucaro et al. (2008), Stasiewicz-Jarocka et al. (2000, 2004), Tranebjaerg et al. (1984), Wiland et al. (2007), and Šumanović-Glamuzina et al. (2017), and personal communication, AT Midro. cSome figures come from direct segregation analysis, and in others from applying this rule: Halving the risk for the lesser of the two risks, which would otherwise have applied to each translocated segment when viewed as a single-segment imbalance (and see text). 140  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 5–30.  A Double-Segment Translocation Seen in Two Extensive Kindreds. Notes: This double-segment translocation, t(1;11)(p36.22;q12.2), was studied in two extensive four-generation pedigrees, the two quite possibly connected. The larger of the two is depicted here; the balanced translocation carriers are shown with bulls-eye symbol. The large numbers enable the derivation of a quite precise risk estimate (see text). The only viable imbalanced combination from this translocation was the adjacent-1 malsegregant leading to monosomy for distal 1p and trisomy for much of 11q. As the reader may determine, such a karyotype would be 46,der(1)t(1;11): that is, the der(1) in the company of two no. 11 chromosomes. The malformative phenotype was lethal in early infancy, as shown with the filled symbols. The many miscarriages (the small black circles) presumably reflect unviable malsegregant outcomes. Source; From AT Midro et al., Recurrence risks for different pregnancy outcomes and meiotic segregation analysis of spermatozoa in carriers of t(1;11)(p36.22;q12.2), J Hum Genet 59:667–674, 2014. Courtesy M Gajęcka, and with the permission of Springer. Autosomal Reciprocal Translocations  141 142  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY The different scenario implied by preimplantation analysis is seen, by way of example, in the double-segment translocation t(3;11)(q27.3;q24.3) carried by a brother and sister (Coonen et al. 2000). At least 15 out of 18 embryos of the brother were karyotypically unbalanced, and only one was normal or balanced. This one embryo was transferred, amniocentesis showed 46,XX,t(3;11), and a healthy carrier daughter was in due course born. His sister, a carrier of the same translocation, underwent two treatment cycles, with two out of six embryos apparently normal, but neither transferred successfully. In another PGT case, relating to a couple one of whom carried a t(2;17)(qter;qter), 13 of 18 embryos showed 2:2 segregation for the translocation (six alternate, seven adjacent-1) consistent with either two independent 1:1 events or 2:2 disjunction from a quadrivalent (McKenzie et al. 2003). The remaining five malsegregants displayed 3:1 segregation. ADJACENT-2 SEGREGATION Very few translocations are capable of producing viable adjacent-2 segregant products, and the data on specific risk levels are limited (Table 5–8). Where the potential imbalance has considerable viability (for example, trisomy 9p and trisomy 21q) the risk is likely to be substantial and may be in the range of 20%–30%. The t(9;21) carrier mother in Figure 5–14, for example, would have, from Table 5–8, an 18% risk for the recurrence of trisomy 9p. 3:1 SEGREGATION, TERTIARY ANEUPLOIDY In contrast to 2:2 segregation, the probabilities for unbalanced 3:1 outcomes differ between the sexes, with the female (and especially if of older maternal age) having the Table 5–8.  Risks in the Case of Adjacent-2 Segregation Specific Risk Figures for Liveborn Aneuploid Child due to Imbalance from 2:2 Adjacent-2 Segregation CENTRIC SEGMENT THAT WOULD BE IMBALANCED RISK % S.D. 4pter→q11–q13 ?0 8pter→q12–q13 ? 9pter→q11–q13 18.4 4.5 10pter→q11–q21 ? 12pter→q11–q13 ? 13pter→q14–q21 ? 14pter→q21–q22 ? 15pter→q13–q24 11.8 7.8 20pter→q11.1 27.3 13.4 21pter→q11.1–q22 ? Note: Figures are expressed as a percentage of all live births. No obvious difference exists according to sex of parent. For the very many segments not listed, no specific data are recorded in Stengel-Rutkowski et al. (1988). ?, Rare cases have occurred, but data are too few to derive a figure; ?0, Probably no risk. Source: From Stengel-Rutkowski et al. (1988).

Autosomal Reciprocal Translocations  143 greater risk (Figure 5–10). For translocations other than the common t(11;22)(q23;q11), the risk is generally small and less than 2%. Nevertheless, each translocation is entitled to its individuality, and atypically higher risks are possible, as may be exemplified in the t(12;13) noted earlier and shown in Figure 5–17, in which two out of four children had a tertiary monosomy. In this case, it could be that the tiny derivative segregated independently, at random. The Common t(11;22). Practically the only segregation mode to produce a viable abnormal baby in the common t(11;22)(q23;q11) is 3:1 with tertiary trisomy (Emanuel syndrome) (Figure 5–16). Different figures have been proposed for the level of risk. From the data of Stengel-Rutkowski et al. (1988) as listed in Table 5–9, the risk is 3.7% and <0.7%, respectively, for the female and the male carrier. In a very large collaboration, with data from 110 families seen in 15 countries (there being some overlap with the material in Stengel-Rutkowski et al.), Iselius et al. (1983) arrived at risk figures for the female and male heterozygote, respectively, of 2.1% and 1.8%. Notably, in most of these families the index case was the only one known definitely to have the unbalanced karyotype. However, it could be supposed that reported malformed stillborn infants in these families were rather likely also to have had the unbalanced karyotype, and if this assumption is accepted, the risk figures for a live- or stillborn affected infant would increase to 5.7% and 5%, respectively. A rather higher risk figure for the female carrier, namely ~10%, is due to Zackai and Emanuel (1980). These authors also observed that the chance of transmitting the translocation in balanced state is significantly greater than the theoretical 50%, with a probability of >70% in the families studied (a form of meiotic drive). An earlier concern about a breast cancer risk to the heterozygote has since been dismissed (Carter et al. 2010). 3:1 SEGREGATION, INTERCHANGE ANEUPLOIDY The risk to have a child with Patau, Edwards, or Down syndrome from an interchange trisomy is remarkably small. It may be in the vicinity of 0.5% in the female, and less than this in the male (Stengel-Rutkowski et al. 1988). Upper limits of the estimated risks are given in Table 5–9. The figures for PGT can be much higher: 5.4% in the survey of Xie et al. (2022), and as illustrated by the case of Conn et al. (1999) noted above, in which a woman with the karyotype 46,XX,t(6;21)(q13;q22.3) had 9/9 embryos with chromosome imbalance, including two with interchange trisomy 21 and one with probable interchange monosomy 6. MORE THAN ONE UNBALANCED SEGREGANT TYPE It is prudent to assume that where more than one mode of segregation can lead to a viable outcome, the overall risk will be cumulative and will be given by the sum of the individual risks. Thus, the carrier mother of the t(11;18)(p15;q11) shown in Figure 5–19 would have a risk comprising three components: duplication 18q11qter due to adjacent-1; tertiary trisomy 18pter-q11 due to 3:1; and trisomy 18 due to 3:1 interchange. From Tables 5–4 and 5–9, and choosing the closest listed segments, these risks are 2.5%, <1.3%, and <0.2% respectively, for a total of up to 4.0%. IMPRINTABLE CHROMOSOMES AND UNIPARENTAL DISOMY Any translocation of which a participating chromosome has an imprintable segment is to be considered from this specific perspective. Here, the gender of the transmitting parent becomes relevant. But in practice, this is a very rarely observed circumstance 144  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Table 5–9.  Risks in the Case of 3:1 Segregation, with Double-Segment Imbalance Specific Risk Figures for Liveborn Aneuploid Child due to Imbalance from 3:1 Single-Segment Segregation A. TERTIARY TRISOMY OR MONOSOMY Segment That Would Be Imbalanced RISK % S.D. 4pter→q12–q13 ? 8pter→q12–q13 ? 9pter→q11–q32 1.7 (mat) ?0 (pat) 1.7 10pter→q11.1–q21 ? 11qter→q23* 3.7% (mat) <0.7% (pat) 12pter→q11–q13 ? 13pter→q12–q33 2.6 (mat) 0 (pat) 1.8 14pter→q11.1–q24 2.6 (mat) <0.8 (pat) 2.6 15pter→q11.1–q24 <0.9 16pter→q11.1 <1.8 (mat) 0 (pat) 18pter→q11.1–q21 <1.3 (mat) 0 (pat) 20pter→q11.1 <4.4 (mat) ?0 (pat) 21pter→q11.1–q22 6.9 (mat) 4.7 22pter→q11.1–q13 <3.5 (mat) ? (pat) B. INTERCHANGE TRISOMY Chromosome That Would Be Trisomic RISK % S.D. 13 <0.2 (mat) 0 (pat) 18 <0.2 (mat) <0.3 (pat) 21 0.5 (mat) <0.6 (pat) 0.5 Notes. Figures are expressed as a percentage of all live births. Risks for maternal transmission (mat) are typically greater than for paternal (pat) in 3:1 segregations. For segments not listed, no specific data recorded in Stengel-Rutkowski et al. (1988). ?, Rare cases have occurred, but data are too few to derive a figure; ?0, Probably no risk. *The common t(11;22)(q23;q11). Source: From Stengel-Rutkowski et al. (1988).

Autosomal Reciprocal Translocations  145 (Table 19–6). Liehr (2025a) recorded only eight examples of uniparental disomy (UPD) for chromosome 7, 15, 16, and 20, in the setting of reciprocal (not Robertsonian) translocations. For example, Silver-Russell syndrome due to UPD(7) has been reported just twice in association with a maternal translocation involving chromosome 7 (Behnecke et al. 2012). A potential risk for UPD following post-zygotic “correction” is noted above. What looks like alternate segregation in the fetus could actually have been 3:1 interchange trisomy, with a post-conceptual loss of the homolog in question. In practice, this appears to be an exceedingly rare outcome (Dupont et al. 2002; Kotzot 2008a; Heidemann et al. 2010). An example is the case in Calounova et al. (2006): A child with Prader-Willi syndrome had the same 46,XX,t(8;15)(q24.1;q21.2) karyotype as her mother, with absence of a paternal chromosome 15, and thus with UPD(15)mat. This much is certain: Any translocation involving chromosome 15 in particular is to be approached very circumspectly. Phenotype and Survivability A major degree of dysmorphogenesis, involving several body systems, and globally disordered brain function, is the typical picture in classical viable autosomal imbalance resulting from a parental reciprocal translocation. The physical phenotype is usually less markedly abnormal in imbalances detectable only on molecular karyotyping, and indeed sometimes essentially physically unscathed, although neurocognitive and behavioral difficulty is often of important degree. Many patients will come with the knowledge of the particular phenotype of at least one of the viable segregant outcomes—the proband in their own family. The same imbalance in a future pregnancy would be expected to lead to a similar physical and mental phenotype.13 Survivability is less predictable because, for many conditions, there is a fine line between relative robustness and a fragile hold on existence, intrapartum and post-natally. Whether there is a heart defect (a frequent malformation in many chromosomal disorders) may be a major factor in this. As for the phenotype of potentially survivable outcomes other than those already exemplified in the family, reference to the chromosomal catalogs and databases and to the journal literature provides a guide. For imprintable chromosomes, there may be an influence of the parental origin of the aneuploid segment, as noted above. THE PARENTAL BALANCED TRANSLOCATION IN A FETUS The conventional wisdom has been that if the same (balanced) karyotype found in the carrier parent is detected at prenatal diagnosis, there is no increased risk for phenotypic abnormality in the child: Like parent, like child. Some have doubted this, and Fryns et al. (1992) measured a 6.4% risk of mental and/or physical defects in the heterozygous children of translocation carriers (this figure including the background risk of 2%–3%). Others remained skeptical and imputed ascertainment bias as the confounding factor (Steinbach 1986). Theoretical mechanisms whereby an ABT could have a deleterious consequence in a child, the parental normality notwithstanding, are discussed above. 13 Similar may only mean “quite similar, but a little different.” Just as trisomy 21 presents quite a range in intellectual capacity, variation may be observed with the identical segment, duplicated or deleted, in different family members. The rest of the (balanced) genome, which will of course differ, may, in (usually) small degree, dictate a relative vulnerability or resistance to the damaging effects of the imbalance. 146  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY If an important additional risk due to one or other of the aforementioned scenarios really does exist, it is surely very small, perhaps no more than “a fraction of a percent” that a child with the “balanced” parental karyotype might have a defect of mostly unpredictable severity and extent. In the meantime, it remains true that in the great majority the balanced translocation really is balanced, structurally and functionally, and of itself will have no detrimental effect (beyond an eventual influence upon the child’s reproductive health). Thus, in practical terms, it would be appropriate to advise continuing a pregnancy when the fetal karyotype is the same as that of the carrier parent, and with very considerable (if not absolute) confidence of a normal physical and mental outcome. If the above advice failed to reassure, this presumably tiny residual risk could be addressed, if this facility is available, by selection at preimplantation diagnosis of only those embryos in which a normal 46,XY or 46,XX chromosome constitution has been inherited (Chow et al. 2020; Pei et al. 2022). This would also have the advantage of eliminating the reproductive risk for the next generation. But, as noted above, the small numbers of embryos available with a balanced karyotype may not allow the luxury of choice in that regard. Infertility and Pregnancy Loss INFERTILITY Both male and female translocation carriers may be affected by infertility, as discussed above, and the infertility can be pregestational (failure to conceive) or gestational (pregnancy loss). Assisted conception, with particular reference to ICSI in the male case, may enable some to become parents (Jesus et al. 2019; Cui et al. 2022; Shetty et al. 2022). But of course in any event, the translocation will convey a genetic risk. MISCARRIAGE Conceptions with large imbalances will abort. Against the background population risk of 15% for a recognized pregnancy to miscarry,14 the risk for the translocation carrier is rather greater, in the range of 20%–30% (Stengel-Rutkowski et al. 1988). For a few, the risk is very high, well over 50%. An increasing viability of conceptuses implies a corresponding declining likelihood of pregnancy loss by miscarriage. Not to diminish the distress felt at the loss of a welcomed and wanted pregnancy, patients can perhaps be heartened that miscarriage in this setting is the natural elimination of a severe abnormality, which provides the opportunity to make a fresh, and hopefully a more fortunate, start. For a couple having lost all pregnancies to miscarriage, karyotyping in the previous generation may be helpful. The consultand would, in her- or himself, embody the proof that the heterozygote can have a normal child, should one of his or her parents also be a carrier. Optimism has to be muted, however, in the setting of a family history of many miscarriages, which may indicate a propensity for the production of unbalanced gametes. 14 This figure applies with respect to clinically diagnosable miscarriage, mostly occurring in the period 8 to 16 weeks of gestation. Severely imbalanced forms may be lost as very early or even occult abortions.

Autosomal Reciprocal Translocations  147 Other Issues OTHER FAMILY MEMBERS WITH THE SAME TRANSLOCATION It appears to be the case that a translocation studied in one family member will typically display similar meiotic behavior in other carriers in the family; at least this applies to the male, in whom gametic analysis is more readily pursued (Benet et al. 2005; Wiland et al. 2007). Thus, genetic advice can be, in practice, the same for one and all. ASSOCIATED MENDELIAN CONDITION Rare translocations are associated with a Mendelian disorder due either to the breakpoint disrupting or influencing a locus, or with coincidental linkage to a mutation near the breakpoint. We note some examples in the earlier section on “Biology.” In such families, over and above any risk associated with unbalanced segregants, one should discuss the risk of transmitting the abnormality peculiar to that chromosome. A BELATED CHROMOSOMAL DIAGNOSIS Some familial syndromes have turned out to be due to a segregating translocation. Examples include Pitt-Rogers-Danks syndrome, which is actually due to a 4p deletion and thus a form of Wolf-Hirschhorn syndrome, and Ruvalcaba syndrome, due to a del/ dup of 2q37.3qter and 5q35.2qter (Boyd et al. 2025). CANCER RISK In rare familial translocations, the rearrangement may disrupt or otherwise influence a cancer-associated gene, or promote mitotic malsegregation and thus comprise a “hit” in the cascade of events leading to the cellular phenotype of cancer, over and above any risks to the heterozygote for offspring of theirs. A more detailed treatment is offered in Chapter 25 (p. 780). Interchromosomal Effect There had originally been concern that a reciprocal translocation heterozygote might be prone to produce gametes aneuploid for a chromosome not involved in the translocation, specifically in this context, chromosomes 13, 18, 21, or X. And there has been the occasional report of a translocation carrier having offspring with chromosomal imbalance not related to the family’s translocation (Couzin et al. 1987). Warburton (1985) reviewed the associations of reciprocal translocations and trisomy 21 from unbiased (amniocentesis) data and found no evidence to support the contention. Uchida and Freeman (1986) and Schinzel et al. (1992) studied families in which a child with trisomy 21 also had a balanced translocation, and while in several the translocation was of paternal origin, in fact the extra chromosome 21 came from the mother. More directly, numerous sperm karyotyping studies have, for the most part, shown no increase in disomies unrelated to the translocation, although some workers have raised doubts. Pellestor et al. (2001) suggest that carrier males with poor semen indices are the only ones in whom any such effect might exist; in which case, it might be the altered testicular environment, rather than the translocation of itself, that is the cause (Kirkpatrick et al. 2008). Analysis of embryos at preimplantation diagnosis largely supports the view of little or no evidence that there exists an interchromosomal effect due to 148  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY a balanced translocation (Mateu-Brull et al. 2019; Oğur et al. 2023), but with a contrary opinion from Verdoni et al. (2021), who point to an increased risk for an unrelated aneuploidy only in female carriers. Certainly, blastocysts from translocation carriers very often have an aneuploidy due to chromosomes other than those involved in the translocation (Zhou et al. 2024, as noted above). But equally, aneuploidy of the embryo is also very frequent in the case of 46,XX and 46,XY parents. To conclude: it may well be that some specific translocations15 do have a very small individual risk, perhaps confined to the female rcp heterozygote of an older maternal age, but there seems little reason to withdraw from the generality of Jacobs’s assessment from 1979; and in practical terms we expect her view to prevail, albeit that we add cautionary comments in brackets: “There is no [definite] indication that parents with a structural abnormality are at a [discernibly] increased risk of producing a child with a chromosomal abnormality independent of the parental rearrangement . . . and their recurrence risk for such an event is [practically] the same as the [maternal-age specific] incidence rate in the population.” 15 Note that a true interchromosomal effect does indeed exist with the Robertsonian carrier.

6 SEX CHROMOSOME TRANSLOCATIONS THE SEX CHROMOSOMES (gonosomes) are different,1 and sex chromosome translocations need to be considered separately from translocations between autosomes. A sex chromosome can engage in translocation with an autosome, with the other sex chromosome, or even with its own homolog. The unique qualities of the sex chromosomes have unique implications in terms of the genetic functioning of sex-autosome translocations. Unlike any other chromosome, the X chromosome is capable of undergoing “transcriptional silencing”—or, as is more usually spoken, facultative2 X chromosome inactivation (XCI)—of almost all of its genetic content. This fact has crucial consequences for those who carry an X-autosome translocation, in both the balanced and the unbalanced states. And, unlike any other chromosome, the Y is composed of chromatin which is, in large part, permanently inert; only a small, mostly male sex–related segment, is active. Some translocations of this inert material can thus be of no clinical significance. BIOLOGY The X-Autosome Translocation Both females and males can carry, as heterozygotes or hemizygotes respectively, an X-autosome translocation, in balanced or in unbalanced state. But the implications for the two sexes are rather different, and we therefore need to treat the two cases separately. First, we need to review the concept of X-inactivation. X-INACTIVATION The normal 46,XX female has two X chromosomes, and yet the possession of only a single X is sufficient to produce normality in the 46,XY male. Are the sexes really so genetically different? Does the female really need a second X? In fact, the second X is largely surplus to requirement, and in order to maintain an appropriate functional balance, it is “switched off ”—or, as usually spoken, inactivated. Very early in female embryonic existence,3 a process is initiated whereby one of the two X chromosomes in 1 But about 200 million years ago in mammalian evolution they were the same, and functioning as autosomes. The sex chromosomes as they are now comprise an older X-conserved region, shared across marsupial and placental mammals, and a more recent X- and Y-added region (an autosomal sequence translocated to the X and Y chromosomes) evolving only in placental mammals, which happened about 100 million years ago (Cotter et al. 2016). 2 “Facultative” refers to inactivation that can occur, or not, as circumstances demand. In other words, in the current context, if the karyotype includes a number of X chromosomes greater than one, such supernumerary X chromosome(s) are inactivated. The opposite is “constitutive” inactivation, which refers to chromatin that is permanently inactive. 3 The process may commence at different times in different cell lineages. Both Xs are inactive in the zygote, and both become active by the 8-cell stage. Selective inactivation of one X—that is, definitive XCI—then 150  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY every cell of the conceptus is randomly genetically inactivated, such that transcription of most of its genes cannot occur (X chromosome inactivation, XCI). This process of transcriptional silencing is initiated at an X-inactivation center (XIC) in Xq13 (Figure 6–1), and it spreads outwards in both directions along the chromosome. The process is called (after Dr. Mary Lyon) Lyonization. In all descendant progeny cells thereafter, the same X chromosomes remain inactive or active, respectively. This “dosage compensation” allows for a necessary functional monosomy of most of the female XX chromosomal genome, analogous to the normal monosomic X state of the XY male: hence, in terms of the expression of genes on the X chromosome, the sexes are, in fact, genetically very similar. Within the XIC is a gene XIST that is cis-acting (that is, it can influence only the chromosome that it is actually on), and XIST is transcribed only from the inactivated X. This transcript—named “XIST” for X (inactive) specific transcript—is not translated into protein, but functions as a long-noncoding RNA molecule (lncRNA). The XIST RNA “coats” the X chromatin and influences the degree of acetylation and other modification of the histones, and this, in turn, prevents the DNA from being transcribed.4 This commences with some tissues of the blastocyst, progresses to other lineages thereafter, and is completed embryo-wide by the gastrulation stage, that is, by week 2 to 3 (Khan and Theunissen 2023). 4 An intriguing suggestion that XIST could have a therapeutic role in trisomic conditions, by inserting an XIST transgene into the aneuploid chromosome and thereby “dosage-compensating” the trisomy, is a theoretical concept well beyond the current scope of this book (Gupta et al. 2024). Figure 6–1.  Notable regions of the sex chromosomes. AZF, azoöspermia factor regions a–d. Dots show specific loci: DAZ, deleted in azoöspermia locus; MLS, microöphthalmia with linear skin lesion gene; SHOX, short stature homeobox gene (X chromosome); SHOXY, short stature homeobox gene (Y chromosome); SRY, testis-determining locus. CR1, 2 show Xq critical regions 1 and 2 (p. 156). A more detailed view of the AZF loci is show in Figure 6–19.

Sex Chromosome Translocations  151 inactive state is then “locked in” by methylation of CpG islands,5 and this methylation status thereafter remains in place in the descendant daughter cells of the 46,XX embryo (except for the cells destined to become oögonia, in which the inactive X is subsequently reactivated; Khan and Theunissen 2023). Normal 46,XX women can have ratios of active Xm and inactive Xp chromosomes6 from fairly even to quite skewed, even more than 90:10; and there can be differences in ratios between different tissues in a woman (Sharp et al. 2000). The inactive X replicates late during the cell cycle; the active X replicates early, along with the autosomes. But the foregoing is not to say that the female’s second X chromosome is unnecessary (a rather obvious statement, considering the difference between 46,XX and 45,X women). This is the reason: not all genes on the second X chromosome are inactivated, and thus some loci are, in the normal female, functionally disomic. This partial functional X disomy is an absolute requirement for normal female development. Since the major regions in which this active disomy invariably applies are functioning as autosomes do, they are referred to as pseudoautosomal regions (PARs). There are two such PARs, a primary and a secondary—PAR1 and PAR2—and, as well as existing on the X, homologous PARs are located on the Y. Thus, the normal 46,XX female has a pair of functioning PAR1s and PAR2s, and likewise so does the normal 46,XY male. These PARs are sited at the terminal segments of each sex chromosome (Figure 6–1). The wave of inactivation, proceeding in either direction along the X chromosome from the XIC, is blocked when it reaches the PARs; thus, both PARs on the X remain genetically active.7 PAR1 on the X comprises the terminal 2.6 Mb of Xp in band p22.3 and carries at least 25 genes, of which SHOX, a gene associated with short stature, is a notable representative.8 This segment has its homolog on distal Yp. PAR2 extends over 320 kb within distal Xq, holding only four genes and having homology with distal Yq (Mangs and Morris 2007). An obligate recombination event occurs in the PAR1 of the X and the Y chromosome at male meiosis; recombination between the secondary PARs, if it occurs at all, is very infrequent. Otherwise, certain other loci on the X other than in the PARs “escape” inactivation, at least in some tissues, and disomic expression of these genes in the female is normal (Navarro-Cobos et al. 2020). The end result of XCI is that X-linked gene expression between the sexes is near-equalized: each sex has one X, two PAR1s, and two PAR2s, all fully functioning. Measuring Inactivation Status. Inactivation status can be assessed cytogenetically (replication-banding, or R-banding), which enables, in principle, distinction of the early-replicating (active) and the late-replicating (inactivated) X chromosomes and allows a precise estimate of the ratio of normal-Xactive to translocation-Xactive cells. Mostly, however, the analysis is done using molecular methodologies. The androgen receptor locus at Xq13 (quite close to the XIC) is often used as the basis of this test, although results are not informative in all women. There is no consistent cut-off for 5 Dinucleotide clusters consisting of a cytosine (C) base followed immediately by a guanine (G) base. 6 Denoting the one from her mother as Xm and the one from her father as Xp. 7 Similarly, the PARs on the Y are constitutively—in other words, always—active. Thus, both the 46,XX female and the 46,XY male are functionally disomic for PAR1 and PAR2. 8 SHOX deletion leads to a particular skeletal anomaly, Leri-Weill dyschondrosteosis, which includes a distinctive forearm defect, the Madelung deformity. Reflecting the pseudoautosomal nature of this chromatin, the clinical picture is similar between the sexes (Figure 6-2). 152  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY what qualifies as skewing, but a survey of normal adult women identified skewing of >80:20 in 14%, >90:10 in 3.6%, and >95:5 in 1.7% (Sharp et al. 2000). Interestingly, skewing increases with age, at least in blood, and is much less frequent in newborn girls, the corresponding percentages being 4.9%, 0.5%, and 0.2%. In the phenotypically normal heterozygote, the observation of a complete skew of translocation-Xactive and normal-Xactive in the representative tissue analyzed would indicate that the same 100:0 proportion applies elsewhere in the soma. Since it is impossible ever to test the entire soma (and in particular the brain), it would have to remain an open question, in a phenotypically abnormal but structurally balanced X-autosome heterozygote, that a more random skewing pattern might apply in some tissues, notwithstanding a complete skew in the peripheral tissue(s) tested. Abnormal individuals may show incomplete inter-tissue concordance of inactivation status, with sometimes quite different ratios in different tissues—for example, 80:20 in blood and 30:70 in skin (Schmidt and Du Sart 1992). The importance of the foregoing in relation to the X-autosome translocation is this: Transcriptional silencing—inactivation—can spread into the autosomal component of an X-autosome translocation (Cotton et al. 2014). This process can act to mitigate, or equally to exacerbate, an abnormal phenotype. Figure 6–2.  The Forearm Skeletal Picture in Males and Females with a SHOX Deletion. Notes: Forearm X-rays of a brother (A) age 13½, and sister (B) age 11, their respective karyotypes 46,Y,del(X) (p22.2) and 46,X,del(X)(p22.2) (the maternal karyotype was not available, but presumably the same deletion). The radius (the upper forearm bone in these images) is short and abnormally curved, and its articulation with the wrist bones is aberrant (Madelung deformity). The notable point is that the degree of the deformity due to Xp SHOX deletion is similar between the genders, and if anything, more marked in the female (these siblings also showed other clinical features relating to other loci within the deleted segment). Source: From E-H Cho et al., A case of 9.7 Mb terminal Xp deletion including OA1 locus associated with contiguous gene syndrome, J Korean Med Sci 27:1273–1277, 2012. Courtesy J-K Kim, and with the permission of The Korean Academy of Medical Sciences.

Sex Chromosome Translocations  153 THE BALANCED FEMALE X-AUTOSOMAL HETEROZYGOTE The phenotypically normal balanced X-autosome female translocation carrier has two translocation chromosomes, the der(X) and the der(autosome). The X segment in one of these, most commonly the der(X), contains the XIC; and the X segment in the other, usually on the der(autosome), lacks the XIC. The latter segment, having no XIC of its own and being beyond the influence of the XIC on the other derivative, is always active. The only way, then, for the karyotypically balanced female X-autosome heterozygote to achieve a functionally balanced genome is to use, as her active X complement, the two parts of the X in the two translocation chromosomes. Together, they add up to an equivalent whole and functioning X chromosome. The other chromosome, the normal X, is inactive. The cartoon karyotype in the 46,X,t(X;12) carrier mother in Figure 6–3 shows the normal X as inactive (dotted outline), and the X-segments of the der(X) and der(12) as active (solid outline). Probably, the mechanism to bring about this asymmetric inactivation is as follows. Inactivation is initiated at random in each cell, at either one of the XICs. Some cells will be functionally balanced, with the intact X inactive as described above. Others, in Figure 6–3.  Inactivation Patterns. Mother with a balanced X-autosome translocation, showing patterns of inactivation in herself and in her two chromosomally unbalanced children with partial Turner and partial Klinefelter syndrome, respectively. Dashed outline indicates inactivated chromosome. The inactivation pattern of a theoretical third child with a partial X trisomy is shown at right. Note that the balanced carrier inactivates her normal X chromosome, while it is the abnormal X which is inactivated in the unbalanced offspring (and, in the third child, one of the additional normal X chromosomes as well). Based on family in Figure 6–11. 154  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY which the intact X is active, will have a functional disomy for the X chromosome segment that is translocated to the der(autosome), due to this X segment not being subject to transcriptional silencing and thus genetically active. According to this theory, cell selection then eliminates the cells which are functionally disomic X (Figure 6–4, sequence a→b→c). This mechanism is successful in a fraction of translocation heterozygotes, and aside from a possible gonadal effect or rare position effect (see below), such individuals are phenotypically normal. The phenotypically abnormal balanced X-autosome female translocation carrier will often reflect a failure of the mechanism to achieve a functionally balanced X genome. According to one study, such a failure, and with phenotypic consequence, may affect as many as 25% of apparently balanced female carriers (Schmidt and Du Sart 1992). If some functionally disomic cells should survive and come to comprise part of the soma (Figure 6–4, sequence a→b→d), this would, presumably, have some deleterious effect. The natural prediction is that only cells with small partial disomies would be capable of survival. Thus, in these phenotypically affected carrier females, we might more commonly expect to observe translocation breakpoints in distal Xp or distal Xq (Xp22 and Xq28), which would impart disomy for only a very small segment of either distal X short arm, or distal X long arm. But while this is sometimes so, the pattern is not consistent (Du Sart et al. 1992; Schmidt and Du Sart 1992; Waters et al. 2001; Huang et al. 2023a). Yuan et al. (2021) give an example of such inconsistency in describing an otherwise normal mother heterozygous for an X-autosome translocation (X;1)(q28;p31.1), but Figure 6–4.  Skewing of X Inactivation. Notes: Skewing or non-skewing of X chromosome inactivation, as a theoretical explanation for the X-autosome carrier being of either normal or abnormal phenotype (and see text). (a) Before X-inactivation occurs, both the normal and the der(X) are active in all cells (shown in light gray). (b) X-inactivation occurs as a random, cell-autonomous process. Cells shown in white have the der(X) as the active chromosome, and thus the genetic activity of these cells is balanced with respect to X chromosomal output. The cells shown in dark gray have the normal X-active, and in consequence their X chromosomal activity is imbalanced, due to the additional output from the X-segment of the der(autosome). Subsequently in embryonic development: Either (c) the cells with the normal X-active (dark gray) die out, due to their functional genetic imbalance, leaving only the cells with the der(X) active (white). These latter cells functionally are genetically balanced, and the phenotype is normal. The individual has a skewed X-inactivation pattern. Or (d) the dark gray cells persist, despite their functional genetic imbalance (the defect is not severe enough to be lethal), and the individual is a mosaic of functionally balanced tissue (white cells) and imbalanced tissue (dark gray cells). In consequence, the phenotype is abnormal. Source: Adapted from MC Lanasa and WA Hogge, X chromosome defects as an etiology of recurrent spontaneous abortion, Semin Reprod Med 18:97–103, 2000.

Sex Chromosome Translocations  155 whose infant daughter with the same karyotype was of poor developmental status and had a heart and laryngeal defect. Upon X-inactivation studies, while the mother’s picture was appropriately skewed toward inactivation of the normal X, in her child it was the der(X)—not the normal X—that was preferentially inactivated, and this inactivation had spread into part of the 1p component of the translocation chromosome, the segment 1p33-p31.1. Thus, the child had a partial functional monosomy within this segment of 1p. A tiny distal Xq functional disomy may or may not have contributed to the phenotype (Figure 6–5).9 Otherwise, the phenotypically abnormal but apparently balanced carrier may reflect, just as with autosomal rearrangements, disruption of loci at the site of breakpoint (Table 6–1; Figure 6–6). Since her normal X will be preferentially inactivated, the disrupted locus is exposed. An example is seen in Morleo et al. (2008) concerning a girl whose early development was apparently normal, but then regressing with seizure onset (West syndrome) at age 15 months and, at age 12, remaining with no speech. She had a de novo X;20 translocation, which disrupted the IQSEC2 locus at Xp11.22, this being a known brain-expressed gene. As is typically the case, X-inactivation in this child was extremely skewed, with the der(X) the active and the normal X the inactive; but this attempt at functional balancing could not outweigh the severe effect of the IQSEC2 mutation, now “exposed” on the active der(X). Molecular analysis of the Figure 6–5.  The same structurally balanced X-autosome translocation in a normal mother and her abnormal daughter. Notes: The translocation is (X;1)(q28;p31.1); the Xq breakpoint is right at the qter tip of the chromosome, whereas the 1p breakpoint is about midway along the short arm. The dotted outlines on the cartoon (left) indicate inactivation. The karyotypes (right) present X-inactivation studies, the inactivated chromosome indicated with red lettering, the active with green; the pale segments of chromatin reveal inactivation. The mother’s normal X (arrowed) is (appropriately) preferentially inactivated; but in the daughter, it is the der(X) (arrowhead) which is (inappropriately) inactivated. This inactivation has spread into a small part of the 1p component of the der(X), the segment 1p33-p31.1, effectively determining a functional partial del(1p). Source: From S Yuan et al., Reproductive risks and preimplantation genetic testing intervention for X-autosome translocation carriers, Reprod Biomed Online 43:73–80, 2021. Courtesy F Gong and Y-Q Tan, and with the permission of Elsevier. 9 “Inappropriately” skewed X-inactivation can be driven by hidden variants on the X chromosome. Ziegler at al. (2024) studied a family in which two females expressed severe hemophilia A with X-inactivation 99.5% skewed. Exome sequencing identified a variant in the gene VMA21, located on the opposite X chromosome to the F8 variant, which was predicted to drive skewing by imposing a selective disadvantage on cells expressing the variant. 156  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY apparently balanced translocation may reveal a more complicated picture than initially had been seen (Figure 6–7). OVARIAN FUNCTION AND THE X “CRITICAL REGIONS” In the balanced female carrier, breakpoints at certain locations in the X may affect ovarian function (Table 6–2). An Xq critical region spans from Xq13 to Xq27 and is bookended by two smaller segments (at Xq13.1-Xq21.33 and Xq24-Xq27), labeled CR1 and CR2 (critical regions 1 and 2) respectively (Figure 6–1). A breakage and reunion within either of CR1 and CR2 is characteristically associated with premature ovarian insufficiency; these regions are thus also called POI2 and POI1, respectively). CR1/ POI2 is the more commonly implicated, as most X-autosome translocations have their breakpoint within Xq21. The deleterious effect upon ovarian function appears not to be due to gene disruption, but rather to a position effect, a “perturbation of the regulatory Table 6–1.  Girls with X-linked Mendelian Disorders due to an X-Autosome Translocation SYNDROME LOCUS TRANSLOCATION REFERENCE Aarskog FGD1 46,X;t(X;8)(ql3;p21) Bawle et al. 1984 Duchenne DMD 46,X,t(X;17)(p21.1;q23.2) Segarra-Casas et al. 2024 Hunter IDS 46,X,t(X;9)(q28;q12) Lonardo et al. 2014 Lowe OCRL 46,Xt(X;3)(Xq25q27) Attree et al. 1992 Nance-Horan NHS 46,X,t(X;1)(p22.13;q22) Gómez-Laguna et al. 2018 Menkes ATP7A 46,X,t(X;2)(ql3;q32.2) Kapur et al. 1987 OTC deficiency OTC 46,X,t(X;5)(p21.1;q11) Zenker et al. 2005 Notes: These disorders involve an X breakpoint at a particular well-known Mendelian locus. Several other apparently balanced X-autosome translocations are also seen in girls in whom no Mendelian syndrome diagnosis is made, but whose abnormal phenotypes are probably due to the disruption of a known locus yet to be associated with a named Mendelian syndrome (Morleo et al. 2008 above; Moysés-Oliveira et al. 2015). Figure 6–6.  Mendelian Disease in the Balanced Carrier. Notes: A de novo X-autosome translocation 46,X,t(X;4)(p21;p16) in which the dystrophin locus at the Xp21 breakpoint is presumed to be disrupted, in a 7-year-old girl. In consequence, very little dystrophin is produced, and the girl has a Becker-like muscular dystrophy. The approximate position of the dystrophin locus is indicated (arrowhead) on the intact X. The intact X is preferentially inactivated, as shown here with replication-banding and indicated in dashed outline on the cartoon karyotype. Early replicating (active) chromatin and the late replicating (inactivated) chromatin stain dark and light, respectively (Case of JA Sullivan).

Sex Chromosome Translocations  157 landscape” (Figure 6–8). In one series of 30 women presenting with premature ovarian insufficiency, in whom the cytogenetic findings were reviewed, Devi and Benn (1999) recorded just one to be an X-autosome translocation heterozygote; thus, it is an infrequent cause of this problem. The Unbalanced Near-Normal Female X-Autosomal Heterozygote The female carrying an unbalanced translocation may yet be of near-normal phenotype if the inactivation process proceeds favorably. Such a scenario is seen in four women in Figure 6–7.  Molecular Analysis of an Apparently Balanced X-Autosome Translocation. Notes: This translocation was initially interpreted as t(X;22)(q13;q13)dn; the corrected karyotype is t(X;22)(q11.1;q12.2). Black = chromosome 22, orange = X chromosome, circles = centromeres, rectangles = telomeres. Red dot-and-dash lines = breakpoints. A very short segment within 22q12.2 is duplicated, and the loci noted (LIMK2 at 22q12.2 and LINC01278 at Xq11.1) disrupted. Presumably, the der(X) translocation chromosome would have remained active, since the XIC is distal to LINC01278, and thus located on the der(22). The genetic perturbation in consequence of these several factors would lead to phenotypic expression. Source: From C Redin et al., The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies, Nat Genet 49:36–45, 2017. Courtesy ME Talkowski, and with the permission of Springer Nature. Table 6–2.  Gonadal Dysgenesis Occurrence of Gonadal Dysgenesis (Primary or Secondary) in 118 t(X-autosome) Women According to X Chromosome Breakpoint BREAKPOINT GONADAL DYSGENESIS NORMAL GONADAL FUNCTION Xpter-q12 5 37 q13 4 8 q13-q22 20 1 q22 11 6 q22-q25 7 1 q26 3 5 q27-qter 1 9 Source: From E Therman et al., The critical region on the human Xq, Hum Genet 85:455–461, 1990. 158  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY three generations in the family described in Ciaccio et al. (2020) (Figure 6–9). Each had a genomic imbalance comprising a 23.4 Mb deletion of Xq26.2q28,10 and an 11.7 Mb autosomal duplication in 7q35q36; and yet the phenotypes were mild, with cognitive capacity within a normal range. The two women in generation II had difficulty conceiving; and autoimmune disease in three of the women may have been an effect of the imbalance. XCI studies in two showed a complete skewing of activation in favor of the normal X. The Male X-Autosomal Hemizygote Almost invariably, the cytogenetically balanced X-autosomal male hemizygote is, without intervention, infertile due to spermatogenic arrest; disruption of the sex vesicle11 is the presumed proximate cause of the obstruction (Hwang et al. 2007). In two such men subject to testicular biopsy, Quack et al. (1988) showed germ cell maturation arrest mostly at the pachytene stage of meiosis I, although a few cells managed to make the first, and some even the second, meiotic metaphase, and thus might have become spermatozoa. This outcome of a very modest success might more likely be achieved in those men in whom the breakpoints are more centromerically placed. A man reported in Perrin et al. (2008), hemizygous for a whole-arm translocation (X;18)(q11;p11.1), was subject to Figure 6–8.  The “Regulatory Landscape” of the POI2 Region, Xq13q22. Notes: Numbers 1–6 refer to the Xq breakpoints in six cases of premature ovarian insufficiency, each woman having a balanced X-autosome translocation. Each red triangle represents a Topologically Associating Domain (TAD), within which several loci interact. Perturbation of this interaction, consequential upon the breakpoint within a TAD, can influence ovarian function accordingly, as loci are inappropriately up- or down-regulated. Source: From A Di-Battista et al., Premature ovarian insufficiency is associated with global alterations in the regulatory landscape and gene expression in balanced X-autosome translocations, Epigenetics Chromatin 16:19, 2023. Courtesy MI Melaragno, and with the permission of Springer Nature. 10 With monosomy for distal Xq, a fragile X test for subfertility in II:2 showed only a single copy of FRAXA; the significance of this escaped notice at the time. 11 The sex vesicle (or sex-body, or XY-body) can be considered as a “peripheral nuclear subdomain” within which the X and Y chromosomes lie, genetically inactivated, during the pachytene stage of meiosis (Turner 2007). Sex Chromosome Translocations  159 Figure 6–9.  An Unbalanced X;Autosome Translocation in a Family with Mild Phenotype. Source: From the report in C Ciaccio et al., Unbalanced X;Autosome translocations may lead to mild phenotypes and are associated with autoimmune diseases, Cytogenet Genome Res 160:80–84, 2020. sperm chromosomal FISH analysis; he had presented with infertility and “very severe oligoasthenoteratozoöspermia.” Analysis showed a range of segregant types in the small number of 447 cells able to be studied: alternate segregation in just over 50% (with half of these normal 23,Y), and adjacent-1, adjacent-2, 3:1, and 4:0 in 8%, 5%, 22%, and 2%, respectively. If sperm could be retrieved, intracytoplasmic sperm injection (ICSI) may be attempted in order to enable fertility. The man with severe oligoasthenoteratozoöspermia described in Chamayou et al. (2018) had inherited his X;3 translocation from his otherwise normal carrier mother (Figure 6–10). After IVF with ICSI, blastocyst biopsy on 11 embryos showed two 46,XY, two apparently 46,XX (but necessarily X-3 heterozygotes), four with adjacent-2 imbalance, one likely interchange monosomy, and two with other unrelated imbalances. Patterns of Inactivation in the Unbalanced Offspring FEMALE OFFSPRING OF THE X-AUTOSOMAL HETEROZYGOTE OR HEMIZYGOTE As a rule (but one that can be broken), the pattern of inactivation that is observed in the chromosomally unbalanced offspring will be the one that allows the least amount of functional imbalance, as discussed above. This is typically arrived at in the karyotypically unbalanced daughter by inactivation of the abnormal chromosome, always supposing that the choice exists (and the choice can exist only if the abnormal chromosome contains an XIC). We may consider these categories: translocations in which the autosomal component is very small; those in which the autosomal component is larger; and those in which the derivative X component lacks an XIC. The autosomal component is very small. If the abnormal chromosome is a der(X) from an effectively single-segment exchange, containing no autosomal material other than a telomeric tip, it comprises, essentially, a deleted Xp or Xq chromosome. In a girl with the 46,X,der(X) karyotype, preferential inactivation of this

160  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY deleted X leads simply to a phenotype of partial Turner syndrome. Consider the family segregating a t(X;12) shown in Figures 6–3 and 6–11. The segregation shown in Figure 6–3 (daughter from adjacent-1) and Figure 6–11a (daughter) illustrates the case for an Xq deletion. Here, the normal X is active (shown as solid outline in Figure 6–3), and the der(X) is inactivated (dotted outline). Leichtman et al. (1978) provide an example of the Xp deletion circumstance in a three-generation family with seven persons having an Xp– Turner syndrome variant on the basis of a segregating t(X;1). In a tertiary trisomy combination with a 47-chromosome count (Figure 6–3, daughter from 3:1), a partial form of the XXX syndrome (Chapter 15) would result. The autosomal component is larger. If the der(X) carries a larger translocated autosomal segment—conferring, therefore, a partial autosomal trisomy in the 46,X,der(X) subject—the effects of this imbalance may be mitigated by selective inactivation of the abnormal chromosome. Transcriptional silencing could spread, albeit patchily, into the autosomal chromatin on the der(X), at least partially converting a structural autosomal trisomy into a functional autosomal disomy (Sharp et al. 2002). Figure 6–12 shows an example of blocked spread of inactivation into the autosomal (16p) segment of an inherited X;16 translocation. Observe the der(X) in the lower row, with pale (inactivated) long arm and dark (active) short arm. In one case proceeding only to the 8th week of pregnancy, a female embryo with 47,XX,+der(5) from 3:1 malsegregation had trisomy for most of Xq, and almost all of no. 5, the mother being 46,X,t(X;5)(q13;p14) (Van Echten-Arends et al. 2013). That Figure 6–10.  Assisted Reproduction for a Male X-Autosomal Translocation Carrier. Notes: This is a three-generational translocation, (X;3)(p11.2;p15). N = normal karyotype; half-filled symbol = heterozygote/hemizygote for the translocation. Smaller symbols in Generation III = blastocysts. Individual II:2, an otherwise normal man, had presented with infertility with a very low sperm count (20,000/ml). Generation III comprises 11 blastocysts created after ICSI. Diamond = adjacent-2 malsegregant embryo; filled circle = embryo with 45,X, likely reflecting interchange monosomy; filled squares = embryos with other unrelated aneuploidy. One normal 46,XY embryo, III:1, was successfully transferred. The X-3 balanced embryos, III:3 and 4, were not chosen, given a possible risk for phenotypic abnormality, as discussed above. Source: From the case in S Chamayou et al., The decision on the embryo to transfer after preimplantation genetic diagnosis for X-autosome reciprocal translocation in male carrier, Mol Cytogenet 11:63, 2018. Sex Chromosome Translocations  161 such a near double trisomy advanced even to week 8 may reflect quite substantial inactivation within the very large (longer than no. 1) der(5) chromosome. The X component of the derivative autosome lacks an XIC. If, in the female with a 46,XX,der(autosome) karyotype, the derivative chromosome has no XIC in its translocated X segment, this segment cannot be inactivated; a functional partial X disomy, Figure 6–11.  The Autosomal Component of the der(X) is Very Small. (a) Mother with balanced X;12 translocation, showing two different segregant outcomes. Her daughter had presented with clinical Turner syndrome, in whom the karyotype was initially interpreted as del(X)(q22). Her son was subsequently studied, and he had a partial Klinefelter syndrome (Case of JA Sullivan). (b) The presumed pachytene configuration during gametogenesis in the mother (X chromatin, open; chromosome 12 chromatin, cross-hatched; dot indicates X-inactivation center). Light arrows indicate movements of chromosomes to daughter cells in adjacent-1 segregation, as observed in the daughter with partial Turner syndrome. Heavy arrows show the tertiary trisomy combination seen in the son with partial Klinefelter syndrome. These two segregations are represented in b and c in Figure 6–14. 162  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 6–12.  The Autosomal Component of the der(X) is Larger. Spread of inactivation into autosomal segment. (a) Mother with balanced X;16 translocation (above), and her daughter with a 46,X,der(X) karyotype from adjacent-1 segregation (below). The translocation is t(X;16)(p11;p12). Replication-banding shows active (darker-staining) and inactive (lighter-staining) chromosome segments. The normal X is inactivated in all cells analyzed in the mother (dashed box on cartoon karyotype; dot indicates X-inactivation center). The daughter’s abnormal X lacks Xp and contains distal 16p material. This chromosome is preferentially inactivated (dashed outline of box), but in 76% of cells analyzed (lymphocytes) the inactivation has not continued through the translocated 16p segment (dotted outline of box). The phenotype is the combined result of the Xp monosomy and a “partial” 16p trisomy. The child is short and has a developmental age of about 2½ years at a chronological age of 4 years (Case of CE Vaux). One other daughter had the same balanced translocation as the mother and showed consistent inactivation of the normal X chromosome in blood lymphocytes, but she suffered intellectual deficit. (b) The presumed pachytene configuration during gametogenesis in the mother (X chromatin, open; chromosome 16 chromatin, cross-hatched; dot indicates X-inactivation center). Arrows indicate movements of chromosomes to daughter cells in adjacent-1 segregation; heavy arrows show the combination observed in this family. This is essentially the segregation i in Figure 6–14, with an Xp breakpoint in this case.

Sex Chromosome Translocations  163 of distal Xp or distal Xq, is the consequence. Figure 6–13 demonstrates a functional disomy for a part of Xp (Xp22.31pter) in a chromosomally unbalanced daughter, from a maternal X;10 translocation; in this instance, since the autosomal breakpoint is at the 10q telomere, we assume there to be little or no effect from a 10q monosomy. As for translocations involving distal Xq, a functional disomy of Xq28qter has been reported sufficiently often that a clear core phenotype can be described, and the Rett syndrome MECP2 locus at chrX:154.0-154.1 Mb is considered a key pheno-contributory factor (Collins and Neul 2022). Such a picture is seen in the girl described in Shimada et al. (2013), a child with no meaningful words and intractable epilepsy, with the karyotype 46,XX,der(12)t(X;12)(q28;q24.33). The distal 12q component involved only the tip of that chromosome, and so the child’s essential functional imbalance reduces to an Xq28 duplication. De Novo Unbalanced X-Autosome Translocations in the Female. In order to illustrate some aspects of inactivation behavior we may usefully consider de novo unbalanced translocations, some of which could be, in principle, the same as if they had Figure 6–13.  The der(X) Lacks an XIC. Notes: (a) Mother with balanced X;10 translocation (above), and her daughter with a 46,XX,der(10) karyotype from adjacent-1 segregation (below). The translocation is t(X;10)(p22.31;q26.3). Dashed box on cartoon karyotype indicates the mother’s preferentially inactivated chromosome; dot indicates X-inactivation center. The der(10) contains Xp material in the translocated segment, which cannot be inactivated, and so the daughter has functional X disomy. Since the 10q breakpoint is in the terminal band, we may regard this as an effectively single-segment exchange, with the phenotype of severe mental deficit and minor dysmorphism due entirely to disomy for the small Xp22.31→pter segment (Case of A Ma and HR Slater). (b) The presumed pachytene configuration during gametogenesis in the mother (X chromatin, open; chromosome 10 chromatin, cross-hatched; dot indicates X-inactivation center). Arrows indicate movements of chromosomes to daughter cells in adjacent-1 segregation; heavy arrows show the combination observed in this family. This is essentially the segregation a shown in Figure 6–14. 164  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY been transmitted from a carrier parent. Giorda et al. (2008) analyzed cells from a girl with mild dysmorphology, arthritis, obesity, microcephaly, and intellectual and behavioral disability, who had the karyotype 46,X,der(X)t(X;5)(q22.1;q31)dn and was thus partially trisomic for the large segment 5q31qter. Of itself, this partial 5q trisomy would otherwise have been nonviable. Giorda and colleagues were able to show that of 17 interpretable genes tested in this translocated segment, nine had been inactivated while another eight were active (as measured by methylation status). This inactivation did not “weaken” as it spread further into 5q31qter segment, and indeed the autosomal gene closest to the Xq-5q breakpoint remained active; thus, some autosomal genes were susceptible and some were resistant to the spreading influence from the XIST of the der(X). King et al. (1998) describe an intriguing example of a de novo X-autosome translocation 46,X,der(X)t(X;17)(p22.1;p11.2) in a mildly disabled female who had Charcot-Marie-Tooth neuropathy (CMT; Chapter 14). The extra segment of 17p attached to Xp produced an attenuated picture of partial 17p trisomy, presumably reflecting an extension of inactivation into the 17p segment from the X-inactivation center of the der(X). However, the “supernumerary” PMP22 gene on the 17p segment was apparently fully functioning, since the neuropathy was typical for CMT. The inactivation process, as it spread along 17p, could be supposed to have “hopped over” the PMP22 region. A most remarkable scenario is that of an “incorrect” inactivation of the der(X) comprising the “first hit” in a tumor cascade. An intellectually disabled woman in her 20s developed schwannomas, and she was found to carry a de novo t(X;22)(p21.3;q11.21); these breakpoints are very close to the t(X;22) discussed elsewhere and shown in Figure 6–17. Although the X-inactivation pattern on blood was appropriate, in tumor tissue the der(X) was inactivated (Bovie et al. 2003). This inactivation may have spread through to the 22q segment, which contains two loci (NF2 and SMARCB1) associated with schwannoma susceptibility. MALE OFFSPRING OF THE FEMALE X-AUTOSOME HETEROZYGOTE Analogous to the female, the male inheriting a der(autosome) in unbalanced state is affected according to whether the X-translocated segment does or does not contain an XIC. There is, however, a gender difference relating to X deletion states. In the male, this would lead to a nullisomy and, unless very small, would not be viable. The phenotypes due to X duplication states will depend upon whether or not there has been inactivation. The autosomal component is very small. If the autosomal segment is so small that its effect can be discounted, and if X segment contains an XIC, the X segment is inactivated and, other things being equal, a Klinefelter-like phenotype might be expected in those sons inheriting the maternal der(autosome) (Figure 6–14d). But this expectation might not be met, and a more severe clinical picture—whether due to incomplete inactivation or to the effect of a concomitant autosomal deletion—could result. Balci et al. (2007) report a three-generation family with a t(X;19)(q11;p13.3): a normal grandmother and mother with the balanced translocation, and a severely disabled boy (physically somewhat resembling Prader-Willi syndrome) whose karyotype was 46,XY,der(19) t(X;19). Virtually the entire Xq—including the XIC—was present in disomic dose on the der(19); but in spite of its inactivation, the phenotype was a great deal more severe than “Klinefelter-like.” The der(19), although the breakpoint appeared to be at 19qter, might Sex Chromosome Translocations  165 Figure 6–14.  Malsegregation in the Female X-Autosome Carrier. Major categories of adjacent-1 and 3:1 malsegregation in the X-autosome female carrier. The top row shows quadrivalents at maternal meiosis, and the following rows various combinations of segregant products. Open, X chromatin; cross-hatched, autosomal chromatin; dot indicates X-inactivation center. “Single-segment” and “double-segment” are defined in the text. X exchanges can occur in either Xp or Xq; only Xq exchanges are shown here. Circled letters provide reference points for text comments. *Effect of autosomal duplication may be lessened by spreading of transcriptional silencing into the autosomal segment of the der(X). **Blocking of spread of inactivation into the autosomal segment of the der(X) may avoid further functional autosomal monosomic effect.

166  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY yet have lost functional material (and recalling the extraordinary gene load of this chromosome; Figure 1–4). The X component of the derivative chromosome lacks an XIC. As with the female child, the male from an X-autosome mother in which the translocated X segment lacks the XIC can suffer a viable functional disomy, if the X segment is “small” (Figure 6–14a). For example, the mother in Giudice-Nairn et al. (2019) carried an Xq;14p translocation, while in her der(14) son, the duplicated distal Xq segment, attached to the short arm of 14, remained active (there would have been no effect of the 14p imbalance). The child was diagnosed with dup MECP2 syndrome (Chapter 15), and died at age 11 months after a stormy cardiorespiratory course. DETAILS OF MEIOTIC BEHAVIOR: FEMALE MEIOSIS In oögenesis, a quadrivalent presumably forms, just as in the two-way translocation between autosomes. 2:2 alternate segregation with the intact X and intact autosome can lead to 46,XX or 46,XY conceptions, while transmission of the translocation in balanced state produces heterozygous or hemizygous conceptions. As for malsegregation, Figures 6–14 and 6–15 set out certain outcomes that may be viable for various categories of single-segment and double-segment translocation, as discussed below. Given the greater survivability of X imbalances due to inactivation, and likewise a possible lessened effect of autosomal imbalance, a greater number of conceptuses are potentially viable than those from the autosome-autosome translocation. The “rules” of segregation (Chapter 5) may not apply; for example, a viable adjacent-2 malsegregation can occur with a derivative chromosome having a large centric segment. The coexistence of tertiary monosomy and adjacent-2 aneuploidy in the family described in Figure 6–17, two otherwise very uncommon segregations, reflects the unique characteristics of the X-autosome translocation. Categories of Translocation and Modes of Malsegregation We consider here various chromosomal scenarios that ought to cover the majority of clinical circumstances. Concerning terminology with respect to the size of translocated segments: If one of the translocation breakpoints is at the telomeric tip of either the autosome or the X chromosome, and thus only one of the translocated segments (X or autosomal) comprises an important amount of chromatin, this may be considered an effective “single-segment exchange.” If both translocated segments are of significant size, this is a “double-segment exchange.” SINGLE-SEGMENT EXCHANGE, X-TRANSLOCATED SEGMENT The first two columns in Figure 6–14 and the first column in Figure 6–15, segregations a–c and segregation a, respectively, depict the general form of a translocation in which the single important exchanged segment comprises X chromatin. A particular example Sex Chromosome Translocations  167 is shown in Figure 6–11, in which the derivative X chromosome is deleted for a large segment of Xq and has only the telomeric tip of 12p in exchange. A child receiving this abnormal “Xq–” in place of a normal X, or as an additional chromosome, could present with a partial form of a sex chromosome aneuploidy syndrome. Thus, a daughter with 46,X,der(X) from adjacent-1 malsegregation (b in Figure 6–14) would have a variant form of Turner syndrome. From tertiary trisomy (c in Figure 6–14), a son with 47,XY,+ der(X) would have incomplete Klinefelter syndrome, and a 47,XX,+der(X) daughter might show the 47,XXX phenotype to a diminished degree. More severe consequences follow the countertype adjacent-1 segregation: a in Figure 6–14. Conceptions with 46,der(12) from adjacent-1 segregation would, in the Figure 6–15.  Adjacent-2 Malsegregation in the Female X-Autosome Carrier. Notes: Three categories of adjacent-2 malsegregation in the X-autosome female carrier. The top row shows quadrivalents at maternal meiosis, and the next row various combinations of adjacent-2 segregant products. Note that these potentially viable outcomes occur only in the setting of the transmitted derivative chromosome, be it the der(X) or the der(autosome), having an X-inactivation center (XIC). In the first two columns, the der(autosome) has the XIC; here, the X breakpoint must be in proximal Xq, above the XIC, as depicted. In the third column, in which the der(X) has the XIC, X exchanges can occur either in Xp or in Xq distal to the XIC; only an Xp exchange is shown here. Open, X chromatin; cross-hatched, autosomal chromatin; dot indicates XIC; der(A), der(autosome). Circled letters provide reference points for text comments. *Effect of autosomal duplication may be lessened by spreading of transcriptional silencing into the autosomal segment of the der(A). **Blocking of spread of inactivation into the autosomal segment of the der(X) may avoid further functional autosomal monosomic effect.

168  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY family in Figure 6–11, be functionally disomic for a large and unsurvivable amount of Xq, and would abort. However, if the translocated X segment is small, the functionally disomic X state may yet be viable. This is shown in Figure 6–13, in which the intellectually disabled and dysmorphic daughter has a 46,XX,der(10) karyotype and is functionally disomic for the small amount of Xp22.31pter. As for adjacent-2 segregation (Figure 6–15a), such a gamete would, in theory, have viability only if it is the der(autosome) that is transmitted along with the intact autosome and if the X segment of the der(autosome) includes the XIC. In that case, inactivation could spread through the autosomal material, at least partially converting a structural autosomal trisomy into a functional autosomal disomy. Of course, there would be a partial X monosomy as well. This scenario is discussed in more detail in the section on “Double-Segment Exchange, Adjacent-2.” A truly single-segment X-autosome translocation, the translocated segment comprising X material, is recorded in de Vries et al. (1999). A mother had a submicroscopic segment of the PAR1 in distal Xp (p22.31pter) translocated across to the short arm of a chromosome 14—but, as far as could be seen, there was no reciprocal movement back to the X of any 14p material. She transmitted the der(X) to a son, who presented signs interpreted as consistent with nullisomy for certain genes in the distal PAR1: the SHOX, MRX, CDPX, and STS genes, their absences responsible respectively and collectively for short stature, short limbs, developmental delay, and ichthyosis. SINGLE-SEGMENT EXCHANGE, AUTOSOMAL TRANSLOCATED SEGMENT The single segment being of autosomal origin, with only the telomeric tip of Xp or Xq translocated in exchange, is shown in the middle column of Figure 6–14, segregations d–g. The imbalanced conceptions from 2:2 adjacent-1 malsegregation would be partially monosomic or partially trisomic for the autosomal segment: 46,der(autosome) and 46,der(X), respectively (segregations d and e in Figure 6–14). In the 46 X,der(X) female, the partial autosomal trisomic state may have an attenuated phenotype due to spreading of transcriptional silencing from the XIC of the der(X) into the autosomal segment. The 46,Y,der(X) male conceptus, in which no X-inactivation occurs, would show the undiluted effect of the partial autosomal trisomy. The partially monosomic state—46,XX,der(autosome) or 46,XY,der(autosome)—would be no different than if the other chromosome participating in the translocation had been an autosome instead of an X, and the typical clinical consequence associated with that autosomal deletion would be expected. DOUBLE-SEGMENT EXCHANGE, ADJACENT-1 In a double-segment exchange with adjacent-1 segregation (right column, Figure 6–14, segregations h–i), there may be, in the unbalanced conceptus, effects of a combined X functional disomy and autosomal monosomy, or of X monosomy (or nullisomy) and autosomal trisomy. Such combinations would often be lethal in utero or failing to implant. But in the 46,X,der(X) female (segregation i), the effects may be very considerably modified by spreading of inactivation. Consider the t(X;16) illustrated in Figure 6–12. The 46,X,der(X) daughter has both a monosomy for most of Xp, giving a Turner-like phenotype and a structural trisomy for most of 16p. Following spread of inactivation in the der(X) into its autosomal segment in a fraction of cells, the 16p trisomy has been Sex Chromosome Translocations  169 converted in these cells into a functional 16p disomy. However, in 76% of cells (at least in blood) and in the cell illustrated, the inactivation has not extended into the 16p segment. Thus she has, effectively, a functional mosaic 16p trisomy/16p disomy. This same combination with a Y replacing the X as the intact sex chromosome—46,Y,der(X) with nullisomy Xp/trisomy 16p—would not be viable, and thus affected sons are not observed. The other adjacent-1 conceptions with 46,XX,der(16) and 46,XY,der(16) (light arrows in Figure 6–12; h in Figure 6–14) would not be similarly “modifiable” and would have a very large functional imbalance, and they would also be expected to abort early in the pregnancy or to fail to implant. If the translocated segments are small, survival may be possible notwithstanding the inactivation status. Ben-Abdallah-Bouhjar et al. (2012) describe a mother with 46,X,t(X;3)(q27.3;p26.3) whose son, with severe psychomotor delay and a somewhat Prader-Willi-like phenotype, inherited the der(3) in unbalanced adjacent-1 state. The imbalance conveyed a dupX:147.42 Mb-qter (this includes the region of the dup Xq28 syndrome; Chapter 15), and superimposed upon this, a distal 3p monosomy, del chr3:pter-1.42 Mb. DOUBLE-SEGMENT EXCHANGE, ADJACENT-2 Adjacent-2 segregation typically produces trisomy for much of one chromosome along with monosomy for much of the other, and this is not, in the usual autosome-autosome translocation, remotely viable (e.g., segregation (5) in Figure 5–4). But such an enormous degree of structural imbalance can be accommodated in some X-autosome translocations, in a female conceptus. First, consider the case of the intact autosome and the derivative autosome being transmitted together: 46,X,–X,+der(autosome). Provided the X segment of the der(autosome) includes the XIC (segregation b in Figure 6–15), inactivation can spread from the XIC in both directions and into the autosomal segment, counteracting the effect of the autosomal duplication, at least partially. The concomitant partial X monosomy is, of itself, a viable state. The child would be expected to display a partial Turner phenotype, upon which the effect of a variably inactivated partial autosomal trisomy would be added. This is illustrated in Leisti et al. (1975), who record a mother carrying a t(X;9)(q11;q32) and her daughter being 46,X,–X,+der(9). In the daughter, transcriptional silencing spread through much of the autosomal segment which, very substantially although not completely, neutralized the effect of the partial trisomy 9: She had a Turner syndrome picture with superadded microcephaly and intellectual disability. The case in Williams and Dear (1987) is similar, with an intellectually disabled and dysmorphic child having the karyotype 46,X,–X,+der(10),t(X;10) (q11;q25)mat, but in this instance inactivation into the autosomal segment was apparently blocked at the centromere of the der(10). This left the child with an effective duplication of 10p, along with the X deletion (Figure 6–16). Concerning a male conception in this setting, of course, an adjacent-2 conceptus with an X nullisomy could not survive. Second, viability is also possible in one very rare circumstance of an intact X and the der(X) being transmitted together, with the adjacent-2 karyotype 46,XX,–(autosome),+ der(X), segregation c in Figure 6–15. The der(X) must contain an XIC; its autosomal segment must comprise a very substantial amount of the chromatin of that autosome; and there must be little or no spread of inactivation beyond the X segment of the translocation chromosome into the autosomal segment. In this way, the autosomal component can maintain sufficient disomic genetic activity to produce a viable phenotype. Only

170  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY autosomes with “genetically small” short arms could enable these criteria to be met. An example from a maternal t(X;22)(p21.3;q11.21) is shown in Figure 6–17b (daughter with adjacent-2, bottom row). The der(X) comprises most of an X and all, or almost all, of 22q. If its 22q segment were blocked from inactivation, there would be, in effect, a near-normal functional disomy 22 along with a partial XXX syndrome. In fact, this woman had a mild intellectual disability and attended a special school; the relative contributions to her phenotype of the two components of the cytogenetic abnormality are open to speculation. Figure 6–16.  Adjacent-2 Segregation. Notes: (a) Mother with balanced X;10 translocation (above), and her daughter with a 46,X,–X,+der(10) karyotype (below), on G-banding. The translocation is t(X;10)(q11;q25). Replication-banding showed the normal X to be inactivated in all 30 lymphocytes analyzed in the mother (dashed box on cartoon karyotype; dot indicates X-inactivation center). The daughter’s der(10) was preferentially inactivated (dashed outline of box) in 50/50 cells, but the inactivation did not continue through to the 10p segment (dotted outline of box). The phenotype is the combined result of the 10p duplication and Xp monosomy. Case of J Williams; in J Williams and PRF Dear, An unbalanced t(X;10) mat translocation in a child with congenital abnormalities, J Med Genet 24:633, 1987. (b) The presumed pachytene configuration during gametogenesis in the mother (X chromatin, open; chromosome 10 chromatin, cross-hatched; dot indicates X-inactivation center). Arrows indicate movements of chromosomes to daughter cells in adjacent-2 segregation; heavy arrows show the combination observed in this family. This is segregation b in Figure 6–15. Sex Chromosome Translocations  171 Figure 6–17.  Adjacent-2 and 3:1 Segregation. Notes: 3:1 tertiary monosomy and adjacent-2 segregation both occurring in the same family (and see text). (a) Pedigree of family segregating a t(X;22)(p21.3;q11.21). Filled symbol, imbalanced state; half-filled symbol, heterozygote/hemizygote; N = 46,XX. (b) Partial karyotypes of heterozygotes (top) and of the two unbalanced states (lower). On replication-banding, the normal X is inactivated in all cells analyzed in the heterozygotes, whereas the der(X) is inactivated in the two affected persons (dashed box on cartoon karyotype; dot indicates X-inactivation center). In the affected child in generation III with a 45,X,–X,+der(X),–22 karyotype (middle karyotype), the der(X) was positive for a probe recognizing a sequence in the DiGeorge critical region. The der(X) chromosome showed, in 50/50 cells, apparently no inactivation going through to its 22 component (dotted outline of box), but the clinical picture might suggest otherwise (see text). Her hemizygous brother, III:2, will presumably be infertile. The affected woman II:1 has the adjacent-2 karyotype 46,XX,+der(X),–22 (Case of T Burgess). (c) The presumed pachytene configuration during gametogenesis in the heterozygote (X chromatin, open; chromosome 22 chromatin, cross-hatched). Heavy arrow indicates movement of the der(X) chromosome to one daughter cell in 3:1 segregation (essentially segregation k, Fig. 6–14). Dashed arrows show the movement of chromosomes in the adjacent-2 combination (segregation c, Fig. 6–15).

172  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY DOUBLE-SEGMENT EXCHANGE, 3:1 SEGREGATION WITH TERTIARY MONOSOMY The same criteria noted in the preceding paragraph may also obtain in the rare situation of tertiary monosomy being viable (in essence, this is segregation k in Figure 6– 14). The t(X;22) in Figure 6–17 again provides an example. In the index case in this family having the tertiary monosomy state 45,X,–X,+der(X),–22 (middle row, Figure 6–17b), the der(X) chromosome is preferentially inactivated, but inactivation has not (at least on blood lymphocytes) spread through to the 22q component of the der(X). Thus, a functional 22 disomy is maintained, or nearly so. The important structural imbalance, one might have predicted, could have been limited to the Xp21.3pter deletion (loss of 22p being without effect) with the phenotype confined to a Turner syndrome-like picture. In the event, however, there were minor congenital anomalies, and she was assessed as being intellectually disabled. This does suggest that the pattern of inactivation elsewhere in the soma may have differed from that observed on peripheral blood, and there might have been a degree of functional 22q monosomy in other tissues, including brain. 3:1 SEGREGATION, INTERCHANGE TRISOMY/MONOSOMY From each of the categories of single- and double-segment exchange, 3:1 interchange trisomy could theoretically produce Klinefelter syndrome or XXX syndrome along with the balanced translocation, and interchange monosomy could produce typical 45,X Turner syndrome. We are aware of only one such outcome from oögenesis: an infertile woman with 47,XX,t(X;12) from her 46,X,t(X;12)(q22;p12) mother, with the imbalance being equivalent to 47,XXX (Madan et al. 1981). 4:0 SEGREGATION With a trisomically viable autosome, say chromosome 21, as part of an X-autosome translocation, a 48,XX,+der(X),+der(21) karyotype might be equivalent to the potentially viable 48,XXX,+21 state: a combined Down syndrome plus XXX syndrome. But we know of no such report in a liveborn child. At the embryonic stage, however, 4:0 is regularly observed, and this becomes a relevant consideration for the translocation carrier proceeding to IVF with blastocyst biopsy (Zhang et al. 2018). DETAILS OF MEIOTIC BEHAVIOR: MALE MEIOSIS Meiosis in the X-autosome hemizygote is typically compromised due to failure of formation of the sex vesicle, and spermatogenesis arrests. Infrequently, some sperm may be made, albeit in small numbers. Perrin et al. (2008) propose formation of a quadrivalent in which the Y chromosome participates with apposition of its PAR1 and PAR2 to the homologous regions on the der(X) and the der(A) (Figure 6–18). As with the female, some malsegregant forms might have viability due to the potential lesser effects of X imbalance. Similarly, according to the principles as set out above for the female but with the additional factor of a Y chromosome to be considered, the reader can determine the range of possibilities in a particular case for this rarely encountered circumstance. The X;3 example of Chamayou et al. (2018) (Figure 6–10) illustrates some of this range: of 11 blastocysts from the male hemizygote presented in this case, two were alternate normal, two were alternate balanced, Sex Chromosome Translocations  173 four were adjacent-2, and one was likely 3:1 with monosomy X, along with two having an unrelated aneuploidy. Y-Autosome Translocations Y-autosome translocations fall into two major Yq-breakpoint categories, one of which has important clinical implications, and the other of which does not. Certain other rare forms exist. First, some brief comments on the nature of the Y chromosome are in order. THE ROLE AND BEHAVIOR OF THE Y CHROMOSOME The particular raison d’être of the Y chromosome is to bring about male development. The testis-determining gene, SRY, lies in the euchromatic region on the short arm, just 5 kb proximal to the primary pseudoautosomal (PAR1) boundary. As noted above, and see Figure 6–1, the PAR1s of the Y and X short arm contain homologous loci, and certain other loci elsewhere in the Y have homologs on the X. The secondary pseudoautosomal region (PAR2) is located at distal Yq and distal Xq; its loss from Yq seems to be without phenotypic consequence (Kühl et al. 2001). From the point of view of reproductive health, three “azoöspermia factor regions” on Yq are of importance, named AZFa, b, and c; the internal structure of AZFb and c includes segments that can be duplicated or deleted (Figure 6–19). Besides sex determination, the Y has certain other, including Figure 6–18.  Meiosis in the Male X-Autosome Carrier. Notes: (a) Father with balanced X;18 translocation, from whom pregnancy was achieved following in vitro fertilization with intracytoplasmic sperm injection. (b) The presumed pachytene configuration during gametogenesis in the father (X chromatin, open; Y chromatin, gray; chromosome 18 chromatin, cross-hatched). According to this construction, the X segments and the Y align only at the respective pseudoautosomal regions (PARs), and otherwise lie free. Heavy arrows indicate movement of chromosomes to daughter cells in one of the 2:2 alternate segregations, to produce a normal gamete, as observed in the 46,XY son. Light arrows show the other alternate combination, which could lead to a carrier daughter (Drawn after the case in Perrin et al., 2008).

174  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY immune-related, loci (Maan et al. 2017). Otherwise, half or more of the Y comprises the genetically inert heterochromatic region of the long arm (Yq12), which contains highly repetitive DNA sequences. The Y is the most variable in length of any chromosome, ranging from about 45 to 85 Mb (Hallast et al. 2023). MEIOSIS During normal meiosis in the male, the X and Y chromosomes recombine, synapsing at the PAR1 at the tips of Xp and Yp. The two sex chromosomes joined together in this way but otherwise unsynapsed comprise the sex vesicle. A properly formed sex vesicle is necessary for normal spermatogenesis, and anything that interferes with its normal formation—such as the presence of a translocation chromosome—will compromise the process of sperm development. Y-Autosome Translocation Types Y LONG-ARM AND ACROCENTRIC SHORT-ARM TRANSLOCATIONS This essentially harmless rearrangement is the most common form of the Y-autosome translocation, accounting for some two-thirds of all cases. The autosome is one of the acrocentrics, most commonly chromosome 15, der(15)t(Y;15)(q12;p12) (which may be particularly prevalent in an Israeli Ethiopian community; Chen-Shtoyerman et al. 2012), followed by chromosome 22. There is no loss or gain of euchromatin; the result is that one acrocentric carries some phenotypically irrelevant Y heterochromatin, looking rather like (and sometimes mistaken for) a very long short arm (Neumann et al. 1992). The breakpoints are sited in the acrocentric short arm (p11p13) and in the heterochromatin of the Y long arm (Yq12) (Figure 6–20). Males and females can equally be carriers. Neither phenotypic abnormality nor infertility has been associated. Chen et al. (2021b) tested for a theoretical risk of UPD(15) in a prenatally diagnosed case; no such association has actually been reported. The only instance of a possibly related untoward effect is suggested in the case in Rajcan-Separovic et al. (2001), who document the instance of a woman with a Yq;15p chromosome, of older childbearing age, who had had two trisomic 15 pregnancies; no other such cases have since been reported. The countertype of the common Y;15 is the circumstance in which the other reciprocal product, the der(Y), replaces a normal Y. Hoshi et al. (1998) identified a perfectly normal man, the father of three, who had a 46,X,–Y,t(Y;15)(q12;p13) karyotype. The Figure 6–19.  The AZF loci on Yq, and Showing the Internal Structure of AZFb and c. Source: From R Zhou et al., Identifying novel copy number variants in azoospermia factor regions and evaluating their effects on spermatogenic impairment, Front Genet 10:427, 2019. Courtesy Z Xu, and with the permission of Frontiers in Genetics. Sex Chromosome Translocations  175 der(Y) contained the necessary male-determining and fertility regions. He was only investigated because his sister had had a gonadal tumor of testicular origin, she having the mosaic karyotype 46,X,Y,t(Y;15)/45,X. BALANCED RECIPROCAL Yq AND AUTOSOME TRANSLOCATION This translocation is seen only in the male. Reciprocal exchange between the Y long arm and an autosome produces a balanced Y-autosome translocation. In the form being considered here, the Y breakpoint is usually given as q11.2 or q12, and the autosomal breakpoint is anywhere on the autosomal karyotype (other than at an acrocentric short arm, a different entity as discussed in the preceding section) (Braun-Falco et al. 2007). In most, the rearrangement may be truly balanced, with the physical and intellectual phenotype being normal, and male infertility is the usual presenting factor. Given this latter fact, it follows logically enough that the translocation would typically arise as a de novo event, and this is indeed the observation (Pinho et al. 2005). There are associated phenotypic abnormalities in a few individuals, and this may be due to a disruptive effect at the breakpoints or a deletion of autosomal material distal to the breakpoint (Erickson et al. 1995). Azoöspermia is typical (Kim et al. 2012). Incomplete pairing at meiosis, with failed or abnormal formation of a sex vesicle, may lead to spermatogenic arrest (Figure 6–21). In other cases, loss of the AZF region may explain the infertility (Brisset et al. 2005). But if spermatogenesis is able to proceed, there is a risk for the generation of unbalanced forms, and a few examples are on record. Mademont-Soler et al. (2009) describe a fertile couple, the father having the karyotype 46,X,t(Y;12) (q12;q24.33). The der(12) was deleted for a very small distal segment of chromosome 12 (12q24.33qter), whereas the der(Y) carried this material. In two pregnancies, the two different adjacent-1 segregations were observed: 46,der(12) in one, and 46,der(Y) in the other. Both pregnancies, with thus an autosomal deletion and a duplication respectively, were terminated. A very few familial cases have been reported with father and son having the same balanced rearrangement. Teyssier et al. (1993) document a man with severe oligoasthenospermia who had a t(Y;1)(q11;q11) and whose father proved to carry the same translocation. Intact fertility is well illustrated in the family described by Sklower Brooks et al. (1998), depicted in Figure 6–22. One son in a sibship of five males and two females, he himself a university graduate, had presented for genetic counseling when his wife had a third miscarriage (they also had a normal daughter). The deceased father must have carried a t(Y;8)(q12;p21.3), with three sons showing the balanced state Figure 6–20.  A Familial Y-Autosome Translocation. Notes: An example of the Y-autosome translocation involving an acrocentric autosome, the der(15) depicted here, with the breakpoint in the acrocentric short arm. Normal chromosome 15 and normal Y shown alongside for comparison (chromosome 15 chromatin, cross-hatched; Y heterochromatin, filled; Y euchromatin, open). The translocation chromosome can be carried equally by males and females. The karyotype appears unbalanced, but the phenotype is normal.

176  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY and two sons having inherited 46,X,der(Y), an unbalanced complement. The unbalanced state conferred a partial trisomy for 8p22pter, which was associated with a mild learning difficulty. With access to intracytoplasmic sperm injection (ICSI), biological paternity becomes possible for some carriers. The man we had seen with the 46,X,t(Y;18) (q11.2q21) translocation shown in Figure 6–23 had been karyotyped in the course of investigation for infertility with severe oligospermia, he being an otherwise normal person. In this Y;18 case, of the 16 possible embryos more than half, including one of the 4:0 segregants, would in theory be viable; the reader may wish to work out which ones these might be. Only one sperm, the 23,X, is capable of producing a phenotypically and karyotypically normal child; the other gamete from alternate segregation, 23,t(Y;18), would produce a son who would likely have similar infertility. At preimplantation genetic testing, the chromosomally unbalanced embryos could be discarded. With a small number of eggs retrieved on each stimulation cycle, a normal combination might well not happen, given that there are 14 unbalanced possibilities, if each outcome were equally likely. But in fact, the observations of Sklower Brooks et al. (1998; see above) provide some encouragement that the odds for the Y-autosome carrier (in other words, the meiotic predisposition) may be tipped in favor of the normal Figure 6–21.  Meiosis in an infertile man, otherwise normal, with a balanced Y;1 translocation. Notes: An immunostained pachytene spermatocyte (top panel) from a man 46,X,t(Y;1)(p11.3;p31). The lower panel interprets synapsis of the PAR1s of the X (purple) and the short Yp segment (green) of the der(1). Otherwise, synapsis between the 1p and 1q segments of the normal homolog and the der(1) is incomplete (occurring only at the double red lines). Blue circles = centromeres; yellow circles = cross-over points. Similar meiotic studies are reported in Delobel et al. (1998) and Sun et al. (2005). Source: From G Li et al., Meiotic defects and decreased expression of genes located around the chromosomal breakpoint in the testis of a patient with a novel 46,X,t(Y;1)(p11.3;p31) translocation, Int J Mol Med 40:367– 377, 2017. Courtesy Y Zhang and D Yu, and with the permission of Spandidos Publications. Sex Chromosome Translocations  177 and balanced forms. As it turned out in this Y;18 case, one embryo was indeed 46,XX, and this was successfully implanted. This question of a tendency toward an asymmetric segregation is more directly answered in Giltay et al. (1999), these workers undertaking a sperm analysis in a man with a t(Y;16)(q11.21;q24). Sperm were present but few in number, with many abnormal forms (oligoasthenoteratozoöspermia). Although alternate segregation accounts for only two out of the 16 segregation possibilities, in fact in this case half of all morphologically normal spermatozoa were normal or balanced, with about 40% showing adjacent segregation and about 10% with 3:1. But the fractions were less favorable if Figure 6–22.  A Familial Y-Autosome Translocation. Notes: A Y-autosome translocation, not involving an acrocentric short arm. In this particular example, and somewhat unusually, fertility is apparently normal. The autosomal translocated segment is of small size, structurally and functionally, and the aneuploid state with a dup(8p) is not only viable but also associated with only a mildly abnormal intellectual phenotype and an essentially normal physical appearance. (a) Family tree. Filled symbol, unbalanced karyotype; half-filled symbol, balanced carrier. The deceased grandfather is presumed to have been a translocation heterozygote. (b) Partial karyotype of a translocation heterozygote (above), showing the Y;8 translocation, and one of the individuals with the unbalanced complement (below). (c) The presumed pachytene configuration during gametogenesis in the heterozygote (chromosome 8 chromatin, open; Y and X chromatin, cross-hatched). Arrows indicate movements of chromosomes to daughter cells in “adjacent-1” segregation; heavy arrows show the combination observed in this family. (Case of S Sklower Brooks et al. 1998.) 178  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY abnormal sperm were included. With reference to assisted conception and using ICSI, Giltay and colleagues speak of in vitro and in vivo selection (the former artificial, the latter natural) combining to effect a considerable reduction in the risk for an unbalanced offspring. In fact, this man had had three children by ICSI, two normal daughters and a carrier son. Rare Forms Yp MATERIAL-TO-AUTOSOME TRANSLOCATION, 45-CHROMOSOME COUNT, INCLUDING “45,X Male” The testis-determining region of the Y, containing the SRY gene, can be translocated onto an autosome, usually an acrocentric and most often no. 15. The individual, phenotypically male, has 45 chromosomes, including the Y+autosome fusion product. The translocated Y segment may be beyond the level of cytogenetic resolution, and the classic karyotype can appear as 45,X (“45,X male”) until further studies cast light (Qin et al. 2022). Typically, the reproductive, and sometimes the physical, phenotype is affected. Azoöspermia is a frequent finding. The oligoasthenozoöspermic man in Jia et al. (2019) had smallish testes but was otherwise normal: he had a 45,X,psu dic(Yp;22p) karyotype of paternal origin. These authors speculate that the infertility in his case may have been due rather to a del/dup of the b2/b3 and b3/b4 segments within Yq (Figure 6–19), since the AZF loci were otherwise intact. The Y component may be translocated insertionally, as Yenamandra et al. (1997) demonstrated in a phenotypically abnormal “45,X” boy, in one of whose chromosomes 4, at 4p15.3, the SRY-bearing segment was accommodated. Rather more obvious cytogenetically was the de novo dicentric Y;13 translocation, 45,X,dic(Y;13)(p11.3;p11.2) described in Shanske et al. (1999): The translocation comprised almost a complete 13+Y composite. Their patient was a very short and otherwise normal 10-year-old boy in whom the SHOX growth control gene, normally located in Figure 6–23.  The Y-Autosome Translocation and Fertility. Notes: This t(Y;18)(q11;2q21) was identified in a man presenting with oligospermia during investigation for infertility. The fact that some sperm are still being produced allows the option of in vitro fertilization with intracytoplasmic sperm injection. A considerable number of these unbalanced gametes could, in theory, be viable. Only a 46,XX daughter could be both karyotypically and phenotypically normal. (Case of L Harris and L Wilton.)

Sex Chromosome Translocations  179 the PAR1, was absent. A more markedly affected case is the “45,X” boy in Suntharesan et al. (2022) presenting with short stature and a pervasive developmental disorder, whose unbalanced Yp;2p translocation dictated a partial 2p monosomy; the Y+2 derivative chromosome included SRY. The translocation may occasionally be of no phenotypic or reproductive effect, as Callen et al. (1987) record in a family identified quite by chance in the course of a research study, in which a man and two sons had the karyotype 45,X,dic(Y;22) (q11.23;p11.2). A similar story is presented in Morales et al. (2007b), in this case the karyotype being 45,X,psu dic(Y;22)(qter;p11.2), with the Y+22 chromosome comprising almost an entire Y and almost an entire 22. The chromosome very evidently did not affect fertility in 10 carrier fathers in this large family; curiously, it was segregation of the 22 chromosomes that was the sex-determining mechanism in the offspring of these men. It was interesting that only normal children were born, whereas in theory, segregation might also have led to 45,X Turner syndrome and 46,XX,psu dic (Y;22) Klinefelter syndrome. Yqh MATERIAL ON A NON-ACROCENTRIC CHROMOSOME, 46-CHROMSOME COUNT If Yq heterochromatin is translocated to the tip of a non-acrocentric autosome, there may be no reproductive implication. A der(1)t(Y;1)(q12;p36) in a French family could be traced back to a couple married in 1773, with self-evident fertility, male and female, for more than two centuries (Morel et al. 2002); and Vozdova et al. (2011) showed normal seminal indices in a man with a familial der(4)t(Y;4)(q11.23;p16.3) identified serendipitously. Specific Very Rare Cases FAMILIAL t(Y;15) WITH PRADER-WILLI SYNDROME A very few cases of Prader-Willi syndrome (PWS) have been due to a fusion between a Y and a chromosome 15, having the karyotype 45,X,t(Y;15) with varying breakpoints, either de novo or familial (Vickers et al. 1994; Puvabanditsin et al. 2007). A remarkable example concerns a familial t(Y;15)(p11.2;q12) described in Gole et al. (2004). The father with the balanced translocation had a daughter with presumed PWS, she having inherited his X chromosome and the der(Y) which comprised almost all of 15q but lacking the PWS region, and most of the Y but lacking SRY. Her karyotype 46,XX,–15,+der(Y) reflected what might be called a “version” of adjacent-2 segregation. The absence of a paternally originating PWS region led to the development of that syndrome, while the absence of SRY was the basis of female sex. Her brother had the countertype “standard” adjacent-2 combination, 46,X,–Y,+der(15): He was of below-average intelligence, presumably due to duplication of the proximal 15q region, 15cen→q12, and had required treatment for hypogonadism. DE NOVO t(Yq;1q) WITH 1q TRISOMY A few cases are on record of a recurrent de novo unbalanced translocation t(Y;1) (q12;q21) seen in mosaic state (mos 46,X,der(Y)t(Y;1)/46,XY), with the abnormal cell line imposing an essentially complete 1q trisomy. The rearrangement arises at a

180  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY post-zygotic mitosis; presumably, similar sequences on 1q21 and Yq21 predispose to this recurrent rearrangement. The phenotype, unsurprisingly, is very severe, somewhat resembling Fryns syndrome (Bone et al. 2017). X-Y Translocations Liu et al. (2023) proposed a classification of the X-Y translocation, and this is set out in Table 6–3. The major division is between those with an Xp22 breakpoint (Types I–V), and all others. Within the Xp22 category, there is a distinction between those in which the Y breakpoint is below the centromere, in Yq11 (I, II, and V), and those in which it is above, in Yp11 (III and IV). Types I and II t(X;Y). Of the major types of X-Y translocation the classical form, Types I and II, is the most frequently seen (Figure 6–24a, b). The X and Y breakpoints are broadly constant at the cytogenetic level, involving Xp22 in the distal X short arm and Yq11/q12 in the proximal Y long arm. It is readily recognized cytogenetically, and has the karyotypic notation 46,Y (Type I) or 46,X (Type II), der(X),t(X;Y)(p22;q11) (the full form of the karyotype is set out in Table 6–3). The important genotypic defect is deletion of the distal Xp segment, Xp22→pter, with the loss of chromatin including PAR1. At the molecular level, there is variation in the amount of Xp deleted; and the phenotype, in large part, depends upon which of the following distal Xp genes (listed here in order from Xpter toward centromere) may be lost: SHOX (short stature homeobox, for Leri-Weill dyschondrosteosis), ARSE (arylsulfatase E, for chondrodysplasia punctata), STS (steroid sulfatase, for ichthyosis), KAL1 (Kallmann syndrome), OA1 (ocular albinism), CLCN4 (intellectual disability), and HCCS (for microphthalmia linear-skin defects). The Y-originating segment does not contain SRY. The (female) person who is 46,X,der(X)t(X;Y) has a partial monosomy for this Xp segment, and the (male) individual with 46,Y,der(X)t(X;Y) is partially nullisomic. The female t(X;Y) heterozygote is characteristically fertile and of normal intelligence, but intellectual disability, skeletal findings, facial dysmorphism, and uterine anomaly (Figure 6–25) are associated in a minority (Daghsni et al. 2025). If SHOX is deleted (as is frequently so), the monosomic/heterozygous state for this gene determines a particular form of short stature and wrist deformity (Leri-Weill dyschondrosteosis). The pattern Table 6–3.  A Classification of the X-Y Translocation and the Associated Gender Phenotypes Sex Types I-V, with an Xp22 breakpoint I 46,Y,der(X)t(X;Y)(Xqter→Xp22::Yq11→Yqter) Male II 46,X,der(X)t(X;Y)(Xqter→Xp22::Yq11→Yqter) Almost all female III 46,X,psu dic(X;Y)(Xqter→Xp22::Yp11→Yqter) Similar male:female IV 46,X,der(X)t(X;Y)(Xqter→Xp22::Yp11→Ypter) Male>female V 46,X,der(Y)t(X;Y)(Ypter→Yq11::Xp22→Xpter) Male All other types, the X breakpoint elsewhere than Xp22 Various Source: From S Liu et al., Comprehensive analysis of three female patients with different types of X/Y translocations and literature review, Mol Cytogenet 16:7, 2023. Sex Chromosome Translocations  181 of X-inactivation tends toward preferential inactivation of the der(X)t(X;Y), but this is variable and unpredictable (Gabriel-Robez et al. 1990). The male t(X;Y) hemizygote is typically the son of a t(X;Y) mother (Jiang et al. 2020a). Some may be cognitively normal, in those in whom the breakpoint is more distal. If the male is of short stature along with Leri-Weill dyschondrosteosis, it is no more marked than in the female, reflecting the fact that the SHOX locus is in the PAR1 and that each Figure 6–24.  X-Y Translocations. The four more frequent ways in which X-Y translocations are seen. (a) The classical t(X;Y)(p22.3;q11) together with a normal X (in a female; Type II). (b) The classical t(X;Y) together with a normal Y (in a male; Type I). (c) The cryptic t(Xp;Yp), with the Yp segment containing the SRY gene, in a “46,XX male.” (d) The cryptic t(Xp;Yp) as the sole gonosome, in a “45,X male.” Y chromatin: White indicates Y euchromatin, black indicates that part of distal Yp euchromatin encompassing the pseudoautosomal region and the SRY locus, and cross-hatching indicates Yq heterochromatin. Note that gonadal sex accords with the absence (a) or presence (b–d) of the SRY gene. Figure 6–25.  Uterine Anomaly in an X-Y Translocation Carrier. Notes: Bicornuate (or possibly septate) uterus in a woman with a classic 46,X,der(X),t(X;Y)(p22.3;q11) translocation. The two “horns” (cornua) are outlined by the dark imaging, diverging from each other as a letter V. The arrow points to free spill of the contrast medium, due to patency of the right fallopian tube. Source: From WA Dobek et al., Long-term follow-up of females with unbalanced X;Y translocations— Reproductive and nonreproductive consequences, Molec Cytogenet 8: 13, 2015. Courtesy LC Layman, and with the permission of Elsevier.

182  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY sex still retains one copy of the gene, as a heterozygote, on their normal X or Y, respectively. Should a more proximal molecular breakpoint expose a Mendelian “brain gene” such as CLCN4 mentioned earlier, intellectual disability results. Infertility is almost invariable due to spermatogenic arrest (Gabriel-Robez et al. 1990). The two unkaryotyped fathers in Liu et al. (2023) (Figure 6–26) may be exceptions to that rule. Sperm production was documented in a single case, (albeit at a very low level: 125,000 per ml) in a man with the type I karyotype (Morel et al. 2001). He was of normal intelligence, height 165 cm (5 feet 5 inches), with normal external genitalia and normal endocrine indices, and he had presented with infertility. There were equal numbers of 23,der(X) and normal 23,Y sperm, but about 20% of sperm were otherwise abnormal, the most common defect being 24,Y,der(X). The majority of cases are familial and almost always of matrilineal transmission. Presumably, the X-Y chromosome arose following a reciprocal exchange between the X and Y during spermatogenesis in the man fathering the originating (female) translocation carrier in the family. This event is facilitated by the apposition of X and Y segments having a high degree of homology; for example, a crossover between the Kallmann locus on the X chromosome and a Kallmann-like nonfunctional pseudogene on the Y chromosome long arm (Guioli et al. 1992). Type III t(X;Y). This is readily recognized cytogenetically with much of a Y chromosome, encompassing some of Yp and the complete q arm, having been attached to distal Xp. The nomenclature pseudodicentric refers to the presence of both an X and a Y centromere, with only one of these remaining functional. It is certainly rare. The phenotypic sex relates to the presence or absence of SRY within the Yp segment. In the 46,X,psu dic t(X;Y) SRY+ case, the t(X;Y) chromosome, containing a near-complete amount of (inactivated) X material, may impose a Klinefelter-like physical phenotype. Mosaicism with a 45,X line may be seen, whether in male, female, or intersex state (Mazen et al. 2013). Fertility is almost unknown (Pavlistova et al. 2016). Figure 6–26.  Pedigree of a t(X;Y) family. Notes: The translocation is Liu Type II, 46,X,der(X),t(X;Y)(p22;q11), demonstrated in **some, and presumed in *others. Half-fill symbol = short stature; fill symbol, arrowed = proband with short stature and infertility; open symbol = normal stature; small diamond = biochemical pregnancy; P-in-diamond = 30/40 pregnancy. The deleted Xp segment chrX:251888-1772154 includes SHOX. It is possible, but unproven, that the unkaryotyped fathers II:2 and II:6, being of short stature (150 cm), are hemizygotes. If so, their fertility is certainly notable; and it would be consistent that their sons III:1 and III:5 are obligate normal, and the one daughter, III:6, obligate heterozygous. Source: From S Liu et al., Comprehensive analysis of three female patients with different types of X/Y translocations and literature review, Mol Cytogenet 16:7, 2023. Courtesy X Zhang, and with the permission of Springer Nature. Sex Chromosome Translocations  183 Type IV t(X;Y). This category has been known as the XX male (also as de la Chapelle syndrome) and the 45,X male. In the early days of cytogenetics, a very small translocation of Yp onto Xp could not be discerned, but as technology improved, including in particular the use of FISH probes recognizing Yp material, their true status as X;Y translocations became apparent (Figure 6–24c, d). The translocation arises from an abnormal X-Y recombination during paternal meiosis (Weil et al. 1994). The X breakpoint is within Xp22.3, and the Y breakpoint is in the short arm, proximal to the SRY testis-determining gene. The genotypic consequences are loss of the distal region of the X chromosome and the transfer of the SRY gene onto an almost intact X chromosome. Thus, the person is typically a male; rare female cases may result from X-inactivation extending into the Yp segment (Liu et al. 2023). This translocation accounts for most supposed XX males and some 45,X males (Y-autosomal forms of 45,X male are discussed above). Almost always, it occurs sporadically, and the affected males are infertile.12 The extra X in the 46,X,der(X)t(X;Y) case determines a Klinefelter-like physical phenotype. If there is loss of one copy of the SHOX gene, Leri-Weill dyschondrosteosis is the expected consequence. Type V t(X;Y). This rare form comprises a quite small derivative chromosome containing key Yp functional components (including the SRY locus) but lacking several Yq loci, and along with the presence of the p arm tip of an X. All cases are male. As an example, the Yq breakpoint of the 46,X,der(Y),t(Y;X)(q11.221;p22.33) azoöspermic man in Bukvic et al. (2013) was at Yq11.221, such that AZFa was retained but AZFb and c lost: this disruption was presumably the basis of the compromised spermatogenic function. These authors perceived a “small reduction of mental capability” in this man, which might possibly have reflected the functionally disomic state of about 8 Mb within Xp22.33pter.13 Other Variant Forms. There is a very considerable range of other types of t(X;Y), and Liu et al. (2023) list 22 various rearrangements. The counselor seeing a case not falling within the Types I–V as discussed above but listed in Table 6–4 is referred to the Table in Liu et al. for further detail. X-X Rearrangements There are barely double-digit of numbers of reports of this very rare observation. While it is sometimes referred to as an X;X translocation, the expression rea(X) may perhaps be more useful than t(X;X), given that the chromosomal status is always unbalanced, while a lone “t” is often indicative of a balanced-carrier setting. The general karyotype in the heterozygous female is written 46,X,rea(X),t(Xp;Xq), and the resultant imbalance is a dup/del of Xp/Xq, or vice versa. The imbalance can be substantially mitigated due to inactivation of the der(X). Pubertal and/or menstrual abnormality is the usual presentation, and infertility is the rule; a SHOX deletion in distal Xp can be the basis of short stature (Reinehr et al. 2001; Tayebi and Khodaei 2011). The de novo rearrangement 12 A most extraordinary exception, indeed a unique case, is seen in the family reported in Sharp et al. (2004). Two individuals, 46,X,der(X)t(X;Y)(p22.33;p11.2), likely distantly related, presented with an ovotesticular disorder of sex development. One was the child of a 46,X,t(X;Y) mother, and the other was the child of a 46,Y,t(X;Y) father. It may be that SRY in the two affected offspring was only partially operating within gonadal tissue, due to a variably penetrant position effect. 13 And in fact, PAR1 would have been in trisomic state: PAR1 from his normal X, PAR1 from the Yp component of the der(Y), and PAR1 from the Xp component of his der(Y).

184  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY could have arisen following unequal recombination between the two X chromosomes in the oöcyte. Or, the rearrangement could have occurred within the one X chromosome, folding in upon itself, in which case the origin is more likely paternal (Giglio et al. 2000). Xp11.23 and Xq21.3 are favored as breakpoints, and the translocated del/dup segments may therefore be large. If female fertility is retained, the rea(X) is transmissible, as is of course the normal X, presumably a 50:50 probability for each. Heterozygous daughters may display a similar phenotype to their mothers, X-inactivation permitting. Viable hemizygous males, in whom the rea(X) is not subject to inactivation, can be severely affected, and especially if the MECP2 locus is duplicated (Magini et al. 2015; Grams et al. 2016); major fetal malformation may be seen (Lin et al. 2024). Table 6–4.  Some Recorded X-Y Translocations, Several Being Unique, Having X Breakpoints Elsewhere than at Proximal Xp22 TRANSLOCATION PHENOTYPIC SEX 46,X,der (X)t(X;Y)(p11.2;q11)dn F 46,X,psu dic(X;Y)(p11.3;p11.1) F 46,X,der(X)t(X;Y)(p11.4,p11.2)mat* F 47,XY,der(Y)t(X;Y)(p21.1;p11.2) F 46,X,der(Y)t(X;Y)(p21.1;q11)dn F 46,X,der(Y)t(X;Y)(p21.3;q11.21) M 46,t(X;Y)(p22.3;p11.2)* M 46,X,dic(X;Y)(p22.33;p11.32)* M 46,X,t(X;8)(q13;q11.2) F 46,X,der(Y)t(X;Y)(q13.1;q11.223) F 46,X,der(X)t(X;5)(q21;q31) F 46,X,psu dic(X)t(X;Y)(q22;p11) F 46,X,der(X)t(X;Y)(q22;q11)dn F 46,X,der(X)t(X;Y)(q25;q12) F 46,X,t(X;22)(q25;q11.2) F 46,Y,t(X;8)(q26;q22) M 46,Y,t(X;1)(q26;q23) M 46,Y,t(X;3)(q26;p24) M 46,X,der(X)t(X;Y)(q26.2;q11.223)mat F 46,X,der(X)t(X;Y)(q26.3;q11.223) F 46,der(X)t(X;Y)(q28;p11.2)mat** F 46,X,der (X)t(X;Y)(q28;q11.2)dn F 46,X,der(Y)t(X;Y)(q28;q11.23)dn M Notes: Translocations are listed in “numerical order” of the Xp and then Xq breakpoints. A few are *mosaic. **The notable case of Politi et al. (2024) concerning the translocation (X;Y)(q28;p11.2) records the extraordinary observation of three generations of phenotypically normal female heterozygotes being SRY+, a reflection of very skewed X-inactivation, such that SRY function within the Y component of the der(X) was suppressed. Source: From S Liu et al., Comprehensive analysis of three female patients with different types of X/Y translocations and literature review, Mol Cytogenet 16:7, 2023, with the addition of the case in Politi et al., and six cases of Huang et al. (2023).

