Thompson & Thompson Genetics in Medicine, 8th Edition

CHAPTER 5. Principles of Clinical Cytogenetics and Genome Analysis

Clinical cytogenetics is the study of chromosomes, their structure, and their inheritance, as applied to the practice of medicine. 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. 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. Today, chromosome analysis—with increasing resolution and precision at both the cytological and genomic levels—is an important diagnostic procedure in numerous areas of clinical medicine. Current genome analyses that use approaches to be explored in this chapter, including chromosomal microarraysand whole-genome sequencing, represent impressive improvements in capacity and resolution, but ones that are conceptually similar to microscopic methods focusing on chromosomes (Fig. 5-1).

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FIGURE 5-1 Spectrum of resolution in chromosome and genome analysis. The typical resolution and range of effectiveness are given for various diagnostic approaches used routinely in chromosome and genome analysis. See text for details and specific examples. FISH, Fluorescence in situ hybridization.

Chromosome disorders form a major category of genetic disease. They account for a large proportion of all reproductive wastage, congenital malformations, and intellectual disability and play an important role in the pathogenesis of cancer. Specific cytogenetic disorders are responsible for hundreds of distinct syndromes that collectively are more common than all the single-gene diseases together. Cytogenetic abnormalities are present in nearly 1% of live births, in approximately 2% of pregnancies in women older than 35 years who undergo prenatal diagnosis, and in fully half of all spontaneous, first-trimester abortions.

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 whole-genome sequencing encompasses literally the entire field of medical genetics (see Fig. 5-1). In this chapter, we present the general principles of chromosome and genome analysis and focus on the chromosome mutations and regional mutations introduced in the previous chapter. 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. Application of these principles to some of the most common and best-known chromosomal and genomic disorders will then be presented in Chapter 6.

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. To be examined by chromosome analysis for clinical purposes, cells must be capable of proliferation in culture. The most accessible cells that meet this requirement are white blood cells, specifically T lymphocytes. To prepare a short-term culture that is suitable for cytogenetic analysis of these cells, a sample of peripheral blood is obtained, and the white blood cells are collected, placed in tissue culture medium, and stimulated to divide. After a few days, the dividing cells are arrested in metaphase with chemicals that inhibit the mitotic spindle. Cells are treated with a hypotonic solution to release the chromosomes, which are then fixed, spread on slides, and stained by one of several techniques, depending on the particular diagnostic procedure being performed. They are then ready for analysis.

Although ideal for rapid clinical analysis, cell cultures prepared from peripheral blood have the disadvantage of being short-lived (3 to 4 days). Long-term cultures suitable for permanent storage or further studies can be derived from a variety of other tissues. 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. White blood cells can also be transformed in culture to form lymphoblastoid cell lines that are potentially immortal. 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. Its main use is in the diagnosis of suspected hematological malignancies. 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. Chorionic villus cells can also be analyzed directly after biopsy, without the need for culturing. Remarkably, small amounts of cell-free fetal DNA are found in the maternal plasma and can be tested by whole-genome sequencing (see Chapter 17 for further discussion).

Molecular analysis of the genome, including whole-genome sequencing, can be carried out on any appropriate clinical material, provided that good-quality DNA can be obtained. 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. 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 Box).

Clinical Indications for Chromosome and Genome Analysis

Chromosome analysis is indicated as a routine diagnostic procedure for a number of specific conditions encountered in clinical medicine. Some general clinical situations indicate a need for cytogenetic and genome analysis:

• Problems of early growth and development. Failure to thrive, developmental delay, dysmorphic facies, multiple malformations, short stature, ambiguous genitalia, and intellectual disability are frequent findings in children with chromosome abnormalities. Unless there is a definite nonchromosomal diagnosis, chromosome and genome analysis should be performed for patients presenting with any combination of such problems.

• Stillbirth and neonatal death. The incidence of chromosome abnormalities is much higher among stillbirths (up to approximately 10%) than among live births (approximately 0.7%). It is also elevated among infants who die in the neonatal period (approximately 10%). Chromosome analysis should be performed for all stillbirths and neonatal deaths that that do not have a clear basis to rule out a chromosome abnormality. In such cases, karyotyping (or other comprehensive ways of scanning the genome) is essential for accurate genetic counseling. These analyses may provide important information for prenatal diagnosis in future pregnancies.

• Fertility problems. Chromosome studies are indicated for women presenting with amenorrhea and for couples with a history of infertility or recurrent miscarriage. A chromosome abnormality is seen in one or the other parent in 3% to 6% of cases in which there is infertility or two or more miscarriages.

• Family history. A known or suspected chromosome or genome abnormality in a first-degree relative is an indication for chromosome and genome analysis.

• Neoplasia. Virtually all cancers are associated with one or more chromosome abnormalities (see Chapter 15). Chromosome and genome evaluation in the tumor itself, or in bone marrow in the case of hematological malignant neoplasms, can offer diagnostic or prognostic information.

• Pregnancy. There is a higher risk for chromosome abnormality in fetuses conceived by women of increased age, typically defined as older than 35 years (see Chapter 17). Fetal chromosome and genome analysis should be offered as a routine part of prenatal care in such pregnancies. As a screening approach for the most common chromosome disorders, noninvasive prenatal testing using whole-genome sequencing is now available to pregnant women of all ages.

Chromosome Identification

The 24 types of chromosome found in the human genome can be readily identified at the cytological level by specific staining procedures. The most common of these, Giemsa banding (G banding), was developed in the early 1970s and was the first widely used whole-genome analytical tool for research and clinical diagnosis (see Figs. 2-1 and 2-10). 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.

