Part 2

PART 2: Genetic Diversity and Clinical Cytogenetics

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Ch4 — Human Genetic Diversity — Genomic Variation (16) Ch5 — Principles of Clinical Cytogenetics and Genome Analysis (18)

Human Genetic Diversity — Genomic Variation

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Human Genetic Diversity Genomic Variation The study of DNA variation is the conceptual cornerstone for genetics in medic…
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Human Genetic Diversity Genomic Variation The study of DNA variation is the conceptual cornerstone for genetics in medicine and for the broader field of human genetics.人类遗传多样性 基因组变异：DNA变异的研究是医学遗传学以及更广泛的人类遗传学领域的概念基石。
During the course of evolution, the steady influx of new variation has ensured a high degree of genetic diversity and individuality, and this theme extends through all fields in human and medical genetics.在进化过程中，新变异的持续涌入确保了高度的遗传多样性和个体性，这一主题贯穿于人类遗传学和医学遗传学的所有领域。
Genetic diversity may manifest as differences in the organization of the genome, as nucleotide changes in the genome sequence, as variation in the copy number of segments of DNA or entire chromosomes, as balanced or unbalanced alterations, as alterations in the structure or amount of proteins found in various tissues, or as any of these in the context of clinical disease.遗传多样性可表现为基因组结构的差异、基因组序列中的核苷酸变化、DNA片段或整条染色体的拷贝数变异、平衡或非平衡改变、各组织中蛋白质结构或数量的改变，或在临床疾病背景下上述任何一种表现。
This chapter is one of several in which we explore the nature of genetically determined differences among individuals.本章是探讨个体间遗传决定差异本质的若干章节之一。
Considering all classes of genetic variation, the sequence of nuclear DNA is ~99% identical between any two unrelated humans.考虑到所有类别的遗传变异，任意两个无关人类之间的核DNA序列约有99%相同。
Yet it is precisely the small fraction of DNA sequence difference among individuals that is responsible for the genetically determined variability evident both in one’s daily existence and in clinical medicine.然而，正是个体间DNA序列差异的那一小部分，决定了在日常生活和临床医学中均显而易见的遗传变异性。
Many DNA sequence differences have little or no effect on outward appearance, whereas other differences are directly responsible for disease.许多DNA序列差异对外观影响很小或没有影响，而其他差异则直接导致疾病。
Between these two extremes is the variation responsible for genetically determined variability in anatomy, physiology, dietary intolerances, susceptibility to infection, predisposition to cancer, therapeutic responses or adverse reactions to medications, and perhaps even variability in various personality traits, athletic aptitude, and artistic talent.在这两个极端之间，变异导致了遗传决定的变异，涉及解剖学、生理学、饮食不耐受、感染易感性、癌症易感性、治疗反应或药物不良反应，甚至可能包括多种人格特质、运动能力和艺术天赋的变异。
One of the important concepts of human and medical genetics is that diseases with a clearly inherited component are only the most obvious and often the most extreme manifestation of genetic differences: one end of a continuum of variation that extends from rare deleterious variants that cause illness, sometimes representing a spectrum of clinical phenotypes, through more common variants that can increase susceptibility to disease, to the most common variation in the population that is of uncertain relevance with respect to disease.人类和医学遗传学的重要概念之一是，具有明确遗传成分的疾病仅仅是遗传差异中最明显且往往最极端的表现：这是变异连续谱的一端，该连续谱从导致疾病的罕见有害变异（有时代表一系列临床表型），到可增加疾病易感性的更常见变异，再到人群中最为常见但与疾病相关性尚不明确的变异。
THE NATURE OF GENETIC VARIATION As described in Chapter 2, a segment of DNA occupying a particular position or location on a chromosome is a locus (plural loci).遗传变异的本质 如第2章所述，占据染色体上特定位置或位点的一段DNA称为基因座（复数loci）。
A locus may be large, perhaps containing many genes, such as the major histocompatibility complex locus involved in the response of the immune system to foreign substances; it may be a single gene, such as the β-­globin locus we introduced in Chapter 3; or it may be just a single base in the genome, as in the case of a single nucleotide variant (SNV) .一个基因座可以很大，或许包含多个基因，例如参与免疫系统对外来物质反应的主要组织相容性复合体基因座；它可以是单个基因，例如我们在第3章介绍的β-珠蛋白基因座；或者仅仅是基因组中的一个碱基，例如单核苷酸变异（SNV）。
Alternative versions of the DNA sequence at a locus are called alleles.一个基因座处DNA序列的不同版本称为等位基因。
For many genes, there is a single prevailing allele, usually present in more than half of the individuals in a population, that geneticists call the wild-­type or common allele.对于许多基因，存在一个主要等位基因，通常出现在群体中一半以上的个体中，遗传学家称之为野生型或常见等位基因。
(In lay parlance, this is sometimes referred to as the normal allele; however, because genetic variation is itself very much normal, the existence of different alleles in normal individuals is commonplace.（在通俗说法中，这有时被称为正常等位基因；然而，由于遗传变异本身非常正常，正常个体中存在不同等位基因是司空见惯的。
Thus one should avoid using normal to designate the most common or major allele.) The other versions of the gene are variant alleles that differ from the wild-­type allele because of the effect of a mutation having changed the nucleotide sequence or arrangement of DNA.因此应避免使用“正常”来指代最常见或主要的等位基因。）基因的其他版本为变异等位基因，它们因突变改变了DNA的核苷酸序列或排列而与野生型等位基因不同。
Note that the terms mutation and mutant apply to DNA, but not to individuals.注意，术语突变和突变体适用于DNA，而非个体。
They denote a change in sequence without any connotation with respect to the function or fitness of that change.它们表示序列的改变，而不带有关于该改变的功能或适应性的任何含义。
The frequency of different variants can vary widely in different populations, as we will explore in Chapter 10.不同变异的频率在不同人群中可能差异很大，我们将在第10章探讨这一点。
If a locus in a population has two or more relatively common alleles (typically defined by convention as having an allele frequency >1%), the locus is said to exhibit polymorphism (literally “many forms”) in that population; thus such a locus is polymorphic.如果一个群体中的某个基因座有两个或更多相对常见的等位基因（通常按惯例定义为等位基因频率>1%），则该基因座在该群体中表现出多态性（字面意思为“多种形态”）；因此这样的基因座是多态的。
Most variant alleles, however, are rare; some are so rare as to be found in only a single family and are known as private alleles.然而，大多数变异等位基因是罕见的；有些极为罕见，仅在一个家庭中发现，称为私有等位基因。
Common jargon in genetics came to use polymorphism in reference to a variant rather than a locus, but following expert guidance, for clarity, we suggest use of common variant (rather than polymorphism) or rare variant遗传学中的常见行话曾用多态性指代变异而非基因座，但根据专家指导，为清晰起见，我们建议使用常见变异（而非多态性）或罕见变异。
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(rather than mutation).
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(rather than mutation).（而非突变）。
An exception is for the use of single nucleotide polymorphism (SNP) in the context of microarrays, where it is strongly entrenched in the lexicon.一个例外是在微阵列背景下使用单核苷酸多态性（SNP），该术语在词汇中根深蒂固。
The Concept of Variation In this chapter we begin by exploring the nature of genomic variation, ranging from the change of a single nucleotide to alterations of an entire chromosome.变异的概念 在本章中，我们首先探讨基因组变异的性质，范围从单个核苷酸的变化到整个染色体的改变。
To recognize a change means that there has to be a gold standard, compared to which the variant shows a difference.识别一个变化意味着必须有一个金标准，与之相比，变异显示出差异。
As we saw in Chapter 2, there is no single individual whose genome sequence could serve as such a definitive standard for the human species, and thus one arbitrarily designates the most common sequence or arrangement in a population at any one position in the genome as the so-­called reference sequence .正如我们在第二章中所见，没有一个人的基因组序列能够作为人类物种的这样一个明确标准，因此人们
As more and more genomes from individuals around the globe are sampled (and thus as more and more variation is detected among the currently 7. 9 billion genomes that make up our species), this reference genome is subject to constant evaluation and change.[TL:missing]
Indeed, a number of international collaborations share and update data on the nature and frequency of DNA variation in different populations in the context of the reference human genome sequence and make the data available through publicly accessible databases that serve as essential resources for scientists, physicians, and other health care professionals ( As we learn more about variation and, in particular, as long-­read sequencing allows us to fill holes in the reference genome, updated genome The draft sequence of the genome was released in 2001, and the “essentially complete” reference genome assembly was published in 2004.[TL:missing]
Gateway The Single Nucleotide Polymorphism Database (db SNP) and the Structural Variation Database (db Var) are databases of small-­scale and large-­scale variations, including single nucleotide variants, microsatellites, indels, and CNVs. ncbi. nlm. nih. gov/­snp/­ ncbi. nlm. nih. gov/­dbvar/­ The 1000 Genomes Project created a catalogue of common human genetic variation, using openly consented samples from people who declared themselves to be healthy.[TL:missing]
All data are publicly available.[TL:missing]
The International Genome Sample Resource (IGSR) maintains and shares the human genetic variation resource. www. internationalgenome. org The Genome Aggregation Database (gnom AD) reports variants from 125,748 exomes and 15,708 genomes (141,456 unrelated individuals) aligned on GRCh 37 in v 2. 1 and 76,156 genomes from unrelated individuals aligned on GRCh 38 in v 3. 0. gnomad. broadinstitute. org Clin Var is a freely accessible, public archive of reports of the relationships among human variants and phenotypes, with supporting evidence. www. ncbi. nlm. nih. gov/­clinvar The Human Gene Mutation Database is a comprehensive collection of published germline variants associated with or causing human inherited disease (currently including over >210,000 mutations in 8519 genes). www. hgmd. cf. ac. uk/­ac/­index. php The Database of Genomic Variants is a curated catalogue of structural variation in the human genome.[TL:missing]
As of 2023, the database contains over 8 million entries. dgv. tcag. ca CNV, Copy number variant; SNV, single nucleotide variant.[TL:missing]
Updated from Willard HF: The human genome: a window on human genetics, biology and medicine.[TL:missing]
In Ginsburg GS, Willard HF, editors: Genomic and personalized medicine, ed 3, New York, 2016, Elsevier. builds are released by the human genome reference committee; the current reference is h GRC38.[TL:missing]
Because errors are corrected and new sequences added, it is very important to always specify the build used to annotate a genomic variant.[TL:missing]
Variants are sometimes classified by the size of the altered DNA sequence and, at other times, by the functional effect of the change on gene expression.[TL:missing]
Although classification by size is somewhat arbitrary, it can be helpful conceptually to recognize the spectrum of changes at three different levels: Variation in chromosome number that leaves chromosomes intact but changes the number of chromosomes in a cell (aneuploidy) Alterations that change only a portion of a chromosome and might involve an unbalanced change of a subchromosomal segment or a structural rearrangement involving parts of one or more chromosomes (regional variation or copy number variation [CNV]) Alterations of the sequence of DNA, involving the substitution, deletion, or insertion of DNA, range from an SNV through small repetitive units (such as trinucleotide repeats) and insertion-­deletion variants (indels) up to an arbitrarily set (and evolving) limit of approximately 1 kb where such a change becomes a CNV.[TL:missing]
The basis for and consequences of this third type of variation are the principal focus of this chapter, whereas both chromosome and regional variation will be presented at length in Chapters 5 and 6.[TL:missing]
The functional consequences of DNA mutations, even those that change a single base pair, run the gamut from being completely innocuous to causing serious[TL:missing]
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Human Genetic Diversity 47 illness, all depending on the location, nature, and size of the resulting variant.
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Human Genetic Diversity 47 illness, all depending on the location, nature, and size of the resulting variant.人类遗传多样性 47种疾病，完全取决于所产生变异的位置、性质和大小。
For example, even a change within a coding exon of a gene may have no effect on how a gene is expressed if the change does not alter the primary amino acid sequence of the polypeptide product; even if it does, the resulting change in the encoded amino acid sequence may not alter the functional properties of the protein.例如，如果基因编码外显子内的变化不改变多肽产物的主要氨基酸序列，则即使发生变化也可能对该基因的表达没有影响；即使发生了变化，所导致的编码氨基酸序列改变也可能不改变蛋白质的功能特性。
Not all variants, therefore, manifest in a clinical phenotype, though they will be reflected as DNA sequence variants.因此，并非所有变异都会表现为临床表型，尽管它们会以DNA序列变异的形式反映出来。
The Concept of Common Variants The DNA sequence of a given region of the genome is remarkably similar among chromosomes carried by many different individuals from around the world.常见变异的概念 来自世界各地许多不同个体的染色体上，基因组特定区域的DNA序列惊人地相似。
In fact, any randomly chosen segment of human DNA of ~1000 bp in length, on average, will differ by only one base pair between the homologous segments inherited from that individual’s parents (assuming the parents are unrelated).事实上，随机选取一段约1000 bp的人类DNA片段，在该个体父母（假设父母无亲缘关系）遗传的同源片段之间，平均仅相差一个碱基对。
However, across all human populations, hundreds of millions of single nucleotide differences and over a million more complex variants have been identified and catalogued.然而，在所有人类群体中，已识别并编录了数亿个单核苷酸差异以及超过一百万个更复杂的变异。
Because of limited sampling, these figures are likely to underestimate the true extent of genetic diversity in our species.由于采样有限，这些数字可能低估了我们物种遗传多样性的真实程度。
Many populations have yet to be adequately studied.许多群体尚未得到充分研究。
Even in those that have been well studied, the number of individuals examined is too small to reveal most variants with minor allele frequencies below 1% to 2%.即使在那些已深入研究的群体中，所检测的个体数量也太少，无法揭示大多数次要等位基因频率低于1%至2%的变异。
Thus, as more people are included in variant discovery projects, additional (and rarer) variants will certainly continue to be uncovered.因此，随着越来越多的人被纳入变异发现项目，必然还会发现更多的（且更稀有的）变异。
Whether a variant is formally considered common or not depends entirely on whether its frequency in a population exceeds a certain threshold, such as 1% of the alleles in that population.一个变异是否被正式视为常见变异，完全取决于其在群体中的频率是否超过某个阈值，例如该群体中等位基因的1%。
It does not depend on what kind of mutation caused it, how large a segment of the genome is involved, or whether it has a demonstrable effect on the individual.它不取决于引起该变异的突变类型、所涉及的基因组片段大小，也不取决于其对个体是否具有可证明的影响。
Although most common sequence variants are located between genes or within introns and are most often inconsequential to the functioning of any gene, others may be located in the coding sequence of genes themselves and result in different protein variants that may lead in turn to distinctive differences in human populations.尽管大多数常见序列变异位于基因之间或内含子内，并且通常对任何基因的功能无关紧要，但其他变异可能位于基因本身的编码序列中，导致不同的蛋白质变异，进而可能引起人类群体中显著差异。
Still, others are in regulatory regions and may have important effects on transcription or RNA stability.还有一些变异位于调控区域，可能对转录或RNA稳定性产生重要影响。
One might expect that deleterious variants that cause rare monogenic diseases are unlikely to become considered common variants.人们可能会认为，导致罕见单基因疾病的有害变异不太可能被视为常见变异。
Although it is true that the alleles responsible for most clearly inherited clinical conditions are rare, some alleles that have a profound effect on health—­such as alleles of genes encoding enzymes that metabolize drugs (e. g., sensitivity to abacavir in some individuals infected with human immunodeficiency virus) (Case 1), the sickle cell allele in African populations and others of African and Mediterranean ancestry (see Chapter 12) (Case 42), or the p.尽管大多数明确遗传的临床病症的致病等位基因确实罕见，但一些对健康有深远影响的等位基因——例如编码药物代谢酶的基因的等位基因（如某些人类免疫缺陷病毒感染者对阿巴卡韦的敏感性）（案例1）、非洲人群及其他非洲和地中海血统人群中的镰状细胞等位基因（见第12章）（案例42），或p.
Phe 508del variant in CFTR that causes cystic fibrosis (see Chapter 13) (Case 12)—­are relatively common.CFTR基因中导致囊性纤维化的Phe508del变异（见第13章）（案例12）——却相对常见。
Nonetheless, these are exceptions.尽管如此，这些都是例外。
As more and more genetic variation is discovered and catalogued, it is clear that the vast majority of variants in the genome—­whether common or rare—­reflect differences in DNA sequence that have no overt significance to health.随着越来越多遗传变异被发现和编录，显然基因组中的绝大多数变异——无论是常见还是罕见——都反映了对健康无明显意义的DNA序列差异。
Common variants are key elements for the study of human and medical genetics.常见变异是人类遗传学和医学遗传学研究的关键要素。
The ability to distinguish different inherited forms of a gene or different segments of the genome provides critical tools for a wide array of applications, both in research and in clinical practice (see 1)..区分基因不同遗传形式或基因组不同片段的能力，为研究和临床实践中的广泛应用提供了关键工具（见第1章）。
INHERITED VARIATION IN HUMAN AND MEDICAL GENETICS Allelic variants can be used as markers for tracking the inheritance of the corresponding segment of the genome in families and in populations.人类遗传学和医学遗传学中的遗传变异 等位基因变异可作为标记，用于追踪家族和群体中相应基因组片段的遗传。
Such variants can be used as follows: As powerful research tools for mapping a gene to a particular region of a chromosome by linkage analysis or by allelic association (see Chapter 11) For prenatal diagnosis of genetic disease and for detection of carriers of deleterious alleles (see Chapter 18) In blood banking and tissue typing for transfusions and organ transplantation In forensic applications such as identity testing for determining paternity, identifying remains of crime victims, or matching DNA from a crime investigation to that of a perpetrator To provide genomic-­based precision medicine (see Chapter 19), medical care is tailored, for example, to whether an individual carries variants that increase or decrease the risk for common adult disorders (such as coronary heart disease, cancer, and diabetes; see Chapter 9) or that influence the efficacy or safety of particular medications (see Chapter 19) INHERITED COMMON VARIATION IN DNA The original Human Genome Project and the subsequent study of many millions of individuals worldwide have provided vast DNA sequence information.此类变异可用于以下方面：作为通过连锁分析或等位基因关联（见第11章）将基因定位到染色体特定区域的有力研究工具；用于遗传疾病的产前诊断和有害等位基因携带者的检测（见第18章）；用于输血和器官移植的血库及组织配型；用于法医学应用，如亲子鉴定的身份检测、识别犯罪受害者遗骸，或匹配犯罪调查中DNA与犯罪嫌疑人的DNA；为实现基于基因组的精准医学（见第19章），例如根据个体是否携带增加或降低常见成人疾病（如冠心病、癌症和糖尿病；见第9章）风险或影响特定药物疗效或安全性的变异（见第19章）来定制医疗护理。
With this information in hand, one can begin to characterize the types and frequencies of common variation found in the human genome and to generate catalogues of the world’s human DNA sequence diversity.有了这些信息，就可以开始描述人类基因组中常见变异的类型和频率，并编制世界人类DNA序列多样性目录。
Such variants can be classified according to how the DNA sequence differs among the different alleles ( 4. 1 and 4. 2).此类变异可根据不同等位基因之间DNA序列的差异进行分类（4.1和4.2）。
Single Nucleotide Variants The simplest and most common of all variants are SNVs.单核苷酸变异 所有变异中最简单且最常见的是SNV。
Those that occur at a high population frequency (typically defined as >1% or >5%) have been called SNPs, but more recently, common SNVs.那些在群体中出现频率高（通常定义为>1%或>5%）的曾被称为SNP，但近期更常称为常见SNV。
A polymorphic locus characterized by a common SNV usually has以常见SNV为特征的多态性位点通常具有
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C – G – SNV Indel A Indel B G G G G A T T T T T C T C...
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C – G – SNV Indel A Indel B G G G G A T T T T T C T C...C – G – 单核苷酸变异 插入缺失A 插入缺失B G G G G A T T T T T C T C...
A G C A T G C A...A G C A T G C A...
A A Allele 1 Allele 2............A A 等位基因1 等位基因2............
A A A A Allele 1 Allele 2............A A A A 等位基因1 等位基因2............
A A A A Allele 1 Allele 2.........A A A A 等位基因1 等位基因2.........
A T A A Reference sequence 5 20 15 10 6).A T A A 参考序列 5 20 15 10 6).
The single nucleotide variation (SNV) at position 8 has two alleles, one with a T (corresponding to the reference sequence) and one with a C.位于第8位的单核苷酸变异（SNV）有两个等位基因，一个带有T（对应参考序列），另一个带有C。
There are two indels in this region.该区域有两个插入缺失。
At indel A, allele 2 has an insertion of a G between positions 11 and 12 in the reference sequence (allele 1).在插入缺失A处，等位基因2在参考序列（等位基因1）的第11位和12位之间插入了一个G。
At indel B, allele 2 has a 2 ­bp deletion of positions 5 and 6 in the reference sequence.在插入缺失B处，等位基因2在参考序列的第5位和6位有一个2碱基对的缺失。
A B C D E F G H ABCDEFGH ABCDEFGFGFGH ABCDEFGH ABEDCFGH Allele 1 Allele 2 Allele 3............A B C D E F G H ABCDEFGH ABCDEFGFGFGH ABCDEFGH ABEDCFGH 等位基因1 等位基因2 等位基因3............
A C G G...A C G G...
A G C C C A A A Allele 1 Allele 2 Allele 1 Allele 2 Microsatellite polymorphism Mobile element insertion polymorphism Copy number variant LINE Allele 1 Allele 2 Inversion polymorphism Clockwise from upper right: The microsatellite locus has three alleles, with four, five, or six copies of a CAA trinucleotide repeat.A G C C C A A A 等位基因1 等位基因2 等位基因1 等位基因2 微卫星多态性 移动元件插入多态性 拷贝数变异 LINE 等位基因1 等位基因2 倒位多态性 从右上角顺时针方向：微卫星位点有三个等位基因，分别具有CAA三核苷酸重复序列的四、五或六个拷贝。
The inversion variant has two alleles corresponding to the two orientations (indicated by the arrows) of the genomic segment shown in green; such inversions can involve regions up to many megabases of DNA.倒位变异有两个等位基因，对应于以绿色显示的基因组片段的两个方向（由箭头指示）；此类倒位可涉及长达数兆碱基的DNA区域。
Copy number variants involve deletion or duplication of hundreds of kilobase pairs to over a megabase of genomic DNA.拷贝数变异涉及数百千碱基对至超过一兆碱基的基因组DNA的缺失或重复。
In the example shown, allele 1 contains a single copy, whereas allele 2 contains three copies of the chromosomal segment containing the F and G genes; other possible alleles with zero, two, four, or more copies of F and G are not shown.在所示的例子中，等位基因1包含一个拷贝，而等位基因2包含三个包含F和G基因的染色体片段拷贝；其他可能的等位基因（具有零、二、
The mobile element insertion variant has two alleles, one with and one without insertion of a ~6-­kb LINE repeated retroelement; the insertion of the mobile element changes the spacing between the two genes and may alter gene expression in the region. ) Basis for the Variant Number of Alleles Single nucleotide variant 1 bp Substitution of one or another base pair at a particular location in the genome Usually 2 Insertion/­deletions (indels) 1 bp–­1 kb Simple: Presence or absence of a short segment of DNA 1–­1000 bp in length Microsatellites: Generally, a 2-­, 3-­, or 4-­nucleotide unit repeated in tandem 5–­25 times Simple: 2 Microsatellites: typically ≥5 Copy number variant 1 kb–­> ≅ 3 Mb Typically the presence or absence of 1-­kb to 1. 5-­Mb segments of DNA, although tandem duplication of 2, 3, 4, or more copies can also occur ≥2 Inversions Few bp–­>1 Mb A DNA segment present in either of two orientations with respect to the surrounding DNA 2 bp, Base pair; kb, kilobase pair; Mb, megabase pair.[TL:missing]
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Human Genetic Diversity 49 only two alleles, corresponding to two different bases at that particular location .