Sex Chromosome Translocations  185 Y Rearrangements For the sake of completeness, the presumed existence of this very rare circumstance is noted. Similarly to the rea(X;X) just discussed, rea(Y) may be a more useful nomenclature than the sometimes-seen t(Y;Y). A number may in fact have been isodicentric Yq chromosomes (Chapter 15) (Hsu 1994; Hernando et al. 2002). GENETIC COUNSELING The X-Autosome Translocation Fertility is affected in the X-autosome heterozygote and hemizygote. About half of the female carriers and almost all males are likely to be infertile. The Female Heterozygote If fertile, the female heterozygote has a substantial risk for having abnormal offspring due to transmitting an imbalanced chromosomal constitution. At one end of the scale, the abnormality might be mild (e.g., partial Klinefelter syndrome) or barely discernible (e.g., partial X trisomy). At the other end, it could be severe (e.g., partial X disomy or autosomal aneuploidy, not modified by inactivation). The counselor should determine the theoretical gametic combinations from the particular category of translocation, with reference to the examples described in the prior section on Biology. Adjacent-1 and 3:1 tertiary trisomy are the major malsegregation modes to be considered. Figures 6–14 and 6–15 provide a guide, but each translocation needs to be assessed on its own merits. General comments follow. 1. A “single-segment” translocation (that is, the autosomal segment is very small) with an X segment of large size would imply risks, in viable offspring, for partial Turner, partial Klinefelter, and partial XXX syndromes (Figures 6–3 and 6–11; Figure 6–14b, c). 2. A single-segment translocation with an X segment of small size would imply a risk not only for one of these three partial gonosomal aneuploidies, albeit in milder form, but also—given the fact of a small segment implying possible viability—for a functional disomy for a small distal Xp or Xq segment. A functional disomy in a child of either sex would have a severe outcome (Figure 6– 13b, segregation as per heavy arrows; Figure 6–14a) (Sanlaville et al. 2005). The other possibility is a nullisomy. While nullisomy in the female would lead only to an attenuated form of Turner syndrome, in the male, for all but the smallest segments, this would be lethal in utero (Figure 6–13b, segregation as per light arrows; Figure 6–14b). The borderline between viable (but severe) and nonviable Xp deletion in the male may be at Xp22.2, in which about 10 Mb of DNA is removed (Melichar et al. 2007). 3. A single-segment translocation with an autosomal translocated segment of “viable size” (Figures 6–14d-f) implies a risk for partial autosomal monosomy or trisomy 186  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY from adjacent-1 segregations, or 3:1 imbalance. In the female conceptus, the trisomy may be modified by spreading of inactivation, but this is unpredictable. 4. Any 2:2 unbalanced segregant from a double-segment translocation (Figure 6– 14h-j) has a combined duplication/deficiency, and spontaneous abortion is probable. But spreading of inactivation in a female conception may attenuate a partial autosomal trisomy and allow for survival, albeit with phenotypic defect of unpredictable degree. 5. Adjacent-2 possibilities need individual assessment (Figure 6–15). THE LEVEL OF RISK The risk for many female heterozygotes who are fertile will be “substantial.” An otherwise nonviable unbalanced conception may survive because inactivation tempers the imbalance; and some conceptions with the structurally balanced complement may be functionally unbalanced due to aberrant inactivation patterns. The counselor should go through the exercise of determining possible malsegregant outcomes, as depicted in Figures 6–14 and 6–15. The risks to have a liveborn child with a structural and/or functional aneuploidy may be in the range 20% or higher. In Stene and Stengel-Rutkowski (1988), and with specific reference to single-segmental translocations involving Xp, the risk for adjacent-1 malsegregants was 24%, although interestingly the risk associated with 3:1 segregation leading to interchange trisomy X was very low, less than 0.8%. At the level of the blastocyst, in one small series the fractions of normal/balanced and malsegregants were similar (Table 6–5). As we discussed above, the components making up the total risk may comprise a very mild abnormality through to severe disability. There is the difficulty of knowing what risk might apply to a child with the same balanced translocation as their parent (see below). The only clear statement that can be made is this: Only with the 46,XX and 46,XY karyotype can one be confident of normality, other things being equal. Even more so than with the common autosomal translocation, the risks relating to each X-autosome translocation will be specific to that particular rearrangement, and extrapolation from other translocations will be fraught. Panasiuk et al. (2004) have made a start in deriving specific risk figures for four different translocations, in each case the X breakpoint involving the short arm (Table 6–6). The one circumstance in which they consider data pooling to be permissible is in rearrangements in which the autosomal breakpoint is in the short arm of an acrocentric. The risks, both for an unbalanced form or for a balanced form but with phenotypic abnormality due to unfavorable inactivation could, in principle, be bypassed using PGT blastocyst biopsy with fine-tuned molecular analysis to distinguish the normal from the balanced carrier. The attraction of PGT is obvious. In essence, this might make the detailed assessments of segregation risks, as just discussed, of somewhat academic interest. Yuan et al. (2021) demonstrate the application of this approach in their management of three female X-autosome carriers, all three happening to be X-1 heterozygotes but with different breakpoints in each. In quite small numbers of embryos created at IVF, each carrier had one or two normal embryos (Table 6–5). These normal embryos were, naturally, chosen for transfer, and eventually a normal 46,XX and a normal 46,XY baby were born. While FISH is no longer applied at PGT, diagramming the use of color-coded FISH probes can rather nicely demonstrate segregation at embryo biopsy (Figure 6–27).

Sex Chromosome Translocations  187 The Male Hemizygote Infertility is almost inevitable, barring the possibility of medical intervention. If sperm can be accessed from an ejaculate or via testicular sperm extraction, IVF using ICSI may be attempted; greater spermatogenic success may attend translocations with pericentromeric or centromeric breakpoints (Perrin et al. 2008). The only outcome from which normality could be expected, other things being equal, is the alternate segregation leading to 46,XY; such a child will also be free of the family genetic risk. Normality in a (necessarily heterozygous) daughter would require inactivation in her to have been Table 6–5.  The Karyotypes of Embryos from Three Female X-autosome Carriers MOTHER BLASTOCYST DIAGNOSIS NORMAL CARRIER UNBALANCED t(X;1)(q28;p31.1) 1* 1 1 (adj-1) t(X;1)(p22.31;q21) 2** 1 2 (adj-1) t(X;1)(p22.33;p36.22) 1*** 2 (adj-1, + unrelated trisomies) Notes: adj-1 = adjacent-1 malsegregant *This embryo transferred, but implantation failed. **One embryo transferred, and a 46,XX baby born; one cryopreserved. ***This embryo transferred, and a 46,XY baby born. Source: From S Yuan et al., Reproductive risks and preimplantation genetic testing intervention for X-autosome translocation carriers, Reprod Biomed Online 43:73–80, 2021. Table 6–6.  Risks Relating to Four Specific X-Autosome Translocations Estimated Risk Figures for Having a Liveborn Aneuploid Child, or a Child Stillborn or Dying as a Neonatea Because of Imbalance Due to X-Autosome Malsegregation (Adjacent and/or 3:1), in Four Specific Translocations, Three Double Segment, and One, the X;22, Effectively Single Segmentb TRANSLOCATIONS RISKc (%) t(X;5)(p22.2;q32) 4.2 t(X;6)(p11.2;q21) 3.3d t(X;7)(p22.2;p11.1) 2.1 t(X;22)(p22.1;p11.1)e 17 aFigures may be considered as expressing the percentage risk to have an aneuploid liveborn or stillborn infant, from a pregnancy which had proceeded to at least 28 weeks gestation. bFamilies published or cited in Panasiuk et al. (2004). cThe figure in one family (X;22), in which the autosomal breakpoint is in the p arm of an acrocentric chromosome, comes from direct segregation analysis, and combining with literature cases of another X;acrocentric p arm translocation (of chromosome 15). In the remaining three, the figure is indirect and derived from applying this rule: halving the risk for the lesser of the two risks, which would otherwise have applied to each translocated segment when viewed as a single-segment imbalance. dThis carrier mother had presented having had an unkaryotyped malformed stillbirth at 42 weeks gestation, suggesting that at least one of the malsegregant combinations might be compatible with survival to term. The figure of 3.3% might thus be an underestimate, if the risk figure were taken to include stillbirth. eThis translocation is very close to, and might possibly be the same as, the t(X;22) in Figure 6–17. 188  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY skewed in favor of the normal X, which, as discussed above, may not always happen. Phenotypic normality in the hemizygous father would allow the inference of a truly balanced rearrangement, and thus no question should arise about a cryptic deletion/duplication. The segregant fractions can vary quite considerably between men, and may suggest optimism for IVF, or pessimism, accordingly (Perrin et al. 2009b). In the IVF/ PGT cases of Chamayou et al. (2018) and Yuan et al. (2021), the ratio of normal/balanced to malsegregant embryos was about equal, ignoring otherwise unrelated aneuploidies (Figure 6–10; Table 6–5). The presumption of an approximately 50% risk was, for example, brought to the attention of the man with an (X;18)(q11;p11.1) translocation noted earlier (Figure 6– 18); nevertheless, and given the practical matter of a long wait for PGT, the couple went ahead with IVF and ICSI, having prenatal diagnosis in the pregnancy, and they had a normal 46,XY son (Perrin et al. 2008). Ma et al. (2003) describe a successful outcome in a man with a whole-arm translocation, t(X;20)(q10;q10), maternally inherited, and from whose ejaculate only about 50 sperm were able to be retrieved; an embryo created at IVF went on to become a carrier daughter, who was normal physically and developmentally on assessment at age 12 months. The child and her heterozygous paternal grandmother both displayed skewed X-inactivation. Interestingly, the man’s brother, also an X;20 hemizygote, had had 7 years of infertility but then had two normal daughters. These girls’ karyotypes and paternity status had not been evaluated. Figure 6–27.  Embryo Biopsy from an X;Autosome Carrier. Notes: The carrier mother had the karyotype 46,X,t(X;2)(q27;p15). Bl = blastomere (that is, a single cell from the embryo). Two blastomeres (Bl1, Bl2) were biopsied from each of the six day-3 embryos, indicated as A through F. FISH for appropriate parts of the involved chromosomes, using probes with the colors as shown, was applied. The pattern of colors enabled determination of segregation, and thus an interpretation of the genomic state of the embryos. Only one embryo was normal or balanced, embryo A, a male: note one X chromosome (green), two no. 2 chromosomes (red + yellow), and one Y (blue), and the two blastomeres concordant. This embryo was therefore transferred, but miscarried at 6 weeks. Source: From F Ferfouri et al., Is the resulting phenotype of an embryo with balanced X-autosome translocation, obtained by means of preimplantation genetic diagnosis, linked to the X inactivation pattern? Fertil Steril 105:1035–1046, 2016, with the permission of Elsevier and the American Society of Reproductive Medicine.

Sex Chromosome Translocations  189 The Balanced Inherited X-Autosome Detected Prenatally. This is a vexed question. Consider the circumstance of a phenotypically normal carrier mother who has prenatal diagnosis, or PGT. A balanced X-autosome karyotype identified in a female fetus, or in a female embryo (the balanced translocation and normal states not routinely distinguishable) might eventually lead to a normal daughter, but by no means can this be made as a firm statement (Scriven 2013). Indeed, Ferfouri et al. (2016), writing about the detection of a balanced X-autosome at PGT, speak of “the resulting phenotype remaining a mystery.” As yet, we lack a good understanding of the consistency of the mechanism of aberrant X-inactivation in causing phenotypic abnormality. A normal carrier mother (and she having a “perfect” 100:0 normal:derivative X-activation ratio) could yet have an abnormal carrier daughter if the daughter’s inactivation ratio were “imperfect” (e.g., Figure 6–5). There is a need for a large study, with unbiased ascertainment, of the carrier daughter offspring of the (normal) carrier mother in order to address this issue; those seeing such cases are encouraged to publish. Too little information exists concerning the phenotype of the male hemizygote born to a female X-autosome heterozygote for any firm advice to be offered. Normality has been recorded in this setting, but so has major genital defect, which in one case was the consequence of compromised function of the androgen receptor gene (Buckton et al. 1981; Kleczkowska et al. 1985; Callen and Sutherland 1986; Ma et al. 2003). Fetal ultrasonography may be useful to check for normal male genital development. This approach was offered to the mother whose karyotype appears in Figure 6–17, and who had a 46,Y,t(X;22) result at amniocentesis in her second pregnancy. A normal baby boy was subsequently born, whose infant development was quite normal. Otherwise normal male carriers would almost certainly be infertile. Y-AUTOSOME TRANSLOCATIONS The Apparently Balanced Y-Autosome Translocation It is notable that the same balanced Y-autosome translocation can behave differently in different male members of a family in terms of fertility, this presumably reflecting the importance of the background genetic contribution to the control of the mechanics of spermatogenesis (Teyssier et al. 1993; Rumpler 2001). For those who are fertile, risk data are too few to form a secure base for genetic counseling. From first principles, unbalanced forms are probable, several of which will often be viable (according to the autosome in question, and the site of the autosomal breakpoint), and the option of prenatal diagnosis is appropriately offered or (especially if IVF is needed,) PGT. As discussed in the Biology section, despite there being several more imbalanced than balanced possibilities, there are tentative grounds for supposing that alternate segregations (normal and balanced forms) may be favored. The t(Y;8) family of Sklower Brooks et al. (1998) noted above and shown in Figure 6–22 demonstrated three of the four predicted alternate and “adjacent-1” karyotypic outcomes: 46,XX, the 46,X,t(Y;8) balanced carrier, and 46,X,der(Y), the former two outnumbering the latter. The 46,X,der(Y) karyotype produced sons with an 8p duplication; the other unbalanced karyotype, 46,XX,der(8), would have produced a daughter with an 8p deletion. Manifestly, the carrier male, while he could have a normal 46,XX daughter, could never conceive a 46,XY child. Sperm karyotyping, if available, may be a helpful investigation. In the man with a 190  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY rare Yp;13p fusion recorded in Alves et al. (2002), having demonstrated that most sperm had a balanced complement, reassurance could be offered that if pregnancy were achievable, there would be a good chance of producing a normal child in this particular case. For the infertile man, assisted reproduction may offer the possibility of paternity (Mackie Ogilvie et al. 2010). A sperm count way below the level needed for natural conception may yet allow retrieval of sperm for ICSI. Testicular aspiration may provide sperm even when they are completely absent in the ejaculate. With the need for IVF, PGT becomes attractive because of the probable substantial genetic risk, in most cases, for unbalanced forms, and considering the practical point that the embryo is nicely accessible. Taking the example of the oligospermic man with a 46,X,t(Y;18)(q11.2;q21) karyotype, shown in Figure 6–23, he could, in theory and through IVF, have a 46,XX daughter or a 46,X,t(Y;18) son like himself. The substantial fraction of unbalanced forms that could be viable in this case, out of the 16 total possible conceptions, does becomes a relevant matter at PGT. These issues of IVF and PGT are discussed in more detail in Chapter 23. THE Yqh-ACROCENTRIC TRANSLOCATION Probably, these translocations can be regarded as being no more than interesting variant chromosomes, and of no clinical significance. In the case of the t(Yq;15p), a theoretical risk for trisomy 15 with correction to uniparental disomy (White et al. 1998; Rajcan-Separovic et al. 2001) is prudently not to be completely ignored, but certainly not to be overstated. The “45,X” Yp-Acrocentric Translocation. These chromosomes are probably stable, and not (if fertility is achievable) implying a risk for phenotypically abnormal offspring (Callen et al. 1987). The Classical X-Y Translocation The female with the classic Type II X-Y translocation is usually fertile and of normal intelligence. She has a 50% risk for having a child, whether a son or daughter, who would have the translocation. An X-Y translocation son may be abnormal, according to the extent of distal Xp nullisomy and the loci involved. If the mother is short, an X-Y translocation daughter would also be short, likely because of deletion of the SHOX locus. As with Turner syndrome, growth hormone treatment may be appropriate for such a child. She would probably be, like her mother, fertile. A child receiving the mother’s normal X would of course be normal, 46,XX or 46,XY. Prenatal diagnosis or PGT is appropriately offered. The male (Type I) X-Y translocation carrier is almost invariably infertile. A sperm chromosome study has been undertaken in only one 46,Y,der(X)t(X;Y) man (Morel et al. 2001, above). He had severe oligozoöspermia and, notably, sex chromosome aneuploidy was recorded in 20% of sperm. Otherwise, 40% of sperm were normal 23,Y, and 40% had the t(X;Y). Conception in such a case could only ever be achieved via IVF. If preimplantation testing were to be attempted, the choice of a 46,XY embryo (the only normal gonosomal possibility) would allow avoiding the genetic risk for the next generation. Other rare X-Y translocation types (Table 6–4) will need individual assessment.

Sex Chromosome Translocations  191 X-X Translocations Infertility is the expectation, and a theoretical question of genetic risk will usually be academic. In a small imbalance, fertility may be retained, as in the exceptional examples of Reinehr et al. (2001) and Grams et al. (2016) discussed above. A daughter receiving the X-X translocation would be expected to have a phenotype similar to that of her mother. A male pregnancy would be very likely to miscarry at any early stage, due to an X nullisomy/disomy. If the del/dup segments were very small, viability might be possible, but with probable major phenotypic defect. Children receiving the mother’s normal X chromosome would of course be normal, other things being equal. If IVF is proposed, PGT would also be a suitable option.

7 ROBERTSONIAN TRANSLOCATIONS THE AMERICAN INSECT CYTOGENETICIST WRB Robertson first described translocations of chromosomes resulting from the fusion of two acrocentrics in his study of insect speciation in 1916, and this type of translocation is named Robertsonian1 (abbreviation rob) in his honor. There are five human acrocentric autosomes—chromosomes 13, 14, 15, 21, and 22 (the 13, 14, and 15 are the D group chromosomes, and the 21 and 22 comprise the G group)—and all are capable of participating in this type of translocation. The composite chromosome produced includes the complete long-arm chromatin of the two fusing chromosomes, although it lacks at least some of the short-arm chromatin. Robertsonian translocations are common, with a population frequency of around one in 800 (Poot and Hochstenbach 2021). Historically, the most important are the D;21 and G;21 translocations, which are the basis of most familial translocation Down syndrome. Uniparental disomy is of relevance, although uncommonly so, with respect to the two imprintable acrocentrics, chromosomes 14 and 15. In this chapter we consider the case of the phenotypically normal person who carries, in balanced form, a Robertsonian translocation, with necessarily a 45-chromosome count. We generally use a short cytogenetic description for the carrier state, thus, 45,XX,rob(14q21q) or simply rob(14q21q), or even just 14;21 when the meaning is clear. The formally correct ICSN designation for a short-arm to short-arm fusion Robertsonian translocation, for example, is 45,XX,der(14;21)(q10;q10) or 45,XX,rob(14;21)(q10;q10).2 BIOLOGY The great majority of balanced Robertsonian translocations involve two different chromosomes (a heterologous or nonhomologous translocation); those involving the formation of homologs (homologous translocation) are rare. Heterologous translocations can be transmitted through many generations of phenotypically normal heterozygotes, whereas the homologous translocation is almost always seen only as a de novo event in the consultand. As Table 7–1 attests, the rob(13q14q) and the rob(14q21q) are the most predominant; these two are the Class I robs, and all the rest are Class II. The rob(13q14q) accounts for about three-quarters of all Robertsonian translocations in unbiased studies, and indeed it is the most common single chromosome translocation in the human race: around one person in 1,000 is a carrier. Karyotypes of the 13q14q and 1 Many authors continue to write Robertsonian with an uppercase R; the honor accorded Mendel, whose name-related adjective mendelian increasingly has a lowercase m, seems not yet to have flowed through to Dr. Robertson. 2 The reader may have queried this nomenclature, which would seem, prima facie, to indicate a chromosome without a centromere. However, given the complexity of formation of this translocation (Figure 7–5), we can simply take this as a pragmatic oversimplification. 194  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 14q21q carrier states, and of the unbalanced 14q21q state leading to translocation Down syndrome, are shown in Figures 7–1 through 7–3. Balanced carriers for any of the five homologous translocations are of about equal rarity. Nucleolar Organizing Regions The nucleolar organizing regions (NORs) of the acrocentric chromosomes have a key role in the formation of the rob translocations. The NORs are located in the short arms of these chromosomes within the p12 band, along with multiple satellite DNA classes and segmental duplications coded at p11 and p13 (Poot and Hochstenbach 2021; McStay 2023) (Figure 7–4). Nucleoli (“little nuclei”) have a role in the control of transcription in interphase cells. Only about half of all NORs per cell are actively functioning (van Sluis et al. 2020), and so it is not surprising that a loss of some NORs due to the rob translocation appears to be without consequence. Formation of the Nonhomologous (Heterologous) Translocation Pseudo-homologous regions (PHRs) at band p11 in each acrocentric chromosome co-locate in three-dimensional space within the nucleus, due to a mutual attraction between the NORs in p12 (Figure 7–5 center). This apposition facilitates meiotic crossing-over Table 7–1.  The Relative Frequencies of Robertsonian Translocations in Two Selected Populations Translocation Chinese European Averages 13;13 1% 0.1% 0.5% 13;14 59% 63% 61% 13;15 4% 3% 3% 13;21 2.5% 1% 2% 13;22 2.5% 1% 2% 14;14 0.7% 0.3% 0.5% 14;15 4% 2.6% 3% 14;21 15% 20% 17% 14;22 2.5% 3% 3% 15;15 1% 0.1% 0.5% 15;21 2.5% 2% 2.5% 15;22 1.5% 2% 2% 21;21 1% 0.3% 0.6% 21;22 2.5% 2% 2% 22;22 0.5% 0.5% 0.5% Note: Relative frequencies (%) are taken from large studies in Chinese and in European populations based upon diagnostic screening, mostly infertility or childhood abnormality in the former, and cancer diagnoses in the latter. Chinese n = 583, European n = 1,987. The figures are, in essence, very comparable, and thus the averages are likely to apply universally. Fractions greater than 1.0 are rounded. Source: From Zhao et al. (2015) and Schoemaker et al. (2019). Robertsonian Translocations  195 between non-homologs (Guarracino et al. 2023; de Lima et al. 2025). Uniquely, the PHR of chromosome 14 is inverted (Figure 7–5 right), and this leads to its preeminent role (85% of all translocations) within the rob landscape. The common rob(13q14q) and rob(14q21q) translocations are formed predominantly during female meiosis, with Figure 7–1.  The Balanced rob(13q14q) in a Phenotpyically Normal Male. Figure 7–2.  The Balanced rob(14q21q) in a Phenotypically Normal Male. 196  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY consistent breakpoints at the molecular level (Bandyopadhyay et al. 2002). Variable breakpoints in the Robertsonian uncommon translocations point to a more inconsistent process (Wiland et al. 2020; Poot and Hochstenbach 2021). Rare cases are due to post-zygotic joining together, a point that can be proven when the two component chromosomes can be shown to have come one from one parent, and one from the other (Bandyopadhyay et al. 2003). Just as a Robertsonian translocation can form de novo from the fusion of chromosomes, so can it (very rarely) revert to two separate chromosomes by a “back-mutational” fission (Pflueger et al. 1991) (Chapter 12). Figure 7–3.  The Unbalanced rob(14q21q) in a Girl with Translocation Down Syndrome. Figure 7–4.  The Structure of the Short Arms of the Acrocentric Chromosomes. Note: rDNA = ribosomal DNA; the other abbreviations refer to satellite (Sat) DNA classes and segmental duplications. The distal and proximal junctions encompassing the rDNA segment are indicated in green and orange, respectively. Source: Adapted from McStay, The p-arms of human acrocentric chromosomes play by a different set of rules, Annu Rev Genomics Hum Genet 24:63–83, 2023. Courtesy B McStay, and with the permission of Annual Reviews of Genomics and Human Genetics.

Robertsonian Translocations  197 Formation of the Homologous Translocation The rare balanced homologous Robertsonian chromosome may arise from fusion in the zygote of the paternal and maternal homologs, in which case it is a true translocation. The site of formation may be at the first mitosis, a conclusion we drew from studying a woman with 45,XX,rob(13q13q), who showed no mosaicism on biopsy samples from a number of different tissues taken during surgery for tubal ligation (Gardner et al. 1974a). Alternatively, it may be an isochromosome, with the stage having been set in meiosis: A nullisomic egg due to a maternal nondisjunction leads to a monosomic conceptus, which is then “rescued” by reduplication of the paternal homolog as an isochromosome, and thus with uniparental disomy for the chromosome in question (discussed below).3 THE HETEROLOGOUS ROBERTSONIAN TRANSLOCATION Details of Meiotic Behavior This type of Robertsonian translocation chromosome comprises the long-arm elements of two different acrocentric chromosomes. At meiosis in the 45-chromosome Figure 7–5.  Formation of the Non-Homologous Robertsonian Translocation. Notes: Pseudo-homologous regions (left) within each short arm of the acrocentric chromosomes facilitate (center) physical proximity of a chromosome pair. Arrowheads show orientation of the segment; note that in no. 14 the segment is inverted cf. nos. 13 and 21. In the case of nos. 13 and 14 (right), recombination between the inverted PHR in the no. 14 and the no. 13 PHR leads to formation of the common rob(13q14q). A very small bi-satellited product is sometimes seen (Schmutz and Pinno 1986) as a by-product, and one is depicted here (curly arrow, right). Source: A Guarracino et al., Recombination between heterologous human acrocentric chromosomes, Nature 617:335–343, 2023. Courtesy E Garrison, and with the permission of Springer Nature. 3 Berend et al. (1999) showed a de novo 45,i(13q),upd(13)pat in a normal infant to have complete isozygosity for chromosome 13 markers, indicative of this scenario of post-zygotic monosomy rescue. In another instance, they could show a paternal meiotic origin of the i(13q) in a normal adolescent with 45,i(13q),upd(13) pat. This individual would have had trisomy 13, had it not been for gametic complementation: the mother contributed a nullisomic 13 ovum (she being a rob13;14 heterozygote). These two cases came to attention only through fortuitous discovery at prenatal diagnosis, and subsequently followed up: a maternal-age indication in the former and a rob13;14 family history in the latter. 198  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY heterozygote, the translocation chromosome and the two normal acrocentric homologs synapse as a trivalent. Following 2:1 segregation, six types of gamete are produced (Figure 7–6). “Alternate” segregation leads to the production of normal and balanced gametes, and adjacent segregation produces two types of disomic and two types of nullisomic gamete. 3:0 segregation occurs, but it is rare. In obvious contrast to what happens with the reciprocal translocation, the chromosomally abnormal conceptuses have a complete aneuploidy. Only unbalanced conceptuses that are effectively trisomic for chromosome 13 or 21 can survive substantially through the course of the pregnancy (whether to fetal death in utero, stillbirth, or live birth). Fetal trisomy 14, 15, and 22 are expected to end in miscarriage in the first or early second trimester, and the monosomies would typically abort in early embryogenesis. Of these six possible outcomes (eight if we include 3:0 segregants), some are much more likely to occur than others. Judging from the outcomes at birth, one might conclude that alternate segregation is favored. From the male heterozygote, translocation Down syndrome (DS) and translocation trisomy 13 are scarcely ever seen in the offspring, and for DS in only a minority (5%–15% of children) from the female (Table 7–2). But of course, as just mentioned, there has been complete prenatal selection against some unbalanced forms, plus a variable prenatal selection against the two potentially viable imbalances, trisomy 13 and trisomy 21. Gametes. Insight comes from gamete analysis. Sperm and oöcyte studies show considerable fractions, but still a minority, of unbalanced forms. (Naturally, most if not all of the individuals proceeding to gamete testing in these reported studies will have experienced reproductive difficulty, and thus the data from their gametes may not necessarily be applicable to the larger number of carriers with apparently normal fertility.) Zhu et al. (2022a) analyzed nearly a quarter of a million sperm from ten male 13;14 heterozygotes, Figure 7–6.  Meiotic behavior of the Robertsonian translocation. (a) Trivalent at synapsis. (b) Normal and (c) carrier gametes from “alternate” segregation. (d) Disomic and (e) nullisomic gametes from adjacent segregation. Note that there are six possible combinations (ignoring 3:0 segregation), of which two are normal/balanced, and four are unbalanced.

Robertsonian Translocations  199 showing segregation ratios tilted substantially in favor of balanced forms: an average of 74% of sperm were balanced, ranging from 62% to 85% per subject in this series. Otherwise, an average of 23% of sperm were unbalanced due to adjacent segregation, and just 1.5% with 3:0. The numbers from pooled series are similar, with a ratio of close to 80%:20%, for balanced:unbalanced in both of the Class I cases, 13;14 and 14;21 (Table 7–3). Across the range of rare Class II rob translocations, Wiland et al. (2020) derived estimates from pooled literature reports, and these data are shown in Table 7-4. The similar picture is graphed in Figure 7–7. What is notable from these data is that the fractions are so similar between all the Class I and Class II rob translocations and that of all imbalanced possibilities in sperm, it is only adjacent segregation that occurs with any substantial frequency. Ova are somewhat more prone to error. The ingenious approach of FISH analysis on polar bodies allows an inference of what must be the chromosomal constitution of the oöcyte. For example, if a polar body from a 45,XX,rob(14;21) heterozygote has a chromosome 14 but is lacking a number 21 (say, polar body (e) in Figure 7–6), then the 14;21 Table 7–2.  Estimates of Risks to Have a Child with Aneuploidy, for the Heterologous rob Carrier rob MOTHER FATHER 13q14q 1% <1% 13q15q 1% <1% 13q21q 10%–15% <1% 13q22q 1% <1% 14q15q – – 14q21q 10%–15% <1% 14q22q – – 15q21q 10%–15% <1% 15q22q – – 21q22q 5%–10% <1% Notes: Estimates for the uncommon rob translocations are extrapolated from data for the common robs. Unbal., unbalanced, with a full aneuploidy for chromosome 13 or 21. The risks for a UPD syndrome from a 14- or 15-containing translocation are uniformly very low (0.06%; Moradkhani et al. 2019). Sources: From Harris et al. 1979; Ferguson-Smith 1983; Boué and Gallano 1984; Daniel et al. 1989. Table 7–3.  Male Meiotic Behavior of rob 13q14q and 14q21q. Rob Alternate Adjacent 3:0/2n Other 13;14 79% 20% 0.8% 0.2% 14;21 79% 19% 1.4% 0.6% Note: Shown are segregation patterns in the sperm of carriers of the two common (Class I) rob translocations. Note the substantial bias toward alternate segregations in both cases. 2n = diploidy. Source: From pooled data in Wiland et al. (2022). 200  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY translocation and a number 21 must be present in its fellow oöcyte (say, gamete (d) in Figure 7–6). Such a gamete would, if fertilized, give rise to the karyotype of translocation DS. Munné et al. (2000) and others have shown that typically, slightly over one-half of oöcytes are balanced; 15% of oöcytes from the 14;21 carrier would potentially be viable (as translocation DS), and from the 13;14 carriers, the corresponding figure is 10% (as translocation trisomy 13) (Table 7–5). Embryos. The data from analysis of blastocysts at PGT show, as might have been expected, a rather similar spread to that observed in gametes (Table 7–6, Figure 7–8). Alternate segregation with a balanced genotype is the most commonly observed from all categories of the male rob carrier. Alternate segregation is somewhat less seen in the female carrier, but nevertheless, with the exception of the 46,XX,rob(21q22q) case, half Table 7–4.  Male Meiotic Behavior of the Rare Robertsonian Translocations Rob Alternate Adjacent 3:0/2n Other 13;15 76% 23% 0.9% 0.1% 13;21 89% 11% 0.1% 0.3% 13;22 81% 17% 0.8% 0.3% 14;15 84% 16% 0.4% 0% 14;22 81% 18% 0.7% 0% 15;21 78% — — — 15;22 86% 13% 1% 0% 21;22 80% 19% 0.5% 1% Averages 82% 17% 0.65% 1% Notes: Observe the substantial bias, averaging 82%, toward alternate segregations in every case. Note also how closely these percentages match those in the two common rob translocations (Table 7–3). 2n = diploidy. Source: From pooled data in Wiland et al. (2022). Figure 7–7.  Meiotic Segregation in Sperm. Notes: Each column represents a rob heterozygote. Cases grouped according to the particular rob, y axis. Source: From A Lamotte et al., Is sperm FISH analysis still useful for Robertsonian translocations? Meiotic analysis for 23 patients and review of the literature, Basic Clin Androl 28:5, 2018. Courtesy S Hennebicq, and with the permission of Springer Nature. Robertsonian Translocations  201 Table 7–5.  Female Meiotic Behavior of rob 13q14q and 14q21q Rob 2:1 Alternate 2:1 Adjacent (fractions with the potential viable disomy) 13;14 56% 33% (10%) 14;21 55% 42% (15%) Total 56% 39% (12%) Note: These data are derived from oöcyte analysis of 19 13;14 carriers and six 14;21 carriers. Only 2:1 segregants are listed, not 3:0; thus, shortfalls per case from 100% totals are due to 3:0 forms. The potentially viable disomies noted could give rise to trisomy 13 or trisomy 21. Sources: From Munné et al. (2000), Durban et al. (2001), Pujol et al. (2003), and Molina Gomes et al. (2009). Table 7–6.  The rob 13q14q and 14q21q in Blastocysts Segregation Female 13;14 Male 13;14 Female 14;21 Male 14;21 Number of blastocysts 1972 2093 668 403 Alternate 1254 1746 389 316 Adjacent 693 342 267 85 3:0/others 25 5 12 2 Alternate % 64% 83% 58% 78% Notes: These data are combined from three studies: Zhang et al. 2021a, Dang et al. 2023, and Benn and Merrion 2025. Source: From P Benn and K Merrion, Chromosome segregation of human nonhomologous Robertsonian translocations: insights from preimplantation genetic testing, Eur J Hum Genet 33:711–717, 2025. Figure 7–8.  The Rates of Alternate Segregant Products in the Blastocysts of Every Category of Heterologous rob Carrier. Note: In only one type, the rob 21q22q in the female, are balanced segregants in a minority. Source: From S Zhang et al., Meiotic heterogeneity of trivalent structure and interchromosomal effect in blastocysts with robertsonian translocations, Front Genet 12:609563, 2021. Courtesy C Xu and X Sun, and with the permission of Frontiers in Genetics.

202  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY to three-quarters of blastocysts result from alternate segregation. Embryos resulting from adjacent segregation will, in the considerable majority, be nonviable, and as noted above, it is only trisomies for 13 and 21 that are potentially viable from this segregant category (and very rare “corrected” uniparental disomies). Interchromosomal Effect. The concept of an interchromosomal effect (ICE) has been invoked in the setting of the balanced Robertsonian heterozygote. Could a translocation somehow influence the distribution of another chromosome not involved in the rearrangement, with the production of a gamete aneuploid for a chromosome not involved in the translocation? Anecdotal reports of DS children born to 14q22q and 13q14q rob carriers (Farag et al. 1987; Sikkema-Raddatz et al. 1997b) seemed to support this notion. However, formal segregation studies in large numbers of families with a rob(13q14q) or with trisomy 21 showed no apparent excess of trisomic offspring or of parental Robertsonian translocations, respectively (Harris et al. 1979; Lindenbaum et al. 1985). Therman et al. (1989) ascertained no Robertsonian translocation through a trisomic child other than one that included the trisomic chromosome. Observations in the cleavage-stage embryo suggest that an ICE may apply during the mitoses immediately after the formation of the zygote. Using CGH microarray, Alfarawati et al. (2012) recorded malsegregation of chromosomes not involved in the translocation in 70% of the embryos of Robertsonian translocation carriers, giving 6% over and above the background rate of 64% in controls. As these authors write, “out of every 11 euploid zygotes produced by a Robertsonian translocation carrier, one is expected to become abnormal by the cleavage stage due to an ICE.” Zhang et al. (2021a), applying the methodology of single nucleotide polymorphism (SNP) genotyping of whole genome amplification (WGA) products, identified a range of aneuploidies and mosaicisms in 977 blastocysts of rob carriers, showing overall only a very slightly increased risk due to an ICE (Figure 7–9), consistent with Alfarawati et al. (2012) and with other recent studies (Shetty et al. 2022). The practical conclusion to be drawn is that an ICE may indeed exist and is to be taken into account, although in terms of a rob risk, it is a minor player. Meiotic Drive. Meiotic drive is an influence whereby one of the products at meiosis may be favored and have a better-than-even chance of coming to be in the successful gamete. The Robertsonian translocation provides an example. At the level of the offspring produced, de Villena and Sapienza (2001) demonstrated that children of female carriers of rob translocations have a ratio close to 60:40 for the balanced rob, compared to normal karyotypes. No such effect could be confirmed for the male rob carrier. Daniel (2002) has confirmed these interpretations in a retrospective analysis of prenatal diagnosis data, with rigorous attention to the need to avoid bias, showing a 116:81 ratio in favor of balanced carrier offspring versus normal karyotypes where the mother is the carrier parent, compared to a near unity 42:41 ratio for carrier fathers. Other esoteric differences in ratios are dealt with in Kovaleva (2019). POST-ZYGOTIC “CORRECTION” AND ASSOCIATED UNIPARENTAL DISOMY Trisomic Correction. An initially translocation trisomic conception where one parent is a rob carrier may be “corrected” in very early embryonic existence by the mitotic loss of one of the free homologs. If the lineage of this newly produced normal cell is destined to give rise to the inner cell mass, then a chromosomally balanced (albeit rob heterozygous) embryo may result, and the embryo will have uniparental disomy (UPD). UPD has no untoward effect if the chromosome is not subject to imprinting (except for the question Robertsonian Translocations  203 of isozygosity for a recessive gene; see below), and chromosomes 13, 21, and 22 are in this category. But when chromosome 14 or 15 is a partner in a rob translocation, a risk (albeit small) exists for the birth of a child with an imprinting syndrome, chromosomes 14 and 15 being subject to parent-of-origin imprinting (Chapter 19). For example, a presumed mechanism whereby UPD(15) could arise from a rob(13q15q) parent is outlined in Figure 7–10. Essentially, adjacent segregation produces a trisomic 15 conception, and then loss of the chromosome 15 contributed from the other parent,4 at a very early post-zygotic stage, “corrects” the quantitative chromosomal content. Observations such as these are very rare. Liehr (2025a) assembled a total of 40 cases in which a UPD syndrome had been associated with a nonhomologous Robertsonian translocation, comprising 22 cases of UPD(14)mat (Temple syndrome), five of UPD(14)pat (Kagami-Ogata syndrome), seven of UPD(15)mat (Prader-Willi syndrome), and six of UPD(15)pat (Angelman syndrome). Most of these nonhomologous robs had been inherited. Nonetheless, UPD due to a parental rob is extremely rare; the overall risk to have a child with a UPD syndrome, as determined from prenatal diagnosis data where one parent is a heterologous rob carrier, is on the order of only 0.06% (Moradkhani et al. 2019). Figure 7–9.  Interchromosomal effect, at the level of the blastocyst, from carriers of rob translocations. Notes: Every type of heterologous rob is represented. The graph shows the range of aneuploidies, and of mosacisms, across the whole karyotype, as seen in 977 blastocysts of rob carrier couples, cf. 785 of control couples. The controls are from blastocysts of couples of quite similar ages (actually, 2-3 years older) at risk for a mendelian condition, and these defined a background rate of aneuploidy affecting any embryo. On simple visual inspection, an increased risk for an ICE in the rob carriers appears, overall, only slightly greater compared with the control group, and only with some chromosomes (no. 16 a spectacular outlier). On formal statistical analysis, the whole group of rob carriers gives an odds ratio of 1.3 cf. controls for an aneuploid embryo due to an ICE. Mosaic and segmental aneuploidies, which are typically of mitotic origin, were not increased in the embryos of rob carriers. Source: From S Zhang et al., Meiotic heterogeneity of trivalent structure and interchromosomal effect in blastocysts with robertsonian translocations, Front Genet 12:609563, 2021. Courtesy C Xu and X Sun, and with the permission of Frontiers in Genetics. 4 Note that with one or other chromosome 15 being the candidate to be lost, the risk for UPD to be generated is 50%. This is in contrast with correction in standard trisomy in which, with three candidate chromosomes, the chances are 1 in 3 for the “wrong” one to be lost.

204  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 7–10.  Uniparental Disomy. Uniparental disomy 15 from a rob(13q15q) parent, due to “trisomy rescue.” The heterozygous parent produces a malsegregant gamete with the translocation, and with a free chromosome 15. The conception thus has trisomy 15. Subsequently, as a postzygotic event, the chromosome 15 from the other parent is lost. Since most malsegregations will have been of maternal origin, the UPD in this setting will usually be a maternal heterodisomy. (Chromosome 13 elements, white; chromosome 15 elements, cross-hatched. The two chromosome 15 elements from the carrier parent are asterisked.) Robertsonian Translocations  205 Monosomic Correction. Hypothetically, correction may also go the other way—that is, the conversion of a monosomic conceptus, due to a nullisomic gamete from 2:1 adjacent segregation in the rob parent, into a disomic conceptus. This conversion to disomy, or “correction,” would be achieved by the replication of the homolog contributed in the (normal) gamete of the other parent. A replicate “free” chromosome might be produced, in which case the karyotype would appear normal. Or, the homolog could replicate as an isochromosome, which would produce the intriguing circumstance of a de novo Robertsonian-like chromosome in the setting of a true Robertsonian parent. This event, whichever one, would take place at a very early post-zygotic stage and would necessarily lead to uniparental isodisomy (Berend et al. 2000). It is, apparently, very rare. Association with Infertility Heterozygosity for a rob translocation is an occasionally identified association with infertility in the male. Of men with abnormal sperm indices, more particularly oligospermia rather than azoöspermia, the rob carrier rate will be above the population figure, and similarly in those whose partners had suffered recurrent pregnancy loss (Kuroda et al. 2020; Tunç and Ilgaz 2022; Yuan et al. 2023). Estimates of the excess of rob carriers in an infertile population range from three-fold to around ten-fold. In those rob carriers with an abnormal spermiogram, there is an associated increase in levels of aneuploidy in sperm, and the disposition of the individual bivalents at meiosis I may be disturbed due to the presence of a rob trivalent (Solé et al. 2017) (Figure 7–11). As discussed above, this infertility, if indeed it is a direct consequence of the translocation, could operate at the level of gametogenesis or could be having its effect during very early embryogenesis: pregestational or gestational infertility. In other words, the translocation chromosome may of itself impose an obstructive influence during spermatogenesis, leading to a low sperm count with abnormal forms; or the translocation could, of itself, following a successful fertilization, then compromise the process of chromosome segregation in the cleavage-stage embryo, leading to a lethal imbalance with non-implantation or later miscarriage. And yet, there is the conundrum that a number of infertile rob men will have rob male relatives of normal fertility (Wiland et al. 2020). It is less straightforward to tease out a causal association concerning female rob-related infertility in an individual case, and there is always the fact of a background rate of 1 in 800 women being a rob carrier and many women in the population suffering infertility. In a large Chinese cohort of infertile5 couples, Yuan et al. (2023) identified 21 female (and 33 male) rob carriers, giving percentages of 0.25% and 0.38% respectively, against the population figure of 0.125%. The doubled rate in the female rob carriers is to be noted, but the numbers studied were small. It remains possible that the infertility in at least some such women might be coincidental. In a review of causes of recurrent pregnancy loss (a different question, in that a conception had occurred), Tunç and Ilgaz (2022) noted in a small fraction (under 1%), one partner is a rob(13q14q) carrier, more usually the female. 5 Infertility in the sense of infecundity, that is, the inability to achieve a pregnancy. 206  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY RARE COMPLEXITIES Homozygosity for a Robertsonian Translocation Due to Both Parents Being Carriers. An interesting curiosity is the rare case of a union between Robertsonian heterozygotes, usually in the setting of a consanguineous marriage (Figure 7–12). The rob(13q14q) is, unsurprisingly, the most frequently observed—unions of 45,XY,rob(13q14q) × 45,XX,rob(13q14q)—but other robs are also on record in this context (Table 7–7). Thus, the child of a rob(13q14q) × rob(13q14q) union could have all their 13s and 14s in the form of a rob, with the karyotype 44,rob(13q14q)mat, rob(13q14q)pat. Intriguingly, these 2n = 44 homozygous individuals have been, for the most part (but not all) of normal phenotype and with intact fertility. The reader may care to construct a hypothetical balanced karyotype with 2n = 41 and five Robertsonian translocation chromosomes. Some “carrier couples” have presented with multiple miscarriages, and two have had an aneuploid child: a translocation DS child with 45,XY,rob(14q21q),rob(14q21q),+21mat, from rob(14q21q) × rob(14q21q) parents, and an infant with translocation trisomy 13, from rob(13q15q) × rob(13q15q) parents (Rajangam et al. 1997; Mori et al. (1985). In the latter case, due to a founder effect, this otherwise rare Robertsonian translocation was rather common in their small village in the province of Cuidad Real in Spain, and this couple were surely distantly related, even though they were unaware of any link. Figure 7–11.  Sperm Observations in the rob Carrier. Notes: The rates of alternate (balanced) segregation in sperm of men heterozygous for a rob, according to findings on semen analysis. Those with abnormal indices, and who may have presented with infertility, have a lesser frequency of normal/balanced forms. Source: From A Lamotte et al., Is sperm FISH analysis still useful for Robertsonian translocations? Meiotic analysis for 23 patients and review of the literature, Basic Clin Androl 28:5, 2018. Courtesy S Hennebicq, and with the permission of Springer Nature. Figure 7–12.  Homozygosity for a Robertsonian Translocation. The karyotype is 44,rob(14;15),rob(14;15). The parents of this case, a phenotypically normal man, were first cousins, and both were rob(14;15) heterozygotes (Song et al. 2016).

Robertsonian Translocations  207 Robertsonian Fission. The Robertsonian translocation arises through a “fusion” of the short-arm sequences. Equally, it can, in somatic tissues, revert to “normality” by fission (Perry et al. 2005). Although the resulting two acrocentric chromosomes would have somewhat truncated short arms that lacked NORs, this appears to be without any clinical consequence. The Homologous Robertsonian Translocation, or Acrocentric-Derived Isochromosome This Robertsonian translocation chromosome comprises the long-arm elements of two acrocentric chromosomes that are the same. With a 45-chromosome count, the carrier has an essentially balanced genome and is, other things being equal, of normal phenotype. The site of formation is typically postmeiotic (Gardner et al. 1974a; Robinson et al. 1994). If the translocation forms from the fusion of the two parental homologs, then manifestly there is biparental inheritance (Abrams et al. 2001). If, on the other hand, the rearrangement is actually an isochromosome, each long arm is an exact copy of the other, and there will be uniparental isodisomy. Such an isochromosome may have arisen as a “correction” of monosomy in the one-cell zygote, or at a post-zygotic stage (Riegel et al. 2006). A person carrying an isochromosome from this mechanism can be normal, except in the case of iso14q or iso15q (these chromosomes being subject to parent-of- origin imprinting). DETAILS OF MEIOTIC BEHAVIOR In principle, only two segregant outcomes are possible at meiosis in the homologous 45,rob heterozygote. Either the gamete will receive the translocation chromosome and be effectively disomic or it will not, and be nullisomic. Essentially, this is 1:0 segregation (or “1+1”:0 segregation). No balanced gamete is possible. Thus, if the other gamete is normal, only trisomic or monosomic conceptions are possible. Occasionally, conceptuses with translocation trisomy 13 are viable, and translocation trisomy 21 not infrequently survives to term. None of the other unbalanced possibilities (trisomies 14, 15, and 22, nor any of the monosomies) are viable. Post-zygotic “trisomic correction” is a mechanism that could, extremely rarely, enable the carrier to have a phenotypically normal child. If, for example, in the case of an Table 7–7.  Cases of Homozygosity for a Robertsonian Translocation Translocation Number of cases References rob (13q14q) 9 Bahçe et al. 1996; O’Neill 2010; Miryounesi et al. 2016 rob(13q15q) 1 Mori et al. 1985 rob(14q15q) 4 Song et al. 2016; Sasi et al. 2020; Sahraeean et al. 2023; Xu et al. 2024b rob(14q;21q) 3 O’Neill 2010 rob(21q22q) 1 O’Neill 2010 Notes: Most cases listed are from the review in O’Neill (2010); subsequently reported cases are noted individually. The infertile man in Sasi et al. was heterozygous for a rob(13q14q) as well as having the 14q15q homozygosity.

208  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY unbalanced 46,–22,rob(22q22q) conception, the free chromosome 22 were lost at a very early mitosis, genetic balance in this cell line would be restored, with a 45,rob(22q22q) karyotype. Provided the unbalanced cell line contributed negligibly or not at all to the embryo, and provided there was no effect due to uniparental disomy (and in the case of chromosome 22, there is not), the child would be normal. A very few such cases are recorded, with the 13q13q and 22q22q thus represented (Slater et al. 1994, 1995; Engel and Antonarakis 2002; Ouldim et al. 2008). “Monosomic rescue” is another theoretical and as yet unobserved mechanism in this context, whereby the homolog from the other parent could be duplicated post-zygotically as two separate homologs, or as an isochromosome, to produce a pregnancy with either a normal karyotype or 45,iso. Finally, for completeness (but almost never in reality), gametic complementation is to be mentioned, whereby the non-rob parent contributes a gamete that happens to lack the homolog for which the rob parent’s gamete is disomic (Berend et al. 1999). For the rob(14q14q) and rob(15q15q) carrier, even if one of these rescuing mechanisms did happen, the child would in any event be abnormal, since these UPDs lead, of themselves, to an abnormal phenotype. GENETIC COUNSELING The Heterologous Robertsonian Translocation Carrier RISKS OF HAVING ABNORMAL OFFSPRING FROM INDIVIDUAL TRANSLOCATIONS Figures for the risks to have an abnormal child, or for the probability of detecting an unbalanced form at prenatal diagnosis, are taken (making a few assumptions about extrapolating to the rare translocations) from data of a number of North American and European collaborative studies from the 20th century (Harris et al. 1979; Ferguson-Smith 1983; Boué and Gallano 1984; Daniel et al. 1989) and set out in Table 7–2. These data relate essentially to the risk for a full trisomy. Earlier estimates of risks for a UPD syndrome due to Shaffer (2006) have since been seen as likely overestimates, and in fact a very low risk figure of 0.06% may be appropriate (Moradkhani et al. 2019) (see below, “Uniparental Disomy”). Detailed comments on each individual translocation6 follow, with general comments thereafter on the theoretical risks of uniparental disomy (14- and 15-containing translocations), “isozygosity” for a recessive gene, residual low-level trisomy mosaicism, and interchromosomal effect. The gamete data (Tables 7–3, 7–4, 7– 5) may be helpful for those considering PGT (see also below, “Preimplantation Genetic Testing”). THE COMMON (CLASS I) TRANSLOCATIONS rob(13q14q). The karyotype of the balanced rob(13q14q) is shown in Figure 7–13 and above. Translocation trisomy 13 can result from adjacent-1 segregation, with a 6 The illustrative partial karyotypes are taken mostly from W-W Zhao et al., Robertsonian translocations: an overview of 872 Robertsonian translocations identified in a diagnostic laboratory in China, 2015; the 21;22 from S Vujisic et al., Chromosomal segregation in sperm of the Robertsonian translocation (21;22) carrier and its impact on IVF outcome, 2020; the 22;22 from N Alhalabi et al., De novo balanced Robertsonian translocation rob(22;22)(q10;q10) in a woman with recurrent pregnancy loss: A rare case, 2018; and the homozygous 14;15 case from J Song et al., A family with Robertsonian translocation: a potential mechanism of speciation in humans, 2016. Robertsonian Translocations  209 typical Patau syndrome phenotype. The risk for this is very small. Almost all instances are index cases in families, not secondary cases. Engels et al. (2008) identified no cases of translocation trisomy 13 in live births, after correction for bias, notwithstanding that a number of their families had come to attention through an index case with translocation trisomy 13. These authors propose risk estimates of <0.4% for female carriers to have a liveborn child with translocation trisomy 13, and <0.6% for the male; and if the genders are combined, one arrives at a lower figure of <0.23%. They did, however, document a 7% (3/42) incidence in amniocenteses (12% from maternal rob; none from paternal rob). Further, one translocation trisomy infant had been stillborn; and it is a fine point, in undertaking this sort of analysis, to make a distinction between a stillborn baby versus one that survives only a few days (the usual in Patau syndrome). A risk estimate of ¼% to ½%, or more conservatively <1%, may be a practical figure to offer. If there is male infertility needing IVF with intracytoplasmic sperm injection (ICSI) to achieve pregnancy, the additional exercise of PGT would be reasonable to improve the chances of producing a normal/balanced conception; PGT may also be an appropriate choice for some female heterozygotes. Otherwise, an offer of prenatal diagnosis remains a discretionary matter. A focused ultrasound should be capable of detecting the great majority of trisomy 13, and any residual risk could be virtually eliminated by a normal noninvasive prenatal test (NIPT). Exclusion of the very small risk of UPD(14) would require invasive testing. rob(14q21q). The rob(14q21q) (Figure 7–14) is the most important Robertsonian translocation in terms of its frequency and genetic risk, and it shows a marked difference according to the sex of the parent. Most familial translocation Down syndrome is due to the rob(14q21q) (Figure 7–2). Adjacent segregation may lead to the conception of translocation trisomy 21 (Figure 7–3). At amniocentesis, the female heterozygote has a risk for translocation trisomy 21 of about 15% (Ferguson-Smith 1983; Boué and Gallano 1984; Stene and Stengel-Rutkowski 1988; Daniel et al. 1989). The risk of having a liveborn child with translocation DS is a little less (in the range 10%–15%). This likely reflects the loss, through spontaneous abortion, of a fraction of DS fetuses after the time Figure 7–13.  rob(13;14). Figure 7–14.  rob(14;21).

210  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY during gestation when prenatal diagnosis is done. PGT is a very suitable option, at least in the case of the female 14q21q carrier (Scriven et al. 2001; Dang et al. 2023). The risk for the male heterozygote is very different, and a figure of <1% for a liveborn child with DS is appropriate to offer. Those choosing PGT, whether the carrier parent is male or female, might also see benefit in avoiding transmission of the carrier state. The matter of UPD(14) is noted below. THE RARE (CLASS II) TRANSLOCATIONS rob(13q15q). Few data are available concerning genetic risks to the carrier (Mori et al. 1985; Daniel et al. 1989). We would expect these individuals are no more likely to produce adjacent segregants than the rob(13q14q) carrier, and a similar risk of <1% for translocation trisomy 13 may therefore apply. The risk for UPD(15) is noted below. rob(13q21q). In Boué and Gallano’s (1984) study, the risk for translocation DS, in terms of the likelihood of detection at amniocentesis, was 10% for the female; and in Daniel et al.’s (1989) study, the figure was 17%. This 10%–17% range suggests there may be no real difference from the 10%–15% that applies to the common rob(14q21q). The risk for the male heterozygote is low, and probably similar to the <1% proposed for the male rob(14q21q) carrier. The segregation ratio of 13% rob-related disomy/nullisomy in sperm in one case of a 45,XY,(13;21) carrier was very similar to that of the Class I robs, and embryos of his had essentially the same (12%) rate of rob-related aneuploidy (Bernicot et al. 2012). An additional 1% or less risk for translocation trisomy 13 may apply, for either sex. Figure 7–15.  rob(13;15). Figure 7–16.  rob(13;21). Figure 7–17.  rob(13;22). Robertsonian Translocations  211 rob(13q22q). We expect the risk for translocation trisomy 13 would be “small,” and perhaps similar to that for the rob(13q14q). In Boué and Gallano’s (1984) study of 262 Robertsonian prenatal diagnoses not involving chromosome 21, there were only three rob(13q22q) cases, and in fact one of these showed trisomy 13; no unbalanced karyotypes were diagnosed in Daniel et al.’s (1989) seven cases. The 13q22q man subjected to a sperm study in Anahory et al. (2005) had presented with infertility, and oligospermia was shown. rob(14q15q). Adjacent segregants (translocation trisomy 14, translocation trisomy 15) are invariably lethal in utero. UPD(14) or UPD(15) are possible outcomes, as noted below. Normality in offspring remains open if a gamete from alternate segregation is produced. rob(14q22q) and rob (15q22q). The potentially trisomic states from these translocations (trisomy 14, 15, or 22) would all be anticipated to abort spontaneously. Neu et al. (1975) record the segregation of a rob(14q22q) chromosome in a large family in which some carriers had an increased miscarriage rate. Infertility may be associated, but treatable with IVF and PGT (Sobotka et al. 2015). UPD would be a theoretical risk from a “corrected” conception (see below). Figure 7–18.  rob(14;15). Figure 7–19.  robs(14;22) and (15;22). Figure 7–20.  rob(15;21). 212  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY rob(15q21q). From Boué and Gallano’s (1984) small series of nine carrier mothers, one (11%) had translocation trisomy 21 detected at amniocentesis; and in Daniel et al.’s (1989) data, the fraction was 0/9. These figures derive from too small a body of data to be sure, as yet, that the risk is really any different from the more solidly based 10%–15% that applies to the rob(14q21q) female carrier. Again, we suppose a low risk (<1%) for the male carrier in terms of DS. The possibility of UPD is noted below. rob(21q22q). In a large kindred of our study, the segregation ratios according to gender of the parent and the outcome of a DS child were 6.8% for the female and an upper limit of 2.8% for the male (Chapman et al. 1973). UPD need not be a concern, nor, practically speaking, trisomy 22. Homozygosity in a Carrier Since some Robertsonian translocations are not uncommon, it is not surprising that a few instances are known where both of a couple are carriers (see above, “Homozygosity for a Robertsonian Translocation Due to Both Parents Being Carriers”). It is possible, then, for these couples to have children who are homozygous and phenotypically normal, and also fertile—for example, the homozygous 44,rob(13q14q)×2 mother in Miryounesi et al. (2016), who had a healthy 45,XY,rob(13q14q) son, albeit also four other pregnancies ending in first-trimester loss. PRE-CONCEPTION GENETIC DIAGNOSIS Testing an oöcyte before fertilization in vitro has been proposed as an alternative to PGT but seems not to have caught on as a regular procedure. In a pilot study, Molina Gomes et al. (2009) analyzed the first polar body of oöcytes from six women heterozygous for rob(13;14) and one for rob(14;21). The first polar body, if balanced, can represent the opposite balance of the ovum; thus, a polar body showing rob13;14 in balanced state would reflect the ovum having a normal chromosomal content. Any imbalance in the polar body would imply a matching imbalance in the egg. From 32 embryos transferred in this pilot study, three successful pregnancies resulted. PREIMPLANTATION GENETIC TESTING PGT for a Robertsonian scenario has been available for much of this century. Initially, it was the day-3 cleavage-stage embryo at IVF that was analyzed, but latterly it has been the day-5 blastocyst that is chosen (Chapter 23). As noted above (Table 7–6), there is a gender difference, with blastocysts of male rob carriers being considerably more likely to be normal/balanced, at 80%, versus 60% in the female. The key datum of practical Figure 7–21.  rob(21;22).

Robertsonian Translocations  213 interest is that of the chance per embryo transferred to have a healthy baby: in the series of Oğur et al. (2023), that figure was 54% for mothers under age 35 years and 64% for those over that age.7 The miscarriage rate, at 9%, was in fact less than that of the general population risk. A SNP-based methodology may enable the distinction between a carrier and a normal embryo, clearly an attractive option to parents who will be very well aware of the complicated reproductive implications of the carrier state (Zhai et al. 2022). The apparent existence of an interchromosomal effect, albeit one of very small influence (discussed above), is seen by some as strengthening the rationale for using 24-chromosome PGT in couples with a Robertsonian translocation, although others are not convinced that this is a realistic concern (Oğur et al. 2023). UNIPARENTAL DISOMY UPD in a setting of parental Robertsonian heterozygosity is very rare. We need consider only those acrocentric chromosomes subject to imprinting: chromosomes 14 and 15. The four syndromes that can arise, as mentioned above and as described in detail in Chapter 19, are maternal UPD(14) (Temple syndrome), paternal UPD(14) (Kagami-Ogata syndrome), maternal UPD(15) (Prader-Willi syndrome), and paternal UPD(15) (Angelman syndrome). The potential mechanisms are, as discussed above, adjacent segregation followed by “correction” of trisomy with loss of a homolog, or (hypothetically) by “correction” of monosomy with replication of a homolog. In the review of Shaffer (2006), combining prenatal diagnostic data from seven groups and including both familial and de novo cases, four instances of UPD were identified out of 482 prenatal diagnoses, for a point risk estimate, therefore, of 0.8%. The two familial cases were UPD(13)mat due to a rob(13q14q)mat, and UPD(14)mat due to a rob(14q22q)mat; for the record, the de novo cases were UPD(14)mat with a rob(13q14q), and UPD(14)mat with a rob(14q21q). More recently, Moradkhani et al. (2019) reviewed the large total of 1,747 prenatal diagnoses done on the basis of a parental 14- or 15-containing rob, and identified just one in which a UPD syndrome had resulted: UPD(14)mat (Temple syndrome), from a 13;14 mother. From this observation, they refined the risk figure down to 0.06% and suggested that specific UPD testing via an invasive procedure might be seen as unjustified. But if prenatal karyotyping is otherwise proposed, adding in a UPD assessment might be seen as discretionary, if the same 45,rob karyotype as the parent’s is observed. As for maternal and paternal UPD 13, 21, and 22, these are apparently without phenotypic effect, and need not be a cause for concern. “Isozygosity” for a Recessive Gene. Monosomic rescue, whether producing an isochromosome or a 46,N karyotype, theoretically has the potential to cause an autosomal recessive disorder should the non-rob parent happen to be heterozygous for a Mendelian condition, the locus for which was on the chromosome in question. But the risk is likely to be very low. In one small series in which a specific search was made for UPD due to monosomic rescue from a rob parent, no such case came to light (Ruggeri et al. 2004). Barring knowledge of such a condition8 elsewhere in the family, molecular testing is not currently practicable. Of the more common recessive genes that might be suitable for 7 Only seven cases were in this category compared to 23 in the <35 age group. 8 For example, Wilson syndrome, locus on chromosome 13; Krabbe disease, on chromosome 14; Bloom syndrome, on chromosome 15; Knobloch syndrome, on chromosome 21; metachromatic leukodystrophy, locus on chromosome 22. 214  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY population screening in some jurisdictions (cystic fibrosis, thalassemia, sickle cell disease, Tay-Sachs disease), in fact none has its locus on an acrocentric chromosome. Risk to Pass on the Balanced Carrier State to Offspring As noted above, “meiotic drive” applies in gametogenesis of the female rob heterozygote, such that a child is about one-and-a-half times more likely to be him- or herself a carrier than to have a normal karyotype. In the event that PGT is being applied, typically for reasons of infertility, an approach using SNP microarray can distinguish the two states, potentially allowing choice in favor of an embryo of normal karyotype (Zhang et al. 2017). Infertility and Miscarriage The Robertsonian translocation involving non-homologs is occasionally associated with repeated spontaneous abortion and with male and (to a lesser extent) female infertility (Table 7–8). The risks for miscarriage are set out in Table 7–9. It may be unclear, in an individual case, whether the association is causal or fortuitous. We can theorize that in some miscarrying couples, there may have been a majority of zygotes with nonviable adjacent segregants; and in some infertile males, the translocation may have disrupted spermatogenesis. Cytogenetic analysis of products of conception and of testicular tissue, respectively, may cast some light. It remains possible that some other cause could underlie the problem. The infertile male usually produces some sperm, and may thus be a candidate for IVF using ICSI, and optionally PGT (Vujisic et al. 2020; Yuan et al. 2023). THE HOMOLOGOUS ROBERTSONIAN TRANSLOCATION CARRIER We refer to these rearrangements as “rob,” recognizing as discussed above that most such cases do actually involve an acrocentric-derived isochromosome (“rob-iso”). Virtually all conceptions of the 45-chromosome heterozygote result in either trisomy or monosomy. Monosomy results in occult abortion. Trisomy 14 and 15 always, and trisomy 22 virtually always, miscarry. Most trisomic 13 pregnancies miscarry, although some survive until the third trimester, while of course many trisomic 21 pregnancies will proceed through to the birth of a child with Down syndrome. Practically speaking, no normal child could be produced from homologous rob or isochromosome carrier individuals (the scenario of post-zygotic correction, discussed earlier, can scarcely be Table 7–8.  Rates of Robertsonian Translocations Identified in a Large Series of Infertile Couples Number couples studied Number and incidence of rob In females In males 17,054 21 (0.25%) 33 (0.38%) Source: J Yuan et al., Detection of chromosome aberrations in 17 054 individuals with fertility problems and their subsequent assisted reproductive technology treatments in Central China. Hum Reprod 20;38(Suppl 2):ii34-ii46, 2023.

Robertsonian Translocations  215 raised as a realistic hope). Appropriate advice for these carriers is to use contraception. Alternatively, the use of donor gametes may allow the couple to have a normal child. In the very rarely recognized parental mosaic case, a child may yet be possible, as in the rea(13;13), rea(14;14), and rea(21;21) discussed below. Specific Translocations Specific comments relating to the risk for abnormal offspring in each type of rob follow. rob(13q13q). In principle, the carrier parent can produce only monosomic or trisomic 13 conceptions, and these would either miscarry or, in the case of trisomy, produce a very abnormal child (Patau syndrome). Three recorded exceptions to this statement are given in Slater et al. (1994, 1995) and Stallard et al. (1995), of a normal rob(13q13q) parent having a normal child with rob(13q13q). The translocations in the children were probably 13q isochromosomes (and so perhaps we should have written iso(13q) for their karyotypes) arising from post-zygotic correction, and thus the children had uniparental isodisomy. Parental somatic-gonadal mosaicism for a rob(13;13) may leave open the possibility of having a normal child. Bint et al. (2011) report a woman having had a child with translocation trisomy 13, her own karyotype being 45,XX,rob(13;13)[27]/46,XX[33]. At subsequent PGT, a normal embryo was transferred and a normal 46,XX baby born. Table 7–9.  Risk of Miscarriage per Pregnancy, and Proportions of Pregnancies that are Trisomic at Prenatal Diagnosis, for the 13q14q and 14q21q Robertsonian Translocations, According to Gender of the Carrier rob(13q14q) rob(14q21q) MISCARRIAGE TRISOMIC PREGNANCY MISCARRIAGE TRISOMIC PREGNANCY Mother 28% 12% 24% 10%–15% Father 20% <1% 33% 1% Note: The miscarriage rates are to be seen in the context of a background population risk for miscarriage, per pregnancy, of 15%. The rates above that are substantially higher than background might reflect, in part, a maternal-age influence (Cohain et al. 2017) within the rob clinical material. The risk for a trisomic pregnancy refers to the rate at second trimester prenatal diagnosis. Source: Table adapted from pooled 14;21 data in Kim et al. (2008) and Shaffer (2002), and 13;14 data in Engels et al. (2008). Figure 7–22.  rob(13;13). 216  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY rob(14q14q), rob(15q15q). Trisomies and monosomies for chromosomes 14 and 15 are not viable, and thus all pregnancies of these heterozygotes would be expected to terminate in occult abortion or miscarriage. Proven gonadal (testicular) mosaicism, with a normal cell line in spite of 100% rob(14q14q) on peripheral blood, may allow for having a normal child, but with a risk also for multiple miscarriage (Cinar et al. 2011). Likely confined gonadal (ovarian) mosaicism for a rob(14;14) in the case of Gonzalez et al. (2024) was associated with recurrent pregnancy loss and recurrent failure of embryo implantation. Even if post-zygotic correction did happen, the child would have a UPD syndrome, according to the translocation and the sex of the transmitting parent. Thus it is, in theory and in reality, impossible to have a normal child from any gamete of the heterozygote. rob(21q21q), or iso(21q). Although the balanced rob(21q21q) carrier is extremely rare, every counselor knows about this famous translocation. It is a classic example of a risk of (essentially) 100% to have a chromosomally abnormal child: all pregnancies continuing to term can be expected to produce a child with DS. Sudha and Gopinath (1990), for example, report a couple who had 13 pregnancies, with four children proven or presumed to have had DS, and nine miscarriages. The mother was 45,rob(21q21q). Similarly, Kolgeci et al. (2012) describe a 21q;21q mother having had ten miscarriages and two children with DS. The curious case in Yan et al. (2007) of a 45,XY(21;21) father having had a mosaic 46,XX/46,XX(21;21) child is the only such instance on record of an apparent post-zygotic partial correction for this translocation. Figure 7–23.  rob(14;14) and rob(15;15). Figure 7–24.  rob(21;21). Robertsonian Translocations  217 Parental mosaicism for this rearrangement, as an isochromosome, is on record and has been associated with the birth of a normal child. Hervé et al. (2015) review the small number of cases. In their own case, a mother of one normal child, herself of 46,XX karyotype on a 1,000-cell count on blood, had had two 46,iso21q pregnancies, thus declaring herself a gonadal, if not somatic, mosaic for the isochromosome. These authors note the importance of distinguishing between a true rob and an isochromosome in the case of parental “45,rob21q,” and they comment that “when an i(21q) is detected, extensive cytogenetic analysis of at least 500 cells (from a variety of tissues, if possible) might enable the detection of low-grade parental mosaicism, and thus the provision of appropriate genetic counseling.” rob(22q22q). All conceptions would be monosomic or trisomic 22, other things being equal. For example, one carrier woman had 24 miscarriages, but no normal child (Farah et al. 1975). Two cases are mentioned above of post-zygotic correction with the birth of a normal child, but this is not a realistic hope to offer in the individual case. Gamete donation or surrogacy are potential options (Alhalabi et al. 2018). Figure 7–25.  rob(22;22).

8 INSERTIONS INSERTIONS ARE A TYPE OF TRANSLOCATION. Sometimes the expressions insertional translocation, interstitial translocation, or nonreciprocal translocation are used. In the common, simple insertion, three breaks are required. The first two breaks release an interstitial segment of chromatin, which is then inserted into the gap created by the third break. In the simple one-way interchromosomal insertion, a segment from one chromosome is intercalated into another chromosome. This is the most commonly observed form, at 80% of all insertions (Zhang et al. 2023c). A rarely seen, more complicated four-break rearrangement is the reciprocal insertion, whereby two nonhomologous chromosomes exchange intercalary segments. In the intrachromosomal insertion, a segment is intercalated into another part of the same chromosome. The segment may be inserted “right way around”—that is, with the same orientation to the centromere as before—this is a direct insertion (dir ins). Or it may be reversed—an inverted insertion (inv ins). Intrachromosomal insertions account for 10% of the total. More complicated scenarios, which may involve both insertional and terminal translocated segments, are more appropriately dealt with in Chapter 10 (Complex Chromosomal Rearrangements). In this chapter, we consider the case of the phenotypically normal heterozygote, in whom the rearrangement is assumed to be balanced. Insertions are uncommonly recognized rearrangements, but less uncommonly in the molecular age than previously, and Nascimento et al. (2023) propose a carrier frequency for all types of insertion of around one in 4,000 births. All autosomes are on record as having been donor and recipient chromosomes, with no. 11 the most frequently seen donor and no. 22 the most seen recipient chromosome (Zhang et al. 2023c). THE INTERCHROMOSOMAL INSERTION BIOLOGY The formation of the simple one-way interchromosomal insertion is depicted in Figure 8–1. The recipient chromosome now carries the insertional segment, and the donor chromosome lacks it. Van Hemel and Eussen (2000) estimated a prevalence, on classical cytogenetics, on the order of one in 80,000 persons; with molecular methodology, the true figure may actually be severalfold this estimate (Nowakowska et al. 2012). Details of Meiotic Behavior In theory, two categories of meiotic behavior are possible, according to whether the homologs pair independently or as a quadrivalent. 220  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Independent Synapsing of Homologous Pairs Meiosis could proceed in the usual fashion, with homologs pairing independently as bivalents. In essence, we can suppose that the insertional segment is disregarded and that the homologs synapse, with segments matching for as much of their length as they are able. In theory, and perhaps only with larger insertions, the insertional segment could fold out1 to accommodate this requirement (Figure 8–2, upper). (Some crossing-over will presumably occur between synapsed regions, but this would not alter segregation outcomes.) Alternatively, homologs may pair along their full lengths, which would bring some nonmatching segments “incorrectly” alongside each other (“heterosynapsis”). Then, with normal segregation of the two bivalents, independently of each other, two alternative pairs of gametes are possible. Overall, there would be gametes of four possible segregant types, in the ratio 1:1:1:1. Two of these would have a correct amount of genetic material, and two would not. The former two combinations are 46,N and the balanced insertion carrier. The two unbalanced combinations would produce conceptuses, one with a partial trisomy (duplication), and the other with a partial monosomy (deletion), for the insertional segment (Figure 8–2, lower). As discussed further below, studies of testicular biopsies and sperm have shown that (at least with smaller insertions) the homologs can indeed pair normally as bivalents, and that the expected 1:1:1:1 ratio does hold true. It makes no difference whether the insertion is direct or inverted. The foregoing scenario of independent synapsing is more likely to apply when the insertional segment is of small size. The case illustrated in Figure 8–3 exemplifies this: a small (0.4% of haploid autosomal length, HAL) segment from 8q inserted into 10q, with the duplication and deletion outcomes depicted (this case discussed further below). Formation of a Quadrivalent Probably only in exceptional cases, with larger insertional segments, a quadrivalent forms, and this would enable recombination within the insertional segments. In the review of Van Hemel and Eussen (2000), the mean size of the inserted segment in recombining Figure 8–1.  The formation of an interchromosomal insertion. Notes: Single and double asterisks indicate orientation of the insertion segment. The direct insertion has the same orientation to the centromere; the inverted insertion has the opposite orientation. 1 Described also as ballooning out, looping out, or as translocation loops. Insertions  221 cases was 1.5% HAL, compared with 1.0%2 and 0.5% HAL in non-recombining families in which the imbalances were due, respectively, to duplication and to deletion. With the direct insertion, a recombinant chromosome would be monocentric and therefore functional. Inverted insertions, on the other hand, could produce dicentric or acentric recombinant chromosomes, with the resulting gametes presumably nonviable. Consider the large direct insertion depicted in Figures 8–4 and 8–5. Most of the material within the chromosome 5 long arm (q11q22) has been removed and inserted within the distal long arm of chromosome 1. A configuration at meiosis I such as that depicted, with the insertional segments thrown into an overlapping loop, would allow for complete synapsis of homologous segments. If no crossover occurred in the insertional loop (and assuming 2:2 disjunction with symmetric segregation of centromeres), the same four outcomes noted in the preceding section would eventuate. The gametic combination [a,c] would produce a del(5)(q11q22), and the combination [b,d] would produce a duplication for this same segment (Jalbert et al. 1975). But if a crossover did occur, two recombinant chromosomes would be formed, and now three further unbalanced outcomes from symmetric 2:2 disjunction would be possible: gametes [b′,d′], [b′,c], and [a,d′] in Figure 8–4. The duplication/deletion combinations, [b′,c] and [a,d′], are judged to be nonviable, although they might cause miscarriage. The “least imbalanced, least monosomic” combination is the “dup ins” [b′,d′], which Figure 8–2.  Meiosis at independent pairing of the two sets of homologs. Notes: The insertional segment is shown in black, both in its original and in its translocated positions. The horizontal line marks the site whence came the segment from the donor (cross-hatched) chromosome, and the site of its destination on the recipient (white) chromosome. 2 1% of HAL equates to approximately 29 Mb of DNA.

222  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY leads to a partial trisomy for the insertional segment, 5q11q22. This was, in fact, the karyotype of the proposita in this family (Figure 8–5). Actually, this karyotype endows the same genetic imbalance as would the non-recombinant [b,d] gamete; so in practical terms, it made no difference that this recombination did happen. SEGMENT CONTENT AND VIABILITY The viability of the conceptuses—in other words, the level of risk to the heterozygote of having an abnormal child—depends on the degree of the aneuploid states. Consider the example illustrated in Figure 8–3. A small segment from the middle of chromosome 8 long arm, 8q21.2q22, has been removed and is inserted within the chromosome 10 long arm. This segment comprises about 0.4% of HAL. The heterozygote for this rearrangement could produce two types of unbalanced conceptus: one with a duplication of the segment 8q21.2q22 (Figure 8–3b), and one with this segment deleted (Figure 8–3c). In this family (Figure 8–6), only the duplication was observed. These individuals had mild to moderate intellectual disability and minor physical anomalies (Bowen et al. 1983). A segregation analysis of the family was done, and the segregation ratio was close to 1:1:1:0 for normal:balanced:partial trisomy:partial monosomy. This implies viability for the partially trisomic conceptus, and nonviability for the partially monosomic state. Figure 8–3.  An Illustrative Case. Notes: An insertion from chromosome 8 to chromosome 10, ins(10:8)(q21;q21.2q22), showing (a) the balanced carrier, (b) the duplication, and (c) the deletion states. In this family, the duplication was the only unbalanced form to be observed. Case of PA Bowen; in Bowen et al., Duplication 8q syndrome due to familial chromosome ins(10;8)(q21;q212q22), Am J Med Genet 14: 635–646, 1983. Insertions  223 Thus in this family, the risk for having an aneuploid child is estimated to be 1/1 + 1 + 1 + 0, or 33%. (This assessment is an example of a “private” segregation analysis.) A genetically smaller insertional segment has the potential to be viable in both the duplicated and deleted states. For example, Doheny et al. (1997) describe two first cousins, one with a duplication of a segment of 10q, the other with a deletion. The connecting relatives carried an ins(12;10)(q15;q21.2q22.1).3 The insertional segment, 10q21.2q22.1, was small, comprising about 0.5% HAL. The child with the duplication was identified with learning difficulty in first grade, and her IQ measured at 74; the physical phenotype was rather mild. Her cousin with the deletion had considerable lag in neurodevelopmental progress as an infant, which would lead one to anticipate a more Figure 8–4.  Meiosis at Quadrivalent Formation. Notes: Gamete production following formation of a quadrivalent in the interchromosomal insertion, with a single crossover having occurred in the insertion loop. Only one of each sister chromatid is shown. Recombinant chromosomes noted as b′ and d′. (Based on the case shown in Figure 8–5.) 3 In the ISCN nomenclature, the recipient chromosome is noted first, followed by the donor chromosome. 224  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 8–5.  Recombinants from an Interchromosomal Insertion. Notes: Interchromosomal insertion with recombinant chromosomes in phenotypically abnormal offspring. Partial karyotypes of 46,ins(1;5)(q32;q11q22) carrier parent (above) and her recombinant child with 46,rec(1)rec(5)dup(5q)ins(1;5)(q32;q11q22) (below). The latter is the [b′,d′] combination in Figure 8–4. The child is trisomic for the segment 5q11q22. Cartoon karyotype: white, chromosome 1; criss-cross-hatched, 5q11q22; cross-hatched, remainder of 5. Source: From P Jalbert et al., Partial trisomy for the long arms of chromosome no. 5 due to insertion and further ‘aneusomie de recombinaison’, J Med Genet 12:418–423, 1975. Figure 8–6.  An Insertional Translocation Family Tree. The pedigree of the family in which the insertion illustrated in Figure 8–3 was segregating, quite probably the most extensive on record. Another such is the 4-generation ins pedigree in Arens et al. (2004).

Insertions  225 serious intellectual disability at older age, and she had a more obviously dysmorphic appearance. A similar circumstance is illustrated in Arens et al. (2004), who describe a family in which an ins(3;5)(q25.3;q22.1q31.3) is segregating in four generations, with 10 persons having inherited the del or dup state for the 5(q22.1q31.3) segment. Those with the deletion were more markedly affected than those inheriting the duplication state Insertional segments of smaller size, shading into the measurement lengths associated with copy number variants, may present the remarkable circumstance of pathogenicity due to deletion but normality with the duplication. Such a story is seen in Nowakowska et al. (2012), who describe a family segregating an ins(1;2)(p13q36.3q37.1), the inserted segment 2q36.3q37.1 of size 2.1 Mb. Six family members presented severe intellectual disability and minor dysmorphism, and they each had deletion for the 2q36.3q37.1 segment. But one family member with the duplication was normal, and this observation informed prenatal advice for her carrier nephew. If an insertional segment coincides with that of a known segmental aneuploidy, the particular syndrome may be observed in the family. Consider the story in Fernández et al. (2016): Two family members, related as uncle and nephew, presented some aspects of the HDR syndrome of hypoparathyroidism, deafness, and renal disease, which is due to monosomy 10p14 (Chapter 14). In this instance, the deletion comprised the segment chr10:2,471,915-14,544,442. The heterozygotes in the family carried a balanced insertion, ins(16;10)(q22;p13p15.2). The Two-Way Insertion. A two-way reciprocal insertion (a rare observation) has the potential for two different imbalances: a partial monosomy from the segment of one chromosome with the reciprocal partial trisomy of the segment from the other chromosome; or the opposite, with a partial trisomy of one chromosome and a partial monosomy of the other. Gametogenesis Studies. Gametic analysis has been reported in two male insertion heterozygotes. Goldman and Hultén (1992) examined testicular material from an ins(6;7) heterozygote, and demonstrated independent synapsis of the no. 6 and no. 7 homologous pairs at diakinesis, with the two bivalents occupying quite separate parts of the nucleus. This is a direct demonstration that the segregation scenario set out in Figure 8–2 does happen. Testicular tissue and sperm were studied from one ins(3;10) carrier in whom a very small segment of chromosome 10 (p13p14) was inserted into chromosome 3 at q13.2 (Goldman et al. 1992). In meiosis I, the pairing chromosomes did not loop out the nonhomologous segments; but in fact the normal chromosome 3 appeared to pair fully with the der(3), and likewise the chromosome 10 and the der(10). This is likely heterosynapsis. Sperm karyotyping from the ins(3;10) carrier in Goldman et al. (1992) showed, as expected from the theoretical considerations noted earlier, similar proportions of gametes with normal, balanced, duplication, and deletion chromosomes. The actual figures were 22%, 32%, 24%, and 22%, respectively. No recombinant forms were seen. This may be the typical meiotic behavior in small insertions. Spermatogenesis may be compromised in some carriers, a conclusion drawn from the observation that only half as many index cases have carrier fathers as they do carrier mothers (Van Hemel and Eussen 2000). Blastocyst Studies. The segregation ratio with respect to the insertional chromosome, at the level of the blastocyst, essentially reflects the symmetrical balanced:unbalanced ratio as observed in the sperm studies, albeit that unrelated aneuploidies may be 226  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY superadded. In a study of blastocysts from nine couples in S Zhang et al. (2024), 59% were imbalanced (Table 8–1), and in Z Zhang et al. (2023c), 15 couples had, on average, only 30% of blastocysts testing as normal/balanced. In almost all, no insertional crossovers had happened. Instructive Cases. Because nonreciprocal insertional translocations lead to “pure” single segmental imbalances, they can be helpful in delineating genes or phenotypes, and numerous such cases are on record. One example is an ins(13;11)(q14.1p11.2p12) segregating in a family, in which the deletion individuals had biparietal foramina (skull bone deficiencies), multiple exostoses (bone growths), and developmental delay (Shaffer et al. 1993). The description of this family led to the recognition of other deletion individuals, and eventually to the discovery of genes involved in multiple exostoses and biparietal foramina (Wakui et al. 2005; and see Potocki-Shaffer syndrome, Chapter 14). An insertional translocation involving the critical region for Down syndrome provides an interesting illustration that this small segment is indeed sufficient, of itself, to produce the phenotype. Lee et al. (2005) describe a father with 46,XY,ins(4;21)(q21q22.13q22.2) who had a child with typical Down syndrome, having inherited the paternal ins(4) with the small 21q segment, along with two normal chromosomes 21. RARE COMPLEXITIES We may include here mention of insertions which are present in unbalanced state in the transmitting parent, with the parent’s (the mother’s) phenotype presumably protected, Table 8–1.  The Range of Findings at Blastocyst Biopsy from Nine Interchromosomal Insertion Carriers INSERTION BLASTOCYSTS BIOPSIED RESULTS NORMAL CARRIER UNBALANCED INVERSION OR ANEUPLOIDY 46,XX,ins(1;2)(q23.1;q31.1q32.2) 17 5 3 9 46,XX,ins(1;13)(p22.1;q22q34) 2 1 0 1 46,XY,ins(3;2)(q27;q22q31) 5 0 0 5 46,XX,ins(4;5)(q21;q13q22) 3 1 1 1 46,XX,ins(5;11)(q33;q24.2q14.2) 8 1 2 5 46,XX,ins(6;5)(q24;q31.1q34) 7 2 0 5 46,XX,ins(6;15)(q24;q22.1q25) 4 0 1 3 46,XY,ins(7;2)(q11.2;q22q34) 2 0 0 2 46,XX,ins(9;18)(q32;q12.3q21.2) 11 2 5 4 TOTALS 59 12 12 35 Notes: These carriers had presented due either to having had a history of miscarriage or to having had a child with an aneuploidy due to the insertion. The lengths of the insertional segments lay between 20 Mb and –60 Mb, except for the case of the ins(9;18), in which the insertional segment was 12 Mb in length. The fraction of imbalanced embryos is 59%; the “unbalanced” category included aneuploidies. The normal cf. balanced carrier state was distinguished by haplotype phasing. A skewed ratio of female carriers may reflect a degree of infertility in the male. Source: From S Zhang et al., Comprehensive preimplantation genetic testing for balanced insertional translocation carriers, J Med Genet, 61:794-802, 2024.

Insertions  227 partially or fully, by X-inactivation. An ins(X;5)(p22.1p13.2p13.2) is described in the family of Walters-Sen et al. (2015). Two brothers had autistic features and mild dysmorphism, and their two sisters had poor language development, one with a major unilateral limb defect. Their mother was of mild physical phenotype and normal development. All five had duplication of the 5p13.2 segment; the mother showed skewed X-inactivation (the X with the 5p segment being preferentially inactivated), while her daughters had random skewing. The inserted segment is chr5:36,669,467-37,010,647(hg19), containing only two genes and indeed, only parts of these genes, SLC1A3 and NIPBL; an abbreviated form of the NIPBL protein might plausibly have been the pathogenic factor. There can be a link with cancer if a tumor suppressor gene is located in the insertional segment (Barber et al. 1994). An extraordinary case is seen in a father who had had Wilms tumor as a child, and whose daughter had retinoblastoma due to an insertion that was apparently balanced in him and unbalanced in his child. A segment from 13q14 including the retinoblastoma (RB) gene was inserted into 11p13, this being the site on chromosome 11 of the WT1 Wilms tumor locus (Punnett et al. 2003). Familial dominantly-inherited Alzheimer disease4 is rarely due to an APP duplication. A quite extraordinary case is in Kalfon et al. (2022), in which a small insertional translocation containing APP has been transmitted in unbalanced state for at least seven generations, co-segregating with a phenotype of early-onset Alzheimer disease and/or intracerebral hemorrhage. A segment of chromosome 21q21.3 containing the APP (and CYYR1) locus, along with a segment from chromosome 5, have together been insertionally translocated into chromosome 18. The consequential duplication of APP is presumably the proximate cause of the familial disease, although adjunctive roles for the eight chromosome 5 loci, or the disrupted gene within chromosome 18, are also possible. GENETIC COUNSELING Insertions are among rearrangements implying the highest reproductive risk. Pooled data from a number of insertion families (Van Hemel and Eussen, 2000) indicate an average risk of having an abnormal child of 32% for the male carrier and 36% for the female. It may reach 50%. Of the phenotypically normal offspring, approximately half will have normal chromosomes and half will be insertion heterozygotes. Broadly speaking, the risk for liveborn unbalanced offspring is greater in the small-segment insertion, and smaller in the large-segment insertion; larger segments will typically be lethal in utero. Offering prenatal or preimplantation (Table 8–1, Figure 8–7) testing should, in many cases, be the rule given the high risks for either abnormal offspring, or for miscarriage. Zhang et al. (2024) reviewed results in nine interchromosomal insertion carriers undergoing PGT. Of 59 blastocysts, 24 were euploid, and 36 were imbalanced due to malsegregation of the insertion, or otherwise aneuploid. Applying family-based haplotyping, the euploid embryos could be distinguished as balanced or non-carrier, and were seen in equal proportion. Where the choice was available, non-carriers were chosen for transfer to the uterus. 4 The least rare form is due to the PSEN1 gene. 228  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Short Insertion Segment For the short insertion (<1% HAL), the segregation ratio at conception would be expected to be 1:1:1:1 for normal:balanced:duplication:deletion (as discussed above). If the insertional segment is not only short but also genetically “small,” both trisomically and monosomically, the maximum risk of having a liveborn aneuploid child would approach 50% (1 + 1/1 + 1 + 1 + 1). The segment 18q11q21 (HAL = 0.8%), for example, meets these criteria, as seen in the insertion family presented in Chudley et al. (1974). Carriers for this insertion had all four karyotypic classes of offspring—insertion heterozygotes, karyotypically normal individuals, individuals with a duplication of a small segment of 18q, and individuals with the same segment deleted—in approximately equal numbers. A similar scenario is seen in Marinescu et al. (1999) with a family segregating an insertion ins(16;5)(q22p14p15.3). Here, the “small” segment comprised 5p14p15.3. In two generations from a heterozygous grandparent, there were two children with 5p–, two with 5p+, four normals, and three carriers. The same level of risk, with a 1:1:1:1 segregation as above, will also apply to the very small insertion that requires molecular karyotyping for its recognition. If viability is reduced or impossible for the trisomic or monosomic conceptuses, the risk to have an affected liveborn child would be correspondingly less, but the risk increased for miscarriage or for failed embryo transfer. Trisomic lethality presumably increases with an increasing fraction of HAL, with monosomic imbalances being more lethal. It may not be possible to make a clear judgment based on the literature about the qualitative content of the imbalance, because the insertion involves an interstitial segment of chromosome, whereas most data on record relate to distal segments. A review of the insertional data on record up to the year 2000, taken from nearly 90 families, is Figure 8–7.  Preimplantation genetic testing. Notes: The mother was heterozygous for an interchromosomal insertion of substantial size, of karyotype 46,XX,ins(13;5)(q32;q12.1q34). Test results in three embryos are shown; the imbalances in the samples of the lower two embryos are clearly seen. The large insertion segment, comprising chr5:61,805,642-162,688,727, would not have been viable in an unbalanced form. The analysis was done on whole genome analysis of trophectoderm cells taken at blastocyst biopsy. Source: From Z Zhang et al., Clinical outcomes in carriers of insertional translocation: a retrospective analysis of comprehensive chromosome screening results, F S Rep 5:55–62, 2023. Courtesy P Xie, and with the permission of Elsevier.

Insertions  229 provided in Van Hemel and Eussen (2000), and Figure 8–8 is taken from their paper. Any insertion involving the same red bar (deletion) or green bar (duplication) segment, or part thereof, will have a significant risk. Schinzel’s (2001) cytogenetic database and the Internet sources DECIPHER and the phenotype tracks of the UCSC genome browser may also be consulted. Of course, any unbalanced child in the counselee’s family will provide proof of viability, and an illustration of that particular phenotype. A study of the wider family may provide a guide to the recurrence risk—a “private” segregation analysis, as illustrated above in the “Biology” section. But in any case, the starting point with a patient having a short insertion is that the risk for an abnormal child is high, by which we mean in the range 10%–50%. Longer Insertion Segment A longer insertion may yet be viable, as the longer green bars (dups) in Figure 8–8 attest, and some of the red bars (dels). Consider these examples. The child in Dittner-Moormann et al. (2020) had deletion of 13q13.3q14, from a paternal insertion 46,XY,ins(12;13)(q21.2;q12.3q14.3), one of the largest ins-related dels (16 Mb) on record, making the point that the nature of the imbalanced segment is key in determining risk. And rather obviously, a risk for viability in the countertype dup form, which would be a partial trisomy 13, must be high, approaching the 1:1:1:1 short-segment risk discussed above. In the family of Jalbert et al. (1975) mentioned above (Figure 8–5), the insertional segment (5q11q22) comprised 2.2% HAL (about 60 Mb), and this duplication did allow survival, although the child was dysmorphic and severely disabled. This case is the sole example of dup(5)(q11q22) in Schinzel’s (2001) database. The risk for recurrence in this family, or occurrence in another family, must surely be small, and perhaps x is only a low single-digit number. Many longer insertions will not imply a risk for an affected liveborn, although the miscarriage risk may be high. In a family such as that in Abuelo et al. (1988), with an insertional segment comprising most of 3p (3p26p13, approximately 75 Mb), one could be rather confident that any imbalanced conception would miscarry. The closest viable segment in Schinzel’s database is 3p14pter, and the closest overlapping CNV in DECIPHER is a 43 Mb duplication at 3p24.3p14.2. A risk of “close to 0%” for an abnormal child could be offered. Prenatal diagnosis in cases judged to be of this very low risk category would be discretionary; a normal NIPT result and ultrasonographic fetal anatomy scan would likely be considerably reassuring of itself. As noted above, PGT may be seen as valuable in avoiding the transfer of embryos that would inevitably fail. With longer insertions, there is theoretically an additional risk for the formation of recombinant duplication and deletion chromosomes. But in fact the deletion for a long segment (whether the result of a non-recombinant or recombinant chromosome) would usually impose a nonviable degree of partial monosomy. The dup/del combinations (see Figure 8–4) are even more unbalanced, leading to spontaneous abortion. Thus, only the duplication (whether non-recombinant or recombinant) is likely to allow for viability. In the great majority of cases, therefore, the segregation ratio for pregnancies going to term is 1:1:x:0 for normal:balanced:partial trisomy:other imbalances, where x is less than 1, and probably very much less than 1. The corollary is that a miscarriage risk will be high, and the attraction of PGT is evident given a likely 1:1:1:1 segregation at the blastocyst stage. 230  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 8–8.  Segregations from an Interchromosomal Insertion. (Above and opposite) Presentation of chromosome segments in which recombinant imbalances have been recorded (on classical cytogenetics), in the child of a parent heterozygous for an interchromosomal insertion. Segments seen only as duplications are shown in green, those seen only as deletions in red, and green and red bars connected show segments observed in either state. Insertions seen only in the balanced state are identified with open bars. Numbers alongside bars refer to the numbers of recorded cases. Heterochromatin is in blue. Source: From JO Van Hemel and HJ Eussen, Interchromosomal insertions: Identification of five cases and a review, Hum Genet 107: 415–432, 2000. Courtesy JO Van Hemel, and with the permission of Springer-Verlag. Insertions  231 Figure 8–8.  Continued.

232  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Intermediate-Length Segment Intermediate-length segments (1%–1.5% HAL) might imply a risk in the range 5%–10%. But each segment needs to be judged on its merits, both according to the reproductive history in the family and with reference to the cytogenetic databases. THE INTRACHROMOSOMAL INSERTION BIOLOGY Intrachromosomal insertions are rare indeed. These insertions can be between-arm or within-arm (pericentric or paracentric), and direct or inverted. Domínguez et al. (2017), in their literature review, accumulated 70 cases, of which 40 were between-arm and 30 within-arm. Most of these were based upon classical analysis, and the inserted segments were of at least size 5 Mb, and several much larger. The cytogenetic recognition can be difficult, with some having originally been interpreted as paracentric inversions with unbalanced meiotic products (Madan and Nieuwint 2002). The formation of the intrachromosomal insertion is outlined in Figure 8–9, and there may be incomplete or complete synapsis. These differences may have practical reproductive consequences, and it is useful to consider each separately. The Between-Arm Insertion The between-arm5 insertion has a segment of chromatin from one arm inserted into a point in the other arm (Figure 8–9, right). If we consider the part of the chromosome containing the centromere as the fixed reference point of a chromosome, we can regard the centromeric segment as “staying still” while the insertion segment shifts from one arm to the other. This somewhat arbitrary point of view allows us to use the term inserted segment unambiguously, in the context of the between-arm insertion. Thus, in Figure 8–9, the segment shown in black has moved “up” from the long arm and is inserted into the short arm (rather than the segment containing the centromere moving “down” into the long arm). Incomplete Synapsis. Perhaps in most cases of the direct between-arm insertion, the inserted segments fold out so as to allow a good degree of synapsis of the bivalent. This synapsis would include that part of the chromosome between the two inserted segments—that is, the centromeric segment. There would be no difference, at least in theory, if the insertion is direct or inverted. One (or any odd number) crossover within the centromeric segment will produce recombinant chromosomes: one with a duplication of the insertion segment, and the other with a deletion (Figure 8–10). The centromeric segment may be quite long as a proportion of the whole chromosome, and provide considerable opportunity for crossover. Thus, the genetic risk is expected to be high, and in theory could approach 50%. In other words, the segregation ratio for the four possible segregant outcomes of normal:balanced insertion:duplication:deletion may be close to 1:1:1:1. 5 Also called inter-arm, centromere shift, and pericentric insertion. Insertions  233 Figure 8–9.  The Formation of the Intrachromosomal Insertion. Left, the within-arm insertion, with the inserted segments cross-hatched. The normal chromosome is on the left, and the insertion chromosome on the right. Right, the between-arm insertion, with the inserted segment in black. The normal chromosome is on the left, and the insertion chromosome on the right. Figure 8–10.  Meiosis in the Between-Arm Insertion. Gamete production following a recombination between the sites of rearrangement in the between-arm intrachromosomal insertion. At the top of the figure, the normal chromosome is on the left, and the insertion chromosome on the right. There is incomplete synapsis, with ballooning out. (Cf. the ins(5) shown in Figure 8–13.) 234  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY The level of reproductive risk will lie according to the level of in utero genetic compromise imposed by the recombinant duplicated and deleted states, respectively. An insertion segment of substantial size, in either the duplicated or deleted state, may imply a risk only for miscarriage, such as the ins(6)(p24q21q27) reported in Elkarhat et al. (2019). Siblings in Xanthopoulou et al. (2010) with ins(7)(p22q32q31.1) had had two liveborn children and one prenatal diagnosis with the duplication, but no recorded pregnancy from the deletion. Contrariwise, in the family illustrated in Figure 8–11, with a between-arm insertion involving the small Potocki-Shaffer segment (11p11.2), both imbalanced outcomes are observed. Here, it may be the case that with no reduced viability of either imbalanced state in utero, the risk for the carrier to bear liveborn affected children is indeed in the region of the theoretical 50%. The interpretation can be difficult with a smaller insertion, as Lybæk et al. (2009) discuss in their case of a “19p13-into-19q” insertion, an ins(19)(q13.3p13.2p13.3). A profoundly disabled infant girl with precocious puberty had a distal 19p duplication of 8.9 Mb, and her mother had a rea(19), initially assessed as a pericentric inversion. It took FISH to reveal the true nature of the abnormal chromosome as being due to a between-arm shift. Complete Synapsis, Direct Between-Arm Insertion. For complete synapsis to be achieved, the insertion and the centromeric segments and their matching segments on the normal homolog would need to loop back and forth into each other, forming a double loop (Figure 8–12, upper panel). Crossing-over within the centromeric segment will lead Figure 8–11.  Familial Transmission of an Intrachromosomal Insertion. Family tree (a) showing segregation of an intrachromosomal insertion ins(11)(q23.1p11.2p12), with both deletion and duplication observed in the family, and (b) cartoon karyotype to show the nature of the rearrangement. The insertional segment is of approximately 2 Mb in length. Half-filled symbol, balanced carrier; filled symbol, 11p deletion (Potocki-Shaffer syndrome); cross-hatched symbol, 11p duplication. The formal karyotypes of the deletion and duplication states are rec(11)del or dup(11)(p11.2p12)ins(11)(q23.1p11.2p12). (Case of J Gastier-Foster and C Astbury.) A very similar ins(11) case is reported in Chen et al. (2024d). Insertions  235 Figure 8–12.  The range of possible recombinants from crossing-over in one or other insertion loop following complete synapsis of the intrachromosomal insertion. The four panels show, from above down, the direct between-arm insertion, the inverted between-arm insertion, the direct within-arm insertion, and the inverted within-arm insertion. In the loop diagrams, the dots signify the centromere, and the × shows the point of crossover. The insertion segment DE is shown in thick line in the loop and in the recombinant chromosomes. Circled letters provide reference points for text comments. Source: Adapted from K Madan and FH Menko, Intrachromosomal insertions: a case report and a review, Hum Genet 89:1–9, 1992.