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. Figure 5-2 is an ideogram of the banding pattern of a set of normal human chromosomes at metaphase, illustrating the alternating pattern of light and dark bands used for chromosome identification. The pattern of bands on each chromosome is numbered on each arm from the centromere to the telomere, as shown in detail in Figure 5-3 for several chromosomes. The identity of any particular band (and thus the DNA sequences and genes within it) can be described precisely and unambiguously by use of this regionally based and hierarchical numbering system.

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FIGURE 5-2 Ideogram showing G-banding patterns for human chromosomes at metaphase, with approximately 400 bands per haploid karyotype. As drawn, chromosomes are typically represented with the sister chromatids so closely aligned that they are not recognized as distinct entities. Centromeres are indicated by the primary constriction and narrow dark gray regions separating the p and q arms. For convenience and clarity, only the G-dark bands are numbered. For examples of full numbering scheme, see Figure 5-3SeeSources & Acknowledgments.

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FIGURE 5-3 Examples of G-banding patterns for chromosomes 5, 6, and 7 at the 550-band stage of condensation. Band numbers permit unambiguous identification of each G-dark or G-light band, for example, chromosome 5p15.2 or chromosome 7q21.2. SeeSources & Acknowledgments.

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 (see Fig. 5-2): metacentricchromosomes, with a more or less central centromere and arms of approximately equal length; submetacentric chromosomes, with an off-center centromere and arms of clearly different lengths; and acrocentricchromosomes, with the centromere near one end. A potential fourth type of chromosome, telocentric, with the centromere at one end and only a single arm, does not occur in the normal human karyotype, but it is occasionally observed in chromosome rearrangements. The human acrocentric chromosomes (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). 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.

In addition to changes in banding pattern, nonstaining gaps—called fragile sites—are occasionally observed at particular sites on several chromosomes that are prone to regional genomic instability. Over 80 common fragile sites are known, many of which are heritable variants. A small proportion of fragile sites are associated with specific clinical disorders; the fragile site most clearly shown to be clinically significant is seen near the end of the long arm of the X chromosome in males with a specific and common form of X-linked intellectual disability, fragile X syndrome (Case 17), as well as in some female carriers of the same genetic defect.

High-Resolution Chromosome Analysis

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 of greater than approximately 5 to 10 Mb anywhere in the genome (see Fig. 5-1). 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.

To increase the sensitivity of chromosome analysis, high-resolution banding (also called prometaphase banding) can be achieved 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). High-resolution banding is especially useful when a subtle structural abnormality of a chromosome is suspected. Staining of prometaphase chromosomes can reveal up to 850 bands or even more in a haploid set, although this method is frequently replaced now by microarray analysis (see later). A comparison of the banding patterns at three different stages of resolution is shown for one chromosome in Figure 5-4, demonstrating the increase in diagnostic precision that one obtains with these longer chromosomes. Development of high-resolution chromosome analysis in the early 1980s allowed the discovery of a number of new so-called microdeletion syndromes caused by smaller genomic deletions or duplications in the 2- to 3-Mb size range (see Fig. 5-1). However, the time-consuming and technically difficult nature of this method precludes its routine use for whole-genome analysis.

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FIGURE 5-4 The X chromosome: ideograms and photomicrographs at metaphase, prometaphase, and prophase (left to right). SeeSources & Acknowledgments.

Fluorescence In Situ Hybridization

Targeted high-resolution chromosome banding was largely replaced in the early 1990s by fluorescence in situ hybridization (FISH), a method for detecting the presence or absence of a particular DNA sequence or for evaluating the number or organization of a chromosome or chromosomal region in situ (literally, “in place”) in the cell. This convergence of genomic and cytogenetic approaches—variously termed molecular cytogenetics, cytogenomics, or chromonomics—dramatically expanded both the scope and precision of chromosome analysis in routine clinical practice.

FISH technology takes advantage of the availability of ordered collections of recombinant DNA clones containing DNA from around the entire genome, generated originally as part of the Human Genome Project. Clones containing specific human DNA sequences can be used as probes to detect the corresponding region of the genome in chromosome preparations or in interphase nuclei for a variety of research and diagnostic purposes, as illustrated in Figure 5-5:

• DNA probes specific for individual chromosomes, chromosomal regions, or genes can be labeled with different fluorochromes and used to identify particular chromosomal rearrangements or to rapidly diagnose the existence of an abnormal chromosome number in clinical material.

• Repetitive DNA probes allow detection of satellite DNA or other repeated DNA elements localized to specific chromosomal regions. Satellite DNA probes, especially those belonging to the α-satellite family of centromere repeats (see Chapter 2), are widely used for determining the number of copies of a particular chromosome.

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FIGURE 5-5 Fluorescence in situ hybridization to human chromosomes at metaphase and interphase, with different types of DNA probe. Top, Single-copy DNA probes specific for sequences within bands 4q12 (red fluorescence) and 4q31.1 (green fluorescence). Bottom, Repetitive α-satellite DNA probes specific for the centromeres of chromosomes 18 (aqua), X (green), and Y (red). SeeSources & Acknowledgments.

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, and thus its use is limited by the need to target a specific genomic region based on a clinical diagnosis or suspicion.