Ch4 — Segment 5
Human Genetic Diversity 49 only two alleles, corresponding to two different bases at that particular location .人类遗传多样性49中仅存在两个等位基因，对应特定位置的两个不同碱基。
Common SNVs are observed, on average, once every 1000 bp.常见SNV平均每1000个碱基对出现一次。
However, their distribution is uneven around the genome; many more are found in noncoding parts of the genome, in introns and in sequences that are some distance from protein-­coding genes.然而，它们在基因组中的分布不均匀；在非编码区、内含子以及距离蛋白质编码基因一定距离的序列中发现更多SNV。
Nonetheless, a significant number of SNVs, both common and rare, occur in genes and other known functional elements in the genome.尽管如此，相当数量的SNV（包括常见和罕见）发生在基因及基因组其他已知功能元件中。
Approximately half of these do not alter the predicted amino acid sequence of the encoded protein and thus are termed synonymous, whereas those that do alter the amino acid sequence are called nonsynonymous.其中约半数SNV不改变所编码蛋白质的预测氨基酸序列，因此称为同义SNV，而改变氨基酸序列的则称为非同义SNV。
Other SNVs are candidates to have significant functional consequences, as they introduce or change a stop codon (see The significance for health of the vast majority of common SNVs is unknown and is the subject of ongoing research.其他SNV可能具有显著功能影响，因为它们引入或改变终止密码子（参见：绝大多数常见SNV对健康的意义尚不明确，且是持续研究的课题）。
The fact that these variants are common does not mean that they are without detrimental or protective effect on health or longevity.这些变异常见并不意味着它们对健康或寿命没有有害或保护作用。
What it does mean is that any effect of common SNVs is likely to involve a relatively subtle altering of disease susceptibility rather than be a direct cause of serious illness.这实际意味着常见SNV的任何效应可能涉及对疾病易感性的相对微小改变，而非严重疾病的直接原因。
Insertion-­Deletion Variants A second class of variants result from insertion or deletion (indels) of segments that range from a single base pair up to ~1 kb.插入-缺失变异 第二类变异源于长度从单个碱基对到约1 kb片段的插入或缺失（indels）。
Over a million indels have been described among human genomes, numbering in the hundreds of thousands for any one individual.人类基因组中已描述超过一百万个indels，任何个体个体中均有数十万个。
Approximately half of all indels are referred to as simple because they have only two alleles—­that is, the presence or absence of the inserted or deleted segment .约半数indels称为简单indels，因为它们仅有两个等位基因——即插入或缺失片段的存在与否。
Microsatellite Variants Other indels, however, are multiallelic due to variable numbers of a segment of DNA in tandem at a particular location.微卫星变异 然而，其他indels由于特定位置串联排列的DNA片段拷贝数可变而呈多等位基因性。
The term satellite comes from the early observation that this fraction of DNA has a different density, causing separation during centrifugation.“卫星”一词源于早期观察，即这部分DNA具有不同密度，在离心过程中发生分离。
Sometimes called variable number of tandem repeats, these microsatellites are highly vulnerable to mutation.这些微卫星有时称为可变数目串联重复序列，极易发生突变。
They consist of DNA cassettes composed of units of several nucleotides—­such as TG, CAA, or AAAT—­ repeated in tandem between one and a few dozen times .它们由DNA盒组成，这些DNA盒包含数个核苷酸单元（如TG、CAA或AAAT），以串联方式重复1至数十次。
The numbers of repeated units determine the different alleles, sometimes also referred to as short tandem repeats (STRs).重复单元的数目决定不同的等位基因，有时也称为短串联重复序列（STRs）。
A microsatellite locus often has many alleles (repeat lengths) that can be rapidly evaluated by standard laboratory procedures to distinguish different individuals and to infer familial relationships .一个微卫星位点通常具有多个等位基因（重复长度），可通过标准实验室程序快速评估，以区分不同个体并推断家族关系。
Many tens of thousands of microsatellite loci are known throughout the human genome.整个人类基因组中已知数万个微卫星位点。
Microsatellites are particularly useful for genetic mapping.微卫星对遗传作图尤为有用。
Determining the alleles at multiple microsatellite loci is currently the method of choice for DNA fingerprinting used for identity testing.测定多个微卫星位点的等位基因是目前用于身份鉴定的DNA指纹图谱的首选方法。
For example, the US Federal Bureau of Investigation (FBI) currently uses 20 STRs for its DNA fingerprinting panel.例如，美国联邦调查局（FBI）目前使用20个STR进行DNA指纹图谱分析。
Two individuals (other than monozygotic twins) are so unlikely to have exactly the same alleles at all 20 loci that the panel will allow effectively definitive determination of whether samples came from the same individual.两个个体（除同卵双胞胎外）在所有20个位点上具有完全相同等位基因的可能性极低，因此该组合可有效确定样本是否来自同一人。
The information is stored in the FBI’s Combined DNA Index System (CODIS).该信息存储在FBI的联合DNA索引系统（CODIS）中。
Mobile Element Insertion Variants Nearly half of the human genome consists of dispersed families of repetitive elements (see Chapter 2).移动元件插入变异 人类基因组近一半由分散的重复元件家族组成（见第2章）。
Although most of the copies of these repeats are stationary, some of them are mobile and contribute to human genetic diversity through the process of retrotransposition.尽管这些重复的大部分拷贝是稳定的，但其中一些具有移动性，并通过逆转座过程促进人类遗传多样性。
As introduced in Chapter 3 in the context of processed pseudogenes, this involves transcription into an RNA, reverse transcription into a DNA sequence, and insertion (i. e., transposition) into another site in the genome.如第3章中关于加工假基因的介绍，这一过程涉及转录为RNA、逆转录为DNA序列，以及插入（即转座）到基因组中的另一个位点。
The two most common mobile element families are the Alu and long interspersed nuclear elements (LINE) families of repeats, and nearly 10,000 mobile element insertion variants have been Unrelated Individuals Allele length Family Members Mother Father Child 1 Child 2 Child 3 7 6 5 4 3 2 1 The different-­sized alleles (numbered 1–­7) correspond to fragments of genomic DNA containing different numbers of copies of a microsatellite repeat, and their relative lengths are determined by separating them by gel electrophoresis.最常见的两种移动元件家族是Alu和长散在核元件（LINE）重复家族，且已描述近10,000种移动元件插入变异。无关个体 等位基因长度 家庭成员 母亲 父亲 子女1 子女2 子女3 7 6 5 4 3 2 1 不同大小的等位基因（编号1–7）对应于含有不同拷贝数微卫星重复的基因组DNA片段，其相对长度通过凝胶电泳分离确定。
The shortest allele (allele 1) migrates toward the bottom of the gel, whereas the longest allele (allele 7) remains closest to the top.最短的等位基因（等位基因1）向凝胶底部迁移，而最长的等位基因（等位基因7）停留在最靠近顶部的位置。
Left, For this multiallelic microsatellite, each of the six unrelated individuals has two different alleles.左图，对于这个多等位基因微卫星，六名无关个体各有两个不同的等位基因。
Right, Within a family, the inheritance of alleles can be followed from each parent to each of the three children.右图，在一个家族内，可以追踪每个父母传给三个子女的等位基因遗传模式。
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described in different populations.
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described in different populations.在不同人群中描述。
Each polymorphic locus consists of two alleles, one with and one without the inserted mobile element .每个多态性位点由两个等位基因组成，一个带有插入的移动元件，另一个不带。
Mobile element variants are found on all human chromosomes; although most are found in nongenic regions, a small proportion of them are found within genes.移动元件变异存在于所有人类染色体上；虽然大多数位于非基因区域，但其中一小部分位于基因内部。
For many of these loci the insertion allele has a frequency of greater than 10% in various populations.对于其中许多位点，插入等位基因在不同人群中的频率大于10%。
Copy Number Variants Another important type of human polymorphism includes CNVs, which are conceptually related to indels and microsatellites but involve larger segments of the genome, operationally defined as from 1000 bp to ~3 million bp (i. e., the span between limits of sequencing detection and cytogenetic analysis, respectively).拷贝数变异 另一种重要的人类多态性类型包括CNV，其在概念上与插入缺失和微卫星相关，但涉及更大的基因组片段，操作上定义为从1000 bp到约300万 bp（即分别介于测序检测和细胞遗传学分析的极限之间）。
In the general population, variants larger than 500 kb are found in 5% to 10% of individuals, and those encompassing more than 1 Mb in 1% to 2%.在一般人群中，大于500 kb的变异见于5%至10%的个体，而涵盖超过1 Mb的变异见于1%至2%。
The largest CNVs are sometimes in regions of the genome characterized by repeated blocks of homologous sequences called segmental duplications (or segdups).最大的CNV有时位于基因组中具有重复同源序列块（称为片段重复或segdups）的区域。
The importance of these regions in mediating duplication and deletion of the corresponding segments is discussed further in Chapter 6 in the context of various chromosomal syndromes.这些区域在介导相应片段重复和缺失中的重要性将在第6章结合各种染色体综合征进一步讨论。
As with indels, smaller CNVs may have only two alleles (i. e., the presence or absence of a segment).与插入缺失类似，较小的CNV可能只有两个等位基因（即片段的存在或缺失）。
Some large CNVs have multiple alleles due to the presence of different numbers of tandem copies of a DNA segment .一些大的CNV由于存在不同数量的DNA片段串联拷贝而具有多个等位基因。
In terms of genome diversity, the amount of DNA involved in CNVs vastly exceeds the amount that differs because of SNVs.就基因组多样性而言，CNV涉及的DNA量远远超过因SNV而不同的DNA量。
Compared to the reference genome, the content of any given individual’s genome can differ by as much as 30 Mb because of copy number and indel differences.与参考基因组相比，任何给定个体的基因组内容因拷贝数和插入缺失差异而可能相差多达30 Mb。
Notably, since their variable segments can include from one to several dozen genes, CNV loci are frequently implicated in traits that involve altered gene dosage.值得注意的是，由于它们的可变片段可包含一到几十个基因，CNV位点常涉及基因剂量改变相关的性状。
When a CNV is frequent enough, it represents a background of common variation that must be understood to properly interpret alterations in copy number for medical purposes.当CNV足够常见时，它代表了常见变异的背景，必须理解这一点才能正确解释医学用途中的拷贝数改变。
As with all DNA variation, the significance of different CNV alleles in health and disease susceptibility is the subject of intensive investigation.与所有DNA变异一样，不同CNV等位基因在健康和疾病易感性中的意义是深入研究的主题。
Inversions A final group of structural variants is inversions.倒位 最后一组结构变异是倒位。
These regions of the genome, from a few base pairs up to several Mb, are found in either of two orientations .这些基因组区域，从几个碱基对到几Mb，以两种方向之一存在。
Most inversions are characterized by regions of sequence homology at the edges of the inverted segment, implicating a process of homologous recombination in their origin.大多数倒位的特点是在倒位片段边缘具有序列同源性区域，提示其起源于同源重组过程。
Regardless of orientation, an inversion that does not involve a gain or loss of DNA is balanced.无论方向如何，不涉及DNA获得或丢失的倒位是平衡的。
Some can achieve substantial frequencies in the general population.有些在一般人群中可达到相当高的频率。
However, anomalous recombination can result in the duplication or deletion of DNA located between the regions of homology—­a process associated with clinical disorders that we will explore further in Chapters 5 and 6.然而，异常重组可导致位于同源区域之间的DNA重复或缺失——这一过程与临床疾病相关，我们将在第5章和第6章进一步探讨。
THE ORIGIN AND FREQUENCY OF DIFFERENT TYPES OF MUTATION Along the spectrum of diversity from rare to common variants, the different kinds of mutation occur in the context of such fundamental processes of cell division as DNA replication, DNA repair, DNA recombination, and chromosome segregation in mitosis or meiosis.不同类型突变的起源和频率 在从罕见到常见变异的多样性谱中，不同类型突变发生于细胞分裂的基本过程中，如DNA复制、DNA修复、DNA重组以及有丝分裂或减数分裂中的染色体分离。
The frequency of mutation per locus per cell division is a basic measure of how error prone these processes are, which is of fundamental importance for genome biology and evolution.每个位点每次细胞分裂的突变频率是衡量这些过程易错性的基本指标，对基因组生物学和进化具有根本重要性。
However, of greatest importance to medical geneticists is the frequency of mutation per disease locus per generation, rather than the overall mutation rate across the genome per cell division.然而，对医学遗传学家最重要的是每个疾病位点每代的突变频率，而非整个基因组每次细胞分裂的总体突变率。
Measuring disease-­causing mutation rates can be difficult, however, because many mutations cause early embryonic lethality before the result can be recognized in a fetus or newborn.然而，测量致病突变率可能很困难，因为许多突变在胎儿或新生儿中能被识别之前就已导致早期胚胎致死。
Further, some people with a disease-­causing variant may manifest the condition only late in life or may never show signs of the disease.此外，一些携带致病变异的人可能仅在生命晚期才表现出该疾病，或者从不显示疾病症状。
Despite these limitations, we have made great progress in determining the overall frequency—­sometimes referred to as the genetic load—­of all mutations affecting the human species.尽管存在这些限制，我们在确定影响人类的所有突变的总体频率（有时称为遗传负荷）方面取得了巨大进展。
These major types of mutation occur at appreciable frequencies in many different cells in the body.这些主要突变类型在体内许多不同细胞中以可观的频率发生。
In the practice of genetics, we are principally concerned with inherited genome variation; however, all such variation had to originate as a new (de novo or spontaneous) change in a germ cell.在遗传学实践中，我们主要关注遗传的基因组变异；然而，所有这些变异最初都必须作为生殖细胞中的新发（新生或自发）变化出现。
From this unique start in the population, the ultimate frequency of each variant over time depends on chance and on the principles of inheritance and population genetics (see Chapter 10).从这种在群体中的独特起点开始，每个变异随时间的最终频率取决于随机性以及遗传和群体遗传学原理（见第10章）。
Although the original mutation would have occurred only in the DNA of a cell in the germline, any progeny derived from that cell would then carry it as a constitutional variant in essentially all the cells of the body.尽管最初突变仅发生在生殖系细胞的DNA中，但源自该细胞的任何后代随后将把它作为体质性变异携带至身体几乎所有细胞。
In contrast, somatic mutations, depending on when they arise, occur in different proportions of cells throughout the body, but they cannot be transmitted to the next generation of individuals (unless they involved a germline cell).相比之下，体细胞突变根据其发生时间，以不同比例出现在全身细胞中，但不能传递给下一代个体（除非涉及生殖系细胞）。
Given the rate of mutation (see later in this section), one would predict that every cell in an individual has a slightly different version of the genome, depending on the number of cell divisions that have occurred since conception.鉴于突变率（见本节后面），可以预测个体中的每个细胞都有略微不同的基因组版本，取决于自受孕以来发生的细胞分裂次数。
Such genomic heterogeneity is particularly likely to be apparent in highly proliferative tissues, such as intestinal epithelia or hematopoietic cells.这种基因组异质性在高度增殖的组织中尤其明显，例如肠上皮或造血细胞。
However, most such variants are not typically detected because, in clinical testing, one usually sequences DNA from many millions of cells, among which the base sequence present at conception will predominate, and rare somatic mutations will be largely invisible and unascertained.然而，大多数此类变异通常未被检测到，因为在临床检测中，通常对来自数百万个细胞的DNA进行测序，其中受孕时存在的碱基序列占主导，而罕见的体细胞突变大多不可见且无法确定。
Such variants,此类变异，
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Human Genetic Diversity 51 however, can be of clinical importance in disorders associated with somatic mosaicism, caused…
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Human Genetic Diversity 51 however, can be of clinical importance in disorders associated with somatic mosaicism, caused by mutation in only a subset of cells in certain tissues (see Chapter 7).人类遗传多样性51然而，在与体细胞嵌合体相关的疾病中可能具有临床重要性，这类疾病由仅在某些组织的部分细胞中发生的突变引起（见第7章）。
While somatic mutations will typically remain undetected within any multicell DNA sample, cancer provides the major exception.尽管体细胞突变通常在任何多细胞DNA样本中难以检测，但癌症是主要的例外情况。
The mutational basis for the origins of cancer and the clonal nature of tumor evolution drive certain somatic changes to be present in essentially all the cells of a tumor.癌症起源的突变基础以及肿瘤演化的克隆特性，使得某些体细胞变化存在于肿瘤的几乎所有细胞中。
Indeed, 1000 to 10,000 somatic variants (and sometimes many more) are readily found in the genomes of most adult tumors, with mutation frequencies and patterns specific to different cancer types (see Chapter 16).事实上，在大多数成人肿瘤的基因组中可轻易发现1000至10000个体细胞变异（有时更多），其突变频率和模式因癌症类型而异（见第16章）。
Chromosome Alterations Events that produce a change in chromosome number because of chromosome missegregation are among the most common sources of variation seen in humans, with a rate of one event per 25 to 50 meiotic cell divisions.染色体畸变：因染色体错误分离导致染色体数目改变的事件，是人类中观察到的最常见变异来源之一，其发生率为每25至50次减数分裂细胞分裂一次。
This estimate is clearly minimal because the developmental consequences of many such events are likely so severe that the resulting embryos are aborted spontaneously shortly after conception without being detected (see Chapters 5 and 6).这一估计值显然是最低值，因为此类事件的发育后果可能非常严重，以至于由此产生的胚胎在受孕后不久即自发流产而未被检测到（见第5章和第6章）。
Structural Variation Alterations affecting the structure or regional organization of chromosomes can arise in a number of different ways.结构变异：影响染色体结构或区域组织的改变可通过多种不同方式产生。
Duplications, deletions, and inversions of a segment of a single chromosome are predominantly the result of homologous recombination between DNA segments with high sequence homology at more than one chromosomal site.单条染色体某区段的重复、缺失和倒位，主要是由于在不同染色体位点具有高度序列同源性的DNA片段之间发生同源重组所致。
Not all structural mutations are the result of homologous recombination, however.然而，并非所有结构突变都是同源重组的结果。
Others, such as chromosome translocations and some inversions, can occur at the sites of spontaneous double-­stranded DNA breaks.其他类型，如染色体易位和某些倒位，可发生在自发性DNA双链断裂的位点。
Once breakage occurs at two places anywhere in the genome, the two broken ends can be joined together, even without any obvious sequence homology between the two ends (a process termed nonhomologous end-­joining repair).一旦基因组中任意两处发生断裂，两个断裂末端可连接在一起，即使两个末端之间没有任何明显的序列同源性（此过程称为非同源末端连接修复）。
Examples of such mutations will be discussed in Chapter 6.此类突变的例子将在第6章中讨论。
Mutation in Genes Gene or DNA variants, including base pair substitutions, insertions, and deletions , can originate by either of two basic mutational mechanisms: errors introduced during DNA replication or arising from a etc. etc.基因突变：基因或DNA变异，包括碱基置换、插入和缺失，可通过两种基本突变机制之一产生：DNA复制过程中引入的错误，或由等等。
Reference sequence Substitution Deletion Insertion T A G C The first base pair of the second codon in the reference sequence (shaded in blue) is mutated by a base substitution, deletion, or insertion.参考序列 置换 缺失 插入 T A G C 参考序列中第二个密码子的第一个碱基对（蓝色阴影）通过碱基置换、缺失或插入发生突变。
The base substitution of a G for the T at this position leads to a codon change (shaded in green) and, assuming that the upper strand is the sense or coding strand, a predicted nonsynonymous change from a serine to an alanine in the encoded protein (see genetic code in Both the single base pair deletion and insertion lead to a frameshift mutation in which the translational reading frame is altered for all subsequent codons (shaded in green), until a termination codon is reached.该位置上T被G碱基置换导致密码子改变（绿色阴影），并假设上链为有义链或编码链，则预测所编码蛋白质中丝氨酸变为丙氨酸（非同义改变）（参见遗传密码）。单碱基对缺失和插入均导致移码突变，即所有后续密码子的翻译读框发生改变（绿色阴影），直至遇到终止密码子。
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failure to properly repair DNA after damage.
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failure to properly repair DNA after damage.损伤后DNA未能正确修复。
Many such mutation events are spontaneous, arising during the normal (but imperfect) processes of DNA replication and repair, whereas others are induced by physical or chemical agents called mutagens.许多此类突变事件是自发发生的，源于DNA复制与修复的正常（但不完美）过程，而其他突变则由称为诱变剂的物理或化学因素诱导产生。
DNA Replication Errors Typically, the process of DNA replication is highly accurate.DNA复制错误 通常，DNA复制过程具有高度精确性。
Most replication errors (i. e., bases other than the complementary bases inserted into the double helix) are rapidly removed from the DNA and corrected by a series of DNA repair enzymes.大多数复制错误（即插入双螺旋的非互补碱基）会迅速被一系列DNA修复酶从DNA中移除并纠正。
A process termed DNA proofreading first recognizes which strand in the newly synthesized double helix contains the incorrect base and then replaces it with the proper complementary base.一种称为DNA校对的过程首先识别新合成双螺旋中哪条链含有错误碱基，然后将其替换为正确的互补碱基。
DNA replication needs to be a remarkably accurate process; otherwise, the burden of mutation on the organism and the species would be intolerable.DNA复制必须是一个极其精确的过程；否则，突变对生物体及物种的负担将不可承受。
The enzyme, DNA polymerase, faithfully duplicates the two strands of the double helix based on strict base-­pairing rules (A pairs with T, C with G) but errs about once in every 10 million bp.酶DNA聚合酶基于严格的碱基配对规则（A与T配对，C与G配对）忠实地复制双螺旋的两条链，但大约每1000万个碱基对发生一次错误。
Additional proofreading then corrects more than 99. 9% of these errors of DNA replication.额外的校对随后纠正了超过99.9%的这些DNA复制错误。
Thus the overall mutation rate per base as a result of replication errors is a remarkably low 1 × 10−10 per cell division—­fewer than one mutation per genome per cell division.因此，由复制错误导致的每个碱基的总体突变率极低，为每次细胞分裂1×10⁻¹⁰——即每次细胞分裂每个基因组少于一个突变。
Repair of DNA Damage In addition to replication errors, about 10,000 to 1,000,000 nucleotides are damaged per human cell per day by (1) spontaneous chemical processes such as depurination, demethylation, or deamination, (2) reaction with chemical mutagens (natural or otherwise) in the environment, or (3) exposure to ultraviolet or ionizing radiation.DNA损伤修复 除了复制错误外，每个人类细胞每天约有10,000至1,000,000个核苷酸因以下原因受损：(1)自发化学过程，如脱嘌呤、去甲基化或脱氨基；(2)与环境中的化学诱变剂（天然的或其他）反应；或(3)暴露于紫外线或电离辐射。
Some but not all of this damage is repaired.这些损伤中有一部分（而非全部）被修复。
Even if such damage is recognized and excised, the repair machinery may introduce incorrect bases.即使此类损伤被识别并切除，修复机制也可能引入错误的碱基。
Thus in contrast to replication-­related DNA changes, which are usually corrected through proofreading mechanisms, nucleotide changes introduced by DNA damage and repair are often permanent.因此，与通常通过校对机制纠正的复制相关DNA改变相反，由DNA损伤与修复引入的核苷酸改变往往是永久性的。
A particularly common spontaneous mutation is the substitution of T for C (or A for G on the other strand).一种特别常见的自发突变是T替代C（或在另一条链上A替代G）。
The explanation for this observation comes from considering the major form of epigenetic modification in the human genome: DNA methylation, introduced in Chapter 3.对这一观察结果的解释源于考虑人类基因组中表观遗传修饰的主要形式：DNA甲基化，在第3章中介绍。
Spontaneous deamination of 5-­methylcytosine to thymine (compare the structures of cytosine and thymine in in the Cp G doublet gives rise to C to T or G to A mutations (depending on which strand the 5-­methylcytosine is deaminated).5-甲基胞嘧啶自发脱氨基为胸腺嘧啶（比较胞嘧啶和胸腺嘧啶的结构，在CpG双核苷酸中）导致C到T或G到A的突变（取决于5-甲基胞嘧啶在哪条链上脱氨基）。
Such spontaneous mutations may not be recognized by the DNA repair machinery, thus becoming established in the genome after the next round of DNA replication.此类自发突变可能不被DNA修复机制识别，从而在下一轮DNA复制后固定于基因组中。
More than 30% of all single nucleotide substitutions are of this type, and they occur at a rate 25 times greater than those of other single nucleotide mutations.所有单核苷酸替代中超过30%属于此类，其发生速率是其他单核苷酸突变的25倍。
Thus the Cp G doublet represents a true hot spot for mutation in the human genome.因此CpG双核苷酸代表了人类基因组中真正的突变热点。
Overall Rate of DNA Mutation The rate of DNA mutation at specific loci has been estimated using a variety of approaches.DNA突变的总体速率 特定基因座的DNA突变率已通过多种方法进行评估。
The impact of replication and repair errors on the occurrence of new variants throughout the genome can now be determined directly by whole genome sequencing (WGS), using trios consisting of a child and both parents, looking for new sequences in the child that are not present in either parent.复制与修复错误对全基因组新变异发生的影响现在可以直接通过全基因组测序（WGS）来确定，使用由孩子及其双亲组成的三人家系，寻找孩子中父母双方均不存在的新的序列。
The overall rate of new mutations, averaged between maternal and paternal gametes, is ~1. 2 × 10−8 per base pair per generation.新突变的总体速率，在母方和父方配子间取平均值，约为每代每碱基对1.2×10⁻⁸。
This rate, however, varies from gene to gene and perhaps from population to population, or even individual to individual.然而，该速率因基因而异，可能因人群而异，甚至因个体而异。
This rate of change, combined with considerations of population growth and dynamics, predicts that there must be an enormous number of relatively new (and thus very rare) variants among the current worldwide population of 7. 9 billion individuals.这一变化速率，结合人口增长与动态的考量，预测在当前全球79亿人口中必然存在大量相对较新（因而非常罕见）的变异。
As might be predicted, the vast majority of these will be single nucleotide variants in noncoding portions of the genome and will probably have little or no functional significance.正如可以预见的，其中绝大多数将是基因组非编码区的单核苷酸变异，且可能几乎没有或完全没有功能意义。
Nonetheless, at the level of populations, the potential collective impact of these new mutation changes on genes of medical importance should not be overlooked.尽管如此，在群体层面，这些新突变变化对具有医学重要性的基因的潜在集体影响不应被忽视。
In the United States, for example, with over 4 million live births each year, ~6 million new changes will occur in coding sequences; thus even for a single protein-­coding gene of average size, we can anticipate several hundred newborns each year with a new variant in the coding sequence of that gene.例如，在美国，每年有超过400万活产，约600万新变化将出现在编码序列中；因此，即使对于一个平均大小的蛋白质编码基因，我们也可以预期每年有数百名新生儿在该基因的编码序列中携带一个新变异。
Conceptually similar studies have determined the rate of mutation for CNVs, where the generation of a new length variant depends on recombination, rather than on errors in DNA synthesis.概念上类似的研究已确定了拷贝数变异（CNV）的突变率，其中新长度变异的产生依赖于重组，而非DNA合成错误。
The measured rate of formation of new CNVs (≈1. 2 × 10−2 per locus per generation) is orders of magnitude higher than that of base substitutions.测得的新的CNV形成率（约每个基因座每代1.2×10⁻²）比碱基替换的速率高出数个数量级。
Rate of Disease-­Causing Variations The most direct way of estimating the rate of disease-­ causing mutation, resulting in a pathogenic variant, for a given locus is to measure the incidence of new cases of a genetic condition that is clearly recognizable in all neonates who have a particular genetic alteration.致病性变异的速率 估计给定基因座导致致病性变异的致病突变率最直接的方法是，测量一种在具有特定遗传改变的所有新生儿中可明确识别的遗传病的新发病例发生率。
Achondroplasia, a condition of reduced bone growth leading to short stature (Case 2), is a condition that meets these requirements.软骨发育不全是一种骨生长减少导致身材矮小的疾病（病例2），符合这些要求。
In one series of 242,257 consecutive births, 7 children with achondroplasia were born to parents of average stature; because achondroplasia always manifests when a pathogenic variant is present, all were considered to represent new mutations.在一系列242,257例连续出生的婴儿中，有7名患有软骨发育不全的儿童出生于身材平均的父母；由于软骨发育不全在存在致病性变异时始终表现，所有这些病例均被视为新突变。
Thus the new mutation rate at this locus can be calculated to be 7 new mutations in a total of 2 × 242,257 copies of the relevant gene, or ~1. 4 × 10−5 pathogenic因此，该基因座的新突变率可计算为在相关基因共2×242,257个拷贝中有7个新突变，即约1.4×10⁻⁵致病性。
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Human Genetic Diversity 53 variants per locus per generation.
