Genetics PDF

49 Chromosomal Aberration (Numerical & Structural) ILOs By the end of this lecture, students will be able to 1. Interpret the different types of chromosomal abnormalities. 2. Differentiate between aneuploidy and polyploidy. 3. Differentiate between balanced and unbalanced karyo...

49 Chromosomal Aberration (Numerical & Structural) ILOs By the end of this lecture, students will be able to 1. Interpret the different types of chromosomal abnormalities. 2. Differentiate between aneuploidy and polyploidy. 3. Differentiate between balanced and unbalanced karyotypes. 4. Correlate the phenotypic outcome with types of chromosomal aberrations. Numerical aberrations Euploidy: The normal number of chromosomes for a species. In humans, the euploid number of chromosomes is 2n (46) in somatic cells and n (23) in gametes. Types of numerical chromosomal abnormalities: A. Polyploidy: It is a condition in which the chromosome number is a simple multiple of a haploid chromosome set. Triploidy:  69 chromosome with XXX or XXY or XYY; there are 3 copies for each chromosome (3n) (Figure 1).  Caused by failure of reduction division in meiosis in an ovum or sperm.  Alternatively it can be caused by fertilization of an ovum by two sperm: this is known as dispermy.  Usually results in early spontaneous miscarriage.  Example: Partial vesicular mole occurs when triploidy results from an additional set of paternal chromosomes, in which placenta is severely malformed and appears as bunch of small vesicles, and the embryo is abnormal. Figure 1. Karyotype from products of conception showing triploidy. Tetraploidy:  92 chromosome with XXX or XXYY; There are 4 copies for each chromosome (4n)  Occurs due to failure of the first cleavage zygotic division resulting in doubling of the chromosome numbers immediately after fertilization (4n).  Very rare and always lethal. Page 1 of 5 B. Aneuploidy It is an abnormal chromosome number due to an extra or missing chromosome but does not involve the whole chromosome set. When the abnormality involves the autosome the abnormal phenotype is more severe than involvement of sex chromosomes. Aneuploidy is caused by: 1. Non-disjunction: failure of homologous chromosomes segregation during meiosis I or failure of segregation of sister chromatids during meiosis II or mitosis. Mostly, it is due to the aging effect on the primary oocyte in old age mothers. 2. Anaphase lag: Failure of chromosome or chromatid to be incorporated into one of the daughter nuclei following cell division, as a result of delayed movement (lagging) during anaphase. Trisomy:  It is the presence of three copies instead of two for an autosome or sex chromosome in an otherwise diploid cell (2n+1) (Figure 2).  The karyotype is describes as (47, sex chromosomes, + the number of the chromosome with an extra copy). Ex: Down syndrome male karyotype (47, XY, +21). Figure 2. Karyotype of Down syndrome. Monosomy:  It is the absence of a single chromosome  Monosomy for an autosome is almost always incompatible with survival to term.  The X chromosome monosomy including Lack of contribution of an X or a Y chromosome results in a (45, X) karyotype, which causes the condition known as Turner syndrome is the only live birth example of monosomy. The phenotype of Turner Syndrome is of a female with close to normal intelligence but may have some learning disability. They are infertile and show some physical features including webbing of the neck, low hairline, as well as short stature. Page 2 of 5 C. Mixoploidy Having two or more genetically different cell lineages within one individual is called mixoploidy. The genetically different cell lineages could arise from the same zygote resulting in mosaicism or may result from fusion of 2 different twin zygotes resulting in chimerism (Figure 3).  Mosaic Down Syndrome occurs when the two chromatids of chromosome 21 fail to separate at the second mitotic division in a human zygote, this would result in the four-cell zygote having two cells with 46 chromosomes, one cell with 47 chromosomes (trisomy 21), and one cell with 45 chromosomes (monosomy 21). It accounts for 1% to 2% of all clinically recognized cases of Down syndrome and usually milder than pure disjunction Down Syndrome.  Dispermic Chimeras: These are the result of double fertilization whereby two genetically different sperms fertilize two ova and the resulting two zygotes fuse to form one embryo. If the two zygotes are of different sex, the chimeric embryo can develop into an individual with true hermaphroditism and an XX/XY karyotype having an ovary and a testicle either as separate organs or as ovitesticle on both sides. Figure 3. Mixoploidy: Mosaicism and Chimerism. Structural Aberrations: It refers to chromosome breakage with subsequent reunion in a different configuration that occurs between homologous chromosomes during crossing over in meiosis or between non- homologous chromosomes in case of abnormal rejoining of broken chromosomes. They can be: 1. Balanced rearrangements: the chromosome complement is complete, with no loss or gain of genetic material. Consequently, balanced rearrangements are generally harmless with the exception of rare cases in which one of the breakpoints damages an important functional gene. However, carriers of balanced rearrangements are often at risk of producing children with an unbalanced chromosomal complement. Page 3 of 5  2. Unbalanced rearrangements: the chromosomal complement contains an incorrect amount of chromosome material and the clinical effects are usually serious. Types of structural chromosomal abnormalities (Figure 4): Deletions (del)  A deletion involves loss of part of a chromosome.  