Genome Analysis Using Microarrays

Although the G-banded karyotype remains the front-line diagnostic test for most clinical applications, it has been complemented or even replaced by genome-wide approaches for detecting copy number imbalances at higher resolution (see Fig. 5-1), extending the concept of targeted FISH analysis to test the entire genome. Instead of examining cells and chromosomes in situ one probe at a time, chromosomal microarray techniques simultaneously query the whole genome represented as an ordered array of genomic segments on a microscope slide containing overlapping or regularly spaced DNA segments that represent the entire genome. In one approach based on comparative genome hybridization (CGH), one detects relative copy number gains and losses in a genome-wide manner by hybridizing two samples—one a control genome and one from a patient—to such microarrays. An excess of sequences from one or the other genome indicates an overrepresentation or underrepresentation of those sequences in the patient genome relative to the control (Fig. 5-6). An alternative approach uses “single nucleotide polymorphism (SNP) arrays” that contain versions of sequences corresponding to the two alleles of various SNPs around the genome (as introduced in Chapter 4). In this case, the relative representation and intensity of alleles in different regions of the genome indicate if a chromosome or chromosomal region is present at the appropriate dosage (see Fig. 5-6).

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FIGURE 5-6 Chromosomal microarray to detect chromosome and genomic dosage. A, Schematic of an array assay based on comparative genome hybridization (CGH), where a patient's genome (denoted in green) is cohybridized to the array with a control reference genome (denoted in red). The probes are mixed and allowed to hybridize to their complementary sequences on the array. Relative intensities of hybridization of the two probes are measured, indicating equivalent dosage between the two genomes (yellow)or a relative gain (green) or loss (red) in the patient sample. B, A typical output plots the logarithm of the fluorescence ratios as a function of the position along the genome. C, Array CGH result for a patient with Rett syndrome (Case 40), indicating a duplication of approximately 800 kb in band Xq28 containing the MECP2 gene. LogR of fluorescence ratios are plotted along the length of the X chromosome. Each dot represents the ratio for an individual sequence on the array. Sequences corresponding to the MECP2 gene and its surrounding region are duplicated in the patient's genome, leading to an increased ratio, indicated by the green arrow and shaded box in that region of the chromosome. SeeSources & Acknowledgments.

For routine clinical testing of suspected chromosome disorders, probe spacing on the array provides a resolution as high as 250 kb over the entire unique portion of the human genome. A higher density of probes can be used to achieve even higher resolution (<25-50 kb) over regions of particular clinical interest, such as those associated with known developmental disorders or congenital anomalies (see Fig. 5-6; for other examples, see Chapter 6). This approach, which is being used in an increasing number of clinical laboratories, complements conventional karyotyping and provides a much more sensitive, high-resolution assessment of the genome. 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. Based on this significantly increased yield, genome-wide arrays are replacing the G-banded karyotype as the routine frontline test for certain patient populations.

Two important limitations of this technology bear mentioning, however. 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. Thus confirmation of suspected chromosome or genome abnormalities by karyotyping or FISH is important to determine the nature of an abnormality and thus its risk for recurrence, either for the individual or for other family members. And second, high-resolution genome analysis can reveal variants, in particular small differences in copy number, that are of uncertain clinical significance. An increasing number of such variants are being documented and catalogued even within the general population. As we saw in Chapter 4, many are likely to be benign copy number variants. Their existence underscores the unique nature of each individual's genome and emphasizes the diagnostic challenge of assessing what is considered a “normal” karyotype and what is likely to be pathogenic.

Genome Analysis by Whole-Genome Sequencing

At the extreme end but on the same spectrum as cytogenetic analysis and microarray analysis, the ultimate resolution for clinical tests to detect chromosomal and genomic disorders would be to sequence patient genomes in their entirety. Indeed, as the efficiency of whole-genome sequencing has increased and its costs have fallen, it is becoming increasingly practical to consider sequencing patient samples in a clinical setting (see Fig. 5-1).

The principles underlying such an approach are straightforward, because the number and composition of any particular segment of an individual's genome will be reflected in the DNA sequences generated from that genome. Although the sequences routinely obtained with today's technology are generally short (approximately 50 to 500 bp) compared to the size of a chromosome or even a single gene, a genome with an abnormally low or high representation of those sequences from a particular chromosome or segment of a chromosome is likely to have a numerical or structural abnormality of that chromosome. To detect numerical 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 (Fig. 5-7). This concept is now being applied to the prenatal diagnosis of fetal chromosome imbalance (see Chapter 17).

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FIGURE 5-7 Strategies for detection of numerical and structural chromosome abnormalities by whole-genome sequence analysis. 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. A, Alignment of sequence reads from a patient's genome to the reference sequence of three individual chromosomes. Overrepresentation of sequences from the red chromosome indicates that the patient is aneuploid for this chromosome. 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. This indicates a translocation in the patient's genome involving the blue and orange chromosomes at the positions designated by the dotted lines.

To detect balanced rearrangements of the genome, however, in which no DNA in the genome is either gained or lost, a more complete genome sequence is required. Here, instead of sequences that align perfectly to the reference human genome sequence, one finds rare sequences that align to two different and normally noncontiguous regions in the reference sequence (whether on the same chromosome or on different chromosomes) (see Fig. 5-7). 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 (see Chapters 6 and 15).