Ch4 — Segment 9
Human Genetic Diversity 53 variants per locus per generation.人类遗传多样性：每个基因座每代有53种变异。
This high mutation rate is particularly striking because virtually all cases of achondroplasia are due to the identical variant: a G to A transition that changes a glycine codon to an arginine in the encoded protein.这种高突变率尤为引人注目，因为几乎所有软骨发育不全病例均由同一变异引起：一个G到A的转换，将编码蛋白中的甘氨酸密码子变为精氨酸密码子。
The rate of pathogenic mutation has been estimated for a number of other disorders in which the occurrence of a new variant was identified by the appearance of a detectable disease ( The measured rates for these and other disorders vary over a 1000-­fold range, from 10−4 to 10−7 mutations per locus per generation.已对其他多种疾病估算出致病突变率，这些疾病中可通过可检测疾病的发生来识别新变异（针对这些及其他疾病测得的突变率范围跨达1000倍，从每基因座每代10⁻⁴到10⁻⁷突变）。
The basis for these differences may be related to some or all of the following: the size of different genes, the fraction of all variants in that gene that will lead to the disease, the age and sex of the parent in whom the mutation occurred, the mutational mechanism, and the presence or absence of mutational hot spots in the gene.这些差异的基础可能与以下部分或全部因素相关：不同基因的大小、该基因中会导致疾病的变异比例、突变发生时的父母年龄和性别、突变机制，以及基因中是否存在突变热点。
Indeed, the high rate of the particular site-­specific mutation event in achondroplasia may be partially explained by it being at a hot spot for mutation by deamination, as discussed earlier.实际上，软骨发育不全中特定位点特异性突变事件的高发生率，可部分解释为其位于脱氨基作用的突变热点，如前所述。
Notwithstanding this range of rates among different genes, the median gene mutation rate is ~1 × 10−6.尽管不同基因之间突变率范围如此之大，中位基因突变率约为1 × 10⁻⁶。
Given that there are at least 5000 genes in the human genome in which variants are currently known to cause a discernible disease or other trait (see Chapter 7), ~1 in 200 persons is likely to receive a new pathogenic variant in a known disease-­associated gene due to mutation in one or the other parent.鉴于人类基因组中目前已知至少有5000个基因的变异会导致可辨识的疾病或其他性状（见第7章），约每200人中就有1人可能因父亲或母亲的突变而获得已知疾病相关基因的新致病变异。
Sex Differences and Age Effects on Mutation Rates Because the DNA undergoes far more replication cycles in sperm than in ova (see Chapter 2), there is greater opportunity for errors to occur in sperm, suggesting that new variants will be more often paternal than maternal in origin.性别差异与年龄对突变率的影响：由于精子中的DNA复制周期远多于卵子（见第2章），精子中发生错误的机会更大，这表明新变异通常源于父亲而非母亲。
Indeed, where this has been explored, new variants responsible for certain conditions (e. g., achondroplasia, as just discussed) are usually missense variants that arose nearly always in the paternal germline.事实上，在已进行相关研究的情况下，导致某些疾病（例如，刚讨论的软骨发育不全）的新变异通常是错义变异，且几乎总是发生在父亲生殖细胞系中。
Furthermore, the older a man is, the more rounds of replication have preceded the meiotic divisions, thus the frequency of new paternal variants might be expected to increase with the age of the father.此外，男性年龄越大，减数分裂前的复制轮次就越多，因此新的父源变异频率预计会随父亲年龄增长而增加。
Indeed, increased paternal age is correlated with increased incidence of SNVs for a number of disorders (including achondroplasia) and with the incidence of CNVs in autism spectrum disorders (Case 5) and intellectual disability.确实，父亲年龄增加与多种疾病（包括软骨发育不全）中单核苷酸变异（SNV）发生率的增加，以及与自闭症谱系障碍（病例5）和智力障碍中拷贝数变异（CNV）发生率的增加相关。
For other diseases, however, the parent-­of-­origin and age effects on mutational spectra are, for unknown reasons, not as striking.然而，对于其他疾病，亲本来源和年龄对突变谱的影响，由于未知原因，并不那么显著。
TYPES OF MUTATION AND THEIR CONSEQUENCES In this section we consider the nature of different types of mutation and their effect on the genes involved.突变类型及其后果：本节我们将探讨不同类型突变的性质及其对所涉及基因的影响。
Each type of mutation discussed here is illustrated by one or more disease examples.此处讨论的每种突变类型均以一个或多个疾病实例加以说明。
Notably, the specificity of the pathogenic variant found in almost all cases of achondroplasia is the exception rather than the rule, and the variants that underlie a single genetic disease are typically heterogeneous among a group of affected individuals.值得注意的是，几乎所有软骨发育不全病例中发现的致病变异的特异性是特例而非普遍规律，而单基因疾病的变异在受影响的个体群体中通常是异质性的。
Different cases of a particular disorder will therefore usually be caused by different underlying pathogenic variants in one gene (allelic heterogeneity), sometimes in different genes (locus heterogeneity).因此，特定疾病的不同病例通常由同一基因中不同的潜在致病变异（等位基因异质性）所致，有时则由不同基因（基因座异质性）中的变异引起。
In Chapters 11 and 12 we will turn to the ways in which variants in specific disease-­ associated genes cause these disorders. 4 × 10−5 Aniridia PAX6 (Pax 6) 2. 9–­5 × 10−6 Duchenne muscular dystrophy (Case 14) DMD (dystrophin) 3. 5–­10. 5 × 10−5 Hemophilia A (Case 21) F8 (factor VIII) 3. 2–­5. 7 × 10−5 Hemophilia B (Case 21) F9 (factor IX) 2–­3 × 10−6 Neurofibromatosis, type 1 (Case 34) NF1 (neurofibromin) 4–­10 × 10−5 Polycystic kidney disease, type 1 (Case 37) PKD1 (polycystin) 6. 5–­12 × 10−5 Retinoblastoma (Case 39) RB1 (Rb 1) 5–­12 × 10−6 a Expressed as mutations per locus per generation..在第11章和第12章中，我们将探讨特定疾病相关基因中的变异如何导致这些疾病。4 × 10⁻⁵ 无虹膜症 PAX6（Pax6）2.9–5 × 10⁻⁶ 杜氏肌营养不良（病例14） DMD（肌营养不良蛋白）3.5–10.5 × 10⁻⁵ 血友病A（病例21） F8（凝血因子VIII）3.2–5.7 × 10⁻⁵ 血友病B（病例21） F9（凝血因子IX）2–3 × 10⁻⁶ 神经纤维瘤病1型（病例34） NF1（神经纤维蛋白）4–10 × 10⁻⁵ 多囊肾病1型（病例37） PKD1（多囊蛋白）6.5–12 × 10⁻⁵ 视网膜母细胞瘤（病例39） RB1（Rb1）5–12 × 10⁻⁶ a 表示为每基因座每代突变数。
Types of Variation in Human Genetic Disease Type of Variation Percentage of Disease-­Causing Variants Nucleotide Substitutions Missense variants (amino acid substitutions) 40% Nonsense variants (premature stop codons) 10% RNA processing variants (destroy consensus splice sites, cap sites, and polyadenylation sites or create cryptic sites) 10% Splice-­site variants leading to frameshift mutations and premature stop codons 10% Long-­range regulatory variants Rare Deletions and Insertions Addition or deletions of a small number of bases 25% Larger gene deletions, inversions, fusions, and duplications (may be mediated by DNA sequence homology either within or between DNA strands) 5% Insertion of a LINE or Alu element (disrupting transcription or interrupting the coding sequence) Rare Dynamic variants (expansion of trinucleotide or tetranucleotide repeat sequences) Rare人类遗传疾病中的变异类型 变异类型 致病变异百分比 核苷酸置换 错义变异（氨基酸置换） 40% 无义变异（提前终止密码子） 10% RNA加工变异（破坏共有剪接位点、加帽位点和多聚腺苷酸化位点，或生成隐蔽位点） 10% 导致移码突变和提前终止密码子的剪接位点变异 10% 长程调控变异 罕见 缺失与插入 少量碱基的添加或缺失 25% 较大的基因缺失、倒位、融合和重复（可能由DNA链内或链间的DNA序列同源性介导） 5% LINE或Alu元件插入（破坏转录或中断编码序列） 罕见 动态变异（三核苷酸或四核苷酸重复序列的扩增） 罕见
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Nucleotide Substitutions Missense Variants A single nucleotide substitution (or point mutation or SNV) in a gene sequenc…
Ch4 — Segment 10
Nucleotide Substitutions Missense Variants A single nucleotide substitution (or point mutation or SNV) in a gene sequence, such as that in the example of achondroplasia, can alter the code in a triplet of bases and cause the nonsynonymous replacement of one amino acid by another in the gene product (see the genetic code in 4. 4).核苷酸替换 错义变异 基因序列中的单个核苷酸替换（或点突变或单核苷酸变异，SNV），例如软骨发育不全中的例子，可以改变三联体碱基中的编码，并导致基因产物中一个氨基酸被另一个氨基酸非同义替换（参见4.4中的遗传密码）。
Such events are called missense mutations, creating missense variants because they alter the coding (or sense) strand of the gene to specify a different amino acid.此类事件称为错义突变，产生错义变异，因为它们改变了基因的编码链（或有义链），以指定不同的氨基酸。
Although not all missense variants lead to an observable change in the function of the protein, the resulting protein may fail to work properly, may be unstable and rapidly degraded, or may fail to localize in its proper intracellular position.尽管并非所有错义变异都会导致蛋白质功能的可观察变化，但产生的蛋白质可能无法正常工作，可能不稳定并迅速降解，或者可能无法定位于其正确的细胞内位置。
In many disorders, such as β-­thalassemia, most of the variants detected in different patients are missense variants (see Chapter 12).在许多疾病中，例如β-地中海贫血，在不同患者中检测到的大多数变异是错义变异（参见第12章）。
Nonsense Variants Point mutation in a DNA sequence that causes the replacement of the normal codon for an amino acid by one of the three termination (or “stop”) codons creates a nonsense variant or premature termination codon (PTC; also called stop gain).无义变异 DNA序列中的点突变，导致氨基酸的正常密码子被三个终止密码子（或“终止”密码子）之一替换，从而产生无义变异或提前终止密码子（PTC；也称为获得终止密码子）。
Because translation of messenger RNA (mRNA) ceases when a termination codon is reached (see Chapter 3), a variant that converts a coding codon into a termination codon causes translation to stop prematurely.由于信使RNA（mRNA）的翻译在遇到终止密码子时停止（参见第3章），将编码密码子转变为终止密码子的变异会导致翻译提前停止。
In general, mRNAs harboring a PTC are targeted for rapid degradation through a cellular process known as nonsense-­mediated mRNA decay (NMD), and no translation is possible.通常，含有PTC的mRNA通过一种称为无义介导的mRNA降解（NMD）的细胞过程被靶向快速降解，无法进行翻译。
Rarely, transcripts harboring a PTC escape NMD, most predictably if the premature stop codon occurs in last 50 bp of the penultimate exon or anywhere in the final exon of a gene.少数情况下，含有PTC的转录本逃脱了NMD，最可预测的情况是如果提前终止密码子出现在倒数第二个外显子的最后50 bp内或基因的最后一个外显子中的任何位置。
In this circumstance, a nonsense mutation can often give rise to a truncated protein with altered function.在这种情况下，无义突变通常会产生功能改变的截短蛋白。
Rarely, an SNV can alter the normal termination codon (called a stop loss variant), permitting translation to continue until another termination codon in the mRNA is reached further downstream.极少数情况下，SNV可以改变正常的终止密码子（称为终止密码子丢失变异），使翻译继续进行，直到在mRNA下游更远处遇到另一个终止密码子。
Such a variant can lead to an abnormal protein product with additional amino acids at its carboxy-­terminus.这种变异可能导致异常蛋白质产物在其羧基末端带有额外的氨基酸。
Alternatively, access of a translating ribosome into the 3′ untranslated region downstream of the normal stop codon can displace proteins that regulate mRNA stability and/­or translation.或者，翻译核糖体进入正常终止密码子下游的3′非翻译区，可能取代调节mRNA稳定性和/或翻译的蛋白质。
Variants Affecting RNA Transcription, Processing, and Translation The normal mechanism by which initial RNA transcripts are made and then converted into mature mRNAs (or final versions of noncoding RNAs) requires a series of modifications, including transcription factor binding, 5′ capping, polyadenylation, and splicing (see Chapter 3).影响RNA转录、加工和翻译的变异 初始RNA转录本被制造并随后转化为成熟mRNA（或非编码RNA的最终版本）的正常机制需要一系列修饰，包括转录因子结合、5′加帽、多聚腺苷酸化和剪接（参见第3章）。
All of these steps in RNA maturation depend on specific sequences within the RNA.RNA成熟中的所有这些步骤都依赖于RNA内的特定序列。
In the case of splicing, two general classes of splicing variants have been described.在剪接的情况下，已经描述了两种一般类型的剪接变异。
For introns to be excised from unprocessed RNA and the exons spliced together to form a mature RNA requires particular nucleotide sequences located at or near the exon-­intron (5′ donor site) or the intron-­exon (3′ acceptor site) junctions.为了从未加工的RNA中切除内含子并将外显子拼接在一起以形成成熟RNA，需要位于或靠近外显子-内含子（5′供体位点）或内含子-外显子（3′受体位点）连接处的特定核苷酸序列。
Variants that substitute the required bases at either the splice donor or acceptor site prevent normal RNA splicing.在剪接供体或受体位点替换所需碱基的变异会阻止正常的RNA剪接。
Substitution of less conserved adjacent bases has a variable impact on splicing efficiency.较不保守的邻近碱基的替换对剪接效率有不同的影响。
A second class of splicing variants involves base substitutions that do not affect the donor or acceptor site sequences themselves, but instead create alternative donor or acceptor sites that compete with the normal sites during RNA processing.第二类剪接变异涉及碱基替换，这些替换不影响供体或受体位点序列本身，而是在RNA加工过程中产生与正常位点竞争的可替代供体或受体位点。
Activation of these so-­called cryptic splice sites can lead to inappropriate exclusion or inclusion of exonic or intronic sequences, respectively, in the mature mRNA.这些所谓的隐蔽剪接位点的激活可能导致成熟mRNA中分别不适当地排除或包含外显子或内含子序列。
Thus at least a proportion of the mature mRNA or noncoding RNA in such cases may contain improperly spliced intron sequences.因此，在这种情况下，至少一部分成熟mRNA或非编码RNA可能含有错误剪接的内含子序列。
Examples of both types of variation are presented in Chapter 12.两种类型变异的例子在第12章中给出。
For protein-­coding genes, even if the mRNA is made, SNVs in the 5′ and 3′ untranslated regions can contribute to disease by changing mRNA stability or translational efficiency, thereby reducing the amount of protein product.对于蛋白质编码基因，即使mRNA被制造出来，5′和3′非翻译区中的SNV也可以通过改变mRNA稳定性或翻译效率来导致疾病，从而减少蛋白质产物的数量。
Deletions, Insertions, and Rearrangements Mutation can also involve the insertion, deletion, or rearrangement of DNA sequences.缺失、插入和重排 突变还可能涉及DNA序列的插入、缺失或重排。
Some deletions and insertions involve only a few nucleotides and are generally most easily detected by direct sequencing of that part of the genome.一些缺失和插入只涉及少数核苷酸，通常通过直接测序基因组的那部分最容易检测到。
In other cases, a substantial segment of a gene or an entire gene is deleted, duplicated, inverted, or translocated to create a novel arrangement of gene sequences—­collectively called structural variants.在其他情况下，基因的一个实质性片段或整个基因被缺失、重复、倒位或易位，从而产生新的基因序列排列——统称为结构变异。
Depending on the exact nature of the deletion, insertion, or rearrangement, a variety of different laboratory approaches can be used to detect the genomic alteration.根据缺失、插入或重排的确切性质，可以使用多种不同的实验室方法来检测基因组改变。
Some deletions and insertions affect only a small number of base pairs.一些缺失和插入只影响少量碱基对。
When such a variant occurs in a coding sequence and the number of bases involved is not a multiple of three (i. e., not an integral number of codons), the reading frame will be altered beginning at the point of the insertion or deletion.当这种变异发生在编码序列中，且涉及的碱基数不是三的倍数（即不是整数个密码子）时，从插入或缺失点开始，阅读框将被改变。
The results are called frameshift variants .其结果称为移码变异。
From the point of the insertion or deletion, a different sequence of codons is thereby generated that encodes incorrect amino acids followed by a termination codon in the shifted frame.从插入或缺失点开始，由此产生不同的密码子序列，编码错误的氨基酸，随后在移码中遇到终止密码子。
This typically leads to degradation of the altered transcript via activation of NMD or, more rarely,这通常通过激活NMD导致改变的转录本降解，或更罕见地，产生一种异常的延长蛋白。
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Human Genetic Diversity 55 an altered and truncated protein product.
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Human Genetic Diversity 55 an altered and truncated protein product.人类遗传多样性55一种改变且截短的蛋白质产物。
In contrast, if the number of base pairs inserted or deleted is a multiple of three, then no frameshift occurs, and there will be a simple insertion or deletion of the corresponding amino acids in the otherwise normally translated gene product.相比之下，如果插入或删除的碱基对数目是三的倍数，则不会发生移码，而会在其他正常翻译的基因产物中简单插入或删除相应的氨基酸。
Larger insertions or deletions can affect multiple exons of a gene and cause major disruptions of the coding sequence.较大的插入或缺失可影响基因的多个外显子，并导致编码序列的严重破坏。
One type of insertion mutation involves insertion of a mobile element, such as those belonging to the LINE family of repetitive DNA (LINE-­1 [L1] elements).一种插入突变类型涉及移动元件的插入，例如属于重复DNA的LINE家族（LINE-1 [L1]元件）的那些。
Any of the 146 putatively active L1 elements currently recognized in the human genome are capable of movement by retrotransposition (introduced earlier).目前人类基因组中已识别的146个假定活跃的L1元件中的任何一个都能够通过逆转座作用（如前所述）进行移动。
Such movement not only generates genetic diversity in our species but can cause disease by insertional mutagenesis.这种移动不仅在我们物种中产生遗传多样性，还可能通过插入诱变导致疾病。
For example, in some patients with the severe bleeding disorder hemophilia A (Case 21), LINE sequences several kilobases long are found within an exon in the factor VIII gene, interrupting the coding sequence and inactivating the gene.例如，在一些患有严重出血性疾病血友病A（病例21）的患者中，在因子VIII基因的一个外显子内发现了数kb长的LINE序列，中断了编码序列并使该基因失活。
LINE insertions throughout the genome are also common in colon cancer, reflecting retrotransposition in somatic cells (see Chapter 16).基因组中的LINE插入在结肠癌中也常见，反映了体细胞中的逆转座作用（见第16章）。
As we discussed earlier in this chapter, duplications, deletions, and inversions of a larger segment of a single chromosome are predominantly the result of homologous recombination between DNA segments with high sequence homology .正如本章前面所讨论的，单个染色体较大片段的重复、缺失和倒位主要是具有高度序列同源性的DNA片段之间同源重组的结果。
Disorders arising as a result of such exchanges can be due to a change in the dosage of otherwise wild-­type gene products when the homologous segments lie outside the genes themselves (see Chapter 6).此类交换导致的疾病可能是由于当同源片段位于基因本身之外时，其他野生型基因产物的剂量发生改变（见第6章）。
Alternatively, such events can lead to a change in the nature of the encoded protein itself when recombination occurs between different genes within a gene family (see Chapter 12) or between genes on different chromosomes (see Chapter 16).或者，当重组发生在基因家族内不同基因之间（见第12章）或不同染色体上的基因之间（见第16章）时，此类事件可导致编码蛋白质本身性质的改变。
Abnormal pairing and recombination between two similar sequences in opposite orientation on a single strand of DNA leads to inversion.在单条DNA链上，两个方向相反的相似序列之间的异常配对和重组会导致倒位。
For example, nearly half of all cases of hemophilia A are due to recombination that inverts a number of exons, thereby disrupting gene structure and rendering the gene incapable of encoding a normal gene product .例如，近一半的血友病A病例是由于重组导致多个外显子倒位，从而破坏基因结构，使该基因无法编码正常的基因产物。
Repeat Expansion Variants The pathogenic variant in some disorders involves amplification of a simple nucleotide repeat sequence.重复扩增变异 某些疾病中的致病变异涉及简单核苷酸重复序列的扩增。
For example, simple repeats such as (CCG)n, (CAG)n, or (CCTG)n—­located in the coding portion of an exon, in an untranslated region of an exon, or even in an intron—­may expand during gametogenesis in repeat expansion or dynamic mutation, and interfere with normal gene expression or protein function.例如，简单重复如(CCG)n、(CAG)n或(CCTG)n——位于外显子的编码部分、外显子的非翻译区甚至内含子中——可能在配子发生过程中因重复扩增或动态突变而扩增，并干扰正常的基因表达或蛋白质功能。
An expanded repeat in a coding region will generate an abnormal protein product; in the untranslated regions or introns of a gene, it may interfere with transcription, mRNA processing, or translation.编码区中的扩增重复将产生异常的蛋白质产物；在基因的非翻译区或内含子中，它可能干扰转录、mRNA加工或翻译。
How repeat expansions occur is not completely understood; they are conceptually similar to microsatellites but expand at a much higher rate.重复扩增的发生机制尚未完全阐明；它们在概念上类似于微卫星，但以更高的速率扩增。
The involvement of simple nucleotide repeat expansions in disease is discussed further in Chapter 7.简单核苷酸重复扩增在疾病中的参与将在第7章进一步讨论。
In such disorders, marked parent-­of-­origin effects are A B 23 22 21 1 23 1 A B 23 22 21 1 Mispairing and recombination Hemophilia A mutation Remainder of gene Upstream of gene Remainder of gene Upstream of gene Factor VIII gene A/B A/B 21 22 Inverted segment within gene Intrachromosomal mispairing and recombination results in inversion of exons 1 through 22 of the gene, thereby disrupting the gene and causing severe hemophilia.在这些疾病中，显著的亲本效应是 A B 23 22 21 1 23 1 A B 23 22 21 1 错配与重组 血友病A突变 基因剩余部分 基因上游 基因剩余部分 基因上游 因子VIII基因 A/B A/B 21 22 基因内倒位片段 染色体内错配与重组导致基因第1至22外显子倒位，从而破坏基因并引起严重血友病。
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well known and appear characteristic of the specific disease and/­or the particular simple nucleotide repeat involved (s…
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well known and appear characteristic of the specific disease and/­or the particular simple nucleotide repeat involved (see Chapter 13).众所周知，这些特征具有特定疾病和/或所涉及的特定简单核苷酸重复的特征（见第13章）。
Such differences may be due to fundamental biologic differences between oogenesis and spermatogenesis but may also result from selection against gametes carrying certain repeat expansions.这种差异可能源于卵子发生与精子发生之间的基本生物学差异，也可能源于对携带某些重复扩增的配子的选择排斥。
VARIATION IN INDIVIDUAL GENOMES The most extensive current inventory of the amount and type of variation in any given genome, relative to the (composite) human reference genome sequence (see Chapter 2), comes from the analysis of individual diploid human genome sequences.个体基因组中的变异：目前关于任何给定基因组相对于（复合）人类参考基因组序列（见第2章）的变异数量和类型的最全面清单，来自对个体二倍体人类基因组序列的分析。
The first such sequence, that of a male individual, was reported in 2007.首个此类序列（一名男性个体的序列）于2007年报道。
Now, hundreds of thousands of individual genomes have been sequenced, some as part of large international research consortia exploring human genetic diversity in health and disease, and others in the context of clinical sequencing to determine the underlying basis of disorders in particular patients.如今，已有数十万个个体基因组被测序，其中一些是探索健康与疾病中人类遗传多样性的大型国际研究联盟的一部分，另一些则是在临床测序背景下，用于确定特定患者疾病的潜在基础。
What degree of genome variation does one detect in such studies?在此类研究中，人们能检测到多大程度的基因组变异？
Individual human genomes typically carry ~3. 5 million SNVs when compared to the reference genome, of which—­depending in part on the population—­currently 1% are novel (i. e., not previously documented) (see 2).与参考基因组相比，个体人类基因组通常携带约350万个单核苷酸变异（SNV），其中——部分取决于人群——目前有1%是新的（即此前未记录）（见2）。
This suggests that the number of SNVs described for our species is still incomplete, although presumably the novel fraction will decrease as more genomes from more populations are sequenced.这表明，人类物种已描述的SNV数量仍不完整，不过随着更多人群的基因组被测序，新变异所占比例预计将下降。
Within this variation lie variants with clinical impact that are either known, likely, or suspected.在这些变异中，存在已知、可能或怀疑具有临床影响的变异。
Each genome carries 50 to 100 variants that have previously been implicated in known inherited conditions.每个基因组携带50至100个此前已知与遗传性疾病相关的变异。
In addition, each genome carries thousands of nonsynonymous SNVs in protein-­coding genes, some of which would be predicted to alter protein function.此外，每个基因组在蛋白质编码基因中携带数千个非同义SNV，其中一些预计会改变蛋白质功能。
Each genome also carries ~200 to 500 likely loss-­of-­ function variants, some of which are present at both alleles of a gene in that individual.每个基因组还携带约200至500个可能的功能丧失型变异，其中一些在该个体的一个基因的两个等位基因上同时存在。
Within the clinical setting, this realization has important implications for the interpretation of genome sequence data from patients, particularly when trying to predict the impact of variants in genes of currently unknown function (see Chapter 13).在临床环境中，这一认识对解释患者的基因组序列数据具有重要意义，尤其是在试图预测目前功能未知的基因中变异的影响时（见第13章）。
An interesting and unanticipated aspect of individual genome sequencing is that each new genome reveals some sequence that is still undocumented or unannotated in the reference human genome assembly.个体基因组测序中一个有趣且出乎意料的方面是，每个新基因组都会揭示一些在参考人类基因组组装中尚未被记录或注释的序列。
It is estimated that, once fully elucidated, the complete genome sequence representing the current world population will be 20 to 40 Mb larger than the extant reference assembly.据估计，一旦完全阐明，代表当前世界人口的完整基因组序列将比现有的参考组装大20至40 Mb。