Loss of more than 2% of the total haploid genome will have a lethal outcome. Inversions (inv)  An inversion is a two-break rearrangement involving a single chromosome in which a segment is reversed in position (i.e., inverted).  Inversions are balanced rearrangements that rarely cause problems in carriers unless one of the breakpoints has disrupted an important gene. Insertions (ins)  It occurs when a segment of one chromosome becomes inserted into another chromosome.  If the inserted material has moved from elsewhere in another chromosome then the karyotype is balanced. Otherwise an insertion causes an unbalanced chromosome complement. Duplication (dup) Represent a gain of chromosomal material through production of one or more copies of a gene or region of a chromosome. Figure 4. Structural Chromosomal aberrations. Translocations A translocation refers to the transfer of genetic material from one chromosome to another. 1. A reciprocal translocation:  It is formed when a break occurs in each of two chromosomes of metacentric and submetacentric types with the segments being exchanged to form two new derivative chromosomes (Figure 5). Page 4 of 5   Usually the chromosome number remains 46. 2. Robertsonian translocation:  It results from the breakage of two acrocentric chromosomes (numbers 13, 14, 15, 21, and 22) at or close to their centromeres, with subsequent fusion of their long arms (Figure 5).  The short arms of each chromosome are lost, this being of no clinical importance as they contain genes only for ribosomal RNA, for which there are multiple copies on the various other acrocentric chromosomes.  The total chromosome number is reduced to 45.  Because there is no loss or gain of important genetic material, this is a functionally balanced rearrangement. Figure 5. Receprocal and Robertsonian translocations. Isochromosomes (i) Results from abnormal centeromeric division that is at right angle to the normal separation (The centromere has divided transversely rather than longitudinally) (Figure 6). The most commonly encountered isochromosome is that which consists of two long arms of the X chromosome. Figure 6. Isochromosome. Ring Chromosomes A ring chromosome is formed when a break occurs on each arm of a chromosome leaving two ‘sticky’ ends on the central portion that reunites as a ring (Figure 7). The two distal chromosomal fragments are lost so that, if the involved chromosome is an autosome, the effects are usually serious. Figure 7. Ring chromosome. Page 5 of 5 35 Mendelian Inheritance Autosomal Dominant vs Recessive Disorders ILOs By the end of this lecture, students will be able to 1. Determine patterns of Mendelian inheritance. 2. Identify characteristics of autosomal inheritance. 3. Calculate the recurrence risk of monogenic autosomal disorders using Punnett square. 4. Interpret pedigrees for autosomal dominant and recessive modes of inheritance. 5. Correlate hereditary disorders with autosomal dominant and recessive modes of inheritance. Mendelian inheritance Simple Mendelian inheritance refers to the inheritance of traits controlled by a single gene with two alleles, one of which may be completely dominant to the other. The pattern of inheritance of simple traits depends on whether the traits are controlled by genes on autosomes (autosomal inheritance) or by genes on sex chromosomes (sex-linked inheritance). Mendelian inheritance follows the laws of segregation and independent assortment in which a gene inherited from either parent segregates into gametes at an equal frequency. More than 16000 traits or disorders in humans exhibit single gene or simple mendelian inheritance. However, characteristics such as height, and many common familial disorders, such as diabetes or hypertension, usually follow a non-mendelian inheritance. Studying Inheritance Patterns There are two very useful tools for studying how traits are passed from one generation to the next: 1. Pedigree: A pedigree is a chart representation of an individual ancestry and relatedness of family member constructed from detailed family history with use of standard symbols (Figure 1). It shows relationships and identifies individuals with a given trait. It shows how a trait is passed from generation to generation within a family. It determines the mode of inheritance of a trait; whether a trait is an autosomal dominant, autosomal recessive or X-linked trait. It allows accurate risk calculation for family members. Page 1 of 4  Figure 1. Symbols commonly used in pedigree charts. 