236  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY to recombinant chromosomes deficient or duplicated for the inserted segment (Figure 8–12 a, b). If, however, following complete synapsis, there is crossing-over within the inserted segment, this will lead to the generation of new recombinant forms: chromosomes that are duplicated for terminal p and deleted for terminal q, or vice versa (Figure 8–12 c, d). A notable such example is illustrated in Ardalan et al. (2005), concerning a mother who carried a dir ins(20)(p13q11.21q13.33) (initially thought to be a pericentric inversion). The “shifted” segment was relatively large, about half the length of the chromosome, and the del qter/dup pter recombinant karyotype conveyed a survivable imbalance. Complete Synapsis, Inverted Between-Arm Insertion. Recombination in the inverted between-arm insertion, in the setting of complete synapsis, has the same consequences as for the direct insertion as discussed above, when crossovers take place within the centromeric segment (Figure 8–12 e, f ). The case illustrated in Figure 8–13 demonstrates this. The recombinant child with a dup(5) could equally have arisen from recombination in a partial synapsis (Figure 8–10) or in a complete synapsis (Figure 8–12 f ), but in either event, the crossover is within the centromeric segment. The duplication comprises the inverted insertion segment. If, however, the crossover is within the inserted segment, dicentric and acentric products will result, and the compromised conceptus will likely degenerate very early and may not even implant (Figure 8–12 g, h). The Within-Arm Insertion A shift of chromatin within the same arm is called, logically enough, a within-arm6 insertion (Figure 8–9, left). Since both segments shift, essentially switching positions, each could be called an “inserted segment.” If both segments maintain the same orientation toward the centromere, it is a direct insertion. If the orientation of one segment is reversed, it is an inverted insertion. In the case of the inverted inversion, we can distinguish one segment from the other by referring to respective inverted and noninverted segments. In the direct insertion, the shorter of the two segments can be arbitrarily labeled as the inserted segment, and the longer as the “noninserted” or “interstitial” segment (Madan and Menko 1992; Barber et al. 1994); since they are both really insertion segments, we can also speak of the “shorter inserted” and the “longer inserted” segments. Incomplete Synapsis. The within-arm shift, in the case of the direct insertion, can have a similar folding out of one inserted segment, and its homolog on the normal chromosome, to enable synapsis of the other inserted segment and its homologous region. In Figure 8–14, we depict the shorter insertion segment folded out, with synapsis of the larger inserted segment; equally, it could have been drawn the other way around, with synapsis involving the smaller inserted segment. Recombination within the larger segment will lead, respectively, to duplication or to deletion of the shorter segment in the recombinant products, thus giving rise to the gametocytes. Or, if there is synapsis of the shorter inserted segments, followed by recombination, there would be duplication of the larger inserted segment in one gametocyte, and deletion of this segment in the other. 6 Also called intra-arm, and paracentric insertion. Insertions  237 In theory, the longer the larger segment is, the more likely it is that recombination will happen; but nevertheless, cases are on record of crossing-over taking place in very short inserted segments (Webb et al. 1988; Barber et al. 1994). A molecular example is the following: A girl with a severe intellectual disability, autism, and minor facial dysmorphism had a 3.4 Mb microdeletion at 14q11.2, chr14:19,663,407-23,061,615, and this was interpreted initially as a de novo rearrangement, as a FISH probe for the deleted region hybridized to 14q11.2 in both parents. The family requested that the girl’s uncle, a jovial man with mild intellectual disability, be tested—and he proved to have the countertype duplication. It then needed further three-color FISH analysis to reveal the subtlety of the insertion of the 3.4 Mb segment, the whole rearrangement taking place within a single band. The rea in the heterozygote is described broadly (but inadequately) as ins(14)(q11.2q11.2q11.2) (R Beddow and K Gibson, personal communication, 2016). Complete Synapsis, Direct Within-Arm Insertion. If complete synapsis is achieved in the direct within-arm shift, there is no new category of recombinant form beyond the four that could be generated from incomplete synapsis with folding out of one of the segments (as in Figure 8–14); indeed, distinction between the two processes is not possible. Crossing-over within the longer inserted segment will lead to recombinant chromosomes deficient or duplicated for the shorter inserted segment (Figure 8–12 i, j). Vice versa, crossing-over within the shorter inserted segment will lead to recombinant chromosomes deficient or duplicated for the longer inserted segment (Figure 8–12 k, l). We illustrate such a case from Quinonez et al. (2012), who describe an insertion of 6.33 Mb at 1q21.3q23.3 into 1q42.12, in the mother of two children with multiple malformations, severe intellectual deficit, and anatomic brain abnormalities on imaging. The children were deleted for this 1q21.3q23.3 segment, chr1:153,035,245-159,367,106(hg18). A meiotic crossover within the intervening region (or, within the longer insertion segment) led to gametes deleted for 1q21.3q23.3 (the shorter insertion segment), as per the Figure 8–13.  Recombination from an inverted between-arm shift. Partial karyotypes of an insertion heterozygote mother and her recombinant child. The karyotypes are 46,inv ins(5)(p13q22q33), and 46,rec(5)dup(5q)inv ins(5)(p13q22q33). The child is duplicated for 5q22q33 (indicated by the cross-hatched segment). The recombination may have arisen from crossing-over anywhere between 5p13 and 5q22 at either partial synapsis with ballooning out of segments 5q22q33, as in Figure 8–10, or from complete synapsis following double loop formation, as in Figure 8–12 f. From NJ Martin et al., Duplication 5q(5q22-5q33): from an intrachromosomal insertion, Am J Med Genet 20:57–62, 1985.

238  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY scenarios depicted in Figure 8–14 (del), or Figure 8–12 (imbalance i) and as shown in Figure 8–15. FISH was necessary to clarify the picture. (Of interest, this rearrangement had previously been interpreted as a harmless paracentric inversion, and the two affected children’s karyotypes as normal.) Complete Synapsis, Inverted Within-Arm Insertion. Nonviability is the fate of conceptions from crossovers in the inverted within-arm shift, if crossing-over happens within the inverted segment (Figure 8–12 o, p). But if crossing-over is in the noninverted segment, we see the same imbalances (Figure 8–12 m, n) as in the direct within-arm shift (Figure 8–12 i, j). Thus, Rethoré et al. (1989) describe a child with a duplication for the very short segment 5p13.32p14.2 due to a parental inv ins(5)(p13.31p14.3p15.12) with recombination in the even shorter segment p14.3p15.11, reflecting the scenario set out in either Figure 8–12 n, or Figure 8–14. Offspring with either the deletion or the duplication may be seen, such as Silipigni et al. (2017) show in a kindred segregating a within-arm inverted ins 1q42.13q43. A notable example of a three-generational inverted within-arm insertion is the inv ins(15)(q15q13q11.2) family described in Collinson et al. (2004). The grandmother, her son and her daughter, and one grandchild were heterozygous for the insertion, with the detailed karyotype written inv ins(15)(pter→q11.2::q13→q15::q13→q1 Figure 8–14.  Meiosis in the Within-Arm Insertion. Gamete production following a recombination within one of the insertion segments (the longer segments) of a direct within-arm intrachromosomal insertion. The chromosome pair at upper left could be seen as the normal and inverted, respectively; the dotted line indicates the movement of the inverted segment. There is incomplete synapsis, with “ballooning out”. There are four possible gametic outcomes. The case in Figure 8–15 exemplifies this scenario, with the segment at 1q21.3q23.3 being removed, and translocating to a position elsewhere on the same arm, at 1q42.12 (in this case, with the same orientation to the centromere, and thus a direct within-arm insertion). Insertions  239 1.2::q15→qter). Three grandchildren were abnormal: one with Prader-Willi syndrome (PWS), one with the dup(15)(q11q13) syndrome (p. 428), and the third with Angelman syndrome (AS). As the reader may already have guessed, the AS grandchild was born to the carrier daughter, while the PWS grandchild was fathered by her son: These two grandchildren had each inherited a deletional rearrangement. The grandchild with the dup(15)(q11q13) syndrome, 46,XX,rec(15),dup(15)(q13q11.2) ins(15)(q15q13q11.2)mat, was the carrier daughter’s child, having inherited a duplicational rearrangement. The rearrangements would have arisen following either the scenario set out in Figure 8–14 or Figure 8–12 m (the deletion), or Figure 8–12 n (the duplication). The reader may have discerned a pattern in the various aforementioned constructions. Whichever segment recombination takes place in (the active segment, so to say), it is the other (passive) segment that comes to be duplicated or deleted. This is logical. Figure 8–15.  Meiosis in the Within-Arm Insertion. Meiotic recombination from a direct intrachromosomal insertion (within-arm shift). Above, chromosomes 1 of a carrier mother, 46,XX,ins(1)(q42.12q21.3q23.3), normal on left, insertion chromosome on right. The segment at 1q21.3q23.3 is inserted into 1q42.12. The zigzag line shows the region of crossover between the normal and the ins(1), in the gametes giving rise to her affected children. Below, chromosomes 1 in her affected daughter. FISH with probes for 1q21.3q23.3 shows a normal signal in the normal position on the paternal chromosome 1 (below left), and absence of this signal on the deleted, maternal rec(1) (below right). Source: From SC Quinonez et al., Maternal intrachromosomal insertional translocation leads to recurrent 1q21.3q23.3 deletion in two siblings, Am J Med Genet 158A: 2591–2601, 2012. Courtesy JW Innes, and with the permission of John Wiley & Sons.

240  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY A crossover will create a new version of the active segment that contains a portion from each contributing chromosome—but it will be the same length as it was before. The other, non-crossing-over segments follow, as it were, passively along. Embryogenesis Studies. An insight into meiotic behavior of the direct between-arm insertion is offered in Xanthopoulou et al. (2010), who studied embryos created at preimplantation diagnosis from a sister and brother, who were both heterozygous for ins(7) (p22q32q31.1). The sister had 13/17 analyzable embryos which were normal or balanced, three with dup 7q31, and one with del 7q31, thus with an imbalanced fraction of 24%. Her brother had a majority, nine out of 14 (64%) imbalanced, five deleted and four duplicated for 7q31, and only five normal/balanced. Thus, from smallish numbers. in this sibship the fraction of balanced embryos from the sister (77%) was twice that of her brother (36%). Blastocyst studies in Z Zhang et al. (2023c) and S Zhang et al. (2024), comprising a material of 34 embryos from four carriers of an intrachromosomal insertion (two female, two male) gave findings of 13 embryos (38%) as being normal or balanced. In three carriers the insertion was between-arm, and in one carrier, within-arm. The imbalanced embryos included those with another aneuploidy. Rare Complexity. If one of the breakpoints in an insertion takes place at or near a Mendelian locus, disease may result. This picture is illustrated in Ryu et al. (2024) in their study of a family in which a mother and son were diagnosed with tuberous sclerosis (TSC), and numerous other family members were said to have facial angiofibromas, a classic TSC observation. Mother and son were shown to carry a quantitatively balanced inverted within-arm intrachromosomal insertion. One of the genes for TSC, TSC1, is located at 9q34.13. The 6.6 Mb segment 9q33.3q34.13 was inserted, inverted, into 9q31.2. The 9q34.13 breakpoint occurred within the TSC1 gene, disrupting its function. GENETIC COUNSELING The risk to have an abnormal recombinant liveborn child from an intrachromosomal insertion carrier parent, in the 27 families reviewed by Madan and Menko (1992), was 15%, although they considered this quite possibly to be an underestimate. This is an average figure, and it was derived from families studied with classical cytogenetics. We may presume a range from near 50% to zero in the individual case. Referring to the concept of the “shorter inserted” and the “longer inserted” segments as discussed above, a high risk is likely (1) if the shorter inserted segment is small, so that there is a high survivability in both the duplicated and deleted state for that segment; and (2) if the longer segment is large, in which case recombination may be more likely to take place. In this situation, a figure of 30%–40% may be the appropriate one to offer. Given that the partial aneuploid states will involve interstitial regions of the chromosome, very little data (quite possibly none) may be on record for the viability and phenotype of the particular segment (but of course the appropriate databases should be checked); and an educated assessment will have to be made. In the case of very small insertions detectable at the level of molecular karyotyping, the risk is likely to be at the upper end of the range. Risks are presumably less, and possibly zero, if both segments are long (that is, no recombinants are viable). The risks may also be less—say, below 10%—if both segments are short, which might weigh against recombination; but we have no firm data with which to buttress this suggestion. As always, a “private” segregation analysis, if the family offers that opportunity, may provide the best estimate of risk. For one specific insertion, Insertions  241 Allderdice et al. (1983) calculated a risk of 31% for female inv ins(9)(q22q34.3q34.1) heterozygotes. But prediction is imprecise. One short-segment between-arm shift, 46,dir ins(7)(p22.1p21.4q36.1), with a long centromeric segment for which a high risk might have been predicted from the foregoing, in fact produced no liveborn recombinant child in a three-generation family. A number of first- and second-trimester pregnancy losses in this family may have been due to unbalanced forms, and an increased risk for miscarriage will often apply (Farrell and Chow 1992). Prenatal or preimplantation diagnosis will often be appropriately offered in scenarios in which a high-risk picture is drawn, both to eliminate the risk for a liveborn affected child and to avoid the transfer at IVF of embryos that would inevitably miscarry. From the embryogenesis studies noted above, a high risk applies—at least 60%—albeit likely exaggerated due to aneuploidies unrelated to the insertional chromosome. In this scenario, PGT would clearly have a place. NIPT will be an alternative option to detect larger unbalanced segments, after consultation with the testing laboratory. The ins(14)(q11.2q11.2q11.2) described above (in the section “Incomplete Synapsis, Direct Within-Arm Insertion”) conveys an important message. The presenting child with a deletion was interpreted, following parental analysis, as having a de novo rearrangement; thus, a low recurrence risk for others in the family was assumed. But the discovery of her uncle with the countertype duplication demanded reappraisal, and with the identification then of the (very subtle) insertion in the connecting relatives, in fact a high-risk scenario was recognized. To state the obvious, family histories can be very revealing.

9 INVERSIONS INVERSIONS ARE INTRACHROMOSOMAL STRUCTURAL rearrangements. The commonest is the simple (or single) inversion. (If the inversion coexists with another rearrangement in the same chromosome, it is a complex inversion.) The simple inversion comprises a two-break event involving just one chromosome. The intercalary segment rotates 180 degrees, reinserts, and the breaks unite (Figure 9–1). The rearranged chromosome consists of a central inverted segment, and flanking short-arm (p) and long-arm (q) distal noninverted segments. If the inverted segment includes the centromere, the inversion is pericentric; if it does not, it is paracentric. Note that the pericentric inversion has one break in the short arm and one in the long arm, whereas in the paracentric inversion both breaks occur in the same arm. Thus, when reading cytogenetic nomenclature, one can readily tell which is which. For example, 46,XX,inv(3)(p25q21), with both a p and a q, is pericentric, while 46,XY,inv(11)(q21q23), with both letters the same, is paracentric (inv = inversion). The particular clinical relevance of inversion chromosomes is that they can set the stage for the generation of recombinant (rec) gametes that may lead to abnormal pregnancy. In this chapter we pay attention largely to the circumstance of the familial balanced and phenotypically normal carrier, and that carrier’s risk for abnormal offspring; but we also refer to inversions, familial or (most often) de novo, that are unbalanced, or which disrupt genes, and with an associated phenotypic abnormality. The heterozygote is, other things being equal, a phenotypically normal person. The reorientation of a sequence of genetic material apparently does not influence its function, and breakage and reunion at most sites does not perturb the smooth running of the genome (although subtle imbalances may be detectable at the molecular level; Pettersson et al. 2020). (Some inversions of the X may be an exception to this rule: A breakpoint involving the X long arm within the “critical region” can cause gonadal insufficiency.) As with other balanced chromosome rearrangements, classic inversions will typically not be detected by chromosome microarray. FREQUENCY OF INVERSIONS Excluding variant forms (see further below), classical inversions are an uncommonly recognized rearrangement. Estimates of population frequency range from about 0.12% to 0.7% (pericentric) and about 0.1% to 0.5% (paracentric) of individuals (Van Dyke et al. 1983; Kleczkowska et al. 1987; Worsham et al. 1989; Pettenati et al. 1995). Our focus here concerns the frequencies of carriers of balanced, truly pathogenic inversions—pathogenic in the sense of posing a risk for miscarriage or congenital abnormality in a child. In the review of Liehr et al. (2019), the world-published total of thus-defined inversions was a little over 300, one-third of which related to the recurrent

244  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY inv(8)(p23.1q22.1) of San Luis Valley syndrome (see below). In other words, such inversions are rare. A founder effect may skew the frequency in certain populations, such as the inv(8)(p23.1q22.1) just mentioned; the inv(9)(p23q22.3) seen in persons of Greek ancestry (Sismani et al. 2020), and the inv(22)(p13q12.2) from the Guadalajara region of Mexico (Tonk et al. 2004). Inversions that are smaller, or a great deal smaller, than the classical inversions may be a great deal more common. Dong et al. (2018), using whole genome sequencing, discovered four small paracentric inversions in just over a thousand individuals in the 1,000 Genomes Project. Applying a molecular microscope, Pagnamenta et al. (2024) studied near 34,000 persons, discovering a remarkable range of inversions: some of very small size, and some of which they could deduce as being pathogenic. Be that as it may, inversions of very small length are unlikely to pose a risk for reproductive mischance other than by direct transmission of a known pathogenic abnormal chromosome; we address them here no further. We consider only the classic case. BREAKPOINTS WITHIN GENES In the event that a breakpoint occurs actually within a gene, or within a segment having regulatory influence over a nearby gene, the inversion could be of itself directly pathogenic. Rare de novo examples include an inv(3) with the 3q breakpoint close (7 kb downstream) to the ZIC1 locus at 3q24, the basis of a cerebellar malformation; an inv(17) (q12q25) disrupting SOX9 and causing campomelic syndrome; an inv(X)(p22.1q28) leading to dysregulation of the MECP2 gene in a girl with a Rett-like syndrome; and an inv(16) with breakpoints in two known loci, leading to a phenotype combining tuberous sclerosis and KBG syndrome (Figure 9–2) (Maraia et al. 1991; Vieira et al. 2015; Murakami et al. 2024; Rodrigues Alves Barbosa et al. 2024). In fact, a de novo inv(2) (q35q27.3) provided the entrée to the mapping of a Waardenburg syndrome locus to 2q35 (Ishikiriyama et al. 1989). Figure 9–1.  The structure of the pericentric (left) and paracentric (right) inversions. The inverted segment is cross-hatched. Asterisks provide landmarks at each end of the inversion segment. Inversions  245 Familial examples of inversions with gene disruption include an inv(15)(q11.2q24.3) transmitted from a normal mother to her Angelman syndrome daughter, and which actually led to the cloning of the causative UBE3A gene (Greger et al. 1997). In a family with a number of members suffering from attention deficit disorder, and the affected persons also carrying an inv(3)(p14q21), a locus at each breakpoint was disrupted, these being in an intron of a solute carrier gene (SLC9A9) at the q arm, and in an intron of the DOCK3 gene at the p arm breakpoint (de Silva et al. 2003). SLC9A9 is a fair candidate for having a role in the genesis of this neurobehavioral disorder (Patak et al. 2020). On the X chromosome, an inv(X)(p11.4q22) damaging the Norrie syndrome gene at Xp11.4 and leading to familial Norrie disease (an eye disorder), is described in Pettenati et al. (1993). Xu et al. (2003) report a family with congenital androgen insensitivity (causing a disorder of sex development) segregating an inv(X)(q11.2q27); presumably, the break at Xq11.2 compromised the integrity of the androgen receptor locus. X-linked ectodermal dysplasia has its locus at Xq13.1, and in the affected child in Wu et al. (2017), an inv(X)(p21.3q13.1) had disrupted the gene. Zaum et al. (2022) record the investigation of two brothers with X-linked Duchenne muscular dystrophy, in whom multiplex ligation-dependent probe amplification (MLPA) and whole genome sequencing had been unrevealing. Finally they were able to show an aberration at intron 44 in the dystrophin gene at Xp21 and demonstrate that this was due to an inv(X)(p21.1q13.3) mat. An inversion chromosome with gene damage at both breakpoints is reported in Figure 9–2.  A de novo pericentric inversion inv(16)(p13.3q24.3) associated with phenotypic abnormality, the p and q breakpoints being within two known loci, respectively TSC2 and ANKRD11. Notes: P1, P2 (dark blue), refer to normal genomic sequences within ANKRD11 either side of nt 89518635; and P3, P4 (red), refer to normal sequences either side of nt 2115464 (hg19 coordinates). The hybrid red-blue genetic segments due to the inversion chromosome are non-functional for both TSC2 and ANKRD11; and the consequential haploinsufficiency at these two loci led to a phenotype combining features of the two associated syndromes, tuberous sclerosis and KBG syndrome. Given that the rearrangement is quantitatively balanced, no abnormality was initially detected upon molecular genomic analyses. Source: From V Rodrigues Alves Barbosa et al., Single variant, yet “double trouble”: TSC and KBG syndrome because of a large de novo inversion, Life Sci Alliance 22:e202302115, 2024. Courtesy R Perrier and M Tarailo-Graovac, and with the permission of Life Science Alliance.

246  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Chandrasekhar et al. (2024): An inv(X)(p21q21) mother had two sons, half-brothers, each with Duchenne muscular dystrophy and hearing loss: the inversion breakpoints disrupted dystrophin in Xp21 and POU3F4 in Xq21, the latter a deafness-associated gene. CRYPTIC INVERSIONS An inversion may not necessarily be detected on routine study, and knowing when to mount a directed search requires clinical acumen. Thus, Yokoyama et al. (1997) discovered an inv(17)(p13.1q25.1) in a father whose child had lissencephaly, a particular type of severe brain malformation. At first sight, the inverted chromosome looked normal. They noted a family history of similarly affected children, suspected a diagnosis of Miller-Dieker syndrome (which is due to 17p13.3 deletion; Chapter 14), and went on to demonstrate the cytogenetic abnormality using FISH with a probe recognizing the Miller-Dieker sequence. Molecular methodology was needed to clarify in detail the nature of a chromosome 20 inversion in which classical karyotyping had been interpreted as normal, but MLPA and FISH then revealed a del/dup of distal 20p/20q, respectively, in three adult siblings (Stevens et al. 2009). The mother’s karyotype was 46,XX,inv(20)(p13q13.33), and the siblings each had the identical rec(20)dup(20q)inv(20)(p13q13.33)mat. The imbalances were molecularly very small, the q duplication being of 2.5 Mb, and the p deletion, 1.1 Mb. Dysmorphology was subtle, but the cognitive/behavioral phenotypes were quite abnormal. DELETION OR DUPLICATION AT INVERSION BREAKPOINT A “clean” break and rejoin may not necessarily happen, and rarely, the rearrangement may comprise, or give rise to, an associated deletion or duplication. This is a “complex inversion.” Langer-Giedion syndrome (LGS) is due to a deletion at 8q24.11q24.13 (Chapter 14), and Sasaki et al. (1997) studied a child with LGS who had a de novo inv(8) (q13.1q24.11). Molecular analysis revealed a 4 Mb deletion encompassing the LGS region; presumably this segment had been deleted as part of the process that generated the inversion. A familial inv(18)(q21.1q23)—in which a gene for brain myelination and likely some adjacent genes were deleted—led to some features of the 18q– syndrome in a mother and daughter (Keppler-Noreuil et al. 1998). WAGR syndrome (Chapter 14) is due to abnormality of the PAX6 and WT1 genes at 11p13, and in the complicated case in Marakhonov et al. (2023) the affected child—presenting with hypospadias, aniridia, and Wilms tumor—had an de novo inv(11)(p12q12), along with a t(10;11)(p15;p13); at 11p13, adjacent genes PAX6 and WT1 were both deleted. “Normal Variant” Heterochromatic Inversions. Inversions having a breakpoint within the heterochromatic regions of chromosomes 1, 9, 16, and Y are frequently seen, and they are to be thought of as normal variants, not abnormal chromosomes. In “the world’s largest epidemiological study of the inv(9)”, Šípek et al. (2015) found no significant differences in frequencies between the inv(9)(p12q13) and the normal 9 in populations ascertained for various clinical reasons. Male fertility is, as a rule, unaffected, and

Inversions  247 occasional associations of this inv(9) with reproductive difficulty may simply be coincidental (Ting et al. 2022; Liu et al. 2024c). A single case is recorded of a rearrangement leading to a possibly pathogenic duplication of 9p, from a father with the typical inv(9) (Malinverni et al. 2017). The most common inversion in humans not involving centromeric heterochromatin is the inv(2)(p11.2q13) (Fickelscher et al. 2007); here, just two recorded cases in the world are known of a possibly related pathogenic recombination (see Chapter 18). Other presumed essentially harmless inversion variants include the following: inv(3)(p11q11) and inv(3)(p11q12), inv(3)(p13q12), inv(5)(p13q13), and inv(10) (p11.2q21.2). The inv(10) has been rather extensively studied by a collaborative group of five laboratories in the United Kingdom that between them had 33 families available for investigation (Collinson et al. 1997). They found no excess of infertility or spontaneous abortion among carriers; of interest, all carriers of the inv(10) may be descendant from the same ancient northern European heterozygote (Gilling et al. 2006). THE PERICENTRIC INVERSION BIOLOGY The Autosomal Pericentric Inversion Details of Meiotic Behavior.  The inversion heterozygote may produce chromosomally unbalanced gametes, and in consequence suffer reproductive pathology. The chromosomal imbalance is a result of the formation of a recombinant (rec) chromosome. This is aneusomie de recombinaison—aneusomy due to recombination. Recombination occurs if there is, within the inverted segment, crossover between the inversion chromosome and the normal homolog. The risk of this happening is proportional to the length of the inverted segment. Figure 9–3 shows three pericentric inversions, two with a long and one with a shorter inverted segment. Synapsis and Recombination.  Classically, crossing-over follows the reversed loop model (Figures 9–4 and 9–5). This configuration of the bivalent at meiosis allows alignment and pairing of matching segments of the inversion chromosome and its normal homolog (homosynapsis) to be as complete as possible. One (or an uneven number of ) crossover(s) within the inversion loop, between a chromatid of the normal homolog and a chromatid of the inversion chromosome, leads to the production of two complementary recombinant chromosomes. One of these has a duplication of the distal segment of the short arm, and a deletion of the distal segment of the long arm (chromosome A-A in Figure 9–5), and vice versa in the other rec chromosome (D-D in Figure 9–5). Thus, the conceptuses that result would have both a partial trisomy for one distal segment and a partial monosomy for the other, or vice versa. Typically, only one of these—the least monosomic—is ever viable. Consider the recombinant 7 due to a paternal inversion illustrated in Figure 9–6. There is a duplication of the substantial segment 7p14.2pter, and a deletion of only the tiny segment comprising the distalmost sub-band of 7q (7q36.3qter), this combination being survivable. The countertype conceptus, having a monosomy for 7p14.2pter (and trisomy 7q36.3qter) would, we suppose, fail to implant or would miscarry. 248  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 9–3.  Three different pericentric inversions. Notes: The inverted segments are large in the upper inv(3) and in the lower inv(11), comprising most of the length of the respective chromosomes, and thus potentially predisposing to recombination. With short noninverted segments, rec forms would likely be viable. In the middle inv(3), the inverted segment comprises about half the length of the chromosome, and presumably therefore, with a large noninverted segment, rec forms would be nonviable. The color-staining in the inv(11) (lower) very clearly identifies the large inverted segment. The arrows and arrowheads show the breakpoints. Sources: Cases of NA Adams and LM Columbano-Green; and from T Liehr et al., Recombinant chromosomes resulting from parental pericentric inversions—Two new cases and a review of the literature, Front Genet 14;10:1165, 2019. Courtesy T Liehr, and with the permission of Frontiers in Genetics. Figure 9–4.  Inversion loop in meiosis, direct observation. Left, inversion loop in a mouse study. Right, spermatocyte study of a man with inv(6)(p22q22.2). Source: From A de Perdigo et al., Correlation between chromosomal breakpoint positions and synaptic behavior in human males heterozygous for a pericentric inversion, Hum Genet 83: 274–276, 1989. Courtesy Y Rumpler, and with the permission of Springer-Verlag. Inversions  249 The cytogenetic nomenclature to describe the recombinant karyotype is straightforward. In the above case, for example, we have the following: • Parent: 46,XY,inv(7)(p14.2q36.3) • Recombinant offspring (A-A): 46,XY,rec(7)dup(7p) inv(7)(p14.2q36.3) It is not necessary to put “dup(7p)del(7q)”—the complementary deletion is taken as read (although some may prefer to include both p and q for clarity). More fully, the nomenclature is 46,XY,rec(7)dup(7p)inv(7)(pter→p14.2::q36.3→p14.2::q36.3→qter)pat. This complex twisting of the chromosomes to form a loop may not necessarily take place. In an inversion with a short inverted segment (Figure 9–7a), a partial pairing may occur. Both distal segments (or sometimes just one) align in homosynapsis. The inverted segment and the corresponding part of the normal homolog either “balloon out” (asynapsis of the inversion segment) or lie adjacent but unmatched (heterosynapsis) (Gabriel-Robez and Rumpler 1994; Anton et al. 2005). Thus, no crossing-over can happen within the inverted segment, and recombinant products do not form. Conversely, some inversions with long inverted and very short distal segments may undergo synapsis of the inverted segment only, with the distal segments at each end remaining unpaired (Figure 9–7b). Recombination can occur in this setting. Gamete Studies.  Sperm studies in a small number of inversion heterozygotes give an indication of the frequency with which recombination happens, at least in male Figure 9–5.  Formation of the Inversion Loop. Notes: Inversion loop in meiosis, theoretical recombinant outcomes (cf. the inv(3) shown in Figure 9–3). Both sister chromatids are shown. The inversion (centromeric) segment is blue and white, the long arm noninverted segment is purple, and the short arm noninverted segment is orange. The four possible gametic outcomes following one crossover within the inversion loop are depicted. Compare with the actual observation in Figure 9–4, right. Source: From P Xie et al., Retrospective analysis of meiotic segregation pattern and interchromosomal effects in blastocysts from inversion preimplantation genetic testing cycles, Fertil Steril 112:336–342.e3, 2019. Courtesy G Lin, and with the permission of Elsevier. Figure 9–6.  Pericentric inversion 7 in the father (left) of an abnormal child with a recombinant 7 (right). The recombinant chromosome has a duplication of just over half of 7p, and a minuscule deletion involving the distal-most subband of 7q. The child has a triple amount of the segment 7p14.2pter. The karyotypes are 46,inv(7)(p14.2q36.3) and 46,rec(7) dup(7p) inv(7)(p14.2q36.3)pat. (Case of SM White.)

250  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY gametogenesis (Anton et al. 2005; Morel et al. 2007; Luo et al. 2014). Table 9–1 sets out the findings from a number of such studies, and the data are shown graphically in Figure 9–8. Dual-color FISH methodology, with one color (e.g., green) for the p arm and another (e.g., orange) for the q arm of the inversion chromosome, can show whether a sperm is recombinant. Sperm with non-recombinant chromosomes would show one orange spot and one green spot. A recombinant chromosome with two green spots would reveal the dup(p)/del(q) state, while vice versa, the dup(q)/del(p) chromosome would have two orange spots (Figure 9–9). These several studies confirm the point that the longer the inverted segment, the more likely is recombination to happen. Presumably, a longer inverted segment allows a more ready formation of an inversion loop. We can separate the studied cases into those with a long inversion segment (over 57% of the length of the whole chromosome) and those in which it is shorter. In five examples from Table 9–1 with longer inversion segments, inv(1)(p36.3q43), inv(3)(p25q21), inv(6)(p23q25), inv(7)(p13q36), and inv(8) (p12q24.1), the proportions of dup(p)/del(q) and dup(q)/del(p) recombinant chromosomes were substantial: 31%, 31%, 38%, 24%, and 38%, respectively. The fractions of each vice-versa recombinant type at the level of the gamete, dup(p)+del(q) and dup(q)+ del(p), are essentially the same.1 On the other hand, no recombinants at all were seen in inversions with a short (or a very short) inversion segment: three “normal variant” pericentromeric inversions of chromosomes 2, 3, and 9, and an inv(20)(p13q11.2). In the inv(8)(p23q22) listed in Table 9–1, for example, about equal numbers of sperm showed Figure 9–7.  Alternative models for meiotic pairing, in which only a partial synapsis is achieved. Synapsis of (a) both distal segments; (b) the inverted segment. One crossover is shown in each. 1 Liehr et al. (2019) point out that at the level of observation of viable recombinant forms, in fact p-deletion/ q-duplication is twice as frequently seen as q-deletion/p-duplication; and they propose that, as it happened in evolution overall in the human karyotype, there are fewer dosage-sensitive genes in the short arms than in the long arms. Thus, and given that deletions are phenotypically more crippling than duplications, rec chromosomes with del(p) are typically more survivable than those with del(q). Inversions  251 Table 9–1.  Sperm Analysis from 26 Autosomal Pericentric Inversion Heterozygotes INV SEGMENT SIZE (%) NON-RECOMBINANT* (%) REC DUP(p)/DEL(q) DUP(q)/DEL(p) inv(1)(p11q12) 9 100 0 0 inv(1)(p22q42) 60 80 7 7 inv(1)(p31q12) 30 99.6 0.25 0.13 inv(1)(p32q21) 37 91 4 5 inv(1)(p32q32) 62 83 9 8 inv(1)(p36.3q21) 60 85 7 9 inv(1)(p36q32) 81 83 9 7 inv(1)(p36.2q42) 92 59 20 21 inv(1)(p36.3q43) 95 68 12 19 inv(2)(p11q13) 10 99.4 0 0 inv(2)(p11.2q13) 10 100 0 0 inv(2)(p23q33) 71 61 20 18 inv(3)(p11q11) 5 100 0 0 inv(3)(p25q21) 60 69 14 17 inv(4)(p16q21) 42 99.2 0.8 inv(6)(p23q25) 80 46 19 19 inv(7)(p13q36) 65 75 7 17 inv(8)(p12q21) 31 97 1 0.4 inv(8)(p12q24.1) 61 61 20 18 inv(8)(p23q22) 62 87 6 7 inv(9)(p11q13) 16 100 0 0 inv(10)(p13q22.3) 47 97 3 inv(12)(p11q23) 51 91 4 4 inv(17) (p13.1q25.3) 89 73 0.8 0.6 inv(20) (p12.3q13.33) 84 80 10 8 inv(20)(p13q11.2) 51 100 0 0 AVERAGES ALL 52 85 6.4 6.8 INV SEGMENT >50% 70 76 10 12 Notes: Frequencies of recombinant (rec) and non-recombinant chromosomes are shown as percentages. The size of the inversion segment, as a fraction (%) of the whole chromosome, is noted. Note that, as a rule, the larger the inversion size (especially >50%), the greater the fraction of recombinant forms. Overall, a considerable majority (85%) of sperm are non-recombinant, but somewhat less so (76%) in those of longer inverted segment size; and vice versa, rec forms are 15% and 24%, respectively, in shorter and longer inv segments. The average proportions of the two recombinant forms from each inversion chromosome, dup(p)/del(q) and dup(q)/del(p), are very similar (but see footnote 1). *Whether normal or the inversion. Sources: From the review of Morel et al. (2007), and including also the inv(1)(p22q42) case of Chantot-Bastaraud et al. (2007) and five inv(1) cases of Luo et al. (2014). 252  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY the del(p)/dup(q) state (which is viable) and the dup(p)/del(q) state (which is not), 7% and 6%, respectively. Morel et al. (2007) offer this rule: A high risk of recombination applies when the inversion segment is over 50% in length; the risk is small when the length is between 30% and 50%; and no recombination appears to take place when the inversion segment comprises less than 30% of the chromosome. Figure 9–8 in essence bears this out. And in any event, even if recombination occurred in a small inversion segment, the recombinant chromosome would have such a large duplication and deletion that the risk of an abnormal live birth would, very probably, be negligible. Different inversions in the same chromosome can have quite different recombinant fractions, and this relates, as the reader will have surmised, to the length of the inv segment. Luo et al. (2014) studied the sperm chromosomes in carriers of five different inv(1) cases: inv(1)(p11;q12), inv(1)(p32q21), inv(1)(p36.3q21), inv(1)(p32q32), and inv(1) Figure 9–8.  Recombinant Sperm from Inversion Carriers. Note: Graph shows the proportion of gametes (sperm) that are recombinant, compared with the relative size of the inversion. This is graphical representation of the data from Table 9–1; individual data points and the regression line are shown. The clear trend is that the larger the inversion size, the more frequently recombinants are seen. Source: Adapted from Y Luo et al., Different segregation patterns in five carriers due to a pericentric inversion of chromosome 1, Syst Biol Reprod Med 60: 367–372, 2014. Figure 9–9.  Recombinant Sperm in an Inversion Carrier. Notes: The use of FISH probes to identify rec sperm, from a representative submetacentric inv chromosome. The green probe recognizes the p arm tip, and the red, the q arm (the blue is a centromere probe.) Sperm with a normal or a balanced inv chromosome have one red and one green spot. Rec sperm have both p and q tips of the same color: two green for the dup(p), or two red for the dup(q). The breakpoints 1 and 2 are noted. Source: From E Anton et al., Sperm studies in heterozygote inversion carriers: a review, Cytogenet Genome Res 111:297–304, 2005. Courtesy E Anton, and with the permission of S Karger.

Inversions  253 (p36.2q42), with the size of the inv segments ranging from shortest to longest 9%, 37%, 60%, 62%, and 92% (these men having presented due to infertility or repeated pregnancy loss). The frequencies of recombinant sperm followed accordingly, proportional to segment length: 0% (the shortest inv segment), 9%, 15%, 17%, and 41% (the longest segment). Concerning the common inv(2)(p11q13), Ferfouri et al. (2009) studied seven men presenting either with infertility or during the course of a family study. Of just over 7,000 sperm, 99.7% were non-recombinant; the rate of aneuploidy otherwise did not differ from a control group. This work is interesting in proving that recombination can occur even with this very short inverted segment; equally, the fact of the very tiny fraction manifesting recombination is to be noted. Blastocyst Studies.  In vitro fertilization provides an insight into the behavior of an inversion chromosome before any selection pressure may have been exerted. From 94 carriers of a pericentric inversion, Xie et al. (2019) analyzed 397 blastocysts, of which 58%2 were chromosomally balanced (either a normal karyotype, or with the parental inv). The larger chromosomes, nos. 1 to 12 and the X, were the more often seen. As with sperm, blastocysts show recombination to be related to the length of the inverted segment (Figure 9–10). Recombination was infrequent, about 8%, when the inverted segment was less than 57% of the whole chromosome, whereas with a segment above this length, recombination occurred in 43% of male carriers and 24% of female carriers. It is notable that the male figure of 43% is considerably higher than might have been anticipated from the sperm findings outlined above (24% for an inv segment >50%), a sperm cf. blastocyst discrepancy also observed in some cases of the reciprocal translocation (Haapaniemi Kouru et al. 2017). In a blastocyst study focusing on just one chromosome, namely no. 1, Jia and Xue (2023) came up with analogous findings. From 22 carriers, recombination varied from 2% with an inverted segment under 36%, to 33% with a segment of greater extent. Overall, recombination within the inv from a male parent (24%) was twice that (12%) from the female. 2 Of the remaining 32%, of course, as in any blastocyst study, a considerable fraction of these will be abnormal due to aneuploidy, and unrelated to the inv. Figure 9–10.  Recombinant Blastocysts from Inversion Heterozygotes. Notes: The correlation between inversion size, as a fraction of the whole chromosome length, and the observed frequency of recombination, in a population of blastocysts from 94 inv carriers. Red, female carrier; blue, male carrier. Note the similarity, with respect to the spread of the data points and the slope of the regression line, compared with the graph of gamete (sperm) data in Figure 9–8. Source: Adapted from data in P Xie et al., Retrospective analysis of meiotic segregation pattern and interchromosomal effects in blastocysts from inversion preimplantation genetic testing cycles, Fertil Steril 112:336–342.e3, 2019. 254  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Segment Content and Viability.  While a long inversion segment can set the stage for recombination, what determines the viability of the recombinant conceptus is the functional content of the noninverted (distal) segments. We speak of a “genetically small” content, if the combined effect of duplication p + deletion q, or of duplication q + deletion p, does not cause lethality during the earlier part of pregnancy but allows development to proceed well through the pregnancy and possibly to live birth. Thus, only those heterozygotes who have inversions with genetically small distal segments will ever have a chromosomally unbalanced, phenotypically abnormal, liveborn child. The inversions shown in Figure 9–3 (upper and lower) and Figure 9–6 illustrate this case. Inversion heterozygotes in whom one or both distal segments are genetically large (e.g., Figure 9–3, middle) cannot have an abnormal recombinant child, although they may well have an increased risk for miscarriage. Any recombinants produced by such a person would impart a degree of imbalance that would be lethal in utero. Genetic content corresponds fairly well to chromosome length.3 In inversion families in which recombinant children have been born, the distal (noninverted) p and q segments together add up to a smallish chromosomal burden, whereas in families having no known recombinant offspring, the distal segments together comprise a more substantial load. To put some numbers, in families with rec offspring, on average the distal segments account for just 35% of the total chromosome length, while in those with no rec offspring the figure is almost twice this, at 62% (Kaiser 1988). A larger potential imbalance can still imply a risk to have a viable recombinant child, if the distal segments comprise “genetically small” material. Consider the inv(13)(p11q14) and inv(13)(p12q13), in which the distal segments comprise as much as 75% of the chromosome length. Although the imbalance in the recombinant is large in terms of haploid autosomal length (HAL), the result in the dup(q) form is, in effect, a partial trisomy 13 (imbalance of 13p acrocentric material, here in monosomic state, being of itself without phenotypic consequence). Partial trisomy 13 is, of course, well known to allow intrauterine and postnatal survival. Likewise, consider the case in Ujfalusi et al. (2020), concerning a mother who carried an inversion 46,XX,inv(22)(p13q13.3)(p13), where one of the breakpoints was in the short arm of an acrocentric chromosome. She had two recombinant children, young adults at the time of study, with full-scale IQs of 72 and 79, one with neuropsychiatric symptomatology and mild facial dysmorphism. Their karyotypes are reported as 46,rec(22)dup(22q13.3)inv(22)(p13q13)mat, and at the molecular level, the q arm imbalance encompassed a short 3.3 Mb of DNA, chr22:47,870,362-51,197,766×3(hg19). This imbalance represented only 6.5% of the genomic content of chromosome 22. Similarly, an inversion in chromosome 18 can have distal segments that may be long relative to a short inversion segment, but they are still small genetically, and the dup(q)+del(p) combination can be viable (Schmutz and Pinno 1986; Ayukawa et al. 1994). With specific reference to chromosome 4, Stipoljev et al. (2002) reviewed 20 reported familial inv cases, and showed that recombinant forms have never been seen in those with smaller inversions, but are seen frequently in the larger ones. If the deletion of one segment and the duplication of the other are each associated with a clinical phenotype on their own, a combination of both may be seen in the recombinant child. Thus, Putoux et al. (2013) describe a child in whom they saw features 3 If the reader will forgive this rather crude statement: of course, some larger chromosomes (e.g., no.13) are of relatively sparse genetic content, and no. 19, one of the smallest, is densely packed.

Inversions  255 of both Beckwith-Wiedemann syndrome (which can be due to duplication of paternal 11p) and Jacobsen syndrome (which is due to 11q deletion). The father was heterozygous for an inv(11)(p15.3q24.1), and the child had a rec(11)dup(11p)inv(11) (p15.3q24.1)pat. As noted above, it is typically the case that only one recombinant form is ever viable. This is rather impressively illustrated in Allderdice et al. (1975) in a kindred with the inv(3)(p25q21). Numerous cases of known or suspected dup(3q) children have been born, but none with the countertype del(3q). There is not even an increase in the miscarriage rate, suggesting that the del(3q) is lethal very early post-conception, and either fails to implant or implants only transiently (“occult abortion”). Viability with both recombinant forms from the same inversion, the dup/del and the reciprocal del/ dup, is infrequently seen and includes these reported examples: inv(4)(p15.1q35.1), inv(4)(p15.32q35), inv(4)(p16.2q35.1), inv(5)(p13q35), inv(10)(p15.1q26.12), inv(13) (p11q22), inv(18)(p11q21), and inv(20)(p13q13.3) (Kaiser 1984; Hirsch and Baldinger 1993; Dufke et al. 2000; Maurin et al. 2009; DeScipio et al. 2010a,b; Ciuladaite et al. 2014). These instances have this quality in common: The p and q noninverted segments are very short. It is instructive to consider the inv(4)(p15.32q35) in Hirsch and Baldinger (1993), in which recombinant offspring could be del(4p)/dup(4q) or dup(4p)/del(4q) (Figure 9–11). The four separate segmental imbalances are all well known individually to be viable. Distal 4p is, of course, the basis of the Wolf-Hirschhorn syndrome, and distal 4p trisomy has syndromic, if not eponymic, status. The distal 4q segment is small cytogenetically (0.25% HAL) and functionally, and duplication4 and deletion are quite well tolerated. So the respective imbalances in the combined states—the del(4p)+ dup(4q), and the dup(4p)+del(4q)—remain sufficiently small to be viable, at least much of the time. The index case, with the former imbalance, was a severely disabled child with a Wolf-Hirschhorn phenotype; an aunt, having the latter combination, had rather minor dysmorphism and intellectual disability. The inverted segment is very long: 87% of the total length of chromosome 4. Therefore, crossing-over within the inverted segment is, we assume, very likely to take place. Thus, the genetic risk to heterozygotes for this inv(4) is high. Two other reported families, with slightly different breakpoints (4p16.2, 4q35.1 and 4p15.1, 4q35.1, respectively), also demonstrate a high risk for imbalanced offspring, with both recombinant products observed (Dufke et al. 2000; Maurin et al. 2009). Likewise, a high risk applies to the inv(13)(p11q22) described in Williamson et al. (1980), in a family with several documented, suspected, or possible recombinant abnormal offspring. Here, the contribution of 13p imbalance to the two recombinant states—the del(13p)+dup(13q) and the dup(13p)+del(13q)—has no phenotypic effect, and the effective “single-segment” imbalances of dup(13)(q22qter) and del(13) (q22qter) are each well known to be viable, as discussed above. Applying the principles of “private segregation analysis” as set out in Chapter 4, the risk for a recombinant form in this family comes to a high 50%. We emphasize again the point that while the length of the inverted segment may influence the likelihood of recombination 4 Duplication for a considerably longer segment, 4q31.3→qter, comprising 1.15% of HAL, is viable, as the children in the frontispiece photograph illustrate. 256  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY happening, it is actually the combined genetic content of the distal segments that is the direct determinant of viability of the recombinant form. During the period 1975–2019, about 300 papers were published which reported the birth (or prenatal diagnosis) of offspring having a recombinant chromosome that derived from a parental pericentric inversion. In their review of this body of literature, and adding two families of their own, Liehr et al. (2019) determined the involvement of specific chromosomal segments, and Figure 9–12 depicts the combinations of dup + del genotypes that have been associated with viability. A glance at the figure is enough to see that the gaps—that is, the inverted segments—are mostly longer, and in several a lot longer than the sum of the lengths of the two noninverted segments. Those chromosomes in which the gaps are small (e.g., inv18) are those in which the genome content is “small.” These observations serve to illustrate again the point that inversion chromosomes with large inverted segments, along with those of “small” genetic content are, as a rule, the ones with the greatest genetic risk. It is also to be observed that the green bars (representing duplications) are mostly longer than the red bars (deletions), a reflection of the preferential viability of the least monosomic combination. A Special Case: San Luis Valley Syndrome. By far the most common rec syndrome from an inversion is the inv(8)(p23.1q22.1), leading to offspring of the carrier having a duplication of 8q22qter and deletion of 8p23pter (the breakpoints can Figure 9–11.  An inversion inv(4)(p15.32q35) with small noninverted segments, in which each of the two recombinant possibilities is viable. The del(4p)/dup(4q) karyotype (left recombinant offspring) produces a Wolf-Hirschhorn-like picture, and in the dup(4p)/ del(4q) case (right recombinant offspring) the phenotype resembles the partial 4p trisomy syndrome. The normal chromosome 4 contributed by the other parent is shown grayed out. The 4q segment is so small (indicated by the dots) that it might not make a major contribution, whether duplicated or deleted, to the phenotypes. (Case of Hirsch and Baldinger 1993.)

Inversions  257 vary) (Figure 9–13). Its eponymous name derives from all known cases in the first extended report having been of Hispanic origin from ancestors in Colorado and New Mexico (Smith et al. 1987). These authors calculated a genetic risk of 6% for the inv(8) carrier to have a rec(8) child. Habhab et al. (2020) review the clinical features, usually with facial dysmorphism, multiple malformation, and intellectual compromise. Effect upon Fertility.  Uncommonly, the heterozygote might be infertile, apparently consequential upon the inversion (Groupe de Cytogénéticiens Français 1986b; De Braekeleer and Dao 1991). In their survey of 8,721 men and 8,333 women having presented with a history of reproductive failure, Yuan et al. (2023) identified three men (0.03%) and six women (0.07%) with a pericentric inversion; these fractions lie well within the normal population range, and so a causative link, while plausible, remains speculative. It is suggested that abnormal synapsis of the chromosome pair could affect cellular mechanics at meiosis in the male, more likely if the inversion involves a larger chromosome and in consequence arresting spermatogenesis (Gabriel-Robez and Rumpler 1994). Meschede et al. (1994), for example, describe azoöspermic brothers, one with histologically documented arrest at the level of the primary spermatocyte, and each heterozygous for an inv(1)(p34q23) inherited from their (evidently fertile) female parent. The counselor may be intrigued to learn of the role of a gene familiar in a different setting, namely, BRCA1: The BRCA1 protein may co-locate on the unsynapsed regions of meiotic chromosomes, and this is associated with maturation arrest. Kirkpatrick et al. (2012) showed BRCA1 staining on the inversion segment of an inv(1)(p21q31) in a man who had presented with azoöspermia. There have been numerous reports of infertility associated with the inv(9) pericentromeric variants (Yuan et al. 2023). We remain skeptical of a causal link, and suspect that the concordance of a common malady with a common variant is almost always, if not actually always, simply coincidental (Merrion and Maisenbacher 2019). The large series of Šípek et al. (2015) and of Liu et al. (2024c), which have the important benefit of having accumulated substantial comparison groups, support this view. Parental Mosaicism.  Mosaicism for a (balanced) inversion is rarely recognized. Lazzaro et al. (2001) describe a mother with 46,XX,inv(21)(p12q21.1)[19]/ 46,XX[11] on blood karyotyping, who had a child with a partial form of Down syndrome. The child’s karyotype was non-mosaic 46,XX,rec(21)dup(21q)inv(21) (p12q21.1)mat. Given the mother’s karyotype was from a peripheral blood sample, and she having had a recombinant child, clearly enough this is a case of somatic-gonadal mosaicism. Pericentric Inversions Frequently Innocuous.  Many pericentric inversions are not associated with any discernible reproductive problems. The families of Voiculescu et al. (1986) and Rivas et al. (1987) are not atypical: an inversion chromosome transmitted through several generations with numerous carriers identified, and no difference between the offspring of carriers and those of non-carriers in the incidences of abortion and neonatal death. Interchromosomal Effect.  Some pericentric inversions had originally been discovered in the setting of a child with an aneuploidy such as trisomy 21, and an “interchromosomal effect” was invoked. More likely, it is now appreciated, these associations are fortuitous, and the inversion does not of itself influence the meiotic segregation of other 258  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 9–12.  Recorded deletions (red) and duplications (green) due to a rec chromosome from an inv parent. Note: Every chromosome has been involved, with the obvious exception of the Y (which lacks a partner homolog with which recombination could happen). The chromosomes are ordered according to frequency of involvement, and the small-font numbers below each chromosome refer to the number of recorded cases. The extraordinary contribution of the rec(8), the cause of San Luis syndrome, is evident. Source: From T Liehr et al., Recombinant chromosomes resulting from parental pericentric inversions – Two new cases and a review of the literature, Front Genet 10:1165, 2019. Courtesy T Liehr, and with the permission of Frontiers in Genetics. Inversions  259 Figure 9–12.  Continued.

260  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY chromosomes (Young et al. 2019; Oğur et al. 2023). Sperm analyses, as noted above, and embryo studies endorse this inference (Xie et al. 2019; Jia and Xue 2023). RARE COMPLEXITIES Collectors of remarkable cases will find fascinating the report of Allderdice et al. (1991). They studied a kindred (mentioned also above) with a segregating inv(3) (p25q21), which originated from a couple marrying in 1817 and which was quite widely spread over the maritime provinces of Canada and other parts of eastern Canada, and the northeastern United States. In the course of the study, a normal man was found to have two recombinant 3 chromosomes: one with a dup(q)+del(p), and the other with a complementary dup(p)+del(q), such that his karyotype was balanced. Presumably, both of his (distantly consanguineous) parents were inv(3) (p25q21) heterozygotes, and one parent produced one recombinant gamete and the other parent the other. Likewise, Kariminejad et al. (2011) document a consanguineous couple each heterozygous for inv(18)(p11.31q21.33), who produced a child with a complementary recombinant karyotype—dup(18p)/del(18q) from one parent, dup(18q)/del(18p) from the other—of normal phenotype, and in whom analysis showed segmental UPD(mat) for 18p and segmental UPD(pat) for 18q.5 A similar study is due to Bartsch et al. (2006), in this case a woman with complementary rec(5) chromosomes. Figure 9–13.  The formation of the rec(8) associated with San Luis syndrome, due to inv(8) (p23.1q22.1). Note: The recombinant chromosome has a duplication of the segment 8q22.1qter (shaded), and a deletion of the small segment 8p23.1pter. Source: From SL Graw et al., Cloning, sequencing, and analysis of inv8 chromosome breakpoints associated with recombinant 8 syndrome, Am J Hum Genet 66:1138–1144, 2000. Courtesy SL Graw, and with the permission of Elsevier. 5 These authors raise the intriguing theoretical point that continuing inbreeding in a region with a high prevalence of such a rearrangement could lead to several homozygous individuals being the beginning of a “new” species. Inversions  261 Consanguinity may also lead to homozygosity for the (non-recombined) inversion chromosome. This might be without harm, unless there has been genetic detriment at an inversion breakpoint. Jones et al. (2013) report a couple 46,XY,inv(5)(p15.1q14.1) and 46,XX,inv(5)(p15.1q14.1), whose homozygous inv(5) child had the blood disorder Hermansky-Pudlak syndrome, due to homozygosity for disruption of the relevant gene (AP3B1) at the 5q14.1 breakpoint. In the inversion inv(7)(p15q21) studied in Watson et al. (2016), the 7p15 breakpoint is close to (523 Kb upstream of ) the HOXA13 gene. Consanguineous parents produced a homozygous inv(7) child with the hand-foot-uterus syndrome, typically an autosomal dominant disorder. It may be that a displaced enhancer of HOXA13, in the homozygous state in the child, sufficed to compromise gene activity, while having been without effect in the heterozygous parents. THE PERICENTRIC INVERSION X Pericentric inversions of the X are rare indeed, and of 23 examples reviewed in Ramírez-Velasco and Rivera (2014), only seven were known to be familial; further familial cases are in Kim et al. (2014), Chen et al. (2016a), Damián et al. (2021), and in Chandrasekhar et al. (2024). The inv(X) can be transmitted both by the male and by the female carrier. Baumann et al. (1984) and Schorderet et al. (1991), for example, describe families with an inv(X) transmitted through four generations, with all carriers—female heterozygotes and male hemizygotes—being phenotypically normal. Demonstrably unimpaired fertility is evidenced in the carrier matriarch of the family of Madariaga and Rivera (1997) (Figure 9–14). The X inversion forms in the same way as an autosomal inversion, but the implications may differ. This is because (1) breakpoints in certain parts of the X (its critical region) may have an influence on the phenotype of the female; (2) X chromosomal imbalance in the 46,X,rec(X) female may be mitigated by selective inactivation of the abnormal X; and (3) the 46,Y,rec(X) conceptus will have a partial X nullisomy and functional X disomy. The female and male inv(X) carrier need to be discussed separately. The Female inv(X) Heterozygote Outwardly, the female heterozygote is normal, and not infrequently may be of normal fertility. The concept of “position effect” is of practical importance in the context of X rearrangement. If the long arm breakpoint lies within the segment Xq13q22 or Xq22q26, gonadal dysfunction may occur, but by no means invariably (Therman et al. 1990, and as Figure 9–14 illustrates). There may be primary amenorrhea or, after a fertile period in early adulthood, a premature menopause. Meiosis in the fertile carrier would be expected to proceed according to one of the preceding scenarios (Figures 9–5 and 9–7), with recombination within the inverted segment a possibility. Prima facie, we presume that an ovum with a normal X or the intact (non-recombinant) inv(X) would produce a normal child, whether male or female. In the case of the male, this would require there to have been no compromise of loci at the breakpoints, and evidence of normality in another male family member would be reassuring. A hemizygous son would typically be of normal fertility. If, in the family, the balanced inversion is associated with normal gonadal function in the female, a heterozygous daughter would be expected to have, likewise, normal puberty, fertility, and menopause at the usual time. This family information may not be accessible (or may not exist). In the family of Soler et al. (1981), for example, a hemizygous father, 46,Y,inv(X)(p22q13),

262  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY had three sons and three daughters—each daughter, of course, an obligate heterozygote. He apparently had no gonadal deficiency, but his two older daughters had menopause at ages 37 and 34 years (the youngest was only 30 years old). There was no family history recorded antecedent to him. An ovum carrying a recombinant X would have two very different results, depending on whether it is fertilized by an X- or a Y-bearing sperm, as follows. The 46,X,rec(X) Conceptus.  In their review, Madariaga and Rivera (1997) record outcomes in recombinant cases in 10 families. The del(Xq)/dup(Xp) combination is, in female offspring, characterized by normal or tall stature, and ovarian dysgenesis. The countertype, del(Xp)/dup(Xq), is associated with short stature and, in some, intact ovarian function. These phenotypes presumably reflect the loss or gain of stature genes (in particular SHOX) located on Xp, and ovarian genes located on Xq, respectively. Any effect of the concomitant duplication is presumably mitigated by selective inactivation of the recombinant X chromosome. There is no obvious effect upon intellect. Consider the case presented by Buckton et al. (1981) (Figure 9–15). One of the breakpoints is at the tip of the short arm, and the other is in proximal Xq. The recombinant chromosome, with a deficiency of the tip of Xp and a duplication of distal Xq (Figure 9–15, lower right), was in this family associated only with shortness of stature. The partial Xq trisomy made no discernible contribution to the phenotype. A 26-year-old mother with the rec(X) herself had a rec(X) daughter—unarguable evidence that oögenesis had not (at least by age 26 years) been compromised. A more recent case, with the countertype Xp/Xq imbalance and having molecular study, is reported in Kim et al. (2014): a woman with premature ovarian failure who had the karyotype 46,XX,rec(X)dup(Xp)inv(X)(p22.3q27.3) from a maternal inv(X), the Xp duplication involving chrX:pter-8.9 Mb and the Xq deletion, chrX:145.9-qter Mb. The 46,Y,rec(X) Conceptus.  There will be a nullisomy for the deficient X segment. If this segment constitutes any but the tiniest length of chromatin, the conceptus would not be viable. Nullisomy for a tiny telomeric segment may be viable, but with major dysmorphogenesis and severe neurodevelopmental compromise. Furthermore, the concomitant disomy X is functional, not being subject to inactivation, and therefore of itself produces a major deleterious effect. For example, the carrier mother in Chen et al. (2016a), 46,X,inv(X)(p22.3q26.3), had an abnormal ultrasound, and amniocentesis showed Figure 9–14.  Pedigree of a Kindred Segregating an inv(X)(p22q22). Notes: Carriers have bull’s-eye symbol; two women with gonadal dysgenesis and 46,X,rec(X)dup(Xp) inv(X)(p22q22) have half-filled symbol; normal karyotype shown as N; no annotation, not tested; black dot, miscarriage. The fertility of the heterozygous matriarch is very evident. Source: From Madariaga and Rivera (1997). Inversions  263 46,Y,rec(X)dup(Xq)inv(X)(p22.3q26.3); at 24-week termination, fetal defects were observed. She had a second pregnancy, amniocentesis showing the inversion in balanced state in a male, 46,Y,inv(X)(p22.3q26.3); the baby boy was born prematurely but did well. The Male inv(X) Hemizygote In the male carrier, the rearrangement typically has no apparent effect on phenotype or on reproduction. This is what might have been presumed a priori, given that the inv(X) is regarded as being genetically balanced. Meiosis proceeds unperturbed (rather obviously, there can be no recombination within the inverted segment). All his daughters will be heterozygotes. Sons receive his normal Y and their mother’s (normal) X chromosome, to become 46,XY. A causal association with infertility may be suspected, although not proven, in those presenting with that particular problem. Thus, in Ge et al. (2020), two brothers inherited an inv(X)(p22.3q22) from their mother, and both had severe oligospermia, with “0–1 spermatozoön per high power field.” A role for an effect due to locus disruption at the X breakpoints remains an open question. THE PERICENTRIC INVERSION Y A pericentric inversion of the Y, inv(Y)(p11.2q11.23), is not uncommon in the general population (Verma et al. 1982; Tóth et al. 1984). Three major forms are recognized: types I–III, with differing Yq breakpoints, the Yp site being constant (Knebel et al. 2011). Types I and II, inv(Y)(p11.2q11.23) as noted above, typically have no phenotypic effect and Figure 9–15.  X chromosome inversion. Notes: The mother (above) has the karyotype 46,X,inv(X)(p22q13). Below, The two possible unbalanced reproductive outcomes in daughters, following recombination within the inverted segment; the normal X on the left in each has been contributed by the father. Each type of daughter would have a variant form of Turner syndrome. Male recombinant conceptuses are not shown: The combination of X nullisomy and functional X disomy in the 46,Y,rec(X) conceptus would in this instance be lethal in utero. (Case of KE Buckton et al. 1981.)

264  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY imply no risk for having an abnormal child; these may be regarded as normal variants. The Type III, inv(Y)(p11.2q11.223), which splits the DAZ and CDY fertility gene cluster in AZFc, may be associated with infertility. A molecular-level inversion within Yq11.23, known as r2/r3 and of 1.6 Mb extent, can predispose to partial AZFc deletion, with consequential oligo/azoöspermia (Hallast et al. 2021). UNBALANCED DE NOVO APPARENT RECOMBINANT FROM AN INV Rivera et al. (2013) studied a number of cases, ascertained either pre- or post-natally, in which a rec-like chromosome—that is, deleted for a p segment and duplicated for a q segment, or vice versa—was found. This might have raised a question of gonadal mosaicism for an inversion in a parent and might thus have implied an important genetic risk. But in fact, they could show that the typical mechanism was that of a nonallelic homologous recombination, which spoke for a sporadic, one-off, meiotic generation. GENETIC COUNSELING The Autosomal Pericentric Inversion Variant Forms. It is important to distinguish between the essentially normal variant inversion, of quite frequent observation, versus the uncommon potentially pathogenic inversion. The common inv(2)(p11.2q13), a very small pericentric inversion, is regarded as essentially innocuous (Hysert et al. 2006; Ferfouri et al. 2009). Two possible exceptions are on record to belie its reputation: two abnormal children, one with a 2p duplication and the other a 2p deletion, the proximal boundary at or adjacent to 2p11.2, and the fathers being inversion heterozygotes, described as inv(2)(p11.2q12.2) and inv(2) (p11.2q13), respectively (Magee et al. 1998a; Lacbawan et al. 1999). It may be that the configurations adopted by the chromosome 2 homologs led to an unequal crossing-over and hence the duplication or deletion. With only two such observations of recombination in the decades of history of clinical cytogenetics, some circumspection is required, and Lacbawan et al.’s comment is perfectly reasonable that “at this point, it seems premature to recommend prenatal diagnosis of all couples in this situation.” No genetic risks are known to be associated with the other inversion variants noted in the “Biology” section: inversions of 1, 9, 16, and Y heterochromatin, along with the inv(3)(p11-13q11-12), inv(5)(p13q13), and inv(10)(p11.2q21.2). Concerning the inv(10)(p11.2q21.1), Collinson et al. (1997) offer the practical advice that “family investigation of carrier status is not warranted in view of the unnecessary concern this may cause family members.” We exclude these inversion variants from the discussion below. Risks of Having an Abnormal Child Ascertainment via Recombinant Child. Identification of a family through a recombinant individual proves the viability of at least one of the two recombinant chromosomes. Table 9–2 lists a large number of different inversions for which a carrier is known to have had a recombinant child. There have been various empiric estimates of the overall level of risk to the heterozygote in families ascertained through an abnormal child. From a Inversions  265 number of studies, a consensus range for the usual risk to have a liveborn abnormal child due to recombination is within the range 5%–15% (Groupe de Cytogénéticiens Français 1986b; Sherman et al. 1986; Stene 1986; Daniel et al. 1989). As a general rule, the longer the inversion segment—and, consequently, the shorter the distal segments—the greater the risk to produce a viable recombinant gamete (Figures 9–8 and 9–10). Very long inversions, such as that in Roberts et al. (1989), an inv(10) that comprised 80% of the whole chromosome, or the inv(20) in Stevens et al. (2009) comprising 94%, would imply Table 9–2.  Autosomal Pericentric Inversions Associated with the Birth of a Recombinant Offspring, Listed in “Numerical” Order CHROMOSOME INVERSIONS 1 p36.21q42.13 2 p25q35 p25.3q33.3 3 p25q23 p25q25a 4 p13q28 p15.32q35 5 p13q33 p13q35 p14q35 p15q32 p15.1q33.3 p15.1q35.1a p15.3q35 6 p23q27 p23q25.13 7 p14.2q36.3 p15q36 p15.1q36 p22q22 8 p23q22a,b p23.3q24.1 9 p24.3q34.1 10 p11q26 p11.2q25.2a p12q25 p15q24 11 p11q25 p13q23.3 p15.3q24.1 12 p13q24.3 13 p11q21 p11q22 p12q13 p12q14 p13q21a p13q31 14 p12q31 16 p13q22 p13.1q22 17 p11q25 p13.3q25.1 18 p11q11 p11.2q12.2 p11.2q21.3 19 p13.3q13.33 20 p11.2q13.3 p12q13.3 p13q13.1 p13q13.33 21 p11q21.09 p11.2q22.1 p12q22 22 p11q21 p11.2q13.31 p13q12a p13q12.2 Notes: Inversions listed here are from 55 families, published over the period 1981–2012. These comprise the cases reviewed in Ishii et al. (1997); the case illustrated in Figure 9–5; and more recent cases in Lagier-Tourenne et al. (2004), Mehra et al. (2005), Grange et al. (2005), Schluth-Bolard et al. (2008), Tagaya et al. (2008), Stevens et al. (2009), Honeywell et al. (2012), Mundhofir et al. (2012), Putoux et al. (2013), and Sgardioli et al. (2013). aReported in more than one family. bAssociated with San Luis Valley syndrome.

266  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY the highest risks, possibly up to 50% (Luo et al. 2014). In these two particular cases, two out of the inv(10) carrier father’s three children were recombinant (for 67%), and all three of the inv(20) carrier mother’s children were recombinant (for 100%); of course, n = very few children in these two families. For most families, there is no important risk difference depending on the sex of the heterozygote (Kaiser 1984; Stene 1986) (cf. the quite similar slopes of the blastocyst graph in Figure 9–10); but in some families, the female heterozygote may run a greater genetic risk (Sutherland et al. 1976; Pai et al. 1987). Indeed, for the inv(21)(p12q21.1), recombinant children (with dup(21q) and thus a partial form of Down syndrome) have been seen only where it is the mother who is the carrier parent (Lazzaro et al. 2001). And yet, from the blastocyst data just noted (Figure 9–10), the male carrier in most families has a greater likelihood, if only slightly so, to produce a rec embryo. Each individual inversion carries its own individual risk to have a rec child. This may be arrived at by analyzing the patient’s family (Chapter 4), studying the literature, and assessing the degrees of imbalance potentially arising in the recombinant conceptuses. A specific figure of 6.2% has been derived for one relatively common inversion, inv(8)(p23q22), with more rec children seen of carrier mothers than fathers (Smith et al. 1987): the rec(8) dup(8q)inv(8)(p23q22.1) form leads to the San Luis Valley syndrome, as noted above under “Biology.” Of note, this estimate of 6.2% compares closely with the figure of 7% of sperm with the del(p)/dup(q) form (Table 9–1), attesting to an apparently uncompromised viability of the unbalanced embryo. In contrast, the countertype dup(p)/del(q) recombinant, which is seen in 6% of sperm, is never seen in liveborn offspring, reflecting a zero viability. Concerning chromosome 18, Lustosa-Mendes et al. (2017) reviewed the literature: a heterogeneous material, with inversion breakpoints variously at p11.2 or p11.3, and at q11, q12, q21, q22, or q23. A total of 37% of offspring in 18 families had either the del/ dup or the dup/del combination; but adjusting for ascertainment bias (a little bluntly, by removing one proband in each family), the overall risk figure is 19%. This is still a high figure, presumably reflecting the viability of many of the recombinant forms. In due course, figures may be determined for other inversions seen in more than one family, such as the inv(3)(p25q21), inv(4)(p14q35), inv(10)(p11q25), inv(13)(p13q21), and inv(21)(p12q21.1). The precision that molecular analysis allows will enable subtler distinctions to be drawn, such as Starr et al. (2014) illustrate in comparing with earlier reports their patient with a rec(20) due to a parental inv(20)(p13q13.12). Acrocentric chromosome. The risks to produce abnormal offspring from pericentric inversions in an acrocentric chromosome are again dependent on the size of the inversion, but in this case only the long arm segment needs to be considered; and rather than a composite del/dup imbalance, a recombinant chromosome would simply convey, in functional essence, either a dup(q), for a partial trisomy, or a del(q), for a partial monosomy. A loss or gain of the p arm material would be without phenotypic consequence. The risk associated with a large inversion, with the q arm breakpoint sited distally, may therefore be particularly high. No Family History of Recombinant Form. For families identified by means other than through the birth of an abnormal child (e.g., discovered fortuitously at prenatal Inversions  267 diagnosis), the overall risk is—for what this figure is worth—about 1%. The individual risk, which is what really matters, depends on the actual inversion. Is the inversion chromosome on record (Table 9–2) as being associated with viable imbalance? Or does the inversion segment include and extend beyond the inversion segment of one of these recorded cases? In that circumstance, a significant risk surely does apply. Is the inversion segment much shorter in length than any of those listed in Table 9-2? Here, the risk may be as low as zero. The level of risk can be assessed from a study of the family, noting the reproductive histories of other heterozygotes, and from a consideration of the degrees of potential imbalance in a conceptus. As a rule, any chromosome with a short inversion segment (less than one-third of the chromosome’s length) is most unlikely ever to lead to a viable recombinant product (Kaiser 1988; Morel et al. 2007). Nevertheless, one should determine the composition of the theoretically possible recombinant gametes and gauge whether the resulting partial trisomy and partial monosomy might be viable. This applies in particular to inversions of chromosomes 13, 18, and 21, partial trisomies and partial monosomies of these chromosomes being well recognized as viable. If, in any inversion chromosome, one breakpoint is very close to the telomere, one recombinant form will impose very little partial monosomy. The contribution of the duplication can then be assessed essentially on its own, and reference to the viability of this segment in other cytogenetic contexts (translocation, de novo rearrangement) will likely provide a valid comparison. For example, had the father in Figure 9–6 been identified before he had had children, we could have deduced that the rec(7)dup(7p) genotype might survive to term, knowing that the databases of Stene and Stengel-Rutkowski (1988) and Schinzel (2001) record a viable phenotype for trisomy 7p14pter. Prenatal or preimplantation diagnosis should be offered to the following people: 1. Any heterozygote in whose family a recombinant child has been born. 2. A heterozygote for any of the inversions listed in Table 9–2. 3. A heterozygote for an inversion involving a segment longer than, but including, a region listed in Table 9–2. 4. Any other heterozygote for whom the theoretical recombinant product(s) might be viable. Many inversions of chromosomes 13, 18, and 21 will fall into this category. 5. Molecular analysis to exclude deletion in the Prader-Willi/Angelman region of 15q11q13 may be appropriate in an inversion having a breakpoint within or adjacent to this segment. Of the phenotypically normal offspring, approximately half will have normal chromosomes, and half will be inversion heterozygotes (Groupe de Cytogénéticiens Français 1986b). A question of “transmission distortion,” whereby the 50/50 ratio is skewed, has been proposed in some inversions (Honeywell et al. 2012; Lustosa-Mendes et al. 2017). A risk to the child for some other rearrangement than the classic recombination (see above, “Deletion or Duplication at Inversion Breakpoint”) we presume to be very small,

268  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY likely well under ½%, and prenatal molecular analysis targeted to the breakpoint regions would not normally be warranted. A question of interchromosomal effect appears not to be an issue. Preimplantation Genetic Testing. In theory, PGT might be expected to improve reproductive outcomes, and especially so in the case of a parental inversion with a long inverted segment. This view is supported in the work of Xie et al. (2019) noted above, who showed an increased rate of blastocysts with an imbalance, in those in whom the inverted segment comprised above 57% of the chromosomal length (and see Figure 9–10). Jia and Xue (2023) similarly show an increased rate of imbalance with respect to inv(1) cases, the risk according to the inverted segment length (see “Biology” above). Other studies not showing an apparent benefit (Shao et al. 2020b; Tong et al. 2022a) may have been compromised by the inclusion of many cases with low-risk inversions. Thus, in a known (from previous history) or presumed (from the inv characteristics) high-risk scenario, PGT targeting possible rec forms may well have a place. THE INVERSION X The female heterozygote could have a premature menopause, if the long arm breakpoint is in the critical region, and if there is a family history of early ovarian failure; pragmatic advice might be to have children sooner rather than later. But normal reproductive function is perfectly possible. Recombination may be less likely than for an autosomal inversion (Pinto Leite and Pinto 2001), although a risk to produce an abnormal daughter with a recombinant X does, certainly, exist. The abnormality is, to some extent, predictable according to the deleted segment, Xp or Xq: Short stature is typically seen in del(Xp), and ovarian failure in del(Xq). Hemizygous sons would be expected to be normal, and reassurance in this respect may be drawn from the observation, if it can be made, of normality in a male relative. For the most part, no practical risk exists for having an abnormal son, because recombinant male conceptuses, having partial X nullisomy and disomy, would be nonviable. Only when the breakpoints are very close to the telomere is male viability possible, and such a child would have major physical abnormalities and intellectual disability, probably severe. Due to this male lethality, the sex ratio of the offspring would, in theory, be 1 male:2 females. All daughters of the male heterozygote would be inv(X) heterozygotes. Other things being equal, they will be phenotypically normal. If the long arm breakpoint is in the “critical region,” and if heterozygous female relatives have had ovarian deficiency (e.g., primary amenorrhea, premature menopause), they may develop the same problem. All sons would have a 46,XY karyotype. THE INVERSION Y This inversion—specifically, a macrosopically defined Type I or II inversion, as outlined above—is generally considered a normal population variant of no clinical significance. It is self-evident that all the sons of the inv(Y) carrier will be, themselves, inv(Y) carriers. They are all normal and, other things being equal, have normal gonadal function. All the daughters would be 46,XX. The Type III inv(Y)(p11.2q11.223) may be, but not necessarily so, associated with infertility.

Inversions  269 THE PARACENTRIC INVERSION BIOLOGY Details of Meiotic Behavior According to classical theory, the phenotypically normal heterozygote for an autosomal paracentric inversion would only have children who are karyotypically normal, or with the same balanced inversion. In theory, they could not have viable unbalanced progeny, for the following reasoning. If a recombinant gamete is formed following a crossover in the inverted segment, the chromosome would be either acentric (lacking a centromere) or dicentric (Figure 9–16). An acentric chromosome is never viable, since it lacks a point of attachment to the spindle fibers. The dicentric is considered a lethal impediment, being attached to spindle fibers pulling in opposite directions, with the chromosome thus suspended between the daughter nuclei at telophase, and excluded from either cell. A minor revision of classical theory is necessary, and a very few cases have proved exceptions (Table 9-3). Three possible mechanisms may conspire to yield a functional gamete that could then produce a viable, although imbalanced, conception. Firstly, one centromere of a dicentric rec product might become functionally suppressed, thus allowing the dicentric recombinant to function stably as, in effect, a monocentric (or “pseudodicentric”) chromosome. Thus, the rec chromosomes could successfully attach to the spindle Figure 9–16.  Theoretical recombinant products from classical crossover in a paracentric inversion. One is dicentric, and the other acentric. Notes: The inversion segment is shown in red and blue, and the different colors indicate the parts proximal and distal to the crossover point. This inv(2)(q31.2q33.2) had a possible association with the patient’s history of pregnancy loss. Source: Adapted from J Wincent et al., Genome sequencing differentiates a paracentric inversion from a balanced insertion enabling more accurate preimplantation genetic testing, Acta Obstet Gynecol Scand 103:1564–1569, 2024. Courtesy J Wincent, and with the permission of John Wiley & Sons. 270  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY fiber, using just the one centromere. Each product would have a del/dup combination, and the least imbalanced of these could be viable (Madan 1995). Secondly, a dicentric recombinant chromosome, pulled in two directions, might rupture, yielding functional monocentric products. Thirdly, a crossover within the inversion loop, instead of continuing on in the same direction along the chromatid, could reverse upon itself, known as “U-loop recombination” (Figure 9-17) (Mitchell et al. 1994). Gamete Studies. Yapan et al. (2014) review the findings from a small number of sperm studies, and analyze the extent to which recombination had occurred, showing that the likelihood of recombination is, in considerable part, related to the length of the inv segment. Their own case from a man 46,XY,inv(2)(q21.2q37.3), the largest paracentric inv on record, had the highest level of rec forms, at 28%; presumably, the large size of the inversion, at 103 Mb comprising about three-quarters of 2q, meant that formation of an Table 9–3.  Some Recorded Examples of Parental Paracentric Inversions Associated with the Birth of a Recombinant Child STUDY PARENTAL KARYOTYPE EFFECTIVE IMBALANCE IN THE CHILD Devillard et al. (2010) 46,XX,inv(2) (q14.2q37.3) dup 2q14.1q14.2, del 2q37.3** South et al. (2006) 46,XX,inv(5) (p13.3p15.3) del 5p14.3** Hoo et al. (1982) 46,XX,inv(7) (q11.23q22) dup 7q11.22q11.23 Paskulin et al. (2011) 46,XX,inv(7) (q11.23q33) del 7q31.32q33 Phelan et al. (1993) 46,XY,inv(9)(p13p24) dup 9p12p24** Worsham et al. (1989) 46,XX,inv(9) (q22.1q34.3) dup 9pter-q22.1, del 9q34.3-qter* Douglas et al. (2017) 46,XY,inv(13) (q21.2q32.3) dup 13q21.31q22.3 + 13q32.1q33.3, del 13q33.3qter Lefort et al. (2002) 46,XX,inv(14) (q13q32.2) dup 14pter-q13, del 14q32.2qter* Mules and Stamberg (1984) 46,XX,inv(14) (q24.2q32.3) dup 14q24.2pter, del 14q32.3qter* Whiteford et al. (2000) 46,XXinv(15) (q11.2q26.3) dup 15pter-q11.2, del 15q26.3qter* Yang et al. (1997) 46,XY,inv(17)(p11.2p13) del 17p11.2 Anlaş et al. (2023) 46,XX,inv(18) (q11.2q21.3) dup 18p11.32p11.21 + 18q11.1q11.2, del 18q21.33q23* Chia et al. (1992) 46,XY,inv(18)(q12.1q23) dup 18q12.1q21.3, del 9q21.3q23*** Courtens et al. (1998) 46,XX,inv(18) (q21.1q22.3) dup 18q12.1q21.1, del 18q22.3qter** McClarren et al. (2006) 46,XX,inv(22) (q11.2q13.3) del 22q11.2** Notes: * Dicentric rec chromosome. ** Rupture and reconstitution of rec chromosome. *** U-loop recombinant chromosome. See also Madan (1995) and Pettenati et al. (1995), and Warburton and Twersky (1997). Inversions  271 inversion loop was not hindered, and recombination was enabled. In contrast, those of shorter inv segments had, in fact, zero rec sperm. Meiosis in oögenesis commences during fetal life, and its direct study therefore requires access to fetal tissue. Cheng et al. (1999) analyzed ovarian tissue from a 19-week termination of pregnancy, in which a de novo inv(7)(q11.23q21.2) had been shown at amniocentesis. By using a FISH probe for the Williams syndrome critical region (WSCR), which is at 7q11.23, they could determine whether the inverted segments were aligned alongside each other (homosynapsis) or not (heterosynapsis). Most cells showed the chromosome 7 homologs lined up side-by-side, but with the WSCR signals off from each other: Thus, the inversion segment was unaligned. A classical inversion loop was seen in only 10% of cells. This single example, concerning a small inversion segment, offers an explanation for the rarity with which recombinant forms are seen, given that the necessary prerequisite of homosynapsis often does not apply. A mechanism reminiscent of paracentric inversion U-loop reunion may be the cause of some isochromosome Xq Turner syndrome (Wolff et al. 1996). Two zinc-finger Figure 9–17.  Meiotic Behavior of the Paracentric Inversion. Above, parent with paracentric inversion and child with recombinant (“reunitant”) chromosome. Father has paracentric inversion of 18q, inv(18)(q12.1q23). The inverted segment is shown cross-hatched (cross-hatching changes slope at q21.3). Child has duplication of the segment q12.1q21.3 on the reuniting chromosome (shown cross-hatched) and deletion q21.3q23. (Case of NL Chia and LR Bousfield.) Below, Proposed mechanism of U-loop exchange depicted; asterisk indicates point of U-loop. The position of the point of exchange within the inversion loop (in this case, q21.3) determines the nature of the imbalance. There is duplication of chromatin proximal to the crossover point (q12.1q21.3), and deletion of distal chromatin (q21.3q23), as in the child’s rec(18); and vice versa in the complementary product, rec(18)′. (An alternative interpretation is that the father’s rearrangement is a within-arm insertion of 18q, rather than an inversion, in which case the karyotype of the child would have been derived from recombination in the inserted segment.)

272  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY genes (ZXDA and ZXDB) in proximal Xp, just above the centromere, have about 98% homology and transcribe in opposite directions. In X-to-X synapsis in some meioses, a small inversion loop in proximal Xp might enable ZXDA (the more centromeric locus) in one Xp to match up with ZXDB on the other Xp, and vice versa. Then, a breakage and U-loop reunion between the two ZXD loci would generate an isodicentric chromosome Xqter→cen→ZXDA::ZXDA→cen→Xqter. Similar events at other loci may underlie other Xq isochromosomes (Giglio et al. 2000). Pregnancy Loss.  Several inversion carriers have been ascertained through their having had many miscarriages (Madan 1995). In most of these, surely, the discovery was fortuitous: there had to be a clinical reason for them to have had a chromosome test. One family with an inv(10) was widely studied, and 19 carriers in three generations had only one miscarriage out of 36 pregnancies (Venter et al. 1984). The report in Devine et al. (2000) mentioned above of two brothers with 46,XY,inv(2)(q14.2q24.3) presenting with reproductive pathology may be suggestive, but other causes are quite possible. One brother’s wife had had three miscarriages, and at in vitro fertilization in the partner of the other brother, five of 10 fertilized eggs failed to cleave, and progression in the remaining five failed at the blastocyst stage. No karyotyping was done of any of these several products of conception. In the case in Wincent et al. (2024), illustrated in Figure 9-16, the carrier had presented through having had three pregnancy losses, but untyped; at subsequent PGT, four blastocysts analyzed were all balanced. In a very few cases, theoretical dicentric recombinant products might convey a genetic imbalance that could allow at least some weeks of in utero growth before miscarrying (Bocian et al. 1990; Bell et al. 1991). The nine miscarriages suffered by the carrier grandmother in the family in Worsham et al. (1989) we might more reasonably imagine to have been due (some of them at least) to recombinant gametes, the dicentric state having been proven in her index grandchild. A Special Case, inv(8)(p23). A subtle paracentric inversion of 8p23 is a very common “abnormality,” and indeed should be described as a polymorphism, since it occurs in approximately a quarter to a third of European and Japanese populations, respectively. From the millions, perhaps billions of people who carry this inversion, the tiniest number of abnormal infants have been born, 50 or so known worldwide. In these very rare cases, the inversion has led to a classic recombination with production of a dicentric chromosome, essentially as outlined in Figure 9–17, in which a segment including one centromere is then “clipped off ” to produce a monocentric inv dup del(8p) (8qter→8p23::8p23→proximal 8p) (Huynh et al. 2021b). The recombinant chromosome is typically generated (unusually for a structural rearrangement) in maternal meiosis of the inv carrier (Shimokawa et al. 2004). X Chromosome.  If a paracentric inv(X) is associated elsewhere in the family with normality in both men and women, no defect would be anticipated in future heterozygotes or hemizygotes (Neu et al. 1988a). Breakpoints in the critical regions in Xq might, however, compromise gonadal integrity. For example, Dar et al. (1988) report a woman with a de novo inv(X)(q13q24) who had ovarian dysgenesis with primary amenorrhea and no spontaneous pubertal development, and Németh et al. (2002) describe an infertile man with a Klinefelter-like phenotype having an X inversion with rather similar breakpoints, 46,Y,inv(X)(q12q25); no family study in the latter case was feasible. Inversions  273 Y Chromosome.  A paracentric inv(Yq) is a rare observation (Madan 1995; Liou et al. 1997; Aiello et al. 2007). In Liou et al.’s three-generation family, the normal grandfather and father were 46,X,inv(Y)(q11q21), and the child with the same karyotype had ambiguous external genitalia with Müllerian structures internally and intra-abdominal testes. The inversion Y may well have been coincidental; alternatively, there may have been, in the child, a position effect whereby the expression of a gonadogenesis gene had been compromised. The father and son with 46,X,inv(Y)(q11.2q12) in Aiello et al. were normal (the chromosome having been an incidental observation at prenatal diagnosis). Mendelian Mechanisms Causing Abnormality.  Mendelian loci can be vulnerable when chromosomal rearrangement happens, due to “position effect,” direct disruption, or epigenetic influence, and a few examples with respect to paracentric inversions are on record. Position effect: We have seen a family in which a chromosome 7 paracentric inversion, inv(7)(p22.2p21.2), was associated with Saethre-Chotzen syndrome, this being a Mendelian disorder due to the TWIST gene (locus at 7p21.1). Two heterozygous children showed major craniosynostosis, but the father and grandfather had only the subtlest facial, auricular, and digital signs (it may be that Saethre-Chotzen syndrome due to position effect has a milder phenotype than when it is due to point mutation; Rose et al. 1997). Similar such cases include an inv X(q13q24) likely causing deafness due to an influence upon the nearby POU3F4 locus (Anger et al. 2014), and the small (11.7 Mb) familial paracentric inversion (1)(q42.13q43) in Rigola et al. (2015), which may have compromised the functioning of genes in this region, leading to intellectual deficiency in heterozygous family members. Locus disruption: If a breakpoint occurs within a known gene, a causal link to the observed phenotype may reasonably be assumed, such as the de novo 46,X,inv(X) (q11.1q27.3) in Marco et al. (2008), associated with a syndrome of intellectual disability and hyperresponsiveness, and in which the cognition-related ARHGEF9 gene at Xq11.1 was disrupted. Two siblings with Angelman syndrome in Kuroda et al. (2014) each had an inv(15)(q11.2q26.1), in which the q11.2 breakpoint of the inversion deleted the UBE3A Angelman locus. Their mother (necessarily the parent of origin, p. 555) was of normal karyotype on peripheral blood, and so presumably she was a gonadal mosaic. An epigenetic mechanism may apply in the case of imprintable chromosomes. Norman et al. (1992) described a family in which a mother had one child with Beckwith-Wiedemann syndrome and a presumably affected fetus, all three carrying an apparently balanced inv(11)(p11.2p15.5). The normal imprinting state of the Beckwith region on distal 11p was likely perturbed. Paracentric Inversions Usually Innocuous The above rather extensive compendium notwithstanding, the observed facts attest to the general innocuousness of the autosomal paracentric inversion, concerning either the heterozygous state per se, or a risk for chromosomally unbalanced offspring. Madan (1995) reviewed 184 cases of autosomal paracentric heterozygosity. Many were ascertained fortuitously, and including those discovered during the course of investigation for recurrent miscarriage, 58% were identified in a normal person. Several had an abnormal phenotype, but this was, of course, the reason they had had the chromosome test done in the first place: By definition, they had to be abnormal. No clear consistent pattern among

274  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY phenotypes of presenting cases is apparent. As Madan comments, there may have been a bias in choosing cases for publication, and editors of journals might not find compelling a paper describing an “uninteresting” inversion discovered incidentally in a normal individual (a series of a dozen or more cases might stand a better chance). In their review, Pettenati et al. (1995) could be confident about a causal association with a specific phenotype only with respect to the paracentric inv(X), and not with any of the autosomal inversions. The Groupe de Cytogénéticiens Français (1986a) note that the reproductive fitness of heterozygotes in 32 French families was normal. Two quite common inversions seen in a number of families in more than one part of the world are the inv(3)(p13p25) and the inv(11)(q21q23) (Madan 1995). No abnormalities directly attributable to these inversions have been documented. It may be founder effect, or recurring mutation, that is the basis for their frequency. Interchromosomal Effect.  In the series of 197 preimplantation diagnoses from 57 couples, one of whom was a paracentric inversion heterozygote, due to Xie et al. (2019), no interchromosomal effect was discernible, confirming the earlier view of Pettenati et al. (1995) apropos. Technical Comment.  Paracentric inversions are not detected by microarray and can be technically difficult to detect on classical cytogenetics. Gross chromosome morphology is not altered, and unless major landmark bands are shifted, the rearrangement may go unnoticed. Only with the use of good-quality, high-resolution banding are paracentric inversions likely to be detected regularly. Also, for technical reasons, reported cases of recombination in the literature should be regarded with caution; as mentioned above and noted below, some “inversions” are likely actually to be intrachromosomal insertions (“paracentric/within-arm shifts”). The cytogenetic distinction can be difficult to make, especially so for chromosomal regions without distinctive banding patterns, or where the inverted segments are very small (Callen et al. 1985; Madan 1995). For example, the inverted insertion of chromosome 15 described in Collinson et al. (2004), associated with recombinant offspring having Prader-Willi and Angelman syndrome (and see p. 238), had originally been reported, some 10 years prior, as a paracentric inversion. We have seen a family in which the index case seemed to have an unbalanced translocation at distal 4p, but the normal mother and grandfather had the same anomaly, which could then be reinterpreted as the minimum inversion detectable on routine cytogenetics, a one-band paracentric inversion, in this case inv(4)(p15.3p16.3) (Smith et al. 1992). GENETIC COUNSELING On practical grounds, the reassuring point to note is that practically all paracentric inversion heterozygotes identified have been discovered incidentally, and not through the birth of a child with an abnormality attributable to the parental inversion (Madan 1995). We agree with Madan: “The vast majority of paracentric inversions are likely to be harmless.” Apparently, the genetic risks to offspring are extremely small. In the U.S. collaborative study described in Daniel et al. (1988), there were no unbalanced karyotypes in 30 prenatal diagnoses. The sex chromosomes warrant separate attention, and it may be that some X and Y paracentric inversions have an effect upon gonadal development in the intact (that is, unrecombined) state. Inversions  275 However, a tiny handful of abnormal offspring, and as reviewed at length above, refute a complete harmlessness in the parental paracentric inversion, whether due to classic recombination, or to other forms of rearrangement. Whether this would warrant prenatal diagnosis, when a parent is a carrier of one of these implicated inversions, is a matter for debate. Even where the new chromosome from a classic or U-loop recombinant might on theoretical grounds be viable, the risk for one to be generated, while its exact magnitude is unknown, is surely “extremely small.” “Better than 99.9%” might be a fair estimate that there will be no untoward reproductive outcome due to behavior of the inversion. While molecular karyotyping offers the potential to screen, at prenatal diagnosis, for submicroscopic molecular damage associated with a particular apparently balanced inversion, the case for so doing is very modest. Caution—but in realistic perspective—should be exercised during genetic counseling, in that it is prudent never to say “never.” Thus we suggest that in practice, an offer of prenatal diagnosis be discretionary in the case of a fortuitously discovered inversion in the family; and we would regard it as not inappropriate if the offer were declined (or not made). A firmer stance may be appropriate if there has been a previous history of an apparently associated reproductive abnormality. Inversions on record with a demonstrated recombinant (Table 9–3) would oblige the offer of prenatal diagnosis. But again, we return to the expressions used above: “vast majority,” and “better than 99.9%” in respect of favorable behavior of the inversion. As mentioned above, a diagnosis of a paracentric inversion might be incorrect, and the rearrangement is actually a within-arm insertion, which actually carries a high genetic risk (Chapter 8). Since the distinction in the routine laboratory can be difficult, a practical view might be to risk over-interpreting subtle paracentric inversions as potential insertions in those cases where the cytogeneticist is not absolutely certain. The true picture may emerge by determining the order of a number of FISH probes across the relevant region. The Special Case of the inv dup del(8p) The inv dup del(8p), noted in the “Biology” section earlier, arises from a maternal cryptic (on classical cytogenetics) paracentric inversion. Yet for a couple who have had this happen, the risk of recurrence is in all likelihood still extremely small. Nevertheless, it would be understandable for a couple having had that experience to seek the reassurance of preimplantation or prenatal diagnosis in a subsequent pregnancy. The Paracentric Inversion Detected Prenatally If an apparently balanced paracentric inversion is discovered at prenatal diagnosis, and if the parental karyotypes are normal—in other words, this is a de novo rearrangement— there yet remains a possibility that the rearrangement is not truly balanced, and a risk for abnormality exists (see above, “Mendelian Mechanisms Causing Abnormality”). This question is dealt with in detail in Chapter 22 (p. 702).

10 COMPLEX CHROMOSOMAL REARRANGEMENTS COMPLEX CHROMOSOMAL REARRANGEMENTS (CCRs) occurring in phenotypically normal persons are rare. In her exhaustive review at the time, Madan (2012) recorded 103 published cases. Three or more chromosomes are involved, and a considerable variety of rearrangements are possible. Translocation may involve distal segments, as in the usual reciprocal translocation, or interstitial segments, as in the insertion. Any chromosome may participate in a CCR. Molecular methodology is revealing more complexity among some classical rearrangements than previously appreciated, and the definition of what actually is a “CCR” could become unwieldy (Poot and Haaf 2015). We here largely limit our discussion to those CCRs that may be seen in balanced form in heterozygotes of otherwise normal health, and who may be at risk of producing abnormal pregnancies.1 BIOLOGY Four Major Categories of Complex Chromosome Rearrangement Madan (2012) defines CCRs as those involving three or more chromosomes in which there are three or more breaks. This definition excludes the double two-way reciprocal exchange (Chapter 5). She proposes four major categories of CCR, types I–IV, based essentially upon the number of chromosomes versus the number of breaks and whether there are insertions or inversions. In Type I, there is the same number of breaks as there are chromosomes, and the most common is the three-way exchange in which three segments from three different chromosomes break off, translocate, and unite (Figure 10–1). In Type II, there is one more break than the number of involved chromosomes, and this is due to one chromosome having an inversion. Some apparent Type I CCRs may turn out, upon molecular dissection, to be Type II (Figure 10–2). Molecular dissection may also be needed to reveal the true state of a “cryptic” CCR karyotype initially interpreted as normal (Figure 10–3). Type III is characterized by translocations having one or more insertions (Figure 10–3). The most complex scenario is seen in Type IV (Figure 10–4), in which one (or more) of the derivative chromosomes comprises segments from three or even more chromosomes. In the discussion below, we group Types II–IV as “exceptional CCRs.” The original CCR in a family typically arises as a single complex event, rather than sequential changes, at a meiosis during male gametogenesis (Grossmann et al. 2010). In the familial CCR, transmission thereafter is much more often seen through the mother, 1 Most (~90%) apparently balanced CCRs in abnormal individuals prove in fact to be imbalanced on molecular methodology (Feenstra et al. 2011; Plesser Duvdevani et al. 2020). 278  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 10–1.  A Three-way Complex Chromosome Rearrangement. Notes: Most of 2q is translocated onto 18q; part of 18q is translocated onto 11p; and the tip of 11p is translocated onto 2q. The formal karyotype is 46,XX,t(2;11;18)(2pter→2q13::11p15.3→11pter;11qter →11p15.3:: 18q21.1→18qter;18pter→18q21.1::2q13→2qter). The woman had presented with multiple miscarriages. Source: From RJM Gardner et al., A three-way translocation in mother and daughter, J Med Genet 23: 90, 1986 and with the permission of the British Medical Association. Figure 10–2.  A Type I CCR Revealed to be, in fact, Type II. Notes: This complex chromosome rearrangement was initially interpreted as a simple three-way t(6;7;17) (p23;p22;q25)pat), and thus to be seen as a Type I CCR. As indicated above, on molecular dissection the breakpoints were subsequently refined, and an inverted segment (17q24.3) identified; and the case thus redefined as Type II. Orange = chromosome 6, blue = chromosome 7; black = chromosome 17, circles = centromeres, rectangles = telomeres. Red dot-and-dash lines = breakpoints. Source: From C Redin et al., The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies, Nat Genet 49:36–45, 2017. Courtesy ME Talkowski, and with the permission of Springer Nature. Complex Chromosomal Rearrangements  279 and this is a reflection of the infertility to which the male is often susceptible (although not always so; Figure 10–5). CCRs with up to four breakpoints are more typically familial, and ascertained through the female; those with more breakpoints are usually de novo and discovered through male infertility (Poot and Haaf 2015). Nomenclature of the CCR, as per the ISCN, is straightforward with the Type I CCR, although it can become rather complicated with exceptional CCRs. In principle, the involved chromosomes and breakpoints are listed in the following order: first, the lowest numbered (or X or Y) chromosome; second, the chromosome that receives Figure 10–3.  Unbalanced Transmission of a CCR. Notes: Chromosome 2 in green, 5 in red, and 18 in blue. (a) The father’s karyotype is balanced. At his daughter’s conception, transmitting the der(5) alongside the normal 18 led to imbalance: the der(5) lacks a segment of distal 5p (the red segment with a contained green arrow), and carries additional 18q material (the blue segment annotated a-b). Albeit that the der(5) contains chromosome 2 material (in green), the child is balanced in this respect. The small size of the translocated segments at first misled investigation, and the initial karyotype in the child was 46,XX. The child, with del5p/dup18q, was globally developmentally delayed. (b) The subtleties of the rearrangement within the der(5), revealed by molecular dissection. Jct = breakpoint junction; ONT = Oxford Nanopore Technology. Source: From Z Dardas et al., Genomic balancing act: deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32, Eur J Hum Genet 33:231–238, 2025. Courtesy JR Lupski, and with the permission of Springer Nature.

280  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY a segment from the first; and last, the chromosome donating a segment to the first listed chromosome. Thus, in the simplest Type I case, for example, the karyotype of the CCR shown in Figure 10–1 would be written 46,XX,t(2;18;11)(q13;q21.1;p15.3). Details of Meiotic Behavior The carrier of a CCR has a risk for an abnormal conception due to malsegregation of the derivative chromosomes (or, rarely observed, due to the generation of a recombinant chromosome). Malsegregation follows the general principles as set forth for the simple translocation, assuming that apposition of homologous segments is able to take place; but if so, naturally the range of unbalanced combinations is greater. The broad categories of malsegregation in the Type I three-way translocation are 3:3 (alternate and adjacent), 4:2, and 5:1 and 6:0; in Types II to IV, the theoretical range is enormous. Unsurprisingly the rates of abnormality are much higher in gametes and embryos than in liveborn children, reflecting the lethality in utero of the many possible unbalanced forms. The findings from four sperm studies are set out in Table 10–1; from these men, an average of only 17% of sperm were normal or balanced. In those in which different Figure 10–4.  The Architecture of a CCR at a Molecular Level. Note: This CCR was identified in a woman who had had three abnormal pregnancies: two miscarriages, and an induced termination following an amniocentesis result of dup 7q/del 13q. This is an “exceptional CCR” Type IV, with insertions from 7q into 2p, and from 13q into 7q, along with distal exchanges between 2p and 13q.a The breakpoints are defined at the level of the base pair. a For the record, the detailed karyotype is 46,XX,der(2)(13qter→13q31.1::7q21.2→7q21.11::2p24.2→2qter), der(7)(7pter→7q21.11::13q21.1 →13q31.1::7q21.2→7qter),der(13)(13pter→13q21.1::2p24.2→2pter). Source: From L Xing et al., Long-read Oxford nanopore sequencing reveals a de novo case of complex chromosomal rearrangement involving chromosomes 2, 7, and 13, Mol Genet Genomic Med 10:e2011, 2022. Courtesy H Liu, and with the permission of John Wiley & Sons. Complex Chromosomal Rearrangements  281 malsegregant forms were identified, a very wide range of possible abnormalities were recorded, apparently close to the theoretical maximum. The sperm study in the case in Loup et al. (2010), for example, showed the following proportions among the unbalanced sperm: 34% from 3:3 malsegregations, 38% from 4:2, and even 5:1 (3.5%) and 6:0 (0.05%, representing one sperm out of 1,822). From PGT studies, the results from 155 embryos, from male and female carriers, are listed in Table 10–2. Again, embryos with a normal or balanced constitution are in a small minority. On these small numbers, the risks appear more marked for the female carrier. Gorski et al. (1988) proposed a broad-brush risk to the carrier to have an abnormal liveborn child due to an unbalanced form of the CCR to be about 20%, and for a pregnancy to miscarry about 50%. Of the abnormal forms, Madan (2012) noted adjacent-1 to be the most frequently observed malsegregant mode (72%), 4:2 in 25%, and adjacent-2 in only 3%. Three-Way Complex Chromosome Rearrangement (Type I CCR) At meiosis in the three-way CCR heterozygote, the expectation is that the chromosomes involved in the rearrangement will come together and form a multivalent (Figure 10–6). Figure 10–5.  Familial Complex Chromosome Rearrangement. Notes: On initial classic cytogenetics, a CCR with four breakpoints in chromosomes 2, 6, and 18 was diagnosed. Subsequent FISH-based analysis enabled the recognition of eight breakpoints, with five insertional segments.a The proband at diagnosis was a dysmorphic and developmentally delayed child, whose imbalance due to missegregation comprised a 6p partial trisomy and an 18q partial monosomy. Case III:3 was an 8-month fetal death in utero, unkaryotyped. Atypically in this family, male fertility is retained. a For the record, 46,XX,der(2)ins(2;6)(q37.2;p22.2p22.2)ins(2;6)(q37.2;p21.1p12.3),der(6)ins(6;18) (p12.3;q21.32q21.32), der(18) inv ins(18;6)(q21.32;p22.2p21.1) ins(18;6)(q21.32;p12.3p12.3). Source: Drawn after N Gruchy et al., A paternally transmitted complex chromosomal rearrangement (CCR) involving chromosomes 2, 6, and 18 includes eight breakpoints and five insertional translocations (ITs) through three generations, Am J Med Genet 152A:185–190, 2010. Courtesy N Gruchy, and with the permission of John Wiley & Sons. 282  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Consider how meiosis would proceed in the rcp(2;18;11) translocation illustrated in Figure 10–1. In theory, a hexavalent configuration would allow full synapsis of homologous segments (Figure 10–7). If disjunction were then 3:3, up to 20 possible gametic combinations could occur. The two arising from alternate segregation (arrows in Figure 10–7) would be the only ones to be balanced; the remaining 18 from adjacent segregation would be unbalanced to a greater or lesser degree. Were 4:2, 5:1, or 6:0 segregation to occur, a great number of extremely unbalanced gametes could result, as Rossi et al. (2023) illustrate. Table 10–1.  CCR Sperm Studies Translocation Normal/Balanced Reference t(2;22;11)(q13;q11.2;q23) 14% Cifuentes et al. 1998 t(1;19;13)(p31;q13.2;q31) 15% Loup et al. 2010 t(5;13;14)(q23;q21;q31) 27% Pellestor et al. 2011 t(1;3;6)(p21.1;q22.1;p21.2) 16% Hornak et al. 2014 t(4;7;14)(q12;p21;q11.2) 12% Rossi et al. 2023 Average 17% Table 10–2.  Embryos from CCR Carriers Translocation Carrier Normal/ Balanced Unbalanced Reference t(5;13;16)(q35.1;q32.1;q11.1) F 2 20 Escudero et al. 2008 t(6;11;16)(q16.2;p14.2;q13) M 0 5 Scriven et al. 2014 t(1;4;14)(p32.3;q23;q13) M 4 9 Ibid. t(1;9;18)(p13.3;p22;q23) M 4 13 Ibid. t(1;3;4)(q42.1;q26.2;p15.2) F 0 8 Ibid. t (3;7;9)(q23;q22;q22) M 2 14 Frumkin et al. 2017 t(2;3;4)(p13;q13.2;q21) F 0 2 Hu et al. 2018 t(1;6;3)(p22;q21;p24) F 0 2 Ibid. t(2;12;4)(p13;p11;q33) F 1 5 Ibid. t(1;12;21)(q25;q15;q11) F 1 8 Ibid. t(2;13;9)(p23;q14;p11) M 0 8 Ibid. t(9;16;12)(p22;q22;q15) M 0 1 Ibid. t(1;9;15), t(6;8) F 0 12 Ibid. t(1;4;11)(p31;p16;p22) M 1 3 Brunet et al. 2018 t(3;13;5)(p14;q21;p14) M 0 9 Ibid. t(6;11;21)(q21;q21;q13) F 2 4 Ibid. t(2;4;14)(q21.1;p15.2;q22) M 0 9 Mas et al. 2018 t(2;6;12)(p21;p25;p13) F 0 6 Özer et al. 2022 Averages 11% 89% Note: Some of the unbalanced embryos had aneuploidies unrelated to the chromosomes of the translocation. M = male, F = female. Complex Chromosomal Rearrangements  283 Figure 10–6.  A Multivalent at Meiosis I. Notes: Electron micrograph of a spermatocyte from a testicular biopsy of a man with a type I three-way complex chromosome rearrangement 46,XY,rcp(2;4;9)(p12;q25;p12); line drawing shows component parts of the hexavalent. Source: From N Saadallah and MA Hultén, A complex three breakpoint translocation involving chromosomes 2, 4, and 9 identified by meiotic investigations of a human male ascertained for subfertility, Hum Genet 71:312–320,1985. Courtesy MA Hultén, and with the permission of Springer-Verlag. Figure 10–7.  A Multivalent at Meiosis I, Diagrammed. Notes: Diagrammatic representation of the formation of a hexavalent at meiosis in the three-way 2;18;11 translocation depicted in Figure 10–1. The arrows indicate 3:3 alternate segregation. The breakpoint detail is given in Figure 10–1.