Recently WGS performed on only 94 individuals from 44 African populations revealed 33. 6 million SNVs, of which 5. 7 million (17%) were Clinical Sequencing Studies In the context of genomic medicine, a key question is the extent to which variation in the sequence and/­or expression of one’s genome influences the likelihood of disease onset, determines the natural history of disease, and/­or provides clues relevant to its management.最近，仅对来自44个非洲人群的94名个体进行的全基因组测序（WGS）揭示了3360万个SNV，其中570万个（17%）是新的。在临床测序研究中，对于基因组医学而言，一个关键问题是：基因组序列和/或表达中的变异在多大程度上影响疾病发生的可能性、决定疾病的自然史，以及/或提供与其管理相关的线索。
As just discussed, constitutional genomic variants can have a number of different direct or indirect effects on gene function.正如刚刚讨论的，组成性基因组变异可能对基因功能产生多种直接或间接影响。
Sequencing of entire genomes (WGS, also referred to as genome sequencing) or of the subset comprising all known coding exons (exome sequencing) has been introduced in a number of clinical settings, as will be discussed in greater detail in Chapter 11.对全基因组（WGS，也称为基因组测序）或所有已知编码外显子子集（外显子组测序）的测序已在多种临床环境中引入，这将在第11章中更详细地讨论。
Both exome sequencing and WGS have been used to detect de novo changes (both SNVs and CNVs) in a variety of conditions of complex and/­or unknown etiology.外显子组测序和全基因组测序均已被用于检测多种复杂和/或病因不明疾病中的新生改变（包括SNV和拷贝数变异CNV）。
These include, for example, various neurodevelopmental or neuropsychiatric conditions, such as autism, schizophrenia, epilepsy, intellectual disability, and developmental delay.这些疾病包括例如各种神经发育或神经精神疾病，如自闭症、精神分裂症、癫痫、智力残疾和发育迟缓。
Clinical sequencing studies can target either germline or somatic variants.临床测序研究可针对胚系变异或体细胞变异。
In cancer, especially, various strategies have been used to search for somatic variants in tumor tissue to identify genes potentially relevant to cancer progression (see Chapter 16)..特别是在癌症中，已采用多种策略在肿瘤组织中寻找体细胞变异，以识别可能与癌症进展相关的基因（见第16章）。
VARIATION DETECTED IN A TYPICAL HUMAN GENOME Individuals vary greatly in a wide range of biologic functions, determined in part by variation among their genomes.典型人类基因组中检测到的变异：个体在广泛的生物学功能上存在巨大差异，部分由其基因组变异决定。
Any individual genome will contain (on average) the following: ≈3. 5 million SNVs compared to the reference genome (varies by population) 25,000–­50,000 rare variants (private mutations or seen previously in <0. 5% of individuals tested) ≈65 new (de novo) SNVs and indels not detected in parental genomes ≈200,000 indels (1–­50 bp) (varies by population) 500–­1000 deletions 1–­45 kb, overlapping ≈200 genes ≈102 in-­frame indels ≈132 shifts in reading frame 10,000–­12,000 synonymous SNVs >11,000 nonsynonymous SNVs in 4000–­5000 genes 175–­500 rare nonsynonymous variants 1 new nonsynonymous mutation ≈474 premature stop codons or splice site disrupting variants 250–­300 genes with likely loss-­of-­function variants ≈25 genes predicted to be completely inactivated novel.任何个体基因组平均将包含以下内容：与参考基因组相比约350万个SNV（因人群而异）；25,000–50,000个罕见变异（私有突变或此前在不到0.5%的受检个体中发现）；约65个在亲本基因组中未检测到的新生SNV和插入缺失（indel）；约20万个插入缺失（1–50 bp，因人群而异）；500–1000个缺失（1–45 kb），覆盖约200个基因；约102个框内插入缺失；约132个移码；10,000–12,000个同义SNV；超过11,000个非同义SNV（分布于4000–5000个基因）；175–500个罕见非同义变异；1个新生非同义突变；约474个提前终止密码子或剪接位点破坏变异；250–300个携带可能功能丧失型变异的基因；约25个预测被完全失活的新基因。
This illustrates the extent to which individuals of descent other than European are underrepresented among sequenced cohorts, creating a significant gap in our knowledge of human genetic diversity and our ability to advance genomic medicine.这表明，非欧洲裔个体在测序队列中的代表性不足，这在我们对人类遗传多样性的认识以及推进基因组医学的能力方面造成了显著差距。
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Human Genetic Diversity 57 Direct-­to-­Consumer Genomics Access to laboratory genomic testing has moved into the public …
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Human Genetic Diversity 57 Direct-­to-­Consumer Genomics Access to laboratory genomic testing has moved into the public realm in recent years, no longer with mainstream medicine as its gatekeeper.人类遗传多样性 57 直接面向消费者的基因组学 近年来，实验室基因组检测已进入公共领域，不再以主流医学作为其把关人。
Tests are marketed directly to consumers for information ranging from genealogy and ancestry tracing to information about personal health and inherited traits.检测产品直接向消费者营销，提供从家系和祖先追溯到个人健康与遗传性状等各类信息。
Targeted screening panels are starting to give way to genome sequencing opportunities.靶向筛查组合正在逐步让位于基因组测序机会。
A limited number of specific diagnostic tests have been authorized by the US Food and Drug Administration for marketing.美国食品药品监督管理局已授权有限数量的特定诊断检测上市。
There is considerable public appetite for the sort of individual information being offered commercially, and the massive volume of data being collected and stored has enormous research potential.公众对商业提供的这类个人化信息有相当大的需求，而正在收集和存储的海量数据拥有巨大的研究潜力。
Notwithstanding or minimizing the significant scientific, ethical, and clinical issues that lie ahead, it is certain that individual genome sequences will be an ongoing active part of medical practice and that some of these will be delivered from patient to practitioner, rather than vice versa.尽管或淡化未来面临的重大科学、伦理和临床问题，但个体基因组序列无疑将成为医疗实践中持续活跃的一部分，其中部分序列将由患者传递给医师，而非相反。
IMPACT OF GENOMIC VARIATION Although it will be self-­evident to students of human genetics that new pathogenic or rare variants in the population can have clinical consequences, it may appear less obvious that common variants can be clinically relevant.基因组变异的影响 虽然对人类遗传学学生而言，群体中新的致病性或罕见变异可能具有临床后果是不言而喻的，但常见变异具有临床相关性这一点可能不那么显而易见。
For the proportion of variation that occurs within protein-­coding genes, such loci can be studied by examining variation in the proteins encoded by the different alleles.对于发生在蛋白质编码基因内的那部分变异，可以通过检测不同等位基因所编码蛋白质的变异来研究这些位点。
Any one individual is likely to carry two distinct alleles determining structurally differing polypeptides at an estimated 20% of protein-­coding loci; when individuals from different ancestral groups are studied, an even greater fraction of proteins has been found to exhibit detectable polymorphism.任何个体都可能携带两个不同的等位基因，在大约20%的蛋白质编码位点上决定结构不同的多肽；当研究来自不同祖先群体的个体时，发现更高比例的蛋白质呈现可检测的多态性。
In addition, even when the gene product is unaltered, the levels of expression of that product may be very different among individuals, determined by a combination of genetic and epigenetic variation, as we saw in Chapter 3.此外，即使基因产物未发生改变，该产物的表达水平在个体间也可能差异很大，这由遗传和表观遗传变异的组合决定，正如我们在第3章所见。
Thus a striking degree of biochemical individuality exists within the human species in its makeup of enzymes and other gene products.因此，人类物种在酶及其他基因产物的构成上存在显著程度的生化个体性。
Furthermore, the products of many of the encoded biochemical and regulatory pathways interact in functional and physiologic networks.此外，许多编码的生化与调控通路的产物在功能性和生理性网络中相互作用。
Each individual, therefore—­regardless of state of health—­has a unique, genetically determined chemical makeup and responds in a unique manner to environmental, dietary, and pharmacologic influences.因此，每个个体——无论健康状况如何——都具有独特的、由遗传决定的化学组成，并以独特的方式对环境、饮食和药物影响作出反应。
This concept of chemical individuality first put forward over a century ago by Archibald Garrod, the remarkably prescient British physician introduced in Chapter 1, remains true today.这种化学个体性的概念首次由阿奇博尔德·加罗德（Archibald Garrod）在一个多世纪前提出，这位在第1章中介绍过的极具远见的英国医生，其观点至今仍然成立。
The broad question of what is normal—­an essential concept in human biology and in clinical medicine—­remains very much an open and controversial one when it comes to the human genome.关于“什么是正常”这一广泛问题——人类生物学和临床医学中的一个基本概念——在涉及人类基因组时，仍然是一个开放且充满争议的议题。
The following chapters will explore this concept of individuality in detail, first in the context of structural genome and chromosome variants (Chapters 5 and 6) and then in terms of intragenic variants that determine the inheritance of genetic disease (Chapter 7) and influence its likelihood in families and populations (Chapter 10).接下来的章节将详细探讨这一个体性概念，首先在结构基因组和染色体变异的背景下（第5章和第6章），然后从决定遗传疾病遗传（第7章）并影响其在家族和群体中发生可能性（第10章）的基因内变异角度展开。
Assessing the Clinical Significance of a Gene Variant The American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommend that all variants detected during sequencing of genes for monogenic disease (whether from targeted, exome, or genome sequencing) be classified on a five-­level scale, spanning pathogenic, likely pathogenic, of uncertain significance, likely benign, and benign variants.评估基因变异的临床意义 美国医学遗传学与基因组学学会以及分子病理学协会建议，对单基因疾病基因测序（无论是靶向测序、外显子组测序还是基因组测序）中检测到的所有变异，按五级分类标准进行划分：致病性、可能致病性、意义不明确、可能良性和良性变异。
Specialists in molecular diagnostics, human genomics, and bioinformatics have developed criteria for assessing where a variant sits among these five categories.分子诊断、人类基因组学和生物信息学领域的专家已制定了评估变异在这五类中归属的标准。
None of these criteria are definitive; they must be considered together to provide an overall assessment of the evidence for pathogenicity.这些标准均非决定性；需综合考虑以对致病性证据作出整体评估。
These criteria include the following: Population frequency—­If a variant has been seen frequently in a sizable fraction of the general population, beyond what is expected based on the prevalence of the disease, it is considered less likely to be disease causing.这些标准包括以下内容：群体频率——如果一个变异在相当大比例的一般人群中频繁出现，超出基于疾病患病率的预期范围，则被认为不太可能是致病的。
Being frequent, however, is no guarantee that a variant is benign.然而，频率高并不能保证一个变异是良性的。
Autosomal recessive conditions result from homozygosity for disease-­causing variants that may be surprisingly common, largely harbored by asymptomatic heterozygous carriers.常染色体隐性遗传病由致病性变异的纯合性引起，这些变异可能惊人地常见，主要由无症状的杂合携带者携带。
Conversely, rare variants are not necessarily pathogenic; most variants found in an exome or genome sequence are individually rare.相反，罕见变异不一定致病；在外显子组或基因组序列中发现的大多数变异，每个单独来看都是罕见的。
In silico assessment—­Computational algorithms can evaluate how likely a missense variant is to be damaging to the protein, by using information such as whether the amino acid at that position is conserved in orthologous proteins (in other species), the structural location of the variant, and machine-­learning algorithms.计算机评估——计算算法可以利用如下信息评估错义变异损害蛋白质的可能性：该位置氨基酸在直系同源蛋白质（在其他物种中）是否保守、变异的结构位置以及机器学习算法。
Such tools are limited in their accuracy for predicting functional impact and therefore can never be used alone to definitively determine pathogenicity.此类工具在预测功能影响方面准确性有限，因此绝不可单独用于最终确定致病性。
They are, however, improving with time, and their contribution to variant assessment may strengthen.然而，它们正在随时间改进，其对变异评估的贡献可能会增强。
Other bioinformatics tools assess the pathogenicity of other types of variants, such as potential splice site variants and other noncoding sequence variants.其他生物信息学工具评估其他类型变异的致病性，例如潜在的剪接位点变异和其他非编码序列变异。
Functional data—­If a particular variant adversely affects in vitro biochemical activity, a function in cultured cells, or the health of a model organism, then it is less likely to be benign.功能数据——如果某个特定变异对体外生化活性、培养细胞的功能或模式生物的健康产生不利影响，则其不太可能是良性的。
However, it remains possible然而，它仍有可能。
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that a particular variant will appear benign by these criteria and still be disease causing in humans because of a prolonged human life span, environmental triggers, or compensatory genes present in the model organism but not in humans.根据这些标准看似良性的特定变异，由于人类寿命延长、环境触发因素或模式生物中存在但人类缺乏的代偿基因，仍可能在人类中导致疾病。
Conversely, functional effects demonstrated in systems that do not fully represent the human biologic state may falsely implicate a variant as pathogenic.相反，在未完全代表人类生物学状态的系统中展示的功能效应，可能错误地将某种变异归为致病性。
Caution must be exercised to ensure adequate validation of these assays with variants determined to be pathogenic or benign through other types of evidence.必须谨慎行事，确保这些检测方法已通过其他类型证据确定为致病性或良性的变异得到充分验证。
Segregation data—­If a particular variant is coinherited with a disease in one or more families or, conversely, does not track with a disease in the family under investigation, then it is more or less likely to be pathogenic.分离数据——如果某一特定变异在一个或多个家族中与疾病共同遗传，或者反过来，在所研究的家族中不与疾病共分离，那么它更可能或更不可能具有致病性。
Of course, when only a few individuals are affected, the variant and disease may appear to track by random chance; to be considered strong evidence for pathogenicity, the number of times a variant and disease must be coinherited is generally accepted to be in at least five informative meioses.当然，当只有少数个体受累时，变异和疾病可能看起来是随机共存的；要作为致病性的强证据，一般认为变异与疾病必须至少在有信息的五次减数分裂中共同遗传。
Finding affected individuals in the family who do not carry the variant would be strong evidence against the variant being pathogenic, but finding unaffected individuals who do carry the variant is less persuasive if the disorder is known to have reduced penetrance.在家族中发现未携带该变异的患病个体，将是反对该变异致病性的强证据；但如果已知该疾病具有外显率降低，则发现携带该变异的未患病个体说服力较弱。
De novo variant—­The appearance of a severe disorder in a child along with a new variant in a coding exon that neither parent carries (de novo variant) is additional evidence for that variant to be pathogenic.新生变异——儿童出现严重疾病，同时其编码外显子中出现父母双方均不携带的新变异（新生变异），是该变异具有致病性的额外证据。
However, between one and two new changes occur in the coding regions of genes in every child (see earlier).然而，每个儿童的基因编码区会发生一到两次新的变化（见前述内容）。
Only de novo variants in genes that are associated with the individual’s phenotype are considered evidence for pathogenicity, given a lower prior probability of de novo mutation for a small, targeted set of genes.鉴于针对较小靶向基因集的新生突变先验概率较低，仅当新生变异出现在与个体表型相关的基因中时，才被视为致病性证据。
Variant characterization—­A variant may be synonymous, missense, nonsense, a frameshift with a premature termination downstream, or cause a highly conserved splice site change.变异特征描述——变异可为同义、错义、无义、导致下游提前终止的移码，或引起高度保守剪接位点改变。
The impact on the function of the gene can be inferred but, once again, is not definitive.可推断其对基因功能的影响，但再次强调，这并非决定性。
For example, a synonymous change that does not alter an amino acid codon might be thought to be benign but may have deleterious effects on normal splicing and be pathogenic (see examples in Chapter 12).例如，不改变氨基酸密码子的同义改变可能被认为良性，但可能对正常剪接产生有害影响而具有致病性（见第12章中的例子）。
Conversely, one might assume that premature termination or frameshift variants are always deleterious and disease causing; however, such an alteration at the far 3′ end of a gene may produce a truncated protein that is still functional and, therefore, be a benign change.相反，人们可能认为提前终止或移码变异总是有害且致病；然而，位于基因远3'端的此类改变可能产生仍有功能的截短蛋白，因此为良性改变。
Prior occurrence—­Having been seen multiple times among collections of patients with a similar disorder is important additional evidence that a variant is pathogenic.既往出现——在患有类似疾病的患者集合中多次被观察到，是变异致病性的重要额外证据。
Even if a missense variant is novel (i. e., never described before) it is more likely to be pathogenic if it occurs at the same position in the protein as other known pathogenic missense variants.即使某个错义变异是新型的（即从未描述过），如果它出现在与其他已知致病性错义变异相同的蛋白位置上，则更可能具有致病性。
ACKNOWLEDGMENT We thank Miriam Reuter, Heidi Rehm and Jeff Mac Donald for contributing to this chapter.致谢：我们感谢Miriam Reuter、Heidi Rehm和Jeff Mac Donald对本章的贡献。
GENERAL REFERENCES Olson MV: Human genetic individuality, Ann Rev Genomics Hum Genet 13:1–­27, 2012.一般参考文献：Olson MV: Human genetic individuality, Ann Rev Genomics Hum Genet 13:1–27, 2012.
Strachan T, Read A, editors: Human molecular genetics ed 5, New York, 2018, Garland Science.Strachan T, Read A, editors: Human molecular genetics ed 5, New York, 2018, Garland Science.
The 1000 Genomes Project Consortium: An integrated map of genetic variation from 1,092 human genomes, Nature 491:56–­65, 2012.The 1000 Genomes Project Consortium: An integrated map of genetic variation from 1,092 human genomes, Nature 491:56–65, 2012.
Trost B, Loureiro LO, Scherer SW: Discovery of genomic variation across a generation, Human Molecular Genetics, Volume 30, Issue R2, 15 October 2021, Pages R174–R186, org/­10. 1093/­hmg/­ddab 209.Trost B, Loureiro LO, Scherer SW: Discovery of genomic variation across a generation, Human Molecular Genetics, Volume 30, Issue R2, 15 October 2021, Pages R174–R186, org/10.1093/hmg/ddab209.
Willard HF: The human genome: a window on human genetics, biology and medicine.Willard HF: The human genome: a window on human genetics, biology and medicine.
In Ginsburg GS, Willard HF, editors: Genomic and personalized medicine ed 3, New York, 2016, Elsevier.In Ginsburg GS, Willard HF, editors: Genomic and personalized medicine ed 3, New York, 2016, Elsevier.
REFERENCES FOR SPECIFIC TOPICS Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping, Nature Rev Genet 12:363–­376, 2011.特定主题参考文献：Alkan C, Coe BP, Eichler EE: Genome structural variation discovery and genotyping, Nature Rev Genet 12:363–376, 2011.
Bagnall RD, Waseem N, Green PM, et al: Recurrent inversion breaking intron 1 of the factor VIII gene is a frequent cause of severe hemophilia A, Blood 99:168–­174, 2002.Bagnall RD, Waseem N, Green PM, et al: Recurrent inversion breaking intron 1 of the factor VIII gene is a frequent cause of severe hemophilia A, Blood 99:168–174, 2002.
Crow JF: The origins, patterns and implications of human spontaneous mutation, Nature Rev Genet 1:40–­47, 2000.Crow JF: The origins, patterns and implications of human spontaneous mutation, Nature Rev Genet 1:40–47, 2000.
Fan S, Kelley DE, Beltrame MH, et al: African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations, Genome Biol 20:82, 2019.Fan S, Kelley DE, Beltrame MH, et al: African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations, Genome Biol 20:82, 2019.
Gardner RJ: A new estimate of the achondroplasia mutation rate, Clin Genet 11:31–­38, 1977.Gardner RJ: A new estimate of the achondroplasia mutation rate, Clin Genet 11:31–38, 1977.
Karczewski KJ, Francioli LC, Tiao G, et al: The mutational constraint spectrum quantified from variation in 141,456 humans, Nature 581:434–­443, 2020. 41586-­020-­2308-­7 Kong A, Frigge ML, Masson G, et al: Rate of de novo mutations and the importance of father’s age to disease risk, Nature 488:471–­475, 2012.Karczewski KJ, Francioli LC, Tiao G, et al: The mutational constraint spectrum quantified from variation in 141,456 humans, Nature 581:434–443, 2020. 41586-020-2308-7 Kong A, Frigge ML, Masson G, et al: Rate of de novo mutations and the importance of father’s age to disease risk, Nature 488:471–475, 2012.
Lappalainen T, Sammeth M, Friedlander MR, et al: Transcriptome and genome sequencing uncovers functional variation in humans, Nature 501:506–­511, 2013.Lappalainen T, Sammeth M, Friedlander MR, et al: Transcriptome and genome sequencing uncovers functional variation in humans, Nature 501:506–511, 2013.
Mac Arthur DG, Balasubramanian S, Rrankish A, et al: A systematic survey of loss-­of-­function variants in human protein-­coding genes, Science 335:823–­828, 2012.Mac Arthur DG, Balasubramanian S, Rrankish A, et al: A systematic survey of loss-of-function variants in human protein-coding genes, Science 335:823–828, 2012.
Mc Bride CM, Wade CH, Kaphingst KA: Consumers’ view of direct-­ to-­consumer genetic information, Ann Rev Genomics Hum Genet 11:427–­446, 2010.Mc Bride CM, Wade CH, Kaphingst KA: Consumers’ view of direct-to-consumer genetic information, Ann Rev Genomics Hum Genet 11:427–446, 2010.
Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, Genet Med 17(5):405–­424, 2015.Richards S, Aziz N, Bale S, et al: Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology, Genet Med 17(5):405–424, 2015.
Stewart C, Kural D, Stromberg MP, et al: A comprehensive map of mobile element insertion polymorphisms in humans, PLo S Genet 7:e 1002236, 2011.Stewart C, Kural D, Stromberg MP, et al: A comprehensive map of mobile element insertion polymorphisms in humans, PLo S Genet 7:e1002236, 2011.
Sun JX, Helgason A, Masson G, et al: A direct characterization of human mutation based on microsatellites, Nature Genet 44:1161–­ 1165, 2012.Sun JX, Helgason A, Masson G, et al: A direct characterization of human mutation based on microsatellites, Nature Genet 44:1161–1165, 2012.
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Human Genetic Diversity 59 PROBLEMS 1.
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Human Genetic Diversity 59 PROBLEMS 1.人类遗传多样性 59 问题 1.
Variation can arise from a variety of mechanisms, with different consequences.变异可由多种机制产生，并带来不同的后果。
Describe and contrast the types of variation that can have the following effects: a.描述并对比可产生以下效应的变异类型：a.
A change in dosage of a gene or genes b.一个或多个基因剂量的改变 b.
A change in the sequence of multiple amino acids in the product of a protein-­coding gene c.蛋白质编码基因产物中多个氨基酸序列的改变 c.
A change in the final structure of an RNA produced from a gene d.一个基因产生的RNA最终结构的改变 d.
A change in the order of genes in a region of a chromosome e.染色体某一区域中基因顺序的改变 e.
No obvious effect 2.无明显效应 2.
Aniridia is an eye disorder characterized by the complete or partial absence of the iris and is always present when a pathogenic variant occurs in the responsible gene.无虹膜症是一种以虹膜完全或部分缺失为特征的眼部疾病，且当致病性变异发生在相关基因中时，该疾病总是出现。
In one population, 41 children diagnosed with aniridia were born to parents of normal vision among 4. 5 million births during a period of 40 years.在一个人群中，40年间在450万新生儿中，有41名被诊断为无虹膜症的儿童出生于视力正常的父母。
Assuming that these cases were due to new mutation events, what is the estimated mutation rate at the aniridia locus?假设这些病例是由新突变事件引起的，那么无虹膜症位点的估计突变率是多少？
On what assumptions is this estimate based, and why might this estimate be either too high or too low?这一估计基于哪些假设？为什么这一估计可能偏高或偏低？
Which of the following types of variation would be most effective for distinguishing two individuals from the general population: a single nucleotide variant (SNV), a simple indel, or a microsatellite?以下哪种变异类型最有效于区分来自一般人群的两个个体：单核苷酸变异(SNV)、简单插入缺失还是微卫星？
Explain your reasoning.解释你的理由。
Compare the likely impact of each of the following on the overall rate of mutation detected in any given genome: age of the parents, hot spots of mutation, intrachromosomal homologous recombination, genetic variation in the parental genomes.比较以下各项对任何给定基因组中检测到的总体突变率的可能影响：父母年龄、突变热点、染色体内同源重组、父母基因组中的遗传变异。

Principles of Clinical Cytogenetics and Genome Analysis

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Principles of Clinical Cytogenetics and Genome Analysis Dimitri J.
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Principles of Clinical Cytogenetics and Genome Analysis Dimitri J.临床细胞遗传学与基因组分析原理 Dimitri J.
