1.Answer: B. The denominator of the gene frequency is 100, which is obtained by adding the number of genotyped individuals (50) and multiplying by 2 (because each individual has two alleles at the locus). The numerator is obtained by counting the number of alleles of each type: the 4 homozygotes with the 1,1 genotype contribute 8 copies of allele 1; the 1,3 heterozygotes contribute another 8 alleles; and the 1,4 heterozygotes contribute 3 alleles. Adding these together, we obtain 19 copies of allele 1. Dividing by 100, this yields a gene frequency of 0.19 for allele 1. For allele 2, there are two classes of heterozygotes that have a copy of the allele: those with the 2,3 and 2,4 genotypes. These 2 genotypes yield 5 and 9 copies of allele 2, respectively, for a frequency of 14/100 = 0.14.
2.Answer: E. The incidence of affected homozygotes permits the estimation of the frequency of the recessive mutation in the population. Using the Hardy-Weinberg equilibrium relationship between gene frequency and genotype frequency, the gene frequency can then be used to estimate the frequency of the heterozygous genotype in the population.
Consanguinity (choice A) affects Hardy-Weinberg equilibrium by increasing the number of homozygotes in the population above the equilibrium expectation (i.e., consanguinity results in a violation of the assumption of random mating).
Genotype frequencies can be estimated from gene frequencies (choice B), but gene frequencies can also be estimated from genotype frequencies (as in choice A).
By eliminating a specific genotype from the population (e.g., affected homozygotes), natural selection can cause deviations from equilibrium (choice C).
Only one generation of random mating is required to return a population to equilibrium (choice D).
3.Answer: C. Because the couple shares common ancestors (i.e., one set of grandparents), they are more likely to be heterozygous carriers of the same autosomal recessive disease-causing mutations. Thus, their risk of producing a child with an autosomal recessive disease is elevated above that of the general population.
First cousins share approximately 1/8 of their genes, not 1/2 (choice A).
Because both members of the couple are healthy, neither one is likely to harbor a dominant disease-causing mutation (choice B). In addition, consanguinity itself does not elevate the probability of producing a child with a dominant disease because only one copy of the diseasecausing allele is needed to cause the disease.
Down syndrome (choice D) typically is the result of a new mutation. When it is transmitted by an affected female, it acts like a dominant mutation and thus would not be affected by consanguinity.
Empirical studies indicate that the risk of genetic disease in the offspring of first cousin couples is approximately double that of the general population (choice E).
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4.Answer: E. The frequency of sickle cell disease is elevated in many African populations because heterozygous carriers of the sickle cell mutation are resistant to malarial infection but do not develop sickle cell disease, which is autosomal recessive. Thus, there is a selective advantage for the mutation in heterozygous carriers, elevating its frequency in the population.
Consanguinity (choice A) could elevate the incidence of this autosomal recessive disease in a specific family, but it does not account for the elevated incidence of this specific disease in the African American population in general.
The African American population is large and consequently would not be expected to have experienced elevated levels of genetic drift (choice B).
Although there has been gene flow (choice C) from other populations into the African American population, this would be expected to decrease, rather than increase, the frequency of sickle cell disease because the frequency of this disease is highest in some African populations.
There is no evidence that the mutation rate (choice D) is elevated in this population. In contrast, the evidence for natural selection is very strong.
5.Answer: A. This answer is obtained by taking the square root of the incidence (i.e., the frequency of affected homozygotes) to get a gene frequency for the disease-causing mutation (q) of 1/50 (0.02). The carrier frequency is given by 2pq, or approximately 2q, or 1/25.
6.Answer: C. One must first determine the probability that the man’s
mate will also be a heterozygous carrier. If the frequency of affected homozygotes (q2) is 1/40,000, then the allele frequency, q, is 1/200. The carrier frequency in the population (approximately 2q) is 1/100. Three independent events must happen for their child to be homozygous for the mutation. The mate must be a carrier (probability 1/100), the mate must pass along the mutant allele (probability 1/2), and the man must also pass along the mutant allele (probability 1/2). Multiplying the 3 probabilities to determine the probability of their joint occurrence gives 1/100 × 1/2 × 1/2 = 1/400.