284  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Adjacent segregation can be classified as adjacent-1 and adjacent-2, similarly to the principles set forth in the simple reciprocal translocation. Thus, the segregant gamete shown at left in Figure 10–8, having one of each chromosome pair represented (one of each centromere), would reflect adjacent-1 segregation. An example of 3:3 adjacent-2 segregation is given in Xu et al. (1997). A mother had the karyotype 46,XX,t(5;16;22), and cytogenetic analysis of her morphologically abnormal fetus following intrauterine death at 16 weeks gestation showed 46,XY,der(5),der(16),–22,t(5;16;22). In this case, the abnormal ovum would have had one chromosome 5, two chromosome 16s (one normal, one the derivative), and lacked a chromosome 22. 4:2 segregation particularly characterizes CCRs in which chromosomes with “small content” short arms (9, the acrocentrics) are a component. Schwinger et al. (1975) reported a mother of two children with typical Down syndrome, who herself had a three-way t(7;21;11) CCR. The affected children had an interchange trisomy 21, in that they had, in addition to the maternal translocation pattern, a second intact chromosome 21. Fuster et al. (1997) give an example of a 4:2 malsegregant, diagnosed at chorionic villus sampling, from a three-way paternal t(2;22;11) CCR. The fetal karyotype was interpreted as 47,–2,der(2),der(22)t(2;22;11) (q13;q11.2;q23). The parents continued the pregnancy, and the disabled child with multiple anomalies had a double partial trisomy: a duplication of the segments 11q23qter and 22pter-q11.2. The couple had previously had one normal child and three miscarriages. The risk of having a pregnancy that would go to term but then produce an abnormal child reflects the nature of the rearrangement—that is, the familiar question of whether there are possible chromosomal combinations that would lead to aneuploidy for a survivable amount of genetic material. Thus, considering the preceding rcp(2;18;11) example, three unbalanced combinations—one 3:3 and two 4:2—might be expected to be viable (Figure 10–8). Madan (2012) determined that the criteria applying to simple translocations (Chapter 5) are broadly appropriate for the CCR: If the translocated segments are short, adjacent-1 segregation may lead to liveborn abnormal offspring; and if chromosomes with “small content” short arms (9, the acrocentrics) are involved, 4:2 segregation is usual. Large translocated segments are typically associated only with nonviable products and consequent pregnancy loss. Recombination would add yet further possibility of imbalance, but this is rarely seen. Figure 10–8.  Possibly Viable Segregant Outcomes from a CCR. Notes: Three segregant outcomes of meiosis in the rcp(2;18;11) heterozygote shown in Figure 10–1, that might be expected to produce viable but unbalanced offspring. The 3:3 adjacent-1 gamete on the left may be the one most likely to be observed. Complex Chromosomal Rearrangements  285 Exceptional Complex Chromosome Rearrangement More complex rearrangements imply an even greater potential range of abnormal gametes. Kausch et al. (1988) calculated a minimum of 70 possible unbalanced gametes due to 4:4, 5:3, 6:2, and 7:1 segregations from an octavalent, in the case of a woman with a five-breakpoint CCR with translocations of chromosomes 1, 2, 5, and 11, and an inversion of chromosome 1, who had presented with three first-trimester miscarriages. Van der Burgt et al. (1992) report a similarly complex de novo balanced CCR (chromosomes 5, 11, 12, 16; five breakpoints in all) in a mother who had had one miscarriage, one 46,XY child, the index abnormal child, and, as a quite unexpected outcome, a de novo 45,rob(13q14q) at prenatal diagnosis in her fourth pregnancy. The mother with a particularly complex CCR (chromosomes 1, 4, 14, 18)2 in Campos et al. (2021) had had a normal child and two miscarriages before having her affected son. One of the more complicated familial CCR scenarios described is the case in Röthlisberger et al. (1999). A father carried a de novo CCR, with eight breakpoints altogether—two in chromosomes 6 and 18, three in 7, and one in 21. Most remarkably, among his three children, three different recombinant forms were passed on: a rec(7), a rec(21), and a rec(18). The child with the rec(21) had a balanced karyotype, and he has become a balanced carrier for a simple translocation, 46,t(7;21)(q21.3;q21.3): a “rebuilt” translocation (see below). The other two have partial trisomies for 6q and 7q. The classical karyotype will often fail to reveal the true nature of an exceptional CCR, as the comparison between the G-banded karyotype and the molecular-based diagram in Figure 10–9 illustrates. The coming together of several translocation chromosomes during meiosis may set the stage for recombination that Soler et al. (2005) describe as “rebuilding.” The CCR shown in Figure 10–10 with six breakpoints in five chromosomes offers useful illustration. The woman who carried this rearrangement had four pregnancies, only one of which miscarried, and two produced offspring with a balanced constitution, though different in each child, and different from their mother! Recombination involving the centric segment of chromosome 1 led to a daughter receiving a rebuilt der(1), with just the 6p segment being translocated, and a son with a different rebuilt der(1) having just the 7q segment. A son and a grandson had unbalanced karyotypes, which were different, but each led to partial 7q trisomy. Readers who relish esoteric puzzles may wish to refer to the original paper. Effect upon Fertility. In some complex rearrangements, gametogenesis can accommodate itself to the complexity thrust upon it, and the heterozygote may be fertile and have pregnancies that produce phenotypically normal children. Multi-generation transmission is recorded, but is uncommon (Figure 10–5). The rule of the greater vulnerability of spermatogenesis to chromosomal complexity seems to apply particularly in the case of the CCR, and the male heterozygote is often sterile due to spermatogenic arrest (Liang et al. 2022b). Indeed, in Madan’s (2012) review of 19 patients presenting with infertility, only one was a woman (and in her case, one of the breakpoints in the CCR being at Xq24, a critical ovarigenesis region, was the likely culprit). 2 For the record, 46,XX,ins(1) (pter→p22.3:q41→q43orq43→q41:p22.3→q41:q43→qter),t(4;14;18)(4pte r→4p15.2:4p14→4qter;14pter→14q24.1:4p15.2→4p14or4p14→4p15.2:18q21.1→18qter;18pter→18q21.1: 14q24.1→14qter).

286  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Wang et al. (2015) undertook testicular biopsy in a man presenting with azoöspermia, with a 46,XY,t(5;7;9;13) karyotype. Germ cells were reduced in number, some undergoing apoptosis; but no sperm or spermatids were present. Meiosis had proceeded part way, and octavalents were identifiable in all pachytene cells, albeit that several of the homologous segments had failed to synapse. A similar story is described in Coco et al. (2004) (Figure 10–11). Attempting fertility treatment with intracytoplasmic sperm injection (ICSI)—provided, of course, that sperm are being produced—is controversial (Joly-Helas et al. 2007; Nguyen et al. 2015). Where conception may have taken place, infertility due to multiple miscarriage is a frequent observation; the basis of this may largely be due to the production of only unbalanced conceptions, from either parental sex (Figure 10–12). Figure 10–9.  Extraordinary Complexity Revealed on Molecular Analysis. Notes: The classic banded karyotype (above) cannot reveal the full detail of the CCR. Using FISH and WGS, the true nature of the CCR could be determined, and depicted diagrammatically (below). The rearrangement was de novo. The subject had had four miscarriages, and no successful pregnancies. This is an example of chromoanagenesis (p. 320). Source: From P He et al., Analysis of complex chromosomal rearrangements using a combination of current molecular cytogenetic techniques, Mol Cytogenet 15:20, 2022. Courtesy K Lu, and with the permission of Springer Nature.

Complex Chromosomal Rearrangements  287 GENETIC COUNSELING For the heterozygote (male or female) who is fertile, or for whom fertility can be achieved, a conceptus having either a normal chromosome constitution or the same balanced CCR as the parent would be expected, other things being equal, to produce a normal child. But a very high proportion of conceptions have an unbalanced karyotype, as PGT has been revealing. The male CCR heterozygote who is not otherwise known to be fertile should have a semen analysis to check whether sperm are being produced. If there is oligospermia, IVF will have to be considered, and PGT would be appropriate. Figure 10–10.  A Type IV CCR, with Three Two-Way Exchanges. Note: There are six breakpoints in five chromosomes. Source: From HN Bass et al., A family with three independent autosomal translocations associated with 7q32----7qter syndrome, J Med Genet 22:59–63, 1985. Figure 10–11.  Meiotic Arrest in an Infertile Heterozygote. Notes: This image is from an electron-micrograph of testicular tissue from a man presenting with azoöspermia, and heterozygous for the Type IV CCR t(Y;12;15)t(Y;12) (q11.23;q21.2);t(inv(12);15(p11.2q21.2;q13);t(15;Y)(q13;q11.23). The translocation chromosomes have formed as a pentavalent, and as a small marker. The cartoon karyotype indicates the disposition of the chromosomes, according to this construction. This abnormal configuration was presumed to be the basis of the spermatogenic arrest. Neo Y = euchromatic Y material; PAR = pseudoautosomal region; N = nucleolar mass; M = marker chromosome (the 15;Y element). See also Figure 10–6. Source: From R Coco et al., A constitutional complex chromosome rearrangement involving meiotic arrest in an azoospermic male: case report, Hum Reprod 19:2784–2790, 2004, with the permission of the European Society of Human Reproduction and Embryology. 288  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY An assessment of possible viable imbalances will be helpful, along the lines of the discussion above about the rcp(2;18;11) and as illustrated in Figure 10–8. As noted above, Gorski et al. (1988) calculate an approximately 50% risk for spontaneous abortion, and 20% for a liveborn abnormal child. Liao et al. (2017) derive somewhat different figures of approximately 80% and 10%, respectively. Of course, each CCR is unique, and carries its own particular risk profile. The level of risk is related to the mode of ascertainment— whether through the birth of abnormal infants, multiple miscarriage, male infertility with abnormal spermatogenesis, or fortuitously—and to the family history. If multiple miscarriages have been the pattern in the family in the past, it is likely to continue to be so. In such cases, it may be that all unbalanced forms would lead to miscarriage. If abnormal infants have been born, carriers are likely to have a high risk for the same unfortunate event to happen again. For the three-way CCR, it may tentatively be justifiable to advise that, sooner or later, a normal outcome could possibly be expected. Thus, the couple may be willing to make continued attempts until a successful pregnancy is achieved, but in the realistic awareness that miscarriage may be the only outcome (Figure 10–12). As always, the pedigree should be studied in order to understand what might be the particular pattern of meiotic behavior with that particular CCR. Any optimism may need to be guarded, and the reality faced of a low or very low chance for a normal child. As for the exceptional CCR, from first principles the likelihood for a successful pregnancy would be even less. Prenatal Diagnosis Once a natural pregnancy from a CCR carrier parent is actually achieved, some may prefer initially to rely on first-trimester ultrasonography, declining invasive diagnosis and leaving early abortion to happen naturally if that would be the case, as an unfortunate previous miscarriage history might well cause a heightened sensitivity to the small risk associated with a prenatal diagnostic procedure. A noninvasive methodology could be applied, similar to the genome-wide NIPT approach that has been used in the setting of reciprocal translocations in which at least one predicted unbalanced segment is >15 Mb in size (Flowers et al. 2020). In that case, the CCR will need to be very precisely characterized cytogenetically in the parent and the fetus, in order to ensure accurate diagnosis. If the pregnancy continues normally according to ultrasound criteria into the Figure 10–12.  Multiple Pregnancy Loss. Note: Carriers of a three-way CCR are shown as half-filled symbols, small circles are miscarriages. The karyotype in the carriers is 46,XX or XY,t(1;8;11)(p31;q13;q23). Source: Drawn after N Trpchevska et al., A family study of complex chromosome rearrangement involving chromosomes 1, 8, and 11 and its reproductive consequences, J Assist Reprod Genet 34:659–669, 2017. Courtesy N Trpchevska, and with the permission of Springer.

Complex Chromosomal Rearrangements  289 second trimester, a judgment can be made whether this of itself would be sufficiently reassuring (perhaps in the setting of all unbalanced forms being very unbalanced), or whether amniocentesis would in fact be desirable. On several levels, each case will have to be assessed on its merits. The same balanced state identified at prenatal diagnosis raises the same questions but more pointedly, as in the simple reciprocal translocation: has a cryptic and possibly pathogenic change happened? Molecular methodologies might allow a more precise determination. Prenatal detection of a de novo CCR is discussed on Chapter 22. Preimplantation Genetic Testing Given the high fraction of embryos expected to be chromosomally unbalanced, PGT would have an obvious attraction in order to select in favor of the few embryos—if such there be—that might be normal or balanced (Rossi et al. 2023). The odds are not in favor of the carrier, with a large majority (about 85%) of embryos typically proving to be unbalanced (Table 10–2), and this must be the realistic frame of mind in which couples might approach PGT (Li et al. 2020; Liu et al. 2024b). The case in Mas et al. (2018) is not atypical: from a man of karyotype 46,XY,t(2;4;14)(q21.1;p15.2;q22), all nine of nine biopsied blastocysts were imbalanced. Nevertheless, a faint hope may remain justifiable. For example, the woman carrying the CCR depicted in Figure 10–13 produced 11 embryos at IVF, of which just one had a balanced karyotype, the same as hers, and a normal baby resulted. Figure 10–13.  An Exceptional CCR from which a Baby was Born, following PGT. Notes: The heterozygote for this exceptional CCR had had two previous miscarriages. While just three chromosomes were involved in this CCR, there were 11 breakpoints, revealed at the molecular level following whole-genome low-coverage mate-pair sequencing, as 46,XX,der(1)t(1:4)(p22:q31.1),der(4) ins(5:4)(q22;q25q28)t(1:4),der(5)ins(5:4). Albeit that it was assessed that “there was very little possibility for her to give birth to a normal child through natural pregnancy”, one embryo at PGT proved to have the same balanced CCR, and a normal baby was born. Source: From J Ou et al., Successful pregnancy after prenatal diagnosis by NGS for a carrier of complex chromosome rearrangements, Reprod Biol Endocrinol 18:15, 2020. Courtesy G Fang, and with the permission of Springer Nature.

11 AUTOSOMAL RING CHROMOSOMES AUTOSOMAL RING CHROMOSOMES are uncommon, and it is even more uncommon for a person with a ring (or someone on his or her behalf ) to seek genetic advice about reproductive possibilities. The typical phenotype includes major dysmorphogenesis and intellectual disability, and procreation is not usually a relevant issue. But exceptions exist. Indeed, some persons with a ring chromosome appear to be of entirely normal phenotype. Only mild cognitive impairment or short stature with minor dysmorphism characterizes some other cases. The ring 20 has a unique association with epilepsy. It is these categories of normal or mildly abnormal phenotype—in other words, of possible reproductive potential—we particularly consider in this chapter, although at the outset we can state that only a very few examples of parental transmission of a ring chromosome are known, and almost all rings arise de novo. Rings come in two major categories: larger rings replacing a normal homolog, for a 46-chromosome count; and very small rings existing as a supernumerary 47th chromosome. Rings have been reported for every autosome (Figure 11–1). Mosaicism, typically with a normal cell line, is frequent. The ring X Turner syndrome variant and the “tiny ring X syndrome” are noted on p. 480, and the ring Y on p. 483. BIOLOGY There are two major and quite distinct types of ring chromosome that can be associated with either a normal phenotype or a clinical picture of relatively mild mental compromise, growth restriction, and absence of major malformation. First is the full-length or nearly full-length ring that replaces one of the normal homologs with the karyotype 46,(r), and in which any imbalance is due to loss of distal segments.1 Second is the very small ring typically comprising pericentromeric chromatin, which exists as a supernumerary chromosome, with the karyotype 47,+(r); here, the imbalance comprises gain of proximal segments. On classical cytogenetics, a ring is very obvious to see. With microarray, recognition of a ring is indirect. The observation of p and q telomeric deletions on the same chromosome would point to the likelihood of 46,(r), but a classical karyotype would be needed for definitive confirmation. A 46(r) with deletion of just one arm would not be distinguishable from a simple linear deletion, while 46(r) rings in which the telomeres are retained would typically return a normal microarray result. 47,+(r) rings could be suspected on the basis of a duplication containing a centromere, but again final proof would require classical karyotyping. If, on next-generation sequencing, a DNA fragment 1 A formal report might include the format such as ::p11→q21:: to show the breakpoints :: at p and q, book-ending the chromosomal segment that is retained. 292  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY containing sequences from both p and q arms were seen, this would allow the inference of a probable ring structure (Chai et al. 2020), but a telomere-to-telomere fusion could only be discovered on classical cytogenetics (Burgemeister et al. 2017). Individuals with either of these types of ring, the 46(r) or the 47,+(r), may have intact fertility, and they may present with questions about risks to their offspring. A third type of ring, in which the phenotype would always be abnormal, may have a complex structure at the breakpoint junctions with terminal deletions and duplications (Guilherme et al. 2013); we do not further discuss this category. We deal with the first two categories separately, and list representative reported cases of individual ring chromosomes. The Apparently Balanced or Nearly Balanced Ring Chromosome, 46,(r) We may list these theoretical mechanisms that could lead to the generation of a ring that might appear, at least on classical cytogenetics, to be balanced, and as depicted in Figure 11–2: 1. Deletion of “small” but nevertheless critical amounts of euchromatin at distal p and/or distal q arms, with fusion of the exposed ends (Figures 11–2a). 2. Fusion of telomeres, without loss of other chromosomal material; thus, truly balanced in terms of the amount of chromatin (Figure 11–2b). 3. Deletion of subtelomeric material at terminal p and/or q arms with fusion of the exposed ends, with only some repetitive subtelomeric segments lost (Figure 11–2c). Figure 11–1.  The observed frequency of rings for the individual autosomes. Source: Redrawn from P Li et al., The past, present, and future for constitutional ring chromosomes: A report of the international consortium for human ring chromosomes, HGG Adv 3:100139, 2022. Courtesy T Liehr, and with the permission of Elsevier.

Autosomal Ring Chromosomes  293 In the first scenario (Figure 11–2a), and if the deletions include actual genes, and if these genes are dosage-sensitive, then due to this very fact there would be a phenotypic effect. It is not surprising that those chromosomes with a lesser load of genes are the more often observed (Figures 11–1 and 11–3). Where only telomeric or subtelomeric sequences are lost (Figures 11–2b, c), no genes are lost, and there is thus no haploinsufficiency. Nevertheless, the circular structure of the ring may of itself compromise post-zygotic mitotic cell division. The rings can become entangled, broken, doubled, or otherwise disrupted following sister chromatid exchange during the cell cycle (Figure 11–4). Thus, daughter cells arise that could be partially or totally aneuploid (whether trisomic or monosomic) for the chromosome in question: this is “dynamic mosaicism.” These cells might die; some, however, could survive in the mosaic state and presumably make an unfavorable contribution to the phenotype. This continuous generation and loss of cells could undermine the growth rate, although it might not greatly influence the quality of growth. The result is the “general ring syndrome”—whichever autosome is concerned— of growth retardation, mild to moderate cognitive impairment, minor dysmorphogenesis, and, perhaps, intact fertility (Kosztolányi 1987; Li et al. 2022c). Intriguingly, the trivial but perhaps diagnostically helpful sign of café-au-lait macules is quite often seen (Sodré et al. 2010). MEIOSIS Almost all instances of parent-to-child ring transmission involve the mother as the carrier parent (MacDermot et al. 1990). This reflects the fact that spermatogenesis is compromised in the presence of a ring chromosome, and infertility is the consequence for most male heterozygotes (Rajesh et al. 2011). In the potentially fertile 46,(r) heterozygote, the expectation at gametogenesis would be, in principle, for symmetric disjunction Figure 11–2.  Different Mechanisms that can Lead to the Formation of a Ring. Notes: Breakpoints (red flash) proximal to the telomeres (a), with loss of distal p and q arm specific sequences; Breakpoints within telomeric sequences (b and c), with no loss of unique sequence. Source: From A Peron et al., Ring chromosome 20 syndrome: Genetics, clinical characteristics, and overlapping phenotypes, Front Neurol 11:613035, 2020. Courtesy A Peron, and with the permission of Frontiers in Neurology. 294  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY with 1:1 segregation of the ring and the normal homolog (Figure 11–5). Thus, half of the conceptuses would be entirely normal karyotypically, and half would carry the ring. If “dynamic mosaicism” then occurs, these latter may be lethal in utero, or those surviving to term might have phenotypic abnormality. In fact, at least from the male heterozygote in whom some spermatogenic capacity is retained, there may be an intragonadal selection against ring forms, such that production of normal sperm is favored (Nishikawa et al. 2018). Otherwise, in the case of the heterozygote who has mosaicism with a normal cell line on somatic testing, as is occasionally recognized, the fraction of 46(r) conceptuses would in theory be less, according to the fraction of the gonad-containing ring cells. We list commentaries on the individual ring chromosomes below. In a few, there has been an association with phenotypic normality or near-normality and parenthood, and it is to this category that we pay greater attention. The reader seeking wider and more up-to-date data is directed to the registry websites listed in Li et al. (2022c). Kushwaha et al. (2024) provide a review of considerable number of cases, followed up over some several decades, seen at a single laboratory. Ring 1, 46,r(1). A ring for the largest chromosome is almost unknown (Gardner et al. 1984; Cutenese et al. 2000). Ring 2, 46,r(2). Prenatal and post-natal growth retardation and microcephaly are consistent features (Sarri et al. 2015). Lacassie et al. (1999) summarize eight published cases and provide a photographic record of their own patient from birth to age 10 years, a microcephalic child with some mild cognitive and behavioral compromise, and profoundly growth retarded. The format as shown in Figure 11–2a was proven in the case in Severino et al. (2015), whose severely affected patient had, on microarray, a loss at distal 2p of only chr2:1-0.469 Mb, as well as a substantial 2qter deletion comprising chr2:238.7 Figure 11–3.  The gene-density of chromosomes (green), plotted against the relative frequencies in % of observation (brown) of rings for that chromosome. Note: Overall, the more gene-dense a chromosome is, the less likely it is that a ring of that chromosome is observed; and vice versa. Source: From P Li et al., The past, present, and future for constitutional ring chromosomes: A report of the international consortium for human ring chromosomes, HGG Adv 3:100139, 2022. Courtesy P Li and T Liehr, and with the permission of Elsevier. Autosomal Ring Chromosomes  295 Mb-qter. Prenatal diagnosis is recorded (Chen et al. 2012). A single case of parent-to-child transmission is known (Giardino et al. 2002). Ring 3, 46,r(3). The mechanism of deletion of one arm and fusion with the intact other arm is exemplified in the case in Guilherme et al. (2011), in which there was a 5.7 Mb loss at distal 3p (3p26). The 10-year-old boy was growth retarded, had a mildly Figure 11–4.  Dynamic Mosaicism. The single-chromatid ring chromosome replicates during interphase. Sister chromatid exchanges (SCEs) may, or may not, take place. At meiosis, if there are no SCEs (left), segregation is symmetric (dotted arrows represent spindles drawing homologs to opposite poles). If there is one SCE, a double-sized ring is generated (middle). With each centromere being tugged to opposite poles at anaphase (dotted arrows), the chromosome may break. If there are two SCEs, in the same “direction of rotation” (right), the two rings become interlocked. Breakage, or other mechanical compromise, is the consequence. A second SCE in the opposite direction of rotation would restore the situation.

296  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY dysmorphic facies, and had a degree of intellectual disability. Barely double figures of this ring are recorded in the review of Zhang et al. (2016b); these authors describe their own r(3) case with a 10 Mb deletion at 3p. Ring 4, 46,r(4). Sigurdardottir et al. (1999) describe a growth-retarded infant with normal developmental progress and whorled skin areas of hyperpigmentation and hypopigmentation. The r(4) was a true telomere-to-telomere fusion (Figure 11–2b), as demonstrated with FISH. A similar story is told in Burgemeister et al. (2017), who conclude that the concept of the “general ring syndrome” is supported by such cases in which no genetic material is lost. We have seen a man with 46,XY,r(4) manifesting the presumed general ring syndrome: He was considerably shorter than his brothers, and his occupation of warehouse manager compared with the professional qualifications of his siblings. Nevertheless, he could fully appreciate the genetic implications of his condition, and he and his wife chose to have donor insemination. Irregular synapsis of the ring and the normal homolog at meiosis may be the basis of infertility (Figure 11–6). A single case is on record of presumed maternal gonadal mosaicism for a ring 4, a mother having had two children with this ring, with the same p and q arm deleted segments in each (Phillips et al. 2021b). If the ring formed following terminal deletions, the individual might or might not present a Wolf-Hirschhorn syndrome phenotype, according to the extent of the deletion into 4p (Yao et al. 2014). Ring 5, 46,r(5). Familial transmission of a r(5) is rare, but recorded in a case of mild phenotype reflecting the general ring syndrome (MacDermot et al. 1990). A ring 5 with a substantial 5p deletion may lead to cri du chat syndrome (Nozawa et al. 2020). Ring 6, 46,r(6). Urban et al. (2002) and Liu et al. (2018) reviewed 33 published cases. Hydrocephalus was a common observation. At one end of the spectrum, malformations and microcephaly with severe disability are typical (Zhang et al. 2016c). At the other end of the spectrum, a much milder phenotype of growth retardation evokes the general ring syndrome. An example is provided by the case of a young woman with mild dysmorphism and short stature, but normal psychomotor development and intact fertility (her son had a normal karyotype), reported in Höckner et al. (2008). A single case of parental transmission of a r(6) is described in Dong et al. (2022). A small-for-dates child with r(6) Figure 11–5.  Meiosis in the Ring Carrier. Meiosis with symmetric segregation in the ring heterozygote. Autosomal Ring Chromosomes  297 was born to a mother of normal intellect and short stature, she having the mosaic karyotype 46,XX,r(6)[44]/47,XX,r(6),+r(6)[2]‌/46,XX[15]. Ring 7, 46,r(7). Microcephaly with intellectual disability is a typical presentation. Cleft lip and palate is a common feature (Bangun et al. 2024); Roy et al. (2012) document an association with skin nevi. Ring 8, 46,r(8). Variable cognitive capacity, including normality, was observed in the family described in Le Caignec et al. (2004), in which the ring 8 chromosome, transmitted from mother to son and likely also carried by grandmother and uncle, was determined to have no loss of euchromatin. No other familial case is on record. A man having a ring 8 with megabase-size deletions at 8pter and 8qter, and whose cognitive impairment was less marked than in most r(8) cases, proved to be mosaic, with a upd(8) pat 46,XY cell line (Gradek et al. 2006). The probable sequence was as follows: 46,r(8) at conception; mitotic loss of the ring to give a 45,–8 cell; and subsequent “rescue” of Figure 11–6.  Incomplete Synapsis in Meiosis of the Ring 4 and its Homolog. Notes: This study was made on testicular tissue from a man having presented with severe oligospermia, he showing the mosaic karyotype 46,XY,r(4)(::p16.3→q35.2::)[31]/45,XY,-4[3]‌. Staining (below) with red (SPC3) reveals synaptonemal activity; with green (BRCA1) identifies regions of transcriptional inactivation; and with blue identifies centromeres. The X-Y bivalent is closely associated with the no. 4 bivalent. Diagram (above) shows the ring in green, the normal homolog in blue, and the region of synapsing in yellow. Source: From Q Yao et al., Meiotic prophase I defects in an oligospermic man with Wolf-Hirschhorn syndrome with ring chromosome 4, Mol Cytogenet 7:45, 2014. Courtesy Y-X Cui, and with the permission of Springer Nature.

298  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY the monosomic line by duplication of the normal (paternal) homolog. This mechanism may have operated in some other ring cases in which there is an accompanying normal cell line. Ring 9, 46,r(9). The typical phenotype in the r(9) is comparable to that of deletion 9pter and 9qter cases, according to the extent of the deleted segments (Purandare et al. 2005; Sheth et al. 2007; la Cour Sibbesen et al. 2013). Common elements include dysmorphism, microcephaly, cardiac malformations, growth and psychomotor retardation, and skeletal anomalies. A particular feature may be ambiguous genitalia or, sometimes, sex reversal, caused by deletion of DMRT1 on 9p. 9q deletions including the EHMT1 locus contribute a component due to Kleefstra syndrome (Chapter 14) to the overall picture. The picture may be more complex than a simple end-to-end fusion, as exemplified in the intra-ring duplication seen in the case in Chai et al. (2020). No familial case is known. Nevertheless, if no euchromatin is deleted, infertility may be the only abnormality (Laursen et al. 2015). Ring 10, 46,r(10). Practically every case has presented a picture of growth and psychomotor retardation, congenital malformation, and dysmorphism (Pruccoli et al. 2021). Ring 11, 46,r(11). A notable and unique example of familial transmission of a ring 11 chromosome is given in Hansson et al. (2012), who report a child, her mother, and her aunt each with a r(11), all three short and microcephalic, but only the child with a mild developmental (language) delay. All three had café-au-lait macules. The grandmother presumably carried the same chromosome. A deletion at 11p, chr11:1-565,839(hg19), encompassed 20 genes; there was no loss at 11q. The mosaic complexity that can characterize the ring is well illustrated by the case in Galvão Gomes et al. (2017), with the karyotype 45,XY,‒11[18]/46,XY,r(11)[78]/ 46,XY,dic r(11;11)[4]‌dn. Loss of an 8.6 Mb segment in 11q24.2qter in the major cell line led to a Jacobsen syndrome phenotype (Chapter 14). Ring 12, 46,r(12). Parmar et al. (2003) review the findings in six cases of 46,r(12). Growth retardation and intellectual compromise of varying degree were consistent features. In one 46,XY,r(12)(p13q24.3)[85%]/46,XY[15%] mosaic case, a man in his 20s presented with infertility associated with severe oligospermia; the diagnosis led to retrospective review, and it was noted that he had been assessed as a child for delayed learning and microcephaly (Martin et al. 2008). He also had a number of café-au-lait skin macules, misleadingly the basis of a previous diagnosis of neurofibromatosis; but as noted above, this sign is observed in a number of ring chromosome syndromes. The man described in Chen (2024c), a qualified engineer, presented with infertility due to oligospermia, and in spite of his normal phenotype otherwise, the ring 12 was deleted for twenty loci; it is likely he was protected by mosaicism with a normal cell line. Ring 13, 46,r(13). The typical phenotype, due to the distal 13q deletion component of the ring, presents microcephaly and poor psychomotor development, and genital malformation (Walczak-Sztulpa et al. 2008). The mitotic instability imposed by the presence of the ring is attested in the study of Petter et al. (2019), who, in analyzing 500 cells in each of three cases, documented a long list of variations on the theme of chromosome 13 imbalance. If there is loss only of subtelomeric material (Figure 11–7), familial transmission is possible. Bedoyan et al. (2004) report mother-to-daughter transmission of a ring 13 chromosome: the mother attended a special school, and at age 21 years she “showed no difficulties with speech, could read a newspaper, and worked as an assistant in a day-care center.” Her daughter had presented with delayed language development. A single case of infertility but otherwise normality is recorded in a man with the mosaic Autosomal Ring Chromosomes  299 karyotype 46,XY,r(13)[24]/45,XY,-13[4]‌/46,XY,dicr(13;13)[2] (Zamanian et al. 2023). Somewhat similarly, Kaya et al. (2022) describe a mildly intellectually disabled man having presented with infertility, who was mosaic for a ring 13 in which only 1.5 Mb was deleted at 13qter. Sequential prenatal diagnoses of r(13)/monosomy 13 mosaicism, the parents of normal karyotype, is recorded in Chen et al. (2021a). Quite a substantial length of 13q was deleted. At least in the second studied case, fetal malformation was severe. Marker analysis showed the ring to be of maternal origin, allowing an interpretation of maternal gonadal mosaicism. Ring 14, 46,r(14). This chromosome is somewhat prone to ring formation, with over 60 cases reported (Zollino et al. 2012; Meza-Espinoza et al. 2024). About a quarter of cases are shown on microarray to have no loss of genetic material, and in the remainder, 14q deletions vary in length from 0.3 Mb to 5 Mb. A degree of genotype-phenotype distinction with respect to 14q deletion/nondeletion can be drawn: the characteristic facies and poor behavior are more prevalent with larger deletions. There is a distinctive facies; intellectual disability is practically universal; epilepsy is common; and eye defects of various kinds are frequent. When no genes are lost, the latter two traits may result from silencing of (structurally intact) loci in the proximal long arm, possibly due to a spread of inactivation from nearby 14p material. As direct evidence of an epigenetic effect, Guilherme et al. (2016) showed downregulation at two of eight studied loci in one patient. Given the fact of chromosome 14 being subject to a parent-of-origin effect, it is notable that uniparental disomy is not observed. The scenario of a simple end-to-end fusion in ring formation, as might often be suspected prima facie, may not always reflect reality. Knijnenburg et al. (2007) studied a girl, noting that she showed signs both of deletion and duplication for chromosome 14. She turned out indeed to have a del/dup, and in fact also a triplication rearrangement, within the r(14). Figure 11–7.  FISH demonstration of a 13q subtelomeric deletion in a ring 13 chromosome. Note: Green stain shows hybridization of a centromeric probe (cep) recognizing 13 (and 21) sequence; red shows hybridization of a probe recognizing subtelomeric (13q34) sequence. The absence of red signal in the ring reflects the subtelomeric deletion. Source: From R Guilherme et al., Human ring chromosomes—New insights for their clinical significance, Balkan J Med Genet 16:13-20, 2013. Courtesy T Liehr, and with the permission of the Macedonian Academy of Sciences and Arts.

300  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY As for transmission of the ring, Bowser-Riley et al. (1981) described a 46,XX,r(14) mother “at the lower end of the normal range” of intelligence, who had two intellectually disabled 46,XX,r(14) daughters and a third 46,r(14) pregnancy which was terminated. A curious case is that of Matalon et al. (1990), a mother mosaic for r(14) and a balanced rob(14q21q), who had had two mentally affected r(14) children. In the review of Zollino et al. (2012), one patient had a healthy parent, the father, who had a r(14) in 1% of cells on blood analysis, revealing him to be a somatic-gonadal mosaic for the ring. Ring 15, 46,r(15). The range of clinical phenotype is recorded in Paz-Y-Miño et al. (2018) (Figure 11–8). Short stature is prominent if the deletion includes the IGFR1 locus at distal 15q (Guilherme et al. 2011, 2012). We have seen a young woman in whom a suspicion of Turner syndrome was the grounds for karyotyping (Gardner et al. 1980), as also have Glass et al. (2006) and likely, we imagine, several other observers. Pigmentary mosaicism is quite frequently observed (Figure 11–9) (Boente et al. 2011). Mother-to-child transmission of 46,r(15) is recorded (Horigome et al. 1992). Nishikawa et al. (2018) made the notable observation in the case of a man diagnosed with severe oligospermia and seeking IVF with ICSI and PGT in order to avoid passing the ring 15 on to a child of his, that all sperm were chromosomally normal. Ring 16, 46,r(16). In a child with autism but no physical anomalies, Conte et al. (1997) found an r(16) with apparently no loss of genetic material, and in mosaic company with a normal 46,XY cell line. Six other cases reviewed by these authors had different karyotypes, some with 45,–16 mosaicism, and the phenotypes of these, and of a subsequent case reported in He et al. (2002), were more severe. It is certainly rare (Cignini et al. 2011). Ring 17, 46,r(17). Ring 17 has a particular association with epilepsy which, in the mosaic state, may exist in the context of intellectual normality (Coppola et al. 2017; Tempone Cardoso Penna et al. 2023). The clinical picture can be mild if loss of chromatin is small and LIS1 is retained, but severe if the loss of genes includes LIS1, the Miller-Dieker locus at 17p13.3 (the distalmost 17p band) (Kim et al. 20252). The single instance of familial transmission of r(17) mosaicism is recorded in Surace et al. (2014): a Figure 11–8.  Frequencies of Certain Clinical Features in Ring 15. Note: These data are based upon the authors’ own case, and 98 from the literature. Source: From C Paz-Y-Miño et al., Ring chromosome 15—cytogenetics and mapping arrays: a case report and review of the literature, J Med Case Rep 12:340, 2018. Courtesy C Paz-Y-Miño, and with the permission of Springer Nature. 2 The clinical picture in the child in Kim et al. may have been exacerbated by loss of a VPS53 allele within 17p13.3, exposing a recessive potentially pathogenic variant on the intact homolog; VPS53 is the basis of pontocerebellar hypoplasia type 2E. Autosomal Ring Chromosomes  301 cognitively normal mother displayed only café-au-lait macules, while her daughter suffered epileptic encephalopathy. These authors discuss the intriguing concept that retention of telomeres in a ring may be associated with a milder phenotype, while loss of telomeres, albeit that no genes are removed, could lead to an epigenetic ill-effect. Ring 18, 46,r(18). As Carter et al. (2015) note in their extensive review, this was one of the first ring syndromes to have been discovered, in the early 1960s. They record the interesting historic point that pioneer French cytogeneticist Jean de Grouchy’s prediction that the gene for aural atresia would lie at 18q was vindicated a half-century later. Consistent features include microcephaly, intellectual disability, seizures, maxillofacial dysmorphism, and clefting (Wang et al. 2021). Parental transmission is rarely reported (Balci et al. 2014). Yardin et al. (2001) document the history of a woman with the ring 18 and monosomy 18 mosaicism, her karyotype 46,XX,r(18)(p11.3q23)[32]/45,XX,–18[4]‌. Of six pregnancies, chromosome analysis was done in three, all showing the r(18)—two being children, one similar to herself, and the other apparently normal as a newborn; in addition, there was a terminated pregnancy following amniocentesis, a child dying as a neonate, and two miscarriages that were not karyotyped (Figure 11–10). Ring 19, 46,r(19). Given the rarity of r(19), and with number 19 being the most gene-dense of all the chromosomes (Table 1–1), the fact of even a single familial case is remarkable. Flejter et al. (1996) describe a normal mother having ring 19 mosaicism, 46,XX,r(19)/46,XX, but with only 4% of cells (lymphocytes) having the ring, while her abnormal daughter was 46,XX,r(19) in 98% of cells. Speevak et al. (2003) write of the counseling dilemma at the incidental discovery of non-mosaic r(19) at prenatal Figure 11–9.  Pigmentary Mosaicism in a Child with Ring 15. Note: Both hyperpigmentation and hypopigmentation are to be observed. Source: From C Ribeiro Dias Barroso et al., Cutis tricolor parvimaculata in ring chromosome 15 syndrome: A case report, Pediatr Dermatol 35:e204-e205, 2018. Courtesy C Ribeiro Dias Barroso, and with the permission of John Wiley & Sons.

302  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY diagnosis from a normal mother with the same very low fraction (4%) of cells with r(19), the ring assessed as being an end-to-end fusion (Figure 11–2 b or c). Ring 20, 46,r(20). Two main forms exist: (1) a mosaic karyotype of mitotic origin, with end-to-end fusion of one chromosome 20; and (2) a non-mosaic type, the ring having deletions of p arm or q arm, or of both arms, and having arisen at meiosis (Conlin et al. 2011; Daber et al. 2012). The non-mosaic form presents the more severe picture. Epilepsy is the notable clinical feature, with the onset of seizures typically at a younger age in the non-mosaic form (Peron et al. 2020; Paprocka et al. 2024). There may be an earlier period of normal mental development, which slows following the onset of epilepsy. In childhood onset, a clinical pointer may be an association with terrifying hallucinations as part of the seizure. The age of onset of epilepsy correlates with the degree of mosaicism: the higher the fraction of r(20) cells, the earlier the onset (Figure 11–11). The electroencephalogram (EEG) has a characteristic pattern, with trains of “theta waves.” Any patient with treatment-resistant epilepsy who has long runs of epileptiform activity on the EEG in the non-seizing state (which may or may not be associated with confusion or diminished consciousness) should be tested with this ring chromosome Figure 11–10.  Familial Transmission of a Ring 18 Chromosome. Notes: Half-filled symbols = proven r(18) heterozygosity with mosaicism for monosomy 18; grey symbols = suspected r(18). The mother I:2 was described as manifesting short stature, cleft palate, and mild cognitive impairment, and of karyotype 46,XX,r(18)(p11.3q23)[32]/45,XX,–18[4]‌. Her child II:1 died at age 2 days. The tested cases II:2, 3, and 6 all showed the r(18) along with monosomy 18 in mosaic state, as in the mother. II:3 was a terminated pregnancy; II:4 and 5 were untested miscarriages. Source: Redrawn from C Yardin et al., First familial case of ring chromosome 18 and monosomy 18 mosaicism, Am J Med Genet 104A:257-259, 2001. Courtesy C Yardin, and with the permission of John Wiley and Sons. Figure 11–11.  The Age of Onset of Epilepsy in Ring 20 Mosaicism. Notes: The age of onset is shown correlating with the fraction of cells that are r(20). Source: From A Peron et al., Ring chromosome 20 syndrome: Genetics, clinical characteristics, and overlapping phenotypes, Front Neurol 11:613035, 2020. Courtesy A Peron, and with the permission of Frontiers in Neurology. Autosomal Ring Chromosomes  303 in mind; James et al. (2024) emphasize the need for a classical cytogenetic study, since molecular methodologies will often not discover a ring. The mechanism whereby the genomic alteration due to the ring causes the susceptibility to epilepsy is yet to be clarified (Myers et al. 2021a). Familial transmission is recorded (Unterberger et al. 2019). An otherwise unaffected parent with a lower level of mosaicism can have affected children with the ring chromosome in higher proportion (Canevini et al. 1998). Thus, Herrgård et al. (2007) document a mother with 10% r(20) mosaicism, who had an onset of seizures in her mid-20s and who was intellectually normal. Her daughter had epilepsy from age 7 years, and cognitive capacity fell away in subsequent years; her son was always behind in development, showed poor behavior, and had seizures from age 5 years. These children both had 40% of their cells with the r(20). Ring 21, 46,r(21). The cognitive phenotypes can vary from normal to severe, and the degree of mosaicism for monosomy 21, a frequent concomitant, is likely a major factor in this respect (Ambulkar et al. 2023). A child we followed up into adulthood achieved tertiary education and was a skilled musician; but he was, as can often be the case with the male r(21) heterozygote, infertile, with azoöspermia (Dallapiccola et al. 1986; Gardner et al. 1986b). A sperm study on a ring 21 infertile man with an extremely low sperm count, karyotyping 45,XY,–21[3]‌/46,XY,r(21)[95]/46,XY[2] on blood and with fairly similar proportions on buccal cells, came up with an interesting result: FISH showed most (92%) of 169 spermatozoa to be normal, 7% with the ring, and 1% disomic with the normal 21 and the ring 21. These authors suggested that the (presumed) small fraction in the gonad of normal spermatogonia were selectively favored at meiosis, leading to the majority of gametes being normal (Hammoud et al. 2009). Parent-child transmission, and indeed grandparent-parent-child transmission, is well known (Bertini et al. 2008b). Bertini and colleagues describe a mother-daughter, each having the same karyotype on blood, 46,XX,r(21)/45,XX,–21, the ring being the majority species in each (98% and 94%, respectively). In this instance the rearrangement was due to a subtelomeric 21q deletion of 3.4 Mb, and apparently no critical dosage-sensitive genes had been lost. A transmitting father in Papoulidis et al. (2010) had just one cell out of 100 with the ring (discovered after the birth of his child), presumably reflecting a somatic-gonadal mosaicism; the ring 21 child was normal on assessment at 10 months. Counseling in the event of a prenatal diagnosis of non-mosaic r(21), the parent being mosaic for the ring, is challenging (Mazzaschi et al. 2011). Three-generation kindreds are described in Falik-Borenstein et al. (1992) and Melnyk et al. (1995). In one family, a 46,XX,r(21) heterozygote had had seven pregnancies with four early miscarriages, one normal son, one son with Down syndrome, and one 46,XX,r(21) daughter, the latter herself having a 46,XX,r(21) daughter (Figure 11–12). Most karyotyped cells in these individuals were 46,r(21), but a few were 45,–21, and some had a double-size or multi-size rings. Short stature, but normal IQ/development, accompanied the abnormal karyotype in these females; one male heterozygote may have had a low-normal intelligence. In another family, a 46,XX,r(21) mother had a prenatal diagnosis that showed one 46,XY twin and the other with 46,XX,r(21)/45,XX,–21 mosaicism. Both babies were normal, and the girl’s post-natal karyotype was non-mosaic 46,XX,r(21). The ring 21 might of itself predispose to the generation of a trisomy 21 karyotype, either 47,+r(21) or a recombinant 21 (Kosztolányi et al. 1991; and Figure 11–12). In their review of this circumstance, Muroya et al. (2002) illustrate a reverse picture: a normal

304  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY mother with a rather complex der(21) who had a mildly intellectually disabled son with 46,XY,r(21) and 4/100 cells 45,XY,–21. Ring 22, 46,r(22). A handful of inherited cases are on record (Teyssier and Moreau 1985; Crusi and Engel 1986; Wenger et al. 2000). In some, the ring was inherited from a phenotypically normal parent to phenotypically normal offspring, and presumably in these no crucial genetic material had been deleted. Male infertility may be a concomitant (Zuccarello et al. 2010; Sha et al. 2012). In other cases, one or more of the family members with the ring have had mental compromise or other clinical features. A parent may be mosaic and the child has inherited the ring in a non-mosaic state, which may substantially explain observed parent-offspring differences in phenotype. In one notable case, the mother’s tip-to-tip r(22) underwent change in transmission to her affected child, in whom part of the 22q segment had been deleted (Jobanputra et al. 2009). The r(22) mother in Wenger et al. (2000) had required special education in high school. Her son had bowel and heart defects, with very little language development by age 20 months. (By a strange coincidence he had, on his other chromosome 22, a de novo del 22q11.2.) Phelan-McDermid Syndrome. Some ring 22s have a more proximal q arm breakpoint and are deleted for the 22q13.33 region, which is the basis of the Phelan-McDermid syndrome (Chapter 14); haploinsufficiency for the SHANK3 gene is the key pathogenetic factor. The severity of the phenotype is proportional to the length of the deleted segment. The ring formation can be complicated, and Khalifa et al. (2022) describe a child in whom a r(22) carried a concomitant 4.4 Mb deletion at 22q13.31q13.33 and a 3 Mb duplication at 22q13.2q13.31. While a number of loci were present in deleted or duplicated state, the authors concluded that the loss of one SHANK3 allele in the deleted segment was likely the major contributor to the phenotype, but that imbalance of the other loci would also have had an influence. Koza et al. (2023) propose a recurrence risk for r(22)-associated Phelan-McDermid syndrome of <2% if parental karyotypes are normal, but an increased risk if there is parental mosaicism for the ring, and a 50% risk if a parent is non-mosaic. Figure 11–12.  Pedigree of a Kindred within which is Segregating a Ring 21 Chromosome. Note: Half-filled symbol = heterozygote for r(21); N = normal chromosomes; Filled symbol = Down syndrome. Small symbols in generation III refer to miscarriages. The ancestral couple at generation I had not been karyotyped, but presumably one or the other was an obligate heterozygote (or at the very least, a gonadal mosaic). Source: From TC Falik-Borenstein et al., Stable ring chromosome 21: molecular and clinical definition of the lesion, Am J Med Genet 42:22–28, 1992. Courtesy JR Korenberg, and with the permission of John Wiley and Sons.

Autosomal Ring Chromosomes  305 A ring 22 may, of itself, function as a “first hit” in the generation of certain tumors. The gene for neurofibromatosis type 2 (NF2) is located at 22q12. The neural crest is the embryonic tissue that gives rise to the investing membranes of nervous system structures. Due to its mitotic instability, a cell line in this tissue might lose the ring and thus become monosomic for 22. Subsequently, a mutation occurring in the NF2 gene on the remaining intact homolog would be “exposed” and allow the development of a classic NF2 tumor, a schwannoma of the eighth cranial nerve, or a meningioma of the cranial or spinal meninges (Koza et al. 2023). NF2 may be present in as many as 16% of r(22) individuals (Ziats et al. 2020). A similar scenario has been shown with respect to the SMARCB1 gene, in a child (who also had Phelan-McDermid syndrome) presenting with an atypical teratoid rhabdoid tumor of the brain (Byers et al. 2017). THE SUPERNUMERARY SMALL RING, 47,+(R) The small, or very small ring as a 47th chromosome could as well be dealt with under the category “small supernumerary marker chromosome” (sSMC), but we nevertheless record them here, acknowledging their particular ring identity. These rings may have formed as in the 46,(r) story above, with (large) distal deletions and end-to-end fusion; or, the “Barbara McClintock mechanism” involving breaks at the centromere and in one arm, with material from only that arm then represented in the ring (Quinonez et al. 2017a). A supernumerary chromosome implies, naturally, a partial trisomy (but see “Supernumerary Ring with a Balancing Deletion” below). Generally, it is only when the ring chromosome is very small, or when there is mosaicism with a substantial fraction of normal cells—in other words, where the overall load of genetic imbalance is small—that a question of genetic risk for offspring of the heterozygote will be relevant. Post-natally ascertained cases have naturally presented with an abnormal phenotype, and some have been ascertained through (especially male) infertility (Slimani et al. 2020); but a fraction of cases come to attention fortuitously, some being phenotypically normal. The challenge raised at prenatal diagnosis of a small supernumerary ring chromosome is discussed in Joksic et al. (2024). Mosaicism complicates the interpretation. These very small rings are mitotically unstable, and this is presumably the basis of the frequently observed mosaicism (Spittel et al. 2014). A few cases are known in which a parent with low-level mosaicism has had an abnormal child with a higher proportion of the cells with the ring. The levels of mosaicism as determined from a peripheral blood sample may not necessarily reflect the levels in other tissues, and including brain; and in a number of rings, little correlation is recognized between the degree of mosaicism and the severity of phenotype. Small supernumerary rings have been reported for almost every autosome. Brief sketches of some of these follow, with particular reference to recorded cases in which a parent with the ring has had offspring. For several of the chromosomes, the genetic content of the rings may vary quite considerably, and thus it is not surprising that often no clearly consistent phenotype is observed between cases due to the same chromosome (and the factor of variable mosaicism, as just mentioned above, also influences the picture). Ring 1, 47,+r(1). Callen et al. (1999) and Bernardini et al. (2007) presented series of patients with very small supernumerary r(1) chromosomes ranging in phenotype from normal/infertility to abnormal, and showed that the size of the ring was correlated 306  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY with phenotype. Further cases are listed in Liehr (2025b), several being of normal individuals, discovered incidentally. Chen et al. (2013b) record 24 prenatal diagnoses, just one of which was due to parental (maternal) transmission. Several had fetal anatomical abnormalities; but in some proceeding to birth and followed up at least into infancy, the children developed apparently normally. A remarkable familial example is given in Kosztolányi et al. (2011), concerning a ring 1 chromosome of 28 Mb size, which increased in mosaic fraction with each generation and the phenotypes declining accordingly (Figure 11–13). Ring 2, 47,+r(2). A 47,XX,+r(2)/46,XX mother with minor facial dysmorphology, and apparently otherwise normal, had a son with mosaicism for the same tiny ring chromosome, who presented with intellectual disability and a psychotic disorder (Giardino et al. 2002). The ring was present in 54% of cells (peripheral blood) in the mother, and 80% in the son. A mosaic case in Liehr et al. (2007), a child with a r(2) comprising distal 2q elements with a neocentromere, had severe cognitive impairment and dysmorphic features. Ring 3, 47,+r(3). A normal mother and her normal infant son had the karyotype 47,+ r(3)/46, at frequencies of 33% (mother’s lymphocytes) and 41% (prenatal diagnosis in the son, amniocyte analysis) (Anderlid et al. 2001). Ring 4, 47,+r(4). Bonnet et al. (2006) review the supernumerary ring 4 and describe their own case of a child of low-normal intellect, in whom they demonstrated up to three copies of a very small ring chromosome, about 20 Mb in size, in 82% of cells. Three recorded diagnoses were from amniocentesis; all three pregnancies were terminated, with the very severe brain defect of alobar holoprosencephaly identified in one. Normality, other than male infertility, is on record, but rare (Slimani et al. 2020). Ring 5, 47,+r(5). Masuno et al. (1999) reported a child with minor dysmorphisms and no speech at age three years. A molecular dissection of a ring 5 allowed Hadzsiev et al. (2014) to propose that trisomy for the 21 Mb segment 5p14.1-cen, of which the Figure 11–13.  Pedigree of a Family in which a Supernumerary Ring 1 Chromosome is Segregating. Notes: Half-filled symbols = heterozygotes for a supernumerary r(1), the shading according to the mosaic load, at the level of blood testing. The maternal grandfather in generation I is phenotypically normal. The mother in generation II is very mildly dysmorphic, and cognitively normal. The daughter in generation III has a marked facial dysmorphism and “attends normal school with average performance.” The son is more severely dysmorphic and intellectually disabled.a a  The fact that the fractions of cells with the r(1) have increased with each generation may reflect “pseudo-anticipation,” whereby only those with a lesser fraction of the abnormal chromosome are able to reproduce. In other words, the reverse phenomenon could not happen due to the more severe phenotype, and reproductive incapacity, in those with higher fractions of the ring. Source: From G Kosztolányi et al., Mosaic supernumerary ring chromosome 1 in a three-generational family: 10-year follow-up report, Eur J Med Genet 54:152–156, 2011.

Autosomal Ring Chromosomes  307 ring was comprised, was the basis of the Binder maxillonasal malformation seen in their patient. Ring 6, 47,+r(6). The range of phenotypic abnormality is reviewed in Hurd et al. (2017). James et al. (1995) report a child with paternal uniparental isodisomy 6, in whom a r(6) of maternal origin was also observed. Ring 7, 47,+r(7). Tan-Sindhunata et al. (2000) describe a family in which the mother of low-normal intelligence, and two of her three children, had mosaicism for a very small supernumerary ring, 47,+r(7)/46,N. Although the fractions of mosaicism were similar in the three (~50%), the children were more severely affected, at least with respect to language acquisition, than their mother. Speculatively, this could reflect, in the mother, a lesser “ring load” in the brain. Her other child was normal. Similar 47,+r(7) cases are recorded in the reviews of Lichtenbelt et al. (2005) and Bertini et al. (2008a); in two, Silver-Russell syndrome was due to uniparental disomy (UPD) 7. The additional copies of the STX1A and LIMK1 genes in 7q11.23 (chr7:73.7 and 74.1 Mb, respectively) is common to many r(7) cases, and may contribute importantly to the developmental deficits. Of entirely different origin is the mosaic small r(7) in Louvrier et al. (2015), in which the 7 material was derived from the distal long arm, at 7q22.1q31.1, and in which mitotic stability was enabled due to the generation of a neocentromere. Ring 8, 47,+r(8). The ring 8 is among the less rare of the supernumerary rings (Shao et al. 2020a). It may impose a lesser degree of functional genetic imbalance, possibly reflecting a relatively low chromosome 8 pericentromeric gene density, and indeed normality is recorded. Daniel and Malafiej (2003) report a normal woman karyotyped incidentally (because she had had a child with Wolf-Hirschhorn syndrome) and who turned out to have a very small r(8) in 27% of lymphocytes. A phenotype suggestive of the MURCS3 association was seen in the patient of Loeffler et al. (2003), a mildly disabled teenage girl in whom 70% of cells contained a tiny r(8) chromosome. Filges et al. (2008) studied a developmentally delayed girl mosaic for a small ring 8 of 43.8 Mb size. Bettio et al. (2008) document a prenatally diagnosed de novo very small ring comprising about 5 Mb of proximal 8p and 8q euchromatin in mosaic state (50% of cells with the ring on chorion villus sampling, 90% at amniocentesis, and 96% at post-natal blood sampling). Although early infant development was within the normal range, by age three years it was clear that language acquisition was poor and that behavior was affected. Familial transmission is known. A normal father, a university graduate, with low-level mosaicism for a very small supernumerary r(8), had two non-mosaic 47,XX,+r(8) daughters (Rothenmund et al. 1997). They were intellectually disabled and displayed emotional immaturity, although their physical growth was normal. Ring 9, 47,+r(9). Supernumerary rings derived from the pericentromeric heterochromatin, with which chromosome 9 is well enriched, are likely harmless (Callen et al. 1991). In their review of ring chromosomes and a possible association with uniparental disomy, Anderlid et al. (2001) note a moderately disabled, non-dysmorphic girl with 36% mosaicism for a supernumerary ring 9. This, rather than the concomitant maternal UPD, was presumed to be the basis of her abnormal phenotype. Ring 10, 47,+r(10). A young woman with mosaicism (14% in blood, 16% in buccal mucosa) presenting only with short stature is reported in Trimborn et al. (2005). Sung et al. (2009) review three prenatal reports, and they describe their own case of mosaic 47,XX,+r(10)/46,XX detected at amniocentesis and confirmed in the newborn. The 3 Müllerian and renal aplasia, cervicothoracic somite dysplasia 308  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY child was apparently normal on assessment at age one year. The identity of the ring in the similar mosaic case of Lebedev et al. (2021) as having been derived from chromosome 10 is shown in Figure 11–14. Ring 11, 47,+ r(11). The case in Wang et al. (2023b) exemplifies the scenario of a supernumerary ring which is balanced by a concomitant deletion (See “Supernumerary Ring with a Balancing Deletion” below). Otherwise, supernumerary rings of chromosome 11 are almost unknown. Ring 12, 47,+r(12). No clear clinical phenotype has emerged, other than abnormality in all (Davidsson et al. 2008). Yeung et al. (2009) and Lloveras et al. (2013) document cases in which the supernumerary ring 12 included two copies of 12p, thus determining a Pallister-Killian phenotype (Chapter 14). Ring 13, 47,+ r(13). Surprisingly, for a “survivable” chromosome, supernumerary ring 13 is scarcely ever reported (Zeng et al. 2019). In the normal mother reported in Sun et al. (2023), whose case came to light following an ambiguous result at NIPT, the supernumerary r(13) was of substantial size, but balanced by a deletion of the same segment in one of the other no. 13 chromosomes. Ring 14, 47,+r(14). Infertility was the only presenting complaint in a man with a minute ring 14 reported in Stahl et al. (2007). The detailed formation of a r(14) was determined in the case of Castermans et al. (2008), showing the inverted “mirror” nature of the duplicated 14p13 to 14q12 segment. Ring 15, 47,+r(15). A very small ring 15 may be comparable, in terms of its genetic content, to the relatively common small bisatellited supernumerary chromosome (sSMC) 15 (Chapter 14) (Zou et al. 2006). An exceptional case in Adhvaryu et al. (1998) is that of a sSMC derived from chromosome 15 in grandparent (mosaic) and parent Figure 11–14.  A Supernumerary Ring 10 Chromosome. Notes: This small supernumerary ring 10 chromosome, initially called a marker, was seen following cordocentesis, the indication for the prenatal procedure being fetal nasal bone hypoplasia. Staining with whole chromosome painting confirmed the ring’s identity (less intense staining of the centromeric region of chromosome 1qh is also observed). Mosaicism was shown: 47,XX,+r(8)[18]/46,XX[5]‌. A healthy girl was born at term, and developing normally at age 1 year. Source: From IN Lebedev et al., Prenatal diagnosis of small supernumerary marker chromosome 10 by array-based comparative genomic hybridization and microdissected chromosome sequencing, Biomedicines 9:1030, 2021. Courtesy IN Lebedev, and with the permission of MDPI.

Autosomal Ring Chromosomes  309 (non-mosaic), evolving into a very small ring 15 in the grandchild. All three, and two other siblings with the sSMC, were normal. Ring 16, 47,+r(16). In the only reported case (from a prenatal diagnosis), Cignini et al. (2011) note major fetal abnormalities in association with non-mosaic 47,XY,+r(16). Ring 17, 47,+r(17). A mildly disabled boy with a supernumerary ring 17 is described in Dupont et al. (2003). Ring 18, 47,+r(18). Jenderny et al. (1993) describe a phenotypically normal mother with 47,XX,+r(18) in only 2/100 cells on blood analysis, the remainder being 46,XX, and who had had a daughter with non-mosaic 47,+r(18). Balci et al. (2014) record another normal mother with ring 18 mosaicism, in her case 47,XX,+r(18)(::p11→q21::) [10]/46,XX[90], who had a disabled son with 46,XY,r(18)[75]/46,XY[25] mosaicism; these authors showed more underlying complexity in the structure and formation of the rings than at first appreciated, in undertaking a SNP-array family study. A man with a VACTERL4-like clinical picture, and with a normal intellect, carried at low-level mosaicism a r(18) that endowed “octasomy” for an ~5 Mb segment of pericentromeric chromosome 18 (van der Veken et al. 2010). Ring 19, 47,+r(19). A few cases are on record, with phenotypes from mild (possibly reflecting mosaicism) through severe (Vaz et al. 1999). A familial case involving twins more likely represents a single affected conception than occult parental transmission (Shahwan et al. 2004). A normal mother with r(19) mosaicism came to attention only because she had had a child with defects probably due to a different, coincidental chromosomal imbalance (Argiropoulos et al. 2011). Ring 20, 47,+r(20). Guediche et al. (2010) provide a review of 13 cases, eight ascertained post-natally and five prenatally, with psychomotor and growth retardation as frequent but not universal observations. Kitsiou-Tzeli et al. (2009) document prenatal diagnosis following which the child, at age three months, was judged to be essentially normal; in contrast, Callier et al. (2009) describe dysmorphic features in an aborted fetus. The only example of parental transmission is in Pinto et al. (2005). A mother with borderline intelligence and a degree of body asymmetry had a child with dysmorphism and developmental delay. She karyotyped as 47,XX,+r(20)[8]‌/46,XX[42]; he was 47,XY,+r(20)[25]/46,XY[37]. Ring 21, 47,+r(21). A ring may result from a more complicated process than end-to-end fusions, as Villa et al. (2011) analyze in a child with minor dysmorphism and delay in language development: an initial trisomy 21 at conception gave rise to a large ring, which subsequently “deleted out” a segment, leaving a small ring comprising two noncontiguous regions. Ring 22, 47,+r(22). Mears et al. (1995) document a family in which a phenotypically normal grandfather and father were mosaic for a tiny ring 22 chromosome, 47,XY,+ r(22)/48,XY,+r(22),+r(22). A grandchild, also 47,+r(22)/48,+r(22),+r(22) but whose ring chromosomes had increased in size, had cat eye syndrome (CES) (Chapter 14). These phenotypic differences likely reflect the dosage effect of a CES critical region, with the child having more tissue with a larger ring and/or with two copies of the r(22) of wider body distribution (Figure 11–15). 4 Vertebral, anal, cardiac, trachea-esophageal, renal, limb association.

310  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY RARE COMPLEXITIES Supernumerary Ring with a Balancing Deletion. If a ring chromosome is derived from a segment of chromosome that has been deleted interstitially from an autosome, and if this newly generated ring contains the centromere (or a neocentromere; see below), it can, in some cases, be transmitted stably at mitosis. If so, the karyotype is balanced (Slimani et al. 2020; Sun et al. 2023), but the carrier can be at high risk to produce unbalanced gametes: the ring might be transmitted as a supernumerary chromosome, to give a partial trisomy; or the deleted chromosome is transmitted, for a partial monosomy. Further, mosaicism might supervene. Mantzouratou et al. (2009) studied embryos from a couple, the wife being 47,XX,del(22),+r(22) and herself normal. They had had two natural pregnancies, both mosaic 47,+r(22)/46, with the first producing an abnormal child and the second terminated after prenatal diagnosis. Following two PGT cycles, none of the embryos had received the normal, intact maternal chromosome 22, and thus none were transferred. Better fortune attended the intellectually normal mother in Wang et al. (2023b) with an ocular anomaly, who was mosaic for a del(11) balanced by a supernumerary r(11): mos 47,XX,del(11)(p14.3p11.2),+r(11)(::p14.3→neo→11.12::)[16]/ 46,XX,del(11)(p.14.3p11.2)[4]‌. In her first pregnancy, an abnormal fetus had the del(11) in non-mosaic form. A second pregnancy, enabled through PGT, had the del(11) + r(11) balanced karyotype, and a child born was normal. If a gene is disrupted in the process of ring formation, the phenotype may be impacted upon, such as Quinonez et al. (2017a) propose in an infertile man with Marfan syndrome, who had an apparently balancing supernumerary ring 15 (the fibrillin-1 gene being located at 15q21). If the ring is very small, the balancing deletion may be missed on classical cytogenetics, as Baldwin et al. (2008) describe in a mother whose karyotype at first sight was 47,XX,+r(4)/46,XX; but the small r(4) was in fact derived from a deleted segment of 4p on one of her chromosome 4 homologs. She was described as intellectually normal but with unilateral ear anomalies and minor visual deficiencies; this mild phenotype may have reflected a partial 4p monosomy in body tissue with the “46,XX” (but actually del 4p12-cen, chr4:45-50 Mb) karyotype. Her child, who inherited the small ring but not the balancing deleted 4, and thus with dup chr4:45-50 Mb, had a “mild speech delay.” Figure 11–15.  Pedigree of a Family in which a Supernumerary Ring 22 Chromosome is Segregating. Notes: The grandfather and father in generations I and II are phenotypically normal; the child in generation III has cat eye syndrome. Although there are similar fractions, as shown here, on blood karyotyping, of cells with the + r(22), the affected child had more cells with a larger ring, or with two copies of the ring. Source: From AJ Mears et al., Minute supernumerary ring chromosome 22 associated with cat eye syndrome: further delineation of the critical region, Am J Hum Genet 57:667–673, 1995.

Autosomal Ring Chromosomes  311 Formation of a Neocentromere. A fragment of a chromosome not containing a centromere would not normally be able to be transmitted during cell division. But if a “neocentromere” is generated on this fragment, its survival may be enabled as a “supernumerary marker chromosome.” The supernumerary r(13) seen in the abnormal child in Amor et al. (2005), a chromosome of quite substantial size was studied in detail, and while α-satellite-specific centromere protein CENP-B was absent, the critical histone H3-associated centromere protein CENP-A was present, allowing centromeric function. If the supernumerary ring balances a deletion, the physical phenotype may be normal as noted above, and such as Slater et al. (1999) show in an infertile but otherwise normal man. A segment was deleted from one chromosome 1, and this same segment (1p32p36.1) existed as a tiny supernumerary ring chromosome. This man thus has the karyotype 47,XY,del(1)(p32p26.1)+r(1)(p32p36.1). The ring chromosome was able to activate the formation of certain centromere-binding proteins, which presumably enabled its stable transmission. A similar circumstance is recorded in Knegt et al. (2003), in this case a phenotypically normal woman who had presented with recurrent miscarriage and in whom a tiny ring 13 chromosome was derived from an interstitial deletion of the segment 13q21.31q22.2. Amniocenteses in her fourth and fifth pregnancies demonstrated normal karyotypes. The cases in Wang et al. (2023b) and Quinonez et al. (2017a) described above involved supernumerary rings with a neocentromere. GENETIC COUNSELING Parental Karyotype 46,(r), Non-mosaic or Mosaic The great majority of transmitting parents are 46,XX,(r) mothers, reflecting that most male heterozygotes are infertile. Those offspring inheriting the ring could be expected to present a clinical picture at least similar to, and indeed quite probably more severe than their heterozygous parent. In the review of Kosztolányi et al. (1991), about one-third of familial 46,(r) children were more severely affected mentally than their parent. The 46,(r) parent may be an atypical ring carrier, perhaps having had a fortunate pattern of mitotic disruption, to have reached the level of social phenotype wherein procreation would be likely. The risk is such, certainly for the female carrier, that the attraction of prenatal diagnosis or preimplantation testing is readily apparent. In the case of a male carrier with some retained spermatogenic capacity, and resorting to IVF with ICSI, preliminary data suggests that normal sperm are favored. In the person who is mosaic on somatic (blood) analysis, with a 46,N/46,(r) karyotype, the mosaicism might extend also into the gonad. This would convey an important risk to have a non-mosaic 46,(r) child—and, even if this might overstate the case, this risk would need to be assumed to exist. Quantifying the risk would be most imprecise: as high as 50%, as low as (almost) zero, but anywhere between. In the particular case of the 46,r(21) heterozygote, who is often phenotypically normal, there is a small but as yet unquantified risk of having a child with Down syndrome due to an uncommon karyotype: 47,+r(21), 46,rob(21q;21q), or 46,tan dup(21q;21q) (Kosztolányi et al. 1991). If, in prenatal diagnosis for a pregnancy of a r(21) heterozygote parent, the same r(21) karyotype were demonstrated in the fetus, based on the slender evidence thus far available the chance for phenotypic normality would seem to be “substantial,” but a (probably mild) degree of abnormality could by no means be excluded. As 312  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY noted above (Hammoud et al. 2009), gametogenesis (if fertility is retained) in the mosaic 46,N/46,r(21) male may favor the production of chromosomally normal spermatogonia. Rings of chromosomes 11, 17, 21, and 22 may predispose to cancer, presumed, in some at least, due to sequential events in susceptible tissue of (1) loss of the ring to produce a cell line with monosomy, and (2) a gene mutation on the remaining homolog within that cell line. Loci known in this respect are WT1 on chromosome 11 (Wilms tumor), NF1 on chromosome 17 (neurofibromatosis type 1), chromosome 21 (leukemia), and SMARCB1 and NF2 on chromosome 22 (atypical teratoid rhabdoid tumor; neurofibromatosis type 2) (Carella et al. 2010; Zirn et al. 2012; Byers et al. 2017; De John et al. 2023). Tumor surveillance may be considered in persons carrying these rings. Parental Karyotype 47,+(r) Each ring needs to be assessed individually. Reference to the brief outlines above will give a sense of the range of outcomes. A non-mosaic parent with a very small ring might be expected to transmit the abnormal chromosome with up to 50% probability, assuming (and this may not necessarily be the case) meiotic and mitotic stability. The parental phenotype would, in principle, predict that of a potential 47,+r child, but could underestimate a likelihood of abnormality (recalling that the ascertainment of a parent of sufficient normality to be seeking genetic counseling is biased). Mosaicism in the parent, and potential mosaicism in the child, considerably complicate prediction. A higher-grade mosaicism in the child than in the parent, or complete non-mosaicism in the child, would be expected to produce a more severe phenotype and quite possibly cause lethality in utero. Preimplantation testing or prenatal diagnosis is very appropriately offered. Jiang et al. (2024a) document a series of prenatal diagnoses, in most of which transmission of the ring would have been predicted to be pathogenic. Preimplantation testing has been successfully applied in a few cases of parental small supernumerary ring chromosome (Cheng et al. 2019), and the r(11) case in Wang et al. (2023b) is noted above. Parental Karyotype 47,del(A),+r(A). In the ring with a balancing deletion, normality in an offspring can only be regarded as secure (other things being equal) in the context of the normal homolog (A) having been transmitted from the 47,del(A),+r(A) parent. Even though the carrier parent may be normal, the risk is high that the same balanced karyotype in a conceptus could be followed by post-zygotic misdivision, with the eventual generation of offspring who would be partially trisomic or partially monosomic for the autosome concerned, and thus abnormal. A detailed discussion is offered in Mantzouratou et al. (2009). Actual PGT data is available only in the case of the r(22), and the findings were not promising (Mantzouratou et al. 2009). A carrier mother in whom a supernumerary r(22) was balanced by a del(22), of karyotype 47,XX,del(22)(p10q12),+r(22)(q10q12) had had one affected r(22) child, 47,XY,+r(22)(p11.2q11.2)/46,XY, and one termination. At IVF, 12 oöcytes were fertilized, but none were normal. Mantzouratou and colleagues propose that the abnormal chromosome compromised the very early mitoses of the embryo.

12 CENTROMERE FISSIONS, COMPLEMENTARY ISOCHROMOSOMES, TELOMERIC FUSIONS, BALANCING SUPERNUMERARY CHROMOSOMES, NEOCENTROMERES, JUMPING TRANSLOCATIONS, CHROMOANAGENESIS, AND MULTIPLE DE NOVO CNVs THIS CHAPTER PROVIDES a setting for certain very rare abnormalities that cannot readily be accommodated elsewhere. Barely double-digit numbers, if that, are known for most of these. Centromere fission results when a metacentric or submetacentric chromosome splits at the centromere, giving rise to two stable telocentric products. In a sense, this is the reverse of what happens in whole-arm translocations. The heterozygote, a phenotypically normal individual, thus has 47 chromosomes. The Robertsonian fission reverses the fusion that had originally generated the Robertsonian translocation. Telomeric fusion leads to a 45-chromosome count, due to the joining up of two chromosomes tip-to-tip, not unlike the Robertsonian mechanism. The fusion chromosome has two centromeres, but one of these becomes inactivated. With the balanced complementary isochromosome, two stable exactly metacentric products are generated. A balancing small supernumerary marker chromosome contains material deleted from the normal homolog. A supernumerary chromosome lacking a normal centromere can become stable and functional due to the generation of a neocentromere. In jumping translocations, a segment can move from one chromosome to two or more recipient chromosomes. Chromoanagenesis takes complex rearrangement to a yet more complex level. BIOLOGY Centromere Fission In simple terms, a nonacrocentric chromosome undergoes a horizontal splitting at the centromere (Figure 12–1a), although the true basis may be more complex than this (Rivera and Cantú 1986; Perry et al. 2004). Two new telocentric1 chromosomes result (Figure 12–2). One comprises the short arm of the original, and the other its long arm. It 1 The centromere is at the very end of the chromosome. 314  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY is as though the cell ignores the fact that the split happened and continues on normally, treating each part as a properly functioning whole. The other normal homolog remains intact. The heterozygous person (47,cen fis) may have a balanced complement of genetic material and thus be phenotypically normal. Among the very few families on record, just seven chromosomes—4, 7, 9, 10, 11, 12, and 21—have been involved (Shim et al. 2007; Cetin et al. 2011). The karyotype may be written, for example, 47,XX,–4,+fis(4)(p10),+ fis(4)(q10). Figure 12–1.  Comparing the processes of (a) centric fission of chromosome 7 and (b) complementary isochromosomes of chromosome 2. The chromosome pairs are to be imagined as existing in the zygote (left); they have replicated to give the double-chromatid state. The lightning arrow indicates misdivision of the centromere in one homolog. By the time the cell enters the first mitotic division (right), the abnormal states have been generated. Note that according to the proposed mechanisms in (b), uniparental disomy would necessarily result. Cross-hatching indicates original homolog from one parent; open indicates original homolog from the other. Figure 12–2.  Partial karyotype from a case of 47,cen fis(7). One chromosome 7 exists as a normal homolog, and the other homolog is represented by the 7p and the 7q chromosomes. Rare Abnormalities  315 At meiosis in the heterozygote, the centric fission products presumably form a trivalent with the intact homolog, and 2:1 segregation (essentially as in the Robertsonian carrier) then follows. “Alternate” 2:1 segregation produces normal and balanced centric fission gametes, while adjacent 2:1 segregation leads to gametes disomic or nullisomic for either of the fission products (Figure 12–3). Monosomy would likely be associated with occult abortion, and trisomy with miscarriage or, in exceptional cases, with the live birth of an abnormal child. Thus far, consequential viable trisomies are on record only for 4p, 9p, and 12p. The paucity of data does not allow for a precise assessment of the genetic risk run by the centric fission carrier, other than to suggest that in some, it could be quite high. Dallapiccola et al. (1976) report a chromosome 4 centric fission in a woman who had had two children with trisomy 4p and one normal child. Fryns et al. (1980) describe a man and his normal daughter having a centric fission of chromosome 10. Recurrent miscarriage in the families of Janke (1982) and Shim et al. (2007) may well have been a result of asymmetric segregation of a chromosome 7, and a chromosome 11 centric fission, respectively; in the latter case, the cen fis(11) heterozygous woman then went on to have a normal 46,XX child. Miscarriages and childhood deaths in the family of Del Porto et al. (1984) might have been due to a cen fis 4, which was shown to have been transmitted in balanced state from a mother to her son. Robertsonian Fission The Robertsonian translocation is capable of reversing its evolutionary development, and the fused component chromosomes can separate. Perry et al. (2005) studied two families coming to attention due to a known family history of a segregating rob(13;15). They observed fission products in samplings of somatic tissues (chorionic villus, amniocytes, and blood) in 11 individuals or pregnancies, although mostly at single-digit percentage levels. These “new” acrocentric chromosomes were actually telocentric chromosomes 13 and 15, having no visible short-arm material. This phenomenon appeared to be without any clinical consequence. Xu et al. (2024b) report a person from a rob(14;15) family having mosaicism with a normal cell line alongside the 45,rob(14;15). Figure 12–3.  The six possible gametes arising from 2:1 segregation in a 47,cen fis(9) heterozygote. Two of these would lead to a normal phenotype, the 46,N and the balanced 47,cen fis(9) states. Of the unbalanced states, only the 48,cen fis(9),+9p, in which the imbalance would be a 9p trisomy, might possibly be viable.

316  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Chromosome Fusion (Telomeric Fusion) This is the tip-to-tip fusion of two complete, or practically complete, chromosomes, and the person thus has a 45-chromosome count (Engelen et al. 2000; Lemyre et al. 2001). The fusion occurs at the level of the telomere or the subtelomeric region. All the necessary functional genetic material is “present and correct” (if there is a missing bit, it apparently contains no crucial genes), and the phenotype is normal, other things being equal. The composite chromosome has two centromeres (hence an alternative name of “stable non-Robertsonian dicentric chromosome”), but one of the two centromeres becomes functionally suppressed. The karyotype is written 45,t(A;B), 45,dic(A;B), or 45,tas(A;B), where A and B denote the two chromosomes. The short arm of an acrocentric chromosome is frequently involved, and chromosome 18 is often one of the participating chromosomes. The attachment of an essentially complete long arm of an acrocentric chromosome to the telomeric region of another autosome is a very similar circumstance (Figure 12–4). Ascertainment is typically fortuitous, or through reproductive difficulty (recurrent miscarriage, oligospermia). Familial transmission is recorded. A normal child could be produced following symmetric, essentially 2:1, segregation. That is, either the two normal homologs are transmitted or the composite chromosome. Asymmetric segregation, were it to happen, would lead to trisomy or monosomy of one of the component chromosomes and, according to the nature of the chromosome, in utero viability would be compromised. If the trisomic state were to be “corrected” by loss of the normal homolog from the other parent, a uniparental disomy would result. The case shown in Figure 12–4 is an example of this. On sperm analysis from one such man with 45,XY,der(5;15)(q35.3;q10), symmetric segregation was seen in just over one-half, and adjacent in a little under half, along with rare 3:0 segregants (Pylyp et al. 2014). Xie et al. (2021) examined reproductive outcomes in a series of eight carriers of autosome-autosome fusions, male and female, presenting with infertility. At blastocyst biopsy, a little over half showed adjacent segregation, the embryos being trisomic or monosomic for one of the involved autosomes but with most of the remainder being balanced (symmetric segregation), along with a single 3:0 Figure 12–4.  A telomeric fusion translocation, 45,XY,t(8;15)(p23.3;q11). The normal father with this karyotype has all the functionally necessary part of chromosome 15 attached to the telomere of a chromosome 8. His child with Angelman syndrome has the same karyotype, but haplotyping with DNA markers showed that both chromosome 15 elements derived from the father, with no chromosome 15 contributed from the mother. Probably, this reflected a “corrected” interchange trisomy. Source: From A Smith et al., Familial unbalanced translocation t(8;15)(p23.3;q11) with uniparental disomy in Angelman syndrome, Hum Genet 93:471–473, 1994. Rare Abnormalities  317 case. More favorable results were obtained in four carriers of Y-autosomal fusions, with only one of 19 blastocysts showing an unbalanced translocation. Lemyre et al. (2001) document a 45,XX,dic(14;18)(p11.2;p11.3) mother in whose pregnancy intrauterine fetal death was diagnosed at 32 weeks gestation. The fetal pathology examination was consistent with trisomy 18, and the karyotype, 46,XY,+18,dic(14;18)(p11.2;p11.3), confirmed this diagnosis. An academic fascination in telomeric fusion lies in the theory that such a mechanism may have been a crucial step in the process of human evolution, initiating the separation of Hominina from Pan (chimpanzees). A fusion of the two ancestral primate chromosomes 2A and 2B, in a single 48-chromosome Pan individual, may thus have created the human chromosome 2, around a million years ago (Poszewiecka et al. 2023). It would then have taken inbreeding over some generations to lead to chromosome 2 homozygosity, and this state may then have conferred a survival advantage, ensuring the fixation of a 46-chromosome state in a small population that subsequently, with further genetic change, evolved into Homo sapiens (Stankiewicz 2016). Complementary Isochromosomes The individual has a full complement of the chromosomal material—and may thus be phenotypically normal—but with the two p arms combined in one chromosome and the two q arms in the other (Figure 12–5). A formal karyotype might be written, for example, as 46,XX,i(2)(p10),i(2)(q10). Chromosomes 1, 2, 4, 5, 7, and 9 have been reported with this picture, and at least four instances are known for chromosome 2 (Bernasconi et al. 1996; Shaffer et al. 1997; Björck et al. 1999; Albrecht et al. 2001; Baumer et al. 2007; Guvendag Guven et al. 2011; He et al. 2019). The usual mechanism of formation may be that in the zygote, horizontal fission at the centromere of one homologous chromosome produces not two telocentric products (as happened in the fission discussed above), but two mirror-image metacentric chromosomes: an i(p) and an i(q) chromosome (Figure 12–1b). This is followed by segregation of both isochromosomes into one daughter cell. There is loss (if it had ever been there) of the homologous normal chromosome contributed by the other parent (unlike the Figure 12–5.  Chromosomes from a woman with complementary isochromosomes i(2p) and i(2q) (and see Figure 12–1b). Case of AA Schinzel; in F Bernasconi et al., Normal phenotype with maternal isodisomy in a female with two isochromosomes: i(2p) and i(2q), Am J Hum Genet 59:1114-1118, 1996.

318  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY centric fission, in which the normal homolog is necessarily retained); thus, this is a form of monosomy rescue that engenders a uniparental disomy, usually maternal. In other cases, one isochromosome may be of paternal origin and the other maternally derived, and this may reflect an initial trisomy rescue followed by post-zygotic isochromosome formation (Albrecht et al. 2001; Kotzot 2001; Baumer et al. 2007). A typical clinical presentation has been multiple miscarriage in phenotypically normal women. Rather analogous to the rob(21q21q) carrier, it is practically impossible for such a person to have a normal child. Any pregnancies from “symmetric” segregation would be either dup(p)/del(q) or dup(q)/del(p), and thus hugely imbalanced. In the male, infertility may be the presenting feature. Balancing Supernumerary Chromosomes If deleted material from a chromosome is then accommodated in a newly formed small supernumerary marker chromosome (sSMC), and if this extra chromosome can be stably transmitted, then the carrier individual can be of normal phenotype but may have a risk to have a child with a deletion, or a duplication, of the material in question (Baldwin et al. 2008; Wang et al. 2023b). Figure 12–6 illustrates such a balance, the sSMC in this case in the form of a small ring. A most remarkable example is that of a four-generation family in which several persons carried a chromosome 22 with an atypical q11.2 deletion, but this in company with a small supernumerary ring chromosome that comprised the deleted 22q11 material (Nevado et al. 2009). These people had, therefore, a balanced karyotype, and they were phenotypically normal: 47,del(22)(q11.2),+sSMC. On classical karyotyping, the two chromosome 22 homologs had appeared normal, and it required FISH to reveal the deletion on one homolog; thus, the initial impression in this scenario may simply be 47,+ sSMC, and the sSMC interpreted as “harmless.” In fact, two of these family members had Figure 12–6.  A Balancing Supernumerary Chromosome. Notes: An 8p deletion with an accompanying supernumerary 8p ring chromosome (above), identified in a normal man presenting with infertility. The ring balances the deletion, as demonstrated on the SNP array (below). At PGT with IVF treatment, four embryos were balanced, two were deleted for 8p, and two duplicated for 8p. A balanced embryo was transferred, and a 46,XY baby born. Source: From D Cheng et al., Analysis of molecular cytogenetic features and PGT-SR for two infertile patients with small supernumerary marker chromosomes, J Assist Reprod Genet 36:2533–2539, 2019. Courtesy Y-Q Tan, and with the permission of Springer. Rare Abnormalities  319 a child with atypical deletion 22q11.2 syndrome. The deletion had a different proximal breakpoint to the common 22q11.2 deletion, such that the ring chromosome included some alpha satellite from the chromosome 22 centromere. The other potential imbalance, that of dup(22q11) due to a 47,+sSMC karyotype, had not been observed in the family. Neocentromeres Neocentromeres are ectopic centromeres that originate occasionally from noncentromeric regions of chromosomes (Amor and Choo 2002; DeBose-Scarlett and Sullivan, 2021). Neocentromeres are determined epigenetically by changes in the chromatin structure, such as the incorporation of the histone H3 variant CENP-A, and lack normal centromeric alpha-satellite DNA. The formation of a neocentromere is nearly always associated with a chromosomal rearrangement that generates a fragment lacking a conventional centromere, and provides a useful reminder of the absolute requirement for chromosomes to have both a centromere and a means of capping the chromosome ends, either with telomeres or by the formation of a ring chromosome. Chromosome rearrangements that are most commonly associated with neocentromere formation include inverted duplications of distal chromosome segments, ring chromosomes derived from deletions within chromosome arms, and, less commonly, deletions of the endogenous centromere. “Centromere repositioning,” the formation of a neocentromere in the absence of any chromosome rearrangement, is exceedingly rare (Amor et al. 2004). If material is missing or disrupted from the chromosomal fragment with a neocentromere, pathology may result, such as the man in Quinonez et al. (2017a) with a del(15) and a “balancing” neocentromeric 15-originating sSMC, who had Marfan syndrome due to disruption of the FBN1 gene at 15q21.1. Almost all neocentromeres arise de novo, but familial examples are recorded. The mother in Chuang et al. (2005) had the karyotype 46,XX,del(11)(p11.12p11.2), with the deficit corrected by a neocentromere-containing r(11)(p11.12p11.2). Her child inherited only the del(11), and presented with the Potocki-Shaffer syndrome. Other examples, in which the neocentromeric chromosome formed as a ring, are noted in Chapter 11. Jumping Translocation (“Translocation Sauteuse”) This evocative expression describes a mitotic rearrangement whereby the same piece of one chromosome breaks off, on more than one occasion, and attaches to the tips of other chromosomes. The site of breakage in the donor chromosome is characterized by the presence of an interstitial (internal) telomere, and this region offers the possibility of fusion with the recipient chromosomes (Vermeesch et al. 1997). Jumping translocations are found most commonly in hematological malignancies, but 50 constitutional cases were listed in the review of Reddy (2010). Levy et al. (2000) identified the phenomenon in two couples, themselves karyotypically normal, presenting with recurrent miscarriage and showing evolving “jumping” cell lines in the cultured products of conception. In one of these, for example, the conceptus was initially 46,XX,der(15)t(1;15)(q10;q10). A second line arose, with the 1q

320  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY part of the der(15) replaced by an additional chromosome 15, which then generated an i(15q) along with (presumably independently) trisomy 7. Five further lines then budded off, all with considerable degrees of imbalance; the pregnancy eventually terminated in first-trimester abortion. Lefort et al. (2001) describe in some detail their own case, an otherwise normal boy with a (possibly coincidental) structural cerebellar defect. He had four separate cell lines on blood and skin biopsy samples, with the segment 2p12pter attached to 1pter, 5qter, 6qter, and 12qter, respectively. In each, the rearrangement appeared to be balanced. These authors proposed that these translocations were truly one-way—that is, having no reciprocal exchange, and with healing of the 2p12 stump by the formation of new telomeric sequences. Chromoanagenesis Chromosome microarray and next-generation sequencing technologies have revealed new types of complex chromosomal alterations characterized by multiple structural rearrangements, affecting one or several chromosomes, and arising “all-at-once” (Zepeda-Mendoza et al. 2019; Burssed et al. 2022). Collectively termed chromoanagenesis (“chromosome rebirth”), these events were seen initially as somatic changes in cancer but later observed as germline abnormalities in developmental disorders, although occasionally seen in healthy individuals. Chromoanagenesis is subdivided into three distinct categories: chromothripsis, chromoanasynthesis, and chromoplexy (Table 12–1, Figure 12–7). CHROMOTHRIPSIS Chromothripsis is a word of recent vintage, meaning “chromosome shattering” (Figure 12–7, left). It is mostly a concept applicable in cancer cytogenetics, in which there may be tens to hundreds of chromosomal breaks occurring as a single somatic event, sometimes described as catastrophic, and leading to a jumbled remodeling of a single chromosome which can, of itself, due to inappropriate juxtapositions of certain genes, initiate or maintain a cancer. Deletions can occur if some fragments are not reincorporated into the chromosome. Chromothripsis events take place in micronuclei (Zhang et al. 2015a). The process begins with a lagging mitotic chromosome that is incorporated into a micronucleus where it is “pulverized” to create multiple double strand breaks (DSBs). The DSBs then trigger DNA damage responses that attempt to repair the chromosome via the process of nonhomologous end-joining (NHEJ) but do so imperfectly, leading to a rearranged chromosome that is then reintegrated with the primary nucleus. Constitutional chromothripsis is rare, and may be described as “germline chromothripsis.” In contrast to cancer, germline chromothripsis can involve several chromosomes rather than just one, involve fewer breakpoints, and is more likely to be balanced (or near balanced), the latter being necessary for embryo viability. The paternal gonad is the predominant site of de novo generation, probably due to the higher number of cell divisions in the male germ line. De Pagter et al. (2015) describe three mother-child pairs, the mothers with karyotypes that would certainly qualify as complex Table 12–1.  The Three Categories of Chromoanagenesis, and their Distinguishing Features TERM CHROMOSOMES BREAKPOINTS DISTRIBUTION REPAIR MECHANISM DOSAGE Chromothripsis 1 in cancer, 1–4 when congenital Hundreds in cancer, 5–65 when congenital Clustered c-NHEJ, MMEJ Balanced or deletions Chromoanasynthesis Typically 1 5–25 Clustered FoSTes or MMBIR Complex: gains, losses, inversions, translocations Chromoplexy ≥2 5–25 (fewer than chromothripsis) Interspersed c-NHEJ, MMEJ Typically balanced Notes: c-NHEJ = classic Nonhomologous End-Joining; MMEJ = Microhomology-Mediated End-Joining; FoSTes = Fork Stalling and Template switching; MMBIR = Microhomology-Mediated Break-Induced Replication. Source: From CJ Zepeda-Mendoza and CC Morton, The iceberg under water: Unexplored complexity of chromoanagenesis in congenital disorders, Am J Hum Genet 104:565–577, 2019. 322  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY chromosome rearrangements (Figure 12–8). Further complexity was then visited upon their children due to de novo change within the maternally inherited homologs, with associated severely abnormal phenotypes. As another example, the three-generation familial rcp(3;5)(q25;q31) in Bertelsen et al. (2016), at first sight seeming to be simple two-way reciprocal translocation, proved to be very complicated on analysis by next-generation sequencing, with six different “microrearrangements” at the breakpoint regions. CHROMOANASYNTHESIS Chromoanasynthesis (“chromosome reconstitution”) is a replication-based rearrangement process that involves the mechanisms of serial fork stalling and template switching (FoSTeS) or microhomology-mediated break-induced replication (MMBIR) Figure 12–7.  The Three Categories of Chromoanagenesis. Notes: The chromosome c from chromothripsis (left), after several breakages and joinings (a,b), has lost three segments. The chromosome c from chromoanasynthesis (center), after several breakages and joinings (a,b), has undergone a deletion, and duplications and triplications. The three derivative chromosomes (c) from chromoplexy (right) have undergone breakages with a mutual exchange of segments (b). Abbreviations as in Table 12–1. Source: From B Burssed et al., Mechanisms of structural chromosomal rearrangement formation, Mol Cytogenet 15:23, 2022. Courtesy MI Melaragno, and with the permission of Springer Nature. Figure 12–8.  “Circos Plots” showing Chromothripsis. Notes: Circos plots depict the complexity of the several interconnected breakpoints in the karyotypes of three phenotypically normal mothers, whose abnormal children manifested yet more complicated, and unbalanced, rearrangements. Source: From MS de Pagter et al., Chromothripsis in healthy individuals affects multiple protein-coding genes and can result in severe congenital abnormalities in offspring, Am J Hum Genet 96: 651–656, 2015. Courtesy WP Kloosterman, and with the permission of the American Society of Human Genetics and Elsevier.

Rare Abnormalities  323 (Figure 12–7, center).2 It is seen mostly as a germline abnormality, identified in individuals with developmental disorders. These mechanisms can generate complex local rearrangements that include deletions, duplications, triplications, inversions, and translocations, with microhomology at the breakpoints being a characteristic feature (see Chapter 3). Anzick et al. (2020) provide an example of congenital chromoanasynthesis in a child with Jacobsen syndrome (11q deletion), who had presented with intellectual disability and dysmorphism. The signature features of chromoanasynthesis were the presence of six duplications and five deletions on a single copy of the chromosome 11q, accompanied by microhomology at the breakpoint junctions. Because chromoanasynthesis can produce significant chromosome imbalance, it is typically associated with severe phenotypes of embryonic lethality; yet, stable inheritance can occur. Sabatini et al. (2019) describe a rearranged chromosome 21, derived from chromoanasynthesis, that included seven copy number gains. The chromosome was transmitted stably over at least three generations without phenotypic effect, presumably due to the small size of the duplicated segment. The finding only came to light during the investigation of a child with intellectual disability due to a non-21 abnormality (a causative variant in the gene SYNGAP1 on chromosome 6). CHROMOPLEXY Chromoplexy (“chromosome twisting”) typically occurs as a somatic change in cancer. It bears similarity to chromothripsis, but with the involvement of two or more chromosomes and fewer breakpoints (Figure 12–7, right). The resultant chromosome rearrangements are typically balanced, but there may be oncogenic gene fusions generated by the process of chromosome breakage and rejoining. Although primarily a cancer-related phenomenon, some germline chromothripsis cases might also meet the definition of chromoplexy, according to the number of chromosomes involved and the number and location of breakpoints. The Multiple De Novo CNV (MdnCNV) Phenotype The original cases, through whom the syndrome had been delineated, were defined by the possession of four or more independent de novo CNVs of average size 1Mb, and they had been ascertained at a frequency of 1 in 12,000 among children with “various developmental disorders” referred for clinical microarray testing (Liu et al. 2017). These CNVs are typically duplications, and they may number in the low single digits to just double digits; an example is shown in Table 12–2. They arise in the earliest post-zygotic time interval (within the first few cell divisions) due to a transient fault in the DNA replicative repair process. Thereafter, these CNVs are transmitted stably in the soma. Del Gobbo et al. (2021) report a growth-retarded infant from a pregnancy with confined placental mosaicism for eight 2.4-3.9 Mb duplications. The duplications involved seven different chromosomes of both maternal and paternal origin, and likely affected placental function and thereby fetal growth. 2 Chromoanasynthesis is to be distinguished from chromothripsis by the presence of copy number gains not otherwise explained by the mechanism of chromosome breakage and rejoining, and from the “multiple de novo CNV phenotype” in which several independent de novo copy number variants (CNVs) are generated during the first few mitoses.

324  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY The CNV-generating mechanism may be microhomology-mediated break-induced replication, a form of break-induced replication that occurs when the replication fork has stalled or collapsed. The generation of multiple broken replication forks in a single zygotic cell is indicative of cell-wide replication stress, such as energy or substrate unavailability (Du et al. 2022b). The identification of an increased number of de novo SNVs in the same individuals suggests a more generalized genome instability. The transient nature of the “CNV mutator” phenotype is consistent with it being caused by reduction of quality or quantity of the mRNA that is stored in the oöcyte, impacting upon the first few cell divisions during embryonic development prior to activation of the zygote’s own transcriptional machinery. Oöcyte mRNA is transcribed from the maternal genome, and therefore the “CNV mutator” could be caused by maternal genetic factors that are not necessarily transmitted to the embryo. GENETIC COUNSELING Centromere Fission The centric fission heterozygote has an important risk of having a phenotypically abnormal child in those cases in which a whole-arm aneuploidy is viable. The 4p, 9p, and 12p trisomies are the only examples known so far. In any other combination, spontaneous abortion would be inevitable. Five percent to 25% of the likely risk range is an educated guess where viability is a possibility. Prenatal or preimplantation testing is certainly advisable. Of the phenotypically normal offspring of the heterozygote, half would be expected to have the centric fission and half to have normal chromosomes. For the Table 12–2.  Nine De Novo Copy Number Variants Observed in a Child with the Multiple De Novo Copy Number Variant Phenotype SITE SIZE NATURE PARENTAL ORIGIN 1p34p35 1.7 Mb Dup Maternal 3p14p21 4.2 Mb Dup Maternal 8q24 4.5 Mb Dup Maternal 10q24q25 4.7 Mb Dup Maternal 16p11 322 kb IDD Paternal 16q23 4.2 Mb IDD Maternal 16q24 312 kb Dup Maternal 19q13 4.3 Mb Dup Maternal Xp11 214 kb Dup Maternal Dup = duplication; IDD = insertional double duplication. Source: From P Liu et al., An organismal CNV mutator phenotype restricted to early human development, Cell 168:830–842.e7, 2017. Rare Abnormalities  325 heterozygote in whom neither whole-arm imbalance is viable—an obvious example would be a 47,cen fis(1)—no risk for a liveborn abnormal child exists, but the likelihood of spontaneous abortion may be high. Robertsonian Fission This appears to be a phenomenon of academic interest, seen only in somatic tissues and of no apparent clinical consequence. Complementary Isochromosomes The carrier of the complementary p/q isochromosome carrier, essentially with certainty (that is, barring an extraordinary rescue event), cannot have a normal child. Balancing Small Supernumerary Marker Chromosome The genetic risk is high, and it may approach 50%, if the del or dup imbalance implied by the material contained in the sSMC is “genetically small.” Nevado et al. (2009) emphasize the need to seek a cryptic deletion in persons found to carry an sSMC; if the true state of a cryptic deletion is not recognized, genetic advice would be gravely misplaced. Successful parenthood following PGT is noted above (Figure 12–6). Chromosome Fusion (Telomeric Fusion) Infertility is frequent, and Xie et al. (2021) found impaired spermatogenesis in six out of eight male carriers. If conception is possible, there is likely a high risk for aneuploidy of one or other of the chromosomes involved in the translocation, but equally, a normal child could be conceived. Prenatal or preimplantation testing would have a place (Xie et al. 2021). Uniparental disomy will need to be considered, at least in the case of a chromosome 15 being one of the chromosomes. Jumping Translocation These cases are typically de novo, and the reason for the chromosome suddenly becoming susceptible in the individual is unknown. The genetic implications for the next generation remain uncertain. Yet, normality is on record in the quite extraordinary case of parental transmission described in Hu et al. (2014). A normal father and daughter had translocations involving the same breakpoints at two chromosomes, 16 and 22, but different chromosomes otherwise: t(16;22), t(1;22), and t(22;22) in the father, while the daughter’s translocations were t(16;22), t(9;22), and t(5;22). 326  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Chromoanagenesis If transmission from parent to child is possible (and indeed, cases are on record), the risk for generating further complexity with an associated developmental disorder or miscarriage is likely high. The distinction between a particularly complicated complex rearrangement and a less complicated chromothripsis may be rather subtle. Multiple De Novo CNVs The small number of reported cases have all been sporadic, which is consistent with the proposed post-zygotic origin. However, a heritable contribution to the phenotype— in other words, a genetic susceptibility to the generation of these CNVs—is yet to be excluded.