Stavropoulos Clinical cytogenetics is the study of chromosomes, their structure, and their inheritance, as applied to the practice of medicine.临床细胞遗传学是研究染色体、其结构及其遗传的学科，应用于医学实践。
It has been apparent for over 50 years that chromosome abnormalities—microscopically visible changes in the number or structure of ­chromosomes— could account for a number of clinical conditions that are thus referred to as chromosome disorders.超过50年来已明确，染色体异常——即染色体数目或结构的显微镜下可见改变——可解释多种临床病症，这些病症因而被称为染色体疾病。
With their focus on the complete set of genetic material, cytogeneticists were the first to bring a genome-­wide perspective to the practice of medicine.由于专注于完整的遗传物质集合，细胞遗传学家率先将全基因组视角引入医学实践。
Today, chromosome ­analysis—with increasing resolution and precision at both the cytologic and genomic levels—is an important diagnostic procedure in numerous areas of clinical medicine.如今，染色体分析——在细胞学与基因组水平上具有日益提高的分辨率和精确度——是临床医学众多领域中的重要诊断手段。
Current genome analyses that use approaches to be explored in this chapter, including chromosomal microarrays and whole genome sequencing (WGS), represent impressive improvements in capacity and resolution but ones that are conceptually similar to microscopic methods focusing on chromosomes .当前使用本章将探讨的方法（包括染色体微阵列和全基因组测序）进行的基因组分析，代表了能力和分辨率的显著提升，但这些方法与聚焦于染色体的显微镜分析方法在概念上相似。
Chromosome disorders form a major category of genetic disease.染色体疾病构成遗传病的一个主要类别。
They account for a large proportion of all spontaneous pregnancy losses, congenital malformations, and intellectual disability and play an important role in the pathogenesis of cancer.它们占所有自然流产、先天性畸形和智力残疾的很大比例，并在癌症发病机制中发挥重要作用。
Specific cytogenetic disorders are responsible for hundreds of distinct syndromes that collectively are more common than all the single-­gene diseases together.特定的细胞遗传学疾病导致数百种不同的综合征，这些综合征总体比所有单基因病更为常见。
Cytogenetic abnormalities are present in nearly 1% of live births, in ~2% of pregnancies in women older than 35 years who undergo prenatal diagnosis, and in half of all spontaneous, first-­ trimester pregnancy losses.细胞遗传学异常存在于近1%的活产儿中，在接受产前诊断的35岁以上女性中约占2%的妊娠，以及所有早期自然流产中占一半。
The spectrum of analysis from microscopically visible changes in chromosome number and structure to anomalies of genome structure and sequence detectable at the level of WGS encompasses literally the entire field of medical genetics .从染色体数目和结构的显微镜下可见改变，到在全基因组测序水平可检测的基因组结构和序列异常，分析范围实际上涵盖了医学遗传学的整个领域。
In this chapter we present the general principles of chromosome and genome analysis and focus on the chromosome variants and structural variants introduced in the previous chapter.本章中，我们介绍染色体和基因组分析的一般原理，并重点关注上一章介绍的染色体变异和结构变异。
We restrict our discussion to disorders due to genomic imbalance—either for the hundreds to thousands of genes found on individual chromosomes or for smaller numbers of genes located within a particular chromosome region.我们将讨论限于由基因组失衡引起的疾病——无论是单个染色体上成百上千个基因的失衡，还是特定染色体区域内少数基因的失衡。
Application of these principles to some of the most common and best-­known chromosomal and genomic disorders will then be presented in Chapter 6.这些原理在部分最常见且最广为人知的染色体和基因组疾病中的应用将在第6章中呈现。
INTRODUCTION TO CYTOGENETICS AND GENOME ANALYSIS The general morphology and organization of human ­chromosomes, as well as their molecular and genomic composition, were introduced in Chapters 2 and 3.细胞遗传学与基因组分析导论 人类染色体的一般形态与组织，以及其分子和基因组组成，已在第2章和第3章中介绍。
Chromosome analysis can be performed for clinical purposes by obtaining peripheral blood and stimulating T lymphocytes to prepare short-­term cultures.染色体分析可用于临床目的，通过获取外周血并刺激T淋巴细胞制备短期培养物。
After a few days, the dividing cells are arrested in metaphase with chemicals that inhibit the mitotic spindle, and chromosomes are fixed to glass slides and stained by one of several techniques, depending on the particular diagnostic procedure being performed.数日后，用抑制有丝分裂纺锤体的化学物质将分裂中的细胞阻滞在中期，然后将染色体固定在玻片上，并根据所执行的具体诊断程序，采用若干染色技术之一进行染色。
They are then ready for analysis.至此，它们即可用于分析。
Although ideal for rapid clinical analysis, cell cultures prepared from peripheral blood have the disadvantage of being short lived (3–­4 days).尽管外周血制备的细胞培养物适合快速临床分析，但其缺点是存活时间短（3–4天）。
Long-­term cultures suitable for permanent storage or further studies can be derived from a variety of other tissues.适用于永久保存或进一步研究的长期培养物可从多种其他组织中获得。
Skin biopsy, a minor surgical procedure, can provide samples of tissue that in culture produce fibroblasts, which can be used for a variety of biochemical and molecular studies as well as for chromosome and genome analysis.皮肤活检是一种小型外科手术，可提供组织样本，在培养中产生成纤维细胞，这些细胞可用于多种生化和分子研究，以及染色体和基因组分析。
White blood cells can also be transformed in culture to form lymphoblastoid cell lines that are potentially immortal.白细胞也可在培养中转化，形成潜在永生的类淋巴母细胞系。
Bone marrow has the advantage of containing a high proportion of dividing cells so that little if any culturing is required; however, it can be obtained only by the relatively invasive procedure of marrow biopsy.骨髓的优点是含有高比例的分裂细胞，因而几乎无需培养；但只能通过相对侵入性的骨髓活检手术获取。
Its main use is in the diagnosis of suspected hematologic malignancies.其主要用途在于诊断疑似血液系统恶性肿瘤。
Fetal cells derived from amniotic fluid (amniocytes) or obtained by chorionic villus biopsy can also be cultured successfully for cytogenetic, genomic, biochemical, or molecular analysis.取自羊水的胎儿细胞（羊水细胞）或通过绒毛膜绒毛活检获得的胎儿细胞，也可成功培养用于细胞遗传学、基因组学、生化或分子分析。
Chorionic villus cells can also be analyzed directly after biopsy, without the need for culturing.绒毛膜绒毛细胞在活检后也可直接分析，无需培养。
Remarkably, small amounts of cell-­free fetal DNA are found in the maternal plasma and can be tested by WGS (see Chapter 18 for further discussion).值得注意的是，在母体血浆中发现少量游离胎儿DNA，可通过全基因组测序进行检测（详见第18章讨论）。
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Molecular analysis of the genome, including WGS, can be carried out on any appropriate clinical material, provided that …
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Molecular analysis of the genome, including WGS, can be carried out on any appropriate clinical material, provided that good-­quality DNA can be obtained.包括全基因组测序（WGS）在内的基因组分子分析，可在任何适当的临床材料上进行，前提是能够获得高质量的DNA。
Cells need not be dividing for this purpose, and thus it is possible to study DNA from tissue and tumor samples, for example, as well as from peripheral blood.为此目的，细胞无需处于分裂状态，因此可以研究来自组织、肿瘤样本以及外周血的DNA。
Which approach is most appropriate for a particular diagnostic or research purpose is a rapidly evolving area as the resolution, sensitivity, and ease of chromosome and genome analysis increase (see 1).随着染色体和基因组分析的分辨率、灵敏度及易用性的提高，针对特定诊断或研究目的选择最合适的方法是一个快速发展的领域（参见1）。
Chromosome Identification The different chromosomes in the genome can be identified cytologically by their characteristic banding patterns after applying specific staining procedures.染色体鉴定：基因组中不同染色体可通过应用特定染色程序后呈现的特征性带型，在细胞学上进行鉴定。
The most common of these, Giemsa banding (G-­banding), was developed in the early 1970s and was the first widely used whole genome analytic tool for research and clinical diagnosis that may still apply.其中最常用的是吉姆萨显带（G显带），于20世纪70年代初开发，是首个广泛应用于研究和临床诊断的全基因组分析工具，且至今仍可使用。
It has been the gold standard for the detection and characterization of structural and numerical genomic abnormalities in clinical diagnostic settings for both constitutional (postnatal or prenatal) and acquired (cancer) disorders.它一直是临床诊断中检测和描述结构性及数量性基因组异常的金标准，适用于体质性（出生后或产前）和获得性（癌症）疾病。
Chromosome/ Genome Variation Interchromosomal translocations Ring chromosomes, isochromosomes Marker chromosomes Aneuploidy Aneusomy Segmental aneusomy Chromosomal inversions Intrachromosomal translocations Chromosomal abnormality Heteromorphisms and fragile sites Chromosome deletions – losses Chromosome insertions – gains Copy number variants Segmental duplications/paralogous sequence Inversions, translocations, transpositions Microdeletions, microduplications Variable number tandem repeats (VNTRs) Complex tandem repeat expansions Di-, tri-, tetranucleotide repeats Microsatellites, minisatellites Inversions In Del Structural Variation Sequence Variation Whole chromosomal to genome Microscopic to subchromosomal 1 kb to submicroscopic 2 bp to 1,000 bp Single nucleotide single nucleotide variant In Del Karyotyping flouorscence hybritization Sanger/Capillary sequencing Microarrays/Next generation sequencing Long – read sequencing/FISH Whole – Genome Sequencing The typical resolution and primary methods used to detect them are given for various technologic approaches used routinely in chromosome and genome analysis.染色体/基因组变异：染色体间易位、环状染色体、等臂染色体、标记染色体、非整倍体、异倍体、节段性异倍体、染色体倒位、染色体内易位、染色体异常、异态性与脆性位点、染色体缺失（丢失）、染色体插入（获得）、拷贝数变异、节段性重复/旁系同源序列、倒位、易位、转座、微缺失、微重复、可变数目串联重复（VNTRs）、复杂串联重复扩增、二核苷酸/三核苷酸/四核苷酸重复、微卫星、小卫星、倒位、插入、缺失、结构变异、序列变异：从整个染色体到基因组，从显微到亚染色体，从1 kb到亚显微，从2 bp到1,000 bp，单核苷酸、单核苷酸变异、插入缺失；核型分析、荧光原位杂交、桑格/毛细管测序、微阵列/下一代测序、长读长测序/荧光原位杂交、全基因组测序——对于常规用于染色体和基因组分析的各种技术方法，给出了检测这些变异的典型分辨率和主要方法。
See text for details and specific examples.具体细节和实例请参阅正文。
(Redrawn from Trost B, Loureiro LO, Scherer SW: Discovery of genomic variation across a generation.（改编自Trost B, Loureiro LO, Scherer SW: Discovery of genomic variation across a generation.
Hum Mol Genet 30(2):R174–R186, 2021.) G-­banding and other staining procedures can be used to describe individual chromosomes and their variants or abnormalities, using an internationally accepted system of chromosome classification. can be described precisely and unambiguously by use of this regionally based and hierarchic numbering system.Hum Mol Genet 30(2):R174–R186, 2021.) G显带和其他染色程序可用于描述单个染色体及其变异或异常，采用国际公认的染色体分类系统，通过这种基于区域和分层的编号系统可以精确且无歧义地进行描述。
Human chromosomes are often classified into three types that can be easily distinguished at metaphase by the position of the centromere, the primary constriction visible at metaphase .人类染色体通常分为三种类型，可根据着丝粒（中期可见的初级缢痕）的位置在中期轻松区分。
Metacentric chromosomes have a central centromere and arms of approximately equal length, submetacentric chromosomes have an off-­center centromere and arms of clearly different lengths, and acrocentric chromosomes have the centromere near one end.中着丝粒染色体的着丝粒位于中央，两臂长度大致相等；亚中着丝粒染色体的着丝粒偏离中心，两臂长度明显不同；近端着丝粒染色体的着丝粒靠近一端。
A potential fourth type of chromosome, telocentric, with the centromere at one end and一种可能的第四种染色体类型，即端着丝粒染色体，其着丝粒位于一端且
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Principles of Clinical Cytogenetics and Genome Analysis 63 1 CLINICAL INDICATIONS FOR CHROMOSOME AND GENOME ANALYSIS Chr…
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Principles of Clinical Cytogenetics and Genome Analysis 63 1 CLINICAL INDICATIONS FOR CHROMOSOME AND GENOME ANALYSIS Chromosome analysis is indicated as a routine diagnostic procedure for a number of specific conditions encountered in medicine, and some general clinical indications include: Problems of early growth and development.临床细胞遗传学与基因组分析原理 63 1 染色体与基因组分析的临床指征 对于医学中遇到的若干特定情况，染色体分析被指示作为常规诊断程序，一些常见的临床指征包括：早期生长与发育问题。
Failure to thrive, developmental delay, dysmorphic facies, multiple malformations, short stature, ambiguous genitalia, and intellectual disability are frequent findings in children with chromosome abnormalities.生长迟缓、发育延迟、面部畸形、多发畸形、身材矮小、外生殖器模糊以及智力障碍是染色体异常儿童的常见表现。
Unless there is a definite nonchromosomal diagnosis, genomic analysis should be performed to detect diagnostic genome-­wide copy number and sequence variants for patients presenting with any combination of such problems (see Chapter 11).除非有明确的非染色体诊断，否则对于出现此类问题任意组合的患者，应进行基因组分析以检测诊断性全基因组拷贝数变异和序列变异（见第11章）。
Stillbirth and neonatal death.死产和新生儿死亡。
The incidence of chromosome abnormalities is much higher among stillbirths (up to ~10%) than among live births (~0. 7%).染色体异常的发生率在死产中（高达约10%）远高于活产（约0.7%）。
It is also elevated among infants who die in the neonatal period (~10%).在新生儿期死亡的婴儿中，该发生率也升高（约10%）。
For unexplained stillbirths and neonatal deaths, genome-­wide copy number and sequence analysis may serve to reveal a genetic etiology.对于不明原因的死产和新生儿死亡，全基因组拷贝数及序列分析可能有助于揭示遗传病因。
These analyses may provide important information for prenatal or preimplantation genetic diagnosis (see Chapter 18) in future pregnancies.这些分析可为未来妊娠的产前或植入前遗传学诊断提供重要信息（见第18章）。
Fertility problems.生育问题。
Chromosome studies by G-­banded karyotype are indicated for women with amenorrhea and for couples with a history of infertility or recurrent miscarriage.对闭经女性以及有不孕或复发性流产史的夫妇，建议进行G显带核型染色体研究。
A chromosome abnormality is seen in one or the other parent in 3–­6% of cases in which there is infertility or two or more miscarriages.在存在不孕或两次以上流产的病例中，约3-6%的父母之一可见染色体异常。
Structural characterization of genomic imbalances and family follow-­up studies.基因组失衡的结构表征及家族随访研究。
Copy number variations (CNV) identified by genome-­wide copy number analysis may require additional studies by G-­banding karyotype or metaphase fluorescence in situ hybridization (FISH) to characterize the structure of the alteration.通过全基因组拷贝数分析鉴定的拷贝数变异（CNV）可能需要通过G显带核型或中期荧光原位杂交（FISH）进行额外研究，以表征改变的结构。
A known unbalanced chromosome abnormality may have resulted from a parental balanced rearrangement, which will have implications for future pregnancies and potential prenatal diagnosis, as well as potentially for other family members of the carrier parent.已知的不平衡染色体异常可能源于父母之一的平衡重排，这将影响未来妊娠及可能的产前诊断，也可能影响携带者父母的其他家庭成员。
Neoplasia.肿瘤。
Almost all cancers are associated with one or more chromosome abnormalities (see Chapter 16).几乎所有癌症都与一种或多种染色体异常相关（见第16章）。
Chromosome and genome evaluation in the tumor itself, or in bone marrow for hematologic malignant neoplasms, can offer diagnostic or prognostic information.对肿瘤本身或血液系统恶性肿瘤的骨髓进行染色体和基因组评估，可提供诊断或预后信息。
Pregnancy.妊娠。
Several prenatal risk factors, including advanced maternal age, biochemical markers, and ultrasound findings, are associated with chromosome abnormalities (see Chapter 18).多项产前风险因素，包括高龄产妇、生化标志物和超声检查结果，与染色体异常相关（见第18章）。
Fetal genome-­wide copy number and sequence analysis should be offered as a routine part of prenatal care in such pregnancies.在此类妊娠中，应将胎儿全基因组拷贝数及序列分析作为产前保健的常规部分。
Noninvasive prenatal screening using whole genome sequencing of cell-­free DNA in maternal blood is also available to screen for the most common chromosome disorders. only a single arm, does not occur in the normal human karyotype, but it is occasionally observed in chromosome rearrangements.利用母血中游离DNA进行全基因组测序的无创产前筛查也可用于筛查最常见的染色体疾病。
The human acrocentric chromosomes (13, 14, 15, 21, and 22) have small, distinctive masses of chromatin known as satellites attached to their short arms by narrow stalks (called secondary constrictions).人类近端着丝粒染色体（13、14、15、21和22）的短臂上通过狭窄的茎（称为次缢痕）附着有小而独特的染色质团块，称为卫星。
The stalks of these five chromosome pairs contain hundreds of copies of genes for ribosomal RNA (the major component of ribosomes; see Chapter 3) as well as a variety of repetitive sequences.这五对染色体的茎含有数百个核糖体RNA基因拷贝（核糖体的主要成分；见第3章）以及多种重复序列。
The standard G-­banded karyotype at a 400-­ to 550-­ band stage of resolution, as seen in a typical metaphase preparation, allows detection of deletions and duplications greater than ~5 to 10 Mb .在典型中期制备中可见的400至550条带分辨阶段的标准化G显带核型，能够检测大于约5至10 Mb的缺失和重复。
However, the sensitivity of G-­banding at this resolution may be lower in regions of the genome in which the banding patterns are less specific.然而，在显带模式特异性较低的区域，此分辨率下的G显带敏感性可能较低。
High-­resolution banding (also called prometaphase banding) can achieve 850 or more bands in a haploid set by staining chromosomes that have been obtained at an early stage of mitosis (prophase or prometaphase), when they are still in a relatively uncondensed state (see Chapter 2).高分辨显带（也称为前中期显带）通过对处于有丝分裂早期（前期或前中期）且仍处于相对未浓缩状态的染色体进行染色，可在单倍体组中达到850条或更多条带（见第2章）。
Development of high-­resolution chromosome analysis in the early 1980s allowed the discovery of a number of new microdeletion and microdyuplication syndrome, caused by smaller genomic rearrangements in the 2-to-3 Mb size range .20世纪80年代初高分辨染色体分析的发展使得发现了一系列新的微缺失和微重复综合征，这些综合征由大小为2至3 Mb范围的较小基因组重排引起。
However, the time-­consuming and technically difficult nature of this cytogenetic method precludes its routine use for whole genome analysis.然而，这种细胞遗传学方法耗时且技术难度大，阻碍了其在全基因组分析中的常规应用。
In addition to changes in banding pattern, nonstaining gaps, called fragile sites, are heritable variants that can be observed at particular chromosome sites that are prone to regional genomic instability induced by stress on DNA replication.除了显带模式的变化外，称为脆性位点的非染色间隙是可遗传的变异，可在特定染色体位点观察到，这些位点容易因DNA复制压力而出现区域基因组不稳定性。
Over 100 common and rare (population frequency &lt;5%) fragile sites are documented.已记录超过100个常见和罕见（人群频率<5%）的脆性位点。
Common fragile sites are postulated to drive genomic instability in cancer cells, and a small proportion of rare fragile sites are associated with specific clinical disorders.常见脆性位点被认为驱动癌细胞的基因组不稳定性，而一小部分罕见脆性位点与特定的临床疾病相关。
For example, the rare fragile site located at Xq 27. 3 is caused by an expansion of CGG repeats and is observed in patients with fragile X syndrome (Case 17).例如，位于Xq27.3的罕见脆性位点由CGG重复扩增引起，见于脆性X综合征患者（病例17）。
Fluorescence In Situ Hybridization (FISH) Targeted high-­resolution chromosome banding was largely replaced in the early 1990s by FISH, a method for detecting the presence or absence of a particular DNA sequence or for evaluating the number or structural organization of a chromosome or chromosomal region in situ (literally, “in place”) in the cell.荧光原位杂交（FISH） 靶向高分辨染色体显带在20世纪90年代初被FISH大量取代，FISH是一种用于检测特定DNA序列存在与否，或评估细胞中染色体或染色体区域数目或结构原位组织的方法。
This convergence of genomic and cytogenetic approaches—variously termed molecular cytogenetics or cytogenomics—dramatically expanded both the scope and precision of chromosome analysis in routine clinical practice.这种基因组与细胞遗传学方法的融合——被称为分子细胞遗传学或细胞基因组学——极大地扩展了常规临床实践中染色体分析的范围和精确度。
FISH technology takes advantage of ordered collections of recombinant large-­insert DNA clones containing DNA from virtually any locus in the genome.FISH技术利用有序收集的重组大插入DNA克隆，这些克隆含有基因组中几乎任何位点的DNA。
Clones containing specific human DNA sequences can be labeled with a fluorescent dye and used as probes to detect the corresponding region of the genome in含有特定人类DNA序列的克隆可用荧光染料标记，并作为探针来检测基因组中相应的区域。
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p 1 q p q 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y 36. 2 35 34. 2 33 31 24 22 16 14 12 24 26 22 13. 1 13. 3 22 24 26. 1 26. 3 28 14 12 13 13 22 24 26 28 31. 2 32 34 12 14 12 21 23 14 15. 2 12 14 16 12 22 24 26 22 21. 2 24 31 21 12 33 21 14 23 21. 3 21. 1 12 24. 2 22 12 33 31 21 12 23 21 12 23 21 14 12 25 14 12 14 12 22 24 14 12 23 12 21 24. 2 35 32 34 15. 3 15. 1 12 14. 1 14. 3 22 24 32 34 36 21 12 12 22 24 31 41 43 13 21 31 33 12 21 23 31 12 21 23 21. 2 25 14 11. 2 21 23 13. 2 12 26. 2 12 22 24 12 12 22 11. 3 12 12 13. 2 12 21 12 12 13. 2 11. 22 12 22. 2 21 11. 3 12 11. 3 21 23 25 27 13. 4 13. 2 As drawn, chromosomes are typically represented with the sister chromatids so closely aligned that they are not recognized as distinct entities.p 1 q p q 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y 36. 2 35 34. 2 33 31 24 22 16 14 12 24 26 22 13. 1 13. 3 22 24 26. 1 26. 3 28 14 12 13 13 22 24 26 28 31. 2 32 34 12 14 12 21 23 14 15. 2 12 14 16 12 22 24 26 22 21. 2 24 31 21 12 33 21 14 23 21. 3 21. 1 12 24. 2 22 12 33 31 21 12 23 21 12 23 21 14 12 25 14 12 14 12 22 24 14 12 23 12 21 24. 2 35 32 34 15. 3 15. 1 12 14. 1 14. 3 22 24 32 34 36 21 12 12 22 24 31 41 43 13 21 31 33 12 21 23 31 12 21 23 21. 2 25 14 11. 2 21 23 13. 2 12 26. 2 12 22 24 12 12 22 11. 3 12 12 13. 2 12 21 12 12 13. 2 11. 22 12 22. 2 21 11. 3 12 11. 3 21 23 25 27 13. 4 13. 2 如图所示，染色体通常以姐妹染色单体紧密排列的方式表示，以至于它们不被视为独立的实体。
Centromeres are indicated by the primary constriction and narrow dark gray regions separating the p and q arms.着丝粒以初级缢痕和分隔p臂与q臂的狭窄深灰色区域表示。
For convenience and clarity, only the G-­dark bands are numbered.为方便和清晰起见，仅对G深带进行编号。
For examples of full numbering scheme, see chromosome preparations or in interphase nuclei for a variety of research and diagnostic purposes .完整编号方案的示例可参见染色体标本或间期核，用于多种研究和诊断目的。
Although FISH technology provides much higher resolution and specificity than G-­banded chromosome analysis, it does not allow for efficient analysis of the entire genome.尽管FISH技术提供了比G显带染色体分析高得多的分辨率和特异性，但它无法对整个基因组进行高效分析。
Its use is limited to targeting a specific genomic region based on a clinical diagnosis or suspicion, structural characterization of genomic imbalances and family follow-up studies.其应用仅限于根据临床诊断或怀疑靶向特定基因组区域、基因组不平衡的结构表征以及家系随访研究。
Multiplex Ligation-­Dependent Probe Amplification (MLPA) MLPA is a targeted copy number assay used to detect exon-­level deletions and duplications in a gene or targeted chromosome region.多重连接依赖性探针扩增（MLPA）MLPA是一种靶向拷贝数检测方法，用于检测基因或靶向染色体区域的外显子水平缺失和重复。
This method uses multiplex polymerase chain reaction (PCR) to amplify DNA sequences from multiple exons simultaneously in one PCR.该方法使用多重聚合酶链反应（PCR）在一次PCR中同时扩增多个外显子的DNA序列。
The relative quantity of DNA sequence generated from each exon is then compared to amplification of control regions with normal copy number (two copies).然后将每个外显子产生的DNA序列的相对量与具有正常拷贝数（两个拷贝）的对照区域的扩增进行比较。
Since the total quantity of amplified PCR product is directly proportional to the copy number of each targeted exon in the individual DNA sample, a heterozygous deletion (one copy) will produce approximately half as much PCR product when compared to regions with normal copy number (two copies), and a heterozygous duplication (three copies) will generate ~50% more PCR product when compared to regions with normal copy number.由于扩增的PCR产物总量与个体DNA样本中每个靶向外显子的拷贝数成正比，杂合缺失（一个拷贝）产生的PCR产物量约为正常拷贝数区域（两个拷贝）的一半，而杂合重复（三个拷贝）产生的PCR产物量比正常拷贝数区域多约50%。
This method is limited by the number of targeted regions that can be included in one PCR assay and is not amenable to genome-­wide copy number analysis.该方法受限于一次PCR检测中可包含的靶向区域数量，并且不适用于全基因组拷贝数分析。
It is used to investigate a specific gene (e. g., DMD) or known recurrent microdeletion/­ microduplication syndrome region (e. g., 22q11. 2).它用于研究特定基因（例如DMD）或已知的复发性微缺失/微重复综合征区域（例如22q11.2）。
MLPA can be combined with methylation analysisMLPA可与甲基化分析结合使用。
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Principles of Clinical Cytogenetics and Genome Analysis 65 (MS-­MLPA) to specifically amplify targeted chromosome regions that are methylated, to determine imprinting status.临床细胞遗传学与基因组分析原理 65（MS‑MLPA）用于特异性扩增目标染色体区域中甲基化的部分，以确定印记状态。
As described in Chapter 8, a subset of the genome is differentially imprinted depending on the parent of origin; and abnormal methylation of these regions can be identified by MS-­MPLA to confirm a diagnosis of imprinting disorder (e. g., 15q11. 2q13 in Prader-­Willi and Angelman syndromes; see [Case 38]).如第8章所述，基因组的一个子集根据亲本来源存在差异性印记；这些区域的异常甲基化可通过MS‑MPLA识别，以确认印记障碍的诊断（例如，Prader‑Willi综合征和Angelman综合征中的15q11.2q13；见[案例38]）。
Genome Analysis Using Microarrays Chromosome microarray analysis (CMA) has replaced G-­banded karyotype as the frontline diagnostic test to detect genome-­wide copy number imbalances for most clinical applications.使用微阵列进行基因组分析 染色体微阵列分析（CMA）已取代G显带核型分析，成为大多数临床应用中检测全基因组拷贝数失衡的一线诊断检测方法。
CMA simultaneously queries the whole genome on a glass slide containing regularly spaced DNA probes that represent loci across the entire genome.CMA同时查询整个基因组，使用载玻片上规则排列的DNA探针，这些探针代表整个基因组中的位点。
This technology detects relative copy number gains and losses in a genome-­wide manner by hybridizing equal amounts of control and subject DNA to the DNA probes and calculating the ratio of each DNA sample hybridized to each probe.该技术通过将等量的对照DNA和受检DNA与DNA探针杂交，并计算每个探针上杂交的两种DNA样本的比率，以全基因组方式检测相对拷贝数的增加和缺失。
Microarray probes showing equal ratio of subject and control DNA indicate normal copy number at the respective genomic loci.显示受检DNA与对照DNA比率相等的微阵列探针，表明相应基因组位点的拷贝数正常。
An excess of subject DNA indicates copy number gain, whereas underrepresentation of subject DNA indicates copy number loss at the genomic loci represented by the microarray probes .受检DNA过量表示相应基因组位点拷贝数增加，而受检DNA不足则表示微阵列探针所代表的基因组位点拷贝数缺失。
Microarray platforms may contain copy number probes (see earlier).微阵列平台可能包含拷贝数探针（见前述内容）。
Alternatively, they may comprise single nucleotide polymorphism (SNP) probes that contain versions of sequences corresponding to the variant alleles (as introduced in Chapter 4).或者，它们可能包含单核苷酸多态性（SNP）探针，这些探针含有与变异等位基因对应的序列版本（如第4章所述）。
The data from SNP probes can be plotted on an allele difference plot, which indicates whether a specific SNP locus is homozygous for the A allele (AA), homozygous for the B allele (BB), or heterozygous (AB).来自SNP探针的数据可在等位基因差异图上绘制，该图显示特定SNP位点是A等位基因纯合（AA）、B等位基因纯合（BB）还是杂合（AB）。
Normal copy number across a chromosome typically shows the three allele combinations of AA, AB, and BB along its length .染色体上正常的拷贝数通常显示沿其长度的三种等位基因组合：AA、AB和BB。
A genomic region of homozygosity (ROH), with AA and BB but no AB track, can be observed when the chromosome region is identical by decent (due to parental consanguinity) or when there is uniparental disomy (UPD) with both copies of the chromosome inherited from one parent.当染色体区域因亲本血缘关系而相同（血缘同源）或存在单亲二体（UPD）（两条染色体均来自同一亲本）时，可观察到纯合性区域（ROH），其中包含AA和BB但无AB轨迹。
The identification of several ROHs across the genome of a patient and involving multiple chromosomes suggests parental consanguinity and raises the possibility of a recessive disorder.在患者基因组中识别出涉及多条染色体的多个ROH，提示亲本血缘关系，并增加隐性遗传病的可能性。
While an ROH affecting only one chromosome raises the possibility of UPD, parental genotype analysis is required to confirm that the ROH is in fact due to UPD.而仅影响一条染色体的ROH提示UPD的可能性，但需进行亲本基因型分析以确认该ROH确实由UPD引起。
For routine clinical testing of suspected chromosome disorders, probe spacing on the array provides a resolution as high as 100 kb over the entire unique portion of the human genome.对于疑似染色体疾病的常规临床检测，阵列上探针间距可在人类基因组全部独特区域提供高达100 kb的分辨率。
A higher density of probes can be used to achieve even higher resolution (20 kb) over regions of particular clinical interest, such as those p q 5 6 7 15. 3 15. 2 15. 1 14 13. 3 13. 1 11 11. 1 11. 2 12 13. 1 13. 2 13. 3 14 15 21 22 23. 1 23. 3 31. 1 31. 2 31. 3 32 33. 1 33. 3 34 35. 1 35. 3 35. 2 33. 2 23. 2 12 25 24 23 22. 3 22. 1 21. 3 11. 1 11 12 13 14 15 16. 1 16. 3 21 22. 1 22. 3 23. 1 23. 3 24 25. 1 25. 3 26 27 21. 2 21. 1 12 22. 2 11. 2 16. 2 22. 2 23. 2 25. 2 22 21 15. 3 11. 1 11. 1 15. 1 14 13 12 15. 2 11. 2 11. 22 11. 23 21. 1 21. 2 21. 3 22 31. 1 31. 2 31. 3 32 33 34 35 36 13. 2 11. 21 Band numbers permit unambiguous identification of each G-­dark or G-­light band.可在特定临床关注区域使用更高密度的探针以实现更高分辨率（20 kb），例如那些p q 5 6 7 15.3 15.2 15.1 14 13.3 13.1 11 11.1 11.2 12 13.1 13.2 13.3 14 15 21 22 23.1 23.3 31.1 31.2 31.3 32 33.1 33.3 34 35.1 35.3 35.2 33.2 23.2 12 25 24 23 22.3 22.1 21.3 11.1 11 12 13 14 15 16.1 16.3 21 22.1 22.3 23.1 23.3 24 25.1 25.3 26 27 21.2 21.1 12 22.2 11.2 16.2 22.2 23.2 25.2 22 21 15.3 11.1 11.1 15.1 14 13 12 15.2 11.2 11.22 11.23 21.1 21.2 21.3 22 31.1 31.2 31.3 32 33 34 35 36 13.2 11.21；带号可明确识别每条G深带或G浅带。
The banding nomenclature indicates the chromosome number (1–­22,X,Y), the short arm (p) or long arm (q), the region, band, and subband.带的命名法表示染色体编号（1–22,X,Y）、短臂（p）或长臂（q）、区、带和亚带。
For example, chromosome 5p15. 2 is pronounced as “5-­p-­one-­five-­point-­2.” (Redrawn from Shaffer LG, Mc Gowan-­ Jordan J, Schmid M, editors: ISCN 2013: an international system for human cytogenetic nomenclature, Basel, 2013, Karger.) Metaphase Locus-specific probes Satellite DNA probes Interphase Single-­copy DNA probes specific for sequences within bands 4q12 (red fluorescence) and 4q31. 1 (green fluorescence).例如，染色体5p15.2读作“5-p-1-5-点-2”。（重绘自Shaffer LG, McGowan-Jordan J, Schmid M, 编辑：ISCN 2013：人类细胞遗传学命名国际系统，巴塞尔，2013，Karger出版社。）中期染色体 位点特异性探针 卫星DNA探针 间期细胞 针对4q12（红色荧光）和4q31.1（绿色荧光）带内序列的单拷贝DNA探针。
(Bottom) Repetitive α-­satellite DNA probes specific for the centromeres of chromosomes 18 (aqua), X (green), and Y (red) used to count the number of each chromosome in this individual.（下方）针对18号染色体（青色）、X染色体（绿色）和Y染色体（红色）着丝粒的重复α-卫星DNA探针，用于计数该个体中每条染色体的数目。
(Images courtesy M.（图像由M. Katharine Rudd提供，埃默里遗传学实验室，佐治亚州亚特兰大。）
Katharine Rudd, Emory Genetics Laboratory, Atlanta, Georgia.)[TL:missing]
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associated with known developmental disorders or congenital anomalies (see Chapter 6).