2. Punnett Square (Figure 3 & 5) A Punnett square is a chart that allows determination of the expected ratios of possible genotypes in the offspring of two parents. CHARACTERSTICS OF DIFFERENT MODES OF MENDELIAN INHERITANCE: Autosomal dominant (AD) inheritance: An autosomal dominant trait is one that manifests in the heterozygous state, that is, in a person possessing both an abnormal or mutant allele and the normal allele. It is often possible to trace a dominantly inherited trait or disorder through many generations of a family. Each gamete from an individual with a dominant trait or disorder will contain either the normal allele or the mutant allele. Characteristics of AD inheritance: Affect both males and females in equal proportions. All forms of transmission between the sexes are observed Affected people are usually born to at least one affected parent (unless new mutation). The pedigree usually shows vertical transmission of the trait through generations (Figure 2). Usually involves genes encoding regulatory proteins of complex metabolic pathways or key structural proteins (fibrillin in Marfan syndrome). Affected children are usually heterozygous. Homozygous genotype is rare and when it occurs usually shows a more severe phenotype than heterozygous. Page 2 of 4  NB. The phenotype in AD inheritance usually appears in every generation, each affected person having an affected parent. Exceptions or apparent exceptions to this rule in clinical genetics are: (1) Cases originating from fresh mutations in a gamete of a phenotypically normal parent. (2) Cases in which the disorder is not expressed (non-penetrant). (3) Cases in which the disorder shows variation in the clinical phenotype among generations of the same family (Variable expressivity) as polycystic kidney. Genetic risk of AD inheritance: A child of an affected heterozygous parent has a 50% risk of being affected independent of sex. Usually, unaffected members of the family do not carry the mutant allele; thus they cannot transmit a disease allele to the next generation (Figure 3). Figure 2. Pedigree of AD trait. Figure 3. Punnett square of AD trait. Examples of AD inheritance: Nervous system: Neurofibromatosis. Hematology: Hereditary spherocytosis. Autosomal Recessive (AR) inheritance: In autosomal recessive inheritance, both alleles must be abnormal for the disease trait to be expressed. The unaffected parents of an affected child are obligate heterozygote carriers for the recessive mutant allele. Characteristics of AR inheritance: Males and females are equally likely to be affected. Transmitted by either sex Page 3 of 4  Affected people are usually born to un affected parents (asymptomatic healthy carriers) More commonly observed with consanguineous matings. The pedigree usually shows horizontal transmission of trait with multiple members of one generation affected (Figure 4). Usually involve genes of enzymes and proteins. Affected children may be homozygous for a specific recessive mutant allele, or they may be compound heterozygotes for two different mutations. Genetic risk of AR inheritance: Couples who are heterozygous carriers of a recessive mutant allele have a 25% risk of having an affected child with each pregnancy. The unaffected siblings have a 67% (two-thirds) chance of being a carrier for the mutant allele (Figure 5). Figure 5. Punnett square of AR trait. FIGURE 5. A Punnett square of AR trait. Examples of AR inheritance: The OMIM (Online Mendelian Inheritance in Man) database contains nearly 4,000 traits inherited as autosomal recessives. Metabolic disorders: cystic fibrosis, phenylketonuria, lysosomal storage disorders Haematology: sickle cell anemia, thalassemia. Page 4 of 4 36 Karyotyping and X-linked disorders ILOs By the end of this lecture, students will be able to 1. Determine characteristics of X-linked disorders. 2. Calculate the recurrence risk of monogenic X linked genetic disorders using Punnett square. 3. Interpret pedigrees with X-linked recessive and dominant diseases. 4. Correlate inherited X linked disorders with X-linked recessive and dominant modes of inheritance. 5. Interpret karyogram and karyotype formulae. Sex-Linked Inheritance Sex-linked inheritance refers to the pattern of inheritance shown by genes that are located on either of the sex chromosomes. Genes carried on the X chromosome are referred to as being X-linked, and those carried on the Y chromosome are referred to as exhibiting Y-linked inheritance. X-Linked Recessive Inheritance  Manifests mainly in males. A male with a mutant allele on his single X chromosome is said to be homozygous for that allele.  Females may be affected if the father is affected and the mother is an asymptomatic carrier. Genetic risk X-Linked Recessive Inheritance  For a male affected with X-linked recessive disease has children with a normal female, then all of his daughters will be obligate carriers but none of his sons will be affected “A male cannot transmit an X-linked trait to his son”.  Obligate carriers may transmit the disease to their sons in the future (diagonal pattern of transmission due to affected male relatives on maternal side) (Figure 1). Page 1 of 5   For a carrier female of an X-linked recessive disorder having children with a normal male, each son has a 50% chance of being affected and each daughter has a 50% chance of being a carrier (Figure 2).  