13 DOWN SYNDROME, OTHER FULL ANEUPLOIDIES, POLYPLOIDY, AND THE INFLUENCE OF PARENTAL AGE IN THIS CHAPTER we consider the circumstances in which there may be an increased risk to have a child, or a pregnancy, with an aneuploidy. First we review the case of parents, themselves karyotypically normal, who have had a child, or a pregnancy that aborted, with a full aneuploidy or a polyploidy. Thus, we include the major trisomies (13, 18, 21) as well as the less commonly seen autosomal aneuploidies. The category of polyploidy is substantially devoted to triploidy. In the great majority, these defects arise from an abnormal event during meiosis or (in some triploidy) at conception. In a few, there is post-zygotic generation of aneuploidy. Only in the case of parental gonadal mosaicism, or in the hypothetical setting of an apparent predisposition to meiotic error, will there apply an increased risk of recurrence of aneuploidy over and above that associated with any parental age effect. Triploidy needs separate consideration. Second, we touch briefly on the uncommonly encountered circumstance of possible parenthood in (classically cytogenetic) aneuploid persons. Finally, we rehearse the ways in which parental age may influence the risk to conceive a pregnancy, and potentially to have a child, with an aneuploidy. BIOLOGY Full aneuploidy is presumed in the great majority to be the result of malsegregation of chromosomes at meiosis. A diminished degree of meiotic recombination is typically observed in aneuploid offspring, and this led Hassold and Sherman (2000) to propose a two-hit sequence, the first hit being a less well-tethered bivalent at meiosis I, and the second hit being a consequential aberrant distribution at meiotic metaphase. Meiotic malsegregation can happen at any parental age, but it is more frequent in older mothers, as we discuss in detail below. Alternatively, an abnormality has arisen in a premeiotic gametocyte, with the parent thus having a “wedge” of gonad that carries the abnormality (gonadal mosaicism). Such a parent would, of course, have an increased risk for only the one karyotypic defect. Finally, a small fraction of apparent full aneuploidy may be due to early mitotic nondisjunction in an initially 46,N conceptus with loss, or restriction to extra-embryonic tissue, of the normal cell line. 328  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Autosomal Trisomy TRISOMY 21 (DOWN SYNDROME) Down syndrome (DS) is the archetypal chromosome disorder. It was, along with Klinefelter syndrome, the first medical condition shown to result from a chromosome abnormality, in 1958. It has for many years been recognized as the most common single known cause of intellectual disability, and it has the highest incidence at birth of any chromosome abnormality. Every counselor can expect frequently to deal with problems relating to DS, and thus should be familiar with its genetics. (For convenience, we note here also those forms of DS that are due to translocations.) The Genotype to the Phenotype. The DS phenotype—the characteristic facial appearance, body build, and cognitive impairment—is, in a sense, a “contiguous gene syndrome” in which there is an additional dose of an en bloc set of genes. The entire chromosome 21 was sequenced by the year 2000, and the gene complement turned out to be surprisingly low, only 2251 protein-coding loci in all (Hattori et al. 2000). This gene sparseness is plausibly a factor in the survivability of the trisomic state; it may also be that only a minority of the duplicated loci are dosage-sensitive and thus pheno-contributory (Pritchard and Kola 1999). Along with the brain phenotype, certain organ systems are particularly vulnerable, and Torfs and Christianson (1998) identified characteristic malformations in a population study of nearly 3,000 affected infants (Table 13–1). At the top of the list is the heart abnormality, atrioventricular canal defect, which Kurnit et al. (1985) propose may reflect an increased adhesiveness of cardiomyocytes during the processes of tissue migration as the chambers of the heart are forming. It was logical that attempts be made to define those regions of the chromosome that might contribute predominantly to the DS phenotype—that is, to identify a “DS critical region” (DSCR) that might contain particular “DS genes.” The study of cases with informative incomplete trisomies pointed to the key importance of region 21q22.13 (Figure 13–1). Within this segment, a major gene of import is DYRK1A2, this gene having a role in neurite formation (Park and Chung 2013; Van Bon et al. 2016). Other loci contributing to neurogenesis and neuritogenesis, and which have also been implicated in influencing the DS brain phenotype, are the neural cell adhesion DSCAM gene at 21q22.2 and DSCR1 (also known as RCAN1) at 21q22.13. Shapiro (1997) offers a somewhat different viewpoint, championing the “amplified developmental instability” hypothesis, and comments that “the search for a minimal region on chromosome 21 (the so-called DS critical region) responsible for producing DS has come full circle back to almost the entire chromosome.” In his view, a direct role for one or a few single loci with a one-on-one gene-to-phenotype relationship is simplistic: “Traits that characterize DS are complex, and should be viewed and analyzed accordingly.” His general proposition is not unreasonable: that an excess of chromosome 21 encoded gene products perturbs the functioning of the products of many loci, from all chromosomes, in all manner of developmental and physiological pathways. Entirely differently, might the extra chromosome have a mechanical effect of itself? Kemeny et al. (2018) showed that trisomy 21 nuclei are no larger than euploid nuclei, and so 1 Different sources take different approaches to gene annotation, and therefore arrive at alternative estimates for the number of genes. A large number of non-protein encoding genes on chromosome 21 may also contribute to the DS phenotype. 2 Hypothetically, treatment to inhibit DYRK1A activity might ameliorate some DS features (Kim et al. 2016; McElyea et al. 2016).

Down Syndrome, Other Full Aneuploidies, and Polyploidy  329 chromosomes must be more compacted to fit within the nucleus, potentially displacing them from their usual positions. This altered nuclear spatial architecture might, in turn, alter interactions between different parts of the genome, impacting the activation and silencing of genes. Attempting to draw together the several viewpoints, as do Neri and Opitz (2009)3, we could suppose that the important genetic segments—the “DS loci”—may have their pathogenic role in the modulation, direct or epigenetic (Aït Yahya-Graison et al. 2007), of layer upon layer upon layer of cellular interactions that leads, as the end result, to a phenotypic range that is clinically recognizable as DS. “Complex” may be too simple a word to describe this. What about the characteristic DS facies? Simply to observe one’s fellows is enough to convince one that development of the human face must be the most subtle and complex and precise process. How is it that the DS face is different, and recognizably so? Two proposed contributory factors are the development of the craniofacial skeleton, which might be susceptible to the effects of DYRK1A overexpression, and a failure of the facial musculature to divide into its proper anatomical components during fetal development (Bersu 1980; McElyea et al. 2016). A sophisticated 3D imaging analysis of the facies in 55 DS children, compared to their euploid siblings and unrelated euploid children, is offered in Starbuck et al. (2017). Table 13–1.  Some Malformations Frequently Observed in Down Syndrome MALFORMATION RELATIVE RISK Atrioventricular canal defect* 1,009 Annular pancreas 430 Duodenal atresia 265 Patent ductus arteriosus* 152 Small intestinal atresia/stenosis 142 Ventricular septal defect* 95 Tricuspid valve defect* 84 Hypoplastic aorta* 77 Tetralogy of Fallot* 77 Atrial septal defect* 71 Ectopic anus 67 Cataract 54 Intestinal malrotation 45 Anal atresia/stenosis 34 Tracheo-esophageal fistula 26 Syndactyly 26 *Cardiovascular defect. Source: Data from a population study in California 1983–1993, involving 2,894 infants with Down syndrome (Torfs and Christianson 1998). 3 Their review celebrates the fiftieth anniversary of the discovery of the chromosomal cause of DS, and it provides a fascinating discussion of 19th- and 20th-century thinking leading up to this event. 330  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY One component of the DS phenotype, an early onset dementia (Figure 13–2a), evolves in adult life and is readily explicable. Duplication of the APP locus at 21q21 is the cause, the consequence of a continuing APP overexpression and hence an overproduction of β-amyloid, which, over time, accumulates in the brain (Head et al. 2016). This interpretation is well supported by the observations in the rare form of familial Alzheimer Figure 13–1.  Phenotypic (trisomic) map of chromosome 21. Thick lines represent regions that must be trisomic to produce the particular trait. Thin-line regions may also contribute to that trait; the contribution of dotted-line regions is less clear. M, mild; P, profound. Source: From JR Korenberg et al., Down syndrome phenotypes: The consequences of chromosomal imbalance, Proc Natl Acad Sci USA 91: 4997–5001, 1994. Courtesy JR Korenberg, and with the permission of the National Academy of Sciences. Down Syndrome, Other Full Aneuploidies, and Polyploidy  331 disease due to 21q21 duplication4 as an isolated genomic rearrangement (Figure 14–79). Other genes encoded in chromosome 21 also contribute to the pathology, in particular DYRK1, which alters a number of proteins involved in Alzheimer disease via increased phosphorylation (Kimura et al. 2007; Wegiel et al. 2011). As with 46,XX and 46,XY persons, the apoE genotype influences the age of onset (Figure 13–2b). Different Cytogenetic Forms The usual basis of DS is standard trisomy 21 (Figure 13–3). The disorder has a number of other cytogenetic forms, and Figure 13–4 depicts the proportions graphically. Differences in the source and nature of the genetic errors underlying these various forms require each to be considered separately. STANDARD TRISOMY 21 DOWN SYNDROME The great majority (~95%) of DS is due to simple trisomy of chromosome 21. A little over 90% of these are assumed to reflect a maternal meiotic error, with the rest accounted for by a paternal error or a (post-zygotic) mitotic origin (Vranekovic et al. 2012). About 80% of these maternal errors occur at meiosis I, and the remainder apparently at meiosis II, albeit that the latter may actually have been set up at meiosis I. Meiotic I errors are associated with reduced or actual absence of recombination between the chromatids of the chromosome 21 tetrad. Particularly an absence of recombination (with no chiasma forming, thus an “achiasmate” tetrad) may lead to each homolog being able to segregate without reference to the other, and thus without the imperative to move symmetrically. Among the small fraction (~5%) due to paternal errors, the proportions coming from meiotic I and meiotic II errors are nearly equal. As in the female, a reduced frequency of recombination observed in the meiotic I cases may underlie the cause of this male Figure 13–2.  The Age of Diagnosis of Dementia in Down Syndrome. Notes: The peak age of diagnosis (left) is the mid-fifties, with some as early as in the thirties. One marker of cognitive capacity, the Object memory Z score, declines more markedly in those homozygous for the apoE ε4 allele, or ε3/ε4 heterozygous (right). Source: From SE Antonarakis et al., Down syndrome, Nat Rev Dis Primers 6:9, 2020. Courtesy SE Antonarakis, and with the permission of Springer Nature. 4 Such a duplication is on record as having led to a false-positive finding at noninvasive prenatal testing (Meschino et al. 2016). 332  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY nondisjunction (Savage et al. 1998). Two as yet unexplained observations concerning trisomy 21 due to paternal meiotic errors are these: this fraction is a little greater among prenatally (11%) than post-natally (7%) diagnosed cases, and there is an excess of males among the DS offspring (Muller et al. 2000). Standard trisomy DS typically occurs as a sporadic de novo event, and recurrences are rare. These categories of cause of recurrence can be listed: a parental predisposition to malsegregation, gonadal mosaicism, and chance. Figure 13–3.  Standard Trisomy 21 Karyotype. Figure 13–4.  Origins of Trisomy 21. Notes: Maternal (mat) meiosis is much the major setting (85%–90%) in which the error occurs. Paternal (pat) meiotic errors account for 3%–4%. Robertsonian translocation Down syndrome (TDS) comprises 3% de novo (dn) and 1% familial (fam) of the total. Postzygotic mitotic errors happen in 3%–5%.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  333 Recurrence due to Malsegregation Tendency.  Do some (non-mosaic) individuals, for a certain biological or environmental reason, run an increased risk of producing a trisomic 21 conception? Could a specific sequence within chromosome 21 influence its disjunction (Mastrorosa et al. 2025)? Are some people susceptible to a dietary deficiency affecting meiotic integrity? Is there a range of “meiotic robustness” in the population? These are perfectly respectable concepts, although they remain quite hypothetical. If so, what possibilities might there be? Several theories for a general predisposition to aneuploidy have been put forward, and some of these are discussed on Chapter 3. While some of these various possibilities may be more plausible than others, they are all speculative, and we conclude that there is at present no routinely practicable basis enabling the counselor to identify ahead of time those parents whose risk is high, and those whose risk is low, to have a second pregnancy with trisomy 21. Recurrence due to Mosaicism.  A trisomy 21 cell population in a parent (gonadal, or somatic-gonadal mosaicism) is presumed to be an uncommon cause of the production of disomic 21 gametes, although perhaps less rare than originally thought (Bruyère et al. 2000; Mahmood et al. 2000; Kuo 2002). Pangalos et al. (1992b) studied 22 families in which trisomy 21 had occurred more than once (in siblings, in second- and in third-degree relatives), applying DNA polymorphism analysis. Parental gonadal mosaicism was proposed as the cause of sibling recurrence in five of 13 families (~40%); but other than these, chance alone was enough to explain the recurrences. Sachs et al. (1990) followed 1,211 pregnancies at prenatal diagnosis subsequent to the occurrence of trisomy 21 in a previous pregnancy, and observed six recurrences (for a rate of 0.5%). In two of these instances, mosaicism was shown. One father karyotyped as 47,+21/46,N on skin analysis, and one mother showed trisomic cells in 3%, 14%, 44%, and 47% on culture of, respectively, blood and skin, and—in a more direct observation— of each ovary. James et al. (1998) studied four women, each of whom had had three trisomy 21 conceptions. Two of the mothers were under age 35 years at the time of the trisomic conceptions, and they both showed a very low-level mosaicism (0.5% and 4% on blood karyotyping). Neither had a DS phenotype themselves. In their collaborative series from six Japanese clinics, Uehara et al. (1999b) record the exceptional case of a couple having had five successive pregnancies with trisomy 21 (one DS child, four diagnoses at amniocentesis). Both parents had normal karyotypes on blood and skin analysis. It would seem rather probable that one parent may have had fully trisomic gonadal tissue. Ovarian biopsy proved the point in a mother of three DS children (and one normal child) who typed 46,XX on peripheral blood, but in whom eight out of 20 ovarian cells showed trisomy 21 (Tseng et al. 1994). Other similar examples are on record; we noted Sachs et al. above. Nielsen et al. (1988) report a couple having had six documented pregnancies with standard trisomy 21, and five other unkaryotyped pregnancies ending in neonatal death or abortion. The mother typed 46,XX on peripheral blood, and 47,XX,+21/ 46,XX in ovarian somatic cells. (Even if the oöcytes were all or nearly all 47,+21, it remains perplexing that no known 46,N conception occurred.) An in vitro fertilization (IVF) setting enabled analysis of the gametes themselves in a woman studied by Cozzi et al. (1999). She had had a normal and a DS child at ages 29 and 32 years respectively, and then had prenatal diagnoses of trisomy 21 at 32 and 36 years. No trisomic mosaicism was detected on peripheral lymphocyte analysis. At IVF, of seven embryos, four were trisomy 21 and one tetrasomy 21, with only two showing normal disomy 21. Four unfertilized oöcytes

334  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY were analyzed, and three had a supernumerary chromosome 21.5 A rather elegant demonstration of maternal gonadal mosaicism is described in Cupisti et al. (2003), who, in the study of a woman presenting for fertility treatment, identified three oöcyte–polar body pairs having one copy of chromosome 21 in the egg, and two copies in the first polar body. As for the male parent, Hixon et al. (1998) analyzed sperm samples from 10 men who had fathered a DS child, the additional chromosome 21 having been demonstrated to be of paternal origin. None showed any increase in the fraction of sperm with disomy 21. The concept that parental gonadal mosaicism may be a substantial contributor to the occurrence (and recurrence) of aneuploidy, and not merely a matter of small-print interest, is due in particular to Kovaleva (2010), Delhanty (2011), and Hultén et al. (2013). Kovaleva assembled data from the literature and from local records, from 80 families in which one parent was gonadal/gonadal-somatic mosaic for trisomy 21. Where the origin of the trisomy in the mosaic parent could be determined, three-quarters had been due to post-zygotic rescue of a meiosis I error,6 and one-quarter came from either rescue of a meiosis II error or a post-zygotic mitotic nondisjunction. The sex of the mosaic parent was usually female (61/80 cases), a paucity of mosaic fathers possibly reflecting an impaired spermatogenesis in such men. Kovaleva also proposed a female-specific tendency toward chromosome loss in early embryogenesis (thus allowing trisomy rescue), and suggested that these mosaic females might be not uncommon in the general population. This hypothesis may be supported by observations in the offspring of the mosaic parents. When these parents had non-mosaic DS offspring, the sex ratio was 1.3:1 in favor of males, as observed for DS in the general population. But in the nine instances in which a mosaic DS parent had mosaic DS offspring, in all but one the child was female. The explanation is complex (and unproven), but there may be, first, an intrauterine selection against non-mosaic DS females, and second, a sex-specific tendency for female DS embryos to be converted to the mosaic state by trisomy rescue. Recurrence Risk Estimates After One Affected Child or Pregnancy.  The earliest estimates of risk are due to Penrose (1956),7 prior to the discovery of the chromosomal basis of DS, and to Stene (1970). Penrose proposed the risk of recurrence to be “doubled, or perhaps nearly trebled” compared to the general population risk, irrespective of maternal age; while Stene derived a figure of 1% for mothers under age 30 years, with no increase in the age-specific risk for those over 30 years at the time of birth of their DS child. More sophisticated analyses were subsequently enabled by the collection of amniocentesis data and from population studies, as we present in the sections on parental age and genetic counseling below. It does remain true that for younger mothers the recurrence risk is, in absolute terms, small. Recurrence Risk Estimates After Two Affected Children/Pregnancies.  When a couple have had two (or more) trisomic 21 conceptions, one has to assume an increased risk applies to a subsequent pregnancy, quite possibly a “substantial” risk. The recurrence may well have been due to gonadal mosaicism, but unfortunate chance always remains a possibility, more particularly if the mother is of older age. 5 Two of the no. 21 chromosomes had identical haplotypes, indicating that the mother’s mosaicism was due to post-zygotic error in an initially normal 46,XX conception (Figure 3–15a). 6 If gonadal mosaicism is the result of rescue of an initially trisomic conceptus, then advanced grand-maternal age is expected to be a risk factor, and this indeed appears to be so (Kovaleva 2010). 7 His paper was titled “Some Notes on Heredity Counseling,” and he also referred to “genetical counseling,” one of the first uses of this expression.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  335 Occurrence Risk Estimates with Down Syndrome in a Second- or Third-Degree Relative.  More widely in the family, it appears that a history of standard trisomy DS in second- or third-degree relatives does not, in the main, imply an increased risk (Hook 1992; Pangalos et al. 1992b). Berr et al. (1990) assessed 188 families in which a DS child had been born, and there were comparable numbers of DS cases among the second- and third-degree relatives and in the relatives of 185 control families. MOSAIC DOWN SYNDROME 47,+21/46,N mosaicism accounts for about 2% of individuals with clinically diagnosed DS. With very low-grade mosaicism, an abnormal phenotype may escape recognition. Papavassiliou et al. (2015) provide an exhaustive literature review, from 1961 to 2014, and offer illustrative examples of the milder phenotype. These authors propose that detection of mosaicism can be achieved when present in as little as 1.6%–1.8% of cells using FISH analysis of peripheral blood (1,000 cells scored) and buccal mucosa (500 cells scored). Mosaicism results from a malsegregation of homologs, or an anaphase lag of one homolog, occurring post-zygotically. Probably the majority of individuals with mosaic DS arise from initially trisomic 21 zygotes, losing one of the chromosomes 21 by anaphase lag as a form of “trisomy rescue” (Figure 3–15c). Others may arise from normal conceptuses, with nondisjunction-producing 45,–21/46,N/47,+21 mosaicism, with the 45,–21 line thereafter lost (Figure 3–15a). Whatever the basis, for practical purposes counseling needs to proceed as though the child has standard trisomy 21, recognizing that this will overestimate the risk in some. Genetic counseling for the mosaic individuals themselves is covered on p. 338. Isochromosome 21 Down Syndrome.  After standard trisomy 21, this is the most common chromosomal category of DS. It has often been called a “21q21q Robertsonian translocation,” but in fact it is almost always the case that the two 21q components are identical, from the same parent, and thus isochromosome is the more accurate term, and the karyotype is more accurately 46,i(21q) (Kovaleva and Shaffer 2003). An agnostic nomenclature is rea(21;21). Most arise in an early postmeiotic mitosis (Robinson et al. 1994), and so the risk of recurrence is expected to be low. In one series of 112 de novo rea(21q;21q) DS probands, none of 130 full sibs and 34 half-sibs had DS (Steinberg et al. 1984). Nevertheless, three of the parents actually showed a low-grade mosaicism, and presumably their having had an affected child reflected that the 21q21q cell line had arisen in a premeiotic mitosis and was included in the gonad. Indeed, a few examples of recurrence in subsequently born siblings are recorded, and parental gonadal mosaicism is the presumed or proven basis of such recurrence (Hervé et al. 2015). For example, Mark et al. (1977) studied a woman having had sequential pregnancies with the karyotype 46,i(21q), and she herself typed 46,XX,i(21q)/46,XX on ovarian fibroblast analysis (but 46,XX on blood). Hall (1985) offers the cautionary story of a mother given a low risk of recurrence, who went on to have a second affected child from a second marriage (on resampling of her, a single 46,XX,i(21q) cell was found in 100 cells analyzed). An i(21q) is a recognized cause of a false-negative cfDNA prenatal screening result for DS, this observation attributed to post-zygotic isochromosome formation leading to placental mosaicism (Huijsdens-van Amsterdam et al. 2018). 336  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY ROBERTSONIAN TRANSLOCATION DOWN SYNDROME Almost all translocation DS concerns a Robertsonian translocation (Chapter 7). About one-quarter of Robertsonian translocation DS is familial, and three-quarters is de novo (1% and 3% of all DS, respectively). De Novo Robertsonian Translocation Down Syndrome.  By definition, both parents have normal chromosomes. The abnormal chromosome may usually arise as a sporadic event in maternal meiosis I, from a chromatid translocation (Petersen et al. 1991). Such mutational events are rare and, in the great majority of families, recurrences are not seen. But gonadal mosaicism remains a possibility. The so-called rob(21q21q) is, in most cases at least, actually an isochromosome (see above). Familial Robertsonian Translocation Down Syndrome.  One or the other parent (almost always the mother) is a translocation heterozygote and has transmitted the translocation, in an unbalanced state, to the DS offspring. We discuss this in detail in Chapter 7. Down Syndrome with Reciprocal Translocation The DS phenotype is substantially due, as we noted above, to a duplication of the chromosome segment 21q22.2q22.3. A reciprocal translocation involving chromosome 21 has the potential to produce a duplication of the DS critical region in a gamete from the heterozygote, whether from 2:2 or 3:1 meiotic segregation. The unbalanced adjacent-1 karyotype from the t(18q;21q) illustrated in Figure 5–20 (second row) is an example. Or, interchange trisomy 21 may result (Figure 5–18). These translocation scenarios are extraordinarily rare, the cause of less than 0.1% of DS. Scott et al. (1995) describe a child with DS from a maternal t(12;21)(p13.1;q22.2), and Nadal et al. (1997) and Lee et al. (2005) describe similar cases from a paternal translocation and insertion, respectively. (It is from studies of cases of partial trisomy 21, comparing those with typical DS and those with different phenotypes, that phenotypic maps, as in Figure 13–1, can be drawn; Kondo et al. 2006.) Interchange trisomy 21 was reviewed by Dominguez et al. (2001), with a total of only 23 published families being accumulated. Other Chromosomal Forms of Down Syndrome A number of chromosomally distinct forms of DS result from specific structural changes to chromosome 21. The least rare of these is the terminal rearrangement that produces a mirror-image chromosome around the telomeric region (Pfeiffer and Loidl 1982). The chromosome has two centromeres, one of which is usually inactive, and satellites on both ends. Such chromosomes are always the result of sporadic mutational events, possibly the result of a translocation between sister chromatids (Pangalos et al. 1992a). DS is seen occasionally in association with other aneuploidies, almost always a sex chromosome aneuploidy such as 48,XYY,+21 and 46,X,+21; this is known as double aneuploidy. It is usually the result of a double event of nondisjunction resulting in one abnormal gamete. Rather less likely is a scenario of separate events in gametogenesis in both parents. Interchromosomal effect has been invoked when standard trisomy DS occurs in the setting of a parental karyotypic abnormality not involving chromosome 21 (e.g., a 13;14

Down Syndrome, Other Full Aneuploidies, and Polyploidy  337 Robertsonian translocation, or a reciprocal translocation). It is plausible to imagine that a different “geography” of the chromosomes within the nucleus, imposed by the complicated synapsis of the translocation chromosomes, could perturb the distribution of other “bystander” normal chromosomes at meiosis and including chromosome 21. The question is controversial; if an effect truly exists, it is apparently of infrequent practical consequence; see also Chapter 5 (Anton et al. 2011; Kovaleva 2013; Li et al. 2015). Parent with Down Syndrome Maternal Trisomy 21. At female meiosis, the classical scenario is that the three homologs form either a bivalent and a univalent, or a trivalent (Figure 13–5; Wallace and Hultén 1983). If the former, the bivalent may disjoin and segregate symmetrically, but the univalent passes at random to either daughter cell (1:1 + 1 segregation). If the latter, a trivalent would of itself set the stage for aberrant segregation (2:1 segregation). Speed (1984) has observed trivalents in about 40% of meiotic cells, and a bivalent plus a univalent in the remaining 60%. In either case, the result is disomic (24,+21) and normal (23,N) gametes in equal proportions. An alternative scenario is that the “third” chromosome 21 separates prematurely into chromatids, and each chromatid then passes to a daughter cell (the oöcyte, and the first polar body). Cozzi et al. (1999) provide direct evidence for this mechanism in the FISH study of unfertilized oöcytes from a woman who was presumed to be a 46/47,+21 gonadal mosaic. In a review of the literature, Shobha Rani et al. (1990) list 30 reports of pregnancy in DS women. The ratio of DS to normal offspring was 10:17 (there were three abortions), not significantly different from a 1:1 ratio, but suggestive of a deficit in trisomic offspring. A reasonable interpretation is that 46,N and 47,+21 conceptions occur with equal frequency, but loss of pregnancy is greater with the trisomic fetuses. About one-third of the 46,N offspring were nevertheless abnormal, which may have reflected paternal factors. In a Canadian review of hospital records, there were 184 pregnancies in DS women from 2004 to 2011, but a fetal chromosome abnormality was detected in only 15%; this relatively low figure possibly is due to pregnancy terminations not being recorded (Alnoman et al. 2024). Stern et al. (2016) make the intriguing observation that transmission of DS decreases with the age of a DS mother, and postulate that uterine factors might be responsible. Paternal Trisomy 21.  Spermatogenesis is reduced in the male with non-mosaic DS, but it does not necessarily fail; and a tiny number of examples of proven or suspected Figure 13–5.  Meiosis in Parent with Down Syndrome. Notes: Possible synapsis of three no. 21 chromosomes: (a) as a trivalent and (b) as a bivalent and a univalent. 338  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY fatherhood in DS males have been documented (Pradhan et al. 2006). One notable case concerns the use of IVF with preimplantation genetic screening, with all but one of 10 embryos being euploid; a phenotypically normal child was born (Aghajanova et al. 2015). Parental Trisomy 21 Mosaicism.  In practice, it is usually only those recognized mosaic individuals with a low percentage of +21 cells who seek genetic advice. These people typically come to notice because they are studied as apparently unaffected parents of more than one DS child. The important factor, if it could only be known, is the degree to which the gonad comprises 46,N and 47,+21 cells. The trisomic cells produce disomic and normal gametes in equal proportion; of course normal cells, other things being equal, give rise only to normal gametes. Thus, the proportion of abnormal gametes produced depends on the proportion of germ cells that are trisomic. In the limit, the gonad might be fully 47,+21. Any level of correlation between the degree of mosaicism in lymphocytes and gametes is not readily amenable to study. Familial trisomy 21 mosaicism is on record but is exceptional (Kovaleva 2010). Trisomies 13 and 18 (Patau Syndrome and Edwards Syndrome) These syndromes are much less frequent than DS (about 1 in 12,000 and 1 in 6,000 live births for trisomies 13 and 18, respectively), and both show a maternal-age effect. About 90% originate in maternal meiosis (Bugge et al. 1998; Bugge et al. 2007). As with trisomy 21, correlative phenotypic mapping allows certain segments of chromosomes 13 and 18 to be implicated in the genesis of certain phenotypic traits observed in these syndromes (Tharapel et al. 1986; Epstein 1993; Boghosian-Sell et al. 1994). Parental Trisomy 18 Mosaicism This is extremely rarely recorded in adulthood, and Tucker et al. (2007) review in detail the range of phenotypes. Some individuals had presented with a history of miscarriage, and some due to having had a child with trisomy 18. Because of the usual high rate of lethality of trisomy 18 in utero, the reproductive risks obtaining in such persons would apply substantially to miscarriage. The risk will relate to the gonadal load of trisomic cells; this is not usually known, but some gametic studies are recorded. Bettio et al. (2003) report a woman of normal intelligence with 70% trisomic 18 cells on blood but none on fibroblast karyotyping, presenting with infertility. Ovarian biopsy showed 90% trisomic cells from right ovarian biopsies, and a normal karyotype in left ovarian tissue. A man of normal intelligence and appearance, presenting with severe oligospermia, had approximately 50% trisomy 18 mosaicism on blood and buccal mucosal cell analysis, although only 3% in skin fibroblasts: On sperm study, there was a 10-fold increase in disomy 18 compared with control data, although the absolute fraction was small, 0.68% (Perrin et al. 2009a). Both testes may be free of the trisomic line, as apparently in the father of a normal daughter described in Lim and Su (1998). He was of normal intelligence and worked as a sales representative, and had “slightly unusual facial features.” The trisomic line was found only in blood (76%) and not in skin fibroblasts, and the disomic 18 rate in sperm was similar to that of a control.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  339 OTHER AUTOSOMAL TRISOMY It is extremely rare for any other non-mosaic autosomal trisomy to survive through to (or near to) term. About two dozen examples of each of trisomy 9 and 22 are known (Table 13–2), and the phenotypes have been universally severe. The mosaic state, which in some may have reflected a post-zygotic “trisomy rescue,” may allow otherwise universally lethal trisomies to survive to term, and most chromosomes are represented (Table 13–3). Of these, trisomy 9 mosaicism is the most frequently observed, and Li et al. (2021a) were able to accumulate an experience of 16 cases, adding to the literature resource of about 100 cases. The observed neurodevelopmental range was wide indeed, extending from those who were nonverbal through to children able to participate in educational programs with age-appropriate peers, presumably reflecting the degree and distribution of the trisomic lineage. Blood analysis showed no correlation of karyotype and phenotype; testing a more “basic” tissue, such as buccal fibroblasts, would likely achieve a more accurate representation of the whole-body trisomic load. The ranges of phenotype are too great to summarize here, other than to note that hypomelanosis of Ito (Figure 3–22, Chapter 3) is a common observation. The large Table 13–2.  Recorded Post-natal “Rare Chromosome” Non-Mosaic Trisomies TRISOMY REFERENCE 9 Pejcic et al. 2018 22 Phung et al. 2023 Table 13–3.  Recorded Post-natal “Rare Chromosome” Mosaic Trisomies TRISOMY REFERENCE 2 Talantova et al. 2023 3 Kekis et al. 2016 4 Bouman et al. 2016 5 Sánchez-Herrero et al. 2020 6 Destree et al. 2005 7 Gouveia et al. 2016 8 (Warkany syndrome) Sanderson et al. 2021 9 Li et al. 2021a 10 Gao et al. 2018 12 Hu et al. 2021 14 Godfrey et al. 2018 15 McPadden et al. 2015 16 Nguyen et al. 2020 17 Baltensperger et al. 2016 19 Chen et al. 1981 20 Montplaisir et al. 2019 22 Nardelli et al. 2023 340  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY influence upon phenotype will be due to the distribution of mosaicism, which could range from almost pure trisomy through to a majority-normal cell line, with phenotypes from fetal lethality through to near-normal. The examples cited here were typically, but not universally, of severe phenotype. In contrast, trisomies are very common in miscarrying pregnancies, a matter dwelt upon in detail in Chapter 20. A risk of recurrence, for the same (“homotrisomy”) or a different trisomy (“heterotrisomy”) is very slightly increased, and this is discussed in the “Genetic Counseling” section. Parental Trisomy Mosaicism, of Near-Normal or Normal Phenotype MOSAIC TRISOMY 7 A single instance of familial low-grade trisomy 7 mosaicism is on record: a mother and daughter of normal physical phenotype, both with a psychiatric condition (DeBault & Halmi 1975). MOSAIC TRISOMY 8 In most cases mosaic trisomy 8 arises post-zygotically8 from an initially normal conceptus (Robinson et al. 1999). Habecker-Green et al. (1998) review reports of reproductive status in 47,+8/46 individuals, and there is only a tiny number of cases, usually in persons in whom the diagnosis would not have been suspected clinically. They describe a woman with mosaic trisomy 8 having a history of four spontaneous losses, including a 46,XX fetal death at 27 weeks; her next pregnancy produced an apparently normal 46,XX daughter. Rauen et al. (2003) report a woman who presented a more typical clinical picture of trisomy 8 mosaicism having a 46,XX child (phenotypic abnormality in the child probably reflected paternal characteristics). Mercier and Bresson (1997) studied an otherwise healthy man whose partner’s recurrent miscarriage was the presenting problem, and in whom the peripheral blood karyotype was 47,XY,+8[8]‌/46,XY[92]. On FISH analysis of 25,000 spermatozoa, 398 (1.6%) showed disomy 8, which, although elevated compared with the rate in control sperm of 0.2%, is unlikely to explain recurrent miscarriage. We have seen a somewhat similar case, a man of above-average intelligence and excellent physical health with infertility due to oligospermia, in whom low-level trisomy 8 mosaicism was shown on two separate blood samplings; in his case, one could not exclude that the abnormal cell line was confined to hematological tissue and the oligospermia coincidental. Autosomal Mosaicism, Age-Related Analogous to age-related mosaic loss of the Y chromosome (mLOY, Chapter 15), age-related mosaicism for autosomal chromosomes has been associated with increased morbidity, including hematological malignancy and infection, and with an increased mortality. This hematological mosaicism is not of itself causative but is merely an epiphenomenon, the reflection of an underlying cellular susceptibility. Concerning a risk 8 Trisomy 8 mosaicism of meiotic origin is sometimes found in miscarriage samples, but when detected postnatally, appears to cause a phenotype distinct from Warkany syndrome (p. 687)

Down Syndrome, Other Full Aneuploidies, and Polyploidy  341 for infection (sepsis, pneumonia including Covid-19, digestive system, genitourinary), this susceptibility is manifest in a diminished immune response (Zekavat et al. 2021). The analysis is based upon DNA genotyping array intensity data, and is presently seen as a research endeavor rather than a clinically-applicable test. AUTOSOMAL MONOSOMY Many non-mosaic autosomal monosomies are presumed to end in arrested growth in the first few mitoses at the morula/blastocyst phase, prior even to the time of implantation, with a few possibly proceeding to the stage of “occult abortion.” The existence of most monosomies would have been unproven had it not been for the window of observation afforded by preimplantation testing. The two exceptions may be monosomy 21 and monosomy 22, albeit that most earlier reports of monosomy 21 have since been reinterpreted as being due, for the most part, to an unbalanced translocation involving chromosome 21 (Cardoso et al. 2008). For some other monosomies, mosaicism can allow for survival (Table 13–4 and below). Clinical suspicion should be piqued when asymmetry or Blaschko-linear hyperpigmentation (Figure 3–22) is seen. Monosomy 14.  Three cases of monosomy 14 mosaicism have been reported, all in the setting of a 46,r(14) cell line. McConnell et al. (2004) reported a profoundly disabled girl with complete monosomy of chromosome 14 in 18% of cells, and the remaining 82% cells having a ring 14 chromosome. The diagnosis was made prenatally in amniocytes, and confirmed after delivery in blood lymphocytes. The child had severe intellectual disability, microcephaly, seizures, and dysmorphic features, and died at age four years. Other cases were reported by Portoian-Shuhaiber et al. (1986) and Ono et al. (1999). Monosomy 18.  Only two cases of monosomy 18 mosaicism are on record. Khalifa et al. (1996) reported a toddler with severe developmental delay, nystagmus, optic atrophy, and hypotonia, in whom 5% of lymphocytes were monosomic 18, but fibroblasts were normal. The child in Jackson et al. (2000) had cleft lip and palate but near-normal neurodevelopment. His peripheral blood karyotype was 45,XY,−18[14]/46,XY[86]. Monosomy 20.  Hochstenbach et al. (2014) summarized four cases of mosaic monosomy 20 from the literature and added their own, a boy with an IQ of 54, poor muscular development but not dysmorphic, and whose brain MRI was normal. Multiple samples (blood, skin, buccal mucosa) were monosomic in ½%–4% of cells. As these authors note, this low level of mosaicism would have escaped detection at molecular karyotyping. In other reported cases, the abnormal cells were detected at low percentages, and Table 13–4.  Recorded Post-natal Monosomies MONOSOMY NON-MOSAIC (N) MOSAIC (N) REFERENCE 14 0 3 McConnell et al. 2004 18 0 2 Jackson et al. 2000 20 0 5 Hochstenbach et al. 2014 21 9 9 Viana et al. 2022 22 2 5 Pinto-Escalante et al. 1998 Source: Adapted from Bunnell et al. (2017).

342  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY the phenotype ranged from clinically normal to delayed motor and intellectual development, with mild dysmorphic signs and asymmetry. In two of the five cases, a trisomy 20 cell line was also detected, suggesting origin in a post-zygotic mitotic nondisjunction; and in one, the monosomy 20 was seen only in urine cells. Monosomy 21.  This is the most common full monosomy, and Viana et al. (2022) summarized data from nine mosaic and nine non-mosaic cases. Their own case, a 13-year-old boy, was the oldest surviving patient with mosaic monosomy 21. He presented with microcephaly, low weight, facial dysmorphisms, and severe intellectual disability; monosomy 21 was seen in 81% of lymphocytes. A similar phenotype has been described in other cases. When non-mosaic, monosomy 21 typically results in miscarriage or neonatal death, and is likely incompatible with life. In some reported cases, there may have been undetected mosaicism for a tissue-limited cryptic cell line. Burgess et al. (2014b) emphasize this point in their description of a growth-retarded and dysmorphic neonate, who karyotyped full monosomy 21 on blood and buccal swab, but fibroblast study revealed a cryptic ring chromosome karyotype 45,XX,-21[8]‌/46,XX,r(21)[42]. Monosomy 22.  Pinto-Escalante et al. (1998) reported a dysmorphic and malformed infant, delivered at 30 weeks gestation and who died from septicemia on day 11; 15% of lymphocytes were monosomic. The authors reviewed six other literature cases, noting recurrent observations of growth retardation, microcephaly, facial dysmorphism, joint abnormalities, and cardiac defects. Early death was usual, although two children were alive at age two years. In three cases, 100% of lymphocytes and fibroblasts were monosomic, yet the phenotype was not obviously more severe. Cryptic mosaicism for a normal cell line may have been present. POLYPLOIDY Triploidy The chromosome count in triploidy is 3n = 69, with a double (2n) chromosomal contribution to the conceptus from one or other parent (Figure 13–6). Triploidy can reflect di-andry or di-gyny, with the double contribution coming from the father or mother, respectively (Figure 13–7). The very great majority of triploid conceptions abort during the first or early second trimester. Increasing maternal age does not increase the risk for triploidy. The Two Distinct Forms of Triploidy.  Diandry is usually the consequence of dispermy—that is, two sperm simultaneously fertilizing the ovum (Zaragoza et al. 2000; McFadden et al. 2002).9 A shorthand description is P1 P2M. The fundamental basis in this instance may lie in the “zona reaction,” which is the response of the investing shell of the ovum, the zona pellucida, to prevent further sperm entering after the first has penetrated. Digyny is most commonly due to a diploid egg, which may be the result of nondisjunction of the entire chromosome set at either the first or the second meiotic division in oögenesis, meiosis II being the more vulnerable—or, a polar body may fail to be 9 Dispermy could be deduced simply from the cytogenetic analysis in the case reported in Lim et al. (2003), the man carrying a translocation 46,XY,t(2;6)(p12; q24). The 69,XXY mole had both the balanced translocation and one unbalanced form, reflecting fertilization with one sperm from alternate segregation and the other from adjacent-1. A dispermic mole, at the center of a criminal case, posed a challenge to the assigning of paternity (Budowle et al. 2017). Down Syndrome, Other Full Aneuploidies, and Polyploidy  343 extruded (Filges et al. 2015). An individual susceptibility may exist, as discussed below. A very rare cause may be the fusion of two eggs (whimsically called “dieggy”). Diploidy can be presumed to exist in the “giant binucleate oöcyte,” and these visibly abnormal gametes have actually been shown at IVF to lead to a triploid embryo (Balakier et al. 2002; Rosenbusch et al. 2002). Natural History.  Triploidy is not uncommon in early pregnancy (~1% of recognized conceptions and 10% of recognized miscarriages), but about 99.99% are lost as first-trimester miscarriage or second-trimester fetal death in utero. Of those aborting at the embryonic stage, most are digynic, while in contrast, most fetal losses reflect a diandric state (McFadden and Robinson 2006). The appearances on morphological examination at the stage of the embryo do not differ according to a digynic versus diandric origin, Figure 13–6.  Triploidy. Note: The 69,XXY karyotype of a triploid embryo (the embryo shown in Figure 20-18) Figure 13–7.  Triploidy Origins. Notes: The three major routes whereby triploidy may arise. A complete failure of a meiotic division produces a diploid egg (left) or sperm (middle). Simultaneous fertilization by two sperm is dispermy (right).

344  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY whereas the clinical presentations are readily distinguishable by the time of the fetal stage of development, as follows: Diandric triploids mostly abort in the first or early second trimester, presenting as hydatidiform mole (Scholz et al. 2015). The very few diandric triploid pregnancies that survive to the second trimester typically show partial hydatidiform mole; growth retardation of the fetus is usual but not invariable (Daniel et al. 2001). Dygynic triploids are non-molar, and mostly abort early (mean 10 weeks), although those exceptional few that remain are able to continue through to the third trimester. These surviving digynic triploids develop as a severely growth-retarded fetus with marked head-body disproportion, the head being relatively large, and with an abnormally small and non-molar placenta (McFadden and Langlois 2000; Daniel et al. 2001). In one case of a digynic 69,XXX triploid coexisting with a normal 46,XY twin, survival to 20 weeks (when selective feticide was done) may have been supported by the normal fetus (Gassner et al. 2003). Intrauterine survival may also be promoted if there is fetal-placental karyotypic discordance, with the placenta being diploid (Kennerknecht et al. 1993a). Survival through to the third trimester progresses almost invariably to perinatal death. Of those liveborn, hardly any digynic triploids survive for more than a month; there is one extraordinary instance of death not until 312 days (Sherard et al. 1986; Hasegawa et al. 1999). From Hawaiian data, of 38 recognized triploid pregnancies over the period 1986– 1999, ~40% were XXX, 60% XXY, and a single case of XYY. Most (80%) aborted early, a few (10%) presented as fetal deaths in utero, and 10% were electively terminated (Forrester and Merz 2003a). In a large Danish series, 84% of triploids were diandric. Of the diandric cases, 69,XXX, 69,XXY, and 69,XYY karyotypes were seen in the proportions 7:8½:1. Of the digynic cases, XXX and XXY cases were of similar frequency (Joergensen et al. 2014). Of all 16-week pregnancies, only one in 30,000 are estimated to be triploid, and at 20 weeks only one in 250,000 (Snijders et al. 1995). RECURRENCE Given that triploidy affects 1% of recognized pregnancies, most recurrence is a chance event, and after one digynic triploid pregnancy the risk of a second is no greater than the background figure. Nonetheless, the question remains whether specific risks might apply to a small subset of women, including those having had three (Huang et al. 2004; Brancati et al. 2003) or even four (Khawajkie et al. 2017) triploid pregnancies. Filges et al. (2015) make the case for a failure of maternal meiosis II as a common basis for this predisposition. There may be a genetic basis for some of these recurrences. In the study of an extraordinary mother-daughter pair, both of whom had had multiple miscarriages known or likely due to recurrent triploidy, Filges et al. analyzed a number of candidate genes. One was PLCD4, for which mother and daughter were both heterozygous for a predicted pathogenic mutation; and this gene may have a role in the extrusion of the second polar body. Two other candidate genes, each with a role in maternal meiosis, have since been identified in single consanguineous families: Liang et al. (2024) identified a homozygous truncating variant in HORMAD2 in a woman with recurrent digynic triploid miscarriage, and Fatemi et al. (2021) identified a homozygous missense variant in CCNB3 in two sisters who both had recurrent pregnancy losses, two of which were confirmed as digynic triploidy. Confirmation of the role of these loci awaits the identification of additional families.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  345 Recurrence of diandric triploidy with partial hydatidiform mole is also well reported, although in the series of Nguyen et al. (2018), none of eight patients had more than two. In a registry study of partial hydatidiform mole, 0.3% of women had a recurrence in a subsequent pregnancy, including one woman with three confirmed dispermic triploid pregnancies (Eagles et al. 2015). Recurrent diandric triploidy is to be distinguished from the autosomal recessive form of recurrent hydatidiform mole, which occurs in the setting of a diploid biparental genome in which the cause is biallelic variants in the oöcytes, the major causal genes being NLRP7 and KHDC3L (Slim et al. 2022) (p. 619). Coincidence is the most likely explanation for the occurrence of triploidy of both digynic and diandric etiologies to the one couple, and for the occurrence of both partial hydatidiform mole (due to diandric triploidy) and complete mole (the rare type associated with biparental disomy) to the same couple (Kircheisen et al. 1991; Deveault et al. 2009). The risk of a triploidy is lower in IVF pregnancies, first because intracytoplasmic sperm injection can ensure the ovum is fertilized by only one sperm, and second by excluding embryos with three pronuclei (5% of all embryos) (Nickkho-Amiry et al. 2019). Having made that point, Capalbo et al. (2024) note that pronuclei number is a poor predictor of embryo ploidy, and that PGT can provide a more accurate ploidy assessment (Caroselli et al. 2023). The prevention of chromosomal pathology, as a direct exercise, largely involves secondary prevention: in essence, the selective termination of pregnancies in which a chromosomal abnormality has been identified, or the discarding of abnormal embryos following PGT. Primary prevention is indirect, and encouraging a younger maternal age may be the only feasible approach absent any clear understanding of environmental factors that might compromise the chromosomal integrity of gamete or zygote. But one remarkable exception to this state of affairs concerns the actual correction of a chromosomally abnormal zygote; this involves the diandric triploid zygote, otherwise destined to undergo implantation failure or, in the minority that actually implant, to proceed to a severe fetal defect. A triploid zygote due to dispermy will possess three pronuclei. In vitro removal of one pronucleus at IVF would restore normality. In the case of dispermy, this would have to be one of the paternal pronuclei, thus leaving one maternal and one paternal pronucleus. Escribá et al. (2006) applied this approach to tripronuclear embryos in the research laboratory, removing the pronucleus farthest from the second polar body (the one closest to the polar body being very likely maternal), and followed the embryo through to the blastocyst stage. They were able to confirm restoration of diploidy and could also observe that these corrected embryos showed normal development at day 5, unlike the uncorrected embryos in which no inner cell mass was seen to form. And in the first ever example of “chromosomal cure” of a child-to-be, Kattera and Chen (2003) corrected a tripronuclear zygote, implanted the embryo, and a normal 46,XY boy was subsequently born. These authors comment, cautiously, that this approach should be used “only as a last resort.” Diploid/Triploid Mosaicism.  Van de Laar et al. (2002) accumulated 25 cases from the literature, and reported three of their own. These three came from a population catchment of 15 million over a 20-year period, attesting to the rarity of the condition. Characteristic features include learning difficulties, seizures, short stature, truncal obesity, syndactyly, and body asymmetry. Phenotypic overlap with imprinting disorders is

346  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY to be noted. The triploid line typically reflects digyny, and the basic mechanism may be inclusion of the second polar body at a very early stage after conception of a diploid zygote. Similarly in diandric cases, the mechanism may be dispermy, but with one sperm pronucleus sequestered in the cytoplasm for a few divisions before being incorporated into the nucleus (Daniel et al. 2003b; Wegner et al. 2009). Daniel et al. refer to “delayed digyny” and “delayed dispermy” respectively, as the course of events whereby the extra pronucleus sits to one side, so to speak, while the diploid lineage is in the process of being established, and the pronucleus is then taken up into the nucleus of one blastomere to give rise to the triploid cell line. Survival of the affected fetus in utero is presumably promoted by the diploid cell line. In most cases the triploid line is not seen on a blood analysis, and fibroblast culture is necessary (Boonen et al. 2011). A single instance of a false-negative amniocentesis due to diploid/triploid mosaicism is on record (Flori et al. 2003). Rare Complexities.  “Hypotriploidy” describes the circumstance of a 68-chromosome constitution. The usual mode of formation may be fertilization of a diploid egg with a 22,–X sperm, leading to a 68,XX karyotype; the phenotype resembles that of digynic triploidy (Pasquini et al. 2010). 45,X/69,XXY mosaicism is recorded in a single case, an infant presenting with genital ambiguity, and who displayed complete soft tissue syndactyly of the index and middle fingers of one hand (this being a feature of triploidy) (Quigley et al. 2005). On blood, the karyotype was non-mosaic 45,X, and on skin fibroblast culture, 45,X[3]‌/69,XXY[77]. Quigley and colleagues propose an initial 46,XY zygote which lost an X in one cell at possibly the first cell division, giving rise to the 45,X lineage, followed by delayed dispermy of a (or the) 46,XY cell, to give the 69,XXY cell line. TETRAPLOIDY Several mechanisms may lead to a conceptus with 92 chromosomes, four of each homolog (4n = 92). The simplest is a reduplication of the diploid set in the zygote. At the first mitosis, the chromosomes replicate, but the cell fails to divide. These would karyotype as either 92,XXXX or 92,XXYY. In the case of a 92,XXXY karyotype, a different mechanism would need to be supposed. In a review of Danish cases having presented as hydatidiform mole, Sundvall et al. (2013) showed two-thirds to reflect the former scenario. In a minority, it is necessary to invoke such processes as trispermy, retention of a polar body with concomitant dispermy, or dispermy with a haploid and a diploid sperm; Sundvall et al. rehearse these and other (rather complicated) possibilities and propose very early mitotic events that could further modify the karyotype, with consequential mosaicism. Two examples are on record of women having had a previous digynic triploid, and subsequently a 92,XXXX and 92,XXXY conception, respectively, the latter case proven to reflect an extraordinary coincident maternal and paternal gametic diploidy (Check et al. 2009; Soler et al. 2016). The typical phenotype is that of miscarriage with complete hydatidiform mole, or “hydropic abortion” (Fukunaga 2004). Tetraploidy in a term pregnancy is exceedingly rare. Okamura et al. (2024) summarized 10 cases of liveborn triploidy from the literature and contribute the oldest known survivor, a 4-year-old girl. Predictably, the phenotype is of severe physical and intellectual disability, multiple malformations, and growth retardation.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  347 Mosaic diploidy/tetraploidy in a person has been described in association with severe intellectual disability, and it may only be detectable on skin fibroblast study (Edwards et al. 1994). A complex case is that reported in Leonard and Tomkins (2002) of an intellectually disabled woman with body asymmetry and hypomelanosis of Ito, in whom some fibroblasts cultured from hypopigmented skin showed 92,XXXX, others being 46,XX and 46,XX,t(1;6)(p32;q13), and 46,XX on blood. True diploid/tetraploid mosaicism may be quite frequent at the blastocyst stage of development, but either the abnormal embryo is cast off shortly thereafter or, especially if the proportion of tetraploid cells is small and the blastocyst is otherwise of good quality, the polyploid component may be confined to the trophoblast and in due course come to comprise a minor fraction of placenta (Bielanska et al. 2002; Clouston et al. 2002). Possibly for this reason, tetraploidy can occasionally be seen at chorionic villus sampling (CVS) and at amniocentesis, reflecting a functionally unimportant tetraploidy of part of the placenta, with the remaining extrafetal and fetal tissues being karyotypically normal (Benkhalifa et al. 1993). Alternatively, tetraploidy at prenatal diagnosis may be artifactual. THE INFLUENCE OF PARENTAL AGE IN PREDISPOSING TO ANEUPLOIDY The maternal-age association in Down syndrome was known long before its chromosomal basis. In 1909, Shuttleworth wrote that “with regard to parentage . . . the outstanding point is the advanced age of the mother at the birth of the child. . . . The next point that strikes one is the large proportion of Mongol children that are lastborn, often of a long family.” He considered that either age or parity could be an etiologic factor. Subsequently, Penrose (1933, 1934) demonstrated that it was the mother’s age that was the key factor. A powerful insight into the actual nature of the maternal-age effect has been afforded by Battaglia et al.’s (1996) study in normal women, showing that the oöcyte’s meiotic apparatus deteriorates with age (Figure 3–13). As well as no. 21, the influence of maternal age operates on all the “survivable” aneuploidies (Figure 13–8). Sherman et al. (1994) stated that “increasing maternal age is one of the most important factors in human reproductive failure, as well as being a leading contributor to mental retardation among live-borns.” Hassold et al. (1993) commented that “the association between increasing maternal age and trisomy is arguably the most important etiologic factor in human genetic disease. Nevertheless, we know almost nothing about its basis.” The maternal-age effect in DS—whatever it may be—has been considered to operate upon oögenesis, predisposing to nondisjunction of chromosome 21, predominantly at the first meiotic division. In more general terms, segregation of some of the other chromosomes is vulnerable to the maternal-age effect. Thus, “older women” who are pregnant run an increased risk for having a pregnancy with trisomies 13, 16, and 18, 47,XXX and 47,XXY, as well as trisomy 21. There is also a slight maternal-age association with disorders due to maternal uniparental disomy with trisomy rescue (Ginsburg et al. 2000), this point being discussed in more detail in Chapter 19. 348  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY The oöcyte being the key player, studies have been directed to this gamete. Segregation errors within female meiosis fall into three categories (Franasiak et al. 2014; Gruhn et al. 2019): (1) meiosis I nondisjunction (NDJ); (2) precocious separation of the sister chromatids (PSSC); and (3) reverse segregation (RS) (sister chromatids separate at meiosis I and homologs separate at meiosis II). These are illustrated in Figure 13–9. The relative contribution of these three mechanisms varies according to the chromosome involved, and with maternal age. Oöcytes from young girls and women are more vulnerable to meiosis I NDJ events that particularly affect the largest chromosomes Figure 13–8.  The Likelihood of a Survivable Aneuploidy according to Maternal Age. Notes: These data are based on a whole population cohort in Denmark, and record pregnancies in which trisomy 21, 18, or 13, triploidy, or monosomy X were diagnosed. Mothers in the age group 30-34 had a small increased risk (Odds Ratio, OR, of 1.7) above the baseline of 20 to 29-year-olds, to have a pregnancy with one of these aneuploidies; those in the 35-39 age group had an OR of 4.7; 40 to 44-year-olds had a 16-fold risk; while the oldest group, 45 and older, had a 36-fold increased likelihood. Source: From L Elmerdahl Frederiksen et al., Maternal age and the risk of fetal aneuploidy: A nationwide cohort study of more than 500 000 singleton pregnancies in Denmark from 2008 to 2017, Acta Obstet Gynecol Scand 103:351–359, 2024. Courtesy CK Ekelund, and with the permission of John Wiley and Sons. Figure 13–9.  Segregation Patterns in Female Meiosis Leading to a Trisomic Conceptus. Notes: Pericentromeric haplotypes shown in orange and green. MI NDJ, meiosis I nondisjunction; PSSC, precocious separation of sister chromatids; MII NDJ, meiosis II nondisjunction. Source: From CS Ottolini et al., Genome-wide maps of recombination and chromosome segregation in human oocytes and embryos show selection for maternal recombination rates, Nat Genet 47:727–735, 2015. Courtesy CS Ottolini, and with the permission of Springer Nature.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  349 (chromosomes 1 to 5).10 In contrast, oöcytes from older women are more likely to be affected by PSSC and RS errors of the smaller acrocentric chromosomes (Gruhn et al. 2019). These findings explain the “U-curve” of aneuploidy against maternal age, with peaks at both ends of the age spectrum, and the lowest chance of aneuploidy corresponding to maternal age 27.5 years (Figure 13–10). The age-dependent increase in PSSC and RS likely relates to the prolonged oöcyte arrest and potential protein deterioration over time, with degradation of cohesin proteins and proteins involved in spindle function contributing to aneuploidy formation. Paternal age generally does not usefully enter the equation, at least with respect to the numerical full aneuploidies (Donate et al. 2016).11 Fathers of DS children are older than average, but simply because couples are usually of similar ages, a point determined by Penrose in 1934. On meta-analysis, a paternal age >40 years was associated with a relative risk of 1.13 for Down syndrome compared to paternal age <40 years, a difference that was just statistically significant (Oldereid et al. 2018). In contrast, Steiner et al. (2015) made the surprising observation of a subtle but definite effect of younger age of the father (Figure 13–11), the proposed explanation being that of a reduced intrauterine survival for the trisomic pregnancy from older fathers. 10 Trisomies of these chromosomes will seldom result in recognized pregnancies, therefore the main consequence of these aneuploidies will be reduced fertility in girls and young women, possibly having provided an evolutionary advantage in prehistoric times. 11 As for structural rearrangements, a true paternal-age effect is considered to exist, albeit at an order of magnitude less than the maternal/aneuploidy association (Sloter et al. 2004). Figure 13–10.  Chromosome Missegregation Patterns across the Lifespan. Notes: Aneuploidy rates in human oöcytes (dashed red line) peak in both young girls (<20 years) and in women of older maternal age (≥33 years). This increase at either end of the age spectrum reflects a combination of three different chromosome missegregation patterns, with young oöcytes being affected primarily by MI NDJ (red), and advanced maternal age oöcytes impacted by PSSC (blue) and RS (yellow). Source: From JR Gruhn and ER Hoffman, Errors of the egg: The establishment and progression of human aneuploidy research in the maternal germline, Annu Rev Genet 56:369–390, 2022. Courtesy ER Hoffmann, and with the permission of Annual Reviews. 350  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Concerning gametic studies in older men, numerous sperm analyses have been done, with somewhat conflicting findings (Robbins et al. 1997; Shi and Martin 2000; Eskenazi et al. 2002; Shi et al. 2002; Iwarsson et al. 2015). Some have shown slight increases in some autosomal disomies, and some have shown increases in sex chromosome disomies, with XY disomy being more consistently noted. Other studies report no significant differences in at least autosomal abnormalities comparing older and younger men (one group even using testicular sperm from men in their 80s; Guttenbach et al. 2000). Given that trisomy 21 is of paternal origin in only 5% to 10% of cases, it is unlikely that a small increase in sperm disomy from older fathers, even if real, would lead to a measurable increase in birth prevalence for DS, if paternal age profiles should increase. Dviri et al. (2021) reviewed evidence from embryos derived from young oöcyte donors, to minimize maternal-age effects, and concluded that advanced paternal age is not associated with higher rates of aneuploidy in PGT-tested embryos. Risk Figures According to Maternal Age How old is “older,” and what is “advanced” maternal age at childbearing? Conventionally, the mid- to late thirties is taken as the boundary. The risk curve for DS, the major condition of concern, begins to steepen during this period, although there is no sudden jump. Risk figures for individual ages with respect to this and other aneuploidies have been collected in various jurisdictions, and estimates refined according to certain statistical assumptions, and the information from these studies has long been used as the basis of preconceptional and prenatal genetic counseling. These data are also useful in screening Figure 13–11.  Parental Age and Down Syndrome. Notes: Parental ages compared to risk to have a child with Down syndrome. Note that younger paternal age is a slight risk factor, against the well-known and marked older maternal age effect. Source: From B Steiner et al., An unexpected finding: Younger fathers have a higher risk for offspring with chromosomal aneuploidies, Eur J Hum Genet 23: 466–472, 2015. Courtesy B Steiner and A Schinzel, and with the permission of Springer Nature.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  351 programs for fetal trisomy (Chapter 21), the woman’s age-related risk being an important datum to be included, along with the various laboratory test results, in order to derive her overall risk estimate. For trisomies 13, 18, and 21, spontaneous abortion is more likely than for a normal conceptus. Thus, the prevalence of chromosome abnormality is greater at the time of prenatal diagnosis than at term, and we need access to stage-specific figures. Looking through these different windows of observation—at CVS and noninvasive prenatal testing (10 or 11 weeks), at amniocentesis (about 15–17 weeks), at screen-triggered amniocentesis (may be closer to 20 weeks), and at term—the frequency of chromosomal abnormality for a particular maternal age progressively reduces. For trisomy 21, it is estimated that about one-third of all pregnancies existing at the time of CVS spontaneously abort between then and term, and one-quarter abort during the period from amniocentesis to term (Table 13–5 and Figure 13–12). Trisomies 13 and 18 (and monosomy X) have high rates of fetal lethality, with the majority of pregnancies aborting. For XXX and XXY, in contrast, there appears to be very little if any selective loss in the latter part of pregnancy. These matters may be of particular importance to those women who, having had an abnormal result, nevertheless decide to continue a pregnancy. How likely is it that they will have a liveborn baby with the trisomy in question, or that fetal death in utero will supervene? Won et al. (2005) reviewed 392 women who had continued a trisomy 21 pregnancy, and 106 with trisomy 18; the diagnoses had been given somewhat later than might be usual, because these women had entered a public maternal serum screening program at gestations ranging from 15 weeks to 20 weeks, with amniocentesis then offered to those who returned an increased risk result. For trisomy 21, fetal demise occurred in 10%, and for trisomy 18, 32%. About one-third of the trisomy 21 losses happened before the stage of viability (i.e., 24 weeks), the comparable figure in trisomy 18 being 15%. In those pregnancies proceeding beyond 24 weeks, the losses were evenly spread according to duration. More recent figures for trisomies 13 and 18 are due to Cavadino and Morris (2017), derived from a whole-population study in England and Wales. From their work, a surprisingly high 50% of fetuses diagnosed at 12 weeks with trisomy 13 will survive to term, and for trisomy 18, the figure is 30%. These authors discuss possible reasons for the very considerable differences between studies. It is their more recent data that we use in Table 13–5. Table 13–5.  Natural Fetal Loss Rates from Early Pregnancy Through to Term, Estimated for the Three Major Autosomal Trisomies and X Monosomy ESTIMATED AVERAGE NATURAL PREGNANCY LOSS RATE (%) CHROMOSOME ABNORMALITY FROM 9–14 WEEKS TO BIRTH FROM 15–20 WEEKS TO BIRTH FROM >20 WEEKS TO BIRTH Trisomy 13 50 44 40 Trisomy 18 70 65 64 Trisomy 21 32 25 10 Monosomy X 65 52 Note: 9–15 and 15–20 weeks approximate to the stages at which CVS and amniocentesis are performed. Sources: From Snijders et al. (1995), Won et al. (2005), Savva et al. (2006), and Cavadino and Morris (2017).

352  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Down Syndrome The largest body of data to be collated for the age-related risk of trisomy 21 is that of Morris et al. (2002), who examined records from a 10-year period, 1989–1998, in England and Wales. We have used their material as the basis of the age-related livebirth figures to age 44 years presented in Table 13–6, as it is probably the best available; although in fact, the estimates for younger women (up to age 34 years) have been very similar in all studies, and quite similar in the 35- to 44-year age bracket (Morris et al. 2003). However, and contrary to earlier interpretations, the risk of having a baby with trisomy 21 does not increase from age 45 years and older (Cuckle and Morris 2021). This might reflect a greater tendency to miscarry an abnormal fetus in women into their 40s and early 50s (Stern et al. 2016); or hypothetically, a “meiotic robustness” in some women of this age who are yet able to achieve pregnancy. Estimates for the likelihoods of detection of trisomy 21 at prenatal diagnosis, at the maternal ages at which the procedures would be done, are given in Table 13–7. OTHER ANEUPLOIDY The figures for DS are of most interest because this condition (1) produces significant disability; (2) implies a major burden for parents, in that survival well into adult life is now the norm; and (3) is the most common chromosome defect in newborns. But the data for other aneuploidies are important. Women seeking advice on their age-related risk and considering prenatal diagnosis should know also that some other rather uncommon trisomies of severe effect (13 and 18) might be detected; and know that on the other hand, there are some age-related sex chromosome aneuploidies (XXX, XXY) that Figure 13–12.  Trisomy 21 Prevalences. Notes: Prevalence of Down syndrome for maternal ages 36–43 years, at three “windows of observation”: the time at which CVS is done (~10 weeks), amniocentesis (15–17 weeks), and at live birth. Source: From JL Halliday et al., New estimates of Down syndrome risks at chorionic villus sampling, amniocentesis, and livebirth in women of advanced maternal age from a uniquely defined population, Prenat Diagn 15:455–465, 1995. Courtesy JL Halliday, and with the permission of John Wiley and Sons. Down Syndrome, Other Full Aneuploidies, and Polyploidy  353 have much milder, but not trivial, effects. Tables 13–8 and 13–9 set out age-related risk estimates for these other categories of aneuploidy. There is also the possibility, irrespective of maternal age, that some other type of chromosome abnormality might exist. Table 13–10 sets out the risk for any chromosomal abnormality, whether maternal-age associated or not, to be detected at prenatal diagnosis. To put these figures into some perspective, we remind the reader that the prevalence of unbalanced chromosomal abnormality in the whole newborn population is ~1%, or 1 in 100 (Tables 1–2 and 1–3). Another window of observation is afforded at preimplantation testing; rates of aneuploidy increase, according to the mother’s age, in biopsied embryos (Figure 20–11). No Parental Age Effect in Some Defects There is no discernible increasing risk with increasing maternal age for the following chromosomal abnormalities: de novo rearrangement, XYY, triploidy, and unbalanced karyotype due to transmission of parental translocation. For monosomy X, the risk Table 13–6.  Maternal Age–Specific Risks for Trisomy 21 at Live Birth MATERNAL AGE (YEARS) PREVALENCE AT LIVE BIRTH MATERNAL AGE (YEARS) PREVALENCE AT LIVE BIRTH % 1 IN % 1 IN 14 0.09 1,108 32 0.14 695 15 0.04 2,434 33 0.17 589 16 0.05 2,013 34 0.23 430 17 0.06 1,599 35 0.30 338 18 0.06 1,789 36 0.39 259 19 0.07 1,440 37 0.50 201 20 0.07 1,441 38 0.62 162 21 0.07 1,409 39 0.88 113 22 0.07 1,465 40 1.2 84 23 0.07 1,346 41 1.5 69 24 0.07 1,396 42 1.9 52 25 0.07 1,383 43 2.7 37 26 0.08 1,187 44 2.6 38 27 0.08 1,235 45 3.2 30 28 0.09 1,147 46 3.9 26 29 0.10 1,002 47 4.3 23 30 0.10 959 48 3.0 33 31 0.12 837 49 or older 2.0 50 Note: The figures to age 44 years are based on data from just over 6 million births in England and Wales 1989–1998; the figures for 45 years or older come from a review of several sources internationally. Prenatal diagnostic data were included in this material, weighted according to the probability of survival to term. No trisomy 21 pregnancies were recorded at ages 11–13 years (274 births) or at ages 53–55 years (169 births). The percentage figures are rounded. Source: From Table 2 in Morris et al. (2002), the data up to age 44 years; and from Cuckle and Morris (2021) for age 45 years or older. 354  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Table 13–7.  Maternal Age–Specific Risks for Trisomy 21 Calculated at 10 Weeks Gestation (the Usual Time for CVS) and at 16 Weeks (Amniocentesis) DOWN SYNDROME RISK AT GESTATION (1 in) MATERNAL AGE* (YEARS) 10 WEEKS 16 WEEKS 20 800 1050 25 710 930 30 470 620 31 410 540 32 350 460 33 290 380 34 235 310 35 185 245 36 150 195 37 115 150 38 90 115 39 65 90 40 50 70 41 40 50 42 30 40 43 20 30 44 15 20 *Age at the indicated gestation. Source: From Table 2 in Snijders et al. (1995). Figures are rounded. Table 13–8.  Maternal Age–Specific Risks for Trisomies 13 and 18 Calculated at 10 Weeks Gestation (the Usual Time for CVS), 16 Weeks (Amniocentesis), and at Live Birth TRISOMY 13 (1 in) TRISOMY 18 (1 in) MATERNAL AGE* (YEARS) 10 WEEKS 16 WEEKS LIVE BIRTH 10 WEEKS 16 WEEKS LIVE BIRTH 20 6,500 11,000 14,300 2,000 3,600 10,000 25 5,600 9,800 12,500 1,750 3,200 8,300 30 3,700 6,500 11,100 1,200 2,100 7,200 35 1,500 2,600 5,300 470 840 3,600 36 1,200 2,000 4,000 370 660 2,700 37 900 1,600 3,100 280 510 2,000 38 700 1,200 2,400 220 390 1,500 39 530 920 1,800 170 300 1,000 40 400 700 1,400 130 230 740 41 300 530 1,200 95 170 530 42 230 400 970 70 130 400 43 170 300 840 55 95 310 44 130 220 750 40 70 250 *Age at the indicated gestation or at birth, respectively. Source: Prenatal data from Tables 3 and 4 in Snijders et al. (1995), and modeled livebirth estimates from Appendix A in Savva et al. (2010). Figures are rounded.

Down Syndrome, Other Full Aneuploidies, and Polyploidy  355 Table 13–9.  Maternal Age–Specific Risks for 47,XXX and 47,XXY at Amniocentesis and at Live Birth XXX XXY MATERNAL AGE (YEARS) AMNIO (%) LIVE BIRTH (%) 1 IN AMNIO (%) LIVE BIRTH (%) 1 IN 33 0.04 2,500 0.04 2,500 34 0.05 2,000 0.04 2,500 35 0.04 0.05 2,000 0.05 0.06 1,650 36 0.05 0.06 1,650 0.06 0.07 1,450 37 0.07 0.08 1,250 0.08 0.09 1,100 38 0.09 0.09 1,100 0.11 0.11 900 39 0.11 0.11 900 0.14 0.14 700 40 0.14 0.13 770 0.18 0.17 600 41 0.18 0.16 630 0.24 0.22 450 42 0.22 0.19 530 0.31 0.27 370 43 0.28 0.22 450 0.41 0.34 300 44 0.36 0.27 370 0.54 0.43 230 45 0.45 0.32 310 0.70 0.54 180 46 0.57 0.38 260 0.90 0.68 150 47 0.70 0.45 220 1.2 0.85 120 48 0.90 0.55 180 1.5 1.1 95 49 1.1 0.65 150 2.0 1.3 75 Source: From data in Tables 20.4 and 20.7 in Hook (1992). Figures are rounded. Table 13–10.  Maternal Age–Specific Risks for All Unbalanced Chromosomal Abnormalities at Chorionic Villus Samplinga and at Amniocentesis,b for the Age Range 33–45 Years CHORIONIC VILLUS SAMPLING AMNIOCENTESIS MATERNAL AGEC (YEARS) % 1 IN % 1 IN 33 0.5 200 34 0.6 160 35 0.9 115 0.8 120 36 1.2 85 1.0 100 37 1.5 65 1.2 80 38 2.0 50 1.5 65 39 2.5 40 2.0 50 40 3.5 30 2.5 40 41 4.5 22 3 33 42 6.0 17 4 25 43 7.5 13 5 20 44 10 10 6 17 45 13 8 7 14 aIncluding invariably lethal defects. bIncluding those for which there is no maternal-age effect. cAge at time of procedure. Source: Taken from “averaging” data for ages 33–45 years in Tables 20–7 and 20–8 (amniocentesis) and for ages 35–45 years from Table 20–10 (CVS) in Hook (1992). Figures are rounded.

356  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY actually lessens with increasing maternal age. With only the barest paternal-age association (Figure 13–11), advanced paternal age is not of itself a particular indication for chromosomal prenatal diagnosis, although a case might hypothetically be made for a much older (60s and older) father, in respect of de novo structural rearrangement. SECULAR CHANGES IN MATERNAL AGE DISTRIBUTION AND DOWN SYNDROME PREVALENCE Changing maternal-age profiles in a population will influence the birth prevalence of DS. In the England of Shakespeare’s time, few women lived long enough to bear children in older age, and along with the effects of poor survival in DS, perhaps no more than 100 individuals with trisomy 21 then existed in that country, in a total population of 4 million (Berg and Korossy 2001); a similar situation exists in some developing countries today. (Nevertheless, Levitas and Reid (2003) were able to record a number of probable and possible depictions in art from centuries past, and indeed Martínez-Frías (2005) has presented a photograph of a terracotta head, made in about 500 AD in Mexico, that convincingly captures the essence of the DS facies.) In New Zealand in the 1920s, maternal mortality was much less of an issue, but family planning was rudimentary, and about 45% of all mothers were aged 30 years or older. The great majority (~90%) of all DS babies from that period, at least those surviving to the 1960s to have a chromosome study, were born to mothers in this age group. Over the next four decades, family planning practices became gradually more widespread. By the late 1960s most women were completing their families while still in their 20s, and “older mothers” made much less contribution to the overall birth rate. Only 20% of all mothers were aged 30 years or older; and the proportion of all DS babies born to this age group had fallen to 53% (Gardner et al. 1973). We presume, therefore, that the birth prevalence of DS in New Zealand progressively fell over the period 1920–1970. Hook (1992) reviewed the prevalences of DS in various areas of the world during the early 1980s, in relation to the proportions of mothers aged 35 years or older. The former Czechoslovakia had the lowest proportion, 3.6%, of older mothers, and Northern Ireland, at 11.1%, the highest. As expected, the observed rates of DS births showed a relationship, with 0.106% in Czechoslovakia, and 0.16% in Northern Ireland. In the 1980s and 1990s there was a reversal of the maternal-age trend in several areas of the world, with older mothers closing the gap on their younger counterparts. In South Australia, for example, after falling to a trough around 1975–1978, the fraction of mothers older than age 35 years progressively rose, and the birth prevalence of DS was anticipated to rise from a low point of about 0.09% in the late 1970s to greater than 0.15% in 1990–1994 (Staples et al. 1991). In Israel, maternal age dipped in 1978 to a low of 8% of Jewish mothers being age 35 years or older, and rose to 17% by 1992; and in Alberta, Canada, the comparable figures are 4% in 1980, to 16% in 2007 (Shohat et al. 1995; Lowry et al. 2009). These trends are similar in most affluent countries. Trisomies 13 and 18 have a maternal-age association, and so it is not surprising that similar changes in prevalence are observed. From UK and Australian data (and adjusting for prenatal diagnosis and termination), the live birth rates increased by 13% and 25% for the two trisomies, respectively, from 1989–1996 to 1997–2004 (Savva et al. 2010). The DS birth prevalence is considerably influenced by the use of prenatal diagnosis and selective pregnancy termination, these options becoming widely available in many

Down Syndrome, Other Full Aneuploidies, and Polyploidy  357 countries from the 1970s and 1980s, and then with serum screening becoming adopted into the 1990s, and latterly NIPT. In England and Wales over the period 1974–1987, 14% of potential DS births were avoided by selective abortion, reducing the birth prevalence from 0.126% to 0.108% (Cuckle et al. 1991). In Belgium, Verloes et al. (2001) calculated a theoretical halving in the incidence of DS, from 1/800 to 1/1,600 from the 1980s to the 1990s, with at least 90% of trisomic 21 pregnancies terminated. The South Australian figures noted above are estimates of the birth prevalences had termination not been used; in fact, the actual prevalences were correspondingly less (Cheffins et al. 2000). More recent data have come from large studies from England and Wales (Morris and Alberman 2009) and from the United States (Antonarakis et al. 2020) (Figure 21–4), and these reflect the increasing access to noninvasive screening. In England and Wales from 1989 to 2008, while the number of DS diagnoses overall rose very substantially by 71%, concomitant with a changing maternal-age profile, the number of actual DS births fell marginally, from 755 to 743. The proportion choosing termination over this period remained constant at 92%. A similar “even-ing out” was seen in 15 countries of the European Union over the period 1980–1999, with both the highest rise in maternal age and the highest use of termination seen in Paris, and the DS prevalence in that city remaining stable at 0.076% (Dolk et al. 2005). Similarly in Switzerland, the mean maternal age rose from 26 years in 1980 to 30 years in 1996, but the incidence of DS remained practically unchanged (Mutter et al. 2002). In the United States over the period 1989–2006, the reduction in DS births has varied according to region, with the observed births 44% of expectation in the West, compared with 68% in the Midwest; in the Northeast and the South, the figures fell between, but tending more toward those of the West. From their analysis, Egan et al. (2011) conclude that “a Down syndrome fetus is more likely to be prenatally diagnosed and terminated in the West and least likely to be diagnosed and terminated in the Midwest.” In China, residence in a rural or urban setting has a strong influence upon the prevalence of DS. Deng et al. (2015) surveyed findings over the period 1996–2011 and showed a birth rate rising to 0.199% by 2003, and falling thereafter. An increasing utilization of prenatal diagnosis and termination over the 2003–2011 period led to substantial reductions in birth prevalence—by 62% in an urban population and 36% in a rural population—over that time frame. In Hawaii, the birth rate has been fluctuating but is overall static, at about 0.08%, over the period 1997–2005 (McDermott and Johnson 2011). The influence of termination may be more noticeable among older women: In Alberta, Canada, in 2007 the birth rate of DS to mothers in their 40s was 1.32%, but it would have been 2.15% had not termination been available, whereas the comparable rates for 20- to 24-year-olds were 0.055% and a not much greater 0.076% (Lowry et al. 2009). A somewhat different picture is reported from Japan, where recourse to termination is less frequently sought; the DS birth incidence has been rising as the maternal-age spectrum moved to the right (Takeuchi et al. 2008). Prevalence is also influenced by the greater survival of children and adults with DS in recent decades. The survival figure to age one year for Western Australia rose from 83% in those born during 1966–1975 to 94% for the period 1991–1996, and survival to age 10 years rose to 85% (Leonard et al. 2000). In Sweden, Englund et al. (2013) reviewed mortality in a DS population over the period 1969–2003 and determined that the median age at death was rising by 1.8 years per year, and approaching 60 years. Dementia (a well-recognized and understood concomitant of DS; Figure 13–2) was a main or contributing cause of death in one-third.

358  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY ETHNICITY Systematic calculations from other than Caucasian ethnic groups have come from Nigeria, China, Japan, South America, and Hawaii. Adeyokunnu (1982) showed no difference in incidence of trisomy 21 in Nigeria compared with Europeans; and in a study encompassing nine South American countries, Carothers et al. (2001) demonstrated incidence data and maternal-age correlations very similar to those recorded from other jurisdictions. In Japan, Yaegashi et al. (1998) collected data from four clinics, comprising, in all, 5,484 pregnancies of women aged 35 years or older. The risks for trisomy 21 (and for aneuploidies) overall were, on the face of it, somewhat less than in a European population. The raw figures did, however, fluctuate somewhat, with rather small numbers of affected fetuses at each age category. A question might be raised whether some cases could have escaped ascertainment by earlier screening and not otherwise recorded. It may be premature to suppose that aneuploidy rates could differ to any important degree between Japanese and other ethnic groups, a view that is supported by the observation otherwise of no significant differences in a Hong Kong population (Lau et al. 1998); but bearing in mind also data from Hawaii suggesting that at older maternal ages, the DS rate may be somewhat less in a Pacific Island population (Forrester and Merz 2003b). Within the US population, the birth prevalence of DS is highest among the Hispanic population and lowest among blacks, with whites having an intermediate prevalence (Mai et al. 2019); these data differences likely reflect social and cultural rather than genetic factors. Taking a more fundamental viewpoint, Ghosh et al. (2009) demonstrated that rates of meiotic recombination in families with a DS child in India were essentially the same as in a US population, pointing to a basic identity of nondisjunctional mechanism across these populations. And taking a refined view of ethnicity (by genotyping of “ancestry informative markers”), Franasiak et al. (2016) saw no differences among patients attending an IVF clinic, and whose embryos had been tested for aneuploidy, among those of European, African, East Asian, or Central/South Asian ancestry. GENETIC COUNSELING Down Syndrome The central requirement for accurate genetic advice in DS is knowledge of the chromosomal form in the affected family member. If a child diagnosed as having DS has died and no chromosome studies were performed—and more so in a case of younger maternal age—it may be reasonable to check for the possibility of a familial translocation in the consultand. PREVIOUS CHILD WITH STANDARD TRISOMY 21 (INCLUDING MOSAICISM) If the child has standard trisomy 21, or is a 47,+21/46 mosaic, it is unnecessary routinely to study the parents’ chromosomes.12 One can assume with considerable confidence that they will type as 46,XX and 46,XY. The risk of recurrence of trisomy 21 (homotrisomy), 12 But parental chromosome studies should be considered following the prenatal diagnosis of trisomy 21 by microarray, since microarray cannot distinguish translocation DS from standard trisomy 21. Down Syndrome, Other Full Aneuploidies, and Polyploidy  359 or occurrence of a different aneuploidy (heterotrisomy), is typically small, but above that of a same-age maternal population. Broad-brush estimates of increased risk are listed in Table 13–11. More precise data are shown in Table 13–12. Small differences between these estimates may relate to simple statistical variation, but note also that Table 13–11 refers to risk for the birth of an affected child, whereas Table 13–12 relates to the risk at the time of amniocentesis. In any event, regardless of the exact figure, the practical point is that the risk for a recurrence of DS is comfortingly low, only approaching the 1% mark by the mid-30s of maternal age. Nevertheless, most couples seek the reassurance of prenatal diagnosis in pregnancies after having had a child with DS. Many may choose the option of noninvasive prenatal diagnosis, which relieves the couple of having to balance the risk of recurrence against the risk of a procedure-related pregnancy loss. Elkins et al. (1986b) observe that some of these parents declare they would not abort a trisomy 21 fetus, and the counselor needs to be sensitive to possible ambivalent feelings of the parents in this setting. TWO PREVIOUS TRISOMIC 21 CONCEPTIONS One can only offer an educated guess that the risk for a third trisomic conception will be “substantial.” A skin biopsy study of a parent would be largely academic. If gonadal mosaicism (rather than de novo recurrence) is the cause, a considerable fraction of whichever gonad it is must be involved, since two separate samplings have already come from this Table 13–11.  Risk after Previous Trisomy Increases in Recurrence Risk, Given as Multiples Compared with the Maternal Age–Related Baseline, for Women Who Have Had a Previous Trisomic Pregnancy FOLD INCREASED RISK OF RECURRENCE FOR: PREVIOUS ABNORMAL PREGNANCY SAME TRISOMY OTHER VIABLE TRISOMY Trisomy 21 at maternal age <30, current maternal age <30 8.2× 2.4× Trisomy 21 at maternal age <30, current maternal age ≥30 2.2× 2.4× Trisomy 21 at maternal age <35 3.5× 1.3× Trisomy 21 at maternal age ≥30 1.6× 1.7× Trisomy 21 at maternal age ≥35 1.7× 1.5× Trisomy 13 overall 8.6–9.5× 1.5× Trisomy 18 overall 1.7–3.1× 1× Trisomy 13 or 18 at maternal age <35 7.8× 1.6× Trisomy 13 or 18 at maternal age ≥35 2.2× 1× Trisomies 13, 18, XXX and XXY 2.3× 1.6× Nonviable trisomy in spontaneous abortion* 1.8× Notes: The above figures relate to the probability of trisomy at livebirth. Separate figures are given for the risk of recurrence of the same trisomy (homotrisomy) or of a different trisomy (heterotrisomy). If wished, the appropriate multiple for a particular case can be applied to the woman’s current age-related risk, as listed in Tables 13–6 to 13–9, in order to generate an adjusted recurrence risk figure. Figures are from the prenatal data of Warburton et al. (2004) and pre- and post-natal data of De Souza et al. (2009), and they are grouped in various ways according to the formats of these papers. Specific age-related figures for previous trisomy 21 are also given in Table 13–12, column B. *But cf. Robinson et al. (2001), who discerned no increased risk following an aneuploid miscarriage.

360  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Table 13–12.  Trisomy 21 Recurrence Risk Estimates of Recurrence Risk for Trisomy 21, According to the Mother’s Current Age (Column A) and According to Her Age at the Birth of the Affected Child (Column B) A. BASIC AGE-SPECIFIC RISK B. ADDITIONAL RISK DUE TO PREVIOUS DS MATERNAL AGE AT THIS CURRENT PREGNANCY (YEARS) RISK (%) AGE AT THE EARLIER DS PREGNANCY (YEARS) RISK (%) 20 0.09 20 0.62 21 0.09 21 0.62 22 0.09 22 0.61 23 0.09 23 0.60 24 0.09 24 0.58 25 0.10 25 0.57 26 0.10 26 0.54 27 0.11 27 0.52 28 0.11 28 0.48 29 0.12 29 0.44 30 0.14 30 0.40 31 0.16 31 0.35 32 0.19 32 0.29 33 0.23 33 0.24 34 0.29 34 0.19 35 0.37 35 0.15 36 0.49 36 0.11 37 0.66 37 0.08 38 0.88 38 0.06 39 1.17 39 0.05 40 1.52 40 0.04 41 1.92 41 0.03 42 2.35 42 0.02 43 2.78 43 0.02 44 3.20 44 0.02 45 3.58 45 0.02 46 3.92 46 0.01 47 4.21 47 0.01 48 4.45 48 0.01 49 4.64 49 0.01 50 4.80 50 0.01 Notes: Risks A and B are then to be summed. This combined risk figure relates to the probability of detection of trisomy 21 at early second-trimester amniocentesis. For example, a woman who is now pregnant and due to deliver at age 30 years (risk = 0.14% from column A), and who had had a DS pregnancy when she was 25 years old (additional risk = 0.57% from column B), has an overall risk for trisomy 21 in the current pregnancy of 0.14 + 0.57 = 0.71%, or 1 in 141. Note how, with advancing maternal age at the current pregnancy (A), the additional risk component due to having had a previously affected child (B) progressively diminishes; in other words, at these older ages, the maternal-age factor becomes the overwhelming contributor to the risk. DS = Down syndrome. Source: From Morris et al. (2005). Down Syndrome, Other Full Aneuploidies, and Polyploidy  361 fraction. A risk in the range of 10%–20% may be a fair figure to offer. Preimplantation genetic testing would have an obvious attraction. ISOCHROMOSOME 21 DOWN SYNDROME From the 0/164 fraction among siblings of de novo isochromosome 21q DS in Steinberg et al.’s (1984) series, the risk for recurrence was originally presumed to be small. Nevertheless, three parents (3%) in this series were demonstrably mosaic; and subsequently Hervé et al. (2015) listed 10 cases of recurrence due to known or suspected parental gonadal mosaicism. A concerted search for parental mosaicism (more than one tissue, high cell count) could reasonably be proposed. While the overall risk figure may be low, perhaps in the region of 1%–2%, a cautious approach is certainly prudent. If parental mosaicism is actually detected, a considerably higher risk figure would apply, likely approaching a double-figure percentage. PREVIOUS CHILD WITH ROBERTSONIAN TRANSLOCATION DOWN SYNDROME Obviously, distinction between de novo and familial forms of translocation DS is crucial; this distinction is made by chromosomal studies of the parents. For the de novo translocation, a recurrence risk figure of <1% is applicable (Gardner and Veale 1974). In the case of familial Robertsonian translocation DS, the genetic risk for the female carrier is substantial. The risk to have a liveborn child with translocation DS is about 10%, while the likelihood to detect translocation trisomy 21 at amniocentesis is about 15%. For the male carrier, the risk to have a child with translocation DS is small, about 1% (and see Chapter 7). PREVIOUS CHILD WITH NON-ROBERTSONIAN TRANSLOCATION DOWN SYNDROME In the rare instance that translocation DS is associated with a familial reciprocal translocation, the principles presented in Chapter 5 are to be followed. PREVIOUS CHILD WITH OTHER CHROMOSOMAL CATEGORY OF DOWN SYNDROME For sporadic structural changes such as the terminal rearrangements, the risks are presumed to be very low (<0.5%). For the double aneuploidies, there is no evidence to suggest the risks are any different from the recurrence risks for standard trisomic DS. WIDER FAMILY HISTORY OF DOWN SYNDROME There is no conclusive evidence of an increased risk for second- and third-degree relatives of individuals with standard trisomic DS themselves to have offspring with the condition. The appropriate action in the setting of “a family history of DS” is to determine whether the affected member has standard trisomy 21. If this is so, the family may be reassured that there is no discernibly increased risk, which advice could also reasonably be offered if a single case was associated with older maternal age. If the karyotype of the index case is unknown, and the mother had been younger, the small possibility of a familial translocation may be checked by chromosome study of the counselee. TRISOMY 21 IN PRODUCTS OF CONCEPTION The finding of trisomy 21 in products of conception after spontaneous abortion (in those centers where this testing may be done) presents a problem. Should this finding,

362  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY for genetic counseling risk assessment, be regarded as equivalent to having had a child with DS? From about 10 weeks gestation through to term, about one-third of trisomic 21 conceptions are lost, and it may be stochastic events in utero (in part correlating with maternal age) rather than intrinsic genetic differences that distinguish those that abort and those that survive. It may be prudent to err on the side of caution and provide a risk figure as though the abortion had been a liveborn child. PARENT WITH DOWN SYNDROME The risk to the female with DS is clearly high, as discussed above, although nearer a one-third figure (reflecting natural trisomy 21 miscarriage) rather than a theoretical one-half. It is almost but not absolutely unknown for a male with DS to achieve fatherhood (Parizot et al. 2019). A genetic risk may in fact be small, due to selection against disomic sperm. Ethical issues arising in these circumstances are discussed in Chapter 27. PREVIOUS PREGNANCY WITH TRISOMY 13, TRISOMY 18, OR OTHER AUTOSOMAL TRISOMY Recurrence of trisomy 13 or 18 is a very rare observation. The recurrence risk is, in fact, very small, as displayed in Table 13–11. In a registry study that followed up 676 pregnancies in women who had a previous trisomy 18 pregnancy, there were five instances of trisomy 18 recurrence (0.7%), which was a threefold increase in risk (De Souza et al. 2009). In the same study, there were two recurrences from 381 pregnancies (0.5%) in women with a previous trisomy 13 pregnancy. This represented a relative risk of 9.5, but the confidence intervals were wide due to the small sample size. Relative risks are higher for women aged <35 years at previous trisomic pregnancy. As for an increased risk for a different potentially viable trisomy, such as trisomy 21 (“heterotrisomy”), again in absolute terms it is very small but does exist. Warburton et al. (2004) derived an overall 1.6-fold increased risk factor. In their large study of a UK population, Alberman et al. (2012) recorded two heterotrisomic recurrences (both trisomy 13) from mothers of a previous child with trisomy 18, but no recurrences (hetero- or homotrisomic) following a pregnancy with trisomy 13.13 They commented that these mothers were “relatively elderly,” and perhaps this may have been the basis of the recurrences. In the case of a previous pregnancy with some other type of autosomal trisomy (typically identified in products of conception following spontaneous abortion), from Warburton there is an overall increased risk (1.8-fold), which Grande et al. (2017) refine in terms of maternal age (Table 13–13). As this Table shows, the additional increased risk, over and above that due to maternal age per se, lowers as age increases, from 0.37% at age 20 years, and by the late 40s it is barely perceptible at 0.01%. Recurrence of any trisomy following one of the rare trisomies (Table 13–3 above) is unrecorded. Any theoretical increased risk would presumably be very small. PARENT WITH MOSAIC TRISOMY 18 OR TRISOMY 13 In those in whom a genetic risk is a realistic question, in other words, those being of a normal or near-normal phenotype, the trisomic component of the soma is likely to be low. This may well reflect a similar low fraction in the gonad, and the theoretical risk may thus be low, but not dismissible. Wei et al. (2000) describe a man, presumably otherwise normal, presenting with severe oligoasthenozoöspermia, zero to one sperm per 13 They also mention one unfortunate mother who had had three trisomic pregnancies, of 21, 18, and 13. Down Syndrome, Other Full Aneuploidies, and Polyploidy  363 high-power field, and with trisomy 18 in 20% (on blood) a surprising finding. With intracytoplasmic sperm injection and IVF, he was able to father a normal daughter. We may recount the case of a child with a 1/150 cell count on umbilical blood following prenatal diagnosis of a trisomy 13 mosaicism (Delatycki et al. 1998; Figure 22–6). The child has developed very normally; however, genetic counseling as an adult in his case would need to acknowledge a theoretical gonadal mosaicism. Table 13–13.  Maternal Age–Dependent Excess Risks of Trisomy 21 in a Subsequent Pregnancy, Over and Above that Due to Maternal Age, after a Trisomy Other than Trisomy 21 (Heterotrisomy) MATERNAL AGE AT INDEX PREGNANCY EXCESS RISK PER 1000 PREGNANCIES EXCESS RISK 1 IN 20 3.7 272 21 3.7 272 22 3.6 278 23 3.5 284 24 3.5 290 25 3.4 296 26 3.2 310 27 3.1 325 28 2.9 351 29 2.6 381 30 2.4 417 31 2.1 476 32 1.7 580 33 1.4 702 34 1.1 889 35 0.9 1,111 36 0.7 1,481 37 0.5 2,222 38 0.4 2,667 39 0.3 3,333 40 0.2 4,444 41 0.2 6,667 42 0.2 6,667 43 0.2 6,667 44 0.2 6,667 45 0.2 6,667 46 0.1 13,333 47 0.1 13,333 48 0.1 13,333 49 0.1 13,333 50 0.1 13,333 Source: From Grande et al. (2017). 364  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY PARENT WITH MOSAICISM FOR OTHER AUTOSOMAL ANEUPLOIDY An adult with a low-level mosaicism for some other autosomal trisomy, and presenting for genetic advice, will likely have a low or very low trisomic load in tested somatic tissues. The likelihood of a gonadal mosaicism will also probably be very low. Should there be a conception due to a disomic gamete, this—being non-mosaic, and if remaining non-mosaic—would inevitably miscarry. Triploidy Diandric triploidy associated with partial hydatidiform mole has an overall <1% risk of recurrence; we discuss this in more detail on p. 623. As noted in the “Biology” section, some women may have a predisposition for digynic triploidy, and recurrence is on record (Pergament et al. 2000). However, the level of risk for recurrence of triploidy, or occurrence of an aneuploidy, must usually be small, since in the series of Robinson et al. (2001) no increased risk was discernible for women having had more than one previous spontaneous abortion due to triploidy (or aneuploidy) to have yet another chromosomally abnormal pregnancy. Conception by IVF, with or without PGT, would reduce the risk as noted above. Prenatal karyotyping and/or early pregnancy ultrasonography may reasonably be offered. Tetraploidy Tetraploidy is too rare for a clear picture to have emerged. Sporadic occurrence, in almost all, would seem very probable.

Autosomal Structural Rearrangements  367 et al. (2009) propose that many “deletions” according to cytogenetic analysis are actually inverted duplications contiguous with terminal deletions. Some patients, indeed quite a number, previously testing normal on classical karyotyping have since been revealed on molecular testing as having a chromosomal imbalance. This belated discovery may make no real difference to management, but it is often a source of considerable relief to the parents to have, finally, a definite explanation for the problem. And of course, precise genetic advice can now be offered to others in the family. CONTIGUOUS GENE SYNDROME Recollect that loci are arranged in linear order along a chromosome. Some neighboring loci may be functionally related, but in others the contiguity is mere happenstance. The non-significance of two loci being adjacent has been likened to the unimportance one would attach to “Appalachian Mountains” being next to “apple” in an encyclopedia. Our genome differs from an encyclopedia in that about one-third of all the entries relate to one topic: the development and functioning of the brain—unsurprisingly so, this organ being, as it is said, the most complex structure in the known universe. Many of the other entries (loci) relate to the control of morphogenesis during embryonic life. Figure 14–2.  The Spread of 686 Autosomal Duplications and Deletions in a Cohort of 3,380 Cases Studied by Chromosomal Microarray over the Period 2016–2021 in Colombia. Notes: The cases studied had presented due to the typical reasons for ordering a chromosome study, mostly neurodevelopmental delay, intellectual disability, autism spectrum disorder, short stature, and dysmorphisms. Not shown here are an additional 87 cases with sex chromosomal dup/dels. Source: From YD Carrillo et al., Diagnostic yield of chromosomal microarray in the largest Latino clinical cohort, Am J Med Genet 194A:218–225, 2024. Courtesy JJ López-Rivera, and with the permission of John Wiley & Sons.

368  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY If a length of chromosome is deleted or duplicated, a sequence of adjacent (contiguous) genes will be lost or gained, and so the phenotype resulting from this imbalance can be described as a contiguous gene syndrome (Schmickel 1986; Tommerup 1993). In almost any deletion or duplication detectable cytogenetically, some of the loci deleted or in excess will be brain loci, while others could be for anything, but likely including some morphogenesis loci. Thus, we have the classic clinical picture in del/dup syndromes of intellectual deficit of some degree, dysmorphism, and in some, organ malformation. The deletion produces a monosomy—or “haploinsufficiency”—for the region of the chromosome that has been removed, and the outflow of genetic information is halved. Duplication causes a trisomy for the additional segment: a “triplo-excess” with a 150% amount of genetic information. PHENOTYPES While our focus in this book is substantially upon genetic risk, of course we must make reference to the clinical pictures observed in the setting of the several chromosomal aberrations we consider. Some of the deletions and duplications occur sufficiently frequently and/or present a sufficiently distinctive phenotype that they have acquired eponymic status, and the reader will be familiar with such names as Wolf, Hirschhorn, Williams, and cri du chat. The classical route whereby a chromosomal syndrome came to be established followed the recognition of a group of patients with a very similar clinical picture, often with a characteristic dysmorphology: the “phenotype-first” approach. Subsequent cytogenetic studies revealed the underlying chromosomal basis in common. Williams syndrome is a typical example: The facies and the cardiovascular malformation added up to a distinctive picture, recognized in 1961; but it was not until decades later, 1993, that the chromosomal basis was discovered. Nowadays, taking the molecular approach, the typical path is “genotype-first,” or “reverse dysmorphology.” Subtle deletions and duplications may not present a distinctive enough phenotype that would allow the clinician to “call” a syndrome. But in the laboratory, data on recurrent rearrangements—whether seen in-house or often in collaboration with other cytogenetic services, nationally or internationally—can be collected. It is then up to the clinicians to draw together the observations from the patients thus identified and to construct the core features of the new syndrome. This approach of identifying the chromosomal abnormality first-up can reveal the natural clinical variation of the genomic rearrangements, which might scarcely have been possible with the traditional phenotype-first approach. The brain is the organ exquisitely vulnerable to the effect of a genomic imbalance, and the phenotypes observed reflect this. The affected phenotype due to a small imbalance may be confined to a neurocognitive or behavioral disability; and many of the del/dups listed below include autism as a clinical manifestation (and see Figure 25–2). In some of the smaller-size del/dups detectable on molecular karyotyping, the natural clinical variation may include a brain-functional phenotype well within the range of essential normality. Otherwise, epilepsy, also a brain-functional trait, is a concomitant of several of the del and dup syndromes (Figure 25–7). Some of the loci whose haploinsufficiency/triplo-excess contributes to the phenotype in the various deletion syndromes are being defined. It seems likely that many such genes will have their untoward outcome not in a simple one-to-one relationship with a

Autosomal Structural Rearrangements  369 single gene product, but rather in a complex layering and interlacing of consequential effects (Figure 3–21). As yet, however, it is mostly just the simple case that we can understand quite well: such as, for example, the brain white matter abnormality of the 18q– syndrome, which is presumably a direct consequence of the loss of one structural myelin gene, MBP, on 18q (Lammert et al. 2019). As molecular karyotyping defines del/dups of very small extent, only a few genes may be located within the particular segment, and the counselor blessed with a scientific curiosity has the opportunity to check which genes these are, and perhaps to make an informed speculation (which some parents might find helpful) as to which of these might have contributed to a child’s phenotype. If two or more Mendelian disorders coexist in the one person, a contiguous gene deletion is a strong possibility. In order to prove the point, molecular methodology can be brought to bear; or a direct chromosomal test using FISH offers an immediate visual demonstration of the deletion. We have, for example, seen a young woman presenting with a history of recurrent bacterial infections since childhood, and night blindness and diminishing peripheral vision since teen age, leading to diagnoses of, respectively, chronic granulomatous disease and retinitis pigmentosa (Coman et al. 2010b). The X-linked forms of these conditions being very closely linked, a contiguous gene deletion suggested itself, and a FISH probe targeted to a DNA sequence between the two loci was generated. Its non-hybridization to one X chromosome confirmed the supposition of a deletion. Furthermore, this led the way to another diagnosis, that of a partial protein intolerance, due to deletion of the OTC (ornithine transcarbamylase) gene that lies in the same Xp region. BIOLOGY Origin Intra-, Pre-, or Post-Meiosis The “recurrent” category of de novo deletion or duplication is considered typically to reflect an origin during meiosis. Thus, for a number of deletion syndromes involving a recurrent segment—such as Williams, Prader-Willi, and Smith-Magenis syndromes, along with several others—a risk of recurrence is taken to be very low, because typically only the particular gamete from that particular parental meiosis carried the defect (Giglio et al. 2001; Saitta et al. 2004). These cases arise anew—“de novo”—with the affected child. On the other hand, imbalances which are single observations (or which are of a group involving a cytoband or bands in common, but with relatively distant breakpoints) are “non-recurrent,” and knowledge about the likely origin for these may be scant. Some may indeed have been of meiotic origin, and therefore without increased risk of recurrence. But, alternatively, a non-recurrent imbalance could have originated in a premeiotic mitosis. In that case, the abnormal cell line is confined to a “wedge” of the parental gonad (gonadal mosaicism), and the parent will have a normal phenotype and (on routine tissue sampling) a normal chromosome analysis (Figure 14–3). If, however, the abnormal cell line is present in the parental gonad and also in non-gonadal tissues (somatic-gonadal mosaicism), the parent may have an (often very subtly) abnormal phenotype, and the imbalance may be detectable, in a mosaic form, in parental blood. In either scenario, there is risk of the imbalance being passed to a child (in whom it would 370  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY be in non-mosaic form); although in actual fact, a second affected child of such a parent is only rarely seen. Finally, a rearrangement arising at a post-zygotic mitosis from an initially normal conceptus would lead to mosaicism in the child, typically for a normal and for the abnormal cell line, both with a 46-chromosome count. In a sense, this is a similar scenario to that of the parent having a premeiotic mitosis just discussed, except that the abnormal event took place much earlier in embryonic life, such that development of the soma was overtly compromised. Typically, no increased risk of recurrence would apply for potential future siblings of this child. Somatic mosaicism for a structural rearrangement of this sort is discussed in the comprehensive review of Kovaleva and Cotter (2016). It is often appropriate to check the parental karyotypes in any event for reassurance, and in order to test the possibilities that one parent may be either a carrier of a balanced rearrangement or a low-grade mosaic for the abnormal chromosome. An example is illustrated in Figure 3–23 of an interstitial deletion del(1)(q25q31.2) which was identified at amniocentesis, and which led to the discovery of 46,XY,del(1)[80%]/46,XY[20%] mosaicism on blood karyotyping of the father, thus revealing him to be a somatic-gonadal mosaic. Normal parental karyotypes do not exclude absolutely the possibility of mosaicism, as exemplified in two sisters with a chromosome 16 deletion whose parents’ karyotypes on blood were normal (Hoo et al. 1985); nor in a case of recurrent interstitial 1p36 deletion in two sisters from a gonadal mosaic mother, who did not have any evidence of the deletion on blood testing (Gajecka et al. 2010). Figure 14–3.  Recurrence Risk according to Different Scenarios. Notes: The purple coloring represents a gamete or tissue with an apparently de novo structural rearrangement, and here considering a deletion or a duplication. From panels left to right, for the male- (blue) and female- (pink) originating gametes respectively, each parental couple shows a conception resulting from one of these three scenarios: a “one-off ” rearrangement present in only a single gamete; parental gonadal mosaicism for the rearrangement; and parental somatic-gonadal (mixed) mosaicism. The seventh (green) panel shows a child with mosaicism, euploid at conception, the rearrangement having arisen at a postzygotic stage. Source: Adapted from M Bernkopf et al., Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation, Nat Commun 14:853, 2023. Courtesy A Goriely, and with the permission of Springer Nature.