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associated with known developmental disorders or congenital anomalies (see Chapter 6).与已知的发育障碍或先天性异常相关（见第6章）。
This approach is being used in clinical laboratories to provide high-­ resolution analysis of targeted clinically significant genes and lower resolution backbone coverage across the rest of the genome.这种方法正被临床实验室用于对靶向临床相关基因进行高分辨率分析，并对基因组其余部分进行较低分辨率的骨架覆盖。
Microarrays have been used successfully to identify chromosome and genome abnormalities in children with unexplained developmental delay, intellectual disability, or birth defects, revealing a number of pathogenic genomic alterations that were not detectable by conventional G-­banding. , genome-­wide arrays have replaced the G-­banded karyotype as the routine frontline test for these patient populations.微阵列已成功用于识别不明原因发育迟缓、智力障碍或出生缺陷儿童的染色体和基因组异常，揭示了许多传统G显带无法检测的致病性基因组改变，全基因组阵列已取代G显带核型分析成为这些患者群体的常规一线检测方法。
Two important limitations of this technology bear mentioning, however.然而，这项技术的两个重要局限性值得一提。
First, array-­based methods measure only the relative copy number of DNA sequences but not whether they have been translocated or rearranged from their normal position(s) in the genome.首先，基于阵列的方法仅测量DNA序列的相对拷贝数，而不测量它们是否从基因组中的正常位置发生易位或重排。
Thus further characterization of copy number variants (CNVs) by karyotyping or FISH is important to determine the nature of an abnormality and thus its risk for recurrence for other family members.因此，通过核型分析或FISH对拷贝数变异（CNVs）进行进一步表征对于确定异常的性质及其对其他家庭成员的复发风险至关重要。
Second, high-­resolution genome analysis can reveal variants in particular, small differences in copy number, that are of uncertain clinical significance.其次，高分辨率基因组分析可揭示变异，特别是拷贝数的微小差异，这些变异的临床意义尚不确定。
An increasing number of such variants are being documented and catalogued even from the general population.即使是来自普通人群，此类变异也正被越来越多地记录和编目。
As we saw in Chapter 4, many are likely to be benign CNVs.正如我们在第4章所见，其中许多可能是良性CNVs。
Their existence underscores the unique nature of an individual’s genome and emphasizes the diagnostic challenge of assessing what is considered normal and what is likely to be pathogenic.它们的存在凸显了个体基因组的独特性，并强调了评估何为正常、何为致病所面临的诊断挑战。
Genome Analysis by Whole Genome Sequencing On the same spectrum as cytogenetic and microarray analysis, the ultimate resolution for clinical tests to detect chromosomal and genomic disorders would be to sequence genomes in their entirety.全基因组测序的基因组分析 与细胞遗传学和微阵列分析处于同一谱系，临床检测染色体和基因组疾病的最终分辨率将是完整测序基因组。
Indeed, as the efficiency of WGS has increased and its costs have fallen, it is becoming increasingly practical to sequence samples in a clinical setting .事实上，随着WGS效率的提高和成本的下降，在临床环境中对样本进行测序正变得越来越实用。
The most widely used WGS approach generates millions of short-­sequence reads that range between 100 and 500 bp in length, depending on the sequencing platform.最广泛使用的WGS方法可生成数百万个长度在100至500 bp之间的短序列读段，具体取决于测序平台。
A B Log 2 Ratio AA AB BB Region of Homozygosity Log 2 Ratio Allele Difference Allele Difference AA AB BB Deletion Chromosome 17: G-banding ideogram, followed by an example of copy number and single nucleotide polymorphism (SNP) microarray output, showing the Log 2 ratio of fluorescence intensity and allele difference plots.A B Log2比值 AA AB BB 纯合区域 Log2比值 等位基因差异 等位基因差异 AA AB BB 缺失 染色体17：G显带模式图，随后是拷贝数和单核苷酸多态性（SNP）微阵列输出示例，显示荧光强度的Log2比值和等位基因差异图。
DNA probes (blue dots) with a Log 2 ratio of 0 indicate diploid copy number.Log2比值为0的DNA探针（蓝点）表示二倍体拷贝数。
In chromosome region 17p11. 2, consecutive probes with a Log 2 ratio of −­1 indicate a heterozygous deletion of ~3. 7 Mb, associated with Smith-­Magenis syndrome.在染色体区域17p11.2中，Log2比值为-1的连续探针表示约3.7 Mb的杂合缺失，与Smith-Magenis综合征相关。
(B) Chromosome 18: SNP microarray output plot showing a region of homozygosity of ~6. 052 Mb.(B) 染色体18：SNP微阵列输出图显示约6.052 Mb的纯合区域。
The total copy number is unaffected, but the allele difference plot shows a stretch of only homozygous genotypes (AA or BB) with no heterozygous genotypes (AB).总拷贝数未受影响，但等位基因差异图显示一段仅含纯合基因型（AA或BB）而无杂合基因型（AB）的区域。
(Microarray images courtesy of Genome Diagnostics, The Hospital for Sick Children.)（微阵列图像由多伦多病童医院基因组诊断科提供。）
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Principles of Clinical Cytogenetics and Genome Analysis 67 An individual’s genome is represented by overlapping sequence…
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Principles of Clinical Cytogenetics and Genome Analysis 67 An individual’s genome is represented by overlapping sequence reads, with typically 30 to 40 reads corresponding to any particular segment of the genome.临床细胞遗传学与基因组分析原理67 个体的基因组由重叠的序列读段表示，通常基因组任何特定片段对应30到40个读段。
A genomic region or chromosome with an abnormally low or high representation of those sequence reads is likely to have a numeric or structural abnormality of that genomic region.具有这些序列读段异常低或高代表的基因组区域或染色体可能存在该基因组区域的数目或结构异常。
To detect numeric abnormalities of an entire chromosome it is generally not necessary to sequence a genome to completion; even a limited number of sequences that align to a particular chromosome of interest should reveal whether those sequences are found in the expected number (e. g., equivalent to two copies per diploid genome for an autosome) or whether they are significantly overrepresented or underrepresented .为检测整个染色体的数目异常，通常无需将基因组完全测序；即使有限数量的序列比对到感兴趣的特定染色体，也应能揭示这些序列是否以预期数目（例如，对于常染色体，相当于每个二倍体基因组两个拷贝）出现，或者是否显著过多或过少。
This concept is now being applied to the prenatal diagnosis of fetal chromosome imbalance (see Chapter 18).这一概念目前正应用于胎儿染色体失衡的产前诊断（见第18章）。
To detect balanced rearrangements of the genome, however, in which DNA in the genome is neither gained nor lost, a more complete genome sequence is required.然而，为了检测基因组中既无DNA获得也无缺失的平衡重排，需要更完整的基因组序列。
Here, instead of sequence reads that align perfectly to the reference human genome sequence, one finds rare sequence reads that align to two different and normally noncontiguous regions in the reference sequence (whether on the same chromosome or on different chromosomes) .在此，不再是完美比对到人类参考基因组序列的序列读段，而是发现一些罕见的序列读段，它们比对到参考序列中两个不同且通常不连续的区域（无论是在同一染色体上还是在不同染色体上）。
This approach has been used to identify the specific genes involved in some cancers, and in children with various congenital defects due to translocations, involving the juxtaposition of sequences that are normally located on different chromosomes.该方法已被用于鉴定某些癌症中涉及的特定基因，以及因易位导致各种先天性缺陷的儿童中的基因，这些易位涉及通常位于不同染色体上的序列并置。
More recently, bioinformatics algorithms have been developed to estimate the size of trinucleotide repeat expansions and provide the opportunity to assay known clinically significant loci (such as those involved in fragile X syndrome or Huntington disease) as part of the WGS diagnostic test.最近，生物信息学算法已被开发用于估计三核苷酸重复扩增的大小，并提供机会来检测已知临床意义位点（例如涉及脆性X综合征或亨廷顿病的位点），作为全基因组测序诊断检测的一部分。
Clinical laboratories are beginning to implement WGS to accurately detect sequence-­level variants (single nucleotide variants); insertions/­deletions (indels) up to 50 bp and CNVs for genetically heterogeneous disorders; however, CMA and whole exome sequencing have so far been the predominant tests used for this purpose due to their lower cost.临床实验室正开始实施全基因组测序，以准确检测序列水平变异（单核苷酸变异）、长达50 bp的插入/缺失以及遗传异质性疾病的拷贝数变异；然而，由于成本较低，染色体微阵列分析和全外显子组测序迄今仍是用于此目的的主要检测方法。
Exome sequencing (ES) generates sequence reads from protein-­coding exons, which represent ~1. 5% of the genome.外显子组测序从蛋白质编码外显子生成序列读段，这些外显子约占基因组的1.5%。
This provides accurate detection of exonic sequence–­level variants; however, detection of CNVs is less accurate by ES than by WGS because the number of sequence reads generated for each exon can be less consistent, and there is considerable uncertainty of CNV breakpoints due to the large unsequenced chromosome regions between exons.这提供了外显子序列水平变异的准确检测；然而，通过外显子组测序检测拷贝数变异的准确性低于全基因组测序，因为每个外显子生成的序列读段数量可能不太一致，并且由于外显子之间存在大量未测序的染色体区域，拷贝数变异断点存在相当大的不确定性。
In addition, ES cannot detect balanced rearrangements and noncoding variants.此外，外显子组测序无法检测平衡重排和非编码变异。
As the cost of WGS continues to decrease, it will replace ES and CMA in genomic diagnostics, providing a much more complete representation of all the variants within an individual’s genome.随着全基因组测序成本持续下降，它将在基因组诊断中取代外显子组测序和染色体微阵列分析，提供个体基因组内所有变异更全面的表示。
Although WGS short-­read technologies provide a considerable improvement over microarray and ES, the short-­read lengths limit the ability to resolve complex A B Reference sequence of individual chromosomes Sequence reads: Patient with duplication Reference sequence of individual chromosomes Sequence reads: Patient with translocation Translocation in patient genome Sequences overrepresented in patient genome Although only a small number of reads are illustrated schematically here, in practice, many millions of sequence reads are analyzed and aligned to the reference genome to obtain statistically significant support for a diagnosis of aneuploidy or a structural chromosome abnormality.尽管全基因组测序短读段技术相比微阵列和外显子组测序有显著改进，但短读段长度限制了解决复杂A B个体染色体参考序列 序列读段：重复患者 个体染色体参考序列 序列读段：易位患者 患者基因组中的易位 患者基因组中过多代表的序列 尽管此处仅示意性显示了少量读段，但在实践中，分析并比对到参考基因组的序列读段有数百万个，以获得对非整倍体或结构性染色体异常诊断的统计学显著支持。
(A) Alignment of sequence reads from a patient’s genome to the reference sequence of three individual chromosomes.(A) 将患者基因组的序列读段比对到三个个体染色体的参考序列。
Overrepresentation of sequences from the red chromosome indicates that the patient is aneuploid for this chromosome.来自红色染色体的序列过多代表表明该患者对此染色体为非整倍体。
(B) Alignment of sequence reads from a patient’s genome to the reference sequence of two chromosomes reveals a number of reads that contain contiguous sequences from both chromosomes.(B) 将患者基因组的序列读段比对到两个染色体的参考序列，揭示了一些读段包含来自这两个染色体的连续序列。
This indicates a translocation in the patient’s genome involving the blue and orange chromosomes at the positions designated by the dotted lines.这表明患者基因组中存在涉及蓝色和橙色染色体的易位，位置由虚线标明。
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structural variation, repetitive regions, and genes with homologous sequence in other regions of the genome (e. g., pseu…
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structural variation, repetitive regions, and genes with homologous sequence in other regions of the genome (e. g., pseudogenes).结构变异、重复区域以及基因组其他区域中存在同源序列的基因（例如，假基因）。
The emergence of long-­read sequencing technologies that generate sequence reads greater than 10 kb has made it possible to begin to address many of these challenges that can potentially involve clinically relevant genes.长读长测序技术的出现能够生成超过10 kb的序列读长，使得开始应对许多可能涉及临床相关基因的挑战成为可能。
Notably, this technology is able to (1) sequence genes without interference of homologous sequence from pseudogenes, (2) provide haplotypes and phase variants across large stretches of DNA (&gt;10 kb), (3) sequence large repeat expansions and identify intervening sequence that may affect phenotype and repeat stability (e. g. involved in DMPK, the genes for myotonic dystrophy), and (4) identify balanced and unbalanced translocations, insertions, deletions, duplications, and inversions.值得注意的是，该技术能够（1）在不受假基因同源序列干扰的情况下对基因进行测序，（2）提供跨越大型DNA片段（>10 kb）的单倍型和相位变异，（3）对大的重复扩增进行测序并识别可能影响表型和重复稳定性的间隔序列（例如涉及DMPK，即强直性肌营养不良的基因），以及（4）识别平衡和不平衡的易位、插入、缺失、重复和倒位。
CHROMOSOME ABNORMALITIES Abnormalities of chromosomes may be either numeric or structural and may involve one or more autosomes, sex chromosomes, or both simultaneously.染色体异常 染色体异常可以是数量异常或结构异常，可能涉及一个或多个常染色体、性染色体或同时涉及两者。
The overall incidence of chromosome abnormalities is ~1 in 154 live births , and their impact is therefore substantial, both in clinical medicine and for society.染色体异常的总体发生率约为每154例活产中有1例，因此其对临床医学和社会均产生重大影响。
By far the most common type of clinically significant chromosome abnormality is aneuploidy, an abnormal chromosome number due to an extra or missing chromosome.迄今为止，临床上最重要的染色体异常类型是非整倍体，即因一条额外或缺失的染色体导致的染色体数目异常。
An aneuploid karyotype is typically associated with physical or neurodevelopmental abnormalities, or both.非整倍体核型通常与身体异常或神经发育异常或两者兼有关联。
Structural abnormalities (rearrangements involving one or more chromosomes) are also relatively common .结构异常（涉及一条或多条染色体的重排）也相对常见。
Depending on whether a structural rearrangement leads to an imbalance of genomic content, disruption of coding, or regulatory sequence, these may or may not have a phenotypic effect.根据结构重排是否导致基因组含量的不平衡、编码序列或调控序列的破坏，这些异常可能有或没有表型效应。
However, as explained later in this chapter, even individuals with benign balanced chromosome abnormalities may be at an increased risk for abnormal offspring in the subsequent generation.然而，正如本章后面所述，即使是具有良性平衡染色体异常的个体，其后代出现异常的风险也可能增加。
Chromosome abnormalities are described by a standard set of abbreviations and nomenclature that indicate the nature of the abnormality and (in the case of analyses performed by FISH or microarrays) the technology used.染色体异常通过一套标准的缩写和命名法来描述，指明异常的性质以及（对于通过FISH或微阵列进行的分析）所使用的技术。
Some of the more common abbreviations and examples of abnormal karyotypes and abnormalities are listed in Gene Dosage, Balance, and Imbalance For chromosome and genomic disorders, it is primarily the quantitative aspects of gene expression that underlie disease, in contrast to single-­gene disorders in which pathogenesis often reflects qualitative aspects of a gene’s function.一些较为常见的缩写以及异常核型和异常的示例列于“基因剂量、平衡与不平衡”部分。对于染色体和基因组疾病，主要是基因表达的定量方面构成疾病的基础，而与之相反，在单基因疾病中，发病机制通常反映基因功能的定性方面。
The clinical consequences of any particular chromosome alteration will depend on the resulting imbalance of parts of the genome, the specific genes contained in or affected by the alteration, and the likelihood of its transmission to the next generation.任何特定染色体改变的临床后果取决于由此导致的基因组部分的不平衡、该改变所包含或影响的特定基因，以及其传递给下一代的可能性。
The central concept for thinking about chromosome and genomic disorders is that of gene dosage and its balance or imbalance.思考染色体和基因组疾病的核心概念是基因剂量及其平衡或不平衡。
As we shall see in later chapters, this same concept applies generally to considering some single-­ gene disorders and their underlying etiology.正如我们将在后续章节中看到的，这一概念同样适用于考虑某些单基因疾病及其潜在病因。
It takes on uniform importance, however, for chromosome abnormalities, where we are generally more concerned with the dosage of genes within the relevant chromosomal region than with the actual sequence of those genes.然而，对于染色体异常，这一概念具有统一的重要性，因为我们通常更关注相关染色体区域内基因的剂量，而非这些基因的实际序列。
Most genes in the human genome are present in two doses and are expressed from both copies.人类基因组中的大多数基因以两份剂量存在，并从两个拷贝表达。
Some genes, however, are expressed from only a single copy (e. g., imprinted genes and X-­linked genes subject to X inactivation; see Chapter 3).然而，有些基因仅从单个拷贝表达（例如，印记基因和受X失活影响的X连锁基因；见第3章）。
Extensive analysis of clinical cases has demonstrated that the relative dosage of these genes is critical for normal development.对临床病例的广泛分析表明，这些基因的相对剂量对正常发育至关重要。
One or three doses instead of two are generally not conducive to normal function for a dosage-­sensitive gene or set of genes that is typically expressed from two copies.对于通常从两个拷贝表达的剂量敏感基因或基因集，一个或三个剂量而非两个剂量通常不利于正常功能。
Similarly, abnormalities of genomic imprinting or X inactivation that cause the anomalous expression of two copies or no expression of a gene or set of genes, instead of one, can lead to clinical disorders.类似地，基因组印记或X失活的异常导致两个拷贝的异常表达或一个基因或基因集不表达（而非一个拷贝表达），可导致临床疾病。
Predicting clinical outcomes for chromosomal and genomic disorders can be an enormous challenge for genetic counseling, particularly in the prenatal setting.预测染色体和基因组疾病的临床结局对遗传咨询而言可能是巨大的挑战，尤其是在产前环境中。
Many such diagnostic dilemmas will be presented throughout this section and in Chapters 6 and 17, but there are a number of general principles that should be kept in mind as we explore specific types of chromosome abnormality in the sections that follow (see 2).在本节以及第6章和第17章中将呈现许多此类诊断困境，但在我们探讨后续章节中特定类型的染色体异常时，应牢记一些通用原则（见2）。
Incidence among newborns (%) Aneuploidy Structural abnormalities Total Total Balanced Unbalanced Xand Y chromosomes Autosomes All chromosome abnormalities 0 0. 25 0. 5 0. 75 1. 0 1/154 1/263 1/475 1/375 1/500 1/1600 1/700新生儿中的发生率（%） 非整倍体 结构异常 总计 总计 平衡型 非平衡型 X和Y染色体 常染色体 所有染色体异常 0 0.25 0.5 0.75 1.0 1/154 1/263 1/475 1/375 1/500 1/1600 1/700
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Principles of Clinical Cytogenetics and Genome Analysis 69 Abnormalities of Chromosome Number A human chromosome complem…
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Principles of Clinical Cytogenetics and Genome Analysis 69 Abnormalities of Chromosome Number A human chromosome complement with any number other than 46 is said to be heteroploid.[TL:failed]
An exact multiple of the haploid chromosome number (n) is called euploid, and any other chromosome number is aneuploid.[TL:failed]
Triploidy and Tetraploidy In addition to the diploid (2n) number characteristic of normal somatic cells, two other euploid chromosome complements, triploid (3n) and tetraploid (4n), are occasionally observed in clinical material.[TL:failed]
Both triploidy and tetraploidy have been seen in fetuses.[TL:failed]
Triploidy is observed in 1% to 3% of recognized conceptions; triploid infants can be liveborn, although they do not survive long.[TL:failed]
Among the few that survive at least to the end of the first trimester of pregnancy, most result from fertilization of an egg by two sperm (dispermy).[TL:failed]
Other cases result from failure of one of the meiotic divisions in either sex, resulting in a diploid egg or sperm.[TL:failed]
The phenotypic manifestation of a triploid karyotype depends on the source of the extra chromosome set; triploids with an extra set of maternal chromosomes are typically aborted spontaneously early in pregnancy, whereas those with an extra set of paternal chromosomes typically have an abnormal 3(835185_­1242591)x 1 Deletion in 8p23. 3 at genomic position 835185 to 1242591 using Genome Build GRCh 38 cen Centromere del Deletion 46,XX,del(5)(q 13) Female with terminal deletion of one chromosome 5 distal to band 5q13 der Derivative chromosome der(1) Translocation chromosome derived from chromosome 1 and containing the centromere of chromosome 1 dic Dicentric chromosome dic(X;Y) Translocation chromosome containing the centromeres of both the X and Y chromosomes dup Duplication inv Inversion inv(3)(p 25q21) Pericentric inversion of chromosome 3 mar Marker chromosome 47,XX,+mar Female with an extra, unidentified chromosome mat Maternal origin arr[GRCh 38] 7p22. 3(580556_­1191665)x 3 mat Maternally inherited duplication in 7p22. 3 genomic position 580556 to 1191665 using genome build GRCh 38 p Short arm of chromosome pat Paternal origin q Long arm of chromosome r Ring chromosome 46,X,r(X) Female with ring X chromosome rob Robertsonian translocation 45,XX,rob(14;21)(q 10;q 10) Female with balanced Robertsonian translocation in which breakage and reunion have occurred at band 14q10 and band 21q10 in the centromeric regions of chromosomes 14 and 21; however either rob or der may be used. t Translocation 46,XX,t(2;8)(q 22;p 21) Female with balanced translocation between chromosomes 2 and 8, with breakpoints in bands 2q22 and 8p21 + Gain of 47,XX,+21 Female with trisomy 21 –­ Loss of 45,XY,–­22 Male with monosomy 22 /­ Mosaicism mos 47,XX,+21[20]/46,XX[10] Female with two populations of cells, one with trisomy 21 observed in 20 cells, and one with a normal karyotype observed in 10 cells Abbreviations from Mc Gowan-­Jordan J, Hastings RJ, Adelaide SM editors: ISCN 2020: an international system for human cytogenetic nomenclature, Basel, 2020, Karger..[TL:failed]
UNBALANCED KARYOTYPES AND GENOMES IN LIVEBORNS: GENERAL GUIDELINES FOR COUNSELING Monosomies are more deleterious than trisomies.[TL:failed]
Complete monosomies are generally not viable, except for monosomy for the X chromosome.[TL:failed]
Complete trisomies are viable for chromosomes 13, 18, 21, X, and Y.[TL:failed]
The phenotype in partial (subchromosomal) aneuploidy depends on a number of factors, including the size of the unbalanced segment, which regions of the genome are affected and which genes are involved, and whether the imbalance is monosomic or trisomic.[TL:failed]
Risk in cases of inversions depends on the location of the inversion with respect to the centromere and on the size of the inverted segment.[TL:failed]
For inversions that do not involve the centromere (paracentric inversions), there is a very low risk for an abnormal phenotype in the next generation.[TL:failed]
But, for inversions that do involve the centromere (pericentric inversions), the risk for birth defects in offspring may be significant and increases with the size of the inverted segment.[TL:failed]
For a mosaic karyotype involving any chromosome abnormality, the results from testing one tissue may not accurately represent the extent of mosaicism in other tissues of the body.[TL:failed]
Counseling is particularly challenging because the degree of mosaicism in relevant tissues or relevant stages of development is generally unknown.[TL:failed]
Thus there is uncertainty about the severity of the phenotype.[TL:failed]
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degenerative placenta (resulting in a partial hydatidiform mole), with a small fetus.