Chromosome Abnormalities

Abnormalities of chromosomes may be either numerical or structural and may involve one or more autosomes, sex chromosomes, or both simultaneously. The overall incidence of chromosome abnormalities is approximately 1 in 154 live births (Fig. 5-8), and their impact is therefore substantial, both in clinical medicine and for society. By far the most common type of clinically significant chromosome abnormality is aneuploidy, an abnormal chromosome number due to an extra or missing chromosome. An aneuploid karyotype is always associated with physical or mental abnormalities or both. Structural abnormalities(rearrangements involving one or more chromosomes) are also relatively common (see Fig. 5-8). Depending on whether or not a structural rearrangement leads to an imbalance of genomic content, these may or may not have a phenotypic effect. However, as explained later in this chapter, even balanced chromosome abnormalities may be at an increased risk for abnormal offspring in the subsequent generation.

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FIGURE 5-8 Incidence of chromosome abnormalities in newborn surveys, based on chromosome analysis of over 68,000 newborns. SeeSources & Acknowledgments.

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. Some of the more common abbreviations and examples of abnormal karyotypes and abnormalities are listed in Table 5-1.

TABLE 5-1

Some Abbreviations Used for Description of Chromosomes and Their Abnormalities, with Representative Examples

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Abbreviations from Shaffer LG, McGowan-Jordan J, Schmid M, editors: ISCN 2013: an international system for human cytogenetic nomenclature, Basel, 2013, Karger.

Gene Dosage, Balance and Imbalance

For chromosome and genomic disorders, it is 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. The clinical consequences of any particular chromosome abnormality will depend on the resulting imbalance of parts of the genome, the specific genes contained in or affected by the abnormality, and the likelihood of its transmission to the next generation.

The central concept for thinking about chromosome and genomic disorders is that of gene dosage and its balance or imbalance. As we shall see in later chapters, this same concept applies generally to considering some single-gene disorders and their underlying mutational basis (see Chapters 711, and 12); however, it takes on uniform importance for chromosome abnormalities, where we are generally more concerned with the dosage of genes within the relevant chromosomal region than with the actual normal or abnormal sequence of those genes. Here, the sequence of the genes is typically quite unremarkable and would not lead to any clinical condition except for the fact that their dosage is incorrect.

Most genes in the human genome are present in two doses and are expressed from both copies. 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). Extensive analysis of clinical cases has demonstrated that the relative dosage of these genes is critical for normal development. One or three doses instead of two is generally not conducive to normal function for a gene or set of genes that are typically expressed from two copies. Similarly, abnormalities of genomic imprinting or X inactivation that cause the anomalous expression of two copies of a gene or set of genes instead of one invariably lead to clinical disorders.

Predicting clinical outcomes for chromosomal and genomic disorders can be an enormous challenge for genetic counseling, particularly in the prenatal setting. 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 Box).

Unbalanced Karyotypes and Genomes in Liveborns

General Guidelines for Counseling


• Monosomies are more deleterious than trisomies. Complete monosomies are generally not viable, except for monosomy for the X chromosome. Complete trisomies are viable for chromosomes 13, 18, 21, X, and Y.

• The phenotype in partial 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.

• 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. For inversions that do not involve the centromere (paracentric inversions), there is a very low risk for an abnormal phenotype in the next generation. 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.

• For a mosaic karyotype involving any chromosome abnormality, all bets are off! Counseling is particularly challenging because the degree of mosaicism in relevant tissues or relevant stages of development is generally unknown. Thus there is uncertainty about the severity of the phenotype.

Abnormalities of Chromosome Number

A chromosome complement with any chromosome number other than 46 is said to be heteroploid. An exact multiple of the haploid chromosome number (n) is called euploid, and any other chromosome number is aneuploid.

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. Both triploidy and tetraploidy have been seen in fetuses. Triploidy is observed in 1% to 3% of recognized conceptions; triploid infants can be liveborn, although they do not survive long. 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). Other cases result from failure of one of the meiotic divisions in either sex, resulting in a diploid egg or sperm. 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 degenerative placenta (resulting in a so-called partial hydatidiform mole), with a small fetus. Tetraploids are always 92,XXXX or 92,XXYY and likely result from failure of completion of an early cleavage division of the zygote.

Aneuploidy

Aneuploidy is the most common and clinically significant type of human chromosome disorder, occurring in at least 5% of all clinically recognized pregnancies. Most aneuploid patients have either trisomy(three instead of the normal pair of a particular chromosome) or, less often, monosomy (only one representative of a particular chromosome). Either trisomy or monosomy can have severe phenotypic consequences.

Trisomy can exist for any part of the genome, but trisomy for a whole chromosome is only occasionally compatible with life. 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) (Fig. 5-9). Other trisomies observed in liveborns include trisomy 18 and trisomy 13. It is notable that these autosomes (13, 18, and 21) are the three with the lowest number of genes located on them (see Fig. 2-7); presumably, trisomy for autosomes with a greater number of genes is lethal in most instances. 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). These conditions are considered in greater detail in Chapter 6.

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FIGURE 5-9 Chromosomal and genomic approaches to the diagnosis of trisomy 21. A, Karyotype from a male patient with Down syndrome, showing three copies of chromosome 21. 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). C, Detection of trisomy 21 in a female patient by whole-genome chromosomal microarray. Increase in the fluorescence ratio for sequences from chromosome 21 are indicated by the red arrow. D, Detection of trisomy 21 by whole-genome sequencing and overrepresentation of sequences from chromosome 21. Normalized sequence representation for individual chromosomes (± SD) in chromosomally normal samples is indicated by the gray shaded region. A normalized ratio of approximately 1.5 indicates three copies of chromosome 21 sequences instead of two, consistent with trisomy 21. SeeSources & Acknowledgments.