7.Answer: A. Because males have only a single X chromosome, each affected male has one copy of the disease-causing recessive mutation. Thus, the incidence of an X-linked recessive disease in the male portion of a population is a direct estimate of the gene frequency in the population.
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Cytogenetics 3
Learning Objectives
Interpret scenarios about basic definitions and terminology
Demonstrate understanding of structural chromosome abnormalities
Solve problems concerning advances in molecular cytogenetics
OVERVIEW
This chapter reviews diseases that are caused by microscopically observable alterations in chromosomes. These alterations may involve the presence of extra chromosomes or the loss of chromosomes. They may also consist of structural alterations of chromosomes. Chromosome abnormalities are seen in approximately 1 in 150 live births and are the leading known cause of mental retardation. The vast majority of fetuses with chromosome abnormalities are lost prenatally: Chromosome abnormalities are seen in 50% of spontaneous fetal losses during the first trimester of pregnancy, and they are seen in 20% of fetuses lost during the second trimester. Thus, chromosome abnormalities are the leading known cause of pregnancy loss.
BASIC DEFINITIONS AND TERMINOLOGY
Karyotype
Chromosomes are most easily visualized during the metaphase stage of mitosis, when they are maximally condensed. They are photographed under the microscope to create a karyotype, an ordered display of the 23 pairs of human chromosomes in a typical somatic cell (Figure II-3-1). In Figure II-3-1A, a karyogram represents a drawing of each type of chromosome; the presentation is haploid (only one copy of each chromosome is shown). Figure II-3-1B is a karyotype of an individual male. It is diploid, showing both copies of each autosome, the X and the Y chromosome. Chromosomes are ordered according to size, with the sex chromosomes (X and Y) placed in the lower right portion of the karyotype.
Metaphase chromosomes can be grouped according to size and to the position of the centromere, but accurate identification requires staining with one of a variety of dyes to reveal characteristic banding patterns.
Note
X chromosome contains ~1,200 genes
Y chromosome contains ~50 genes
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Chromosome banding
To visualize chromosomes in a karyotype unambiguously, various stains are applied so that banding is evident.
•G-banding.Mitotic chromosomes are partially digested with trypsin (to digest some associated protein) and then stained with Giemsa, a dye that binds DNA.
G-banding reveals a pattern of light and dark (G-bands) regions that allow chromosomes to be accurately identified in a karyotype. There are several other stains that can be used in a similar manner. The chromosomes depicted in Figure II-3-1 have been stained with Giemsa.
3
2
2
1
1
2
2
p 2
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p 1
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q 2
q 2
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p 1
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q 2
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8 9 10 11 12
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13 14 15
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17 18 19 20
21
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Y
X
Negative or pale staining 'Q' and 'G' bands Positive 'R' bands
(Karyogram) and (B) Photograph of Metaphase Chromosomes (Karyotype)
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Chapter 3 ● Cytogenetics
Chromosome abnormalities in some cases can be identified visually by looking at the banding pattern, but this technique reveals differences (for instance, larger deletions) only to a resolution of about 4 Mb. Smaller abnormalities (microdeletions) must be identified in other ways (FISH), discussed at the end of the chapter.
Chromosome nomenclature
Each mitotic chromosome contains a centromere and two sister chromatids because the cell has gone through interphase and has entered mitosis when the karyotype analysis is performed (metaphase). The long arm of the chromosome is labeled q, and the short arm is labeled p. One of the characteristics described is the relative position of the centromere.
•Metacentric chromosomes (for instance, chromosome 1) have the centromere near the middle. The p and q arms are of roughly equal length.
•Submetacentric chromosomes have the centromere displaced toward one end (for example, chromosome 4). The p and q arms are evident.
•Acrocentric chromosomes have the centromere far toward one end. In these chromosomes, the p arm contains little genetic information, most of it residing on the q arm. Chromosomes 13, 14, 15, 21, and 22 are the acrocentric chromosomes. Only the acrocentric chromosomes are involved in
•Robertsonian translocations, which will be discussed in this chapter.
The tips of the chromosomes are called telomeres.