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degenerative placenta (resulting in a partial hydatidiform mole), with a small fetus.退行性胎盘（导致部分性葡萄胎），伴小胎儿。
Tetraploids are always 92,XXXX or 92,XXYY and likely result from failure of completion of an early cleavage division of the zygote.四倍体总是92,XXXX或92,XXYY，很可能是由于受精卵早期卵裂分裂未能完成所致。
Aneuploidy Aneuploidy is the most common and clinically significant type of human chromosome disorder, occurring in at least 5% of all clinically recognized pregnancies.非整倍体是人类染色体疾病中最常见且具有临床意义的类型，发生在至少5%的临床确认妊娠中。
Most aneuploid individuals have either trisomy (three instead of the normal pair of a particular chromosome) or, less often, monosomy (only one representative of a particular chromosome).大多数非整倍体个体要么具有三体性（某特定染色体有三条而非正常的两条），要么较少见的是单体性（某特定染色体仅有一条）。
Either trisomy or monosomy can have severe phenotypic consequences.三体性或单体性均可能导致严重的表型后果。
Trisomy can involve part of a chromosone, but trisomy for a whole chromosome is only occasionally compatible with life.三体性可涉及染色体的一部分，但整条染色体的三体性仅有偶尔能存活。
By far the most common type of trisomy in liveborn infants is trisomy 21, the chromosome constitution seen in 95% of patients with Down syndrome (karyotype 47,XX,+21 or 47,XY,+21) .迄今为止，活产婴儿中最常见的三体类型是21三体，95%的唐氏综合征患者具有这种染色体组成（核型47,XX,+21或47,XY,+21）。
Other trisomies observed in liveborns include trisomy 18 and trisomy 13.在活产儿中观察到的其他三体包括18三体和13三体。
It is notable that these autosomes (13, 18, and 21) are the three with the lowest number of genes; presumably, trisomy for autosomes with a greater number of genes is lethal in most instances.值得注意的是，这些常染色体（13、18和21）是基因数量最少的三个；推测而言，基因数量较多的常染色体三体在大多数情况下是致死的。
Monosomy for an entire chromosome is almost always lethal; an important exception is monosomy for the X chromosome, as seen in Turner syndrome (Case 47).整条染色体的单体性几乎总是致死的；一个重要的例外是X染色体的单体性，如特纳综合征（病例47）所见。
These conditions are considered in greater detail in Chapter 6.这些情况将在第6章中更详细地讨论。
Although the causes of aneuploidy are not fully understood, the most common chromosomal mechanism is meiotic nondisjunction.虽然非整倍体的原因尚未完全明了，但最常见的染色体机制是减数分裂不分离。
This refers to the failure of a pair of chromosomes to disjoin properly during one of the two meiotic divisions, usually during meiosis I.这指的是在两次减数分裂中的一次（通常是减数第一次分裂）期间，一对染色体未能正常分离。
The genomic consequences of nondisjunction during meiosis I and meiosis II are different .减数第一次分裂和减数第二次分裂期间不分离的基因组后果不同。
If the error occurs during meiosis I, the gamete with 24 chromosomes contains both the paternal and the maternal members of the pair.如果错误发生在减数第一次分裂，含有24条染色体的配子将同时包含该对染色体的父源和母源成员。
If it occurs during meiosis II, the gamete with the extra chromosome contains both copies of either the paternal or the maternal chromosome.如果错误发生在减数第二次分裂，含有额外染色体的配子将包含父源或母源染色体的两个拷贝。
(Strictly speaking, these statements refer only to the paternal or maternal centromere because recombination between homologous chromosomes has usually taken place in the preceding meiosis I, resulting in some genetic differences between the chromatids and thus between the corresponding daughter chromosomes; see Chapter 2.) Proper disjunction of a pair of homologous chromosomes in meiosis I appears relatively straightforward .（严格来说，这些陈述仅指父源或母源着丝粒，因为在之前的减数第一次分裂中，同源染色体之间通常已发生重组，导致染色单体之间以及相应的子代染色体之间存在一些遗传差异；见第2章。）减数第一次分裂中一对同源染色体的正确分离看似相对简单。
In reality, however, it involves a feat of complex engineering that requires precise temporal and spatial control over alignment of the two homologues, their tight connections to each other (synapsis), their interactions with the meiotic spindle, and, finally, their release and subsequent movement to opposite poles and to different daughter cells.然而实际上，这涉及一项复杂的工程壮举，需要精确的时间和空间控制以协调两个同源染色体的排列、它们之间的紧密连接（联会）、它们与减数分裂纺锤体的相互作用，以及最终它们的释放和随后移向两极并进入不同的子细胞。
The propensity for non-­disjunction of a chromosome pair has been strongly associated with aberrations in the frequency or placement, (or both), of recombination events in meiosis I, which are critical for maintaining proper synapsis.染色体对发生不分离的倾向与减数第一次分裂中重组事件的频率或位置（或两者）的异常密切相关，而重组事件对于维持正常的联会至关重要。
A chromosome pair with too few (or even no) recombinations, or with recombination too close to the centromere or telomere, may be more susceptible to nondisjunction than a chromosome pair with a more typical number and distribution of recombination events.具有过少（甚至没有）重组事件，或重组事件过于靠近着丝粒或端粒的染色体对，可能比具有更典型重组事件数量和分布的染色体对更容易发生不分离。
In some cases, aneuploidy can result from premature separation of sister chromatids in meiosis I instead of meiosis II.在某些情况下，非整倍体可源于减数第一次分裂而非减数第二次分裂中姐妹染色单体的过早分离。
If this happens, the separated chromatids may by chance segregate to the oocyte or to the polar body, leading to an unbalanced gamete.如果发生这种情况，分离的染色单体可能随机分配到卵母细胞或极体，导致配子不平衡。
Nondisjunction can also occur in a mitotic division after formation of the zygote.不分离也可发生在受精卵形成后的有丝分裂中。
If this happens at an early cleavage division, clinically significant mosaicism may result (see later section).如果这发生在早期卵裂分裂中，可能导致具有临床意义的嵌合体（见后文）。
In some malignant cell lines and some cell cultures, mitotic nondisjunction can lead to highly abnormal karyotypes.在某些恶性细胞系和一些细胞培养中，有丝分裂不分离可导致高度异常的核型。
Abnormalities of Chromosome Structure Structural rearrangements result from chromosome breakage, recombination, or exchange, followed by reconstitution into an abnormal combination.染色体结构异常 结构重排源于染色体断裂、重组或交换，随后重组为异常组合。
Whereas rearrangements can take place in many ways, they are collectively less common than aneuploidy; overall, structural abnormalities are present in ~1 in 375 newborns .尽管重排可多种方式发生，但总体而言不如非整倍体常见；总体上，结构异常见于约每375名新生儿中1例。
Like numeric abnormalities, structural rearrangements may be present in all cells of a person or in mosaic form.与数目异常类似，结构重排可存在于个体的所有细胞或呈嵌合形式。
Structural rearrangements are classified as balanced if the genome has the normal complement of chromosomal material or unbalanced if material is additional or missing.结构重排分为平衡型（基因组具有正常染色体物质组成）和非平衡型（物质增加或缺失）。
Clearly, these designations depend on the resolution of the method(s) used to analyze a particular rearrangement ; some that appear balanced at the level of high-­resolution banding, for example, may be seen as unbalanced when studied with chromosomal microarrays or by DNA sequence analysis.显然，这些分类取决于分析特定重排所用方法的分辨率；例如，有些在高分辨显带水平看似平衡的重排，在染色体微阵列或DNA序列分析中可能被视为非平衡。
Chromosome rearrangements can be stable, capable of passing through mitotic and meiotic cell divisions unaltered, whereas others are unstable.染色体重排可以是稳定的，能够无改变地通过有丝分裂和减数分裂细胞分裂，而其他则是不稳定的。
Some of the more common types of structural rearrangements observed in human chromosomes are illustrated schematically in both.人类染色体中观察到的一些较常见的结构重排类型在两者中均有示意说明。
Duplication of part of a chromosome leads to partial trisomy for the genes within that segment; deletion leads to partial monosomy.染色体一部分的重复导致该片段内基因的部分三体性；缺失导致部分单体性。
As a general concept, any change that disturbs normal gene dosage balance can result in abnormal development; a broad range of phenotypes can result, depending on the nature of the specific genes whose dosage is altered in a particular case.作为一个总体概念，任何扰乱正常基因剂量平衡的改变都可能导致发育异常；根据特定病例中剂量改变的特定基因的性质，可产生广泛的表型。
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Principles of Clinical Cytogenetics and Genome Analysis 71 Large structural rearrangements involving imbalance of at lea…
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Principles of Clinical Cytogenetics and Genome Analysis 71 Large structural rearrangements involving imbalance of at least a few megabases can be detected at the level of routine chromosome banding.临床细胞遗传学与基因组分析原理 71 涉及至少几个兆碱基失衡的大规模结构重排可在常规染色体显带水平上检测到。
Detection of smaller changes, however, generally requires higher resolution analysis, involving FISH or chromosomal microarray analysis.然而，检测更小的变化通常需要更高分辨率的分析，包括荧光原位杂交或染色体微阵列分析。
B A C D 21 21 Mean fluorescence ratio (Log R) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 X Y -2. 5 -2. 0 -1. 5 -1. 0 -. 5 0. 5 1. 0 1. 5 2. 0 2. 5 Normalized sequence representation 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 22 0. 6 0. 8 1. 0 1. 2 1. 4 1. 6 Karyotype from a male patient with Down syndrome, showing three copies of chromosome 21.来自一名唐氏综合征男性患者的核型，显示21号染色体有三个拷贝。
(B) Interphase fluorescence in situ hybridization analysis using locus-­specific probes from chromosome 21 (red, three spots) and from a control autosome (green, two spots).(B) 使用来自21号染色体（红色，三个斑点）和对照常染色体（绿色，两个斑点）的位点特异性探针进行的间期荧光原位杂交分析。
(C) Detection of trisomy 21 in a female patient by whole genome chromosome microarray.(C) 通过全基因组染色体微阵列检测一名女性患者的21三体。
Increase in the fluorescence ratio for sequences from chromosome 21 is indicated by the red arrow.来自21号染色体序列的荧光比率增加由红色箭头指示。
(D) Detection of trisomy 21 by whole genome sequencing and overrepresentation of sequences from chromosome 21.(D) 通过全基因组测序检测21三体以及21号染色体序列的过度代表。
Normalized sequence representation for individual chromosomes (± SD) in chromosomally normal samples is indicated by the gray-shaded region.染色体正常样本中单个染色体的归一化序列代表（±标准差）由灰色阴影区域表示。
A normalized ratio of ~1. 5 indicates three copies of chromosome 21 sequences instead of two, consistent with trisomy 21.约1.5的归一化比率表示21号染色体序列有三个拷贝而非两个，与21三体一致。
(A, Courtesy Center for Human Genetics Laboratory, University Hospitals of Cleveland; B, courtesy M.(A, 由克利夫兰大学医院人类遗传学实验室中心提供；B, 由M. 提供)
Katharine Rudd, Emory Genetics Laboratory; C, courtesy Daynna J.Katharine Rudd, 埃默里遗传学实验室；C, 由Daynna J. 提供
Wolff, Medical University of South Carolina; D, original data from Dan S, Chen F, Choy KW, et al: Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing.Wolff, 南卡罗来纳医科大学；D, 原始数据来自Dan S, Chen F, Choy KW, 等：通过大规模并行测序进行产前检测非整倍体和失衡染色体排列。
PLo S ONE 7:e 27835, 2012.)PLo S ONE 7:e 27835, 2012.)
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A D E F B C Terminal deletion Isochromosome Robertsonian translocation Reciprocal translocation Interstitial deletion Du…
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A D E F B C Terminal deletion Isochromosome Robertsonian translocation Reciprocal translocation Interstitial deletion Duplication Ring Terminal and interstitial deletions, each generating an acentric fragment that is typically lost.A D E F B C 末端缺失 等臂染色体 罗伯逊易位 相互易位 中间缺失 重复 环状染色体 末端缺失和中间缺失各自产生一个通常丢失的无着丝粒片段。
(B) Duplication of a chromosomal segment, leading to partial trisomy.(B) 染色体片段重复，导致部分三体。
(C) Ring chromosome with two acentric fragments.(C) 具有两个无着丝粒片段的环状染色体。
(D) Generation of an isochromosome for the long arm of a chromosome.(D) 产生染色体长臂的等臂染色体。
(E) Robertsonian translocation between two acrocentric chromosomes, frequently leading to a pseudodicentric chromosome.(E) 两个近端着丝粒染色体之间的罗伯逊易位，常导致假双着丝粒染色体。
Robertsonian translocations are nonreciprocal, and the short arms of the acrocentrics are lost.罗伯逊易位是非相互的，且近端着丝粒染色体的短臂丢失。
(F) Translocation between two chromosomes, with reciprocal exchange of the translocated segments.(F) 两个染色体之间的易位，易位片段相互交换。
Nondisjunction Nondisjunction Normal MEIOSIS I MEIOSIS II Normal Normal Normal Normal Normal Normal If the error occurs at meiosis I, the gametes either contain a representative of both members of the chromosome 21 pair or lack a chromosome 21 altogether.不分离 不分离 正常 减数分裂I 减数分裂II 正常 正常 正常 正常 正常 正常 如果错误发生在减数分裂I，配子要么含有第21号染色体对的两条染色体，要么完全缺失一条21号染色体。
If nondisjunction occurs at meiosis II, the abnormal gametes contain two copies of one parental chromosome 21 (and no copy of the other) or lack a chromosome 21.如果不分离发生在减数分裂II，异常配子含有两条来自同一亲本的21号染色体（而没有另一亲本的拷贝），或缺失一条21号染色体。
Deletions and Duplications.缺失和重复。
Deletions involve loss of a chromosome segment, resulting in chromosome imbalance .缺失涉及染色体片段的丢失，导致染色体失衡。
A carrier of a chromosomal deletion (with one normal homologue and one deleted homologue) is monosomic for the genetic information on the corresponding segment of the normal homologue.染色体缺失的携带者（有一个正常同源染色体和一个缺失同源染色体）对于正常同源染色体相应节段的遗传信息是单体的。
The clinical consequences generally reflect haploinsufficiency (literally, the inability of a single copy of the genetic material to carry临床后果通常反映单倍体不足（字面意思，单个遗传物质拷贝无法执行
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Principles of Clinical Cytogenetics and Genome Analysis 73 out the functions normally performed by two copies), and, whe…
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Principles of Clinical Cytogenetics and Genome Analysis 73 out the functions normally performed by two copies), and, where examined, their severity reflects the size of the deleted segment and the number and function of the specific genes that are deleted.临床细胞遗传学与基因组分析原理 73 指出，由于仅存一个拷贝（而非正常两个拷贝执行的功能），并且在已检测的病例中，其严重程度反映了缺失片段的大小以及缺失特定基因的数量和功能。
Cytogenetically visible autosomal deletions have an incidence of ~1 in 7000 live births.细胞遗传学可见的常染色体缺失在活产儿中的发生率约为1/7000。
Smaller, submicroscopic deletions detected by CMA or WGS are much more common, but as mentioned earlier, the clinical significance of many such variants has yet to be determined.通过染色体微阵列分析或全基因组测序检测到的更小、亚微观的缺失更为常见，但如前所述，许多此类变异的临床意义仍有待确定。
A deletion may occur at the end of a chromosome (terminal) or within a chromosome arm (interstitial).缺失可能发生在染色体的末端（末端缺失）或染色体臂内部（中间缺失）。
Deletions may originate simply from chromosome breakage and loss of the acentric segment.缺失可能仅仅源于染色体断裂和无着丝粒片段的丢失。
Numerous deletions have been identified in the course of prenatal diagnosis or in the investigation of dysmorphic patients or those with intellectual disability; specific examples of such cases will be discussed in Chapter 6.在产前诊断或对畸形患者或智力障碍患者的检查中已发现大量缺失；此类病例的具体例子将在第6章讨论。
In general, duplication appears to be less harmful than deletion.一般来说，重复似乎比缺失的危害小。
However, duplication in a gamete results in chromosomal imbalance (i. e., partial trisomy), and the chromosome breaks that generate it may disrupt genes, and can lead to some phenotypic abnormality.然而，配子中的重复会导致染色体失衡（即部分三体），并且产生重复的染色体断裂可能破坏基因，进而导致某些表型异常。
Marker and Ring Chromosomes.标记染色体与环状染色体。
Very small, unidentified chromosomes, called marker chromosomes, are occasionally seen in chromosome preparations, frequently in a mosaic state.极小的、无法识别的染色体，称为标记染色体，偶尔在染色体标本中可见，常以嵌合状态存在。
They are usually in addition to the normal chromosome complement and are thus also referred to as supernumerary chromosomes or extra structurally abnormal chromosomes.它们通常是在正常染色体组之外附加的，因此也被称为额外染色体或额外结构异常染色体。
The prenatal frequency of de novo supernumerary marker chromosomes has been estimated to be ~1 in 2500 pregnancies.新发额外标记染色体的产前频率估计约为每2500次妊娠中1例。
Because of their small and indistinctive appearance, higher resolution genome analysis (e. g., FISH and/or CMA) is usually required for precise identification.由于其体积小且形态不明显，通常需要更高分辨率的基因组分析（如荧光原位杂交和/或染色体微阵列分析）进行精确鉴定。
Larger marker chromosomes contain genomic material from one or both chromosome arms, creating an imbalance for whatever genes are present.较大的标记染色体包含来自一条或两条染色体臂的基因组物质，从而对所存在的任何基因造成失衡。
Depending on the origin of the marker chromosome, the risk for a fetal abnormality can range from very low to 100%.根据标记染色体的起源，胎儿异常的风险可以从极低到100%不等。
For reasons not fully understood, a relatively high proportion of such markers derive from chromosome 15 and from the sex chromosomes.由于尚未完全理解的原因，此类标记中相当高比例来源于15号染色体和性染色体。
Many marker chromosomes lack telomeres and are ring chromosomes that are formed when a chromosome undergoes two breaks, and the broken ends of the chromosome reunite in a ring structure .许多标记染色体缺乏端粒，是环状染色体，当一条染色体发生两次断裂，且染色体断裂端以环状结构重新连接时形成。
Some rings experience difficulties at mitosis, when the two sister chromatids become tangled in their attempt to disjoin at anaphase.某些环状染色体在有丝分裂时会遇到困难，此时两条姐妹染色单体在后期试图分离时发生缠结。
There may be breakage of the ring followed by fusion, and larger and smaller rings may thus be generated.可能发生环的断裂随后融合，从而产生较大和较小的环。
Because of this mitotic instability it is not uncommon for ring chromosomes to be found in only a proportion of cells.由于这种有丝分裂不稳定性，环状染色体通常仅存在于一部分细胞中。
Isochromosomes.等臂染色体。
An isochromosome is a chromosome in which one arm is missing and the other duplicated in a mirror-­image fashion .等臂染色体是一种其中一条臂缺失而另一条臂以镜像方式重复的染色体。
A person with 46 chromosomes carrying an isochromosome therefore has a single copy of the genetic material of one arm (partial monosomy) and three copies of the genetic material of the other arm (partial trisomy).因此，携带等臂染色体且具有46条染色体的人，一条臂的遗传物质为单拷贝（部分单体），另一条臂的遗传物质为三拷贝（部分三体）。
Although isochromosomes for a number of autosomes have been described, the most common isochromosome involves the long arm of the X chromosome—designated i(X)(q 10)—in a proportion of individuals with Turner syndrome (see Chapter 6, Case 47).尽管已描述了许多常染色体的等臂染色体，但最常见的等臂染色体涉及X染色体长臂——记作i(X)(q10)——出现在一部分特纳综合征患者中（见第6章，病例47）。
Isochromosomes are also frequently seen in karyotypes of both solid tumors and hematologic malignant neoplasms (see Chapter 16).等臂染色体在实体瘤和血液系统恶性肿瘤的核型中也常见（见第16章）。
Dicentric Chromosomes.双着丝粒染色体。
A dicentric chromosome is a rare type of abnormal chromosome in which two chromosome segments, each with a centromere, fuse end to end.双着丝粒染色体是一种罕见的异常染色体类型，其中两个各含一个着丝粒的染色体片段以末端对末端方式融合。
Dicentric chromosomes, despite their two centromeres, can be mitotically stable if one of the two centromeres is inactivated epigenetically or if the two centromeres always coordinate their movement to one or the other pole during anaphase.双着丝粒染色体尽管有两个着丝粒，但如果其中一个着丝粒被表观遗传失活，或者两个着丝粒在后期始终协调地移向同一极或另一极，则可能具有有丝分裂稳定性。
Such chromosomes are formally called pseudodicentric.此类染色体正式称为假双着丝粒染色体。
The most common pseudodicentrics involve the sex chromosomes or the acrocentric chromosomes (so-­called Robertsonian translocations; see later).最常见的假双着丝粒染色体涉及性染色体或近端着丝粒染色体（即所谓的罗伯逊易位；见下文）。
Balanced Rearrangements Balanced chromosomal rearrangements are found in as many as 1 in 500 individuals and do not usually lead to a phenotypic effect because all the genomic material is present, even though it is arranged differently .平衡重排 平衡染色体重排在多达1/500的个体中发现，通常不导致表型效应，因为所有基因组物质虽然排列方式不同但仍然存在。
As noted earlier, it is important to distinguish here between truly balanced rearrangements and those that appear balanced cytogenetically but are really unbalanced at the molecular level.如前所述，在此区分真正平衡的重排和那些在细胞遗传学上看似平衡但实际上在分子水平上不平衡的重排非常重要。
Because of the high frequency of common copy number variants around the genome (see Chapter 4), collectively adding up to differences of many megabases between genomes of unrelated individuals, the concept of what is balanced or unbalanced is subject to ongoing investigation and continual refinement.由于基因组中常见的拷贝数变异频率很高（见第4章），这些变异累积起来导致无血缘关系个体基因组之间多达数兆碱基的差异，因此关于平衡或不平衡的概念仍在不断研究和持续完善中。
Even when structural rearrangements are truly balanced, they can pose a threat to the subsequent generation because carriers are likely to produce unbalanced gametes and therefore have an increased risk for abnormal offspring with unbalanced karyotypes.即使结构重排是真正平衡的，它们也可能对后代构成威胁，因为携带者很可能产生不平衡配子，从而增加产生核型不平衡的异常后代的风险。
There is also a possibility that one of the chromosome breaks will disrupt a gene, leading to a pathogenic variant.还有一种可能性是染色体断裂之一会破坏一个基因，导致致病性变异。
Especially with the use of WGS to examine the nature of apparently balanced rearrangements in patients who present with significant phenotypes, this is an increasingly well-­ documented cause of disorders in carriers of balanced translocations; such translocations can be a useful clue to the identification of the gene responsible for a particular genetic disorder.特别是利用全基因组测序检查具有显著表型患者中看似平衡重排的性质，这日益成为平衡易位携带者疾病的一个充分记录在案的原因；此类易位可为识别特定遗传性疾病的致病基因提供有用线索。
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Translocations.