Although the causes of aneuploidy are not fully understood, the most common chromosomal mechanism is meiotic nondisjunction. This refers to the failure of a pair of chromosomes to disjoin properly during one of the two meiotic divisions, usually during meiosis I. The genomic consequences of nondisjunction during meiosis I and meiosis II are different (Fig. 5-10). If the error occurs during meiosis I, the gamete with 24 chromosomes contains both the paternal and the maternal members of the pair. If it occurs during meiosis II, the gamete with the extra chromosome contains both copies of either the paternal or the maternal chromosome. (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.)

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FIGURE 5-10 The different consequences of nondisjunction at meiosis I (center) and meiosis II (right), compared with normal disjunction (left). 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. 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.

Proper disjunction of a pair of homologous chromosomes in meiosis I appears relatively straightforward (see Fig. 5-10). 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. The propensity of a chromosome pair to nondisjoin 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. 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.

In some cases, aneuploidy can also result from premature separation of sister chromatids in meiosis I instead of meiosis II. If this happens, the separated chromatids may by chance segregate to the oocyte or to the polar body, leading to an unbalanced gamete.

Nondisjunction can also occur in a mitotic division after formation of the zygote. If this happens at an early cleavage division, clinically significant mosaicism may result (see later section). In some malignant cell lines and some cell cultures, mitotic nondisjunction can lead to highly abnormal karyotypes.

Abnormalities of Chromosome Structure

Structural rearrangements result from chromosome breakage, recombination, or exchange, followed by reconstitution in an abnormal combination. Whereas rearrangements can take place in many ways, they are together less common than aneuploidy; overall, structural abnormalities are present in approximately 1 in 375 newborns (see Fig. 5-8). Like numerical abnormalities, structural rearrangements may be present in all cells of a person or in mosaic form.

Structural rearrangements are classified as balanced, if the genome has the normal complement of chromosomal material, or unbalanced, if there is additional or missing material. Clearly these designations depend on the resolution of the method(s) used to analyze a particular rearrangement (see Fig. 5-1); some that appear balanced at the level of high-resolution banding, for example, may be unbalanced when studied with chromosomal microarrays or by DNA sequence analysis. Some rearrangements are stable, capable of passing through mitotic and meiotic cell divisions unaltered, whereas others are unstable. Some of the more common types of structural rearrangements observed in human chromosomes are illustrated schematically in Figure 5-11.

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FIGURE 5-11 Structural rearrangements of chromosomes, described in the text. A, Terminal and interstitial deletions, each generating an acentric fragment that is typically lost. B, Duplication of a chromosomal segment, leading to partial trisomy. C, Ring chromosome with two acentric fragments. D,Generation of an isochromosome for the long arm of a chromosome. E, Robertsonian translocation between two acrocentric chromosomes, frequently leading to a pseudodicentric chromosome. Robertsonian translocations are nonreciprocal, and the short arms of the acrocentrics are lost. F,Translocation between two chromosomes, with reciprocal exchange of the translocated segments.

Unbalanced Rearrangements

Unbalanced rearrangements are detected in approximately 1 in 1600 live births (see Fig. 5-8); the phenotype is likely to be abnormal because of deletion or duplication of multiple genes, or (in some cases) both. Duplication of part of a chromosome leads to partial trisomy for the genes within that segment; deletion leads to partial monosomy. 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.

Large structural rearrangements involving imbalance of at least a few megabases can be detected at the level of routine chromosome banding, including high-resolution karyotyping. Detection of smaller changes, however, generally requires higher resolution analysis, involving FISH or chromosomal microarray analysis.

Deletions and Duplications.

Deletions involve loss of a chromosome segment, resulting in chromosome imbalance (see Fig. 5-11). 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. The clinical consequences generally reflect haploinsufficiency (literally, the inability of a single copy of the genetic material to carry 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. Cytogenetically visible autosomal deletions have an incidence of approximately 1 in 7000 live births. Smaller, submicroscopic deletions detected by microarray analysis are much more common, but as mentioned earlier, the clinical significance of many such variants has yet to be fully determined.

A deletion may occur at the end of a chromosome (terminal) or along a chromosome arm (interstitial). Deletions may originate simply by chromosome breakage and loss of the acentric segment. Numerous deletions have been identified in the course of prenatal diagnosis or in the investigation of dysmorphic patients or patients with intellectual disability; specific examples of such cases will be discussed in Chapter 6.

In general, duplication appears to be less harmful than deletion. However, because duplication in a gamete results in chromosomal imbalance (i.e., partial trisomy), and because the chromosome breaks that generate it may disrupt genes, duplication often leads to some phenotypic abnormality.

Marker and Ring Chromosomes.

Very small, unidentified chromosomes, called marker chromosomes, are occasionally seen in chromosome preparations, frequently in a mosaic state. They are usually in addition to the normal chromosome complement and are thus also referred to as supernumerary chromosomes or extra structurally abnormal chromosomes. The prenatal frequency of de novo supernumerary marker chromosomes has been estimated to be approximately 1 in 2500. Because of their small and indistinctive size, higher resolution genome analysis is usually required for precise identification.

Larger marker chromosomes contain genomic material from one or both chromosome arms, creating an imbalance for whatever genes are present. Depending on the origin of the marker chromosome, the risk for a fetal abnormality can range from very low to 100%. For reasons not fully understood, a relatively high proportion of such markers derive from chromosome 15 and from the sex chromosomes.

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 (see Fig. 5-11). Some rings experience difficulties at mitosis, when the two sister chromatids of the ring chromosome become tangled in their attempt to disjoin at anaphase. There may be breakage of the ring followed by fusion, and larger and smaller rings may thus be generated. Because of this mitotic instability, it is not uncommon for ring chromosomes to be found in only a proportion of cells.