Some X-linked disorders are not compatible with survival to reproductive age and are not, therefore, transmitted by affected males. Duchenne muscular dystrophy is the commonest muscular dystrophy and is a severe disease. Affected males often die in their late teenage years or early 20s. Because affected boys do not usually survive to reproduce, the disease is transmitted by healthy female carriers, or may arise as a new mutation. e trait. Figure 2. Punnett of X-linked recessive trait. X-Linked Dominant Inheritance  Uncommon,  Manifest in the heterozygous female as well as in the male who has the mutant allele on his single X chromosome. Genetic risk X-Linked dominant Inheritance Page 2 of 5   An affected female transmit the trait to both her daughters and sons equally with a 50% chance of being affected regardless the sex (Figure 3 & 4A).  An affected male transmits the trait to all his daughters but to none of his sons (Figure 3 & 4B).  Therefore, in families with an X-linked dominant disorder there is an excess of affected females and direct male-to-male transmission cannot occur.  Females are often less affected than males due to X chromosome inactivation. A B Figure 3. Pe Examples of X-Linked dominant Inheritance Page 3 of 5 X-linked hypophosphatemia, (Vitamin D-resistant rickets): Rickets can be due to a dietary deficiency of vitamin D, but in vitamin D–resistant rickets the disorder occurs even when there is an adequate dietary intake of vitamin D. In the X-linked dominant form of vitamin D-resistant rickets, both males and females are affected with short stature due to short and often bowed long bones, although the females usually have less severe skeletal changes than the males. Y-Linked Inheritance Only males are affected. Genetic Risk Y-Linked Inheritance An affected male transmits Y-linked traits to all of his sons but to none of his daughters. Examples of Y-Linked Inheritance Genes involved in spermatogenesis are carried on the Y chromosome and, therefore, manifest Y-linked inheritance. When these genes are deleted, it leads to infertility from azoospermia (absence of the sperm in semen) in males. If the affected male has a son by the techniques of assisted reproduction (intracytoplasmic sperm injection (ICSI)) the child will also necessarily be infertile as he will inherit this Y-linked infertility from his father. KARYOTYPING Karyotyping is the process of pairing and ordering all the chromosomes of an organism, thus providing a genome-wide snapshot of an individual's chromosomes. Karyotyping detects gross genetic changes either numerical or structural anomalies involving several megabases or more of DNA. A variety of tissue types can be used as a source of these cells. For cancer diagnoses, typical specimens include tumor biopsies or bone marrow samples. For other diagnoses, karyotypes are often generated from peripheral blood specimens or a skin biopsy. For prenatal diagnosis, amniotic fluid or chorionic villus specimens are used as the source of cells. Preparing Karyotypes from Mitotic Cells Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. Without any treatment, structural details of chromosomes are difficult to detect under a light microscope. Thus, to make analysis more effective and efficient, cytologists have developed stains that bind with DNA and generate characteristic banding patterns for different chromosomes. The most frequently used techniques are G- (giemsa), Q- (quinacrine) and R- (reverse) banding. The various banding techniques produce light and dark bands on the chromosomes that are specific to each chromosome and that hence permit unequivocal identification of the individual chromosomes. Page 4 of 5 In general, heterochromatic regions, which tend to be AT-rich DNA and relatively gene-poor, stain more darkly in G-banding. In contrast, less condensed chromatin which tends to be GC-rich and more transcriptionally active appear as light bands in G-banding. According to international consensus, 20–25 should be fully analyzed in order to produce a reliable diagnosis. The karyotype formula An international cytogenetic nomenclature (ISCN: International System of Cytogenetic Nomenclature) provides an exact description of all numerical and structural aberrations in a karyotype formula. The karyotype formula first states the number of chromosomes, followed by the statement of gender chromosomes. Hence, the normal female karyotype is 46,XX, while the normal male karyotype is 46,XY. The karyotype formula denotes:  Gain of a chromosome with a “+” e.g. 47,XX,+8: trisomy of chromosome 8  Loss of a chromosome with “-” e.g. 45,XY,-7, describes monosomy of chromosome 7.  “t” for translocation e.g. t(8;21)(q22;q22) means that a breakpoint has occurred in band q22 of chromosome 8, another one in band q22 of chromosome 21, and that translocation of the fractions has taken place between the chromosomes.  “inv” for inversion: inv(16)(p13q22): i.e. breaks took place in the chromosome bands p13 and q22 of the same chromosome 16, and the segment between both breakpoints was inverted by 180°.  del(5)(q13q31), i.e. the breaks took place in the bands q13 and q31 of the same chromosome 5, and the region between q13 and q31 has been lost. Figure 5. Normal female karyogram Page 5 of 5