Table II-3-1 contains some standard nomenclature applied to chromosomes.
Table II-3-1. Common Symbols Used in Karyotype Nomenclature
1-22
Autosome number
X, Y
Sex chromosomes
(+) or (-)
When placed before an autosomal number, indicates that
chromosome is extra or missing
pShort arm of the chromosome
qLong arm of the chromosome
t
Translocation
del Deletion
NUMERICAL CHROMOSOME ABNORMALITIES
Euploidy
High-Yield
When a cell has a multiple of 23 chromosomes, it is said to be euploid. Gametes (sperm and egg cells) are euploid cells that have 23 chromosomes (one member of each pair); they are said to be haploid. Most somatic cells are diploid, containing both members of each pair, or 46 chromosomes.
Note
Euploid Cells (multiple of 23 chromosomes)
•Haploid (23 chromosomes): gametes
•Diploid (46 chromosomes): most somatic cells
•Triploid (69 chromosomes): rare lethal condition
•Tetraploid (92 chromosomes): very rare lethal condition
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Two types of euploid cells with abnormal numbers of chromosomes are seen in humans: triploidy and tetraploidy.
Triploidy refers to cells that contain 3 copies of each chromosome (69 total). Triploidy, which usually occurs as a result of the fertilization of an ovum by 2 sperm cells, is common at conception, but the vast majority of these conceptions are lost prenatally. However, about 1 in 10,000 live births is a triploid. These babies have multiple defects of the heart and central nervous system, and they do not survive.
Tetraploidy refers to cells that contain 4 copies of each chromosome (92 total). This lethal condition is much rarer than triploidy among live births: Only a few cases have been described.
Aneuploidy
High-Yield
Aneuploidy, a deviation from the euploid number, represents the gain (+) or loss (-) of a specific chromosome. Two major forms of aneuploidy are observed:
•Monosomy (loss of a chromosome)
•Trisomy (gain of a chromosome)
Autosomal aneuploidy
Two generalizations are helpful:
•All autosomal monosomies are inconsistent with a live birth.
•Only 3 autosomal trisomies (trisomy 13, 18, and 21) are consistent with a live birth.
Trisomy 21 (47,XY,+21 or 47,XX,+21); Down Syndrome
•Congenital heart defects in approximately 40% of cases
•Increased risk of acute lymphoblastic leukemia
•Alzheimer disease by fifth or sixth decade (amyloid precursor protein, APP gene on chromosome 21)
•Reduced fertility
•Risk increases with increased maternal age
Trisomy 18 (47,XY,+18 or 47,XX,+18); Edward Syndrome
•Clenched fist with overlapping fingers
•Inward turning, “rocker-bottom” feet
•Congenital heart defects
•Low-set ears, micrognathia (small lower jaw)
•Mental retardation
•Very poor prognosis
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Trisomy 13 (47,XY,+13 or 47,XX,+13); Patau Syndrome
•Polydactyly (extra fingers and toes)
•Cleft lip, palate
•Microphthalmia (small eyes)
•Microcephaly, mental retardation
•Cardiac and renal defects
•Very poor prognosis
Sex chromosome aneuploidy
Aneuploidy involving the sex chromosomes is relatively common and tends to have less severe consequences than does autosomal aneuploidy. Some generalizations are helpful:
•At least one X chromosome is required for survival.
•If a Y chromosome is present, the phenotype is male (with minor exceptions).
•If more than one X chromosome is present, all but one will become a Barr body in each cell.
The two important sex chromosome aneuploidies are Turner syndrome and Klinefelter syndrome.
Klinefelter Syndrome (47,XXY)
•Testicular atrophy
•Infertility
•Gynecomastia
•Female distribution of hair
•Low testosterone
•Elevated FSH and LH
•High-pitched voice
Turner Syndrome (45,X or 45,XO)
•Only monosomy consistent with life
•50% are 45,X
•Majority of others are mosaics for 45,X and one other cell lineage (46,XX, 47,XXX, 46,XY)
•Females with 45,X;46,XY are at increased risk for gonadal blastoma.