Isochromosomes.

An isochromosome is a chromosome in which one arm is missing and the other duplicated in a mirror-image fashion (see Fig. 5-11). 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). 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)(q10)—in a proportion of individuals with Turner syndrome (see Chapter 6). Isochromosomes are also frequently seen in karyotypes of both solid tumors and hematological malignant neoplasms (see Chapter 15).

Dicentric Chromosomes.

A dicentric chromosome is a rare type of abnormal chromosome in which two chromosome segments, each with a centromere, fuse end to end. 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. Such chromosomes are formally called pseudodicentric. The most common pseudodicentrics involve the sex chromosomes or the acrocentric chromosomes (so-called Robertsonian translocations; see later).

Balanced Rearrangements

Balanced chromosomal rearrangements are found in as many as 1 in 500 individuals (see Fig. 5-8) and do not usually lead to a phenotypic effect because all the genomic material is present, even though it is arranged differently (see Fig. 5-11). 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. Because of the high frequency of copy number polymorphisms 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.

Even when structural rearrangements are truly balanced, they can pose a threat to the subsequent generation because carriers are likely to produce a significant frequency of unbalanced gametes and therefore have an increased risk for having abnormal offspring with unbalanced karyotypes; depending on the specific rearrangement, that risk can range from 1% to as high as 20%. There is also a possibility that one of the chromosome breaks will disrupt a gene, leading to mutation. Especially with the use of whole-genome sequencing 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 (see Chapter 6); such translocations can be a useful clue to the identification of the gene responsible for a particular genetic disorder.

Translocations.

Translocation involves the exchange of chromosome segments between two chromosomes. There are two main types: reciprocal and nonreciprocal.

Reciprocal Translocations.

This type of rearrangement results from breakage or recombination involving nonhomologous chromosomes, with reciprocal exchange of the broken-off or recombined segments (see Fig. 5-11). Usually only two chromosomes are involved, and because the exchange is reciprocal, the total chromosome number is unchanged. 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. They come to attention either during prenatal diagnosis or when the parents of a clinically abnormal child with an unbalanced translocation are karyotyped. Balanced translocations are more commonly found in couples who have had two or more spontaneous abortions and in infertile males than in the general population.

The existence of translocations presents challenges for the process of chromosome pairing and homologous recombination during meiosis (see Chapter 2). When the chromosomes of a carrier of a balanced reciprocal translocation pair at meiosis, as shown in Figure 5-12, they must form a quadrivalent to ensure proper alignment of homologous sequences (rather than the typical bivalents seen with normal chromosomes). 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. Alternate segregation, the usual type of meiotic segregation, produces balanced gametes that have either a normal chromosome complement or contain the two reciprocal chromosomes. Other segregation patterns, however, always yield unbalanced gametes (see Fig. 5-12).

image

FIGURE 5-12 A, Diagram illustrating a balanced translocation between two chromosomes, involving a reciprocal exchange between the distal long arms of chromosomes A and B. B, Formation of a quadrivalent in meiosis is necessary to align the homologous segments of the two derivative chromosomes and their normal homologues. C, Patterns of segregation in a carrier of the translocation, leading to either balanced or unbalanced gametes, shown at the bottom. Adjacent-1 segregation (in red,top chromosomes to one gamete, bottom chromosomes to the other) leads only to unbalanced gametes. Adjacent-2 segregation (in green, left chromosomes to one gamete, right chromosomes to the other) also leads only to unbalanced gametes. 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.

Robertsonian Translocations.

Robertsonian translocations are the most common type of chromosome rearrangement observed in our species and involve two acrocentric chromosomes that fuse near the centromere region with loss of the short arms (see Fig. 5-11). 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. 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 acrocentric chromosomes is not deleterious; thus, the karyotype is considered to be balanced, despite having only 45 chromosomes. Robertsonian translocations are typically, although not always, pseudodicentric (see Fig. 5-11), reflecting the location of the breakpoint on each acrocentric chromosome.

Although Robertsonian translocations can involve all combinations of the acrocentric chromosomes, two—designated rob(13;14)(q10;q10) and rob(14;21)(q10;q10)—are relatively common. The translocation involving 13q and 14q is found in approximately 1 person in 1300 and is thus by far the single most common chromosome rearrangement in our species. 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 involved acrocentrics, replaced by two copies of the translocation.

Although a carrier of a Robertsonian translocation is phenotypically normal, there is a risk for unbalanced gametes and therefore for unbalanced offspring. 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. 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.

Insertions.

An insertion is another type of nonreciprocal translocation that occurs when a segment removed from one chromosome is inserted into a different chromosome, either in its usual orientation with respect to the centromere or inverted. Because they require three chromosome breaks, insertions are relatively rare. Abnormal segregation in an insertion carrier can produce offspring with duplication or deletion of the inserted segment, as well as normal offspring and balanced carriers. The average risk for producing an abnormal child can be up to 50%, and prenatal diagnosis is therefore indicated.

Inversions.

An inversion occurs when a single chromosome undergoes two breaks and is reconstituted with the segment between the breaks inverted. Inversions are of two types (Fig. 5-13): 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). Pericentric inversions can be easier to identify cytogenetically when they change the proportion of the chromosome arms as well as the banding pattern.

image

FIGURE 5-13 Crossing over within inversion loops formed at meiosis I in carriers of a chromosome with segment B-C inverted (order A-C-B-D, instead of the normal order A-B-C-D). A, Paracentric inversion. Gametes formed after the second meiosis 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. B, Pericentric inversion. Gametes formed after the second meiosis may be balanced (normal or inverted) or unbalanced. Unbalanced gametes contain a copy of the chromosome with a duplication or a deficiency of the material flanking the inverted segment (A-B-C-A or D-B-C-D).