Autosomal Structural Rearrangements  371 Opposite Deletion/Duplication In a few cases, the duplication (or sometimes triplication) of a locus manifests to some extent as the “opposite” phenotype as that found in the deletion. Thus, triplication of the MMP23 gene on 1p36 results in craniosynostosis, while the deletion is associated with a large, late-closing anterior fontanel (Gajecka et al. 2005). Deletion of the P pigmentation gene in the Prader-Willi/Angelman region causes lighter complexion; an increased copy number of this gene leads to hyperpigmentation (Akahoshi et al. 2004). Deletions and duplications of certain autism-related CNVs are seen with opposite volumes of brain grey matter (Modenato et al. 2021; Figure 25–4). Shinawi et al. (2010) refer to these opposite scenarios as “sister genomic disorders”; Lejeune, in the 1960s, spoke of type and countertype. Complementary Deletion/Duplication The rare observation of a complementary deletion/duplication in the same person offers insight into the likely site of generation of this particular rearrangement. If the del/dup should arise at the very first somatic replication following conception—in other words, the zygote entering into mitosis no. 1—two countertype cell lines will be produced at the two-cell stage, with no normal cell line. In the event that extra-fetal tissues can be studied, and still no normal cell line is seen, the interpretation of a first-mitosis scenario is strengthened; thus, Rodriguez-Revenga et al. (2005) could draw such a conclusion from their prenatal diagnostic case of dup(18q)/del(18q) mosaicism, the chorionic villi showing both karyotypes, although on amniocentesis and fetal blood, only the del(18q) was present. If one of the cell lines is of lesser viability, a child might show the complementary karyotypes at birth, but only one cell line later in childhood. Morales et al. (2007a) report an example, an abnormal infant who as a newborn had dup(7)(q21.1q31.3)[90]/ del(7)(q21.1q31.3)[10] mosaicism, but upon restudy at age 12 and 14 months, only the dup(7) cell line was seen, looking at blood and exfoliated urinary tract epithelial cells. If the del/dup arises at the second or subsequent mitosis, there will be a normal cell line as well; and Tharapel et al. (1999) illustrate this circumstance in a child initially identified at amniocentesis undertaken upon the basis of the ultrasonographic observation of a choroid plexus cyst and echogenic bowel. In this child, the normal cell line was present in about half of cells, with the remaining cells containing either a deletion for 7p11.2p13, or a duplication for this segment. In the similar case in Qi et al. (2015), the normal cell line was presumably predominant in an unaffected mother who had a 46,XX,del(6p25.1p24.3)/46,XX,dup(6p25.1p24.3)/46,XX karyotype (it was her abnormal children who led to the ascertainment; see chromosome 6p25p24 below). Deletions and Mendelian Disorders.  A Mendelian disorder due to autosomal dominant or X-linked inheritance, and typically the result of a gene mutation, may also result if the particular chromosomal locus is deleted. Thus only one functional allele remains, and a state of haploinsufficiency is the consequence. Rubenstein-Taybi syndrome was one of the earliest to exemplify this scenario (the gene CREBBP), and Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary pressure-sensitive palsy provide an instance of both duplications and deletions concerning a single gene (PMP22)—and indeed this genomic mechanism is the most common genetic basis of CMT. Other cases, several of which are also noted below, include Pitt-Hopkins syndrome (the gene 372  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY TCF4), Sotos syndrome (NSD1), Alagille syndrome (JAG1), Saethre-Chotzen syndrome (TWIST), Greig syndrome (GLI3), one type of holoprosencephaly (SHH), CHARGE syndrome (CDH7), one type of lissencephaly (LIS1); and X-linked ichthyosis (STS) in a 46,Y,del(X) individual. If neighboring genes are also deleted, this may contribute to a wider phenotype. A deletion that removes an autosomal recessive gene would not normally, of itself, influence the phenotype. But if, coincidentally, a mutation lies on the other, otherwise intact chromosome, there may result further damage due to an “unmasking heterozygosity” at this locus (Coman and Gardner 2007). Flipsen-ten Berg et al. (2007) reported an infant with Wolf-Hirschhorn syndrome (WHS) due to a deletion on one chromosome 4p, who then went on to develop, over and above the WHS, signs of Wolfram syndrome.3 The WFS1 locus for Wolfram syndrome is on chromosome 4 short arm, which led these workers to examine the gene on the “normal” chromosome 4. A point mutation in WFS1 was discovered. The 4p deletion on the other chromosome allowed this mutation to be “exposed” and the child, being essentially hemizygous, got the syndrome: WHS + WFS, one could say. Similarly, a child with a 22q13 deletion (Phelan-McDermid syndrome), and having an ARSA mutation on the other chromosome 22, would develop the fatal recessive brain disease metachromatic leukodystrophy (Bisgaard et al. 2009). McDonald-McGinn et al. (2013) review a number of cases with the 22q11.2 deletion syndrome, but having an atypical clinical picture in whom an “exposed” mutation on the other 22 led to a more severe phenotype. Direct and Inverted Intrachromosomal (Tandem) Duplication.  Here, the duplication comprises chromatin of the same chromosome, the original and the duplicated segments being ordered in tandem fashion. If the linear orientation of a chromosome A is maintained, the rearrangement is a direct duplication, 46,dir dup(A); if it is reversed, it is an inverted duplication, 46,inv dup(A). Triplication.  A few cases are known, at the level of classical cytogenetic analysis, of a segment of chromosome replicating twice over, being in threefold amount on that homolog. The segment is thus present, in total, in fourfold dose. With molecular karyotyping, we are now seeing several more cases of triplication, and it seems likely that this “rare” complexity may be less rare than initially supposed (Xu et al. 2014; Bouassida et al. 2024). Familial transmission is recorded: The 46,XX,trp(4)(q32.1q32.2) mother in Wang et al. (2009) had three sons with the same imbalance, 46,XY,trp(4)(q32.1q32.2), this being clearly visible on classical karyotyping. Rare Complexity.  A rare (or rarely recognized) complexity is a change in size, from parent to child, of a subtelomeric deletion. Faravelli et al. (2007) observed a mother having a 1.5 Mb 4p deletion, which expanded in size to produce a 2.8 Mb deletion in her child with typical Wolf-Hirschhorn syndrome; in retrospect, the mother had subtle signs to suggest a forme fruste. Similarly, South et al. (2008a) describe a normal mother with a de novo 18q subtelomeric deletion of 0.4 Mb, which increased in size nearly tenfold to 3.7 Mb in her abnormal daughter, who had presented with a clinical picture consistent with 18q deletion syndrome. This parent-to-child “expansion” is presumably due to a recombination mechanism. 3 Wolfram syndrome = diabetes mellitus, diabetes insipidus, deafness, optic atrophy.

Autosomal Structural Rearrangements  373 GENETIC COUNSELING De Novo Deletions and Duplications In most children with deletions or duplications, the parents type as 46,XX and 46,XY on routine tissue analysis, and the defect is “de novo.” The risk for recurrence is very small. Röthlisberger and Kotzot (2007) undertook a review and were surprised at how few actual cases of recurrence had been published. Rare recurrences are presumably due to an occult parental mosaicism, which the routine chromosome study could not detect.4 In that case, the abnormal line in the parent may be gonadal or somatic-gonadal (Figure 14–3). The observation of rarity of recurrence allows us to propose the empiric advice that in the individual de novo case, recurrence is most unlikely. Röthlisberger and Kotzot (2007) offer a figure of “less than 0.3%”; the counselor should note the converse “greater than 99.7%” for a child without the chromosome defect. If the typical mechanism is a meiotic error (as discussed above), the risk might, in principle, fall to the population baseline. Some couples may find “greater than 99.7%” sufficiently encouraging that they would not request preimplantation or invasive prenatal testing in a subsequent pregnancy, or would be satisfied with a normal ultrasound report. Notwithstanding, we acknowledge the unsatisfactoriness that Bernkopf et al. (2023) discuss in the similar situation of counseling for a Mendelian-level mutation, noting a wide range of 1%–50% well-weighted to the left, which is to say almost always near-negligible, but very rarely dreadfully high. Deletions and Duplications with a Parental Rearrangement In quite marked contrast, in those deletions/duplications where a parent is shown to carry a balanced rearrangement, a likely substantial recurrence risk will of course apply, and the appropriate chapter should be consulted. Rarely, the same deletion/duplication might be seen rather unexpectedly in a parent, an observation that underpins the advice that parental karyotyping does need to be undertaken (Sparkes et al. 2009). Extremely rarely, an inverted duplication may in fact be due to recombination within a parental paracentric inversion. Paracentric inversions can be difficult to detect, and a careful and directed search may be appropriate. Commentaries upon Individual Deletions and Duplications Thumbnail sketches of the major deletion and duplication syndromes follow, as well as many (but certainly not all) of the lesser-known ones, in numerical order of chromosomes and “numerical order” of p and q segments.5 Quite a few syndromes are of 4 Campbell et al. (2014) set out to test this hypothesis by using a highly sensitive technique, individual breakpoint-specific polymerase chain reaction, to test parental blood in a cohort of 100 patients with non-recurrent deletion CNVs. Low-level somatic mosaicism was detected in four parents, and presumably these parents would have an elevated risk of recurrence. 5 Thus, reading upwards (or to the left) from the centromere in the p arm, and downwards (or to the right) in the q arm. Note that in formal cytogenetic nomenclature, when two p arm bands are listed, the correct ordering is from telomere to centromere (anti-numerical order), such as del 2p16.1p15. 374  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 2000s–2010s definition, reflecting the widespread application of molecular karyotyping in the early 21st century. All those del/dups listed in the ClinGen Curation of Recurrent CNVs, current at the time of writing, are included and noted with an asterisk (*), and penetrance data for recurrent CNVs is provided in Appendix C. Nucleotide numbers are mostly expressed in build hg38, but some in hg 19. Each chromosomal section is seen with a banded ideogram, taken from ISCN (2004), with particular segments subject to recurrent deletion/duplication indicated along with a selected relevant gene (or other identifier) located within that segment, as a useful “landmark.” Longer or “busier” chromosomes have of necessity been divided into p and q arms. Some are illustrated with a display of the del/dup range against a karyotype, not merely for decoration but to familiarize the reader with this way of demonstrating these abnormalities. Only “pure” imbalances are considered; it is not feasible to include here those due to combination del/dups of different chromosomes. We comment in greater or lesser length upon the genetics of each and, to the extent that knowledge allows, on recurrence risks; those in which recurrence has been recorded are given a more generous hearing. Clinical comments are mostly synoptic and selective, and “intellectual deficiency and facial dysmorphism” very frequently mentioned. Uncommon or distinctive or otherwise interesting phenotypic traits rate particular mentions. More perspectives on recurrent copy number variants are given in Chapter 18. The essays in Cassidy and Allanson’s Management of Genetic Syndromes (2020) offer detailed commentaries for some of the more common of these syndromes. The UNIQUE website (rarechromo.org) has excellent quite detailed descriptions for some of the more common (or less rare) conditions. Chromosome 1 1p21.3 Deletions. This microdeletion is rare (case reports barely in double figures; Willemsen et al. 2011b; D’Angelo et al. 2015), but it is of particular interest in that the reduced amount of a microRNA may be a key factor in determining the clinical picture of intellectual deficit of borderline/mild/moderate degree and abnormal behavior. For the most Figure 14–4.

Autosomal Structural Rearrangements  375 part, deletions are non-recurrent and of variable sizes. The smallest region of overlap, of 1 Mb in extent, runs from chr1:97.5-98.5 Mb, and including the sequence coding for MIR137. This microRNA is particularly expressed in certain brain regions, and it influences the functioning of client genes; its reduced activity has been correlated with psychiatric disease and with obesity (Strazisar et al. 2015; Tucci et al. 2016). Three of the cases in Willemsen et al. were siblings; their deceased parents were known to have been of low cognitive ability, and rather probably one of them had the same 1p21.3 deletion. 1p31.3p32.2 Deletion. This syndrome includes a functional neurocognitive and epileptic phenotype associated with brain malformation, commonly including agenesis of the corpus callosum along with limb and urinary tract defects. Labonne et al. (2016) provide a review and describe in detail their case of a young woman, first diagnosed on classical karyotyping as a 10-year-old. Moyamoya disease (narrowed arteries causing stroke) is associated (Pires de Oliveira-Sobrinho et al. 2024). Most arise de novo, but familial cases are on record. The syndrome could essentially have the alternative name of NFIA deletion (Revah-Politi et al. 2017; Bertini et al. 2022) (Figure 14–5). 1p34.3 Deletions in this cytoband, similarly to del 1p21.3 above, may also have their pathogenic effect through a perturbation of the microRNA system. Tokita et al. (2015) describe deletions of sizes 1.1 Mb–3.1 Mb, with AGO1 and AGO3 (at chr1:36.3 Mb) resident in the 290 kb segment in common. These are “argonaute” genes, whose products direct the process of post-transcriptional gene silencing (that is, RNA interference); their removal may be the basis of the observed phenotype of hypotonia, moderate intellectual disability, and subtle facial dysmorphism. Galesi et al. (2022) analyze in detail the behavioral traits of their patient, a 9⅔-year-old boy, who had particular deficits in hyperactivity and inattention components of ADHD at the 95th–98th percentile, and restlessness/impulsivity at the 95th–98th percentile. A de novo origin has been observed in all tested cases. 1p36.11 Duplication including the ARID1A gene is the basis of this rare, but recurrent condition, albeit that the breakpoints are heterogeneous (Bidart et al. 2017). Microcephaly is common. Figure 14–5.  1p31.3p32.2 Deletions and Duplication. Notes: Deletions in red, duplication in blue. All encompass the NFIA gene. Source: From V Bertini et al., Phenotypic spectrum of NFIA haploinsufficiency: Two additional cases and review of the literature, Genes (Basel) 13:2249, 2022. Courtesy A Orsini, and with the permission of MDPI. 376  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 1p36.22p36.21 Duplication. The physical phenotype is that of “focal facial dermal hypoplasia type 3,” also known as Setleis syndrome, characterized by atrophic facial lesions and otherwise facial dysmorphism, and aberrant hair growth. Duplications (and triplications) are non-recurrent and of varying extents; a set of four duplicated genes are seen in common (Oh et al. 2023). Of the few cases thus far reported, developmental delay has been a feature in most, but an example is also on record of an intellectually normal man with Setleis syndrome, who had inherited the duplication from his phenotypically normal (and non-mosaic) carrier father (Lee et al. 2015). 1p36.3 Deletion. This is one of the more common deletion syndromes, seen in from one in 5,000 to 10,000 births. We may speak of a distal “classical” (Group A) deletion and a more proximal (Group B) deletion. Within these broad categories, Jacquin et al. (2023) delineate four subgroups, clustering around common regions of overlap (Figure 14–6). The most usually encountered is the distal “classical” deletion. GABRD is proposed to be an important pheno-critical locus. The facies is variably dysmorphic, with deep-set eyes and midface retrusion a particular observation, and several minor physical anomalies may be observed (Shimada et al. 2014; Jordan et al. 2015). The intellectual disability is usually severe; an unsurprising observation given that perisylvian polymicrogyria, a major brain malformation is seen in some, and it is plausible that in others, anatomic defect might be beyond MRI resolution. Also, defects in white matter are common (Õiglane-Shlik et al. 2014). A milder phenotype is seen in the mosaic case (Shimada et al. 2014). A phenotypic overlap with Angelman syndrome and Rett syndrome has been noted. In the review of Jacquin et al. (2023), inheritance data was available in 54 cases. Of these 50 (93%) were de novo. The deletion was seen in three parents (mosaic in one) and from a translocation in one. Other rare examples of familial transmission are known, including due to presumed parental gonadal mosaicism (Di Donato et al. 2014; Nistico’ et al. 2020). 1q12q31 Duplication. A very large 50 Mb duplication, ~40% of the length of the long arm, is reported in Sifakis et al. (2014) concerning a fetus of 23 weeks gestation with multiple malformations. They review a very heterogeneous prenatally diagnosed dup(1q) series from the literature; termination had been chosen in almost all, while survival was mostly measured in minutes or days in the pregnancies going to live birth. The even larger duplication described as 1q21qter, a length of fully 100 Mb, causes multiple severe, lethal malformations (Machlitt et al. 2005). 1q21.1* Deletion. Two recurrent deletions reside within this segment (Figure 14–8), each flanked by numbered breakpoint low-copy repeat regions (BPs 2 to 4) that dictate a susceptibility to rearrangement due to unequal crossing-over (Edwards et al. 2021; Pang et al. 2020; Bourgois et al. 2024). Both deletions are characterized by incomplete penetrance, and may thus be discovered when phenotypically normal parents of an affected child are karyotyped. A larger 2.15 Mb recurrent deletion encompasses both smaller deletions.

Autosomal Structural Rearrangements  377 Duplication. The typical recurrent duplication at 1q21.1 involves the same segment as the distal region in the countertype deletion (Figure 14–9). The phenotype of this duplication includes intellectual disability (or at least borderline cognitive functioning) and autism. As the deletion leads to microcephaly, so does the duplication cause macrocephaly; brain scanning may show reduced white matter volume. Dolcetti et al. (2013) document an increased risk for schizophrenia. A range of heart defects are seen (tetralogy of Fallot having a particular association), likely relating to a triplo-excess of GJA5 (Soemedi et al. 2012; Digilio et al. 2013). In the review of Bernier et al. (2016), of those patients whose parents were studied, all but one were familial cases. It is true to Figure 14–6.  The Different Categories of 1p36 Deletions. Notes: There are two major critical regions, seen in patients from Groups A and B respectively: a more common “classic” distal deletion (cases in blue bars), and a proximal deletion (orange bars). The minimal regions of overlap (MRO) that characterize four subgroups within the major grouping are shown as the pink shading. Red asterisk = GABRD site. Source: Adapted from C Jacquin et al., 1p36 deletion syndrome: Review and mapping with further characterization of the phenotype, a new cohort of 86 patients, Am J Med Genet 191A:445–458, 2023. Courtesy C Jacquin, and with the permission of John Wiley & Sons. 378  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY say that incomplete penetrance and variable expressivity complicate interpretation and counseling; an important factor here is likely the role of CNVs elsewhere in the genome (Qiao et al. 2017). Triplication of 1q21.1 is described in Van Dijck et al. (2015). 1q21.1 (proximal)* Deletion. The smaller proximal deletion at BP 2-3 is 0.3 Mb in size and includes RBM8A (Figure 14–8). The 1q21.1 proximal deletion has the particular interest of being a susceptibility factor for thrombocytopenia-absent radius (TAR) syndrome (Strauss et al. 2023). The majority of TAR, 90% or more, is due to having a 1q21.1 deletion on one chromosome and a hypomorphic RBM8A variant (in 3% of European populations) on Figure 14–7.  Figure 14–8.  The Range of Deletions at 1q21.1. Notes: The sequences labelled BP (breakpoint) 2 to 4 comprise low-copy repeats, which promote unequal recombination between them. Imbalances can involve the proximal region (between BP2-3), the distal region (between BP3-4), or can span both regions. †Position of RBM8A, *position of GJA5. Source: From H Pang et al., Disorders associated with diverse, recurrent deletions and duplications at 1q21.1, Front Genet 11:577, 2020. Courtesy S Li and H Gu, and with the permission of Frontiers in Genetics. Autosomal Structural Rearrangements  379 the other. The deletion is usually (75%) familial, but may be de novo. Where one parent is heterozygous for the deletion and the other carries one or other of the RBM8A SNPs, the pattern of inheritance of TAR mimics that of autosomal recessive disease, with its attendant recurrence risk. Goh et al. (2025) calculate a penetrance for proximal 1q21.1 deletion of 18%, but it remains unclear to what extent this penetrance includes neurodevelopmental disability in addition to TAR syndrome. Duplication. The countertype duplication of the proximal 1q21.1 segment (Figure 14–9) may be a susceptibility variant of incomplete penetrance contributing to a largely neurobehavioral but also malformative phenotype in several, although with normality in some carriers (Levy et al. 2023). Goh et al. (2025) calculate a penetrance of 9%. Maternal transmission appears to be more harmful than from the father. Familial epilepsy co-segregating with dup(1)q21.1 is recorded in Fanciulli et al. (2014). 1q21.1 (distal)* Deletion. The distal 1q21.1 microdeletion (GJA5) at BP 3-4 (Figure 14–8) is one of the more common CNVs observed in clinical cohorts. The clinical picture includes cognitive impairment, autism, seizures, cardiac defects, cataract, and minor dysmorphic features. The 1q21.1 distal CNV has a large effect on head circumference, with a high prevalence of microcephaly in deletion carriers and macrocephaly in duplication carriers (Sønderby et al. 2021). Some are de novo cases, some familial with a (usually mildly) affected parent, and some are familial from an apparently unaffected parent; penetrance in Goh et al. (2025) is 30%. A detailed study in Bernier et al. (2016) documents the phenotypic range, with a particular focus on neurocognitive/psychological/behavioral traits. They note that while IQ might “officially” be in a normal range—that is, above 70—the average was about one standard deviation below the mean. Phonological processing, the ability to distinguish the meanings of words, is notably impaired. Digilio et al. (2013) describe a family Figure 14–9.  The Range of Duplications at 1q21.1. Notes: The sequences labelled BP (breakpoint) 2 to 4 comprise low-copy repeats, which promote unequal recombination between them. Imbalances can involve the proximal region (between BP2-3), the distal region (between BP3-4), or can span both regions. Source: From H Pang et al., Disorders associated with diverse, recurrent deletions and duplications at 1q21.1, Front Genet 11:577, 2020. Courtesy S Li and H Gu, and with the permission of Frontiers in Genetics.

380  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY in which a brother had pulmonary valve stenosis and an IQ of 87; his sister had learning difficulties, with an IQ of 58; and the daughter of this sister had moderate intellectual disability (IQ of 48) and difficult behavior, absence seizures, a complex heart defect, and some dysmorphic features. Each had the same 1q21.1 deletion. As can apply in the generality of microimbalances, loci elsewhere, if variant, may exacerbate the clinical phenotype (and indeed bring to medical attention a family that might otherwise have escaped notice). Duplication. Distal 1q21.1 duplication (Figure 14–9) has a nonspecific phenotype comprising mild to moderate cognitive impairment and neuropsychiatric and behavioral findings, along with macrocephaly (Sønderby et al. 2021). There is an increased risk of cardiac disease and diabetes. The duplication is usually inherited, with penetrance of 19% (Goh et al. 2025). A larger, 5 Mb duplication 1q21.1q21.2 in Brisset et al. (2015) was in company with a 16p11.2 deletion, and the phenotype in the child more severe than a simple “sum of the parts”—a multiplicative two-hit. The dup 1q21 had come from the father, and the del 16p11.2 from the mother; the father suffered from psychopathy and mild intellectual disability, and the mother from depression. A yet larger duplication, 1q21.1q44, is recorded in mosaic state in brain tissue from a non-dysmorphic child suffering from intractable epilepsy, who had had surgical resection of a part of one frontal lobe (Conti et al. 2015). On imaging, and subsequently on histopathology, the cerebral cortex was dysplastic. Triplo-excess of AKT3 (see dup 1q43q44, below) may have led to the brain defect. The duplication was not seen in blood or saliva; the abnormality likely arose at a post-zygotic mitosis in neuroectodermal tissue at an early stage of embryonic development, and was confined to this lineage. 1q21.3 Deletion. The few cases on record of this small deletion have involved different breakpoints, but all including these disease-associated loci: GATAD2B, TPM3, and HAX1, of which GATAD2B is likely to have the major role in determining the phenotype, which includes an intellectual disability and a characteristic facies (Tim-Aroon et al. 2017). 1q23.3 Duplication. A familial dup 1q23.3 is described in Speevak and Farrell (2013), a presumed benign copy number variant including two genes, MPZ and SDHC, seen in three generations: a grandfather, father, and one child. But in a second child, the duplication was itself duplicated, to give a 1q23.3 “quadruplication.” This infant presented with a severe form of Charcot-Marie-Tooth (CMT) neuropathy due to the excess dosage of the MPZ gene (mutation in which is the usual basis of CMT type 1B). The quadruplication may represent a second nonallelic homologous recombination (NAHR) event on this no. 1 chromosome in the family, the first having occurred one cannot say how many generations ago. 1q32.1q44 Duplication. These distal long arm duplications are of substantial size, up to 42 Mb, and thus readily detectable on classical cytogenetics; the proximal breakpoint is variable (Balasubramanian et al. 2009). The clinical picture is one of a distinctive facial dysmorphism, due in particular to craniofacial bone maldevelopment along with developmental Autosomal Structural Rearrangements  381 delay. Whether an association with myelodysplastic syndrome in one dup 1q41qter case is causal or coincidental remains to be established (Morokawa et al. 2018). 1q41q42 Deletion. This syndrome is to be numbered among those with an Angelman resemblance. Intellectual disability and seizures are observed. Loci FBXO28 and WDR26 are proposed as key pheno-contributory factors (Yanagishita et al. 2019; Bi et al. 2023); the characteristic facies is notably similar to cases with a point mutation at the WDR26 locus (Skraban-Deardorff syndrome). All cases have been de novo, except for the small (63 kb) deletion in Bi et al., which had been transmitted from a phenotypically unaffected father. 1q43q44 Deletion. There is considerable variation in the extent of these deletions (Figure 14–10). Microcephaly may be due to the AKT3 haploinsufficiency; agenesis of the corpus callosum might be consequential upon deletion of the regulatory factor ZNF238, while seizures could inhere in the HNRNPU gene in those in whom these loci are lost (Ballif et al. 2012; Depienne et al. 2017; Pelle et al. 2020). The ways in which these and other genes within the segment may interact and impact upon head size are rehearsed in Raun et al. (2017). We have seen a young woman—originally and not unreasonably diagnosed as Rett syndrome—with severe epilepsy, but normal on MECP2 mutation study in the early 1990s; microarray some 20 years later showed a microdeletion chr1:244.4-245.3 Mb (hg19) (R Beddow, personal communication, 2012). HNRNPU was the only one of the above-mentioned three genes included in this segment; very similar deletions are reported in Thierry et al. (2012). Figure 14–10.  Deletions of 1q43q44. Notes: Loci within the broad range of deletions, and within the critical region, shown; the pheno-critical locus is proposed to be AKT3. Scale is in hg38. Source: Adapted from B Khadija et al., Clinical and molecular characterization of 1q43q44 deletion and corpus callosum malformations: 2 new cases and literature review, Mol Cytogenet 15:42, 2022. Courtesy B Khadija and S Mougou-Zerelli, and with the permission of Springer Nature.

382  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY De novo inheritance is the norm, but very rare familial cases are recognized (Ballif et al. 2012). Gai et al. (2015) describe a normal father and his microcephalic son, both carrying a 1q44 deletion removing just the AKT3 gene. Parental very-low-level (3.4% on blood) somatic and inferentially gonadal mosaicism has been demonstrated (Campbell et al. 2014). Duplication, triplication, and quadruplication of 1q43q44 are on record (Lopes et al. 2019). The interest here is the proposed role of the AKT3 gene, which is a component of the important PI3K growth control pathway. The macrocephaly typically associated has its counterpart in the microcephaly due to the deletion. A single instance of parental transmission concerns a father and son with a 1 Mb quadruplication. Chromosome 2 2p11.2* Deletion. Ferrario et al. (2023) review the 10 cases then reported. Key loci are taken to be EIF2AK3 and RPIA. The phenotype encompasses an intellectual disability of borderline to moderate degree and, in some, a functional neurological disorder. A single case is known of parental transmission, from a father who had had only surgery for hypoacusia, to an affected daughter who had unilateral microtia and atresia of the external auditory canal; Ferrario and colleagues propose triplo-excess of FOXI3 to be responsible for this latter trait. 2p16.1p15 Deletions of up to 10 Mb within this region are non-recurrent, and all have been de novo. Miceli et al. (2023) determined shortest regions of overlap of the deletion in a review of 38 cases, identifying those including the landmark genes BCL11A alone, USP34/ XPO1 alone, and both BCL11A and USP34/XPO1, the phenotypes differing accordingly (Figure 14–12). Fannemel et al. (2014) describe a man having the smallest recorded deletion (230 kb), removing the USP34/XPO1 gene, who was mildly dysmorphic and intellectually affected but able to have sheltered employment. Figure 14–11. Autosomal Structural Rearrangements  383 Duplication. Twelve cases of dup2p15p16.1 in which the duplication includes BCL11A and PIX13 are listed in Wang et al. (2023a), and another two in which PEX13 was the only gene in common. Little clinical information was available for some of these cases (from the DECIPHER and ISCA databases); the child in Mimouni-Bloch et al. (2015) had a mild developmental delay, attention deficit and oppositional behavior, and mild dysmorphism. The macrocephaly seen in some cases is a countertype to the microcephaly observed with the deletion. BCL11A, in those cases duplicated for this gene, bids fair as a pheno-critical candidate. All those in whom parental studies were noted were of de novo generation. 2p16.3 Deletion. Non-recurrent deletions of NRXN1, at 2p16.3, cause a range of neurodevelopmental phenotypes including intellectual disability, autism, epilepsy, and schizophrenia. The NRXN1 gene is large and generates hundreds of splicing isoforms, complicating the interpretation of exonic deletions (Montalbano et al. 2024). Goh et al. (2025) estimated penetrance of 37% for deletions that include at least one exon of NRXN1, but this may vary with the size of the deletion and exons involved. 2p21 Deletion. This extremely rare syndrome is unusual in being seen in only the homozygous state (Bartholdi et al. 2013), and thus displaying an autosomal recessive mode of inheritance. The loci implicated are PPM1B, SLC3A1, PREPL, and CAMKMT. SLC3A1 is the basis of the cystinuria seen in the syndrome (a smaller deletion including just SLC3A1 and PREPL leads to the hypotonia-cystinuria syndrome). Seizures, intellectual disability, and a Prader-Willi-like facial dysmorphism are observed. 2p22.3-p22.2 Deletion. Quiñones-Pérez et al. (2018) report a 3-generation family in which some members had a clinical picture reminiscent of Marfan or Loeys-Dietz syndrome. The transmission of a 2p22.3p22.2 segment, within which 11 loci were accommodated and of Figure 14–12.  Phenotypic Variation in 2p15p16.1 Deletions, According to the Two Key Loci Lost. Notes: These “radar plots” give a visual indication of how severe a particular trait is, according to its distance from the central 0 point, in relation to which loci have been deleted (BCL11A alone, USP34/XPO1 alone, or both). By eye, severity with both loci deleted is cumulative. IUGR, intrauterine growth retardation; NDD, neurodevelopmental delay. Source: From M Miceli et al., Trait-driven analysis of the 2p15p16.1 microdeletion syndrome suggests a complex pattern of interactions between candidate genes, Genes Genomics 45:491–505, 2023. Courtesy M Fichera, and with the permission of Springer. 384  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY which LTBP1 was the likely basis of the aortopathy observed in the family, co-segregated with the clinical phenotype. 2q11.2 Deletion. The 2q11.2 deletion is ~1 Mb in size, with 20 protein coding genes, TMEM127 a useful landmark. Phenotypes observed include speech delay, ADHD, and dysmorphic features. De novo, and paternal and maternal transmission are all recorded (Riley et al. 2015). Its pathogenicity has been drawn into question due to discovery of the deletion in control cohorts. The penetrance estimate (0%–27%) from Goh et al. (2025) was not statistically significant, and it may be that the 2q11.2 deletion is not pathogenic per se, or at most is weakly penetrant. Duplication. The corresponding 2q11.2 duplication has been seen with short stature, mild facial dysmorphism, and developmental delay, arising de novo or inherited from an affected or (apparently) unaffected parent (Riley et al. 2015). A causal link to these phenotypes is yet to be proven. 2q13* Deletions and duplications within 2q13, and in some extending to the adjacent band 2q12.3, arise within a segment defined by low-copy repeats A through I (Figure 14–14). A subdivision is made among those encompassing the whole segment; those mostly within a proximal (E to G) segment, those more distally (A to D), and a short deletion between D to E. Proximal Deletion and Duplication. These del/dups at low-copy repeats (LCRs) E to G can be of varying extent, but having a shortest region of overlap that includes the RANBP2 locus. A neuropsychiatric phenotype is typical (Aarabi et al. 2022; Huynh et al. 2021a). Mid Deletion and Duplication. A recurrent 2q13 proximal del/dup of size 0.12 Mb (LCRs D to E) is seen commonly in the general population. NPHP1 is the landmark locus (Figure 14–14). Goh et al. (2025) comment that the del penetrance of 4.5% is not above background risk, and the deletion is unlikely to be pathogenic. Homozygosity for NPHP1 deletion causes the kidney disease nephronophthisis. Similarly, the recurrent 2q13 mid-duplication with NPHP1 is not enriched in clinical cohorts compared to controls, and is unlikely to be pathogenic per se (Goh et al. 2025). Figure 14–13.

Autosomal Structural Rearrangements  385 Distal Deletion. The recurrent 2q distal deletion is 1.7 Mb in size (LCRs A to D) and includes the locus BCL2L11 (Figure 14–14). Variability in expression and incomplete penetrance are characteristic. Associated phenotypes include intellectual disability, autism, and dysmorphism, and in some, major cardiac and craniofacial malformation; but more often, carriers are normal (Riley et al. 2015). The carrier parent may or may not show any sign; this may well reflect the influence of variation elsewhere in the genome, and the concept of the “second-hit” CNV is likely germane. Approximately one-third arise de novo. Elron et al. (2025) discuss the counseling issues raised in the context of low penetrance and variable expressivity. The risk will be tempered by the family history: if the finding is made at prenatal diagnosis, with no antecedent family history of note, the risk is likely to be less than had it been through a previously affected child: in the latter case the parents have, in a sense, self-declared the possibility of other interacting genetic factors. Distal Duplication. The recurrent 1.7 Mb distal duplication (BCL2L11) is usually inherited from an unaffected parent. Recurrent features include developmental delay, neuropsychiatric conditions, and nonspecific dysmorphism. In four cases of dup2q13 studied in Riley et al. (2015), developmental delay or intellectual disability was observed in all. Two (an uncle and a nephew) were from a 3-generation kindred, and the connecting relative was described with a learning difficulty. The patriarch in generation I was apparently unaffected. 2q21.1* Deletion. The phenotype associated with these deletions is one of a neurodevelopmental and neuropsychiatric manifestation: intellectual disability, attention deficit hyperactivity disorder, autism, aggressive behavior, and epilepsy (Dharmadhikari et al. 2012; Figure 14–14.  Deletions and Duplications at 2q12.3q13. Notes: These representative data are from cases presenting with developmental delay, intellectual disability, learning deficits, autism spectrum disorders, and congenital anomalies. Deletions are the red bars, duplications the blue. Recurrent del/dups are shown as double entries. Low copy repeats A through I are located along the segment; LCRs A-D and E-G define the two major regions of observed imbalance. Landmark loci are asterisked: from A to I (reading right to left), these are TMEM87B, BCL2L11, NPHP1, RANBP2, SULT1C2, and ST6GAL2. Sources: From M-T Huynh et al., Novel interstitial 2q12.3q13 microdeletion predisposes to developmental delay and behavioral problems, Neurogenetics 22:195–206, 2021. Courtesy M-T Huynh, and with the permission of Springer Nature. Additional cases from Riley et al. (2015) and Aarabi et al. (2022). 386  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Gimelli et al. 2014). Key loci are ARHGEF4 and GPR148. Paralogous sequences in 2q21.1 lead to a propensity for NAHR. It may frequently be inherited from an affected or unaffected parent; in other words, this deletion can, occasionally, be nonpenetrant. Duplication. The case for an effect due to the duplication remains open (Dharmadhikari et al. 2012). 2q23.1 The key locus within 2q23.1 is MBD5, and the expression “MBD5-associated neurodevelopmental disorder” (MAND) has been applied to deletions, duplications, and point mutation of the gene (Mullegama and Elsea 2016). Deletions range considerably in size, from ~300 kb to 20 Mb. There is a resemblance to Angelman and Rett syndromes, with features of severe intellectual disability with absent speech, stereotypic repetitive behavior, microcephaly, ataxia, and a coarse facies. Penetrance is 100% (Goh et al. 2025). Severe epilepsy (infantile spasms) is recorded (Du et al. 2014).6 Familial transmission is very rare, but van Bon et al. (2010) and Tadros et al. (2017) describe transmission from unaffected somatic-gonadal, or presumed confined gonadal mosaic parents, to their children. Duplication. Mullegama et al. (2014) conclude a picture not unlike that of the countertype deletion, although not quite as severe with respect to the core phenotype of intellectual disability, autistic features, and minor dysmorphisms; an “affable personality” is common. The duplicated segments, which are mostly non-recurrent, vary considerably in size; most are less than 10 Mb, and several are less than 1 Mb. All contain the pheno-critical gene MBD5. Most arise de novo, although Mullegama and colleagues do record rare cases of mother-to-child transmission; detailed information was not available for these transmitting parents, but on best advice they were not considered to have been affected. In other words, non-penetrance is observed. 2q31q32 Deletion. Loss of the HOXD cluster, when this is within the deleted segment (Figure 14–15), is the presumed cause of the limb malformation such as great toe duplication and clinodactyly (Dimitrov et al. 2011). Variable dysmorphism, in some presenting a distinctive facial gestalt, and neurocognitive capacity from essentially normal to substantially compromised, may correlate with the compass of the deletion. Parent-to-child transmission, and indeed grandparent-to-grandchild transmission, is recorded (Mitter et al. 2010; Tsai et al. 2009). 2q32q33 Deletion: Glass Syndrome, SATB2-Associated syndrome. There is considerable variation in the extent of the deletion, ranging from 35 kb to over 10 Mb in size. A behavioral phenotype of hyperactivity, and a “happy” affect but with bouts of anxiety or aggression, are reported; intellectual disability can be severe. Dysmorphism may be subtle; a Marfanoid appearance is sometimes observed. The key locus is SATB2. If the deletion 6 MBD5 interacts with several autism-associated loci implicated in other deletion syndromes, including RAI1 in del(17)(p11.2) Smith-Magenis syndrome, TCF4 in del(18q) Pitt-Hopkins syndrome, UBE3A in del(15)(q11.2q13.1) Angelman syndrome, EHMT1 in del(9)(q34.3) Kleefstra syndrome, and MEF2C in the del(5)(q14q21) syndrome; thus, the final common neurobehavioral phenotypic outcome in all these conditions is similar.

Autosomal Structural Rearrangements  387 includes COL3A1/COL5A2 and BMPR2, there is increased likelihood of, respectively, aortic dilatation and primary pulmonary hypertension (Zarate et al. 2021). De novo inheritance is the rule, but parental mosaicism is known. Qian et al. (2019) report a father of two affected children, with an intragenic SATB2 3 kb deletion detected in 13% of blood and 17% of semen DNA. Duplications in this chromosomal region are of varying lengths, and several overlap in the segment containing SATB2, KCTD18, and ADAM23, as Usui et al. (2013) document in their review. Their own case was of a child with severe developmental delay, autism, ataxia, and mild facial dysmorphism. Some duplications extend into 2q31 and 2q24.3; if the imbalance includes the DLX loci (Figure 14–15), this may engender epilepsy (Lim et al. 2014). 2q37 Deletion: Albright-like Syndrome. This well-known deletion should specifically be sought in patients with a morphological phenotype somewhat reminiscent of Albright hereditary osteodystrophy (short stature, short metacarpals), a quite distinctive facies, intellectual disability with autistic behavior, and often obesity (Gavril et al. 2023). It is among the more frequent of the deletion syndromes. Deletions range in size from 2 Mb Figure 14–15.  The Range of Deletions in the 2q31 Syndrome. Notes: For the most part, these deletions are non-recurrent. Some extend well beyond the core region, which is encompassed within the five vertical bars. These vertical bars delineate the positions of key genes deleted within these segments. DLX = the adjacent genes DLX1 and DLX2; HOXD = HOXD cluster; ZNF (mid) = ZNF385B; ZNF (right) = ZNF804A. Source: From E Candelo et al., 2q31 microdeletion syndrome with the velocardiofacial phenotype and review of the literature: a case report, BMC Pediatr 24:641, 2024. Courtesy H Pachajoa, and with the permission of Springer Nature. 388  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY to 10 Mb, and typically include the proposed critical gene HDAC4. Penetrance is complete (Goh et al. 2025). Parent-to-child transmission is very rare, but has been observed in cases in whom the deletion is of smaller extent (Villavicencio-Lorini et al. 2013; Iwata-Otsubo et al. 2022; Jean-Marçais et al. 2015). The latter authors describe a father and his three children with a small 0.49 Mb 2q37.3 deletion, and probably others in the family likewise affected. This case allowed an inference that deletion of the TWIST2 and HDAC4 genes may be necessary to produce the classic phenotypic features. Transmission from a mosaic parent is noted in Freitas et al. (2012). Duplication. The 2q37 duplicated state may be associated with an intellectual capacity within the normal range and little or no dysmorphism (Batstone et al. 2003), in obvious contradistinction to the deletion. Chromosome 3 3p12p14 Deletion. Children with deletion of 3p12p14 have a distinctive facial appearance and are severely developmentally delayed; early childhood death is recorded. The deletions are non-recurrent, the largest recorded being of 27 Mb (Abarca-Barriga et al. 2020). Most overlap the segment 3p13.1p14 within which these particular genes are included: MITF, FOXP1, and PROK2, each of which is plausibly contributory to the phenotype (Dimitrov et al. 2015). 3p25p26 Deletion: Distal 3p deletion syndrome. Deletions at distal 3p are well recognized and command considerable attention (Figure 14–17). Deletions that extend beyond 9 Mb–10 Mb, and which remove some or all of the SRGAP3, SETD5 and BRPF1 loci, are associated with intellectual disability (Fu et al. 2021; Zaghi et al. 2023). Loss confined to the two distalmost bands, 3p26.2 and 3p26.3 and of under 9 Mb in length, may be seen in normal persons. A deletion removing just the CHL1 locus (the very “first” gene in the chromosome in the band 3p26.3) is proposed to affect speech development Figure 14–16. Autosomal Structural Rearrangements  389 (Tsuboyama and Iqbal 2021) but may equally be seen in a normal person (Cuoco et al. 2011). Moghadasi et al. (2014) describe a four-generation family in which all six tested individuals with a 2.9 Mb deletion within these two distalmost bands, including the CHL1 locus, other than the proband were essentially normal people. Similarly, the del(3)(p26.3p25.3) heterozygotes in the three-generation family in Chen et al. (2024f ), ascertained incidentally at prenatal diagnosis, were phenotypically normal. A role for second-hit CNVs (or mere coincidence) in the presenting symptomatology of cognitively affected del(3)(p26.3p26.2) probands remains open. Two genes of interest within distal 3p deletions are ITPR1 (3p26.1) and VHL (3p25.3), and haploinsufficiency of which causes spinocerebellar ataxia type 15 and Von Hippel-Lindau disease, respectively. Thus, a del(3p) patient whose deletion included one or both of these genes, and surviving well into adulthood, might develop the corresponding ataxic and tumor-associated syndrome. Duplication within 3p25p26 has been seen in only two children in whom molecular analysis has been done (Bittel et al. 2006b; Natera de Benito et al. 2014). The segments involved are large, one of 26 Mb and the other contained within 3p25.3p26.2. The GHRL gene is plausibly a basis of the observed obesity, quite strikingly reminiscent of a Figure 14–17.  Some Distal 3p Loci. Notes: The segment from 3p25.3 (the position of the gene BRPF1) to p26.3 comprises the distalmost 10 Mb of DNA. Deletions can encompass as little as the CHL1-containing segment, or the full length up to BRPF1 or further (Shuib et al. 2009). T = telomere. Figure 14–18.

390  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Prader-Willi phenotype. Both had a mild pervasive developmental disorder. At least the larger duplication was confirmed de novo; it is likely both were. 3q22.3q25 Deletion. According to the extent of deletion within this chromosomal region, the phenotype may include features of blepharophimosis-epicanthus inversus syndrome (BPES),7 the Dandy-Walker cerebellar malformation, and the Wisconsin syndrome. Ferraris et al. (2013) define three critical regions within which the deletions of the observed cases have fallen. Deletions that remove FOXL2 (at q22.3) produce BPES; loss of ZIC1 and ZIC4 (q24) likely contributes to the cerebellar defect (but this component of incomplete penetrance); and deletions extending into 3q25.2 may lead to Wisconsin syndrome. Thus, a child described in Ferraris et al. who carried a large 3q22.1q25.1 deletion, 19.2 Mb in length and which removed the FOXL2, ZIC1, and ZIC4 genes, had both BPES and Dandy-Walker malformation as part of the overall complicated clinical picture. The Wisconsin syndrome, characterized by a distinctive facial gestalt, may reside more distally, with the loci MBNL1 and WWTR1 plausibly key factors (Okano et al. 2022). 3q22.2q29 Duplications within this segment are of considerable length and can be 60 Mb or more. This is large enough that the condition—named the “dup(3q) syndrome”—was detectable on classical cytogenetics as early as 1966 by Falek et al. (1966). The clinical phenotype is notable in a resemblance to Cornelia de Lange syndrome (and indeed this dup(3q) misled early efforts to locate the gene). 3q26.32q28 Deletion. This rare syndrome is due to deletion of variable (2 to 8.4 Mb) extent (Robilliard and Caylan 2020), and in some is more accurately described as del 3q26.3q27.2. A distinctive facies, intellectual disability, and severe growth retardation characterize the clinical picture. Where studied, cases have been of de novo origin. Duplication. Two regions declare themselves as recurrent: dups which include 3q26.2, and those including 3q26.32q27.2 (Figure 14–19). There may be complex dysmorphology; the frequent observation of caudal abnormalities in the latter duplication may lie in the loss of DVL3 and/or EPHB3 at 3q27.1 (Pavone et al. 2016; Dworschak et al. 2017). A pheno-contributory role for TBL1XR1 is proposed in Riehmer et al. (2017), who studied a familial case in which a mother and two offspring were duplicated for a very small segment of 521 Figure 14–19.  Duplication Regions of 3q, Common Segments Indicated. Notes: A wide range of duplication within this very large segment are on record, a few encompassing over half of the entire segment (Molck et al. 2018). 7 Isolated BPES may be due to a translocation having one breakpoint in this region, but distant from the actual gene—a laboratory diagnosis that might be missed unless a karyotype is preformed (Yang et al. 2014). Autosomal Structural Rearrangements  391 kb, at 3q26.32. Most of these duplications have arisen following a parental malsegregation of a translocation involving chromosome 3; pure cases are less frequent. 3q27.3 Deletion. This syndrome gained definition through interrogation of the DECIPHER database. Thevenon et al. (2014) collected recorded patients with variable non-recurrent deletions, in whom two shortest regions of overlap (SRO) were identified. A slender and gloomy facial appearance is very distinctive (Castori et al. 2015). The SST gene (within SRO1) may be responsible for the neuropsychiatric picture ranging from autism to psychosis, and the AHSG gene (in SRO2, which extends into q27.2) for the somewhat Marfanoid skeletal phenotype. Most arise de novo, but parental transmission is known. 3q29* Deletion. This recurrent 1.6 Mb deletion encompasses the neighboring DLG1 and BDH loci (Città et al. 2013). Variable behavioral traits, mild to moderate intellectual disability with microcephaly, and mild facial dysmorphism are core features of the phenotype; the facies is sufficiently distinctive that a phenotyping algorithm (Face2Gene) can recognize it (Mak et al. 2021). Some, in addition, have clefting and genitourinary malformation. The deletion predisposes very significantly to schizophrenia, indeed a 41-fold increased risk (Mulle 2015). Glassford et al. (2016) were able to recruit a cohort of 44 cases and documented neuropsychiatric traits including anxiety disorder, panic attacks, depression, and bipolar disorder, as well as schizophrenia. These psychiatric traits reflect, in part at least, a hypoplasia of the cerebellum (Figure 14–20); genes influencing cerebellar formation within 3q29, such as BDH1 and DLG1, may be instrumental in this respect (Sefik et al. 2024). Figure 14–20.  The Cerebellum in 3q29 Deletion. Notes: The red circle shows near-complete absence (hypoplasia) of brain tissue in the midline, between the cerebellar hemispheres. The cerebellum has a major role in cognition and liability for psychopathology, along with its classic role in motor control. Source: From E Sefik et al., Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome, Mol Psychiatry 29:3395–3411, 2024. Courtesy JG Mulle and S Shultz, and with the permission of Springer Nature.

392  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Familial transmission is rare but recorded (Khan et al. 2019), and both abnormal and reportedly normal parental neurocognitive aspects are observed. The penetrance estimate from Goh et al. (2025) is 52%. Duplication. The dup 3q29 has the notable feature that the majority of cases are familial, in contrast to the deletions, which almost always arise de novo. DLG1 and PAK2 may be key loci (Dworschak et al. 2017). Mild to moderate cognitive impairment and microcephaly are the most commonly observed traits in index cases. The normality or near-normality of a transmitting parent which is sometimes observed (Aleixandre Blanquer et al. 2011) may reflect an incompletely penetrant genotype, and other genetic factors may influence expression; Goh et al. (2025) estimate penetrance to be 67%. Chromosome 4 Distal 4p Deletion: Wolf-Hirschhorn Syndrome (WHS). This well-known deletion syndrome identified in the pre-banding era is one of the few that in its typical form can be confidently recognized clinically (Figure 5–29). The “Greek warrior helmet” craniofacial appearance is very characteristic, regardless of ethnicity (Shimizu et al. 2014; Mekkawy et al. 2021). The natural history of WHS is discussed in Battaglia and Carey (2021). Very few ever survive into adulthood, and most who do would require complete care (Carey et al. 2021). The smallest deletions are confined to the distalmost band, 4p16.3, and are of less than 3.5 Mb size.8 Much the commonest observed is a terminal deletion of 5 Mb–18 Mb, which may extend into 4p15. (Larger 22 Mb–25 Mb deletions might be described as “WHS plus.”) Deletions typically include two short contiguous WHS critical regions, WHSCR1 (proximal) and WHSCR2 (distal), within distal 4p16.3 (Figure 14–22). The NSD2 gene (also known as WHSC1) is presumed to have a key role in determining the classic dysmorphology, and LETM1 may influence nervous system functioning; but no one gene commands the phenotype, and this is a true contiguous gene syndrome with a presumed contribution of several p16.3 genes. Figure 14–21.          8 Deletions within 4p16.3 more distally beyond the WHSCRs do not show WHS features (Osundiji et al. 2024). Autosomal Structural Rearrangements  393 While de novo occurrence is the typical observation, almost half may be revealed as having arisen as unbalanced translocations, some showing additional phenotypic features in consequence (South et al. 2008; Wieland et al. 2014). Duplication. Some heterozygotes for this duplication, even if including the WHSCRs, may be of fairly unremarkable phenotype (Carmany and Bawle 2011). In others, in whom the duplication is of greater extent, the intellectual disability can be severe (Mortimer et al. 1980). Macrocephaly and tall stature were observations in a three-generation family described in Schönewolf-Greulich et al. (2013). As with the deletion, familial transmission due to a segregating translocation is often the case, and indeed the del and the dup can be seen in the same family, due to a 4p translocation (Mortimer et al.). 4q21 Deletion. The first major series of patients with this deletion was reported by Bonnet et al. (2010). A number of further cases have since appeared in the literature concerning this syndrome of marked growth and developmental retardation, with poor or absent spoken language along with a quite distinctive facial appearance. The brain defect of polymicrogyria is described (Dobyns et al. 2008). Most deletions are in the range 2.0 Mb–15 Mb; the smallest is 761 kb. Important genes therein are PRKG2 and RASGEF1B, which likely underlie the cognitive phenotype (Hu et al. 2017). If the deletion extends into 4q22 and removes the PKD2 gene, the very specific feature of polycystic kidney disease ensues (Sakazume et al. 2015). Giguet-Valard et al. (2024) describe a prenatal diagnosis, fetal anomalies having been identified. All cases have been de novo; nevertheless, a parental insertional translocation is to be excluded prudently. Duplication of 4q21.22q21.23 is very rarely recognized (Iourov et al. 2018). Intellectual disability is associated. Figure 14–22.  Wolf-Hirschhorn Syndrome Deletions. Notes: These data from eight cases of WHS show the wide range of deletion that is observed. Each deletion encompasses the two WHS critical regions in 4p16.3, WHSCR1 and WHSCR2. WHSCR1 contains the gene NELFA, and WHSCR2 contains LETM1. The gene NSD2, which lies between these two loci, straddles the two critical regions. Source: From T Corrêa et al., Cytogenomic integrative network analysis of the critical region associated with Wolf-Hirschhorn syndrome, Biomed Res Int 2018:5436187, 2018. Courtesy M Riegel, and with the permission of John Wiley & Sons. 394  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 4q3 Deletion. Many cases are on record of distal 4q deletions (“4q deletion syndrome”), mostly terminal or at least subterminal, some interstitial. But this is a heterogeneous collection, as almost all are non-recurrent rearrangements. Heart malformation is frequent, and the HAND2 (in q34.1) and SORBS2 (q35.1) genes are implicated. The very specific observation of ulnar ray defect may reside in 4q34.1 (Lurie 2016). In the review of Strehle et al. (2012), the distal segments in seven patients ranged from 4q32.2q35.2 to 4q35.2q35.2, and of sizes 464 kb to 24.0 Mb. It is not uncommon that a parental rearrangement, typically a balanced translocation, is identified. Smaller distal 4q deletions may be seen in normal persons. Bateman et al. (2010) report a normal woman identified incidentally in the course of a miscarriage investigation, who had a 10 Mb deletion in 4q34.1q34.3. A marginally smaller and more distal deletion at 4q35.1q35.2 was seen in a normal mother and her two daughters in Yakut et al. (2015). This observation speaks to a non-penetrance of these segments. Duplication. A 4q duplication syndrome has been recognized for some time, and Thapa et al. (2014) review several cases from as early as the 1970s in which the breakpoints ranged from q22 to q31.3 proximally, to q32.3 to qter distally. The children whose photo is illustrated in the frontispiece of this book represent the case. Transmission from a parental translocation may be observed (as it was with the children in the photo). It is of interest that 4q34 contains quite a large “gene desert”; this may be a factor in the viability of some quite substantial 4q segments. Chromosome 5 5p13 Duplication. Novara et al. (2013) review dup 5p13, which is associated with a phenotype of intellectual disability that can be severe, along with EEG and brain MRI abnormality, and facial dysmorphism. The key locus, in 5p13.2, is NIPBL (which is well known otherwise as the basis, when deleted, of Cornelia de Lange syndrome). The duplicated segment ranges in size from 0.25 Mb to 13.6 Mb. Figure 14–23.

Autosomal Structural Rearrangements  395 Rare familial examples are on record. In one, four affected children were born to a mother carrying an insertional translocation of 5p13.2 into Xp, of karyotype der(X) ins(X;5) (Walters-Sen et al. 2015). Parental mosaicism was the basis of recurrence in Tian et al. (2022). In another, the remarkable circumstance is recorded of an unaffected father with a small duplication that included NIPBL, with no evidence of mosaicism for a normal cell line (at least on blood and saliva sampling) who had had an affected fetus, raising the possibility of non-penetrance in his case (Kariminejad et al. 2023). 5p13p15 Deletion: Cri du Chat Syndrome. Most of the deleted segments of this famous syndrome are terminal and vary considerably in length, but the segment 5p15.2p15.3 defines a typical core region (Figure 14–24). The clinical severity corresponds substantially, but not always precisely or consistently, to deletion size; differential methylation of loci is proposed also to be a factor in phenotypic variation (Almeida et al. Figure 14–24.  Cri du Chat Deletions. Notes: These data from 15 cases of cri du chat syndrome show the variable breakpoints of deletion that may be observed. Certain loci have been matched with certain phenotypic traits: the “cri” may be due to TERT, and dysmorphisms and cognitive impairment may have their basis, in part at least, in haplo insufficiency of the other four loci shown. Source: From VT Almeida et al., Differences in DNA methylation status explain phenotypic variability in patients with 5p− syndrome, BMC Res Notes 17:121, 2024, with the permission of Springer Nature. 396  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 2024). The cri9 in the newborn is characteristic, and may even allow the diagnosis to be suspected, sight unseen, as one enters the neonatal nursery. Van Buggenhout et al. (2000) document in quite some detail, with several photographs, the phenotypes in seven older individuals, teenagers and adults; and Nguyen et al. (2015) provide detail collected from a support group (the 5p Minus Family Database). Cognitive compromise is typically mild/moderate in more distal small (5p15.31pter) deletions, moderate to severe with deletions from 5pter to 5p14.1, and profound in those extending into 5p13.2p13.3 (Marignier et al. 2012). While most cases are sporadic, about 10% are due to a familial translocation, and this possibility should be checked for in each case; a rare cause is a large parental inversion (Ohnuki et al. 2010). Cases of recurrence of del(5) attest to the reality of parental gonadal mosaicism (Hajianpour et al. 1991; Alkaya et al. 2020). Very seldom, in milder cases, parental transmission may be seen; here, a more distal deletion is common. These transmitting parents typically display a compromised cognitive and behavioral phenotype. Almeida et al. (2024) report a mildly intellectually affected mother and her two moderately affected children, in whom the 6.2 Mb deletion did not include CTNND2. Both children had a high-pitched cry as babies. Remarkably, Zhang et al. (2016a) describe one del(5p) father who had had a cat-like cry as a baby, learning difficulty at school, and who was yet able to graduate with a bachelor’s degree in computer science. The deletion had been transmitted through three generations of his family. More proximal deletions, outside of the core cri du chat region, may not necessarily impose a phenotype. Papoulidis et al. (2013) report a man (a physician) presenting only with infertility, who carried a de novo interstitial 15.5 Mb deletion at 5p13.3p14.3, this segment being described as somewhat of a “gene desert.” 5q11.2 Deletion. This rare disorder has the interest of an associated immunodeficiency, presenting as recurrent infections, along with a learning disorder and mild dysmorphism. Deletions are non-recurrent. A key locus may be DHX29, while the immunodeficiency may reside in loss of IL6ST (Arora et al. 2019; Bayat et al. 2021). All cases have occurred de novo. 5q14 Deletion. This condition has some resemblance to Rett syndrome. The severe intellectual disability is associated with the brain malformation, microcephaly with simplified gyral pattern. Most but not all involve the deletion of MEF2C at 5q14.3 (Fernández Hernández et al. 2021). In some, deletions may be small enough that only MEF2C is removed. Duplication. As with the 5q14 deletion, the neurocognitive phenotype of this rare imbalance inheres in the MEF2C locus. Duplications are of varying size. Cesaretti et al. (2016) documented, at the level of macroscopic fetal neuropathology, partial agenesis of the corpus callosum. All cases have been de novo. 5q22q23 Deletion: Polyposis Plus Syndrome. A minor degree of facial dysmorphism and mild to moderate intellectual disability are nonspecific features seen in these deletions; the 9 The name of the syndrome was whimsically given by nurses at Hôpital Enfants-Malades, Paris.

Autosomal Structural Rearrangements  397 unique feature is adenomatous polyposis of the bowel, and indeed it was such a deletion that led to discovery of the APC (adenomatous polyposis coli) gene (Hockey et al. 1989). Absence of one APC allele of itself allows polyps to develop, and any subsequent mutation/loss of the allele on the intact chromosome 5 then leads to loss of the tumor suppressor function of this gene. If mental capacity is only mildly affected, parenthood is achievable, but of course with a risk of transmission (Tanabe et al. 2024). Duplication. The large 5q22.1q23.2 duplication, of variable extent and obvious on classical cytogenetics, is associated with a clinical picture of variable intellectual disability, typically microcephaly, minor facial dysmorphism, and short stature. In the cases reported in Schmidt et al. (2013) of an affected mother and her two children, the (inverted tandem) duplication extended approximately from the CAMK4 to the ZNF608 loci, encompassing a little over 14 Mb in length. 5q31 Deletion. The clinical picture in this rare 5q31.2q31.3 deletion syndrome is predominantly neurodevelopmental, with severe intellectual disability, marked hypotonia, apneic episodes, and poor feeding. A particular observation is abnormal movements in the neonatal period resembling a seizure, but with no epileptic activity on the electroencephalogram. Brain MRI shows poor frontal lobe structure (Brown et al. 2013). Bonaglia et al. (2015) record the life history of the oldest known patient, who survived to age 26 years. Deletion sizes range from approximately 1 Mb to 5 Mb, and PURA and LRRTM2 are proposed as key loci (Kleffmann et al. 2012). We may need to consider that two “subsyndromes” exist: one defined by loss of PURA, in which epilepsy is a feature (Kofoed et al. 2024), and another by loss of LRRTM2, although most del 5q31.2q31.3 deletions combine the two. All cases have been de novo. 5q35* Deletion: Sotos Syndrome. The central locus in this overgrowth syndrome is NSD1. An alternative name is cerebral gigantism, and macrocephaly is essentially invariable: brain imaging shows cortical malformation in most (Neeman et al. 2024). Mild-to-severe intellectual impairment is universal. A curious observation in the genetics of Sotos syndrome is an ethnic difference: about half of Japanese cases are due to microdeletion 5q35.2q35.3, but only 10% of a UK population (the remainders having an NSD1 point mutation). Furthermore, deletion lengths varied quite considerably in UK cases, from 0.5 Mb to 5.0 Mb; but in the Japanese, most had a recurrent 1.9 Mb deletion, chr5:176.1-178.0 Mb. A similar picture is seen in Korean patients (Sohn et al. 2013). These differences likely reflect an ethnic heterogeneity of “genomic architecture,” and specifically the nature of flanking low-copy repeats, which may predispose to rearrangement (Tatton-Brown et al. 2005; Mochizuki et al. 2008). A large majority of deletions occur de novo on the paternal chromosome. Duplication. The dup (5)(q35.2q35.3) is the countertype of the deletion, and growth is in the opposite direction to Sotos syndrome: length and head circumference are typically more than two standard deviations below the mean, and bone age is delayed. Parental transmission has been recorded, although the majority represent de novo cases. Van der Lugt et al. (2023) report a minimally affected mother and her markedly affected son, raising the matter of a considerable intra-familial variability. A duplication of somewhat greater distal extent, typically to 5qter, is referred to as Hunter-McAlpine syndrome (Jamsheer et al. 2013; Žilina et al. 2013). 398  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Chromosome 6 6p21.1p12.3 Duplication. Savarese et al. (2013) report duplication for a 13.8 Mb segment at 6p21.31p12.3 transmitted from a mildly disabled mother to her daughter; these two bear a most striking facial resemblance to each other. Contained within this segment is band 6p21.1, and Varvagiannis et al. (2013) focus on the syndrome confined to dup(6)(p21.1), noting that the most remarkable feature was a craniosynostosis and proposing that an additional dose of RUNX2 (the gene for cleidocranial dysplasia) may be the basis of this. The duplication may be due to a 6p-containing de novo translocation (Sivasankaran et al. 2017; Türkyılmaz et al. 2023). 6p25p24 Deletion. Terminal deletions at 6p25 may involve just that band, or extend into 6p24 or further (Qi et al. 2015) (Figure 14–26). The “deleted region in common” includes the FOXC1 gene. Eye defects are common (Le et al. 2023). Brain imaging can show a cerebellar malformation and variable leukoencephalopathy (Cellini et al. 2012; Delahaye et al. 2012). Prenatal diagnosis, following ultrasonographic demonstration of multiple anomalies, is recorded (Ergin et al. 2015). Vernon et al. (2013) report an adult, of normal intelligence (certainly an atypical observation), with a CADASIL-like10 leukoencephalopathy, who showed a del 6p25.3p25.2 (chr6:0.2-2.7 Mb) karyotype, FOXC1 included in the deleted segment. A notable familial case is described in Qi et al. (2015): A mother mosaic del(6p)/ dup(6p)/normal for the interstitial segment 6p25.1p24.3 (chr6:4.74-10.38 Mb, R3-8 in Figure 14–26) had a del(6p) daughter with mild speech delay and minor dysmorphism, and a dup(6p) son of normal development and the softest of soft dysmorphic signs. The mother’s chromosomal state likely arose from an unequal sister chromatid exchange in early embryogenesis. Duplication. We note above (Qi et al. 2015) the dup(6p) child of normal development and of soft dysmorphology. Figure 14–25.          10 CADASIL = cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy. Autosomal Structural Rearrangements  399 Figure 14–26.  Distal 6p Deletions. Notes: Some recorded deletions of chromosome 6 distal short arm. Interstitial deletions occurring within the bracketed regions enabled a division into nine subregions (R1–R9). The red asterisk pinpoints the position of FOXC1. Source: From Qi et al., Haploinsufficiency and triploinsensitivity of the same 6p25.1p24.3 region in a family, BMC Med Genom 8: 38, 2015. Courtesy J Yu, and with the permission of Springer Nature. Figure 14–27.

400  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 6q14.1q15 Deletion of 6q14.1q15 can determine a clinical picture of dysmorphic features, congenital malformation, and neurobehavioral difficulty—but within these bounds, quite some variation is seen (Quintela et al. 2015). Body habitus has been described with the opposite observations of a resemblance to Marfan or Prader-Willi syndrome (Lowry et al. 2013). All are intellectually affected. A 5 Mb segment including SNX14 in 6q14.2q14.3 appears to comprise the pheno-critical component of the syndrome. No familial case is known. 6q16 Deletion. Two very closely linked loci, POU3F2 at 6q16.2 and SIM1 at 6q16.3, determine two factors involved in an appetite pathway (the leptin → melanocortin → SIM1 → oxytocin pathway) (El Khattabi et al. 2015; Kasher et al. 2016) (Figure 14–28). A deletion including just one, just the other, or indeed both of these two genes, leads to a syndrome in which obesity associated with hyperphagia is a cardinal observation, along with cognitive compromise; the condition has been called Prader-Willi-like. The breakpoints are almost all non-recurrent. Most cases are de novo, but very rare familial transmission of a ~1 Mb POU3F2-containing deletion is recorded. The penetrance point estimate from Goh et al. (2025) is 17%, but the confidence interval spans 0% to 100%. 6q21q22.1 Deletion. The lengths of deletion cover a wide range (Figure 14–29), but almost all include the segment contained between loci MARCKS and HDAC2, these loci straddling the interface of 6q21 and 6q22.1; several other deletions include CDC40. Structural brain abnormalities are commonly revealed upon imaging. In the review of Minotti et al. (2024), in only one case had there been transmission from a similarly affected parent; every other case in which the information was known had arisen de novo. 6q22.1q22.31 Deletion. Epilepsy and tremors are the notable clinical observations in this deletion; dysmorphology is borderline or essentially absent. Intellectual disability is moderate or severe. Deletion sizes range from 0.2 Mb to 16 Mb; the loci NUS 1 and SLC35 F1 in particular are implicated (Szafranski et al. 2015). Duplication. A very few cases of duplication involving the 6q22 segment are recorded. The clinical picture is rather nonspecific, with mild to moderate intellectual disability, growth deficiency, and facial dysmorphism (Pazooki et al. 2007). In some, it has been interpreted as a benign variant, or possibly as a variant of incomplete penetrance (Srebniak et al. 2016). LAMA4 is a landmark locus. Figure 14–28.  An Obesity-associated Deletion on 6q. Autosomal Structural Rearrangements  401 6q23.2q24.2 Deletion. Only one case is on record, but this is worth noting, given the clinical picture. A 3-year-old girl del(6)(q23.2q24.2), whose development was “completely normal to advanced,” and who had only been karyotyped as a newborn because of low birth weight (Kumar et al. 1999). While the facies was distinctive, she was said to resemble her family. One might imagine that this particular segment contains no critical brain loci. Duplication. The remarkable trait in duplications of the segment 6q24 is transient neonatal diabetes. This reflects an overactivity of a triple dose of loci in this region that are normally subject to parent-of-origin imprinting (Chapter 19). PLAGL1 at 6q24.2 is a suspect gene (Hassan et al. 2024). 6q24.3q25.1 Deletion at the distal long arm, 6q24.3q25.1, is well recognized, albeit that most cases are non-recurrent (Salpietro et al. 2015). A very few cases extend into q24.2 or q25.2, or, as in Stagi et al. (2015), into both. The condition has a resemblance to Noonan syndrome. Notable traits are a joint hypermobility reminiscent of Ehlers-Danlos syndrome, and heart disease, in particular mitral valve disease and cardiomyopathy (Engwerda et al. 2021). Mild to moderate developmental delay is typical. TAB2 is the key locus. 6q25.3 Deletion. The ARID1B gene (mutation in which causes Coffin-Siris syndrome) is the important basis of this syndrome (Paulraj et al. 2018). Deletions are of variable extent, falling within the wide range of 6q24.3 to 6q27 (and thus some having overlap with the del(6)(q24.3q25.1) described above), but nevertheless there are some breakpoints in common. The clinical picture includes intellectual disability, dysmorphism, dysgenesis of the corpus callosum, and hearing loss. An instance of inheritance has been described due to a parental acrocentric translocation (Domínguez et al. 2020). Figure 14–29.  Deletions at 6q21q22.1. Notes: Asterisks show the positions of three loci. The HDAC2 gene is deleted in all, and MARCKS in all but one. Source: From C Minotti et al., Case report: A new de novo 6q21q22.1 interstitial deletion case in a girl with cerebellar vermis hypoplasia and developmental delay and literature review, Front Genet 14:1315291, 2024. Courtesy C Minotti, and with the permission of Frontiers in Genetics. 402  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Chromosome 7 7p13* Deletion: Greig Cephalosyndactyly Syndrome Plus. This acrocephalopolysyndactyly syndrome, classically inherited as an autosomal dominant, is due to mutation at the GLI3 locus. Recorded deletions in this region, which include GLI3, are up to 18 Mb in extent. Loss of other loci is the basis of a combined Greig syndrome with neurodevelopmental disability, seizures, and other abnormalities (Kozma et al. 2021). Loss specifically of the glucokinase gene in 7p13 leads to one form of maturity-onset diabetes of the young (MODY). 7p21.1 Deletion: Saethre-Chotzen Syndrome Plus. Most Saethre-Chotzen syndrome (another type of acrocephalosyndactyly) is due to point mutation in the TWIST gene at 7p21.1. A microdeletion within 7p21.1 may remove TWIST and other genes, and impose a broader phenotype (Cho et al. 2013a). The skull defect in Saethre-Chotzen syndrome is premature fusion of cranial bones (craniosynostosis). Duplication which includes the TWIST locus may lead to underdevelopment of the skull, with a large and confluent fontanelle (Stankiewicz et al. 2001) (Figure 14–31). This is an example of the “type and countertype” of a del/dup: Haploinsufficiency of TWIST causes premature cranial bone fusion, while triplo-excess leads to underdevelopment. 7p22 Deletions in distalmost 7p are rarely reported, and with a variety of segments. One familial example, siblings with del7p22 from a maternal translocation, had the notable trait of an immunodeficiency with hypogammaglobulinemia; loss of CARD11 may be the basis of this (Sloboda et al. 2019). Duplication of 7p22.1 is associated with intellectual disability and craniofacial dysmorphism (Goitia et al. 2015). A triplo-excess of RNF216, a gene with a similar function to the UBE3A of Angelman syndrome, may be a particular factor in the evolution of the behavioral phenotype, which can include an autistic component. Roles otherwise for ACTB, CARD11, and SDK1 are proposed (Ronzoni et al. 2017; Bauleo et al. 2023). De novo inheritance is recorded in all cases in which parental studies have been done. Figure 14–30.

Autosomal Structural Rearrangements  403 7q11.23* Deletion: Williams Syndrome. Most (95%) Williams11 syndrome (WS), also known as Williams-Beuren syndrome, is due to a recurrent 1.5 Mb deletion (Figures 14–33 and 14–34). The characteristic neuropsychological phenotype is that of a mild intellectual disability with impaired language acquisition (Pérez et al. 2022; Hsu 2023), a personality of an overfriendliness to strangers, and a lacking in social judgment; an abnormally developed amygdala (a brain structure subserving social behavior and the recognition of emotional facial expressions) may be the basis of these latter traits (Martens 2013). Abnormal development of another specific brain structure, the right superior longitudinal fasciculus (a major white matter tract), may underlie the visuospatial deficit, of which one commonly given example is a hesitancy in stepping from one type of floor (e.g. carpet) to another (e.g., floorboards) (Hoeft et al. 2007). Affected monozygous twins generally have a rather similar phenotype (Castorina et al. 1997). From an analysis of patients with atypical deletions, GTF2I, GTF2IRD1, and CLIP2 distally (telomerewards) within the critical region, and BAZ1B, FZD9, and STX1A proximally (centromerewards) may be key contributors to the neurodevelopmental picture Figure 14–31.  The Skull in 7p Duplication. Notes: The photo shows widely separated cranial bones in a child with dup(7)(p14.2pter). The ink marker shows the palpable outline of the skull bones, and demarcates the extent of the widely patent fontanelle. This observation reflects duplication of the TWIST gene at 7p21.1, which is included within the imbalanced segment in this child; in contrast, deletion of TWIST is associated with premature cranial bone fusion. 11 The custom of removing the apostrophes from the names of authors associated with syndromes has led to the occasional misspelling of this condition as “William syndrome.” Similarly, the terminal “s” of Edwards and of Sotos is sometimes erroneously dropped. 404  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY (Alesi et al. 2021; Zhou et al. 2022). The basis of the cardiovascular component (supravalvular aortic stenosis) of the phenotype, seen in about a third of cases (Honjo et al. 2022), is well understood: namely, deletion of the elastin gene, ELN. The deletion can arise equally in the gamete of either parent (Pober 2010). Sperm studies in control donors show similar frequencies of deletion and duplication for this segment (the WS critical region, WSCR), consistent with an NAHR mechanism (Molina et al. 2011). A parent who carries an inversion inv(7)(q11.23) including the WSCR (this polymorphism is present in 6% of the general population) has odds tilted in favor of meiotic generation of the deletion; inversion heterozygotes have a prior risk to have a child with WS of about one in 1,750, which is fourfold the overall population risk of one in 9,500 (Hobart et al. 2010). Recurrence of WS in a subsequent child is almost but not entirely unknown. Scherer et al. (2005) describe two instances of recurrence, one of which was associated with the paternal inversion polymorphism noted above. These authors suggested that family members of a WS proband found to be inv(7)(q11.23) heterozygotes consider prenatal testing, albeit that the risk figure is, objectively speaking, very low. In the other instance, maternal gonadal mosaicism was suggested, but not proven. Figure 14–32.          Figure 14–33.  The Williams Syndrome Deletion. Notes: Low copy repeat (LCR) blocks A, B, C, with near-identical sequences, set the stage for non-allelic homologous recombination, leading the deletion or duplication of the intervening region. Recombination between LCR blocks “B cen” (centromeric) and “B mid” results in a 1.5 Mb del or dup; and between “A cen” and “A mid” leads to a 1.8 Mb del or dup. The key locus elastin (ELN) is shown midway within the contiguous gene segment, where it lies along with about 25 other genes. Autosomal Structural Rearrangements  405 An extraordinary case is that of a father who had a deletion at q11.23 on one chromosome 7, and a duplication of this segment on the other; thus, he was genetically balanced and of normal phenotype. He had come to notice due to having had two children with Williams syndrome (Lühmann et al. 2023). As these authors point out, his case represents a rare example of a 100% genetic risk: all potential children of his would have either Williams syndrome or the dup7q11.23 syndrome. Rare instances of parent-to-child transmission are known (Onís Vilches et al. 1998), and Farwig et al. (2010) address the challenging question of counseling persons who themselves have WS. Duplication. This is the reciprocal recombination product to the Williams syndrome deletion, and may be seen with soft dysmorphism, mild cognitive impairment, expressive language deficits (in contrast to the loquacity of WS), and anxiety (Dentici et al. 2020). Macrocephaly and brain anomalies on imaging are observed. The risk for schizophrenia is tenfold (Mulle et al. 2014). Aortic dilatation is recognized (Parrott et al. 2015). Goh et al. (2025) calculate a penetrance of 67%, but this figure may be too low given the presence of mildly affected individuals within control cohorts. Familial cases are not uncommon. Earhart et al. (2017) report an affected father of four affected children. In the series of Morris et al. (2015), about one-fourth of probands had an affected parent. Of the de novo probands in this series, about one-fourth had an inversion of the q11.23 segment on their duplicated chromosome, and in all of these cases, one parent had the WSCR inversion polymorphism noted above. As with WS, this inversion polymorphism is presumed to foster the formation of an intrachromosomal loop, which in turn sets the stage for illegitimate recombination. 7q11.23, Distal A deletion just distal to the WS segment, albeit at least in part within the same cytogenetic band, produces a very different clinical picture of variable epilepsy, cognitive Figure 14–34.  FISH Demonstration of the Williams Deletion. Notes: FISH was the former (20th century) methodology to detect the 7q11.23 deletion, using probes which recognized the ELN gene, along with a control probe more distally on 7q. It remains a useful technique to give a visual appreciation of the deletion.

406  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY impairment, and neurobehavioral disorder (Birca and Myers 2022). The key locus is HIP1, with possibly a contribution from YWHAG in some having a slightly larger deletion. It is typically a de novo event, but familial transmission is on record. 7q21.3 Deletion DLX6 and DLX5 are limb development genes under the control of enhancer DYNC1I1; the SGCE gene codes for epsilon sarcoglycan. Loss of these neighboring two loci contained within 7q21.3 can lead to a split hand/foot malformation and myoclonus-dystonia, respectively; deletion of adjacent loci contributes to a broader phenotype. Deletion of DYNC1I1 alone, DLX6 and DLX5 being intact, may nevertheless also lead to the hand-foot defect in some, this reflecting a loss of the influence of DYNC1I1 over its client loci (Ambrosetti et al. 2023) (Figure 14–35). Duplication. As with the deletion, the split hand-foot malformation is associated (Velinov et al. 2012). 7q21qter Duplication. The q arm of chromosome 7 is long, comprising some 82 Mb of DNA, and yet a partial trisomy of more than half of 7q is viable. Presumably, rather like 13q, which is of similar length, the gene content is such that the qualitative functional imbalance over many loci is nevertheless tolerable, at least in terms of enabling survival through to live birth. Paththinige et al. (2018) report the longest survival, a child of 2⅓ years, in whom the 7q22.1qter duplication encompassed fully 58 Mb. Their case, and six others in their review, had resulted from the transmission of a parental translocation, with imbalances of 7q22qter to 7q21qter. One, a child surviving to 11½ months, carried a der(7q21.2;15p) and therefore represented an essentially “pure” partial 7q trisomy (the 15p segment being without phenotypic effect). 7q31 Deletion. The notable feature of this syndrome is poor speech development, presumed due to haploinsufficiency of FOXP2, a well-known speech apraxia gene. Nagy et al. (2021) report a family segregating a deletion, in which the heterozygotes had an expressive speech disability along with minor dysmorphism. In one notable family, a mother carrying a de novo 4.7 Mb del 7q31.2q31.31 inherited by two children of hers—and all three with impaired speech production and poor language comprehension—FOXP2 Figure 14–35.  Gene Interaction at the 7q21.3 Deletion. Notes: Loss of DLX6 and DLX5 causes a hand-foot malformation. Loss of DYNC1I1 may in some cases (in other words, with reduced penetrance) perturb the function of the (intact) DLX loci, and lead also to the limb defect. Autosomal Structural Rearrangements  407 was intact, but its very close proximity to the deletion suggested a possible position effect (Rieger et al. 2020). 7q33q35 Deletion. There is a wide range of deletion (Kale and Philip 2016). A gene in this region, which will otherwise be familiar to the counselor, is BRAF;12 whether this gene is contributory to the phenotype in the 7q33q35 deletion is an open question. The typical phenotype is of intellectual disability, dysmorphism, epilepsy, and susceptibility to infection. One case of extraordinary interest concerns the IVF clinic (Chalas et al. 2020). Four couples had received sperm from the same donor, with simultaneous ongoing pregnancies. In one, fetal abnormalities were seen at ultrasound, and on amniocentesis, a 7q32.1q33 deletion was found, with termination chosen. Amniocenteses (presumably done with all dispatch) in two of the other couples gave a normal result, and normal babies were born. But upon sperm analysis from the donor, the same 7q deletion was identified in 12% of spermatozoa, attesting to the reality of gonadal mosaicism. 7q36qter Deletion. Terminal 7q deletions can involve as much as q33qter, but are more usually of q36q26 to qter (Ayub et al. 2016). The classic clinical correlate is holoprosencephaly, a developmental brain defect that can vary from devastatingly severe to rather mild. The pheno-critical locus in this deletion is SHH, albeit that penetrance for holoprosencephaly is incomplete. De novo deletion is the rule, but inherited holoprosencephaly has been recorded in the setting of a familial 7q36 translocation (Hatziioannou et al. 1991). The phenotype overall is typically severe (Aneja and Krishnan 2024). Chromosome 8 8p11 Deletion. Notable loci within proximal 8p that can be pathogenic in the event of haploinsufficiency include FGFR1 at 8p11.23 and KAT6A at 8p11.21. Loss (or mutation) of one 12 In the germline, activating missense BRAF mutations cause cardiofaciocutaneous syndrome; somatically, mutations occur in certain “cancer cascades.” Figure 14–36. 408  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY FGR1 allele leads to Kallmann syndrome, and loss (or mutation) of a KAT6A allele is associated with Arboleda-Tham syndrome. The presence or absence of a blood anomaly, spherocytosis, can act as a landmark of the extent of a deletion, this phenotype having its locus, ANK1, at 8p11.21. Dai et al. (2022) review cases reported at the time, the deletions in some of which extended into 8p21. Deletions confined to very proximal segments within 8p11.21, bordering the centromeric region, can lead to distinctive phenotypes such as a syndrome of dystonia and brain calcification reflecting losses of THAP1 and SLC20A2 alleles, respectively (Mu et al. 2019). From the foregoing, it is apparent that a “syndrome” of 8p11 deletion will present a phenotype related to the loci concerned, and the picture may differ quite considerably according to where within the 7 Mb DNA of 8p11 the deletion actually lies. 8p23.1pter* Distal deletions of 8p can be divided into those which are telomeric of the GATA4 locus, which are non-recurrent; and those which include GATA4 and which are recurrent (Figure 14–37). The recurrent deletions involve a core 3.68 Mb segment within 8p23.1. Penetrance in Goh et al. (2025) is 100%. Loss of GATA4 (a cardiac transcription factor) predisposes to heart malformation. Diaphragmatic hernia may be a characteristic component (Keitges et al. 2013). These cases are de novo (except for one remarkable instance of an intellectually disabled but non-dysmorphic mother who had had cardiac surgery as a child, and whose fetus on ultrasound had a major heart defect; she herself died mid-pregnancy, probably of a ventricular arrhythmia; Guimiot et al. 2013). Considering the more distal cases, a landmark locus is DLGAP2 in p23.3, this gene having a role in synaptic integrity and potentially influencing behavioral and cognitive traits. In some individuals with the distal deletion, frustration tolerance is very low, but behavior seems to improve in later adolescence. Some have even been able to gain Figure 14–37.  Recurrent and Non-recurrent Deletion and Duplication Segments of 8p. Notes: The segment at 8p23.1, flanked by Low Copy-number Repeats (LCR), is seen recurrently in both the del and dup state. The position of GATA4 is asterisked, and the dagger is at SOX7. Distal to this segment, six non-recurrent deletions are shown as red bars. Source: From RD Burnside et al., Three cases of isolated terminal deletion of chromosome 8p without heart defects presenting with a mild phenotype, Am J Med Genet 161A:822–828, 2013. Courtesy RD Burnside, and with the permission of John Wiley and Sons.

Autosomal Structural Rearrangements  409 employment. Dysmorphism is mild. Almost all are of de novo generation; parent-to-child transmission is rare. An allied disorder is the inversion duplication/deletion of 8p; this is a more severe condition, in which a duplication of a variable amount of 8p proximal to 8p22 is added to the imbalance of an del 8p23.1 (García-Santiago et al. 2015). The foregoing 8p rearrangements each arise consistently in maternal meiosis—which thus allows the assumption of sporadic generation, and a very low recurrence risk—and had been facilitated by a common (26% population rate) maternal heterozygosity for an inversion polymorphism within p23.1 (Giglio et al. 2001). Duplications. A duplication of the core recurrent 3.68 Mb segment (the blue bar in Figure 14–37) leads to the “8p23.1 duplication syndrome,”,and this does have a phenotype (although this can be quite mild) in terms both of intellect and dysmorphology, with parental genotypes otherwise an important influence (Barber et al. 2015). Penetrance is 100% (Goh et al. 2025). Two key pathogenic loci within the core segment are SOX7 and GATA4. Duplication of SOX7 determines a neurobehavioral phenotype, while GATA4 may be responsible for congenital heart malformation. Duplication of a more telomeric segment within 8p23.1 may be, of itself, without a phenotype; thus, this is seen as a normal variant that can have been transmitted by an unaffected parent, and ascertainment is typically due to a fortuitous coincidental presentation (Barber et al. 2015). 8q23.3q24.11 Deletion: Langer-Giedion Syndrome. The facies is distinctive, the bulbous nose a remarkable feature, and diagnosis can be made with some confidence on clinical grounds. The condition is due to a deletion that removes the gene for trichorhinophalangeal syndrome type I (TRPS1) and a bone growth control gene (EXT1, which causes exostoses), along with several other genes, to give the broader picture of Langer-Giedion syndrome (Maas et al. 2015). Deletions around this segment are of variable extent; some breakpoints are recurrent. Intellect is affected to a degree, but may yet be within a normal range (Schinzel et al. 2013). These latter authors provide a useful narrative about four cases living into young or older adulthood (and comment about the paucity, in general, of long-term data in many of these syndromes of chromosome imbalance). The deletion may arise de novo on the chromosome 8 of either parent (Nardmann et al. 1997). Familial transmission due to an insertional chromosome is on record (Min et al. 2013; Selenti et al. 2015). Figure 14–38. 410  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 8q24.13q24.3 Deletion. If this deletion includes a segment containing KCNQ3, a neurofunctional syndrome typically results. Small deletions either side of this segment appear to be benign (Maya et al. 2021). Chromosome 9 9p24p22 Deletion: Alfi Syndrome. A number of 9p deletion cases involving the p22p24 region are recorded, more than 700, and they present a characteristic phenotype (Sams et al. 2021). Most breakpoints occur in bands 9p22 and 9p24. In about two-thirds, the deletion is terminal; in some, the deletion is accompanied by a duplication elsewhere. Trigonocephaly is a classic craniofacial malformation, and this may relate to loss of FREM1 at 9q22.3. The brain is abnormal, and a curious imaging observation is a widening of the Sylvian fissure, the major cerebral sulcus. Other traits inhere in other regions (Starosta et al. 2024). The deletion is equally likely to have happened on the paternal or maternal chromosome 9. If the deletion extends into 9p24.3, a gonadal phenotype may be seen, as noted in the section below. Most del(9p) arises de novo, but recurrences in a family due to a segregating translocation are on record (Abreu et al. 2014). 9p24.3cen Duplication: Trisomy 9p Syndrome. This is one of the more common partial trisomies, indeed said to be fourth in frequency after the three major full trisomies and known since 1970 (Guilherme et al. 2014). In many, the duplication extends into the 9qh heterochromatic region, 9q11q12, and occasionally as far as q21.11. A paucity of dosage-sensitive loci within 9p, and a concentration of repeat sequences within the pericentromeric region, are the basis, respectively, of its viability and frequency. The craniofacies is characteristic. Intellectual disability is typical, and Martínez-Jacobo et al. (2015) report in addition psychotic behavior; brain abnormality is often seen on imaging. However, Bouhjar et al. (2011) record a few cases, mostly with smaller 9p duplications, in whom intelligence was within a normal range. Figure 14–39.

Autosomal Structural Rearrangements  411 Most cases in fact occur in the setting of a rearrangement with another chromosome (in these, the recurrence risk relates to the parental carrier status; Figure 5–14), but isolated examples are well recorded. Triplication. Tetrasomy 9p typically exists in the form of an isodicentric or pseudodicentric iso(9p). In those who survive, it is seen in the mosaic state (Süleyman et al. 2022). 9p24.3 Deletion. These deletions occur distal to the 9p deletion syndrome core region, and remove the DMRT1 gene. This is the most conserved of any known sex-determining gene, and it is actually on the Z chromosome (the homogametic chromosome) of birds. Its expression is normally greater in the male than in the female embryo, and this dosage is the basis of its testis-inducing action. Loss of one DMRT1 allele in the deleted segment brings the amount of product down below this threshold, thus potentially leading to a disorder of sex differentiation of varying form (hypospadias through to gonadal dysgenesis or male-to-female “sex reversal”) in the 46,XY,del(9)(p24.3) person. This observed variable expressivity—but also, in some, a non-penetrance such that normal male development is seen—may reflect that other loci are intact or absent; that is, a second-hit scenario may apply (Quinonez et al. 2013). Concerning the 46,XX,del(9)(p24.3) female, Bartels et al. (2013) report primary ovarian dysfunction proceeding to menopause in young adulthood, and suggest that this may be a reflection of the DMRT1 haploinsufficiency. 9q22.3 Deletion. A notable feature of this deletion syndrome is the involvement of the PTCH1 gene in 9q22.32, and thus the Gorlin basal cell nevus syndrome is a component of the phenotype (Muller et al. 2012). Deletions are mostly within the range chr9:95-97 Mb, but can extend further into adjacent bands. Other aspects include craniosynostosis with trigonocephaly, hydrocephalus, overgrowth, facial dysmorphism of no consistent character, and intellectual disability. Ewing et al. (2021) describe a curious case of a teenager with a small deletion (0.4 Mb), and yet with an atypically severe phenotype. De novo generation is the rule. 9q34.3 Deletion: Kleefstra Syndrome . This subtelomeric microdeletion syndrome of intellectual disability typically of severe degree, difficult behavior, distinctive facies, and multiple malformation may be, after 1q36 and 22q13, the third most frequent of the subtelomeric deletion syndromes. Haploinsufficiency of (and also point mutation in) the gene EHMT1, the penultimate gene on chromosome 9, determines the core phenotype, and varying degrees of the extent of deletion may impose further compromise (Morison et al. 2024; Figure 14–40). The protein encoded by this gene, Eu-HMTase1, has a role in maintaining the integrity of histones that comprise a key component of the architecture of the chromosome; this syndrome can thus be considered as a disorder of chromatin remodeling. Parental somatic-gonadal mosaicism with recurrence in offspring has been recognized, but the large majority represent a de novo occurrence (Willemsen et al. 2011a). Duplication of the 9q34.3 locus encompassing EHMT1 is associated with mild developmental delay, mild intellectual disability, autism spectrum disorder, and behavioral 412  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY difficulty (Rots et al. 2024). The penetrance estimate in Goh et al. (2025) is 100%. As with the deletion, there are varying lengths of the duplicated segment. It is often inherited from a mildly affected parent, or can be de novo. Chromosome 10 10p12.1p11.23 Deletion. All deletions have been of differing extents and lengths (0.5–10 Mb), but analysis of overlapping segments has allowed proposition of a probable 1.1 Mb critical region at p12.1 (Mroczkowski et al. 2014). Within this, two subregions may determine the phenotypic components of cryptorchidism (MKX the likely culprit) and craniofacial malformation (BAMBI the possible basis). A very specific segment further upstream at 27.1 Mb is associated with familial thrombocytopenia, probably due to MASTL in this region having a role in platelet production (Manohar et al. 2024). The variable pattern of dysmorphism presumably reflects specific deleted regions. Developmental delay in survivors has been universal. Figure 14–40.  Deletions and the Adaptive Behavior Phenotype in Kleefstra Syndrome. Notes: The color coding denotes the severity of adaptive behavior in 103 individuals, from the mildest in pale green, progressively darkening through to the most severely affected in dark blue. No information was available in those with gray bars. The assessment was done using the Vineland II/III ABC scale, ranging from >85 in the green, through to <27 in the blue (the mean for a normal population is 100, SD 15). The pale vertical column reflects the position of the EHMT1 gene. Source: Adapted from LD Morison et al., Expanding the phenotype of Kleefstra syndrome: speech, language and cognition in 103 individuals, J Med Genet 61:578–585, 2024. Courtesy A Morgan. Autosomal Structural Rearrangements  413 10p14 Deletion: “HDR” Syndrome, Barakat Syndrome. All three components of this syndrome— hypoparathyroidism, deafness, and renal dysplasia (HDR)—inhere in deletion (or point mutation) of GATA3. Haploinsufficiency of adjacent genes leads to a broader phenotype, with typically severe intellectual disability; the deletion can extend proximally within p14 or further, and likewise distally within p14 or further—indeed, as far as pter (and thus overlapping with the deletion of the following entry). Centromerically extending deletions may remove a segment within 10p14, which has been labeled the critical region for a DiGeorge-like syndrome, DGS2, although no specific genes have been implicated. But this distinction may not be entirely clear; a DGS-like phenotype is not consistently observed (Benetti et al. 2009; Melis et al. 2012). Sporadic occurrence is typical in 10p14 deletions (but see Chapter 8, familial HDR due to a segregating insertional translocation). 10p15 Deletion: DeScipio Syndrome. Deletions may be confined to subtelomeric p15.3 (which contains only two genes, ZMYND11 and DIP2C) or may extend further into the short Figure 14–41.  Figure 14–42.  10p Deletions. Notes: Deletions declare themselves of two categories: a proximal segment, wherein GATA3 is located; and a distal segment, which includes ZMYND11. The proximal segment is associated with Barakat syndrome and DiGeorge syndrome type 2; deletion of the distal segment leads to DeScipio syndrome. Source: From YQ Pan and JH Fu, Case report: Clinical description of a patient carrying a 12.48 Mb microdeletion involving the 10p13-15.3 region, Front Pediatr 25;9:603666, 2021. Courtesy J-H Fu, and with the permission of Frontiers in Pediatrics.

414  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY arm of the chromosome. The important clinical aspect is typically a severe neurocognitive compromise, often with dystonic cerebral palsy, associated with cortical abnormality identifiable on brain imaging (Poluha et al. 2017). Surprisingly, there is little difference clinically between those with the smaller and those with the larger deletions; this supports the view that the ZMYND11 and DIP2C genes are the likely key pheno-critical factors (Eggert et al. 2016). Almost all cases have been de novo, but two known or assumed transmitting mothers are on record. 10q11.21q11.22 Duplication. A recurrent duplication in 10q11.21q11.22 reflects the agency of low-copy repeats (LCR) C and D (Figure 14–43). There is some controversy concerning the pathogenicity, or not, of this segment. It has been associated with cases of autism, but normal children also have been seen, followed up into early infancy after detection of the duplication at prenatal diagnosis (Ouyang et al. 2024). 10q22.3q23.2* Deletion. This recurrent deletion arises due to flanking low-copy repeats LCR3 in 10q22.3 and LCR4 in 10q23.2. The clinical phenotype is fairly nonspecific, with facial dysmorphism and, in most, delayed language development (but in one case, as an infant, language development was judged to lie within normal limits; Petrova et al. 2014). Juvenile polyposis may arise (Lecoquierre et al. 2020). The BMPR1A gene at 10q23.2 is proposed to be pheno-critical. If the deletion extends more distally into 10q23.2 and removes PTEN, the gene for Cowden syndrome, the result is a severe gastrointestinal syndrome of infantile onset pan-enteric polyposis (an overlap of juvenile polyposis syndrome and Cowden syndrome); treatment with mTOR inhibitors may improve the symptomatology (Taylor et al. 2021). Most del q22.3q23.2 cases have arisen de novo, but inherited cases are known (van Bon et al. 2011). Based on deletion size and gene content, penetrance is likely to be complete (Goh et al. 2025) Duplication 10q22.3q23.2. This is one of several microduplications that raises a dilemma when seen at prenatal diagnosis, due to its incomplete penetrance and a paucity Figure 14–43. Autosomal Structural Rearrangements  415 of recorded information. Goh et al. (2025) propose a penetrance of 27% with respect to a neurodevelopmental phenotype. Kong et al. (2016) describe prenatally diagnosed cases, in the context of one parent being a carrier, and with a causal link between genotype and (variable) phenotype being uncertain. One case concerned a (presumably monozygous) twin pregnancy, both twins heterozygous for a dup 10q22.3q23.2. While the index fetus was growth-retarded and had ventriculomegaly, the “internal control” twin and the carrier mother were considered to be phenotypically normal. This illustrates the point that phenotypic abnormality is often the basis of ascertainment, and thus subject to bias. With this, and with so many other of the del/dups of uncertain significance, the collection of family data beyond the proband, and this being available internationally, is a desideratum of high degree. 10q24.3 Duplication: Split Hand Foot Malformation Syndrome Type 3. Duplications of small (kb size) extent in the 10q24.3 region are associated with this malformation syndrome; dysregulation of the BTRC and SHFM3 genes at 10q24.32 (chr10:101.4 and 101.6 Mb, respectively) may be the key factor (Sowińska-Seidler et al. 2014). Neurocognitive functioning is typically intact, and familial transmission in an autosomal dominant pattern is common (Dai et al. 2013). Sibship recurrence due to maternal somatic-gonadal mosaicism is on record (Dimitrov et al. 2010; Filho et al. 2011); we have seen 30% mosaicism in an unaffected father of a child with split hand foot malformation. 10q25.1q25.3 Duplication: Distal 10q Trisomy Syndrome. Large duplications of distal 10q, involving most or all of 10q25, have been known for some time, the first reports appearing in the 1970s (Al-Sarraj et al. 2014). The clinical picture includes intellectual disability, microcephaly, facial dysmorphism (often with blepharophimosis), and distal limb defects. Most cases have been due to the malsegregation of a parental translocation, but some have reflected a de novo event, the duplication being in that case “pure.” 10q25.3q26.12 Deletion. If EMX2 at10q26.11 is involved, this syndrome is associated very notably with a disorder of sex development, and the XY male may present with genital ambiguity. Piard et al. (2014) describe micropenis, dysgenetic testes, and a “Mullerian recessus” (a uterine rudiment) entering the urethra in a non-dysmorphic child with developmental delay including failure of acquisition of language. 10q26.2q26.3 Deletion. Terminal deletions in distal 10q may comprise loss within only bands 10q26.2q26.3; or, they may be of larger extent and include the segment 10q25.3q26.13 as described in the section above; or, they may involve more proximal segments, such as were identifiable on classic cytogenetics and called the 10q− syndrome. Focusing on those deletions confined to the terminal bands 10q26.2q26.3, the clinical picture is one of moderate intellectual disability, growth retardation, and mild facial dysmorphism. The neurobehavioral phenotype is variable, with some exhibiting attention deficit and hyperactivity; the CALY gene (the seventh-last gene on the chromosome) may be

416  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY implicated (Plaisancié et al. 2014). Lacaria et al. (2017) mention ataxia and hyperemia of hands and feet as notable observations. A familial case, a mother and her two daughters, is recorded in Plaisancié et al., while two siblings in Lacaria et al. came from a mother with an inv(10)(p15.3q26.2). Chromosome 11 11p11.2 Deletion: Potocki-Shaffer Syndrome. The clinical phenotype includes the notable features of multiple exostoses and craniofacial dysostosis with enlarged parietal foramina, along with intellectual disability, and micropenis in males. Most deletions are above 2.1 Mb in extent. These genes are proposed as pheno-critical for these phenotypic aspects: EXT2 for the exostoses, the adjacent ALX4 gene for the skull bone defect, and PHF21A contributory to the cognitive impairment and craniofacial picture (Labonne et al. 2015) (Figure 14–45). A lesser deletion, leaving PHF21A intact, is recorded in a child with a normal intellect, indeed scoring well above the mean in several educational test assessments, although the neurobehavioral phenotype was somewhat affected (McCool et al. 2017). Familial transmission is recorded in the setting of a parental balanced insertion in the original family (Shaffer et al. 1993). An exceptional case is described in Chuang et al. (2005) of a del(11)(p11.2) child whose phenotypically normal mother carried the same deletion but with a supernumerary 11p11.2 neocentromeric marker chromosome, thus having an overall balanced genotype. But de novo occurrence is much the rule. 11p13 Deletion: WAGR Spectrum Disorder. Haploinsufficiency of the PAX6 morphogenesis gene causes aniridia (absence of the iris), with visual loss in consequence. Loss of one WT1 allele can comprise the first hit in the sequence of events to cause Wilms tumor, and it is also responsible for the abnormality of genital development. These two genes, among others, are removed in the 11p13 deletion (Figure 14–45), and the tout ensemble adds up to the WAGR (Wilms tumor, aniridia, genital defects, mental retardation) syndrome. Given the range of phenotype beyond these classic observations, Duffy et al. (2021) proposed the nomenclature WAGR Spectrum Disorder. Figure 14–44. Autosomal Structural Rearrangements  417 Deletions are of quite variable extent; should the deletion include BDNF in 11p14.1, cognitive functioning and adaptive behavior (adjusted for the visual handicap) are negatively impacted upon (Han et al. 2013). Isolated aniridia is often due to deletion restricted to just the PAX6 locus, or in smaller 11p13 deletions which do not include WT1 (Wawrocka et al. 2013). Less commonly, aniridia-causing 11p13 deletions spare PAX6, but affect a PAX6 cis-regulatory element that resides in the adjacent ELP4 gene. Deletions mostly originate on the paternal chromosome (Vasilyeva et al. 2020). A familial case of del 11p13 is recorded in Dolan et al. (2011), due to a father carrying an ins(11)(p13) in balanced state. Duplication. Given the severity of the classic WAGR 11p13 deletion, the mild effect seen in some duplications of the similar segment is notable, as Dolan et al. (2011) emphasize in their patient who had a slight delay in developing language, but by age four years was considered to be at an age-appropriate level; ophthalmology was normal, other than ptosis. (Ascertainment had been via his younger sibling with a typical WAGR syndrome, the father an insertion heterozygote.) However, a child with a small de novo duplication involving only PAX6 had poor vision but no definite anatomic eye malformation; she was microcephalic, of short stature, and developmentally delayed (Aradhya et al. 2011). A different phenotypic effect was seen in Palumbo et al. (2014), who describe a child whose duplication included PAX6 and WT1, presenting a picture resembling Russell-Silver syndrome. These apparent inconsistencies in karyotype–phenotype correlation are perplexing. 11p15.1 Deletion. This segment is well known as containing imprintable growth control loci which can be the basis, when perturbed, of Beckwith-Wiedemann syndrome (BWS), or contrariwise, of Russell-Silver syndrome (RSS). Deletions removing the maternal allele, either de novo or inherited, cause BWS, whereas deletions of the paternal allele can lead to RSS (Begemann et al. 2012). We note here the remarkable case of a healthy father mosaic for a 60 kb deletion, but severe fetal growth retardation occurred in two pregnancies of his partner, with demise at 27 weeks (De Crescenzo et al. 2013). The deletion had removed the growth control factor KCNQ1OT1 (Chapter 19). Duplication at11p15.5 can result in Beckwith-Wiedemann syndrome (BWS), Silver-Russell syndrome (SRS), or no phenotype, depending on the location of the duplication and the parental origin of the duplicated chromosome, as we discuss in detail in Chapter 19. Figure 14–45.  The Region within which WAGR and Potocki-Shaffer Deletions Occur. Notes: The classic WAGR deletion, shown as bracketed, encompasses only the PAX6 and WT1 loci; broader deletions include BDNF. EXT2 is a key locus within Potocki-Shaffer syndrome. Deletions of the full extent as shown above lead to a phenotype combining traits of both conditions (Meng et al. 2020). The four asterisks indicate the relative positions of each locus.