•Short stature
•Edema of wrists and ankles in newborn
•Cystic hygroma in utero resulting in excess nuchal skin and “webbed” neck
•Primary amenorrhea
•Coarctation of the aorta or other congenital heart defect in some cases
•Infertility
•Gonadal dysgenesis
Chapter 3 ● Cytogenetics
Note
Trisomy is the most common genetic cause of spontaneous loss of pregnancy.
Note
Genetic Mosaicism in Turner
Syndrome
Genetic mosaicism is defined as a condition in which there are cells of different genotypes or chromosome constitutions within a single individual. Some women with Turner syndrome have somatic cells that are 45,X and others that are 46,XX or 47,XXX. Mosaicism in Turner syndrome is thought to arise in early embryogenesis by mechanisms that are not completely understood.
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Nondisjunction is the usual cause of aneuploidies
Germ cells undergo meiosis to produce the haploid egg or sperm. Normal meiosis is illustrated in Figure II-3-2A. The original cell is diploid for all chromosomes, although only one homologous pair is shown in the figure for simplicity. The same events would occur for each pair of homologs within the cell.
Figure II-3-2B shows the result of nondisjunction of one homologous pair (for example, chromosome 21) during meiosis 1. All other homologs segregate (disjoin) normally in the cell. Two of the gametes are diploid for chromosome 21. When fertilization occurs, the conception will be a trisomy 21 with Down syndrome. The other gametes with no copy of chromosome 21 will result in conceptions that are monosomy 21, a condition incompatible with a live birth.
Figure II-3-2C shows the result of nondisjunction during meiosis 2. In this case, the sister chromatids of a chromosome (for example, chromosome 21) fail to segregate (disjoin). The sister chromatids of all other chromosomes segregate normally. One of the gametes is diploid for chromosome 21. When fertilization occurs, the conception will be a trisomy 21 with Down syndrome. One gamete has no copy of chromosome 21 and will result in a conception that is a monosomy 21. The remaining two gametes are normal haploid ones.
Some important points to remember:
•Nondisjunction is the usual cause of aneuploidies including Down, Edward, Patau, Turner, and Klinefelter syndromes.
•Nondisjunction is more likely to occur during oogenesis than during spermatogenesis.
•Nondisjunction is more likely with increasing maternal age. Environmental agents (e.g., radiation, alcohol) appear to have no measurable influence.
•Nondisjunction is more likely in meiosis I than meiosis II.
Clinical Correlate: Maternal Age and Risk of Down Syndrome
Surveys of babies with trisomy 21 show that 90–95% of the time, the extra copy of the chromosome is contributed by the mother (similar figures are obtained for trisomies of the 18th and 13th chromosomes). The increased risk of Down syndrome with maternal age is well documented.
•For women age <30 the risk of bearing a child with Down is <1/1,000.
•At age 35 the risk increases to about 1/400.
•At age 40 the risk increases to 1/100.
•At age ≥45 the risk increases to about 1/25.
This increase reflects an elevated rate of nondisjunction in older ova (recall that all of a woman’s egg cells are formed during her fetal development and they remain suspended in prophase I until ovulation).
There is no corresponding increase in risk with advanced paternal age; sperm cells are generated continuously throughout the life of the male.
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The increased risk of trisomy with advanced maternal age motivates >50% of pregnant women in North America to undergo prenatal diagnosis (typically amniocentesis or chorionic villus sampling. Down syndrome can also be screened by assaying maternal serum levels of α-fetoprotein, chorionic gonadotropin, and unconjugated estriol. This so-called triple screen can detect approximately 70% of fetuses with Down.
Gametes
Metaphase of
Meiosis 2
S, G2
Metaphase
Prophase
of Meiosis 1
Disjunction During Meiosis 1
Homologous chromosomes pair with each other at the metaphase plate. During Anaphase 1, homologs disjoin (separate). At the end of Meiosis 1, each daughter cell has one homolog.
Disjunction During Meiosis 2
During Metaphase 2, each chromosome aligns individually at the metaphase plate. In Anaphase 2, sister chromatids migrate to opposite poles and each daughter cell gets one chromatid.
Negative or pale staining 'Q' and 'G' bands Positive 'R' bands
Positive 'Q' and 'G' bands Negative 'R' bands