An inversion does not usually cause an abnormal phenotype in carriers because it is a balanced rearrangement. Its medical significance is for the progeny; a carrier of either type of inversion is at risk for producing abnormal gametes that may lead to unbalanced offspring because, 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 (see Fig. 5-13). When recombination occurs within the loop, it can lead to the production of unbalanced gametes: gametes with balanced chromosome complements (either normal or possessing the inversion) and gametes with unbalanced complements are formed, depending on the location of recombination events. When the inversion is paracentric, the unbalanced recombinant chromosomes are acentric or dicentric and typically do not lead to viable offspring (see Fig. 5-13); thus, the risk that a carrier of a paracentric inversion will have a liveborn child with an abnormal karyotype is very low indeed.

A pericentric inversion, on the other hand, can lead to the production of unbalanced gametes with both duplication and deficiency of chromosome segments (see Fig. 5-13). The duplicated and deficient segments are the segments that are distal to the inversion. Overall, the risk for a carrier of a pericentric inversion leading to a child with an unbalanced karyotype is estimated to be 5% to 10%. Each pericentric inversion, however, is associated with a particular risk, typically reflecting the size and content of the duplicated and deficient segments.

Mosaicism for Chromosome Abnormalities

When a person has a chromosome abnormality, whether numerical or structural, the abnormality is usually present in all of his or her cells. Sometimes, however, two or more different chromosome complements are present in an individual; this situation is called mosaicism. Mosaicism is typically detected by conventional karyotyping but can also be suspected on the basis of interphase FISH analysis or chromosomal microarrays.

A common cause of mosaicism is nondisjunction in an early postzygotic mitotic division. For example, a zygote with an additional chromosome 21 might lose the extra chromosome in a mitotic division and continue to develop as a 46/47,+21 mosaic. 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. 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.

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. 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. Mosaicism can also arise in cells in culture after they were taken from the individual; thus, cytogeneticists attempt to differentiate between true mosaicism, present in the individual, and pseudomosaicism, which has occurred in the laboratory. The distinction between these types is not always easy or certain and can lead to major interpretive difficulties in prenatal diagnosis (see Box earlier and Chapter 17).

Incidence of Chromosome Anomalies

The incidence of different types of chromosomal aberration has been measured in a number of large population surveys and was summarized earlier in Figure 5-8. The major numerical disorders of chromosomes observed in liveborns are three autosomal trisomies (trisomy 21, trisomy 18, and trisomy 13) and four types of sex chromosomal aneuploidy: Turner syndrome (usually 45,X), Klinefelter syndrome (47,XXY), 47,XYY, and 47,XXX (see Chapter 6). Triploidy and tetraploidy account for only a small percentage of cases, typically in spontaneous abortions. The classification and incidence of chromosomal defects measured in these surveys can be used to consider the fate of 10,000 conceptuses, as presented in Table 5-2.

TABLE 5-2

Outcome of 10,000 Pregnancies*

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*These estimates are based on observed frequencies of chromosome abnormalities in spontaneous abortuses and in liveborn infants. It is likely that the frequency of chromosome abnormalities in all conceptuses is much higher than this, because many spontaneously abort before they are recognized clinically.

Live Births

As mentioned earlier, the overall incidence of chromosome abnormalities in newborns has been found to be approximately 1 in 154 births (0.65%) (see Fig. 5-8). 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). Unbalanced rearrangements are likely to come to clinical attention because of abnormal appearance and delayed physical and mental development in the chromosomally abnormal individual. In contrast, balanced rearrangements are rarely identified clinically unless a carrier of a rearrangement gives birth to a child with an unbalanced chromosome complement and family studies are initiated.

Spontaneous Abortions

The overall frequency of chromosome abnormalities in spontaneous abortions is at least 40% to 50%, and the kinds of abnormalities differ in a number of ways from those seen in liveborns. Somewhat surprisingly, the single most common abnormality in abortuses is 45,X (the same abnormality found in Turner syndrome), which accounts for nearly 20% of chromosomally abnormal spontaneous abortuses but less than 1% of chromosomally abnormal live births (see Table 5-2). 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 abortuses.

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 chromosome or regional mutations 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.

However, such mutations also occur in somatic cells throughout life and are a hallmark of cancer, both in hematological neoplasias (e.g., leukemias and lymphomas) and in the context of solid tumor progression. 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. The chromosome and genomic changes seen in cancer cells are numerous and diverse. 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 15.

General References

Gardner RJM, Sutherland GR, Shaffer LG. Chromosome abnormalities and genetic counseling. ed 4. Oxford University Press: Oxford, England; 2012.

Shaffer LG, McGowan-Jordan J, Schmid M. ISCN 2013: an international system for human cytogenetic nomenclature. Karger: Basel; 2013.

Trask B. Human cytogenetics: 46 chromosomes, 46 years and counting. Nature Rev Genet. 2002;3:769–778.

References for Specific Topics

Baldwin EK, May LF, Justice AN, et al. Mechanisms and consequences of small supernumerary marker chromosomes. Am J Hum Genet. 2008;82:398–410.

Coulter ME, Miller DT, Harris DJ, et al. Chromosomal microarray testing influences medical management. Genet Med. 2011;13:770–776.