418  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 11q12.2, 11q21q22.3 Duplication. These two duplications, of 0.3 and 7.5 Mb, have the interest that each is associated, and possibly causally, with a dominantly inherited adult-onset spinocerebellar ataxia: SCAs 20 and 39, respectively (Knight et al. 2008; Johnson et al. 2015). Which actual gene may be responsible for the ataxia is unknown. In SCA20, no other phenotypic effect is seen, presumably reflecting a triplo-insensitivity otherwise of the 10 genes within the 61 Mb segment concerned. Some of the SCA39 family manifested mild intellectual disability, hearing impairment, and chest and foot deformity; these other aspects may inhere in overexpression of one or some of the 44 loci contained within 11q21q22.3. 11q13.2q13.4 Deletion. This uncommon deletion is mediated by low-copy repeats either side of the deleted segment (Figure 14–46). Cognitive compromise and facial dysmorphism are typical concomitants (Shen et al. 2023b). 11q14.1q23.3 Deletion. This deletion, detectable even on “solid-stain” cytogenetics, removes almost half of 11q, pointing to a sparseness of critical survival genes within the region. Shiohama et al. (2016) describe a mildly dysmorphic and globally delayed, blind, 6-year-old with a 34 Mb deletion. She had presented with a neuroblastoma (the fifth such case), which may have reflected a “first-hit” hemizygosity for the neighboring NCAM1 or CADM1 loci within the segment. The visual defect is due to exudative vitreoretinopathy; this is attributed to haploinsufficiency of FZD4. 11q22.1q25 Duplication: Emanuel Syndrome. A variety of duplications are observed, some encompassing the full length of 11q22.1qter—about half of the q arm—and some of Figure 14–46.  The 11q13.2q13.4 Deletion. Notes: The relative positions of the three key loci are indicated, each residing within the segment outlined. The positions of low-copy repeats (LCR), which lead to the propensity for the generation of this deletion, are indicated. The extents of six deletions are shown in the red bars, these cases coming from A Wischmeijer et al., Olfactory receptor-related duplicons mediate a microdeletion at 11q13.2q13.4 associated with a syndromic phenotype, Mol Syndromol 1:176-184, 2011, and Y Shen et al., De novo 11q13.3q13.4 deletion in a patient with Fanconi renotubular syndrome and intellectual disability: Case report and review of literature, Front Pediatr 11:1097062, 2023b. Autosomal Structural Rearrangements  419 more limited extent (Burnside et al. 2009; Chen et al. 2013d). Most are upon the basis of parental rearrangement, but de novo cases are known (Ben-Abdallah-Bouhjar et al. 2013). The Emanuel syndrome, essentially due to dup(11)(q23qter) from an inherited der(22)t(11;22)(q23;q11), is discussed on Chapter 5 and illustrated in Figure 5–16. 11q24qter Deletion: Jacobsen Syndrome. The clinical phenotype includes, along with an intellectual disability, congenital cardiac malformation, pan- or bicytopenia, and immunodeficiency (Dalm et al. 2015; Favier et al. 2015; Blazina et al. 2016; Yamashita et al. 2023). The diagnosis is defined according to the genes deleted: at minimum, BSX, NRGN, ETS1, FLI1, and RICS. Lesser deletions, which may be confined to a phenotype of intellectual disability, produce “partial Jacobsen syndrome.” Specific genes have been linked to aspects of the clinical picture. Thus, ETS1 dictates failure of development of both B and T lymphocytes, hence predisposing to recurrent bacterial and viral infection (Huisman et al. 2022); this gene is also the basis of the heart maldevelopment. FLI-1 is likely the basis of the cytopenia. The classic deletion condition is typically of sporadic occurrence, but it is of historic interest that in the original family, multigenerational inheritance was observed due to an 11;22 translocation (Jacobsen et al. 1973). A case with a complex rearrangement, due to chromoanasynthesis, is described in Anzick et al. (2020). Chromosome 12 12p Duplication of the entire p arm was first reported in the 1970s, and it remains a rare condition. Partial duplications, more often terminal than interstitial, are similarly rare. The phenotype in the full 12p duplication is well recorded, including a distinctive craniofacial appearance and marked intellectual disability. Poirsier et al. (2014) make the case for GRIN2B as contributory to the neurocognitive phenotype in those persons with this gene duplicated. A remarkable story in Lim et al. (2013) describes twins with de novo mosaic full 12p trisomy. A somatic error likely occurred in very early embryogenesis, before the splitting which generated the twinning. Figure 14–47. 420  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Inheritance is about equally de novo or from malsegregation of a balanced parental rearrangement. Only two instances are known of unbalanced parental transmission, both involving small interstitial duplications: a father and son with an inv dup(12) (p12.3p11.2), and a mother and son with inv dup(12)(p12.3p13.1). While these duplicated segments were mostly non-overlapping, the phenotypes of a mild intellectual disability and soft facial dysmorphism were similar. Triplication is only seen in the mosaic state, as the Pallister-Killian syndrome due to an isochromosome of 12p (p. 713). 12p13.1 Deletion. Very few cases are known, but a picture of mild dysmorphism and considerable intellectual handicap, in particular with very poor speech acquisition, is forming (Mishra et al. 2016). GRIN2B may well prove to be the important gene whose haploinsufficiency determines the observed functional neurology. 12p13.33 Deletion. The notable observation in this subtelomeric microdeletion is of a speech apraxia: that is, an inability to “put words together” due both to compromise of voluntary intention of speech generation and to the neural control of the mechanical aspects of vocalization. Speech might be comprehensible only to the parents. The neurobehavioral phenotype includes a proneness to attention deficit and hyperactivity, but the IQ may be within a normal range. Otherwise, any dysmorphism is very mild, or arguably not present. ERC1 is a good candidate as the key gene. Deletions are of variable extent, ranging from 1.3 Mb to 4.8 Mb, and are non-recurrent. Parental inheritance is frequent, perhaps in one-half of cases, and, in retrospect, a history of poor speech development in that parent’s childhood can be elicited (Thevenon et al. 2013). 12q13.13 Duplication. Only single numbers are on record about this duplication (Hu et al. 2017). Three loci are proposed to be the core contributors to the phenotype (Figure 14–48). The phenotype is one of dysmorphism, mild intellectual disability, and minor digit Figure 14–48.  Duplications and Deletions at 12q13.13. Notes: Duplications are in blue, deletions in red. A core segment in common is outlined, containing three notable loci; HOXC is on the borderline. Source: From J Hu et al., Chromosome 12q13.13q13.13 microduplication and microdeletion: a case report and literature review, Mol Cytogenet 10:24, 2017, with the permission of Springer Nature.

Autosomal Structural Rearrangements  421 deformity. The facial appearance is said to resemble that of Wolf-Hirschhorn syndrome. All have been de novo. 12q23q24 Duplication. Bouman et al. (2013) review distal 12q duplications, of which the reported number is small, and most being unique. Their own case was a teenage boy with rudimentary speech, facial dysmorphism, and the inability to walk independently. Several genes that will be familiar to the counselor reside within 12q23q24, including PTPN11, TCTN1, ATXN2, and TRPV4 (respectively genes for Noonan syndrome, Joubert syndrome, spinocerebellar ataxia type 2, and several pleiotropic phenotypes with TRPV4). A physical resemblance to the physical phenotype of Noonan syndrome may reside in the PTPN11 duplication (Geckinli et al. 2015). De novo cases and inheritance due to a parental rearrangement are both observed. 12q24.31 Deletion. Non-recurrent deletions in 12q24.31 typically lead to global developmental delay and a characteristic dysmorphism (Palumbo et al. 2015a). This disorder is added to the list of conditions displaying café-au-lait macules. A 39-year-old man described in Verhoeven et al. (2015) with a 1.7 Mb deletion was notable in being able to have gainful employment (as a clerk), but his intellectual function, while formally within a normal range (IQ of 93; considerable inconsistency between domains), was well below that of his tertiary-educated parents. He had been diabetic since age 10 years, presumably due to haploinsufficiency for the HNF1A gene, the basis of MODY type 3 (Matsukura et al. 2017). SETD1B may be important in determining the intellectual phenotype. Chromosome 13 13q12.11 Deletion. This recurrent 0.2 Mb deletion involving part of the CRYL1 gene is unlikely to be pathogenic (Goh et al. 2025). Figure 14–49. 422  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 13q12.12* Deletion. Three loci determining neuromuscular disorders lie closely together within 13q12.12: SACS, for autosomal recessive spastic ataxia of Charlevoix and Saguenay (ARSACS); SGCG, for autosomal recessive limb-girdle muscular dystrophy type 5; and MIPEP, for a syndrome of left ventricular non-compaction, developmental delay, seizures, and severe hypotonia. A deletion within 13q12.12 may be harmless unless there happens to be, on the other homolog, a recessive mutation in one of these three loci “unmasking” the heterozygosity. We have seen a woman with ataxia and a Charcot-Marie-Tooth-like neuropathy inheriting a (normally non-pathogenic) paternal 0.2 Mb CNV deletion, which removed SACS, and an accompanying maternal SACS mutation on the other homolog, thus enabling a diagnosis of ARSACS. Other such cases are on record (Liu et al. 2016; Eldomery et al. 2016; Dougherty et al. 2018). 13q Deletion. The “13q– syndrome” was first described in detail by Allderdice et al. (1969), and the association with retinoblastoma recorded in the days of “solid-stain” cytogenetics. The no. 13 chromosomes were distinguished from the others of the D group on the basis that no. 13 was later replicating during the cell cycle, using the (long-since discarded) methodology of treating cells in culture with tritiated thymidine (autoradiography). In 1993, Brown et al. reviewed the syndrome in light of the sophisticated cytogenetics of the day, and they proposed three main categories: Group 1 within q12.2q31, with a phenotype of minor abnormalities, mild or moderate intellectual disability, and susceptibility to retinoblastoma; Group 2 within q12.2q32, with particular reference to band q32 in cases with major malformation and severe intellectual disability; and Group 3, comprising those with deletion of the distal segment q33q34, with severe mental compromise but typically without major malformation. The risk for retinoblastoma lay in the RB1 gene in q14, loss of which by deletion comprises a classic first-hit of carcinogenesis, as initially proposed by Knudson (1971). A review in Ballarati et al. (2007) noted that the grouping as above did not always hold true. Mitter et al. (2011) offered an updated and more molecular categorization for deletions which included RB1-containing 13q14: small deletions within q14 of less than 6 Mb; medium deletions within q12.3q21.2 and of size 6–20 Mb; and large deletions within q12q31.2, of greater than 20 Mb in extent (Figure 14–50). The foregoing assessments inform the following entries. (For the record, possibly the largest constitutional deletion ever reported may be del(13)(q13.3qter), encompassing 75.7 Mb, in a fetus diagnosed at 16 weeks gestation with cerebellar hypoplasia; Ballarati et al. 2007.) Duplication. Partial trisomy 13, of large segments, is often viable—an unsurprising fact given observations in the full trisomy. With the availability of G-banding from the 1970s, a number of cases of partial trisomy 13 came to light, and the conclusions from that period quite considerably hold today (Rogers 1984). Duplications are grouped broadly into proximal and distal, with bands 13q14q22 as the dividing region (Figure 14–49). Those of substantial size are invariably associated with psychomotor retardation. Certain features are peculiar to the segment; thus, polydactyly is seen only in the distal duplication. Most cases are due to a parental rearrangement, while some are de novo; and of these, several involve the attachment of a 13q segment to another chromosome as an “add.”

Autosomal Structural Rearrangements  423 13q14.2q14.3 Deletion. Small (less than 6 Mb, and as low as 0.15 Mb) deletions lead to a syndrome of mild or only borderline intellectual disability, with language acquisition in particular affected and a mild, “soft” facial dysmorphism. As noted above, loss of one RB1 gene predisposes to a very high risk for retinoblastoma, 50% or more (Figure 14–50). The considerable majority of deletions arise de novo, but familial cases are recorded, such as a father and two sons with a 3.33 Mb deletion, and an aunt and nephew with a 1.17 Mb deletion, recounted in Mitter et al. (2011). Of these, the father had a retinal scar, likely a spontaneously regressed tumor; one son had a unilateral and the other a bilateral retinoblastoma; and the aunt and nephew both had a unilateral tumor. A parental insertional translocation may be the basis of some familial cases (Punnett et al. 2003). 13q12.3q21.2 Deletions of 6 Mb–20 Mb extent within these chromosomal bands are (as in the entry foregoing, which this larger segment encompasses) at very high risk for retinoblastoma (Figure 14–50). Delayed motor and speech development are the rule, as is growth retardation. Physical features include a distinctive facies. Almost all cases are of de novo origin. 13q12q31.2 Deletions of large size, above 20 Mb, generally produce a more marked phenotype in comparison to the above entry in terms of the neurodevelopmental compromise, and Figure 14–50.  13q Deletions in Retinoblastoma. Notes: Shown here is the range of 13q deletions including the RB1 locus in band 13q14.2 (its position asterisked), from a cohort of retinoblastoma patients. These are divided into large (>20 Mb), medium (6–20 Mb), and small (<6 Mb) sizes. Note that deletions are not recurrent, suggesting nonhomologous end-joining as the generative mechanism. Source: From D Mitter et al., Genotype-phenotype correlations in patients with retinoblastoma and interstitial 13q deletions, Eur J Hum Genet 19:947–958, 2011. Courtesy D Mitter, and with the permission of Macmillan Publishers Ltd. 424  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY a more notable facial dysmorphism. Microcephaly is seen in some. Those deletions removing the EDNRB locus at q22.3 are associated with variable signs of Waardenburg-Shah syndrome13 (Tüysüz et al. 2009). Again, the high risk for retinoblastoma applies. Practically all are de novo. 13q32 Deletions that include this cytoband, and however extensive otherwise, typically present a severe neurodevelopmental picture with major brain malformation. The presumed key loci in this respect are ZIC2 and ZIC5 in sub-band q32.3, with holoprosencephaly and cerebellar dysgenesis the respective concomitants (Mimaki et al. 2015). Other loci determine other aspects of the malformative phenotype (Kotani et al. 2022). Duplication. Jobanputra et al. (2012) observed clinical normality in an infant with a de novo dup 13q32.2; these authors conclude that the ZIC2 gene resident within this segment does not lead, in the dup state, to holoprosencephaly. 13q33q34 Deletion. These distal 13q deletions can be interstitial or terminal. Microcephaly and intellectual disability are typical in those encompassing both cytobands (Sagi-Dain et al. 2019). Genital malformation is often seen in the male, and a considerable resemblance to the VACTERL14 syndrome has been observed (Dworschak et al. 2013). Smaller deletions, restricted to 13q34, may present a different picture, such as the child in Yang et al. (2013), a boy with a borderline IQ of 71, four-limb hexadactyly, and heart disease (a single atrium), who had a 1 Mb terminal deletion. The case in Myers et al. (2017) was due to recombination from a maternal inversion 13. Chromosome 14 14q12 Deletions: FOXG1 Syndrome. Cytoband 14q12 contains the FOXG1 locus, and loss of this gene as part of a typically 0.4 Mb–4.0 Mb microdeletion leads to the “FOXG1 13 Waardenburg-Shah syndrome: deafness; hypopigmented skin, hair, and irides; and Hirschsprung disease. 14 Vertebral, anal, cardiac, trachea-esophageal, renal, limb association Figure 14–51. Autosomal Structural Rearrangements  425 syndrome” of marked post natal microcephaly (head circumference with a standard deviation of –4 to –6), severe intellectual disability, and absent or near-absent language acquisition; a resemblance to Rett syndrome is noted (Brimble et al. 2023; Ellaway et al. 2013). The facies is unremarkable. Epilepsy is frequent. Bertossi et al. (2014) speak of a “dyskinetic encephalopathy of infancy,” a movement disorder which may include jerks, athetosis, chorea, and dystonia. The clinical picture is very similar in 14q12 deletions not actually removing FOXG1, and a dysregulation of the FOXG1 pathway, due to loss of a nearby cis-acting regulatory element, may lead to the same end result of a FOXG1 functional haploinsufficiency. Duplication. A syndrome of epilepsy, cognitive impairment, and dysmorphism, but not microcephaly accompanies a 14q12 duplication that includes the FOXG1 locus (Hettige and Ernst 2019). De novo inheritance is the rule, but malsegregation from a parental translocation is on record. del 14q24q32 Deletions within q24q32 can vary in size from 4 Mb to 20 Mb (Nicita et al. 2015; Stokman et al. 2016). A phenotype of intellectual disability is typical, and brain scans can show structural defects. The facies is abnormal. The region in common between most reported cases includes NRXN3, a “brain gene” (Figure 14–52). The deletion in Stokman et al. (2016) does not quite extend this far; these authors postulate IFT43 as another pheno-contributory gene. Inheritance is typically de novo. 14q32.2 Deletion: Kagami-Ogata Syndrome, Temple Syndrome. See Chapter 19. 14q32.11 Deletion. This new syndrome imposes a neurodevelopmental phenotype, along with mild dysmorphisms (Eno et al. 2021). One child with autism was “good at math.” Transmission from a very mildly affected mother is known. It may be more common than initially supposed. Figure 14–52.  A Series of Deletions within 14q24q32. Notes: These cases are from a series of eight, and another single report. The position of the key locus NRXN3 is asterisked; it lies within the common region outlined. The single case (lowest bar) did not include NRXN3. Sources: From F Nicita et al., Neurological features of 14q24-q32 interstitial deletion: report of a new case, Mol Cytogenet 8:93, 2015; with the additional case from MF Stokman et al., De novo 14q24.2q24.3 microdeletion including IFT43 is associated with intellectual disability, skeletal anomalies, cardiac anomalies, and myopia, Am J Med Genet 170A:1566–1569, 2016, and with the permission of Springer Nature.

426  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 14q32.3 Deletions are mostly in the range 3 Mb–6 Mb, and most include qter; the smallest recorded deletion (of 0.3 Mb) is interstitial (Engels et al. 2012; Holder et al. 2012). The pheno-critical factor may lie in the MTA1 gene, which is deleted in common in all cases. The usual clinical picture is one of malformation in several organs, intellectual disability, and facial dysmorphism. A single familial case is on record, the father-to-son transmission of the 0.3 Mb deletion just mentioned (Holder et al. 2012). Distal 14q24qter Duplication of this large segment is seen with growth retardation, developmental delay, and facial dysmorphism. A parental inversion is always to be considered in the context of a terminal duplication of an acrocentric chromosome, as was the case in the children in Sgardioli et al. (2013) and Kurtulgan et al. (2015), with dup(14)(q31.3qter) and dup(14) (q24qter), respectively. Chromosome 15 We may be, as Homo sapiens, hostage to our evolution, at least in respect of proximal 15q deletions. “Recent” (somewhat less than 1 million years ago) reorganization of the 15q11.2q13.3 region has led to the embedding of segments of LCRs that can now impose a particular vulnerability to nonallelic homologous recombination. The five major LCR segments of our particular interest are referred to as breakpoints 1 through 5 (BP1– BP5) (Figure 14–53). BP1–BP2 relate to Burnside-Butler syndrome; BP2–BP3 deletion is the basis of most Prader-Willi/Angelman deletion; and BP4–BP5 together bookend the segment of the 15q13.3 deletion syndrome. Figure 14–54 outlines points of interest in 15q11.2q13. The 15q11.2q13.3 region contains certain “brain genes,” and autism is a frequent concomitant of imbalance. 15q11.2 BP1-BP2* Deletion: Burnside-Butler Syndrome. This condition is also known as 15q11.2 BP1-BP2 microdeletion syndrome. The minimum deletion region contains the loci NIPA1, Figure 14–53. Figure 14–54.  The Genetic Landscape of Proximal 15q11.2q13. Notes: The regions and loci of interest within the segment 15q11.2q13. AS, Angelman syndrome; BP, (numbered) breakpoint; IC, imprinting center; PWS, Prader-Willi syndrome; T1D, T2D, type 1, type 2 deletion. Source: From DJ Driscoll et al., Prader-Willi syndrome, GeneReviews 2016 (updated 2024). Courtesy DJ Driscoll, and with the permission of the University of Washington. 428  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY NIPA2,15 CYFIP1, and TUBGCP5. While the deletion can vary in size (from 0.25 Mb to 1.5 Mb, most commonly 0.5 Mb), only these four loci are ever lost; Butler (2023) discusses potential roles for each of these. The background population carrier rate may be as high as 0.25% (1 person in 400), and about double that, 0.57%, in a cohort of those of neurobehavioral phenotype (Cafferkey et al. 2014). It is the single most common chromosome finding in large cohorts of those presenting with neurodevelopmental disability and/or autism (Butler 2023). The clinical picture is very largely confined to a neurocognitive/behavioral/psychiatric/autism phenotype (Cox and Butler 2015). Learning is affected, especially with respect to reading and writing. Attention deficit and hyperactivity are commonly seen, as also may be oppositional defiant disorder. Schizophrenia is a risk. This chromosome imbalance is a classic example of the incompletely penetrant microdeletion/CNV. It is typically an inherited deletion (in 80%–85%), but often (50%) the parent is reportedly unaffected; the remaining cases are of de novo origin (Vanlerberghe et al. 2015). A penetrance estimate of 10% (Goh et al. 2025) might be slightly low, and it would likely vary according to the stringency of phenotypic assessment of carriers. In other words, if microsigns of neurobehavioral disorder in parents were sought, the penetrance could well be higher. Duplication. A similar pattern of neuropsychiatric traits is reported in the BP1–BP2 duplication (Meossi et al. 2023), but the penetrance for overt manifestation, at 5%, is no greater than the background risk, arguing against pathogenicity (Goh et al. 2025). 15q11.2q13.1 BP2-BP3* Deletion: Prader-Willi Syndrome, Angelman Syndrome. See Chapter 19. Duplication for the segment 15q11.2q13.1 BP2-BP3 may, but not necessarily will, lead to a syndrome of neuropsychiatric dysfunction; Goh et al. (2025) propose a penetrance figure of 77%. The imbalance can also exist as a triplication, or even as a hexasomy, due to a supernumerary chromosome (inv dup or isodicentric 15) (Chan et al. 2025). The intellectual impairment ranges from borderline to severe (“pervasive developmental disorder”), with autism often a prominent feature (Battaglia 2008; Hogart et al. 2010). Epilepsy is recognized, and gastrointestinal symptoms are common (Coppola et al. 2013; Shaaya et al. 2015). Most (80%) are inherited, and more often recognized from the mother (Bisba et al. 2024). An unaffected parent can transmit the duplication, with children then affected, as Bonuccelli et al. (2017) show in a three-generational pedigree and as Han et al. (2021) report with respect to a sibship of three, two with autism and one with schizophrenia, from their normal mother. Of particular interest is the susceptibility to schizophrenia due to the duplication. Almost exclusively, it is in those in whom the duplication is of maternal origin that this psychiatric disease is seen (Figure 14–55). The penetrance for schizophrenia in the maternally inherited dup15(BP2-BP3) is 12%, compared to only 1%—practically the population figure—in paternal transmission (Isles et al. 2016). Thus it is that the condition is sometimes referred to as “Maternal 15q11.2q13.1 duplication syndrome” (Colijn et al. 2024). The penetrance with respect to developmental disability, autism spectrum disorder, and multiple congenital anomaly also shows a bias, but less markedly so, toward 15 The naming of these two NIPA genes is of interest, according to what they are not: “not imprinted in Prader-Willi or Angelman.”

Autosomal Structural Rearrangements  429 maternal transmission. The respective parental penetrances with respect to these traits are 50% (mat) and 20% (pat). These differences presumably reflect the differing roles of imprinted genes with the segment. 15q13 BP3-BP4* Deletion. This deletion may be a rare cause of familial autism; imbalance of APBA2 is proposed as the crucial factor (Babatz et al. 2009). Duplication. Peycheva et al. (2018) describe the three-generation transmission of a dup15q13.1, the heterozygotes having histories of intellectual compromise, psychopathy, and epilepsy. APBA2 is known of itself to have an association with autism and schizophrenia. 15q13.3 BP4-BP5* Deletion. This 1.5 Mb deletion lies between BP4 and BP5. Uncommonly, larger ~4 Mb deletions can encompass BP3–BP5, or smaller deletions can be “nested” within BP4 and BP5. The associated phenotype is essentially one of neuropsychiatric expression, and Lowther et al. (2015) determined these fractions, corrected for ascertainment: intellectual disability in 58%, epilepsy in 28%, poor speech development in 16%, autism spectrum disorder in 11%, schizophrenia in 10%, mood disorder in 10%, and attention deficit hyperactivity disorder in 7%. A similar inference comes from Torres et al. (2016), who determined high odds ratios for epilepsy, intellectual disability, autism, and schizophrenia. The average nonverbal IQ in the series of Ziats et al. (2016) was 60, and one-third of cases met criteria for a diagnosis of autism spectrum disorder. Galantamine (an acetylcholinesterase inhibitor) may offer some hope as a treatment in order to improve the behavioral component of the phenotype (Casas-Alba et al. 2021). About 85% of cases are inherited, and in 62 transmitting parents studied by Lowther et al. (2015), half had been diagnosed with a neuropsychiatric condition, although none Figure 14–55.  Duplications at 15q11.2q13.3 Causing Schizophrenia. Notes: Duplications comprise segments BP1-BP3, BP2-BP3, BP1-BP4, and BP2-BP4. All include NIPA1, NIPA2, CYFIP1, and TUBGCP5, which lie within BP2-BP3. The very considerable majority of duplications are of maternal origin, presumably an effect of the imprinted status of the contained loci. Source: From AR Isles et al., Parental origin of interstitial duplications at 15q11.2-q13.3 in schizophrenia and neurodevelopmental disorders, PLoS Genet 12: e1005993, 2016. Courtesy MJ Owen and G Kirov, and with the permission of the Public Library of Science. 430  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY had schizophrenia; those with schizophrenia in their study had all been probands in their own right. Thus, we have a further example of a molecular chromosomal imbalance of incomplete penetrance and variable expressivity; however, the fact that Lowther and colleagues found no cases in 23,838 adult controls suggests that penetrance is, in fact, high. Penetrance in Goh et al. (2025) is 54%. The crucial factor, in terms of the phenotype, is haploinsufficiency for one or both of the genes CHRNA7 and OTUD7A, which are located within the deleted segments of both the 1.5 Mb deletion and the smaller nested 0.44 Mb deletion (Unda et al. 2023). Duplication of 15q13.3 BP4-BP5 is one of the most frequently seen of the microduplications; triplication is also known (Soler-Alfonso et al. 2014). It is seen with developmental delay and intellectual disability, poor speech, autism, and subtle dysmorphism (Budisteanu et al. 2021); however, penetrance is quite low, at 8% for the 1.5 Mb duplication and just 3% for the nested 0.44 Mb duplication (Goh et al. 2025). Counseling is complicated by this incomplete penetrance and by the variable expressivity of this genomic disorder (Miller et al. 2009; van Bon et al. 2009). 15q24* Deletion. The breakpoints of this imbalance are for the most part founded upon a series of four low-copy repeats, breakpoints (BPs) A through D, which can promote nonallelic homologous recombination, a 3.1 Mb deletion at BP A–D being the most frequently observed (Mefford et al. 2012). This genomic variation matches a variable but fully penetrant phenotype. Speech development is severely affected in many, some being nonverbal, and some show attention deficit hyperactivity. The BP C–D region, wherein lies SIN3A, may be central to the pathogenesis (the SIN3A protein interacts with the Rett syndrome protein, MeCP2; Witteveen et al. 2016). Facial dysmorphism is mild or “soft,” with a large forehead a common observation. No familial case is known. Duplication. Duplication of 15q24 may cause developmental delay, with or without mild dysmorphism (El-Hattab et al. 2010). Goh et al. (2025) estimate a penetrance of 37%, but with wide confidence intervals. Evidence supports pathogenicity of the larger [A-D] duplication, but is borderline for the smaller [A-B] duplication. 15q24.2q24.3 Deletion. This recurrent but rare 2.2 Mb deletion includes 15 protein coding genes, including FBXO22 and TSPAN3. Goh et al. (2025) calculated a penetrance of 69%, with wide confidence intervals. Duplication. The corresponding 15q24.2q24.3 duplication has a penetrance estimate of 73% (Goh et al. 2025). 15q25.2 and 15q25.2q25.3* Deletion. Low-copy repeat sequences B, C, and D generate recurrent B–C, C–D, and B–D deletions. The 1.5 Mb deletion B–C, at 15q25.2, is proximal; and deletion C–D, at 15q25.2q25.3, is distal. Others, B–D, take in both segments (Figure 14–56). Phenotypic features in the proximal deletion include intellectual disability or developmental delay, short stature, and craniofacial abnormalities. Penetrance is 100% (Goh et al. 2025). Of several plausible candidate genes within the B–C segment, CPEB1 is one that might have a role in the neurocognitive phenotype (Burgess et al. 2014a); HOMER2 is another candidate. The proximal deletion has been implicated in premature ovarian insufficiency; the locus of relevance may be BCN1 (Hyon et al. 2016; Chen et al. 2020d). RPS17 is

Autosomal Structural Rearrangements  431 within this segment, and its haploinsufficiency causes Diamond-Blackfan anemia. The distal deletion may represent a “susceptibility locus” for neurodevelopmental dysfunction (Doelken et al. 2012), but data apropos are few. Duplication. No consistent phenotype is seen in the proximal 15q25.2 duplication. Goh et al. (2025) provide a penetrance figure of 71%, with wide confidence intervals due to small sample size. 15q26.3 Deletion. A particular phenotypic feature of this terminal deletion, which can be of variable extent, is growth retardation, with height and weight often 2 to 4 SD below the mean (Jezela-Stanek et al. 2012). This reflects loss of the IGF1R growth factor gene (as also in the ring 15, p. 300). The intellectual impairment ranges from borderline to severe (“pervasive developmental disorder”), with autism often a prominent feature (Battaglia 2008; Hogart et al. 2010). Facial dysmorphism and genital abnormality are concomitants. The considerable majority of probands are of de novo generation. Duplications at the terminal band 15q26.3 are associated with overgrowth, an IGF1R effect (Tatton-Brown et al. 2009; Cannarella et al. 2017). Intellectual disability and facial dysmorphism are observed. These duplications are often the result of malsegregation of a parental translocation or inversion, but de novo examples exist (Chen et al. 2011a; Kim et al. 2011; Burada et al. 2021). Chromosome 16 Rearrangements in chromosome 16p are among the more often seen in the genetic clinic. As with proximal 15q, the proximal short arm of 16 is of evolutionary interest, being a site of particularly active rearrangement in primate speciation and accumulating, in the time of H. sapiens, loci having putative roles in autism. This region has come to command a major role among CNVs associated with intellectual disability and psychosis. There is also a link with growth as measured by body mass index, and head circumference. There are five listed breakpoint (BP) regions within 16p11.2p12.2, numbering 1–5 from telomeric to centromeric (distal to proximal), enabling classification of different Figure 14–56.  Proximal and Distal Deletions at 15q25.2q25.3. Notes: Low copy repeats generate adjacent deletions, B-C and C-D. The deletion B-D takes in both segments. The relative position of CPEB1 is asterisked; the dagger indicates HOMER2; the double dagger indicates BNC1. 432  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY segmental imbalances (Figure 14–58). There is considerable similarity in phenotypes across these different deletions, and the counselor should take care that it is the correct condition being addressed (Figure 14–59). Again, concomitant CNVs elsewhere in the genome may, as second (or first) hits, aggravate the clinical picture. 16p11.2 proximal* Deletion: BP4-BP5 (Proximal del 16p11.2). This deletion is of sufficient frequency, and of such phenotype, that many counselors could expect to meet a family. BP4 and BP5 define a ~600 kb segment within sequence coordinates chr16:29.5-30.2 Mb, and this is the most commonly encountered of the canonical imbalances within the BP1–BP5 region (Figure 14–58). TBX6 is a useful landmark locus. Deletion presents a neuropsychological picture which may include developmental delay, intellectual impairment, epilepsy, poor language acquisition presenting as childhood apraxia of speech, clumsiness, behavioral disturbance, and certain physical features (Figure 14–60) (Mei et al. 2018; McRae et al. 2025). The clinical picture may quite closely resemble classic autism (and this is one of the most commonly seen CNVs in individuals with autism; D’Angelo et al. 2016), but there are some subtle differences; indeed, Duyzend and Eichler (2015) propose that the genotype-first approach may enable more precise diagnostic categorizations within the autism spectrum. Otherwise, there may be a risk for endometrial cancer (Stylianou et al. 2024). Figure 14–57.          Figure 14–58.  The Distinction between Distal and Proximal Deletions of 16p11.2. Notes: The breakpoints 1 to 5, located at sites of low-copy repeats, are shown in rhomboids. Key loci within each of the major deletion segments, BP2-BP3 distally, and BP4-BP5 proximally, are noted in boxes. Autosomal Structural Rearrangements  433 White matter tracts within the brain are abnormally formed (Owen et al. 2014). Paroxysmal kinesigenic dyskinesia (PKD), in which an abnormal body positioning is triggered by sudden movement, may be due to loss of the PRRT2 gene.16 Macrocephaly is a frequent observation, although the cerebral cortex is thin (this contrasts with the microduplication, with microcephaly). The increase overall in brain size relates to increases in certain brain regions, notably those with roles in the reward pathway and presumably reflecting aberrant neurogenesis; a specific malformation is the Chiari cerebellar defect (Maillard et al. 2015; Steinman et al. 2016). An increased body mass index with marked obesity is common and may have, as its basis, disturbance of the reward pathway such that appetite is excessive. There may or may not be a mild degree of dysmorphism. The overall phenotype, and in contrast to the duplication, is illustrated in Figure 14–60. The deletion is more usually de novo, but can be inherited; the phenotype is more abnormal in the familial case (Duyzend and Eichler 2015). Goh et al. (2025) estimate a penetrance of 47% (95% confidence interval, 40%–55%).17 A concomitant second hit may exacerbate the phenotype (Bassuk et al. 2013; Newbury et al. 2013). Duplication: BP4-BP5 (Proximal dup 16p11.2). This region provides another modern example of Lejeune’s 1960s concept of type and countertype (Figure 14–60). The del (see above) leads to hyperphagia and obesity; the dup is associated with underweight (Jacquemont et al. 2011). Upon a particular type of brain imaging (diffusion tensor imaging) that detects variation in the microstructure of white matter tracts, opposite 16 Mutation within the PRRT2 gene causes familial isolated PKD (Termsarasab et al. 2014). 17 These estimates (and see Appendix C) will be at the level of a clinically diagnosed neuropsychological/ cognitive phenotype. Stefansson et al. (2014) address the question whether subtler personality traits might be seen, on careful observation, that could yet be considered to lie within a normal population range with respect to a number of CNVs. In the case of the 16p11.2 deletion, they note impairments in several cognitive domains tested in control carriers, and record the observation of a reduced verbal IQ. They prefer to speak of “variable expressivity” rather than “reduced penetrance,” and there is some merit in this view. Figure 14–59.  The Relative Frequencies of Deletions and Duplications at 16p11.2. Notes: These data represent relative frequencies in a clinically ascertained population. Within population-based data, 16p11.2 duplications are more common than deletions, consistent with higher penetrance for deletions compared to duplication. Source: From N Vos et al. Evaluation of 100 Dutch cases with 16p11.2 deletion and duplication syndromes; from clinical manifestations towards personalized treatment options, Eur J Hum Genet 32:1387–1401, 2024. Courtesy MM van Haelst, and with the permission of Springer Nature.

434  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY effects are seen in white matter in the del and the dup state (Chang et al. 2016). Applying a neurocognitive assessment tool, subtle distinctions could be teased out between the del and dup phenotypes (Gur et al. 2025). There is a 14-fold risk of psychosis and a 16-fold risk of schizophrenia (Giaroli et al. 2014). From a very large international study (n = 1,006), D’Angelo et al. (2016) show a full-scale IQ in probands of 26 points below that of non-carrier relatives, and in non-probands (whose ascertainment is therefore less biased), about 15 points below. Dysmorphism, if present, is mild. Parental transmission is frequent, and some relatives may be apparently unaffected. Goh et al. (2025) estimate a penetrance of 33% (95% CI, 28%–41%), and thus a majority of heterozygotes would display a phenotype within the normal population range (but again the question arises that more thorough examination might reveal subtler differences, and in comparison with non-carrier relatives). The possession of another CNV elsewhere in the genome may exacerbate the clinical picture (Mitrakos et al. 2024). The discovery of a dup 16p11.2 might not necessarily explain a clinical presentation. Dastan et al. (2016) show this duplication in a child with facial dysmorphism and global developmental delay; his normal mother carried the same dup(16). To cast light on the mother–child difference, a whole exome study was done in the child, and this showed compound heterozygosity at VPS13B; thus, in retrospect, a diagnosis of Figure 14–60.  Phenotypic Contrasts between the Deletion and Duplication at Proximal 16p11.2. Notes: PKD = Paroxysmal kinesigenic dyskinesia; ICCA = infantile convulsion with choreoathetosis syndrome; CAKUT = congenital anomalies of the kidney and urinary tract; ASD = autism spectrum disorders. Source: From C Auwerx et al., The pleiotropic spectrum of proximal 16p11.2 CNVs, Am J Hum Genet 111:2309–2346, 2024. Courtesy A Reymond, and with the permission of Elsevier. Autosomal Structural Rearrangements  435 Cohen syndrome could be appreciated. The dup(16) in the child was merely coincidental, of little or no discernible effect per se. 16p11.2 distal* Deletion: BP2-BP3, distal. A short recurrent 220 kb deletion lies between BP2 and BP3, at chr16:28.8-29.1 Mb. Haploinsufficiency of SH2B1 (Figure 14–58) is presumed to be the basis of the severe early-onset obesity that is typically observed (Barge-Schaapveld et al. 2011; D’Angelo et al. 2016). The phenotype is one of cognitive impairment, difficult behavior, mild facial dysmorphism, and, as mentioned, obesity. An association with schizophrenia is noted (Guha et al. 2013). Penetrance is estimated to be 33% (Goh et al. 2025). It is often inherited. Duplication: BP1-BP3, distal. Duplication of BP1–BP3 may lead to a syndrome including delayed motor development, mild to moderate intellectual disability (mean full-scale IQ of 83), autism, and some with epilepsy (Vos et al. 2024). Most cases are inherited. Goh et al. (2025) estimate a penetrance of 16%. 16p11.2p12.2 This deletion of ~8 Mb includes 16p11.2 distal (SH2B1) deletion but excludes the 16p11.2 proximal (TBX6) deletion. The phenotype is of intellectual disability, autism, and dysmorphism (Tabet et al. 2012). As expected from its size and gene content, the deletion and its corresponding duplication are fully penetrant (Goh et al. 2025). 16p12.2, proximal* Deletion. Girirajan et al. (2010) identified a recurrent 520 kb deletion at 16p12.2, of landmark locus CDR2 (Figure 14–61), which imposed a phenotype of neuropsychiatric disorder and which was especially susceptible to the exacerbating effect of second-hit CNVs elsewhere in the genome: Second-hit CNVs were seen with a much higher frequency in cases (24%) than in controls (0.4%). If a risk for schizophrenia might otherwise have been the case, possession of this deletion, typically as a single-hit imbalance, increases the risk (Rees et al. 2014). Minor craniofacial anomalies may coexist. Just three OMIM genes lie within the segment: CDR2, EEF2K, and UQCRC2, the latter implicated in autism (Kanduri et al. 2016). Social responsiveness is impaired Figure 14–61.  Deletions at 16p12.2. Notes: Two regions are implicated, a proximal and a distal, each flanked by low-copy repeats, breakpoints (BPs) 1 to 3 (Tassano et al. 2019). Landmark loci are noted. This deletion was initially reported as del 16 p12.1, but is more accurately referred to as del 16 p12.2, as genomic precision improved (Girirajan et al. 2010). 436  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY (Figure 14–62). Goh et al. (2025) estimate a penetrance for the 16p12.2 deletion (CDR2) of 16%. Duplication. Penetrance in Goh et al. (2025) is 5%, which, not being above background risk, argues against consistent pathogenicity. Parental transmission is usual: A carrier parent may have had a learning difficulty and mental health disorder, such as depression or bipolar disease, but less severely so than in his or her affected offspring. De novo cases are occasionally seen. 16p12.2, distal* Deletion. A locus of interest in this rarely seen deletion is OTOA, which is the gene for autosomal recessive deafness type 22 (DFNB22), one of only three genes in the deleted segment (the other two METTL9 and IGSF6). A mother who had been deaf from birth proved to be homozygous for this deletion (her parents being cousins). Her child, the proband, had presented with short stature, mild dyslexia, and dysmorphic facial features (Tassano et al. 2019). Figure 14–62.  Developmental Milestones, and Social Responsiveness, in Those with a Proximal 16p12.1 Deletion. Notes: The social responsiveness scale measures the likelihood of a diagnosis of autism. A value ≤ 59 is within the normal range; from 60 to 75 reflects a mild to moderate risk for autism; while over 75 is indicative of a severe impairment. Density is probability per x-unit; the area between two x-values is the proportion of observations in that interval. The range of scores in the del parents of affected children does not differ much from that of the non-deletion parents, but nevertheless, tends slightly towards the direction of their children. (Earlier references to this deletion noted band 16p12.1, but p12.2 is more accurate.) Source: From M Jensen et multi al., Genetic modifiers and ascertainment drive variable expressivity of complex disorders, MedRχiv in press 2025. Courtesy S Girirajan, and with the permission of the Cold Spring Harbor Laboratory.

Autosomal Structural Rearrangements  437 16p13.11* Deletion. This recurrent deletion was discovered “genotype-first” in five patients from a large cohort screened by microarray analysis (Hannes et al. 2009). The typical deletion is 1.65 Mb in size; MYH11 is a landmark locus. It is associated with cognitive impairment, microcephaly, and in some patients, short stature, cleft lip, and other midline defects. Epilepsy has a particular association (Mullen et al. 2013). Paciorkowski et al. (2013) describe a severe structural brain defect in sibs in whom the deletion exposed an NDE1 mutation on the other chromosome 16. Mi et al. (2024) report a similar scenario in a del 16q13.11 mother, in whom no particular phenotype was discerned, she having had a child whose paternal chromosome carried a recessive mutation in MACF1, a gene residing within the deletion segment. Penetrance in Goh et al. (2025) is 23%. Duplication of 16p13.11 may predispose to a range of neurodevelopmental disability, including intellectual disability, attention deficit disorder, autism, and, less often, epilepsy (Ramalingam et al. 2011; Coe et al. 2014). Early-onset schizophrenia is recorded in Kızıltan et al. (2024). Congenital anomalies and dysmorphism are seen in some. Discovery at prenatal diagnosis may be prompted by fetal ultrasound anomaly (Zhao et al. 2024). Segmental repeat sequences define sites of rearrangement, leading to some heterogeneity of duplication extent. The most commonly observed imbalance is of ~1.3 Mb, with MYH11 a sentinel gene. The phenotype may be susceptible to the influence of a second-hit CNV elsewhere. Males are more susceptible, or stated differently, females are more resistant, to the inimical effects of the imbalance (Tropeano et al. 2013). Penetrance in Goh et al. (2025) is 10%. Both de novo and transmitted inheritance are observed, the transmitting parent more often the mother, of either normal or (usually mildly) abnormal neurocognitive phenotype. Homozygosity for the duplication (from a consanguineous union) has been reported, with the neurocognitive phenotype, curiously enough, not particularly different from the heterozygous state (Houcinat et al. 2015). 16p13.3* Deletion. Two important deletion syndromes lie within the large (7.9 Mb) 16p13.1 region. (1) del 16p13.3: α-Thalassemia and Mental Retardation. This is one of two α-thalassemia and mental retardation (ATR) syndromes (the other being an X-linked Mendelian condition). In the del(16p) ATR syndrome, there is monosomy for a segment at the very tip of the chromosome, which includes at least the α chain globin loci. Previously, the thalassemia would have been a key observation leading to the diagnosis; but as Gibbons (2012) somewhat wryly commented, nowadays “the widespread use of array-based screening for genomic deletions is identifying cases with little regard for the phenotype.” Deletions are of variable size. The smallest ones, from about 0.3 Mb to 1 Mb, may present no evident cognitive compromise, but those in the range 1 to 2 Mb usually do. A larger deletion, extending proximally beyond 2 Mb, may determine a broader phenotype, which may include tuberous sclerosis and polycystic kidney disease (due to the TSC2 and PKD1 loci) over and above the ATR syndrome. However, the length of the deletion is not necessarily related to phenotypic severity, and Babbs et al. (2020) study the role of the nature of the content of the other, intact 16p segment and of other sequences 438  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY elsewhere in the genome. They propose that “monosomy for 16p13.3 unmasks the effects of other variants genome-wide”; in other words, the variable expressivity of this deletion syndrome may relate more to loci on other chromosomes than in the del 16p13.3 itself. The only consistent observation is that of the thalassemia. De novo occurrence is often so, but parental rearrangements are not infrequent and should always be sought. Of the 41 cases in Babbs et al., 20 were familial, from five families. (2) del 16p13.3: Rubinstein-Taybi Syndrome. The Rubinstein-Taybi syndrome18 (RTS) has a distinctive phenotype, and the facies and the broad thumbs are very characteristic. Most cases are due to point mutation in the CREBBP gene, but around 10%–25% have a small (1 kb–15 kb) deletion that removes part or all of CREBBP (Wójcik et al. 2010). There is no obvious clinical distinction between those RTS patients with or without the microdeletion, suggesting closely adjacent genes may not be dosage-sensitive (Rusconi et al. 2015). The range of observed severity presumably reflects a variable expressivity of the abnormal genotype, and the case of monozygous twins with RTS having rather different neurobehavioral phenotypes supports this suggestion (Preis and Majewski 1995). The oldest putative case, from 500 AD–900 AD, is that of a skeleton excavated at the Yokem site in Illinois (Wilbur 2000); some kind of record would be set were this case ever to yield to a paleocytomolecular genetic analysis! Duplications in 16p13.3 are the “countertypes” of the Rubinstein-Taybi deletion, include the key CREBBP locus, and are of similarly variable sizes. In the smallest kilobase-size duplications, CREBBP may be the only gene involved (Mattina et al. 2012). Intellectual disability with poor speech, mild periorbital dysmorphism, micrognathia, and proximally implanted thumbs are notable features (Demeer et al. 2013; Li et al. 2013). De novo inheritance is almost always the case, but non-penetrance has been observed in two parents who had “followed normal schooling, function normally in society, and do not present the typical face” (Thienpont et al. 2010). Inheritance from an affected parent is reported in Lee et al. (2016). 16q21q22.1 Deletion. Yamamoto et al. (2008) reported a series of 14 cases, including some of classical cytogenetic description; and Genesio et al. (2013) reviewed six examples of a precise molecular definition. Pre- and post-natal growth retardation, microcephaly with psychomotor retardation, and facial dysmorphism are observed. Loss of HSD11B2 within 16q22.1, consistently observed, might be the basis of the growth retardation. Notably, a partially overlapping region just centromeric of HSD11B2 can be deleted without any effect upon the phenotype; this is a “euchromatic variant,” reflecting a very low gene density in this segment of 16q21 (p. 511). 16q24 Deletion. Three separate or overlapping syndromes involve band 16q24. First, the del 16q24.1 syndrome, as well as implying neurocognitive deficit may also predict certain organ malformations, according to the regions of deletion: the severe and 18 A similar condition due to mutation in the EP300 gene, a paralog of CREBBP, has been called RTS type 2 (Hamilton et al. 2016).

Autosomal Structural Rearrangements  439 usually lethal lung disorder, alveolar capillary dysplasia; bilateral hydronephrosis, likely consequential upon urinary tract obstruction; and heart and gut defects (Stankiewicz et al. 2009). Deletions are non-recurrent and of variable size. FOXF1 is a key pheno-critical candidate in many. This syndrome provides an example of a phenotype which can be due not to haploinsufficiency of a gene, but rather to haploinsufficiency of a distant enhancer of a gene. Thus, Szafranski et al. (2016) show that deletion removing an upstream enhancer of FOXF1 (a long non-protein coding RNA, LINC01081) while the FOXF1 gene itself, some 272 kb away, remains intact, can nevertheless lead to a functional non-expression of the gene and in consequence, the typical lung disease. Second, del 16q24.2 is associated with autism and intellectual disability, often of severe degree, and minor craniofacial dysmorphism (Handrigan et al. 2013). Deletions range from 27 kb to 2.7 Mb in size. One of the contained genes, FBXO31, is plausibly a key factor in the neurobehavioral phenotype. Parental transmission is quite frequently observed, with the deletion size in these being less than 1 Mb; an instance of maternal mosaicism for the deletion is known. Third, deletion of 16q24.3 leads to a syndrome in which intellectual disability, minor facial anomalies, macrodontia, and short stature are typical observations (Kim et al. 2015). Deletions range up to about 2 Mb in size. Loss of ANKRD11 (the gene responsible for KBG syndrome), is the central factor; loss of neighboring genes extends the phenotype (Novara et al. 2017). Familial transmission is recorded, including from a mosaic mother (Sacharow et al. 2012; Khalifa et al. 2013). 16q12qter Duplication. Extensive 16q duplications involving nearly all of the long arm are on record, typically in the context of the concomitant monosomy of another chromosome from a parental translocation. Most are lethal in infancy, but a few “pure” partial trisomies are described, with associated ongoing survival and considerable morbidity (Manor et al. 2021). Figure 14–63. 440  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Chromosome 17 Chromosome 17 short arm has remarkably high density of segmental duplications, and about a quarter of its DNA consists of low-copy repeats (Blazejewski et al. 2018). Thus it is that a number of del/dup conditions due to nonallelic homologous recombination reside in 17p. 17p11.2* Deletion, Smith-Magenis Syndrome. This classic syndrome comprises a picture of dysmorphology, intellectual disability, and fractious behavior. Speech and hearing are substantially affected (Brennan et al. 2024). Brain anatomy may be abnormal (Maya et al. 2014). Sleep disturbance is a characteristic feature (associated in most cases with a reversal of the normal circadian pattern of melatonin secretion); and a habit of self-mutilation and markedly diminished pain sensitivity can manifest as “onychotillomania” (pulling out nails). To the practiced eye, the facies may be distinctive (Allanson et al. 1999). Most (>90%) patients have an ~3.8 Mb deletion, arising by NAHR between low-copy repeats; a larger deletion may be associated with a more complicated phenotype (Park et al. 2002; Vieira et al. 2012). The crucial locus within the deleted segment is RAI1 (Figure 14–64), and the syndrome may result from mutation within this gene alone. Haploinsufficiency of RAI1 may compromise the activity of a number of downstream genes, and each of these, thus compromised, then contribute to a component of the syndrome. Recurrence is very rare, but one case is recorded due to low-level (25% on blood) parental somatic, and inferentially gonadal, mosaicism (Campbell et al. 2014). Otherwise, familial transmission may result from a balanced parental rearrangement. Duplication: Potocki-Lupski Syndrome. This condition was predicted to exist as the reciprocal recombination product of the Smith-Magenis syndrome (SMS) deletion (Potocki et al. 2000). The clinical picture is largely that of a neurobehavioral and neuropsychiatric syndrome; the contrasting phenotypes of Potocki-Lupski syndrome and Figure 14–64. Autosomal Structural Rearrangements  441 SMS are outlined in Neira-Fresneda and Potocki (2015). As with SMS, the key locus is RAI1. Parent-to-child transmission is known (Kolbasin et al. 2024). 17p12* Deletion: Hereditary Pressure-Sensitive Neuropathy. A recurrent 1.4 Mb deletion at 17p12 is the typical basis of hereditary pressure-sensitive neuropathy (HPSN), which has the alternative names of hereditary neuropathy with liability to pressure palsies (HNPP) and tomaculous neuropathy (Chance 2006). The deletion of a particular “nerve gene,” the PMP22 or peripheral myelin protein 22 gene, leads to abnormal myelination of the peripheral nerves, and this compromises their function. A typical presentation is the backpacker who complains of numbness (sensory nerves) and weakness (motor nerves) in the arms after a day’s hiking, and these symptoms are due to the pressure of the shoulder straps on the nerves in the armpit. The former mainstay of cytogenetic diagnosis was by FISH, using a probe that hybridized to the region; Figure 14–65 is still useful in giving a direct pictorial demonstration of the deletion. The deletion can arise de novo or, as is more usual, can be transmitted from an affected parent, in which case the risk to transmit the disease is 50%. Duplication: Charcot-Marie-Tooth Neuropathy. The most common form, by far (two-thirds or more), of all Charcot-Marie-Tooth neuropathy, CMT1A, is due to the recurrent duplication of 1.4 Mb in 17p12, which encompasses the PMP22 (peripheral myelin protein 22) gene (Salpietro et al. 2018).19 It is the reciprocal duplication of the deletion described above which causes pressure-sensitive neuropathy.20 FISH was a formerly used diagnostic method (Figure 14–66). The duplication leads to the production of a 150% amount of the PMP22 protein, and this excess mars the capacity for proper 19 The duplicated segment of chromosome 17 is some 1.7 Mb in size, but it is “gene-sparse.” The very few other genes contained therein appear to imply no phenotypic consequence, due to their being in imbalanced state. 20 An extraordinary coincidence is for one no. 17 chromosome to carry a PMP22 deletion and the other a PMP22 duplication, and thus a balanced genome and the person free of either neuropathy (Hirt et al. 2015). Figure 14–65.  The 17p12 Deletion Causing Hereditary Pressure-Sensitive Neuropathy. Notes: This FISH demonstration, using a probe that recognizes the PMP22 gene, shows normal hybridization (arrow) to one no. 17, but not the other (arrowhead). This reflects the absence of the p12 segment on the deleted chromosome.

442  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY functioning of the peripheral nerve. The sensory nerves are affected, but the major functional effect is on the motor nerves, and weakness is the important consequence. The nerves to the peroneal muscles (on the outside of the leg, with tendons passing around the ankle to the foot) are particularly vulnerable, and an alternative name for the condition is peroneal muscular atrophy. A rare circumstance is that of homozygosity for the duplication, effectively a partial 17p tetrasomy, which leads to a more severe manifestation of the neurological phenotype (Pareyson et al. 2003). About 80% of CMT1A is familial, inherited as an autosomal dominant trait. Of the 20% arising de novo, the considerable majority arose in male gametogenesis, in most cases due to a rearrangement between non-sister chromatids (Lee et al. 2020). Preimplantation testing is appropriately offered to the person with the condition planning a family (Zou et al. 2024). 17p11.2p12 Duplication encompassing both RAI1 and PMP22 produces a syndrome showing features of both Potocki-Lupski syndrome and Charcot-Marie-Tooth type 1A neuropathy (Yuan et al. 2015). Segmental lengths range from 3.2 Mb to 19.7 Mb. These duplications are non-recurrent, and all tested cases have been of de novo origin. 17p13.1 Deletions of 17p13.1 are of differing extents, but typically under 1 Mb in size. Microcephaly with profound intellectual disability is typical, and these children are nonverbal. Carvalho et al. (2014) propose an “oligogenic” model, whereby the microcephaly flows from a perturbed epistatic interaction between five critical genes within the deletion segment (ASGR1, ACADVL, DVL2, DLG4, and GABARAP) rather than an independent effect of each locus (Figure 3–21). In all studied cases, inheritance has been de novo. Duplication encompasses the same critical region as in the deletion. Very few cases are on record, but all include the critical region (Leka-Emiri et al. 2019). Intellectual disability, of varying degree, is seen in common. Almost all cases studied have been de novo, but maternal transmission is recorded. Figure 14–66.  FISH Demonstration of the Charcot-Marie-Tooth Duplication. Notes: These two images are of interphase blood cells from a patient with CMT neuropathy. The probe (pink) recognizes the PMP22 gene. At left, the duplication can be seen at 1 o’clock with two juxtaposed signals, almost overlapping. At right, the signals from the dup(17) at 8 o’clock are somewhat more separated. Source: From H Slater et al., Improved testing for CMT1A and HNPP using multiplex ligation-dependent probe amplification (MLPA) with rapid DNA preparations: comparison with the interphase FISH method, Hum Mutat 24:164–171, 2004. Courtesy KHA Choo, and with the permission of John Wiley and Sons. Autosomal Structural Rearrangements  443 17p13.3 Deletion. A proneness to rearrangement in 17p13.3 reflects a local richness in Alu sequences (Gu et al. 2015), and deletions of variable extents, interstitial or terminal, may remove some or all of these loci. Three loci of particular note are YWHAE, CRK, and PAFAH1B1 (PAFAH1B1 shown as LIS1 in Figure 14–64). According to the pattern of deletion, different syndromes arise (Figure 14–67). In the well-known Miller-Dieker syndrome (MDS) of “lissencephaly plus,” all three genes are deleted. MDS is not uncommonly diagnosed following prenatal ultrasonography (Figure 14–68); it is usually fatal in early childhood. Loss of PAFAH1B1 alone causes isolated lissencephaly, associated with cognitive incapacity, epilepsy, and motor impairment (Cardoso et al. 2003). Deletion of YWHAE and CRK, but not PAFAH1B1, lead to neurodevelopmental compromise, structural brain abnormalities, and epilepsy (Romano et al. 2020). A series of representative del/dups from Liang et al. (2022a) is depicted in Figure 14–69. Most 17p13.3 deletions arise de novo, but a parental balanced rearrangement is occasionally recognized. Duplication of 17p13.3 is divided into a milder Class I and a more severe Class II, based on the absence or presence of PAFAH1B1 in the duplicated segment; both classes include YWHAE (Blazejewski et al. 2018). Intellectual disability and behavioral abnormality—in some diagnosed as autism, speech and motor delay, and subtle facial dysmorphism—characterize Class I. Some have IQs in the normal range, and indeed Liang et al. (2022a) raise a question that this duplication (e.g., the short blue bar in Figure 14–69) might be a variant of uncertain significance. Penetrance in Goh et al. (2025) is 41%. The phenotype in Class II includes microcephaly and other brain abnormality, such as the hypoplasia of the corpus callosum and mild cerebellar volume loss (Curry et al. 2013). The penetrance for duplications that include PAFAH1B in Goh et al. (2025) is 79%. The Class I condition may be familial. Affected parents are typically less affected than their (proband) child; somatic-gonadal and (presumed) confined gonadal mosaicism, with normal parents, are both recorded. Figure 14–67.  Deletions and Duplication at 17p13.3. Notes: The extents of deletions and duplications, with respect to the different syndromes, are shown. The Class I duplication can sometimes extend to include CRK (dotted bracket). PAFAH1B1 was formerly known as LIS1. 444  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Figure 14–69.  A Representative Series of 17p13.3 Deletions and Duplications. Notes: Deletions are in red, duplications are in blue. The Miller-Dieker region is outlined. The relative positions of the three key loci noted are indicated. In one duplication and two deletion cases, PAFAH1B1 remained intact. The duplication case was a prenatal diagnosis, an increased nuchal translucency. The child has since developed normally, and his healthy mother, who had received an undergraduate education, was shown to carry the same duplication. Of the deletion cases with PAFAH1B1 intact, one comprised a fetus with IUGR and a brain cortical anomaly; and the other was a child with intellectual disability and severe motor delay. Source: From B Liang et al., Clinical findings and genetic analysis of patients with copy number variants involving 17p13.3 using a single nucleotide polymorphism array: a single-center experience, BMC Med Genomics 15:268, 2022. Courtesy N Lin, H Huang, and L Xu, and with the permission of Springer Nature. Figure 14–68.  The Lissencephaly of Miller-Dieker Syndrome. Notes: Prenatal brain MRI shows lissencephaly (“smooth brain”) in Miller-Dieker syndrome. This was a 31-week fetus with a de novo del 17p13.3. Frontal lobe in upper part of image, occiput in lower. The surface of the brain (the cortex) is smooth, lacking the normal furrowed appearance at this gestation. The occipital ventricles are mildly enlarged, reflecting a reduction in brain parenchyma. Source: From C-P Chen et al., Chromosome 17p13.3 deletion syndrome: aCGH characterization, prenatal findings and diagnosis, and literature review, Gene 532: 152–159, 2013. Courtesy C-P Chen, and with the permission of Elsevier.

Autosomal Structural Rearrangements  445 17q11.2* Deletion. About 5%–10% of all neurofibromatosis type 1 (NF1) is due to a recurrent 1.4 Mb deletion at 17q11.2, which includes the NF1 gene. The clinical picture is typically more severe than in NF1 due to point mutation. Tritto et al. (2024) hypothesize that the deletion might lead to changes in the 3D chromatin structure in the 17q11.2 region, thus influencing the phenotype for the worse. Duplication. The 17q11.2 microduplication syndrome, reciprocal to the deletion, includes intellectual disability and dysmorphism as the only clinical features in common (Tassano et al. 2017). NF1 signs are not seen. Penetrance in Goh et al. (2025) is 74%. 17q12* Deletion. A key observation is that of renal cystic disease progressing to chronic renal dysfunction (Buffin-Meyer et al. 2024). At fetal ultrasonography, hyperechogenic kidneys may be detected (Zhou et al. 2021). Developmental delay is usually of mild degree, but autism is a possibility. Facial dysmorphism may be moderate, “soft,” or essentially absent. Pancreatic, liver, and genital abnormality may be seen, and some are diabetic, with MODY-521 (Xin and Zhang 2023). The crucial gene is HNF1B (Figure 14–70) which, as a Mendelian mutation, is responsible for the renal cysts and diabetes (RCAD) syndrome. Mother-to-child transmission is recorded. Goh et al. (2025) calculate a penetrance of 63%, but caution that some with RCAD are likely undiagnosed, affecting the validity of this figure. Duplication. Rare 17q12 duplications encompassing HNF1B have been associated with gastrointestinal pathology such as tracheo-esophageal fistula, and choledochal cyst presenting as neonatal cholestatic jaundice. Intellect may be normal, but variable cognitive impairment, difficult behavior, and occasionally epilepsy are observed. Second-hit CNVs elsewhere in the genome may exacerbate the phenotype. Renal function is, as with the deletion, affected; in contrast, diabetes is not over-represented in the duplication (Cannon et al. 2023). Penetrance in Goh et al. (2025) is a low 20%. Inheritance from a normal mother has been seen (Kotalova et al. 2018). 17q21.31* Deletion: Koolen-de Vries Syndrome. This is a condition that could, in retrospect, have been seen as a syndrome, but in which the collection of features did not impress Figure 14–70.          21 Maturity-onset diabetes of the young type 5. 446  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY sufficiently that recognition was likely to have been achieved ahead of the laboratory discovery (“genotype-first”) of this recurrent deletion (Tan et al. 2009). Having made that point, features of the facies are sufficiently distinct that “next-generation phenotyping,” in which facial photographs are assessed by computer, was able to identify a case (Brand et al. 2022). Poor speech development, epilepsy, and “hypersocial behavior” may be seen as having a resemblance to Angelman syndrome. KANSL1 is the relevant gene (point mutation can also produce the syndrome); a 990 kb inversion polymorphism spanning 17q21.31 is a necessary predisposing element (Koolen et al. 2016). Recurrence is very rare. One case is known of mother-to-child transmission (Rendeiro et al. 2016). Koolen et al. (2012) studied two instances of recurrence due to low-grade maternal mosaicism. One mother had 0.5 Mb deletion in 8% of buccal mucosal cells, and in the other mother there was an essentially similar deletion in 3% of peripheral lymphocytes. In the de novo case, Koolen et al. calculate a risk of recurrence of 1/9,446 (0.01%), which is about twice the baseline population risk of 1/16,000. This overall calculation is based upon the separate risks according to the parental genotypes for the inversion polymorphism mentioned above; the interested reader is referred to p. 78 for a fuller exposition. Duplication. The reciprocal duplication of the 17q21.31 deletion is unusual in that the remarkable abnormal phenotype, a dementia, does not emerge until middle age, mean onset at 50 years with a disease duration then of 10 years. In childhood, there may be a mild neurodevelopmental phenotype of borderline cognitive and behavioral capacity (Gregor et al. 2012). Later neurodegeneration is due to duplication of the MAPT gene (adjacent to KANSL1; Figure 14–71), there is abnormal accumulation of tau within certain brain regions, and the disorder can be called a primary tauopathy (Wallon et al. 2021). The typical onset is of an amnestic syndrome, that is, a loss in memory; the condition can evolve to affect other functional neurological domains. Penetrance is high, possibly 100% (Goh et al. 2025). Since the dup can be transmitted, the counseling issues rather reflect those of other adult-onset neurodegenerative conditions such as dominantly inherited Alzheimer disease. Its unanticipated discovery at chromosome analysis would raise an ethical question (p. 810). 17q22 Deletion of the NOG locus is the basis of this syndrome (Carlson et al. 2021). The limbs and the ears are vulnerable anatomy. Symphalangism (fusion of joints of fingers and Figure 14–71.  The Adjacent Loci MAPT and KANSL1 at 17q21.31. Notes: MAPT is the relevant locus in the dup17q21q31, while KANSL1 is the important factor in the deletion. Loss of MAPT in the deletion, and gain of KANSL1 in the duplication, seem without evident effect. Source: Drawn after the UCSC genome browser entry for chr17:45,962,338-46,172,143 (hg38).

Autosomal Structural Rearrangements  447 toes) and other digital defects, joint contractures developing through childhood, and conductive hearing loss are typical. Intellectual disability associated with microcephaly and a distinctive facial dysmorphism are also noted. De novo inheritance is more usual, but parent-to-child transmission is known. 17q23.1q23.2* Deletion. An inconsistency of phenotype mirrors the considerable range of deletions within this region, although a mild to moderate developmental delay, particularly affecting speech, is frequent. In those in whom the deletion removes the adjacent transcription factor genes TBX2 and TBX4, heart and limb defects are characteristic (Ballif et al. 2010). All cases have been de novo. Penetrance in Goh et al. (2025) is complete. Duplication. A phenotype is yet to be established for this rare recurrent duplication, but if a phenotype exists, it is likely to be mild and incompletely penetrant (Goh et al. 2025). Chromosome 18 18p Deletion: de Grouchy Syndrome. The most frequent form of 18p deletion involves a whole-arm loss, the breakpoint at the centromere (thus “centromeric 18p– syndrome”) seen in almost one-half of del 18p cases (Sebold et al. 2015). TGIF1 and AFG3L2 (Figure 14–72) are two of several genes reviewed in Hasi-Zogaj et al. (2015) that may be contributory to the phenotype. Albeit that this is a homogeneous cytogenetic material, the clinical picture can vary quite considerably. Intellectual impairment may be relatively mild, with an IQ range around 50–100, an average of 70 (Hasi-Zogaj et al. 2015). Soileau et al. (2015) provide very detailed data concerning short (and long) arm 18 deletions. Coping with everyday life is difficult. Many will die before adult age. Partial 18p deletion breakpoints are recorded along the whole length of the short arm, very few of which are recurrent. In principle, the milder the phenotype the less the degree of 18p loss. Most cases occur de novo, but there are rare instances of parental transmission. Certainly, in any 18p deletion, parental rearrangement is prudently to be excluded. Figure 14–72. 448  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Duplication 18p. The phenotype of this condition, typically due to an isochromosome of 18p in the company of an 18p deletion, can be quite mild, and compatible with employment. In a notable familial case, Peng et al. (2022) describe a grandfather and his daughter both with 47,del(18)(p11),+i(18)(p10). She had presented in pregnancy, having had the prenatal diagnosis of 18p tetrasomy, 47,i(18p). She was a kindergarten teacher, he a welder. Other instances of maternal transmission are on record; azoöspermia may be a basis of the infrequency of observation of paternity. A case due to tertiary trisomy from transmission of a familial reciprocal translocation is illustrated in Figure 5–19. Triplication 18p. Bawazeer et al. (2018) review this syndrome, characterized by dysmorphism and numerous minor and some major malformations. Intellectual disability ranges from mild or borderline normal to severe and profound. Almost all cases are of de novo generation (but see dup18p, Peng et al. above). 18p11.32p11.31 Duplication. This (genomically and genetically) small segment on distal 18p may be, when duplicated, associated with a mild degree of cognitive impairment and difficult behavior, but without effect upon the physical phenotype. The picture is sufficiently mild that familial transmission is quite possible (Balasubramanian et al. 2016). 18q terminal Deletion 18q. Terminal deletions of differing lengths, up to 30 Mb, are the more usually observed, but about one-fourth are interstitial. The clinical picture may include intellectual disability, difficult behavior, facial dysmorphism, club foot, and scoliosis (Ismail et al. 2023). Cody et al. (2015) assess which genes may contribute to which aspect of the phenotype. Two loci of note in the distal segment are TCF4 and MBP. Mutation in the former is the basis of Pitt-Hopkins syndrome (see below), and the latter directs white matter myelination. De novo and familial origin are both known. 18q21.2 Deletion: Pitt-Hopkins Syndrome. Mutation in, or deletion of, the TCF4 gene is the basis of Pitt-Hopkins syndrome. Whole gene deletion is seen in 30%, and these deletions may extend contiguously, while under 10% are—as is the child in Figure 14–73—due to partial gene deletion (Marangi and Zollino 2015). The condition includes developmental delay, disordered respiratory control with episodes of hyperventilation and apnea, and variable immunodeficiency (Malik et al. 2024). Gonadal mosaicism is well recognized (Figure 14–73), and a small risk of recurrence is to be acknowledged (Kousoulidou et al. 2013). Deletion. In a study of MZ twins with learning difficulty and obesity associated with a del(16)(p11.2), an accompanying very small de novo del(18)(q21.2) was initially interpreted as a variant of unknown significance. Since this deletion included a part of the DCC gene (just 2 Mb upstream of TCF4; see preceding entry), this led clinicians to look for mirror movements, known to be due to DCC deletion (Franz et al. 2015). And indeed, as the video accompanying this paper showed, both boys demonstrated obvious mirror movements of the hands (Kleinendorst and van Haelst 2024). 18q21.31q22.2 Duplication. A 12 Mb duplication involving 18q21.31q22.2 is of interest in that three mildly intellectually disabled children had been born to a (university graduate) mosaic mother, mos46,XX,dup(18)(q21q22)[90]/46,XX[10] (Ceccarini et al. 2007). A slightly larger inherited 18q21q23 is in Henson et al. (2012); but in contrast to the children in

Autosomal Structural Rearrangements  449 Ceccarini et al., the phenotypes in mother and daughter in this latter case could be seen as falling within a normal range. 18q22.1qter Deletion. While most 18q deletions are non-recurrent, Cody et al. (2014) were able to assemble a group of patients in whom the deleted terminal segments all had breakpoints at various sites within a short 2 Mb segment in 18q22.1 between two consecutive genes, SERPINB8 and CDH7, thus all having a length of deletion essentially in common. The deletions removed a suite of 38 genes in q22.1qter, among which TMX3, NETO1, ZNF407, TSHZ1, NFATC, and MBP are judged attractive as contributory to the clinical picture. These authors speak of this as the “distal 18q– reference group.” Diminished cognitive capacity (of borderline or low-normal degree), growth retardation, and hearing loss were commonly observed traits. Of the nine who were adults and with information available, five had graduated from high school and one had a high school completion certificate as their highest level of education; three of these six were at the time in college or had completed college; seven lived with their parents, one with a host family, and one was married and living with their spouse; two had part-time paying jobs, and one had a part-time volunteer job. Chromosome 19 Chromosome 19, while small, is extraordinarily gene-dense (Figure 1–4), and a number of del/dup syndromes “crowd into” the available space. Some separate disorders nevertheless Figure 14–73.  Somatic-Gonadal Mosaicism for Pitt-Hopkins Syndrome. Notes: Mother and child with del(18)(q21), attending a genetic clinic. Daughter is non-mosaic for the deletion, and has Pitt-Hopkins syndrome. Mother, completely normal physically and intellectually, had, on microarray, a “slight negative shift” at 18q21, and on FISH, 4/18 cells showed deletion of TCF4. Blood was the only tissue analyzed, but this was nevertheless sufficient for recognition of somatic-gonadal mosaicism. Source: Case of J Watt, in K Doudney et al. (2013). Photo reproduced with kind permission of the parents. 450  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY occupy the same cytogenetic band, and the reader will need to take care that the correct condition is being addressed. Landmark loci will prove useful in maintaining a distinction. 19p13.12 Deletion. This rare deletion is characterized by intellectual disability, microcephaly, and a rounded face with synophrys and arched eyebrows (de Souza et al. 2018). The region is gene-rich, and full penetrance is assumed based on the gene content (Goh et al. 2025). 19p13.2 Deletion: Malan Syndrome. Microdeletions that include NFIX cause a syndrome of overgrowth and intellectual disability, somewhat resembling Sotos syndrome (Priolo et al. Figure 14–74.          Figure 14–75.  Growth Indices in a Case of Malan Syndrome. Notes: The child in this case had a deletion at 19p13.2 which removed NFIX along with three other genes. Each measurement (weight in blue, height in red, head circumference in green) in the first two years of life is shown in relation to the 98th centile. Note that each measurement begins to cross above the 98th centile between about 3 to 7 months. On the most recent reported measurements at age 14, height at 1.8 m was on the 94th centile, and weight at 61.4 kg on the 75th. Source: From S Makker et al., A patient case of Malan syndrome involving 19p13.2 deletion of NFIX with longitudinal follow-up and future prospectives, J Clin Med 13:6575, 2024. Courtesy CS McIntosh, and with the permission of MDPI. Autosomal Structural Rearrangements  451 2018). The evolution of growth indices is illustrated in Figure 14–75. If the CACNA1A gene is included in the deletion segment, epilepsy may result. Sibship recurrence is recorded: Two sisters had the same del 19p13.13 disrupting NFIX and deleting other loci, but the parents tested normal on (presumably) peripheral blood (Nimmakayalu et al. 2013). Naturally, one must have been a gonadal mosaic. Otherwise, all cases have been de novo. Deletion: Coffin-Siris Type 4 syndrome. While the basis of Coffin-Siris syndrome type 4 (CSS4) resides in the SMARCA4 locus, microdeletion within 19p13.2 that includes SMARCA4, while causing intellectual disability with poor speech acquisition, does not necessarily produce the more distinctive features of the syndrome (Mitrakos et al. 2020). We may speak of “forme fruste” CSS4. 19p13.3 Deletion, distal. This (very) distal segment deletion is reviewed in Peddibhotla et al. (2013), and in two families, transmission from a parent was recorded. THEG is a suitable marker gene. In some, components of the VACTERL association are noted. If the deletion includes the STK11 gene, Peutz-Jegher syndrome will be added to the phenotype otherwise of learning difficulty, dysmorphism, and congenital anomalies (Kuroda et al. 2015). Deletion, proximal. The deletion segment is defined by its containing PIAS4, the gene of presumed pheno-critical role in this syndrome (Tenorio et al. 2020). A phenotype of macrocephaly, facial dysmorphism, multiple health problems, and intellectual disability is seen. All tested cases have been de novo. Duplication, proximal. The clinical picture is quite similar to that of the deletion, other than for a microcephaly (Nevado et al. 2015). 19q12 Deletion of a small segment within the most centromeric band of 19q is associated with a risk for autism, albeit that several reported deletions extend into the adjacent 19q31.11 band (Caubit et al. 2016). Loss of TSHZ3 in 19q12, a gene having a role in development of cortical projection neurons (nerve cells that connect to others in the cerebral cortex), may account for the neuropsychological phenotype. 19q13.11 Deletion. Non-recurrent deletions of varying lengths within this band (and in some extending into the adjacent bands) lead to a clinical picture including intellectual disability, hypospadias in the male, and the notable observation of an ectodermal dysplasia (Figure 14–76). Skin, hair, and nails are affected, and in some, there is an actual cutis aplasia of the scalp. Some children diagnosed as having Dubowitz syndrome, in which eczema and sparse hair are typical, may in fact have had this microdeletion (Urquhart et al. 2015). Two contiguous loci, UBA2 and WTIP, may relate to the ectodermal aspects and the genital defect, respectively (Chowdhury et al. 2014; Melo et al. 2015). Duplication. Variable microcephaly/macrocephaly, developmental delay, obesity, and an unusual facies characterize proximal q duplications within 19q13.11, or extending into 19q13.11q13.2, a segment occupying about one-third of the long arm (Davidsson et al. 2010; Lugli et al. 2011). The several involved segments are non-recurrent. Obesity can be of severe degree, and CEBPA at 19q13.11, whose gene product modulates the

452  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY expression of leptin and influences the insulin receptor, is one of a number of candidate loci. All cases have been de novo. 19q13.32 Deletion. The phenotype of this syndrome may, according to the variable extents of the deletions, include severe intellectual disablement, facial dysmorphism, and certain neuromuscular deficiencies with limb dystonia, and affecting innervation of the eye (with gaze palsy), and gut (with colonic atony and chronic constipation) (Shelby et al. 2022). These traits are not seen in lesser deletions within 19q13.32, and in these a low-normal or mild intellectual deficit and minor dysmorphism are recorded (Castillo et al. 2014). KPTN is a candidate pheno-critical gene. Three-generation transmission is reported in Guadagnolo et al. (2023), with diagnoses of ADHD, anxiety disorder, and developmental delay in the proband child, but without dysmorphism. Duplication. Rim et al. (2017) review the handful of reported cases of dup 19q13.32. Abnormal growth in either direction is seen: macrocephaly or microcephaly, and obesity or growth retardation. Developmental delay is universal. KPTN may have a role. 19q13.33 Duplication. This rare duplication may arise de novo, or upon the basis of a parental translocation. The phenotype comprises neurodevelopmental disability, with epilepsy in some (Pérez-Palma et al. 2018). GRIN2D is a plausible key pheno-contributory locus. Figure 14–76.  Deletions at 19q13.11. Notes: The deletions are non-recurrent; some extend into 19q13.12. The positions of three loci of interest are indicated: CEBPA is asterisked, UBA2 is the single dagger, and WTIP is shown as the double dagger. Source: From KT Abe et al., 19q13.11 microdeletion: Clinical features overlapping ectrodactyly ectodermal dysplasia-clefting syndrome phenotype, Clin Case Rep 6:1300–1307, 2018. Courtesy KT Abe, and with the permission of John Wiley and Sons. Autosomal Structural Rearrangements  453 Chromosome 20 20p11.2 Deletion. The notable aspect of phenotype in this deletion is a panhypopituitarism, and presentation in early infancy with congenital hyperinsulinism is typical. Facial dysmorphism, mental disability, and autism are recorded in some. FOXA2 presents a plausible case as being instrumental in the genesis of the pituitary defect (Laver et al. 2024). In one instance, there had been mother-to-child inheritance, the (normal) mother mosaic for the deletion (Garcia-Heras et al. 2005); all others were de novo. 20p12.2 Deletion: Alagille Syndrome. The characteristic features of this syndrome are stenosis of the peripheral pulmonary arteries and insufficient development of bile ducts within the liver (thus, “arteriohepatic dysplasia”) along with certain eye and skeletal defects, and a distinctive facies; intellect is typically normal. Genomic deletions are an uncommon cause; most are in fact due to mutation in the JAG1 gene. In the <5% of cases of Alagille syndrome with a deletion, those of smaller size (up to 4 Mb) typically convey no further phenotypic burden beyond that imposed by JAG1 haploinsufficiency (Sahoo et al. 2011). Parental transmission is recorded, at least from an affected father and from a mosaic unaffected mother (Laufer-Cahana et al. 2002). 20p12.3 Duplication. This single cytoband duplication is associated with the cardiac conduction anomaly, Wolff-Parkinson-White syndrome (WPWS). The child in Mills et al. (2013) presented as a newborn with heart failure due to tachyarrhythmia, but responded well to treatment. She was otherwise, at age five months, essentially unremarkable. Her father and uncle, both diagnosed with attention deficit and the latter also with WPWS, carried the duplication. WPWS is seen also in the corresponding 20p deletion, supporting the contention of a causal link. BMP2 is a sentinel locus. Another trait observed in dup 20q12.3, and also inhering in BMP2, is a particular form of brachydactyly (Su et al. 2011). Figure 14–77. 454  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 20p13 Deletion. This deletion is sited near the telomere. Fang et al. (2019) define the phenotype as comprising motor and language delay, minor dysmorphic features, and epilepsy; Landau-Kleffner syndrome (loss of speech recognition, nocturnal seizures) is reported. Some achieve an IQ formally within a normal range. Deletions are terminal, and most are non-recurrent, typically from kilobase to 1–2 Mb in extent. The subtelomeric genes NRSN2 and SOX12 are proposed to be pheno-critical. Where tested, de novo inheritance has been universal. 20q11.22q11.23 Deletions that reside within the segment 20q11.22q11.23 determine a heterogeneous range. Clinical presentation typically includes growth retardation, intractable feeding difficulties with gastroesophageal reflux, hypotonia, and psychomotor developmental delay. Bensaid et al. (2024) propose two critical regions, one defined by the locus GDF5, at 20q11.22, and the other by TOP1 at 20q12. One of a pair of non-identical monozygous twins in Meredith et al. (2017) had the smallest recorded deletion, likely in constitutional mosaic state, with only GDF5 deleted of the three genes just named; intriguingly, his phenotypically normal co-twin also showed mosaicism for the deletion, presumably as a consequence of chimerism confined to blood, reflecting that the two had shared a placenta. A mitotic origin of the deletion in one twin, after the splitting of the conceptus, is a probable basis of the abnormality. Duplication. Avila et al. (2013) and Goetzinger et al. (2021) delineate the syndrome due to dup 20q11.22q11.23. A notable clinical feature is trigonocephaly (if ASXL1 is within the deleted segment) with ridging of the metopic suture along with psychomotor delay, poor speech acquisition, and short hands and feet. GDF5 is a plausible pheno-contributory locus. The duplication may exist as an insertional segment into another chromosome. All cases have been of de novo generation. 20q13.33 Deletion. Epilepsy is a particular feature of the phenotype due to this deletion, which might or might not coexist with a neurocognitive component (Okumura et al. 2015; Lewis et al. 2018). A 20q terminal deletion might remove only the last two genes on the chromosome (MYT1 and PCMTD2), or if of wider extent, genes of possible epileptic susceptibility (KCNQ2 and CHRNA4) could be included (Mefford et al. 2012). Chromosome 21 21q21.3 Duplication of 21q21.3 alone, containing the APP (amyloid precursor protein) gene, is of itself a determinant of early-onset dementia (Figure 14–79, 80). Kalfon et al. (2022) report a segregating rea(18) which included the segment dup21q21.3 carrying APP and just one other 21q gene (CYYR1). In this seven-generation family, the heterozygous women had presented with dementia and the men with intracerebral bleeds. Kasri et al. (2024) demonstrate accumulation of amyloid β peptide (Aβ; the product of

Autosomal Structural Rearrangements  455 proteolytic processing of APP) in the brains of dup 21q21.3 carriers (Figure 14–80). As with the17q21.31 duplication (above), counseling will need to follow the norms established for other adult-onset neurodegenerative disease. 21q22.12 Deletion: Braddock-Carey Syndrome. Clinical observations include neurocognitive compromise typically of severe degree, agenesis of the corpus callosum, the Pierre Robin sequence, facial dysmorphism, heart malformation, and in some, congenital thrombocytopenia (Braddock et al. 2016). This latter trait is due to loss of the RUNX1 gene (Figure 14–78); in Braddock-Carey syndrome in which this gene is intact, platelet production is normal. All cases of this syndrome have been of de novo generation. 21q22.13 Deletion. The locus of particular interest within 21q22.13 is DYRK1A, a gene of note with respect to the Down syndrome neurocognitive phenotype. This deletion is close by, but distinct from, the Braddock-Carey deletion. Ji et al. (2015) define a DYRK1A deletion syndrome characterized by growth retardation, microcephaly Figure 14–78.          Figure 14–79.  Duplications at 21q21.3 that Included APP. Notes: These data are from Kalfon et al. (2022) and Kasri et al. (2024). The relative position of the APP gene is asterisked. The smaller duplications included only APP and one other gene (either GABPA on the centromeric side, or CYYR1 telomerically). 456  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY with various types of brain malformation on imaging, global neurofunctional compromise, epilepsy, and a distinctive facial gestalt. Deletions are mostly in the range 0.5 Mb–10 Mb. Sibship recurrence due to a maternal insertional translocation is recorded in Ji et al. Duplication. Broadly speaking, a duplication containing this segment, and more so if it includes DYRK1A, leads to a Down syndrome picture (Schnabel et al. 2018). Chromosome 22 22q11.1q11.21 Duplication, Triplication: Cat Eye Syndrome, Schmid-Fraccaro Syndrome. The cytogenetics of this imbalance varies, and it can be seen typically as a supernumerary inv dup(22)(q11.21) or der(22)(q11.1q11.21) but also as an intrachromosomal duplication or triplication. The eponymous eye sign is iris coloboma; developmental delay, ear tags, renal and anal anomaly, and occasionally the severe cardiovascular malformation, and total anomalous pulmonary venous return are variably associated. The landmark locus is CECR2. Both the intrachromosomal and supernumerary forms can be familial, and it would be obligatory to offer parental testing (Jedraszak et al. 2024). Mosaicism is common. One mother had 4.5% mosaicism in blood, while her two affected sons had levels of 85% and 70%; and reproductive study in one mosaic man, the father of three mosaic children, showed 50% of sperm to carry the inv dup(22) (Kvarnung et al. 2012). Figure 14–80.  Amyloid Accumulation in the Brain in dup21q21.3. Notes: This brain biopsy, of frontal lobe cortex, was taken at post mortem from a person who had suffered dementia, and who was a dup21q21.3 heterozygote, the duplicated segment including the APP gene. The scattered islands of brown staining in brain parenchyma (left) show amyloid β peptide (Aβ) accumulation; none such is to be seen in the control sample. Deposits of Aβ in blood vessels are shown at right. The high-magnified images show a vessel, the lumen patent in the control, but occluded in the dup case. Source: From A Kasri et al., Amyloid-β peptide signature associated with cerebral amyloid angiopathy in familial Alzheimer’s disease with APPdup and Down syndrome, Acta Neuropathol 148:8, 2024. Courtesy H Zetterberg and M-C Potier, and with the permission of Springer. Autosomal Structural Rearrangements  457 22q11.21* Deletion. Before their common cytogenetic basis was understood, the 22q11 deletion clinical presentations had a number of labels, including DiGeorge syndrome (DGS), velocardiofacial (VCF) syndrome, and Shprintzen syndrome.22 DGS was the name typically applied to a child with heart defect, parathyroid abnormality, and immunodeficiency; in Shprintzen syndrome a cleft or deficient palate was the notable feature, while VCF syndrome emphasized the facial appearance along with palatal (“velo”) clefting and a heart defect, typically including a malformation of the great vessels of the outflow tract. Kousseff syndrome and Cayler syndrome were names given to variants with a neural tube defect, and asymmetric crying facies plus cardiac outflow defect, respectively. The intellect is affected; median full-scale IQ is 76 (Campbell et al. 2015). The variable expressivity with respect to IQ is in large part explainable on the basis of the parental IQ levels (Klaassen et al. 2016). Difficulty in social interaction may relate mostly to the degree of intellectual disability. A psychiatric/behavioral component is frequent, with susceptibility to psychosis including schizophrenia (Van et al. 2024). Those in whom the cognitive impairment is more marked have a greater tendency to develop a psychotic disorder (Vorstman et al. 2015). If other features are absent, the chromosomal diagnosis may be delayed until adolescence or adulthood (Furuya et al. 2015; Fonseca-Pedrero et al. 2016). The evolution of the tout ensemble phenotype in the adult, with whom neuropsychiatric disease is the main cause for concern, presents its own challenges (Fung et al. 2015). With a birth incidence of about one in 4,000 (estimates vary), this is the most common human site of deletion, and this vulnerability resides in the existence of LCRs and palindromic AT-rich repeats in the 22q11.21 region (Vervoort et al. 2025). The most frequently observed (~90%) deletion, of 2.54 Mb, lies between LCR A–D (Figure 14–82). Otherwise, 8% span the ~1.5 Mb segment LCR A–B, and rare deletions occur at other sites, including LCRs E through H. TBX1 is the locus seen as key to the cardiac defects, Figure 14–81.          22 In true acknowledgment of the first definition of the syndrome in the Czechoslovakian literature in 1955, Sedlácková syndrome may be the most fitting name (Turnpenny and Pigott 2001).

458  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY and possibly also contributory to the psychopathy (Hiramoto et al. 2011); this gene lies between LCRs A and B (Figure 14–82). An uncommon deletion LCR B–D associated with a clinical picture of immune dysregulation can point to a likely causative role of the immune locus CRKL within this segment (Lin et al. 2021b). Incomplete penetrance for components of the syndrome, and variable expressivity for those that are present, is very much the rule. The overall penetrance estimate in Goh et al. (2025) is 86%, but this would likely increase to near 100% with thorough phenotyping. Monozygous twins are often discordant (Singh et al. 2002b). In the familial case, a parent can, for example, show mild features of the condition or have a predominantly Shprintzen facial and palatal phenotype, with a child showing a characteristic DGS cardiac and endocrine phenotype (Devriendt et al. 1997). Hart et al. (2016) rehearse issues in sensitively raising with parents the risk for psychosis. The condition is typically more severe in second-generation subjects, although ascertainment bias is a likely explanation23 (Cirillo et al. 2014). Variable expressivity with respect to facial appearance is compounded due to ethnic differences, and Kruszka et al. (2017) propose that digital facial analysis technology is a more accurate “observer” than a clinician. In advising about recurrence risk, genetic counseling must take account of the possibilities of a parent being so mildly affected that the condition had not been recognized, and thus parental chromosomal analysis is appropriately offered. Most cases are de novo, but about 10% may be inherited. Gonadal and somatic-gonadal mosaicism are rarely reported but nevertheless have been seen; and a “very small” risk of recurrence, 23 Another is “positive assortative mating.” The de novo case is likely to have arisen from normal parents. But in the next generation, an affected person is more likely to have a partner of a similar level of intellectual capacity, compounding the effect in children of theirs. Figure 14–82.  Deletion and Duplication at 22q11.21q11.23. Notes: Deletions and duplications arise due to recombination between Low Copy Repeats A through H, and are grouped as proximal (A-D) and distal (E-H) imbalances. The considerable majority, 90%, are due to del/dup of LCR A-D within 22q11.21. The distal del/dups are subdivided into Classes I to III, according to the pattern of imbalance. Within the segments between each of the LCRs, a key locus is identified, and their relative positions are shown as the asterisks. In order from centromere to telomere, these loci are TBX1, SCARF2, SNAP29, MAPK1, BCR, SMARCB1, and UBP1. Autosomal Structural Rearrangements  459 following a de novo case, is to be acknowledged (Sandrin-Garcia et al. 2002; Chen et al. 2019). Vergés et al. (2014), in a study of fathers of children with the de novo 22q11 deletion, found two of nine fathers with levels of del(22q11) sperm that were approximately threefold higher than those of controls. Clearly, the recurrence risk from a heterozygous parent will be 50%. Earlier estimates of a larger fraction of affected parents may have been biased due to studying more remarkable families (Swillen et al. 1998). Indeed, Smith and Robson (1999) report only 5% of parents to have had the deletion in an Australian series of 59 cases. However, in the case of the “nested deletions” LCR-B to LCR-D, and LCR-C to LCR-D, a majority, 60%, are familial (Campbell et al. 2018). Rare familial cases can result from a translocation (Peter et al. 2021). The deletion is detectable on maternal blood screening, NIPT (Blagowidow et al. 2023), which could be offered to a whole pregnant population or targeted to couples with a previously affected child or to increased-risk mothers (e.g., heart defect seen on ultrasound). Duplication. The dup22q11.21 most often involves breakpoints LCR-A to LCR-D (Figure 14–82). Curiously, it may be more common than the deletion (Olsen et al. 2018). The clinical picture is quite diverse, ranging from overt normality in many to a degree of neurocognitive compromise. IQ overlaps substantially with the lower fraction of a normal population; one-fifth have a mild intellectual disability, and language acquisition is affected (Lin et al. 2020; Verbesselt et al. 2022, 2023). Penetrance in Goh et al. (2025) is 19%. Congenital anomalies are not infrequent (Bartik et al. 2022). Susceptibility to autism is, to a small degree, increased (Drmic et al. 2022). In perhaps a first for a chromosomal imbalance, dup heterozygotes may have, in at least one respect, better mental health than a general population: There may be a protective effect against schizophrenia (Lin et al. 2020). Familial examples are well recorded, and indeed comprise a majority of cases (Verbesselt et al. 2022; Jiang et al. 2024b); and there is one notable report of a three-generation family in which eight individuals had the dup(22), evincing a range of fairly minor malformation and neurobehavioral phenotypic effects (Yu et al. 2008). This frequent familial observation has enabled a comparison of the phenotype in probands versus non-probands, and unsurprisingly the clinical picture is milder and more often merging into a normal range in those in whom the diagnosis was made only after a proband had brought the family to notice (an example of ascertainment bias, favoring the recognition of a more severe manifestation) (Drmic et al. 2022). This very wide range of expressivity, and merging into non-penetrance, makes for challenging counseling (Dupont et al. 2015); the coexistence of CNVs elsewhere in the genome may be the basis, in part at least, of this phenotypic variation. Recurrence from chromosomally normal parents presenting with a de novo case has not as yet been reported, but a theoretical risk exists due to parental gonadal mosaicism. Demaerel et al. (2016) report siblings of normal parents, one with dup 22q11, the other with del 22q11, both coming from the mother. A smaller, less often seen nested 22q11.21 duplication encompasses the segment bounded by LCR-B and LCR-D (Figure 14–83). Woodward et al. (2019) documented a phenotype of intellectual disability and autism, along with normality in several. PIK4A, located between LCRs C and D, may have an important contributory role to the phenotype. Distal duplication, extending into LCR-E or further (and which, if beyond LCR-F, may include the SMARCB1 locus), is uncommon (Egger et al. 2023).

460  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 22q11.23* Deletion. The distal 22q11.2 region involves LCRs E, F, G, and H, and does not overlap with the classic (TBX1) 22q11 deletion. Deletions with a range of different breakpoint combinations have been reported,24 but meaningful genotype-phenotype correlation is difficult, due to small numbers of reported cases and a marked phenotypic variability. This deletion syndrome is associated with global developmental delay, intellectual disability, growth retardation, cardiac defects, and mild dysmorphism (Pinchefsky et al. 2017). For deletions that extend to G/H, loss of SMARCB1 imposes the additional phenotype of tumor predisposition.25 Distal 22q11 deletions are usually de novo, but are occasionally inherited from a parent with a mild or normal phenotype. Goh et al. (2025) investigated the recurrent 1.8 Mb E–F deletion (including BCR and MAPK1), and noted its virtual absence from control datasets, suggesting penetrance approaching100%. Duplication. 22q11.2 duplications that involve LCRs E, F, G, and H are associated with variable cognitive impairment, speech and language delay, and behavior disturbance. Cardiac defects and minor skeletal abnormalities appear to be part of the phenotype, but there is no common facial gestalt (Tan et al. 2011; Pinchefsky et al. 2017). These duplications are usually inherited, and familial cases with normal phenotypes are known. Goh et al. (2025) report a penetrance of 51% for the distal 22q11.2 duplication, with wide confidence intervals. Figure 14–83.  Central 22q11.21 “Nested” Duplications. Notes: Loci of interest PI4KA and CRKL are shown, respectively asterisked and with a dagger. Duplications are of LCR B-D, B-C, and C-D. Source: From KJ Woodward et al., Atypical nested 22q11.2 duplications between LCR22B and LCR22D are associated with neurodevelopmental phenotypes including autism spectrum disorder with incomplete penetrance, Mol Genet Genomic Med 7:e00507, 2019. Courtesy KJ Woodward and J I-T Heng, and with the permission of John Wiley and Sons. 24 Specifically, D-E, D-F, D-G/H E-F, E-G/H, and F-G/H. 25 SMARCB1 is also a gene of interest in relation to neurodevelopment phenotypes, as non-truncating SMARCB1 variants are a cause of Coffin-Siris syndrome.

Autosomal Structural Rearrangements  461 22q12.1q12.2 Deletion. The clinical picture in this rare deletion includes the notable observations of cleft palate and susceptibility to schwannoma (Breckpot et al. 2016). The MN1 gene may be the basis of the cleft palate, while the nervous system tumors are consequential upon loss of the NF2 gene or its promoter. Other traits include intellectual disability, in some with severe language deficiency, and facial dysmorphism, of which micrognathia is one feature. Breakpoints are non-recurrent. De novo inheritance is seen in all cases in which parental testing has been done. 22q13.3 Deletion: Phelan-McDermid Syndrome. A particular trait of this well-known condition is a failure to develop expressive language, and high pain tolerance is also notable; the physical phenotype comprises rather “soft” dysmorphism, if any. Psychosis may compound the neuropsychiatric picture (Colijn 2024). Seizures happen in near one-half (Levy et al. 2025). Most deletions are terminal (with telomere healing), while a few are interstitial; in scarcely any is the proximal breakpoint recurrent. Size varies from 122 kb to 9 Mb, such that cytogenetic nomenclature can range from del(22)(q13.31q13.33) to del(22)(q13.33) alone (Bonaglia et al. 2011). The key locus is SHANK3, the antepenultimate gene on the chromosome, whose role involves crucial interaction with a neuronal glutamate receptor (Vicidomini et al. 2017). Ricciardello et al. (2021) dissect out which other loci within the deleted segment contribute to which aspect of the clinical picture. SHANK3 deletion is fully penetrant (Goh et al. 2025). Recurrence due to parental gonadal mosaicism for the deletion is very rare but not unknown (Tabolacci et al. 2005). A balanced parental translocation is slightly less rare and should always be checked for. However, almost all cases arise de novo. The deletion may be in the form of a ring chromosome (p. 304). Duplication. The countertype of Phelan-McDermid syndrome presents with developmental delay, very limited language acquisition, and mild dysmorphism (Okamoto et al. 2007). SHANK3 is, as with the deletion, the relevant locus. Both de novo and familial cases due to a parental translocation are known. Mother-to-child transmission is recorded in Granocchio et al. (2024), the mother described as having a speech disorder but without intellectual disability. Large deletions that include SHANK3 and its surrounding regions are likely fully penetrant (Goh et al. 2025). Triplication. A few examples of trp have been included in the dup listing above. With very few cases reported, an empiric recurrence risk cannot usefully be determined for the typical sporadic case. Parental gonadal mosaicism remains a possibility (Eckel et al. 2006). Rare instances are reported of a non-pathogenic duplication in a parent leading to a pathogenic triplication in a child (López-Expósito et al. 2008). SMALL SUPERNUMERARY MARKER CHROMOSOMES: 47,+mar A small (smaller than a chromosome 20) supernumerary chromosome, the identity of which could not readily (or at all) be determined on classical methodology, has been referred to as a “marker” (mar). The expression “mar” is becoming somewhat outdated, as molecular methodology now allows the supernumerary chromosome to be identified

462  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY precisely, and in recurring examples, a specific syndromal status may be assigned (Jafari-Ghahfarokhi et al. 2015). Most are derived from an acrocentric chromosome. A number have been listed above: the 11p11.2 neocentromeric sSMC; the inv dup or isodicentric 15 (pathogenic and non-pathogenic); the 18p sSMC, whose centromere is of 13/21 material; and the inv dup(22)(q11.21) or der(22)(q11.21) sSMC of cat eye syndrome. Some small isochromosomes (next section) have been referred to as sSMCs. If the parental blood karyotypes are normal, parental mosaicism is unlikely but not completely excluded. The load in gametes may be less than seen on peripheral blood, at least in the case of the male (Cotter et al. 2000; Oracova et al. 2009). The dup(22) (q11.21) of cat eye syndrome (above) is exceptional in that mosaicism, which can be familial, is commonly observed. ISOCHROMOSOMES (NON-ACROCENTRIC) We deal in detail with isochromosomes in relation to their discovery at prenatal diagnosis in Chapter 22, and including the following derived from a non-acrocentric26 chromosome: 47,+i(5p), 47,+i(8p), 47,+i(9p), 47,+i(10p), 47,+i(12p), 47,+i(18p), 47,+i(18q), and 46,i(20q). A couple having had a child with an isochromosome, for a chromosome other than an acrocentric, can generally be given encouraging advice, especially if the child is mosaic. The major mechanisms of generation are considered to operate either at meiosis II or post-zygotically, and in either case no discernibly increased risk of recurrence would be implied, albeit that a premeiotic mechanism may apply in some (de Ravel et al. 2004; Rittinger et al. 2015). Very rare exceptions exist: for example, the history in Boyle et al. (2001) of two half-sisters both with 47,XX,i(18p), their mother an inferred gonadal mosaic. 26 As for the acrocentric-derived isochromosome (Chapter 7), a post-zygotic mechanism may be the rule, and thus of optimistic outlook for a subsequent pregnancy (Riegel et al. 2006).