Ch5 — Segment 29
Translocations.易位。
Translocation involves the movement of chromosome segments between two chromosomes.易位涉及染色体片段在两染色体之间的移动。
There are two main types: reciprocal and nonreciprocal.主要有两种类型：相互易位和非相互易位。
Reciprocal Translocations.相互易位。
This type of rearrangement results from breakage or recombination involving nonhomologous chromosomes, with reciprocal exchange of the broken-­off or recombined segments .这种重排源于涉及非同源染色体的断裂或重组，伴随断裂或重组片段的相互交换。
Usually, only two chromosomes are involved, and because the exchange is reciprocal, the total chromosome number and content is unchanged.通常仅涉及两条染色体，且由于交换是相互的，染色体总数和含量不变。
Such translocations are usually without phenotypic effect; however, like other balanced structural rearrangements, they are associated with a high risk for unbalanced gametes and abnormal progeny.此类易位通常无表型效应；然而，与其他平衡结构重排一样，它们与不平衡配子及异常后代的高风险相关。
They come to attention either during prenatal diagnosis or when the parents of a clinically abnormal child with an unbalanced translocation are karyotyped.它们或在产前诊断时被发现，或当临床异常患有不平衡易位的儿童父母接受核型分析时受到关注。
Balanced translocations are more common in couples who have had two or more spontaneous pregnancy losses and in infertile males than in the general population.平衡易位在经历过两次或更多次自然流产的夫妇及不育男性中比普通人群更常见。
Translocations present challenges for the process of chromosome pairing and homologous recombination during meiosis (see Chapter 2).易位对减数分裂过程中染色体配对和同源重组提出了挑战（见第2章）。
When the chromosomes of a carrier of a balanced reciprocal translocation pair at meiosis , they must form a quadrivalent to ensure proper alignment of homologous sequences (rather than the typical bivalents seen with normal chromosomes).当平衡相互易位携带者的染色体在减数分裂时配对，它们必须形成四价体以确保同源序列正确排列（而非正常染色体中见到的典型二价体）。
In typical segregation, two of the four chromosomes in the quadrivalent go to each pole at anaphase; however, the chromosomes can segregate from this configuration in several ways, depending on which chromosomes go to which pole.在典型分离中，四价体中的四条染色体中有两条在后期移向每一极；然而，染色体可从此构型以多种方式分离，取决于哪些染色体移向哪一极。
Alternate segregation, the usual type of meiotic segregation, produces balanced gametes that have either a normal chromosome complement or contain the two reciprocal chromosomes.交替分离是减数分裂的常见分离类型，产生平衡配子，其具有正常染色体组成或包含两条相互易位染色体。
Other segregation patterns, however, always yield unbalanced gametes .然而，其他分离模式总是产生不平衡配子。
Robertsonian Translocations.罗伯逊易位。
Robertsonian translocations are the most common type of chromosome rearrangement observed in our species.罗伯逊易位是人类观察到的最常见的染色体重排类型。
They involve two acrocentric chromosomes that fuse near the centromere region with loss of the short arms .它们涉及两条近端着丝粒染色体，在着丝粒区域附近融合并丢失短臂。
Such translocations are nonreciprocal, and the resulting karyotype has only 45 chromosomes, including the translocation chromosome, which in effect is made up of the long arms of two acrocentric chromosomes.此类易位是非相互的，产生的核型仅有45条染色体，包括易位染色体，该染色体实际上由两条近端着丝粒染色体的长臂构成。
Because, as noted earlier, the short arms of all five pairs of acrocentric chromosomes consist largely of various classes of satellite DNA, as well as hundreds of copies of ribosomal RNA genes, loss of the short arms of two B Quadrivalent formation in meiosis A Chromosomes A B der(A) der(B) C Segregation and gametes Adjacent-1 Unbalanced Unbalanced Unbalanced Unbalanced Normal Balanced Adjacent-2 Alternate Formation of a quadrivalent in meiosis is necessary to align the homologous segments of the two derivative chromosomes and their normal homologues.因为如前所述，所有五对近端着丝粒染色体的短臂主要由各类卫星DNA以及数百拷贝的核糖体RNA基因组成，两条B染色体的短臂丢失——减数分裂中四价体的形成 A 染色体 A B der(A) der(B) C 分离与配子 相邻-1 不平衡 不平衡 不平衡 不平衡 正常 平衡 相邻-2 交替——减数分裂中四价体的形成对于对齐两条衍生染色体及其正常同源物的同源片段是必要的。
(C) Patterns of segregation in a carrier of the translocation, leading to either balanced or unbalanced gametes, shown at the bottom.（C）易位携带者中的分离模式，导致平衡或不平衡配子，如底部所示。
Adjacent-­1 segregation (in red, top chromosomes to one gamete, bottom chromosomes to the other) leads only to unbalanced gametes.相邻-1分离（红色，上方染色体进入一个配子，下方染色体进入另一个配子）仅导致不平衡配子。
Adjacent-­2 segregation (in green, left chromosomes to one gamete, right chromosomes to the other) also leads only to unbalanced gametes.相邻-2分离（绿色，左侧染色体进入一个配子，右侧染色体进入另一个配子）也仅导致不平衡配子。
Only alternate segregation (in gray, upper left/­lower right chromosomes to one gamete, lower left/­upper right to the other) can lead to balanced gametes.仅有交替分离（灰色，左上/右下染色体进入一个配子，左下/右上进入另一个配子）可导致平衡配子。
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Principles of Clinical Cytogenetics and Genome Analysis 75 acrocentric chromosomes is not deleterious; thus the karyotyp…
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Principles of Clinical Cytogenetics and Genome Analysis 75 acrocentric chromosomes is not deleterious; thus the karyotype is considered to be balanced, despite having only 45 chromosomes.临床细胞遗传学与基因组分析原理 75个近端着丝粒染色体并非有害；因此，尽管只有45条染色体，该核型仍被视为平衡的。
Robertsonian translocations are typically, although not always, pseudodicentric , reflecting the location of the breakpoint on each acrocentric chromosome.罗伯逊易位通常（尽管并非总是）是假双着丝粒的，反映了每个近端着丝粒染色体上断裂点的位置。
Although Robertsonian translocations can involve all combinations of the acrocentric chromosomes, two—designated rob(13;14)(q 10;q 10) and rob(14;21) (q 10;q 10)—are relatively common.虽然罗伯逊易位可涉及近端着丝粒染色体的所有组合，但两种——命名为rob(13;14)(q10;q10)和rob(14;21)(q10;q10)——相对常见。
The translocation involving 13q and 14q is found in ~1 in 1300 persons and is thus by far the most common chromosome rearrangement in our species.涉及13q和14q的易位在约1/1300的人群中发现，因此是人类中迄今为止最常见的染色体重排。
Rare individuals with two copies of the same type of Robertsonian translocation have been described; these phenotypically normal individuals have only 44 chromosomes and lack any normal copies of the acrocentrics involved, replaced by two copies of the translocation.已有报道携带两份相同类型罗伯逊易位的罕见个体；这些表型正常的个体仅有44条染色体，缺失所涉及近端着丝粒染色体的任何正常拷贝，取而代之的是两份易位染色体。
Although a carrier of a Robertsonian translocation does not present with any obvious clinical phenotype, there is a risk for unbalanced gametes and, therefore, for unbalanced offspring.尽管罗伯逊易位携带者不呈现任何明显的临床表型，但仍存在产生不平衡配子以及因此产生不平衡后代的风险。
The risk for unbalanced offspring varies according to the particular Robertsonian translocation and the sex of the carrier parent; carrier females in general have a higher risk for transmitting the translocation to an affected child.产生不平衡后代的风险因特定的罗伯逊易位和携带者父母的性别而异；女性携带者通常具有更高的将易位传递给患病孩子的风险。
The chief clinical importance of this type of translocation is that carriers of a Robertsonian translocation involving chromosome 21 are at risk for producing a child with translocation Down syndrome, as will be explored further in Chapter 6.此类易位的主要临床重要性在于，涉及21号染色体的罗伯逊易位携带者有可能产生患有易位型唐氏综合征的孩子，这将在第6章进一步探讨。
Insertions.插入。
An insertion is another type of nonreciprocal translocation that occurs when a segment removed from one chromosome is inserted into a different chromosome or in a different location within the same chromosome, either in its usual orientation with respect to the centromere or inverted.插入是另一种类型的非相互易位，发生于从一个染色体上移除的片段插入到另一个染色体或同一染色体内的不同位置时，插入片段相对于着丝粒的方向可以是正常方向或倒位方向。
Because they require three chromosome breaks, insertions are relatively rare.由于需要三次染色体断裂，插入相对罕见。
Segregation in an insertion carrier can produce offspring with duplication or deletion of the inserted segment, as well as normal offspring and balanced carriers.插入携带者的分离可产生具有插入片段重复或缺失的后代，以及正常后代和平衡携带者。
The average risk for producing an affected child can be up to 50%, and prenatal diagnosis is therefore indicated.产生患病孩子的平均风险可高达50%，因此产前诊断是必要的。
Inversions.倒位。
An inversion occurs when a single chromosome undergoes two breaks and is reconstituted with the segment between the breaks inverted.倒位发生在单一染色体经历两次断裂，并且断裂之间的片段以倒位方式重新连接时。
Inversions are of two types : paracentric, in which both breaks occur in one arm (Greek para, beside the centromere); and pericentric, in which there is a break in each arm (Greek peri, around the centromere).倒位有两种类型：臂内倒位，即两次断裂发生在同一臂内（希腊语para，意为着丝粒旁）；以及臂间倒位，即每臂各发生一次断裂（希腊语peri，意为着丝粒周围）。
Pericentric inversions can be easier to identify cytogenetically when they change the proportion of the chromosome arms as well as the banding pattern.臂间倒位当改变染色体臂的比例以及带型时，在细胞遗传学上可能更容易识别。
An inversion does not usually cause an abnormal phenotype in carriers because it is a balanced rearrangement.倒位通常不会在携带者中引起异常表型，因为它是一种平衡重排。
Its medical significance is for the progeny; a carrier of either type of inversion is at risk for producing unbalanced gametes and offspring.其医学意义在于后代；任一种类型的倒位携带者均有产生不平衡配子和后代的风险。
When an inversion is present, a loop needs to form to allow alignment and pairing of homologous segments of the normal and inverted chromosomes in meiosis I .当存在倒位时，减数分裂I中需要形成一个环，以使正常染色体与倒位染色体的同源片段对齐并配对。
When recombination occurs within the loop, gametes with balanced chromosome complements (either normal or with the inversion) and gametes with unbalanced complements are formed, depending on the location of recombination events.当环内发生重组时，根据重组事件的位置，会形成具有平衡染色体组（正常或带有倒位）的配子以及具有不平衡染色体组的配子。
When the inversion is paracentric, the unbalanced recombinant chromosomes are acentric or dicentric and typically do not lead to viable offspring ; thus the risk that a carrier of a paracentric inversion will have a liveborn child with an abnormal karyotype is very low.当倒位为臂内倒位时，不平衡的重组染色体为无着丝粒或双着丝粒，通常不会导致可存活的后代；因此，臂内倒位携带者生育具有异常核型的活产儿的风险非常低。
A pericentric inversion, on the other hand, can lead to the production of unbalanced gametes with both duplication and deletion of chromosome segments .另一方面，臂间倒位可导致产生同时具有染色体片段重复和缺失的不平衡配子。
The duplicated and deleted segments are those distal to the inversion.重复和缺失的片段是那些位于倒位远端的片段。
Overall, the risk for the child of a carrier of a pericentric inversion to have an unbalanced karyotype is estimated to be 5% to 10%.总体而言，臂间倒位携带者的孩子具有不平衡核型的风险估计为5%至10%。
Each pericentric inversion, however, is associated with a particular risk, typically reflecting the size and content of the duplicated and deficient segments.然而，每个臂间倒位都与特定风险相关，通常反映了重复和缺失片段的大小和内容。
Mosaicism for Chromosome Abnormalities Sometimes, two or more different chromosome complements are present among the cells in an individual; this situation is called chromosomal mosaicism.染色体异常的嵌合体 有时，个体细胞中存在两种或多种不同的染色体组成；这种情况称为染色体嵌合体。
Such mosaicism is typically detected by conventional karyotyping, interphase FISH analysis, or chromosomal microarrays.这种嵌合体通常通过常规核型分析、间期FISH分析或染色体微阵列来检测。
A common cause of mosaicism is nondisjunction in an early postzygotic mitotic division.嵌合体的一个常见原因是早期受精后有丝分裂分裂中的不分离。
For example, a zygote with an additional chromosome 21 might lose the extra chromosome in a mitotic division and continue to develop as a 47,+21/46 mosaic.例如，一个具有额外21号染色体的合子可能在有丝分裂分裂中丢失额外的染色体，并继续发育为47,+21/46嵌合体。
The effects of mosaicism on development vary with the timing of the nondisjunction event, the nature of the chromosome abnormality, the proportions of the different chromosome complements present, and the tissues affected.嵌合体对发育的影响因不分离事件的时间、染色体异常的性质、存在的不同染色体组成的比例以及受累组织而异。
It is often believed that individuals who are mosaic for a given trisomy, such as mosaic Down syndrome or mosaic Turner syndrome, are less severely affected than nonmosaic individuals.通常认为，对于特定三体性呈嵌合体的个体（如嵌合型唐氏综合征或嵌合型特纳综合征），其受累程度比非嵌合体个体轻。
When detected in lymphocytes, in cultured cell lines or in prenatal samples, it can be difficult to assess the significance of mosaicism, especially if it is identified prenatally.当在淋巴细胞、培养细胞系或产前样本中检测到时，评估嵌合体的意义可能很困难，尤其是在产前发现时。
The proportions of the different chromosome complements seen in the tissue being analyzed (e. g., cultured amniocytes or lymphocytes) may not necessarily reflect the proportions present in other tissues or in the embryo during its early developmental stages.在分析的组织（例如，培养的羊水细胞或淋巴细胞）中观察到的不同染色体组成的比例，不一定反映其他组织或胚胎在早期发育阶段中的比例。
Mosaicism can also arise in cells in culture after they were taken from the individual; thus cytogeneticists嵌合体也可能在从个体取出后的培养细胞中出现；因此，细胞遗传学家需谨慎判断。
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attempt to differentiate between true mosaicism, present in the individual, and pseudomosaicism, which has occurred in t…
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attempt to differentiate between true mosaicism, present in the individual, and pseudomosaicism, which has occurred in the laboratory.尝试区分存在于个体中的真正嵌合体与发生于实验室中的假性嵌合体。
The distinction between these types is not always easy or certain and can lead to major interpretive difficulties in prenatal diagnosis (see Incidence of Chromosome Anomalies Visible by Karyotype Analysis The incidence of different types of chromosomal aberration has been measured in a number of large population surveys and was summarized earlier in and four types of sex chromosomal aneuploidy: Turner syndrome (usually 45,X), Klinefelter syndrome (47,XXY), 47,XYY, and 47,XXX (see Chapter 6).这些类型之间的区分并不总是容易或确定的，并可能在前诊断中导致重大的解释困难（见《通过核型分析可见的染色体异常发生率》；不同染色体畸变类型的发生率已在多项大规模人群调查中测量，并总结于前文，以及四种性染色体非整倍体：特纳综合征（通常为45,X）、克兰费尔特综合征（47,XXY）、47,XYY和47,XXX（见第6章））。
Triploidy and tetraploidy account for only a small percentage of cases, typically in spontaneous abortions.三倍体与四倍体仅占病例的一小部分，通常见于自然流产。
The classification and incidence of chromosomal defects measured in these surveys can be used to consider the fate of 10,000 conceptuses ( 5) 1 47,XXY, 47,XXX, 47,XYY 19 4 (21) 15 Unbalanced rearrangements 27 23 (85) 4 Balanced rearrangements 19 3 (16) 16 Other 39 37 (95) 2 a These estimates are based on observed frequencies of chromosome abnormalities in spontaneous pregnancy losses and in liveborn infants.这些调查中测量的染色体缺陷的分类与发生率可用于考虑10,000个胚胎的命运（5）1 47,XXY、47,XXX、47,XYY 19 4 (21) 15 非平衡重排 27 23 (85) 4 平衡重排 19 3 (16) 16 其他 39 37 (95) 2 a 这些估计基于在自然流产和活产婴儿中观察到的染色体异常频率。
It is likely that the frequency of chromosome abnormalities in all conceptuses is much higher than this because many undergo spontaneous pregnancy loss before they are recognized clinically.所有胚胎中染色体异常的发生频率可能远高于此，因为许多在临床识别之前即已发生自然流产。
A B A B C Invert D A C B D Paracentric A B C Invert D A C B D Pericentric A B C D A B C A D B C D A C B D A B C D D B C D Inviable Balanced Unbalanced Balanced A C B D A B C A Paracentric inversion.A B A B C 倒位 D A C B D 臂内 A B C 倒位 D A C B D 臂间 A B C D A B C A D B C D A C B D A B C D D B C D 不可活 平衡 非平衡 平衡 A C B D A B C A 臂内倒位。
Gametes formed after the second meiotic division usually contain either a normal (A-­B-­C-­D) or a balanced (A-­C-­B-­D) copy of the chromosome because the acentric and dicentric products of the crossover are inviable.第二次减数分裂后形成的配子通常含有染色体的正常（A‑B‑C‑D）或平衡（A‑C‑B‑D）拷贝，因为交换产生的无着丝粒和双着丝粒产物不可活。
(B) Pericentric inversion.（B）臂间倒位。
Gametes formed after the second meiotic division may be balanced (normal or inverted) or unbalanced.第二次减数分裂后形成的配子可能是平衡（正常或倒位）或非平衡的。
Unbalanced gametes contain a copy of the chromosome with a duplication or a deletion of the material flanking the inverted segment (A-­B-­C-­A or D-­B-­C-­D).非平衡配子含有染色体的一个拷贝，其中倒位片段侧翼的遗传物质存在重复或缺失（A‑B‑C‑A或D‑B‑C‑D）。
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Principles of Clinical Cytogenetics and Genome Analysis 77 Live Births The overall incidence of chromosome abnormalities…
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Principles of Clinical Cytogenetics and Genome Analysis 77 Live Births The overall incidence of chromosome abnormalities in newborns is ~1 in 154 births (0. 65%) .临床细胞遗传学与基因组分析原理 77例活产：新生儿染色体异常的总发生率约为每154例出生中有1例（0.65%）。
Most of the autosomal abnormalities can be diagnosed at birth, but most sex chromosome abnormalities, with the exception of Turner syndrome, are not recognized clinically until puberty (see Chapter 6).大多数常染色体异常可在出生时诊断，但除特纳综合征外，大多数性染色体异常在青春期前无法通过临床识别（参见第6章）。
Unbalanced rearrangements are likely to come to clinical attention because of abnormal appearance and neurodevelopmental abnormalities in the affected individual.不平衡重排通常因患者出现异常外貌和神经发育异常而引起临床关注。
In contrast, balanced rearrangements are rarely identified clinically unless a carrier of a rearrangement has a child with an unbalanced chromosome complement and family studies are undertaken.相比之下，平衡重排在临床上很少被识别，除非重排携带者生育了染色体组型不平衡的子女，并因此进行了家庭研究。
Spontaneous Pregnancy Loss The frequency of chromosome abnormalities in spontaneous pregnancy loss is at least 40% to 50%, and the kinds of abnormalities differ in a number of ways from those seen in liveborns.自然流产 自然流产中染色体异常的频率至少为40%至
Somewhat surprisingly, the single most common abnormality in pregnancy loss is 45,X (the same abnormality found in Turner syndrome), which accounts for nearly 20% of chromosomally abnormal spontaneous pregnancy losses but less than 1% of chromosomally abnormal live births (see Another difference is the distribution of kinds of trisomy; for example, trisomy 16 is not seen at all in live births but accounts for approximately one-­ third of trisomies in pregnancy losses.[TL:missing]
CHROMOSOME AND GENOME ANALYSIS IN CANCER We have focused in this chapter on constitutional chromosome abnormalities that are seen in most or all of the cells in the body and derive from changes in chromosome structure or number that have been transmitted from a parent (either inherited or occurring de novo in the germline of a parent) or that have occurred in the zygote in early mitotic divisions.[TL:missing]
However, such chromosome abnormalities also occur in somatic cells throughout life and are a hallmark of cancer, both in hematologic neoplasias (e. g., leukemias and lymphomas) and in the context of solid tumor progression.[TL:missing]
An important area in cancer research is the delineation of chromosomal and genomic changes in specific forms of cancer and the relation of the breakpoints of the various structural rearrangements to the process of oncogenesis.[TL:missing]
The chromosome and genomic changes seen in cancer cells are numerous and diverse.[TL:missing]
The association of cytogenetic and genome analysis with tumor type and with the effectiveness of therapy is already an important part of the management of patients with cancer; these are discussed further in Chapter 16.[TL:missing]
ACKNOWLEDGMENT We thank Mary Ann George and Mary Shago for contributing to this chapter.[TL:missing]
GENERAL REFERENCES Gardner RJM, Armor D: Gardner and Sutherland’s chromosome abnormalities and genetic counseling, ed 5, New York, 2018, Oxford University Press.[TL:missing]
Feuk L, Carson AR, Scherer SW: Structural variation in the human genome, Nat Rev Genet 7(2):85–­97, 2006.[TL:missing]
Mc Gowan-­Jordan J, Hastings RJ, Adelaide SM, editors: ISCN 2020: an international system for human cytogenetic nomenclature, Basel, 2020, Karger.[TL:missing]
REFERENCES FOR SPECIFIC TOPICS Baldwin EK, May LF, Justice AN, et al: Mechanisms and consequences of small supernumerary marker chromosomes: from Barbara Mc Clintock to modern genetic-counseling issues, Am J Hum Genet 82:398–­410, 2008.[TL:missing]
Coulter ME, Miller DT, Harris DJ, et al: Chromosomal microarray testing influences medical management, Genet Med 13:770–­776, 2011.[TL:missing]
Dan S, Chen F, Choy KW, et al: Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing, PLo S ONE 7:e 27835, 2012.[TL:missing]
Feng W, Chakraborty A: Fragility extraordinaire: unsolved mysteries of chromosome fragile sites, Adv Exp Med Biol 1042:489–­526, 2017.[TL:missing]
Firth HV, Richards SM, Bevan AP, et al: DECIPHER: database of chromosomal imbalance and phenotype in humans using Ensembl resources, Am J Hum Genet 84:524–­533, 2009.[TL:missing]
Green RC, Rehm HL, Kohane IS: Clinical genome sequencing.[TL:missing]
In Ginsburg GS, Willard HF, editors: Genomic and personalized medicine ed 2, New York, 2013, Elsevier, pp 102–­122.[TL:missing]
Higgins AW, Alkuraya FS, Bosco AF, et al: Characterization of apparently balanced chromosomal rearrangements from the Developmental Genome Anatomy Project, Am J Hum Genet 82:712–­722, 2008.[TL:missing]
Ledbetter DH, Riggs ER, Martin CL: Clinical applications of whole-­ genome chromosomal microarray analysis.[TL:missing]
In Ginsburg GS, Willard HF, editors: Genomic and personalized medicine ed 2, New York, 2013, Elsevier, pp 133–­144.[TL:missing]
Lee C: Structural genomic variation in the human genome.[TL:missing]
In Ginsburg GS, Willard HF, editors: Genomic and personalized medicine ed 2, New York, 2013, Elsevier, pp 123–­132.[TL:missing]
Miller DT, Adam MP, Aradhya S, et al: Consensus statement: chromosomal microarray is a first-­tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies, Am J Hum Genet 86:749–­764, 2010.[TL:missing]
Nagaoka SI, Hassold TJ, Hunt PA: Human aneuploidy: mechanisms and new insights into an age-­old problem, Nat Rev Genet 13:493–­ 504, 2012.[TL:missing]
Reddy UM, Page GP, Saade GR, et al: Karyotype versus microarray testing for genetic abnormalities after stillbirth, N Engl J Med 367:2185–­2193, 2012.[TL:missing]
Riggs ER, Andersen EF, Cherry AM, et al: Technical standards for the interpretation and reporting of constitutional copy-­number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (Clin Gen), Genet Med 22(2):245–­257, 2020.[TL:missing]
South ST, Lee C, Lamb AN, et al: ACMG standards and guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision, Genet Med 15:901-909, 2013.[TL:missing]
Talkowski ME, Ernst C, Heilbut A, et al: Next-­generation sequencing strategies enable routine detection of balanced chromosome rearrangements for clinical diagnostics and genetic research, Am J Hum Genet 88:469–­481, 2011.[TL:missing]
Trost B, Loureiro LO, Scherer SW: Discovery of genomic variation across a generation, Hum Mol Genet 30(R2):R174–­R186, 2021. 209 .[TL:missing]
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PROBLEMS 1.
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PROBLEMS 1.[TL:failed]
You send a blood sample from an infant with multiple congenital anomalies to the chromosome laboratory for analysis.[TL:failed]
The laboratory identifies two copy number variants by chromosome microarray, arr[GRCh 38] 7q33(136240808_159345973)x 3,18q12. 3(45466214_ 80373285)x 1.[TL:failed]
G-banding analysis indicates the child’s karyotype is 46,XY,der(18)t(7;18)(q 33;q 12. 3) a.[TL:failed]
What do these results mean? b.[TL:failed]
The laboratory asks for blood samples from the clinically normal parents for analysis.[TL:failed]
The laboratory reports the mother's karyotype as 46,XX and the father's karyotype as 46,XY,t(7;18)(q 33;q 12. 3).[TL:failed]
What does the latter karyotype mean?[TL:failed]
Referring to the normal chromosome ideograms in Sketch these chromosomes in meiosis in the father.[TL:failed]
What kinds of gametes can he produce?[TL:failed]
A spontaneous pregnancy loss is found to have trisomy 18. a.[TL:failed]
What proportion of pregnancies with trisomy 18 are spontaneously lost? b.[TL:failed]
What is the risk that the parents will have a liveborn child with trisomy 18 in a future pregnancy?[TL:failed]
A newborn child with Down syndrome, when karyotyped, is found to have two cell lines: 70% of her cells have a 47,XX,+21 karyotype, and 30% are normal 46,XX.[TL:failed]
When did the nondisjunction event likely occur?[TL:failed]
What is the prognosis for this child?[TL:failed]
Which of the following persons is or is not expected to be phenotypically normal?[TL:failed]
For questions 4c and 4d, what are the reproductive risks associated with the chromosome rearrangements assuming the other parent is chromosomally normal? a.[TL:failed]
A female with 47 chromosomes, including a small supernumerary marker chromosome derived from the centromeric region of chromosome 15 b.[TL:failed]
A female with the karyotype 47,XX,+13 c.[TL:failed]
A person with a balanced reciprocal translocation d.[TL:failed]
A person with a pericentric inversion of chromosome 6 5.[TL:failed]
For each of the following, state whether chromosome/ genome analysis is indicated or not.[TL:failed]
For which family members, if any?[TL:failed]
For what kind of chromosome abnormality might the family in each case be at risk? a.[TL:failed]
A pregnant 29-year-old woman and her 41-year-old husband, with no history of genetic defects b.[TL:failed]
A pregnant 41-year-old woman and her 29-year-old husband, with no history of genetic defects c.[TL:failed]
A couple whose only child has Down syndrome d.[TL:failed]
A couple whose only child has cystic fibrosis e.[TL:failed]
A couple who has two boys with global developmental delay and severe intellectual disability 6.[TL:failed]
Explain the nature of the chromosome abnormality and the method of detection indicated by the following nomenclature. a. 46,XX,inv(X)(q 21q26) b. 46,XX,del(1)(p 36. 2) c. 46,XX. ish del(15)(q 11. 2q11. 2)(SNRPN−,D15S10−) d. 46,XX,del(15)(q 11. 2q13). ish del(15)(SNRPN−,D15 S10−) e. 46,XX. arr[GRCh 38] 1p36. 33p36. 32(1755688_263 3531)x 3 f. 47,XY,+mar. ish der(8)(D8Z1+) g. 46,XX,der(13;21)(q 10;q 10),+21 h. 45,XY,der(13;21)(q 10;q 10) 7.[TL:failed]
A laboratory performs microarray on a 4 year old male with learning disabilities, ventricular septal defect and immune deficiency.[TL:failed]
This analysis identifies a deletion affecting chromosome 22 at position 18874431 to 20348930 using genome build GRCh 38, in chromosome band 22q11. 21.[TL:failed]
Refer to the ISCN microarray nomenclature in[TL:failed]