Dan S, Chen F, Choy KW, et al. Prenatal detection of aneuploidy and imbalanced chromosomal arrangements by massively parallel sequencing. PLoS ONE. 2012;7:e27835.

Debatisse M, Le Tallec B, Letessier A, et al. Common fragile sites: mechanisms of instability revisited. Trends Genet. 2012;28:22–32.

Fantes JA, Boland E, Ramsay J, et al. FISH mapping of de novo apparently balanced chromosome rearrangements identifies characteristics associated with phenotypic abnormality. Am J Hum Genet. 2008;82:916–926.

Firth HV, Richards SM, Bevan AP, et al. DECIPHER: database of chromosomal imbalance and phenotype in humans using Ensembl resources. Am J Hum Genet. 2009;84:524–533.

Green RC, Rehm HL, Kohane IS. Clinical genome sequencing. Ginsburg GS, Willard HF. Genomic and personalized medicine. ed 2. Elsevier: New York; 2013:102–122.

Higgins AW, Alkuraya FS, Bosco AF, et al. Characterization of apparently balanced chromosomal rearrangements from the Developmental Genome Anatomy Project. Am J Hum Genet. 2008;82:712–722.

Kearney HM, South ST, Wolff DJ, et al. American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genet Med. 2011;13:676–679.

Ledbetter DH, Riggs ER, Martin CL. Clinical applications of whole-genome chromosomal microarray analysis. Ginsburg GS, Willard HF. Genomic and personalized medicine. ed 2. Elsevier: New York; 2013:133–144.

Lee C. Structural genomic variation in the human genome. Ginsburg GS, Willard HF. Genomic and personalized medicine. ed 2. Elsevier: New York; 2013:123–132.

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. 2010;86:749–764.

Nagaoka SI, Hassold TJ, Hunt PA. Human aneuploidy: mechanisms and new insights into an age-old problem. Nat Rev Genet. 2012;13:493–504.

Reddy UM, Page GP, Saade GR, et al. Karyotype versus microarray testing for genetic abnormalities after stillbirth. N Engl J Med. 2012;367:2185–2193.

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. 2011;88:469–481.

Problems

1. You send a blood sample from a dysmorphic infant to the chromosome laboratory for analysis. The laboratory's report states that the child's karyotype is 46,XY,del(18)(q12).

a. What does this karyotype mean?

b. The laboratory asks for blood samples from the clinically normal parents for analysis. Why?

c. The laboratory reports the mother's karyotype as 46,XX and the father's karyotype as 46,XY,t(7;18)(q35;q12). What does the latter karyotype mean? Referring to the normal chromosome ideograms in Figure 5-2, sketch the translocation chromosome or chromosomes in the father and in his son. Sketch these chromosomes in meiosis in the father. What kinds of gametes can he produce?

d. In light of this new information, what does the child's karyotype mean now? What regions are monosomic? trisomic? Given information from Chapters 2 and 3, estimate the number of genes present in the trisomic or monosomic regions.

2. A spontaneously aborted fetus is found to have trisomy 18.

a. What proportion of fetuses with trisomy 18 are lost by spontaneous abortion?

b. What is the risk that the parents will have a liveborn child with trisomy 18 in a future pregnancy?

3. A newborn child with Down syndrome, when karyotyped, is found to have two cell lines: 70% of her cells have the typical 47,XX,+21 karyotype, and 30% are normal 46,XX. When did the nondisjunctional event probably occur? What is the prognosis for this child?

4. Which of the following persons is or is expected to be phenotypically normal?

a. A female with 47 chromosomes, including a small supernumerary chromosome derived from the centromeric region of chromosome 15

b. A female with the karyotype 47,XX,+13

c. A male with deletion of a band on chromosome 4

d. A person with a balanced reciprocal translocation

e. A person with a pericentric inversion of chromosome 6

What kinds of gametes can each of these individuals produce? What kinds of offspring might result, assuming that the other parent is chromosomally normal?

5. For each of the following, state whether chromosome or genome analysis is indicated or not. For which family members, if any? For what kind of chromosome abnormality might the family in each case be at risk?

a. A pregnant 29-year-old woman and her 41-year-old husband, with no history of genetic defects

b. A pregnant 41-year-old woman and her 29-year-old husband, with no history of genetic defects

c. A couple whose only child has Down syndrome

d. A couple whose only child has cystic fibrosis

e. A couple who has two boys with severe intellectual disability

6. Explain the nature of the chromosome abnormality and the method of detection indicated by the following nomenclature.

a. inv(X)(q21q26)

b. 46,XX,del(1)(1qter → p36.2:)

c. 46,XX.ish del(15)(q11.2q11.2)(SNRPN−,D15S10−)

d. 46,XX,del(15)(q11q13).ishdel(15)(q11.2q11.2)(SNRPN−,D15S10−)

e. 46,XX.arrcgh1p36.3(RP11-319A11,RP11-58A11,RP11-92O17) × 1

f. 47,XY,+mar.ish r(8)(D8Z1+)

g. 46,XX,rob(13;21)(q10;q10),+21

h. 45,XY,rob(13;21)(q10;q10)

7. Using the nomenclature system in Table 5-1, describe the “molecular karyotypes” that correspond to the microarray data in Figures 5-6C and 5-9C.

a. Referring to Figure 5-6C, is the individual whose array result is shown a male or a female? How do you know?

b. Referring to Figure 5-9C, is the individual whose array result is shown a male or a female? How do you know?