15 SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT THERE ARE FOUR MAJOR sex chromosome abnormalities1 due to complete aneuploidy. Otherwise unassisted, infertility is practically inevitable in XXY Klinefelter syndrome (KS) and 45,X Turner syndrome (TS). The other two conditions, XXX and XYY, apparently have little effect on fertility; furthermore, they are not discernibly associated with any increased risk for chromosomally abnormal offspring. Mosaic forms need to be considered on their own merits, albeit that infertility is often the case with Klinefelter and Turner mosaicism, at least in those cases coming to clinical attention. As for recurrence, to parents who have had a child with one of these aneuploidies, typically the risks are low. Structural rearrangement of X or Y leads to a partial imbalance. This may involve a large amount of chromatin, such as in substantial deletions, a ring, or an isochromosome. Or, deletion or duplication may involve only a small segment (of kilobase or a few megabases in extent). Some of the latter may have little effect upon fertility, and reproductive risk assessment becomes of practical importance. The recurrence risks vary. BIOLOGY We need briefly to consider why X chromosome aneuploidy can be associated with so little phenotypic abnormality, compared with autosomal imbalance. The important factor is dosage compensation. Only one X in each cell needs to be fully active. Thus, potentially detrimental effects of an X chromosomal imbalance are mitigated (although not exactly canceled out) by inactivating a supernumerary or abnormal X, or by not inactivating a sole remaining X, as the case may be. The conceptus with an X chromosome complement in excess of the normal 46,XX or 46,XY accommodates to this imbalance by inactivating any additional X chromosome— or, as Migeon (2007) emphasizes, by maintaining just one X in the active state in each cell. This is nearly successful in the 47,XXX female and the 47,XXY male, in each of whom there is apparently normal in utero survival and a relatively mild post-natal phenotype. The fact that some loci are not subject to inactivation and may therefore continue to function in the X disomic (XXY), trisomic (XXX), or even quintasomic (49,XXXXX) states, is presumably the predominant reason for the phenotypic abnormalities associated with these karyotypes. 1 The student of history will enjoy Malcolm Ferguson-Smith’s tribute to Victor McKusick, the founding Father of Medical Genetics, on the occasion of the centenary of his birth, which relates some of the early history of cytogenetics in the 1950s and 60s, and with a particular focus on the sex chromosome disorders (Ferguson-Smith, 2021). 464  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY In females with abnormal X chromosomes, the pattern of X-inactivation is usually nonrandom,2 particularly when the imbalance due to the abnormality is “large.” In the 46,X,abn(X) karyotype, with one normal X and one abnormal X—an “abn(X),” as we write it here—the abnormal X is characteristically the inactive one. However, if the abnormality is a small deletion or duplication, the inactivation pattern can be random. In the case of the X-autosome balanced translocation heterozygote, the normal X is usually, although not invariably, inactive (Chapter 6). Laboratory Test for X-Inactivation. Analyzing the pattern of X chromosome methylation with molecular methodology shows whether inactivation is random or nonrandom. A useful assay is methylation-specific polymerase chain reaction based on the androgen receptor gene, located at Xq13 (or any other gene with a convenient polymorphism). A highly skewed pattern, with one X mostly methylated and the other mostly not, is indicative of nonrandom inactivation (Kubota et al. 1999). While this test is performed routinely on a blood sample, there are grounds for believing that the assay result may, at least to some extent, fairly represent the state in other body tissues (Bittel et al. 2008). The former tests of Barr body and late-labeling BrdU analysis are of historic interest; both assays still provide a nice visual illustration of the concept of X-inactivation (Figures 15–1 and 15–2). Y chromosome imbalance is similarly mild in its effects, but for a quite different reason, namely the very low gene carriage of this chromosome and the very narrow scope of activity—male gonadal development—of most of these genes. As discussed elsewhere, the SRY gene on the Y short arm has the critical role of directing the gonad to form as a testis; other loci, most notably the DAZ family of genes within the AZFc region on the long arm, determine aspects of spermatogenesis (Krausz and Casamonti 2017). Complete Aneuploidy DETAILS OF MEIOTIC BEHAVIOR Meiosis proceeds differently in persons with each of the various sex chromosome abnormalities, and each warrants separate consideration. XXX On theoretical grounds, one might have expected the three X chromosomes to display 2:1 segregation, with the production of equal numbers of X and XX ova. But this is not the case. No discernible increased risk for chromosomally abnormal offspring of these women has been demonstrated. In the extensive review of Otter et al. (2010), only one case had ever been reported of an XXX mother having had an XXX daughter. Apparently only normal ova with a single X are regularly produced. It may be that the extra X is lost before meiosis occurs (Neri 1984), with meiosis then proceeding as in the normal XX female. Fertility may, however, be affected, due to premature ovarian insufficiency (Tartaglia et al. 2010). 2 Or, more accurately, random X-inactivation is followed by selection against cells expressing the abnormal X.

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  465 XXY AND XXY MOSAIC STATES In the germ cells of the XXY fetus, the second X chromosome escapes X-inactivation, and the consequent dysregulation of X-linked gene dosage leads to arrest of germ cells at an early stage (Lu et al. 2024). When present, all spermatogonia in non-mosaic KS patients have a 46,XY karyotype, suggesting that these germ cells have lost the extra X chromosome during embryonic, fetal, or neonatal life (Gül et al. 2024). Barring medical intervention, infertility is almost inevitable in non-mosaic Klinefelter syndrome, although some remarkable exceptions exist (Terzoli et al. 1992); undetected XY/XXY mosaicism could account for some of these cases. Van Saen et al. (2012) list three subgroups of adult men with KS, according to findings on testicular biopsy: one group in which mature spermatozoa can be retrieved by testicular extraction, a group with no testicular spermatozoa but in which germ cells are present, and a third group with no germ cells at all. Several workers have karyotyped sperm from XXY men, and all find an excess, albeit not a large one, of 24,XX and 24,XY sperm. Possibly, the abnormal gonadal environment may of itself predispose to gonosomal nondisjunction in the XY tissue; and from that stance, autosomal segregation may also be vulnerable, as indeed sperm studies indicate. There is a higher rate of disomy 21 on sperm studies from KS men, 6.2% versus Figure 15–1.  Buccal mucosal cells from (a) a 45,X female, with no Barr body present; (b) a 46,XX female showing the inactive X as a Barr body; (c) a 47,XXX female showing two Barr bodies; and (d) a 48,XXXX female with three Barr bodies. 466  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY 0.4% in controls (Hennebicq et al. 2001; Bergère et al. 2002). As for XY/XXY mosaicism, Samplaski et al. (2014) showed better androgenization on a number of criteria in these men, including a higher rate of men having sperm in the ejaculate (half, compared to only 4% in non-mosaic XXY). XYY The clinical observation is that XYY men have no discernible increase in risk to have children with a sex chromosome aneuploidy (and XYY or XXY would have been the theoretical risk outcomes from an XYY trivalent at meiosis), and in the UK Biobank study, men with XYY appeared to have normal reproductive function (Zhao et al. 2022). A true increased risk of a fraction of a percent could be distinguished only with great difficulty, when the background population risk is of a similar order of magnitude. The proposed model is that the additional Y chromosome is randomly lost in a germ line precursor, followed by selection in favor of euploid clones due to these having a proliferative advantage (Evans et al. 1970). On laboratory study, XYY spermatocytes proceeding through Figure 15–2.  Partial metaphases showing X-inactivation: (a) a normal X chromosome, (b) an isochromosome of X long arm, (c) an X with a short arm deletion, and (d) a ring X. BrdU had been added for the last 6 hours of culturing. The inactive chromosomes, replicating at this late time in the cell cycle, incorporate BrdU extensively, and thus are palely stained. The active X stains darkly. SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  467 meiosis encounter checkpoints that may lead to elimination of most of the abnormal forms (Milazzo et al. 2006), but nevertheless, some men may have a small increased fraction of 24,YY and 24,XY spermatozoa in the ejaculate and in some, also of autosomal disomies. A distinction may be drawn between XYY men presenting with infertility and those whose fertility is intact, with the sperm aneuploidy rate somewhat higher in the former. Rodrigo et al. (2010) studied the cytogenetics of the preimplantation embryo from five infertile XYY men having had IVF, and identified a significant increase in chromosomally abnormal embryos compared to those of fertile XY controls; however, when compared to embryos of XY males with abnormal spermatogenesis, the proportion of aneuploid embryos was similar. Therefore, the increase in aneuploidy may be a nonspecific feature of abnormal spermatogenesis rather than a direct consequence of the XYY state per se. A unifying mechanism for infertility in XYY men is yet to be identified. In one man with azoöspermia having come to testicular biopsy, both Y chromosomes were present and in synapsis in all meiotic spermatocytes, and in association with—but not synapsing with—the X chromosome; this configuration may possibly have been the cause of spermatogenic arrest (Wu et al. 2016). A different picture was evident in the azoöspermic XYY man studied by Sciurano et al. (2019): At testicular biopsy, 98% of primary spermatocytes were XY, and the authors hypothesized that the XYY Sertoli cells may have contributed to spermatogenesis failure. It may be that in some cases the XYY is an incidental finding, and the male infertility has an alternative explanation. NON-MOSAIC 45,X TURNER SYNDROME Turner syndrome is not uncommon. From a US-wide study 2000–2017, the prevalence was ascertained to be 3.2 per 10,000 female livebirths, or 1 in 3,125 girl babies3 (Martin-Giacalone et al. 2023); and when diagnoses after the first year of life are included, the prevalence increases to 1 in 2,000 (Gravholt et al. 2024). The great majority of women with 45,X TS are infertile and do not spontaneously menstruate or develop secondary sexual characteristics. The ovaries initially appear to be normal but typically begin to degenerate in mid–fetal life. Oöcytes undergo apoptosis and disappear at an accelerated rate and, in most cases, are gone by the age of two years: “The menopause occurs before the menarche” (Federman 1987; Modi et al. 2003). It may be that a 45,X oöcyte could not proceed through meiosis I, given that the sex chromosome has no homolog with which to pair. In one series of 18 45,X girls, none had ovarian follicles on biopsy in childhood or teen age (Borgström et al. 2009). Completed pregnancy in women with an apparent 45,X karyotype is very rare. In a Danish study based on a national TS register, none of 200 45,X women achieved a natural pregnancy (one had twins by ovum donation) (Birkebaek et al. 2002). In a large French study, coming from seven endocrine units nationwide, 480 adult women with TS were recruited (Bernard et al. 2016). Of the 181 with monosomy X, only two had achieved pregnancy, although presumably not all had been attempting motherhood (Table 15–1; other chromosomal forms of TS also listed here). Sybert (2005) was able to record a total of 18 45,X women having had 42 pregnancies, and observed that the 3 The most commonly observed congenital malformation in this cohort was coarctation of the aorta; and the 5-year survivability (excluding cases with hypoplastic left heart syndrome) was 95%.

468  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY risks for spontaneous abortion, sex chromosome aneuploidy, and trisomy 21 were all elevated. Only 17 of the pregnancies proceeded to live birth, including two cases of 45,X and one of trisomy 21. What is the explanation for fertility in these rare cases? An obvious point to consider is gonadal mosaicism, with a 46,XX cell line in the ovary. This has often been suggested, but rarely proven (Birkebaek et al. 2002). Jacobs et al. (1997) undertook a systematic search in 84 subjects with TS whose standard blood karyotype was 45,X with molecular testing of blood and of a second tissue (buccal cells), and found only two cases of X/ XX mosaicism. One very thorough study is that reported in Magee et al. (1998b) concerning a 45,X woman who had had seven pregnancies: five miscarrying, one producing a healthy male, and the last terminated following demonstration of fetal cystic hygroma and a 45,X karyotype on amniocentesis. Biopsies of skin, uterus, and ovary at subsequent gynecological surgery all gave a 45,X karyotype, but molecular testing showed two alleles in ovarian DNA, indicating the presence of occult 46,XX tissue. A similar investigation is reported in Sugawara et al. (2013) of a woman 45,X on standard blood karyotype, but other XX and XXX cell lines seen when 500 cells were analyzed and skin and cumulus tissue studied (and inexplicably, even 4/260 cumulus cells were XY). It is difficult to know, but fair to consider, whether such subtly occult mosaicism might be the explanation for the very rare instances of true natural fertility in (apparently) non-mosaic 45,X TS. X/XX, X/XX/XXX, AND X/XXX MOSAICISM TURNER SYNDROME The relative fractions of the various karyotypes—at least as may be judged on standard peripheral blood analysis—are listed in Tables 15–2 and 15–3 and illustrated in Figure 15–3. In the X/XX state, some gonadal function is likely to be retained if the 46,XX fraction reaches 10%, as evidenced by a spontaneous menarche (Castronovo et al. 2014). Among the TS categories, the X/XX karyotype is associated with the best chance for pregnancy, natural or IVF-assisted. In the cohort of Calanchini et al. (2020) 11/23 Table 15–1.  Turner Syndrome Reproductive Outcomes CHARACTERISTICS PREGNANT TS PATIENTS (N = 27) NON-PREGNANT TS PATIENTS (N = 453) Age at diagnosis* 20 (0–45) 10 (0–64) 45,X 2/27 (7%) 179/453 (40%) 45,X/46,XX 19/27 (70%) 111/453 (25%) Mosaicism with Y 1/27 (4%) 20/453 (4%) Mosaicism with ring X 2/27 (7%) 30/453 (7%) Isochromosome X 1/27 (4%) 27/453 (6%) Other 2/27 (7%) 86/453 (19%) Spontaneous menarche 25/27 (93%) 70/453 (15%) Age at first pregnancy (years) 27.5 (18–38) n/a Delay to conceive (months) 6 (0–84) n/a Notes: These data are from 480 adult women with Turner Syndrome. *Years, median and range. n/a = not applicable. TS = Turner syndrome. Source: From V Bernard et al., Spontaneous fertility and pregnancy outcomes amongst 480 women with Turner syndrome, Hum Reprod 31:782–788, 2016. SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  469 Table 15–2.  Sex Chromosomal Karyotypes, Associated and Not Associated, with Turner Syndrome FREQUENCY (%) DESCRIPTION KARYOTYPES ASSOCIATED WITH TURNER SYNDROME 45,X 40%–50% Monosomy X 45,X/46,XX* 15%–25% Mosaicism with 46,XX 45,X/47,XXX 45,X/46,XX/47,XXX 3 Mosaicism with 47,XXX 45,X/46,XY 10%–12% Mosaicism with 46,XY 45,X/46,X(r)X Rare Ring X chromosome 46, X,i(Xq) 46,X,idic(Xp) 15% Isochromosome Xq Isodicentric Xp 46,XX,del(p11) Proximal deletion of Xp X-autosome translocation, unbalanced Rare Various KARYOTYPES NOT ASSOCIATED WITH TURNER SYNDROME 46,XX,del(p22.3) Distal deletion Xp22.3 (SHOX) 46,XX,del(q24) Premature ovarian insufficiency 46,X,idic(X)(q24) Isodicentric Xq24 Notes: *A diagnosis of Turner syndrome is usually not considered in women with less than 5% 45,X cells. Source: From CH Gravholt et al., Clinical practice guidelines for the care of girls and women with Turner syndrome. Eur J Endocrinol 190:G53–G151, 2024. Table 15–3.  Karyotype-Phenotype Associations in Turner Syndrome KARYOTYPE PHENOTYPE 45,X Higher frequency of comorbidities and a higher mortality compared to individuals with other TS karyotypes. 45,X/46,XX Milder phenotype with left-sided congenital heart defects, obesity, and hypertension being less frequent, age at menarche being near-normal, more likely to experience spontaneous menarche and pregnancies. 45,X/47,XXX Milder external and cardiovascular phenotype compared to 45,X, but neurodevelopmental disabilities and mental health domains remaining a concern. i(Xq) Intermediate severity of left-sided congenital heart defects and spontaneous menarche, and a lower incidence of aortic coarctation. 45,X/46,XY Lowest incidence of autoimmune thyroid disease and severe hearing loss, and a low incidence of aortic coarctation. (r)X Without functional loss of XIST, possible increased risk of metabolic syndrome, low risk of bicuspid aortic valve. With functional loss of XIST, a more severe cognitive phenotype. Source: From CH Gravholt et al. (2024) as above. 470  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY women with 45,X mosaicism achieved a spontaneous pregnancy4 compared to just 2/62 45,X women. Across both categories, all women who achieved spontaneous pregnancy had a history of spontaneous menarche and regular menstruation. Most oöcytes appear to have arisen from 46,XX cells: in the series of Peek et al. (2019), 91% of oöcytes had two X chromosomes despite supporting granulosa cells being 45,X. The survival of 45,X cells in the gonad may be enabled by support from surrounding 46,XX oögonia; such a 45,X cell might, in theory, be able to produce a nullisomic X egg, if its sole X is sequestered to the polar body at meiosis I. This could be the basis of the observation in Uehara et al. (1999b) of a woman with 45,X/46,XX having had three monosomic X pregnancies, all showing fetal hydrops; she also had a normal son. Pubertal development may often be apparently normal in the 45,X/47,XXX case (Lim et al. 2017a). The X/XXX patient in Bouchlariotou et al. (2011) had two normal children, and one (unkaryotyped) deceased, severely growth-retarded baby, while Sahinturk et al. Figure 15–3.  Some sex chromosome complements: (a) normal female XX and normal male XY; (b) X and XXX females; (c) XXY and XYY males; (d and e) abnormal chromosomes from females with a ring X, an isochromosome of X long arm, an X short arm deletion, and an X long arm deletion. 4 In contrast, fertility appears to be minimally impacted in 45,X/46,XX women ascertained from the general population with <20% of 45,X cells (Tuke et al. 2019).

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  471 (2015) report a woman with 45,X[8]‌/47,XXX[12] who had had five miscarriages and one healthy 46,XX daughter. XY/X MOSAICISM TURNER SYNDROME Approximately 10% of women with TS have a mosaic karyotype containing Y chromosome material. The clinical spectrum of patients with 45,X/46,XY mosaicism is wide and includes women with TS, patients with ambiguous genitalia, and infertile males (Guzewicz et al. 2021). These individuals are at risk of gonadoblastoma, a benign tumor that arises in dysgenetic gonads and is subject to malignant transformation. Karila et al. (2022) studied 70 women with 45,X/46,XY TS and identified nine with gonadoblastoma (13%), of which two had undergone malignant transformation. A recommendation for gonadectomy depends upon the nature of the Y: whether it is an intact, or a structurally abnormal chromosome. If intact, gonad removal is advised; if a rearranged Y, careful monitoring can reasonably be offered. The variability of phenotype according to the degree of mosaicism is well illustrated in the report of Lespinasse et al. (1998), who studied monozygous (but not identical) triplets with 45,X/46,XX mosaicism. One child with typical TS had only 6% 45,X cells on blood karyotyping but 99% on fibroblast analysis. One sister with only mild features to suggest TS had 43% of fibroblasts with 45,X, and the third triplet, of normal phenotype, had just 3%. Presumably, the mosaicism existed from a very early stage, and the three-way division of the 45,X/46,XX early conceptus happened to cut across an asymmetric disposition of normal/monosomic cells. MOSAIC LOSS OF THE X CHROMOSOME (MLOX) IN PHENOTYPICALLY NORMAL WOMEN This category is to be distinguished from that of TS due to 45,X/46,XX mosaicism discussed above, and it is supposed to be without reproductive consequence. Advice from the European Cytogeneticists Association a propos is presented on p. 614. Mosaic loss of the X chromosome (mLOX) to give an occasional 45,X cell is a normal characteristic of aging in the 46,XX female (Ziętkiewicz et al. 2009). The phenomenon may reflect variation in a number of cell-cycle factors, similarly to but less markedly than the male equivalent, mosaic loss of the Y, as discussed below (Wright et al. 2017). Russell et al. (2007) reviewed data from a large number of women having had a peripheral blood cytogenetic analysis, and correlated the degree of mLOX with age, documenting a clear association. Up to age 30 years, 1% or less of cells showed mLOX, but rising to an average 2%, 3%, and 5% at median ages of 40, 50, and 65 years respectively. Liu et al. (2024a) analyzed genomic data from ~ 900,000 women participating in various biobanks and detected mLOX in 12%, with a median mLOX fraction of 2%. The frequency of mLOX increased with age, being 3% below 40 years and 35% after 80 years (Figure 15–4). Interestingly, smokers overall had no increased risk of mLOX, but among those who did have mLOX, smokers had a greater proportion of affected cells. mLOX fractions of >10% were associated with a near twofold increased risk of leukemia. Liu et al. propose that mLOX is a polygenic trait, the genes thus implicated being involved in chromosome segregation and cancer predisposition. 45,X/46,XY AND 45,X/47,XYY MOSAICISM IN THE MALE X/XY mosaicism may be diagnosed at birth due to genital abnormality, or be detected later in life in males presenting with hypogonadism and infertility with oligo/azoöspermia; in 472  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY some, the Y chromosome has a deletion at Yq11 (Cui et al. 2007). The maleness presumably reflects the fact that the gonad contained XY cells with a functioning SRY gene, which were able to induce effective testicular differentiation with consequent androgenizing capacity. Reddy and Sulcova (1998) did testicular biopsy on an X/XY man and demonstrated absence of spermatogenesis; about half of the Sertoli supporting cells showed a Y-signal on FISH. Ljubicic et al. (2021) reported on a series of 63 adolescent and adult males with 45,X/46,XY mosaicism, slightly more than half of whom had presented a genital phenotype. Average final adult height was 160cm, but 80% underwent spontaneous puberty. Of those in whom gonadal histology was evaluated, germ cells were detected in 42%, and neoplasia in situ was found in 11%. Newberg et al. (1998) studied sperm from one X[10]/XY[90] man with moderate oligoasthenoteratozoöspermia and showed a two- to threefold rate for XY disomy and 18 disomy in sperm (using 18 as a representative autosome). In contrast, a man with 45,X/47,XYY mosaicism reported in Dale et al. (2002) showed normal gonosomal complements in 99.9% of sperm. He had presented with infertility due to oligospermia; a normal 46,XY pregnancy was achieved with intracytoplasmic sperm injection (ICSI). A meiotic mechanism in these men may favor the production of normal sperm (Ren et al. 2015). Medical and neurodevelopmental manifestations of TS, such as short stature and cardiovascular defects, may be present (Dumeige et al. 2018; Alkhunaizi et al. 2024), and in a registry study, mortality rates were doubled compared to XY males (Stochholm et al. 2024). Mosaic Loss of the Y (mLOY) in Phenotypically Normal Men.  A curious fact is this: Mosaic loss of the Y (mLOY) is the most common chromosome abnormality in the post-natal population. mLOY, when detected on a sample of peripheral blood, is a form of “clonal hematopoiesis,” with loss of the Y appearing to confer a fitness advantage to the cell. Long considered merely to be an incidental observation more prevalent in older men, in more recent years it has been appreciated as having an association with increased morbidity and mortality (Forsberg 2017). The effect is more marked in smokers (Figure 15–5). It may be that mLOY is an epiphenomenon, reflecting an underlying basis in variation in a number of cell cycle factors (Wright et al. 2017); an attractive candidate Figure 15–4.  Prevalence of Mosaic Loss in Women of the X Chromosome (mLOX) by Age Notes: mLOX levels are derived from eight biobanks, as detected from genomic data. Source: From data in A Liu et al., Genetic drivers and cellular selection of female mosaic X chromosome loss, Nature 631:134–141, 2024.

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  473 among these is MAD1L1, which halts the cell cycle until the chromatids are bi-oriented at the equator. This susceptibility could lead to vulnerability of the Y during mitosis in a rapidly-dividing tissue such as blood, the LOY line thereafter having unimpaired survival, as hematogenous tissue has little or no need of Y-based genes. More importantly, the putative cell-cycle susceptibility could predispose to certain diseases, including cancer, atheroma, and Alzheimer disease (Thompson et al. 2019; Vermeulen et al. 2022; García-González et al. 2023). It remains possible that there is a direct causal impact of Y chromosome loss on men’s health, mediated through the white blood cells and the immune system (Sano et al. 2023). The practical value to which this evolving understanding may be put is yet to become clear. SEX CHROMOSOME POLYSOMY The 48,XXXX female characteristically has diminished ovarian function, and fertility in pure XXXX is on record in only one case (ascertained through a Down syndrome child) (Kara et al. 2014). Sterility is presumably invariable in XXXY and XXYY males, who have a further sex chromosome superadded upon the Klinefelter karyotype (Linden et al. 1995). Recurrence to Parents Having Had a Child with a Sex Chromosome Aneuploidy XXY (KLINEFELTER SYNDROME), XXX, AND XYY These aneuploidies occur at roughly similar frequencies, about one per 1,000 of the appropriate sex. About 75% of XXX and 40% of XXY KS is due to a maternal meiotic error, and in three-fourths of each of these it is the first meiotic (MI) division that is involved, this MI group showing a maternal-age effect.5 It is noteworthy that almost half of KS results from a paternal MI error (MacDonald et al. 1994). Fathers of paternally Figure 15–5.  Mosaic loss of a Y chromosome (mLOY) on peripheral blood in older men, and according to smoking status (non, former, current). The y axis shows the proportions of men in whom X/XY is seen, from 2% of nonsmokers age under 65 years to 20% of smokers age 75 years or older. Numbers of subjects in each category are shown under the x axis. Source: From W Zhou et al., Mosaic loss of chromosome Y is associated with common variation near TCL1A, Nature Genet 48: 563–568, 2016. Courtesy SJ Chanock, and with the permission of Springer Nature. 5 For convenience, detailed age-related sex chromosome risk data are included in Chapter 13, Table 13–9, alongside equivalent autosomal risk data. 474  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY originating KS may have marginally elevated levels of disomic XY sperm in comparison with fathers of maternally originating cases, possibly reflecting an inherent tendency among a small minority of these men to produce aneuploid sperm (Eskenazi et al. 2002). Three instances are recorded of KS among non-twin brothers, a number that is surely no greater than would be expected by random chance. In one pair, the karyotype in both brothers reflected a paternal meiosis I error (Woods et al. 1997), but in another, the supernumerary chromosomes were inherited from different parents (Kim et al. 2019). Manifestly, XYY of meiotic origin must be due to a paternal error at MII. All three sex chromosomes aneuploidies can have a post-zygotic mitotic generation, which may present as mosaicism. 45,X TURNER SYNDROME In three-fourths of TS, it is the paternal X chromosome that is absent (Uematsu et al. 2002). Mostly, the error is a meiotic one and resides in paternal gametogenesis, possibly reflecting an absence of pairing along most of the X-Y bivalent with a consequential vulnerability in the process of disjunction (Jacobs et al. 1997). Fathers of non-mosaic 45,Xm TS girls may have a marginally increased risk to produce sperm nullisomic for a sex chromosome. Martínez-Pasarell et al. (1999) analyzed sperm from four fathers and eight controls, and there was a slight increase in nullisomic sperm (0.48%) and 24,XY sperm (0.22%) in the fathers compared to the fractions in controls (0.32% and 0.11%, respectively). This might suggest that some fathers of non-mosaic 45,Xm TS girls have a slight proneness to produce sperm nullisomic for a sex chromosome; but if so, the near-absence of recurrences would point to a very minor influence. An alternative explanation is that the loss occurred post-zygotically, and the “45,X” child is actually a 45,X/46,XX mosaic with a very low proportion of XX cells; but this is apparently an uncommon event (Jacobs et al. 1997). Wiktor and Van Dyke (2005) describe 22 patients with apparently non-mosaic 45,X in whom, upon further study, three had a minor XX cell line, and 19 were apparently pure 45,X; no XY cell lines were seen. To the contrary, Uematsu et al. (2002) suggest that most TS may actually be due to a structurally abnormal gonosome (X or Y) having been generated in paternal meiosis, with a 46,X,abn(X) conception resulting and subsequent mitotic loss of the abn(X) leaving a 45,X karyotype. In a Brazilian cohort of 74 cases of TS, cryptic Y chromosome material was detected in 2.7% (Bispo et al. 2014). These several theories notwithstanding, the observational data point to a very low recurrence risk. In the literature review of Kher et al. (1994), they could find only one instance of 45,X recurrence in sisters. From the Birth Defects Register of Victoria, Australia over the period 2005–2020, of 294 prenatal diagnoses of 45,X, in none had the indication been of a previous chromosome abnormality (Loughry et al. 2023). In the case of a post-zygotic origin, if it could be presumed to have been an event that occurred at random in a single mitosis in the early embryo, the risk of recurrence would not be raised at all. Kher and colleagues did, however, report a unique family with occurrence of 45,X/ 46,XX in sisters. RARE POLYSOMIES Polysomies such as XXXX, XXYY, XYYY, XXXY, XXXXX, and XXXXY are very rare. Successive nondisjunctions in one parent, the other contributing a single sex chromosome, is the mechanism in most if not all (Hassold et al. 1990; Deng et al. 1991). Apart from the extraordinary circumstance of (hypothetically) a familial tendency to

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  475 mosaicism, these polysomies arise sporadically (Bergemann 1962; Kher et al. 1994). Rare reports of coincidence with some other aneuploidy in the family may more likely reflect chance than a causal link (Court Brown et al. 1969). In the particular case of pentasomy X, no maternal-age effect is observed (Pirollo et al. 2015). GENETIC COUNSELING Persons with a Sex Chromosome Aneuploidy XXX XXX mothers have no discernibly increased risk of bearing chromosomally abnormal children. A theoretical increased risk for children with an X aneuploidy has not been demonstrated in practice. Despite reports of chromosomally abnormal children born to XXX women, it should be emphasized— as did Dewhurst and Neri in 1978 and 1984, respectively—that when biased ascertainment is taken into account, no excess of abnormal offspring has been reported. Near silence subsequently in the literature on this issue suggests at least a considerable rarity of X-aneuploid pregnancy outcomes; one such case, an XXX daughter of an XXX mother, is mentioned in passing in Haverty et al. (2004). A possibility of premature ovarian insufficiency with 47,XXX can be brought to the attention of these women, which may assist in decisions about the timing of childbearing. Maternal 47,XXX is a cause of false positive NIPT results for fetal XXX (Tang et al. 2024). XXY Hardly ever will these men father children without recourse to testicular sperm extraction and IVF. This requires the surgical opening of the testis with microdissection of seminiferous tubules under the operating microscope, and on-site analysis by an embryologist, for the presence of sperm; the procedure can be undertaken on the day before programmed oöcyte retrieval from the female partner, or earlier if the sperm are to be frozen. The few single sperm obtained are injected into the egg (ICSI).6 The success rate is variable; although sperm are retrieved in 30%–70% of KS men, only 10% of those who start treatment succeed in having their own biological children (Vloeberghs et al. 2018). Testicular sampling and storage of spermatogonial stem cells at the onset of puberty is feasible (Sá et al. 2023; Kang et al. 2024). Kang et al. identified the highest sperm retrieval rates in 20–29 year olds (71%) compared with 53% in adolescents and just 13% in those >40 years. These authors conclude that sperm retrieval can be deferred until young adulthood. Gamete donor from a brother or father is a means to have a child with shared genetic heritage. The chromosomal outcome for the child conceived from an XXY man appears very promising, with only one case known of fetal XXY in more than 100 pregnancies (Lejeune et al. 2014). Thus, one may propose an approximate risk figure of 1% for a sex-chromosomal abnormality in the child. Tong et al. (2021) report their experience 6 It is an intriguing thought that in those cases proceeding to fatherhood through intervention with assisted reproductive technology, the situation may be presented of the homogametic sex being the one to provide the greater quantum of gametes, albeit by a small margin—an extraordinary contrast from the typical vast imbalance due to the heterogametic male of the species. 476  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY of IVF and PGT in men with KS from whom spermatozoa could be obtained by testicular microdissection. Eighteen couples underwent a total of 22 IVF cycles from which 45 blastocysts were obtained (on average, two blastocysts per IVF cycle). PGT testing showed that 64% were euploid, 18% aneuploid, 18% mosaic aneuploid, and no sex chromosome abnormalities were detected. These aneuploidy and mosaic rates are comparable to other age-matched patients seeking ART. XYY To our knowledge, there is no report of a discernibly increased risk for the XYY male to have chromosomally abnormal children. A slight increase in gonosomal imbalances in sperm (see above, and Rives et al. 2003) might nevertheless lead some to choose prenatal testing, and NIPT provides a suitable option. The risk might, in theory, be greater in those XYY men who need fertility treatment (as some do; Kim et al. 2013) and for whom PGT might therefore be offered as an “add-on” to the IVF process. NON-MOSAIC 45,X TURNER SYNDROME Infertility is almost always the case. However, successful pregnancy outcomes from natural conception, although very few in number, are on record (Bernard et al. 2016). A 45,X woman who has spontaneous menses may possibly be fertile. Endocrine and ultrasound studies may clarify whether ovulation is occurring or likely to occur (Paoloni-Giacobino et al. 2000a). Any period of fertility is likely to be short-lived; thus, a woman with 45,X TS who wishes to have a child should not delay unduly in trying for a pregnancy. Current guidelines do not support fertility preservation using ovarian tissue storage prior to menarche (Gravholt et al. 2024). An increased risk for miscarriage, X aneuploidy, and autosomal trisomy is to be noted (Sybert 2005), as well as a higher risk of maternal and fetal complications. (As discussed above, occult mosaicism may in fact be the basis of retained ovarian function in apparent non-mosaic TS.) Gametes donated from a mother or a sister would, in principle, offer the opportunity to have a child with a shared genetic inheritance (see below). MOSAIC 45,X TURNER SYNDROME Women with 45,X mosaicism and a TS phenotype presumably carry the 45,X cell line in much of the soma and gonad. Categories include X/XX, X/XXX, and X/XX/XXX. Ovarian function is often intact, although early menopause is common (Blair et al. 2001; Sybert 2005; Lau et al. 2009); normal cells in the gonad may provide support for monosomic cells that otherwise would not have survived. As adolescents, a few may have ovarian tissue suitable for biopsy and storage for possible future use, as mentioned above with respect to non-mosaic TS (Talaulikar et al. 2019). There is apparently a small increased risk for X monosomy in a child of hers, and this is consonant with theoretical expectation; autosomal trisomy is also seen (Sybert 2005; Bernard et al. 2016). The risk for miscarriage is increased; it is of interest that the miscarriage rate is greater with natural conception than in pregnancy due to donation of (presumably normal) eggs (Doğer et al. 2015; Bernard et al. 2016). In a large French study, most pregnancies that continued through to live birth produced phenotypically normal children: of 30 newborns, 13 were normal boys, 15 normal girls, and two girls had an X chromosome abnormality presumably related to the maternal karyotype (Bernard et al. 2016). Ovum Donation, Mosaic and Non-mosaic Turner Syndrome.  For the great majority of TS patients, mosaic and non-mosaic, who cannot make their own eggs, ovum

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  477 donation with IVF may be one route to achieve childbearing (Hovatta 2012). Foudila et al. (1999) report their experience with 18 women with TS, and although the rates of embryo transfer were similar to those of other women with primary ovarian failure, the miscarriage rate was high (40%); possibly this may have been due to uterine factors. Bodri et al. (2009) report a similarly discouraging experience. Fénichel and Letur (2008) insist on the advisability of transferring a single embryo only. Any genetic risk to the TS patient bearing children via ovum donation is due to that of the biological donor parents. A related donor (mother, sister) would have obvious attraction, and the improving methodology of ovum storage offers the possibility of maternal donation well ahead of the time of potential use (Schoolcraft et al. 2009). Gidoni et al. (2008) report a 33-year-old mother having “oöcyte vitrification” for the potential use of her daughter with isoXq TS. These authors discuss the ethical issues involved and conclude that the procedure is reasonable and acceptable, with the mother’s motives purely altruistic, and she “is simply providing an option for her daughter.” The foregoing notwithstanding, pregnancies in women with TS are not without risk, particularly for cardiovascular events, and Söderström-Anttila et al. (2019) debate the pros and cons of “gestational surrogacy.” Low-Level 45,X/46,XX Mosaicism in Phenotypically Normal Women.  The discovery of a low level (<20%) of 45,X cells in a woman presenting no phenotype traits of TS is not to be over-interpreted, nor is a reproductive risk to be exaggerated. We have observed a number of healthy pregnant women identified by noninvasive prenatal testing as having low-level 45,X/46,XX mosaicism, the presence of 45,X cells in the mother leading to a “false positive” increased risk result for TS in the fetus. Data from the UK Biobank suggests that the presence of a 45,X cell line in blood does not adversely affect reproductive lifespan or fertility in most cases, as long as more than 20% of cells have two X chromosomes (Tuke et al. 2019). Results from PGT are similarly reassuring, with no discernable increase in the risk of chromosome abnormalities in the embryos of mosaic patients (Luo et al. 2019). Otherwise, mosaic loss of an X chromosome is a normal concomitant of aging (see also “Biology” section). X/XY MALE Infertility is probable, although the considerable bias in clinically ascertained cases is to be noted. In their series of males with 45,X/46,XY mosaicism, Ljubicic et al. (2021) found that 14/17 had complete azoöspermia, and in only one of these were spermatids identified at testicular biopsy. In that series, no patient had fathered a child. Slightly more optimistic data come from Mohammadpour Lashkari et al. (2018): of 49 infertile males with 45,X/46,XY, 28 (57%) were nonazoöspermic (four had a normal spermiogram), 14 underwent an IVF cycle, and three healthy pregnancies resulted. Given a possible increased risk for aneuploidy, gonosomal or autosomal (Newberg et al. 1998), PGT may be considered in that setting. (mosaic loss of the Y in older men is a different matter altogether; see “Biology” section). SEX CHROMOSOME POLYSOMY Many XXXX women are of low-normal or borderline intelligence, and the questions of fertility and genetic risk may well be raised by their carers. In fact, it appears that sterility is almost always the case. XXXY and XXYY men are undoubtedly sterile. 478  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Parents Having Had a Child with a Sex Chromosome Aneuploidy XXX, XXY, XYY, 45,X, AND OTHER SEX CHROMOSOME ANEUPLOIDY There is no firm evidence that a recurrence risk above the age-specific figure exists, and indeed in respect of XXX and XXY, no recurrences of either homotrisomy or heterotrisomy were observed in the study of Warburton et al. (2004). NIPT could be offered for additional reassurance. Structural Rearrangement As in the preceding chapter on autosomal rearrangements, we are dealing here with a segment of a chromosome existing in an imbalanced state, mostly with respect to the X but with the Y chromosome making a small appearance. Broadly, we may consider two categories: large rearrangements that have been known from the early days of cytogenetics; and microrearrangements, originally detected on G-banding and now including deletions and duplications seen only with molecular karyotyping. Typically so, the large rearrangements are associated with disorders of gonadal development, and variant forms of TS predominate among these. Here, X-inactivation enables an otherwise massive genetic imbalance to become functionally viable. The viability of large Y imbalances reflects the very small component of active genes on this chromosome. Contrariwise, microimbalances of the X chromosome in the female are not necessarily subject to “correction” by inactivation, and they may be damaging but not necessarily lethal in the male. Thus, in some respects the implications may be similar to the autosomal microimbalance. We list here selected deletions and duplications of the X and Y chromosomes. As for the X, for the most part we categorize (as commented above) according to (1) large “classic” rearrangements and (2) microdeletions and microduplications. Y abnormalities, although so few, follow suit. Deletions of the X and Y with a particular association with infertility are summarized in Figure 15–6. LARGER X DELETIONS del Xp Turner Variant.  Substantial Xp terminal deletions, many of which had been seen on the solid-stain analysis of the early days of cytogenetics, typically lead to variant or incomplete “formes frustes” of TS (Figure 15–3e). These deletions can remove up to most or even all of the short arm. X-inactivation is markedly skewed toward the abnormal X. Short stature is largely due to haploinsufficiency of the SHOX growth control gene in the pseudoautosomal region. Ovarian function may be retained, in part at least, with the more distal Xp deletions, but is typically absent in proximal deletions (Lachlan et al. 2006). In those women who achieve fertility—and numerous examples of transmission of a del(Xp) are on record (Periquito et al. 2016)—presumably a partial synapsis occurs at meiosis in the 46,X,abn(X) oöcytes, with the intact segment of the abnormal X pairing with the homologous region of the normal X. A segregation ratio of 1:1 would be expected, with equal frequencies of gametes carrying either the normal X, or the abnormal X from that part of the gonad tissue containing the abn(X).

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  479 Not infrequently, mosaicism is recognized. Palka et al. (1994) describe an apparently non-mosaic 45,X woman who had had an abnormal child with an interstitial Xp deletion, del(X)(p22.2p11.3). Upon restudy, the mother herself had one 46,X,del(X) out of 450 cells, allowing the presumption of a somatic-gonadal mosaicism. In a more direct demonstration of gonadal mosaicism, Varela et al. (1991) studied a woman with TS and normal menstruation and who had had a 46,X,del(X)(p21) daughter. They showed 5/ 100 cells with 46,X,del(X)(p21) in one ovary, while all cells from the other ovary, fibroblasts, and lymphocytes were 45,X. Gonadal function can vary in a family, as Zinn et al. (1997) show for a familial del(X)(p21.2). The 45,X/46,X,del(X) mother had had three pregnancies, including one miscarriage, and had normal menses till age 39 years. Her two daughters were both 46,X,del(X). The elder was amenorrheic at age 15 years, while the younger had spontaneous menarche at age 14½ years, with regular cycles one year later. A very similar family is on record in Adachi et al. (2000). An Xp deletion might coexist with an Xq duplication, the consequence of recombination within an inversion chromosome. Stoklasova et al. (2016) report a four-generation family—clearly, fertility was retained—of women with the karyotype 46,X,rec(X) inv(p21.1q27.3). A great-great-grandparent may have been the heterozygote in whom the recombinant arose. del Xp22.12pter.  This deletion, and others of lesser extent, may be associated in the female with only the short stature component of TS, this segment including the SHOX gene. Cho et al. (2012b) report a deletion Xp22.12pter, which had been passed from a mother to her two daughters. The mother’s height was just a little above the range seen Figure 15–6.  Regions of the Sex Chromosomes in which Deletions are Associated with Infertility. Source: From A García-Rodríguez et al., DNA damage and repair in human reproductive cells, Int J Mol Sci 20:31, 2018. Courtesy R Roy and S Johnston, and with the permission of MDPI. 480  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY in classic TS at 149 cm (–3.3 SD); her young daughters plotted somewhat higher, on –2.1 and –1.8 SD, respectively, at their ages of close to 9 and 12 years. The mother’s pubertal development had been normal. del Xq Turner Variant.  Deletions may be of very substantial size, up to 74 Mb, or approximately three-fourths of the q arm length. Mercer et al. (2013) reviewed the clinical picture in a series of 10 del(Xq) cases, of whom eight were non-mosaic (two had a concomitant 45,X cell line). Of the non-mosaic cases, six had terminal deletions, with proximal breakpoints from Xq21.1 to Xq25; where parental testing had been done, all were de novo. The clinical presentations had been due to primary amenorrhea, premature ovarian insufficiency, infertility, and in one child, short stature; few other features characteristic of TS were present. If puberty commences naturally, it remains the case that premature ovarian insufficiency is likely; and it is practical advice that childbearing— if wished, and of course other things being equal—should be embarked upon sooner rather than later. Assuming 1:1 segregation (a fair assumption), the deleted X would be transmitted in 50% of ova. Ring Turner Variants.  The imbalance in the classic 46,X,r(X) TS is essentially due to distal Xp and Xq deletion, the deletions of variable extent. In the series of Cameron-Pimblett et al. (2017), 58% experienced primary amenorrhea. Rare reports of fertility exist. Blumenthal and Allanson (1997) record a woman with mosaic ring X TS, 45,X/ 46,X,r(X), who had been amenorrheic until being given hormone replacement therapy. She had three pregnancies: a healthy 46,XY son, a 12-week miscarriage, and a healthy daughter with the same 45,X/46,r(X) karyotype. The latter was presumably 46,X,r(X) at conception, with post-zygotic loss of the r(X) in some tissue. Other such cases are known (Sybert 2005). A rather different example is that in Matsuo et al. (2000), in which a mother and daughter were 45,X/46,X,r(X)(p22.3q28), the ratios of X:X,r(X) being 97:3 in the mother and 73:27 in the daughter. The ring comprised an almost complete X, but small distal Xp and Xq segments were deleted. The two X chromosomes were randomly inactivated, and presumably in consequence some “brain genes” would have been functionally nullisomic in those cells having the normal X-inactivated. Thus, cognitive function in the mother, and more so in the daughter, was compromised. A male with r(X) is almost unknown, but Ellison et al. (2002) describe transmission from a non-mosaic 46,X,r(X) mother to her non-mosaic 46,Y,r(X) son, mother and son both short-statured. The breakpoints were very distal, within and beyond the Xp and Xq pseudoautosomal regions respectively. The “tiny ring X syndrome” with the karyotype 45,X/46,X,r(X), is a quite different entity. There may be a functional X disomy due to the ring lacking the XIST locus and thus not undergoing inactivation. The syndrome is typically, but not universally, seen with a severe phenotype of physical and intellectual disability, in some resembling Kabuki syndrome. In others, the clinical picture may merely be that of TS (Rodríguez et al. 2008). Similarly, in the male with the tiny ring as a supernumerary chromosome, usually as 46,XY/47,XY,+r(X) mosaicism, the clinical picture is typically abnormal, and in some severely so (Baker et al. 2010). Chen et al. (2006d) report a notable exception from the prenatal diagnosis at amniocentesis of 46,XY[17]/47,XY,+mar[6]‌, the marker chromosome turning out to be a very small XIST-negative r(X). The infant boy, on whose blood the proportions of the two cell lines were similar to the amniocentesis findings, was normal physically and developmentally on follow-up to one year of age. These various phenotypic differences in male and female may reflect the composition, proportion, distribution, and activation status of the abnormal chromosome.

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  481 LARGER X DUPLICATIONS Isochromosome Xq Turner Variant.  The imbalance in i(Xq) TS is a monosomy of Xp and a trisomy of Xq. Outcomes closely match those seen in 45,X TS, other than a lower incidence of congenital heart disease (Cameron-Pimblett et al. 2017). The condition is almost invariably associated with infertility. Isochromosome Xq Klinefelter Variant.  In this rare form of KS, 47,X,i(Xq),Y, there is a monosomy of Xp and trisomy of Xq (as with i(Xq) TS), along with a normal Y complement. Compared to XXY KS, isochromosome Xq KS has been associated with normal height, intelligence, and secondary sexual characteristics (Simsek et al. 2019), and at least in terms of height, this can be attributed to the lack of duplication of Xp. Infertility is usual, but rare fertility with recourse to IVF is on record (Sabbaghian et al. 2011). dup Xq21q26.  Large duplications of (and microduplications within) this segment are noted below. A functional disomy can influence the clinical picture, according to the pattern of X chromosome inactivation (Armstrong et al. 2003). LARGER Y REARRANGEMENTS Y Isochromosome, Isodicentric Y.  The inactivation of one of the two centromeres allows this chromosome to be mitotically functional. The distinction here is between Yp and Yq isochromosomes—or, since typically there are two copies of the centromere, they are usually called Yp and Yq isodicentric chromosomes, thus i(Y)(p) and i(Y)(q), or idic(Y) (p) and idic(Y)(q). Or, more fully, for example, idic(Y)(pter→q11.22::q11.22→pter); note the identical palindromic sequences on either side of the :: breakpoint. Note also that the Yp or Yq designation refers to the site of breakpoint, and that the idic(Y)(p) has two complete Yq copies, while the idic(Y)(q) has two complete copies of Yp.7 There is considerable heterogeneity of size, according to the site of breakpoint (Figure 15–7). An idic(Y)(p) with a breakpoint at distal Yp, with mirror copies of the remainder of the Y, would comprise almost a double copy of the whole chromosome (Figure 15–7a). An idic(Y)(q11.223) would convey a double copy of Yp and a double copy of the proximal long arm (Figure 15–7c). A breakpoint at Yq11.1 would give an idic(Y)(q), with a double copy of only the short arm and absence of long-arm material (Figure 15–7d). Generation is de novo, typically in (obviously) paternal gametogenesis and reflecting a vulnerability due to the apposition of similar Y sequences; uncommon cases may be due to a post-zygotic event. Mosaicism very frequently accompanies as a post-zygotic event, with 45,X and a second abn(Y) the usual additional cell lineages. The clinical presentations range from a majority with male infertility (e.g., the idic(Y)(p11.3) in Figure 15–8), male with mild cognitive impairment, through ovotesticular disorder of sex development (DSD) or mixed gonadal dysgenesis with genital ambiguity, to TS. The gonadal phenotype is presumably directed in keeping with the regional presence or absence of SRY. In a series of 14 cases in Kalantari et al. (2014), all with idic(Y)(q11.22), 13 were men with azoöspermia (note that this chromosome would lack the b and c AZF spermatogenic factors). Most had a concomitant 45,X cell line. Immature germ cells in the ejaculate were, overall, of fairly similar fractions of haploid 23,X and 23,idic(Y) karyotypes, indicating 7 This can sometimes lead to muddling of nomenclature. Beaulieu Bergeron et al. (2011) note that “when referring to an idic with unspecified breakpoints, some authors use idicY(p) or idic(Yp) when two copies of the short arm are present, and idicY(q) or idic(Yq) when two copies of the long arm are present, therefore creating some confusion among readers.” ISCN (2024) does not adjudicate. 482  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY that the first stage of meiosis (division of the primary spermatocyte) had been entered. In the series of Abur et al. (2022), sperm were retrieved from 4/12 men with idic(Y), but no pregnancies were achieved. In the 14 cases reported by Kalantari and colleagues the only woman had a TS-like clinical picture, and about half of cells on blood were 45,X; in comparison, in the series of Beaulieu Bergeron et al. (2011), four women all had gonadal dysgenesis. Ambiguous genitalia with ovotesticular DSD/mixed gonadal dysgenesis was the presenting sign in Figure 15–7.  Formation of the isodicentric Y chromosome (Yp chromatin, gray; Yq chromatin, white). The idic(Y)(p) has mirror copies around a distal (a) or mid (b) Yp breakpoint, whereas the idic(Y)(q) has mirror copies around a Yq breakpoint (c) or practically at the centromere, Yq11.1 (d). Thus, heterogeneity of chromosome length relates to a heterogeneity of breakpoint site. Figure 15–8.  Testicular histology in an infertile man with 45,X[9]‌/46,X,mar[3]/46,X,idic(Y) (p11.3)[33]. There is a maturation arrest at the level of the primary spermatocyte, reflected in the azoöspermia of this man. The idic(Y) had the format as in Figure 15–5a. Source: From KJ Lehmann et al., Isodicentric Yq mosaicism presenting as infertility and maturation arrest without altered SRY and AZF regions, J Assist Reprod Genet 29: 939–942, 2012. Courtesy MA Fischer, and with the permission of Springer.

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  493 of a deletion from Ypter to at least SHOX, but not as far as the sex-determining factor SRY (which is just beyond the PAR1 bound) (Borie et al. 2004). Deletions more proximally within Yp11.2, and which include the AMELY gene, are nonpathogenic copy number variants (Jobling et al. 2007). Yq11.21q11.23 Deletion. This de novo deletion was identified in a man with pervasive developmental disorder (IQ below the first centile), short stature, and some dysmorphisms (Tyson et al. 2009). The deletion is within Yq euchromatin, at chrY:11.6-25.5 Mb. Six cases in Salo et al. (1995), with de novo Yq deletions of varying (but less precise) extents, presented with cognitive compromise of varying degree, and minor dysmorphism. These authors mention a reservation that intellectual impairment could possibly reflect ascertainment bias, acknowledging that normal intellect has been reported in a man with a complete Yq deletion. Transmission is not recorded. Duplication. Y chromosome duplications, which largely refer to the isodicentric Y with a del/dup combination, are noted above. A single family is recorded with an inter-arm insertional Yq duplication of band Yq11.2 into the distal p arm, 46,X,insdup(Y) (pter→p11.32::q12→q11.1::p11.32→qter), presumed transmitted from a normal father to two normal sons; a locus therein is DAZ1 (Figure 15–16). The wife of one had presented with two miscarriages, which may or may not have been related (Engelen et al. 2003). GENETIC COUNSELING Many of the gonosomal structural rearrangements are associated with infertility, or at least subfertility. Some present a phenotype of relatively mild abnormality. Whether preimplantation or prenatal diagnosis is chosen in those who are able to achieve pregnancy may depend on the parents’ perception of the seriousness of the potential abnormal Figure 15–16. 494  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY outcome. Inference from prenatal X-inactivation analysis, in abn(X) cases, may be fraught with uncertainty. Sex Chromosome Deletions and Duplications Del(X), dup(X).  If the female del(X) or dup(X) carrier is fertile, the risk to transmit the abnormal chromosome will presumably reflect symmetric segregation, 1:1. If passed from a 46,X,del(X) mother to a daughter, the daughter’s phenotype may be the same as that of the mother (which may well be quite normal). But a firm statement cannot be made. If the rule of selective Lyonization holds, the abn(X) is consistently the inactivated one, and normality might, in theory, be expected. If the rule fails, random inactivation could, in the case of the duplication, lead to an attenuated functional partial disomy with phenotypic abnormality, such as may be seen in the MECP2 syndrome due to dupXq28. If a del(X) is passed from a 46,X,del(X) mother to a 46,Y,del(X) male conceptus, the hemizygous male fetus will be nullisomic for loci within the compass of the deletion. Viability may be possible, but the absence of loci will lead to a “contiguous gene syndrome.” A classic example is the variable combination of Duchenne muscular dystrophy, adrenal hypoplasia, glycerol kinase deficiency, and intellectual disability, due to deletion within Xp21. Larger microdeletions will often be lethal in utero due to nullisomy for the segment concerned. Fertility is usually an academic question in the male hemizygote for a del(X) or dup(X) (but the reader will well understand that were his Y chromosome to be passed on, the child would, other things being equal, be normal). Del(Y), dup(Y), r(Y).  Fertility is achievable, with medical assistance, in some rea(Y) hemizygotes. In these cases, a 50:50 segregation with respect to the X and the rea(Y) chromosomes is to be assumed. A son inheriting the rea(Y) would very likely recapitulate his father’s reproductive phenotype. IVF may enable fertility in those few males with extractable sperm, but with a high risk to offspring (in principle 50%) and with post-zygotic karyotypic evolution unpredictable, as per the phenotypic range outlined elsewhere (Chapter 20).

484  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY in the isochromosome X, we know only of the single report in the series of Bernard et al. (2016). KLINEFELTER SYNDROME VARIANTS Infertility is the rule. In one example, normal daughters were born to a man with the karyotype 47,X,i(Xq),Y, following IVF with ICSI (Stabile et al. 2008). Deletions and Duplications Chromosome X Xp11.22 Duplication. A distal duplication at Xp11.22 includes the genes SHROOM4 and, in most, also DGKK (Figure 15–10) (Grams et al. 2016). Some recurrent breakpoints are observed, sited at points of long terminal repeats. Males show a phenotype essentially the same as with the female. This may reflect that disomy of the chrX:48.4-52.6 Mb segment expresses the same in the male as in the female (in whom, curiously, the abnormal X is preferentially active, as mentioned below); of course, the male’s single X is active. Intellectual disability ranges from mild to severe degree, with language in particular impaired; in one case the IQ, at 86, was within a normal range. Autistic behavior and epilepsy (or at least an abnormal electroencephalographic pattern) are recorded. Brain scan can show minor anomalies or, in one case, actual cortical atrophy. Early puberty is observed. Facial dysmorphism is of mild or subtle degree. All inherited cases of this duplication have come from a carrier mother. In these, the inheritance pattern could be described, in essence, as X-linked dominant. Most cases, however, have been de novo, and in these, the abnormal X has consistently been of paternal derivation. In female de novo cases, X-inactivation, where measured, has been nonrandom and markedly skewed toward the normal X—a most remarkable observation (Di-Battista et al. 2016). Thus, the abnormal X is preferentially activated, and loci within the duplicated segment may express a functional and therefore potentially damaging disomy. Figure 15–9. SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  485 Duplication. Proximal duplications within Xp11.22 are to be distinguished from the distal ones; overlap is rare (Figure 15–11). Within this group, further distinction is made upon the basis of the loci duplicated, with particular reference to IQSEC2 and HUWE1 (Moey et al. 2016). The observed phenotype in the affected male is one of intellectual disability and attention deficit/hyperactivity; mild facial dysmorphism is noted. In contrast to the distal duplication, epilepsy is not a feature. All cases in Moey et al. were maternally inherited. One child had two affected male cousins, these boys being the sons of three carrier sisters; one of the maternal grandparents was likely a mosaic hemizygote or heterozygote. Xp11.4 Deletion. We have seen a young woman with retinitis pigmentosa, chronic granulomatous disease, and ornithine transcarbamylase (OTC) deficiency, having an Xp deletion Figure 15–10.  Duplications at Xp11.22. Notes: While there is some overlap, duplications largely sort themselves into a distal and a proximal group. The distal group are defined by the particular involvement of SHROOM4, and some extending into Xp11.23, while the proximal group are further subdivided into groups in which KDM5C and IQSEC2, or HUWE1, are the defining loci. Sources: From data in SE Grams et al., Genotype-phenotype characterization in 13 individuals with chromosome Xp11.22 duplications, Am J Med Genet 170A:967–977, 2016; and C Moey et al., Xp11.2 microduplications including IQSEC2, TSPYL2 and KDM5C genes in patients with neurodevelopmental disorders, Eur J Hum Genet 24:373–380, 2016. Dark blue data are due to Grams et al., and light blue to Moey et al. Courtesy SE Grams and C Shoubridge, and with the permission of John Wiley and Sons, and Springer Nature. Figure 15–11.  A Contiguous Gene Deletion at Xp11.4. Notes: The key three loci removed in this deletion are CYBB, the basis of chronic granulomatous disease; RPGR, the basis of one form of retinitis pigmentosa; and OTC, the gene for ornithine transcarbamylase deficiency. 486  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY which removed these neighboring loci (Figure 15–11). She suffered recurrent upper respiratory tract infections and had a history of surgery for mastoid osteomyelitis and lung abscess. Her peripheral vision was poor, and she unconsciously self-managed the OTC deficiency by avoiding high-protein foods. X-inactivation was random. She came to prenatal diagnosis and elected to terminate a male pregnancy with the deletion, the predicted phenotype being severe (Coman et al. 2010b). Xp21 Deletion. Cytogeneticists can claim some credit for the initial location of the gene for Duchenne muscular dystrophy (DMD) at Xp21.1p21.2 (Lindenbaum et al. 1979), and at least for that historical reason we include a mention of deletion in this region. Loss of neighboring loci in the hemizygous male leads to a contiguous gene syndrome, sometimes referred to simply as the “Xp21 deletion syndrome” (Figure 15–12). According to the extent of the deletion, these conditions may comprise the syndrome: DMD, adrenal hypoplasia, and hyperglycerolemia, along with developmental delay. The condition is often familial; while the carrier mother is typically unaffected, rare cases of clinically affected girls with a de novo deletion are reported (Heide et al. 2015). Duplication. A locus of important effect in this duplicated state is NR0B1, which may lead to sex reversal in the 46,dup(X),Y genetic male (in the deleted state, NR0B1 is the basis of the adrenal hypoplasia noted above). Small (<1 Mb) duplications including NR0B1 are associated with sex reversal and isolated gonadal dysgenesis of differing forms, while larger duplications impose a broader phenotype with some dysmorphism and neurodevelopmental compromise (Zheng et al. 2024). Penetrance of the sex-reversal phenotype is incomplete (Veyt et al. 2024). The 46,X,dup(X)(p21) female carrier is normal (seven carriers in the six-generation kindred in Barbaro et al. 2007), and X-inactivation is random. Xp22.31 Deletion of STS in this Xp22.31 causes the skin disorder X-linked ichthyosis. The nature of any additional neurocognitive phenotype is yet to be resolved, but the fact of STS being expressed in the brain raises that question. In the UK Biobank, Brcic et al. (2020) identified STS deletion in 86 males and 312 carrier females and found them to have slightly poorer performance on the Fluid Intelligence Test compared to controls, although not apparently affecting academic achievement. Male deletion carriers had an increased rate of depressive and anxiety-related traits, but which “may feasibly be related to having to live with a potentially stigmatizing lifelong skin condition.” An increased risk of atrial fibrillation might relate to altered steroid hormone levels. Larger deletions Figure 15–12.  The Contiguous Gene Deletion of the Xp21 Syndrome. Notes: The three loci shown here are NR0B1, GK (glycerol kinase), and DMD (Duchenne muscular dystrophy).

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  487 that include the gene NLGN4 have the additional phenotypes of autism and intellectual disability. Duplication of the STS region in Xp22.31 has been reported in patients with a wide range of phenotypes, but is likely to be an incidental finding. STS duplications are common in the general population (0.3%–0.4%) and are not enriched within the clinical population. From 414 male and 938 female carriers in the UK Biobank, health, cognitive function, and academic achievement did not differ from the general population (Gubb et al. 2020). An intriguing finding was of greater happiness among those with the duplication; the authors postulate that this might be the result of STS duplication causing elevated steroid hormone levels. Xp22.2 Deletion. Some deletions in the 46,X,del(Xp) female which include this segment, either as an interstitial or as a terminal deletion, lead to the syndrome of microphthalmia and linear skin defects (MLS). In 90% of cases MLS is caused by deletions that include the HCCS gene, this gene directing a component of the mitochondrial respiratory chain (Morleo et al. 2018).8 The intriguing question is this: Why is MLS seen in only some deletions of Xp22.2? Unfavorable X-inactivation is the reasonable explanation and in theory, inactivation of the normal X could lead to a functional nullizygosity of HCCS. Thus, in tissue derived from neural crest destined to contribute to skin and eye, mitochondrial failure could lead to cell death and hence the MLS phenotype. Favorable inactivation, skewed toward the del(Xp), could see the normal X hold sway. If there is mosaicism with a 45,X cell line, this may be protective by virtue of retained activity of HCCS when the gene is present on a single, active X. Wimplinger et al. (2007) suggest this to be the basis of a mildly affected mosaic 45,X/46,X,del(X)(p22.2) mother with MLS having a more severely affected non-mosaic 46,X,del(X)(p22.2) daughter. Another example of mother-daughter difference is seen in Margari et al. (2014), in this case with a large (and apparently non-mosaic) Xp22.2pter deletion. The mother was of short stature, and she had had one eye removed in infancy; the daughter was blind due to bilateral eye involvement, short, dysmorphic, had lost language ability, and developed signs of autism. Both showed, at least on blood, preferential inactivation of the del(Xp) of ratios 10:90 in daughter and 15:85 in mother. The smallest deletion (of ~200 kb), removing only HCCS and part of one other gene (ARHGAP6), is described in Vergult et al. (2013) and concerned a mother and daughter, both of normal intellect, each with only one eye affected, and skin lesions only in the mother; X-inactivation was completely skewed in both. It is presumed that an Xp22.2 deletion in a male conceptus would lead to inevitable early abortion. Thus, the risk to the female carrier to have a living affected child is one-third, the segregation ratio of 1:1:1 applying to normal female:affected female:normal male. Duplication. Sismani et al. (2011) describe a family in which a mother heterozygous for a 9 Mb duplication Xp22.2p22.13 had four intellectually disabled sons, three of whom died in childhood. She herself and her carrier daughter were of short stature but normal 8 A small minority, MLS is due to other X-borne loci, COX7B at Xq21.1 and NDUFB11 at Xp11.3, which, like HCCS, code for components of mitochondrial function (Indrieri et al. 2012; Van Rahden et al. 2015). Thus far, COX7B and NDUFB11 cases have been due to point mutation or intragenic deletion, not X chromosomal microdeletion. 488  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY intelligence. These authors compare two similar duplications within the region Xp22.11 to Xp22.2, each with different breakpoints but encompassing in common seven known X-linked intellectual disability loci (Figure 15–13). Xq12q13.3 Duplication. Three families (one a five-generational pedigree) are on record segregating very similar duplications, with the gene MED12 in common (Apacik et al. 1996; Kaya et al. 2012; Prontera et al. 2012). The affected males are microcephalic with marked intellectual disability, and in Apacik et al. (with a slightly more extensive duplication) multiple malformations were associated with death in early infancy. Female carriers are phenotypically normal but with completely skewed inactivation of the dup(X); the inheritance pattern is essentially that of an X-linked recessive disorder. A locus of particular interest within this segment is XIST, the X-inactivation center. Xq21.1q21.2 Deletion. Smaller Xq21.2 deletions that include POU3F4 cause the Xq21 deletion syndrome in males, the key phenotypic features being choroideremia (CHM), deafness, and intellectual disability (Bonati et al. 2024). Female carriers are generally asymptomatic, but they may show mild signs of choroideremia and rarely, mild hearing loss. Figure 15–13.  Duplications at Xp22. Notes: Within the full segment Xp21.3 to Xp22.32 outlined, there are seven known X-linked intellectual disability loci, including the three shown. Source: From data in C Sismani et al., 9 Mb familial duplication in chromosome band Xp22.2-22.13 associated with mental retardation, hypotonia and developmental delay, scoliosis, cardiovascular problems and mild dysmorphic facial features, Eur J Med Genet 54:e510–515, 2011. Figure 15–14.

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  489 Xq21.1q21.3 Duplication. Gabbett et al. (2008) describe a boy with poor motor and language development who became a “food seeker” as an infant, and who is described as presenting a Prader-Willi phenocopy, in whom a dup(X)(q21.1q21.31) was identified. His mother, who had had “learning difficulties” at school, proved (on blood analysis) to be a mosaic carrier of the duplication, with a random pattern of X-inactivation. A similar duplication (chrX: 83.6-87.6 Mb) and phenotype in brothers was reported by Sherlaw-Sturrock et al. (2022). Chromosomally adjacent to this case (but not overlapping), Basit et al. (2016) report a family in which five mild to moderately intellectually disabled brothers were the offspring of a consanguineous couple, but in fact a 3.95 Mb dup(X)(q21.31q21.32) proved to be the causative factor. Some displayed a facial dysmorphism; one was epileptic. Hyperphagia with obesity, dry skin, and self-mutilation were further observations. The phenotypically normal carrier mother and one sister showed markedly skewed X-inactivation with respect to the abnormal X. Of the three genes within the duplicated segment, PCDH11X bids fair to be a pheno-critical locus; the other two are TGIF2LX and PABPC5. Yet, some microduplications in this region are not to be over-interpreted: they may in fact be harmless, that is to say a benign copy number variant. Maurin et al. (2017) make this point in their report of a 3.6 Mb microduplication at Xq21.33, discovered incidentally at prenatal diagnosis, and inherited through the mother from a normal grandfather. The fact of this being a gene-sparse region—only two loci resident therein, DIAPH2 and RPA4—is the likely basis of the non-pathogenicity, with these genes tolerating duplication. This principle applies more widely: a large CNV is not necessarily pathogenic. Xq21q26 Large Duplications. A number of dup(Xq) cases have been reported, of varying lengths, within this large (~60 Mb) Xq segment. Some are extensive and readily detectable on classical cytogenetics, while others (see below) warrant the appellation of microduplication. Both genders are seen; the clinical picture in the female, more so in the larger duplication, is often mitigated by skewed X-inactivation. One of the largest in a female is a de novo dup(X)(q21.1q25) initially diagnosed prenatally due to intrauterine growth retardation, in a girl whose circumstance at age two years remained one of a substantial physical and neurodevelopmental disability (Tachdjian et al. 2004). These authors list reports of a variety of relatively large Xq duplications in affected females. Cheng et al. (2005) review a number of reports of male cases of large duplication and present their own patient with 46,Y,dup(X)(q21.32q35), a profoundly disabled 2-year-old boy. Mostly, these are inherited from a heterozygous mother; grandpaternal meiosis may be the usual origin of the duplication. Xq22.1 Deletions that include the TIMM8A and BTK loci at chrX:101.3 Mb cause a contiguous gene deletion syndrome in males comprising deafness and dystonia, and X-linked agammaglobulinemia due, respectively, to loss of these two loci (Rendtorff et al. 2022). Xq22.1q22.3 Deletions of ~3 Mb in Xq22.1q22.3 are seen only in the heterozygous female, and the non-observation of males points to a lethality of the nullizygous state. The resultant “early-onset neurological disease trait” in 46,XX females comprises neonatal hypotonia, 490  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY severe intellectual disability, neurobehavioral abnormalities, and mildly dysmorphic facial features (Yamamoto et al. 2014). Although this region includes the PLP gene that is duplicated in Pelizaeus-Merzbacher syndrome, the critical gene in the Xq22 microdeletion in fact is TCEAL1 (Hijazi et al. 2022). Deletions are nonrecurrent; most have been de novo, but maternal transmission is recorded. Interpretation is not straightforward, and the influence of X-inactivation is uncertain. Xu et al. (2023) report a family in which a 5.29 Mb deletion that included TCEAL1 was associated with a normal phenotype in four carrier females across three generations, suggesting that skewed X-inactivation is likely to be protective for deletions of this size. Xq22.3q23 Deletion. A contiguous gene syndrome within this segment encompasses, in the hemizygous male, Alport syndrome, intellectual disability, midface hypoplasia, and a curious red cell anomaly, elliptocytosis (“AMME complex”) (Gazou et al. 2013). The basis of the Alport syndrome of renal failure and deafness in this syndrome is well understood, namely the COL4A5 gene. Deletions are nonrecurrent, and if COL4A5 is not included, naturally Alport syndrome is not seen; the cognitive impairment may reside in loss of ACSL4, with loss of AMMECR1 contributing the midface hypoplasia and elliptocytosis (Moysés-Oliveira et al. 2018). Familial cases are well known. Mothers can have the slightest sign of renal impairment; it may well be that skewed X-inactivation is protective (Rodriguez et al. 2010). Deletions of COL4A5 that extend in the opposite (centromeric) direction cause a different contiguous gene syndrome in males—“diffuse leiomyomatosis with Alport syndrome,” the smooth muscle overgrowth being due to loss of COL4A6 (Zhou et al. 1993). Xq25 Duplication. Di Benedetto et al. (2014) define a minimal segment of this proposed syndrome, encompassing the loci XIAP and STAG2. Intellectual disability is of mild to moderate degree and may be accompanied by epilepsy, brain malformations, and organ defects (Turchi et al. 2020). Both affected and unaffected female carriers are observed. Xq25q26.2 Duplication. Møller et al. (2014) studied eight families in which a dup(X)(q25q26.2) was segregating, and Herriges et al. (2019) added an additional two families. The 46,Y,dup(X) males manifested growth retardation and microcephaly with facial dysmorphism, digital anomalies, and abnormal genitalia. The heterozygous mothers were less affected, and mostly of normal intelligence; X-inactivation patterns in them were inconsistent. The duplications were nonrecurrent and fell within chrX:128.6-134.8 Mb. Some duplications did not overlap, allowing these authors to propose three pheno-critical segments: chrX:130.13-130.17 Mb containing the genes AIFM1 and RAB33A, predisposing to intellectual disability; chrX:130.49-130.90 Mb leading to microcephaly, ptosis, and digital anomalies; and a broader segment, chrX:130.1-134.2 Mb, the basis of the syndromic facial dysmorphism, small hands and feet, and genital abnormality. They further identified a “polymorphic” segment at chrX:131.5-132.4 Mb, duplication of which was without phenotypic effect. Xq26q27 Duplication. A number of duplications within this region have been recognized, with the observations in common of growth retardation due to pituitary hypoplasia (Stagi

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  491 et al. 2014). The pheno-critical gene is SOX3. Inheritance can be either de novo or due to maternal transmission. Intellectual disability is common but not universal, as demonstrated by Du et al. (2022a), who reported a boy with a 6.2 Mb duplication and marked growth deficiency but normal intellect. Skewed X-inactivation does not necessarily protect the female, as Stankiewicz et al. (2005) illustrate in their study of a short-statured mother and daughter. The dup(X)(q27) is also associated with XX sex reversal, and for example Vetro et al. (2015) describe a de novo 46,X,dup(X)(q27.1q27.3) with random X-inactivation in a mildly developmentally delayed phenotypic male. SOX3 is again implicated. Xq27.3q28 Deletion, This rare deletion removes loci for the fragile X syndrome and Hunter syndrome (a mucopolysaccharidosis): FMR1 at chrX:147.9 Mb and IDS at chrX:149.4 Mb, respectively. X-inactivation in the female heterozygote is variable. If inactivation is skewed to the deleted X, physical signs of Hunter syndrome and fragile X syndrome are not seen, as Marshall et al. (2013) describe in their patient, a 4-year-old girl with global developmental delay having the de novo deletion chrX:145.1-155.6 Mb. Xq28 Deletion, Int22h-1/Int22h-2 Mediated (includes RAB39B). This deletion is an embryonic/fetal lethal in males, but the carrier females reported have been clinically unaffected (El-Hattab et al. 2015). Xq28 MECP2 Duplication Syndrome. The crucial locus in this severe neurodevelopmental disorder is MECP2, the Rett syndrome gene (Lim et al. 2017b); duplication of the close-by L1CAM, FLNA, and IKBKG genes may also be pheno-contributory in some (Peters et al. 2019). Progressive spasticity and a predisposition to infections are additional findings. In the large series of El Chehadeh et al. (2017), most duplications lay within the region chrX:153.6-154.6 Mb; a few may extend well into Xq27.3. Brain malformation is observed on imaging. The condition can be inherited from a carrier mother (who may herself be mildly affected) or of de novo generation. Rare female patients are affected, often but not necessarily less markedly than in the male; this may reflect the influence of random or unfavorable X-inactivation (Fieremans et al. 2014; Scott Schwoerer et al. 2014). While de novo cases are seen, familial transmission is often so, the inheritance being X-linked recessive with sometimes heterozygous manifestation (Xing et al. 2023). The stresses on families of caring for their child are rehearsed in Cherian et al. (2023). Duplication, K/L mediated (includes GDI1). At the chrX:154.3-154.6 Mb locus, low copy repeats lead to complex copy number gains of between one and four extra copies (Leffler et al. 2023; Figure 15–15). The core phenotype is of intellectual disability and seizures in males, with a minority of carrier females experiencing mild learning difficulties. GDI1 is the candidate gene most likely contributing to the phenotype. Duplication, Int22h-1/Int22h-2 Mediated (includes RAB39B). This neurodevelopmental disorder is characterized by variable cognitive impairment and behavioral difficulty, and is due to a recurrent 0.5 Mb duplication mediated by low copy repeats at ChrX:154.9-155.4 Mb (Ballout et al. 2021). The disorder primarily affects males, in whom the duplication can arise de novo or be inherited from a carrier mother who may herself have mild symptoms. Some males are of minimal phenotype, suggesting 492  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY incomplete penetrance in some families (Billes et al. 2024). CLIC2 and RAB39B are the major genes contributing to the phenotype. The corresponding deletion has been identified in females without a phenotype, who are likely protected by skewed X-inactivation. Chromosome Y Deletion. The most common Y deletion is seen in the isodicentric chromosome, as a del/ dup. The deletion in the idic(Y)(q) may involve a distal part of Yq in company with duplication of proximal Yq and all of Yp, and vice versa in the idic(Y)(p), with a partial distal del(Yp) and dup(Yq), as discussed above and in Chapter 20. Yp11.2 Deletion. The pseudoautosomal region 1 (PAR1) on the Y extends from Ypter to about chrY:2.70 Mb in band Yp11.2 (Figure 15–16). Deletions that are confined to within PAR1, and which contain the SHOXY counterpart of SHOX at chrY:0.6 Mb, are rare. And indeed, we know of no example of a “pure” Yp11.2 deletion including SHOX (this locus at the telomeric bound of band Yp11.2, essentially adjacent to Yp13.1). Should one be identified, short stature would be predicted. This was the observation in a boy with a de novo t(Y;22), who was otherwise quite normal and in whom the effective imbalance was Figure 15–15.  The Complexity of K/L Mediated Rearrangement at Xq28. Notes: Low copy repeats K1, K2, L1, L2 (red and blue rhomboids) predispose to recurrent non-allelic homologous recombination within the Xq28 segment. Simple duplications (pink) result, but including also complex triplications (blue), quadruplications (yellow), and quintuplication (green). GDI1 may be the key pheno-contributory gene. Source: From M Leffler et al., Further delineation of dosage-sensitive K/L mediated Xq28 duplication syndrome includes incomplete penetrance, Clin Genet 103:681–687, 2023. Courtesy T Dudding-Byth, and with the permission of John Wiley and Sons.

SEX CHROMOSOME ANEUPLOIDY AND STRUCTURAL REARRANGEMENT  493 of a deletion from Ypter to at least SHOX, but not as far as the sex-determining factor SRY (which is just beyond the PAR1 bound) (Borie et al. 2004). Deletions more proximally within Yp11.2, and which include the AMELY gene, are nonpathogenic copy number variants (Jobling et al. 2007). Yq11.21q11.23 Deletion. This de novo deletion was identified in a man with pervasive developmental disorder (IQ below the first centile), short stature, and some dysmorphisms (Tyson et al. 2009). The deletion is within Yq euchromatin, at chrY:11.6-25.5 Mb. Six cases in Salo et al. (1995), with de novo Yq deletions of varying (but less precise) extents, presented with cognitive compromise of varying degree, and minor dysmorphism. These authors mention a reservation that intellectual impairment could possibly reflect ascertainment bias, acknowledging that normal intellect has been reported in a man with a complete Yq deletion. Transmission is not recorded. Duplication. Y chromosome duplications, which largely refer to the isodicentric Y with a del/dup combination, are noted above. A single family is recorded with an inter-arm insertional Yq duplication of band Yq11.2 into the distal p arm, 46,X,insdup(Y) (pter→p11.32::q12→q11.1::p11.32→qter), presumed transmitted from a normal father to two normal sons; a locus therein is DAZ1 (Figure 15–16). The wife of one had presented with two miscarriages, which may or may not have been related (Engelen et al. 2003). GENETIC COUNSELING Many of the gonosomal structural rearrangements are associated with infertility, or at least subfertility. Some present a phenotype of relatively mild abnormality. Whether preimplantation or prenatal diagnosis is chosen in those who are able to achieve pregnancy may depend on the parents’ perception of the seriousness of the potential abnormal Figure 15–16. 494  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY outcome. Inference from prenatal X-inactivation analysis, in abn(X) cases, may be fraught with uncertainty. Sex Chromosome Deletions and Duplications Del(X), dup(X).  If the female del(X) or dup(X) carrier is fertile, the risk to transmit the abnormal chromosome will presumably reflect symmetric segregation, 1:1. If passed from a 46,X,del(X) mother to a daughter, the daughter’s phenotype may be the same as that of the mother (which may well be quite normal). But a firm statement cannot be made. If the rule of selective Lyonization holds, the abn(X) is consistently the inactivated one, and normality might, in theory, be expected. If the rule fails, random inactivation could, in the case of the duplication, lead to an attenuated functional partial disomy with phenotypic abnormality, such as may be seen in the MECP2 syndrome due to dupXq28. If a del(X) is passed from a 46,X,del(X) mother to a 46,Y,del(X) male conceptus, the hemizygous male fetus will be nullisomic for loci within the compass of the deletion. Viability may be possible, but the absence of loci will lead to a “contiguous gene syndrome.” A classic example is the variable combination of Duchenne muscular dystrophy, adrenal hypoplasia, glycerol kinase deficiency, and intellectual disability, due to deletion within Xp21. Larger microdeletions will often be lethal in utero due to nullisomy for the segment concerned. Fertility is usually an academic question in the male hemizygote for a del(X) or dup(X) (but the reader will well understand that were his Y chromosome to be passed on, the child would, other things being equal, be normal). Del(Y), dup(Y), r(Y).  Fertility is achievable, with medical assistance, in some rea(Y) hemizygotes. In these cases, a 50:50 segregation with respect to the X and the rea(Y) chromosomes is to be assumed. A son inheriting the rea(Y) would very likely recapitulate his father’s reproductive phenotype. IVF may enable fertility in those few males with extractable sperm, but with a high risk to offspring (in principle 50%) and with post-zygotic karyotypic evolution unpredictable, as per the phenotypic range outlined elsewhere (Chapter 20).

496  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY the other two being condensin and the SMC5-SMC6 complex (Uhlmann 2016). SMC complexes are a major component of the chromosomes of all living things; they control chromosome condensation and sister chromosome cohesion, as well as playing a role in DNA repair. CLINICAL GENETICS AND CYTOGENETICS The four classic chromosomal breakage syndromes, as well as Roberts syndrome, Nijmegen breakage syndrome, and the ICF syndrome, are of autosomal recessive inheritance; and the recurrence risk for parents who have had one affected child is the classic 1 in 4. In those rare instances in which parenthood for the affected person is achievable, the risk to the child will in most cases be very low. Cornelia de Lange syndrome is almost always due to a de novo mutation. Fanconi Pancytopenia Syndrome This uncommon disorder of protean manifestation (also known simply as Fanconi anemia, FA) is the least rare of the breakage syndromes (Taylor et al. 2019). Originally described as a disorder of short stature, characteristic facies, and certain malformations along with progressive bone marrow failure, the picture has now widened. In one-third of FA there are no major congenital malformations, although many of these will have minor anomalies, skin pigmentary abnormalities, microphthalmia, and growth indices below the 5th centile (Kee and D’Andrea 2012). Myelodysplastic syndrome and acute myeloid leukemia are common complications, and solid tumors may present at an unusually young age. Some patients whose clinical condition resembles the VACTERL1 association may, in fact, have FA, and tests for chromosome breakage can enable the distinction to be made (Faivre et al. 2005). Males are typically infertile, and females experience early menopause (Petryk et al. 2015). Diagnosis is now commonly made using genomic sequencing, but cytogenetic analysis may be required as an adjunct. Chromosomes show a range of abnormalities, Table 16–1.  The Four Classic Chromosome Instability Syndromes SYNDROME CYTOGENETIC FEATURES Fanconi pancytopenia Increased spontaneous and inducible chromosome breakage Ataxia-telangiectasia Increase in chromosome breaks; presence of clones with translocations having specific breakpoints in 7, 14, and X Nijmegen breakage syndrome Increase in chromosome breaks; presence of clones with translocations having specific breakpoints in 7, 14 Bloom syndrome Increased spontaneous and inducible sister chromatid exchange; increased spontaneous chromatid breakage with production of symmetrical quadriradials 1 Vertebral, anal, cardiac, tracheo-esophageal, renal, limb. CHROMOSOME INSTABILITY SYNDROMES  497 including an increase in chromosome breakage, both spontaneously and upon exposure to DNA cross-linking agents (Figure 16–1). There is little or no hypersensitivity to radiation damage. The increase in chromosome breakage after exposure of cells to a cross-linking agent such as diepoxybutane (DEB) provides, when it is observed, a reliable diagnostic test (Esmer et al. 2004; Castella et al. 2011). Myelodysplasia and acute myeloid leukemia are associated with a specific pattern of chromosome abnormalities, namely, 1q+, 3q+, monosomy 7, and 11q‒ (Quentin et al. 2011). As Joenje et al. (1998) note, most cytogenetic laboratories will see a case of true FA only very infrequently, and it may be difficult to maintain technical expertise in the practice Figure 16–1.  Metaphase from (a) a control and (b) a patient with Fanconi anemia after exposure to diepoxybutane. Note the high level of chromatid breakage in the patient metaphase. One chromatid break is indicated (straight arrow), and a quadriradial figure is shown (curved arrow). 498  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY of clastogen-challenge test protocols. Thus, a negative result might not absolutely exclude the diagnosis. Another reason for a misleading negative result is in vivo “correction” of the functional defect in blood-forming tissue by intragenic homologous recombination, with proliferation of the corrected stem cell population. Joenje and colleagues refer to patients with typical FA who converted from a positive test result on blood sampling to apparent false negative over a period of years.2 Skin fibroblasts maintain the clastogen-sensitive phenotype, and diagnosis following fibroblast study should be reliable. There is much genetic heterogeneity in FA (Figure 16–2), although three genes, FANCA, FANCG, and FANCC account for over 80%. With the exception of the X-linked FANCB and autosomal dominant FANCR (also known as RAD51), all are autosomal recessive. The gene products from these different loci contribute to the control of cellular DNA repair (Kee and D’Andrea 2012). One of the less common of these genes is the breast cancer susceptibility gene FANCD1, better known to the counselor as BRCA2; biallelic mutation leads to a particularly severe form of FA, with a very high cancer risk (Alter et al. 2007). Prenatal diagnosis by mutation detection will be possible in those cases with a known mutation. Preimplantation diagnosis has been successfully applied, not only to select an unaffected embryo but also to select one with the same HLA typing in order to enable blood stem cell donation to a preexisting affected sibling, an approach not without 2 This reversion to a normal cell line may work as a natural “self-treatment,” whereby the normal marrow clone arising could have a proliferative advantage and ameliorate the disease state (Gross et al. 2002). Figure 16–2.  The Genetic and Phenotypic Heterogeneity of Fanconi Anemia. Source: From A Gueiderikh et al., A new frontier in Fanconi anemia: From DNA repair to ribosome biogenesis, Blood Rev 52:100904, 2022. Courtesy A Gueiderikh, F Maczkowiak-Chartois, and F Rosselli, and with the permission of Elsevier.

CHROMOSOME INSTABILITY SYNDROMES  499 controversy (Verlinsky et al. 2001). We have seen a case in which, at routine fetal ultrasonography, upper limb defects were identified, and the couple chose to terminate the pregnancy; subsequent analysis of fetal tissue showed the characteristic cytogenetics of FA. This same cytogenetic testing was offered in subsequent pregnancies. Merrill et al. (2005) report somewhat similar experiences, although they were able to offer targeted testing for a specific mutation enriched in the Jewish population, following ultrasound suspicions of FA. Bloom Syndrome Bloom syndrome (BS) is a rare disorder that has its highest prevalence in Ashkenazi Jews, but also seen in many other ethnic groups. It is characterized clinically by proportionate short stature, a characteristic facies, sun-sensitive skin rash, immunodeficiency, and a marked susceptibility to cancer (German 1993). Infertility seems to be invariable in the male; females have difficulty conceiving, but a few have given birth (Martin et al. 1994). The Bloom gene, BLM, was originally mapped to 15q25qter by the elegant approach of determining the region of isodisomy in a child with BS and concomitant Prader-Willi syndrome due to uniparental disomy 15 (Woodage et al. 1994). BLM codes for a recQ DNA helicase that monitors DNA integrity during the S phase of the cell cycle (German and Ellis 2011). (Other members of this gene family are the basis of Rothmund-Thomson syndrome and Werner syndrome.) The diagnostic cytogenetic finding in BS is a markedly increased level of spontaneous sister chromatid exchange (SCE). The normal is 6–10 exchanges per cell; in BS it is more than 50 per cell (Figure 16–3), although some normal cells may be present in BS patients.3 The other cytogenetic abnormality is an increased incidence of spontaneous chromatid aberrations, giving the classic symmetrical quadriradial configuration. Intriguingly, this effect can manifest in the haploid state, with the heterozygous male producing an excess of sperm with chromosome breaks and rearrangements (Martin et al. 1994). Prenatal Diagnosis. Specific mutation analysis would be applicable if the family mutations were known; a Bloom mutation register is maintained at (https://pediatrics.weill. cornell.edu/research/bloom-syndrome-registry). For the affected woman’s reproductive outlook (in those few surviving to adulthood) the standard Mendelian advice, with consideration of the likelihood of the spouse being heterozygous, applies (Chisholm et al. 2001). Ataxia-Telangiectasia Ataxia-telangiectasia (AT) is the archetype of a group in which the basic pathogenetic process is a failure in one of the monitoring and repair systems that keep watch for DNA damage. The group includes AT itself and Nijmegen breakage syndrome (below), and 3 Interestingly, and analogous to the FA “self-treatment” noted above, the normal cells may be due to a “correcting” genetic event occurring in a bone marrow cell, which then leads to a heterozygous cell line having a normal in vitro phenotype. The correcting event may be either a somatic recombination between the two sites of BLM mutation in the homologs in the BS individual with compound heterozygosity, or a back mutation in a homozygote (Ellis et al. 2001). 500  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY both exhibit chromosome instability. The genes for AT and Nijmegen breakage syndrome encode proteins that are part of a complex that senses abnormal DNA structures and monitors post-replication DNA repair (Michelson and Weinert 2000). Despite exhibiting similar cellular defects, AT and Nijmegen breakage syndrome have contrasting neurological phenotypes: neurodegeneration in AT, and abnormal neurodevelopment in Nijmegen breakage syndrome (Taylor et al. 2019). The clinical presentation of AT is as a brain/immune/cancer syndrome. It is characterized by cerebellar ataxia and oculomotor apraxia (difficulty in performing voluntary eye movements), oculocutaneous telangiectasia, immunodeficiency, and increased cancer predisposition. The cytogenetic hallmarks of AT include frequent nonrandom rearrangements of chromosomes 7, 14, and occasionally X, in T-lymphocytes; nonspecific Figure 16–3.  Metaphase from (a) a control and (b) a patient with Bloom syndrome, showing very high sister chromatid exchange (SCE) in the latter. Three points of SCE are indicated (arrows) on the control metaphase.

CHROMOSOME INSTABILITY SYNDROMES  501 chromosome breakage in fibroblasts; and normal chromosomes in bone marrow. The breakpoints in the lymphocyte rearrangements are at 7p14, 7q35, 14q12, and 14q32, involving the T-cell receptor and immunoglobulin heavy chain genes. Clones with rearrangements may be harbingers of a T-cell malignancy, and these clones evolve as the disease progresses. Breakage is exacerbated in vitro by exposure of cells to ionizing radiation and to radiomimetic chemicals such as bleomycin (Kojis et al. 1991). Most ATM mutations are null, but missense and splicing mutations that allow production of a limited amount of functional product may lead to milder clinical and cytogenetic phenotypes. Prenatal diagnosis is based upon direct mutation analysis of the ATM gene on chorionic villus tissue or at PGT (Gatti and Perlman 2016). Nijmegen Breakage Syndrome This is another brain/immune/cancer syndrome, and it is rare indeed. The clinical picture includes microcephaly with brain dysgenesis, immune deficiency, and risk for lymphoreticular malignancy. It shares with AT certain cytogenetic features (preferential involvement of chromosomes 7 and 14 in rearrangements) and radiation hypersensitivity (Antoccia et al. 2006). The causative gene, called NBN, functions as part of the MRE11-RAD50-NBN complex, and interacts with the ATM gene noted above. A founder mutation, 657del5, is common among the Slavic population, and most patients are 657del5 homozygotes (Seemanová et al. 2006). Prenatal diagnosis is preferably achieved by specific mutational analysis. Roberts Syndrome Roberts syndrome (RS) is a syndrome of craniofacial abnormalities and limb defects that are often severe, and the archetype of the “cohesinopathies.” Cohesinopathies are genetic instability syndromes that are associated with defects in the regulators and structural components of the cohesion complex, which is responsible for maintaining sister chromatid cohesion during mitosis, from synthesis to separation. In RS, the phenotype is so very distinctive that it is unsurprising that case reports date back some centuries, the first appearing in 1672 (a “Portrait d’un enfant monstre”), well before Roberts’ description from 1919 (Bates 2003; Kompanje 2009). Intellect is unaffected. Most affected individuals (~80%) exhibit a chromosomal phenomenon known as premature chromatid separation (PCS), sometimes described as “tram-tracking” or “railroad track appearance” and also referred to as “heterochromatin repulsion,” as the sister chromatids bulge away from each other. The gene is ESCO2 (Vega et al. 2010), and its product enables proper disposition of the chromatids. In its absence, there is an abnormality of sister chromatid apposition around the centromeres, particularly noticeable for those chromosomes with large blocks of heterochromatin (Figure 16–4). It is best seen in plain-stained or C-banded chromosomes; G-banding obscures the phenomenon (Van Den Berg and Francke 1993). In this particular instance, classical cytogenetics is the more powerful diagnostic tool, and it may enable recognition of an atypical case; microarray would miss the abnormality (Gerkes et al. 2010). Prenatal diagnosis is based upon testing for the specific ESCO2 mutation. 502  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Cornelia de Lange Syndrome The clinical phenotype of Cornelia de Lange Syndrome (CdLS) is, in the classic case, very distinctive. Five causative genes are known: NIPBL (the most frequently seen); SMC1A, RAD21, and BRD4 cause autosomal dominant CdLS, typically due to de novo mutations; and mutations in SMC3 and HDAC8 are the basis of X-linked CdLS (Avagliano et al. 2020). The cytogenetic phenotype is PCS, and thus CdLS is another cohesinopathy. Be that as it may, testing for PCS is not useful in the diagnosis of CdLS, with one study showing it to be no more frequent in CdLS patients than in controls (Castronovo et al. 2009). Figure 16–4.  Unusual appearance of the chromosomes in Roberts syndrome: puffing at the centromeres (a and b); a C-banded preparation showing separation of the heterochromatic segments (c) is compared with a C-banded preparation from a control showing the normal centromere appearance (d). Source: From NP Mann et al., Roberts syndrome: Clinical and cytogenetic aspects, J Med Genet 19:116–119, 1982, with the permission of the British Medical Association. CHROMOSOME INSTABILITY SYNDROMES  503 Very Rare Syndromes ICF (Immunodeficiency, Centromeric Instability, Facial Anomalies) Syndrome.  The ICF syndrome is characterized by immunodeficiency, an unusual facies, and growth and developmental retardation, together with a most remarkable tendency of chromosomes 1, 9, and 16 to form “windmill” multiradials by interchange within heterochromatic regions (Figure 16–5). This instability of the pericentromeric heterochromatin reflects hypomethylation of satellites II and III, which are important components of its structure. Hagleitner et al. (2008) document the variability of the phenotypic range. The phenotype, physical and cytogenetic, can be considered to be secondary to a failure of methylation. Five genes have been reported in ICF patients, but most cases are due to autosomal recessive mutations in either DNA methyltransferase 3B (DNMT3B, ICF1), or ZBTB24 (ICF2) (van den Boogaard et al. 2017). Mosaic Variegated Aneuploidy.  The core phenotype of this recessively inherited syndrome comprises microcephaly with functional neurological abnormality, growth retardation, and susceptibility to childhood malignancy, with most of the lymphocytes and about half of skin fibroblasts showing premature chromatid separation. Many cells are aneuploid, with trisomies, double trisomies, and monosomies with almost every chromosome represented (Bohers et al. 2008; García-Castillo et al. 2008). In mosaic variegated aneuploidy (MVA) type 1, the underlying defect in the cell cycle involves one of the checkpoint proteins (BUB1B) that control progression through the mitotic process, maintaining an alert for chromosome malsegregation. The BUB1B heterozygote may display the tendency in a proportion of lymphocytes, and some mitotic cells may present the striking observation of a 92-chromosome count. At least five other MVA loci have been identified. Prenatal diagnosis has been reported based on conventional cytogenetics, the abnormalities being very obvious (Plaja et al. 2003; Chen et al. 2004b). If the molecular basis is known, preimplantation testing would be applicable. Figure 16–5.  A “windmill” or “starburst” multiradial chromosome 1 in the ICF syndrome. Source: From JR Sawyer et al., Chromosome instability in ICF syndrome: Formation of micronuclei from multibranched chromosomes 1 demonstrated by fluorescence in situ hybridization, Am J Med Genet 56: 203–209, 1995. Courtesy JR Sawyer, and with the permission of Wiley-Liss.

504  PARENT OR CHILD WITH A CHROMOSOMAL ABNORMALITY Seckel Syndrome and Primary Autosomal Recessive Microcephalies.  This spectrum of disorders presents with microcephaly of prenatal onset, an absence of visceral malformations, and variable cognitive impairment and short stature. Mutations in at least 16 different genes are responsible. Although these disorders are well suited to diagnosis by multigene sequencing panels, chromosome analysis may also have a role. Premature chromosome condensation, initially described by Neitzel et al. (2002) as a novel syndrome in siblings with microcephaly and cognitive impairment, is now known to be caused by mutations in MPCH1. In a group of five patients with Seckel syndrome of unknown genotype, Bobabilla-Morales et al. (2003) demonstrated excessive chromosomal breakage with mitomycin C, although not an excess of SCEs. Casper et al. (2004) discovered increased breakage rate at known fragile sites in patients with SCKL1 (due to the ATR gene, which interacts with ATM). Warsaw Breakage Syndrome.  A severely growth-retarded and microcephalic teenager showed both chromosomal breakage and premature chromatid separation, and his case represents a further cohesinopathy, named Warsaw breakage syndrome for the city of his residence (van der Lelij et al. 2010). The causative gene is DDX11, having some sequence similarity to the gene for Fanconi anemia type J, and coding for a helicase. Inheritance is autosomal recessive, although there is a hint the heterozygote may have an increased cancer risk. Further families are summarized in van Schie et al. (2020). Bloom-like Syndrome.  We identified a Bloom syndrome variant in two children, the offspring of consanguineous parents, who presented with slow growth and multiple café-au-lait macules and whose cells exhibited a “Bloomoid” phenotype of markedly elevated levels of SCE (Hudson et al. 2016). The siblings were homozygously deleted for the gene RMI2, which encodes for one of the four proteins that make up the BLM complex. Subsequently, variants in RMI2 and TOP3A have also been shown to give rise to a Bloom syndrome-like disorder characterized by microcephalic dwarfism (Martin et al. 2018). Ataxia-Telangiectasia-Like Disorder.  This condition is due to biallelic variants in MRE11, which functions within the MRE11-RAD50-NBN complex noted above with respect to NBS. Despite this, the associated syndrome resembles AT more than NBS; it is characterized by a post-natal cerebellar degeneration and cancer predisposition (Regal et al. 2013). Nijmegen Breakage Syndrome-Like Disorder.  The core phenotype from a study of four cases is documented in Takagi et al. (2023) and includes growth retardation, microcephaly, bone marrow failure, and immunodeficiency. The genetic basis is mutation in RAD50 (this gene encoding DNA repair protein RAD50). Chronic Atrial and Intestinal Dysrhythmia Syndrome.  This rare autosomal recessive disorder, caused by variants in the SGOL1 gene, has the cytogenetic phenotype of “railroad track” heterochromatin repulsion at the centromere (Chetaille et al. 2014). The clinical presentation is with cardiac arrhythmia and intestinal pseudo-obstruction in the first four decades of life, in the absence of birth defects or other signs of cohesinopathy. Syndromes Reported in Only One or Two Families (A Few Examples)  • Ishikawa et al. (2000) reported a single family with a dominantly inherited chromosome instability syndrome. The major clinical observations are mild to moderate intellectual disability, depression, and a spastic ataxia, with striking abnormalities of cerebral white matter and the basal ganglia and an atrophic spinal cord. All three affected individuals having a cytogenetic analysis showed a low frequency of a CHROMOSOME INSTABILITY SYNDROMES  505 t(7;14), with a common 14q11.2 breakpoint in each, and a hypersensitivity to radiation and radiomimetic drugs. • A unique Austrian family appears to present a sex-limited chromosome breakage syndrome with ovarian failure (Duba et al. 1997). The index case had presented with primary hypogonadism, and karyotyping showed a high proportion of cells with breaks, acentric fragments, triradial rearrangements, and dicentric chromosomes. Two healthy brothers had essentially the same chromosome findings. The cytogenetic picture most closely resembled that of Fanconi anemia, and the three siblings also demonstrated an elevation in α-fetoprotein, which is a feature of AT. Lespinasse et al. (2005) report a similar case, but in this instance a sister and a brother were both infertile, and the α-fetoprotein was normal. • Bakhshi et al. (2006) describe a 17-year-old boy with growth retardation and dysmorphic facies, with mitomycin-sensitive chromosomal breakage, who developed a B-cell lymphoma; they proposed this as a new syndrome distinct from FA. • We have described two families in which biallelic mutations in SPRTN caused a novel chromosome instability syndrome, with progeroid features and early-onset hepatocellular cancer (Ruijs-Aalfs syndrome) (Lessel et al. 2014). Nonclonal structural chromosome abnormalities comprising spontaneous breaks, rearrangements, deletions, and marker chromosomes were present in peripheral blood, comparable with “variegated translocation mosaicism,” a phenomenon previously described in cells of the Werner premature-aging syndrome. • van der Crabben et al. (2016) identified a new chromosome breakage disorder associated with defective T and B cell function, and leading to fatal lung disease in four children from two unrelated families. Peripheral blood cells showed multiple de novo chromosome rearrangements and variable numbers of de novo supernumerary marker chromosomes. This is another disorder of the SMC complex (see above), due to biallelic missense mutations in the NSMCE3 gene, which encodes a subunit of the SMC5/6 complex essential for DNA damage response and chromosome segregation. PART THREE CHROMOSOME VARIANTS