Cytogenetics DSR - Harris Fall 2024 PDF

Clinical Cytogenetics (DSR) (Reference: Medical Genetics, Chapter 6) OMS 6111: MEDICAL GENETICS DR. RANDALL HARRIS  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how kar...

Clinical Cytogenetics (DSR) (Reference: Medical Genetics, Chapter 6) OMS 6111: MEDICAL GENETICS DR. RANDALL HARRIS  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome.  Chromosome Abnormalities Important cause of morbidity and mortality Occur in as many as 1 in 150 live births Leading known cause of: ◦ Intellectual disability ◦ Pregnancy loss (spontaneous abortions) ◦ 50% in first trimester ◦ 20% in second trimester Types of chromosome abnormalities Abnormalities in chromosome number ◦ Trisomies, Monosomies ◦ Cause: Nondisjunction events during Anaphase I or II of meiosis Abnormalities in chromosome structure ◦ Translocations, Deletions, Duplications ◦ Cause: Improper chromosome recombination during Prophase I of meiosis  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome. Chromosome anatomy  Chromosome terminology and notation Major regions and bands are systematically numbered, starting at the centromere and moving towards the telomeres (banding patterns are established by various staining procedures) Centromeres are designated as p10 and q10 by convention ◦ Letter = short or long arm ◦ First number = region ◦ Second number = band “14q32” = second band in the third region of the long arm of chromosome 14 Sub-bands can be indicated by decimals (14q32.3)  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome.  Methods of chromosome analysis Karyotyping FISH CGH/microarrays  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome.  Abnormalities in chromosome number Euploidy (“good set”) ◦ Chromosome number is a multiple of 23 (in humans) ◦ Haploid gametes and diploid somatic cells are both euploid Polyploidy ◦ The individual has a complete extra set of chromosomes (can be any number of sets: triploid, tetraploid, etc.) ◦ Results in seedless fruits in plants but spontaneous abortion in humans (generally) Aneuploidy ◦ Total chromosome number is NOT a multiple of 23 ◦ Monosomy: one of the chromosome pairs is present in only ONE copy ◦ Trisomy: one of the chromosome pairs is present in THREE copies  Abnormalities in chromosome number Autosomal monosomies are almost always incompatible with life Autosomal trisomies are also problematic but can be compatible with life ◦ MOST COMMON IN LIVE BIRTHS: 21, 18, 13 Basic rule of thumb: “The body can tolerate excess genetic material more readily than it can tolerate a deficit of genetic material.” (Medical Genetics) Most common cause of aneuploidy is nondisjunction during meiosis  NORMAL disjunction during Meiosis I and II Important features of meiosis: Synapsis during Prophase I Anaphase I: Separation of homologous chromosomes (paternal vs. maternal) Anaphase II: Separation of sister chromatids (splitting at the centromere) Normal haploid gametes produced Compare the trisomic offspring generated by a nondisjunction in Meiosis I with the trisomic offspring generated by a nondisjunction in Meiosis II: in the first case, the offspring has both a paternal and a maternal copy of the chromosome that is duplicated (two DIFFERENT chromosomes), whereas in the second case, the offspring has two of the SAME chromosome (in this case, two copies of the pink chromosome).  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome.  Trisomy 21 (Down syndrome) Karyotype: 47, XY, +21 (sex is irrelevant in this karyotype) Frequency: 1 in every 800 to 1000 live births (most common autosomal trisomy resulting in live births) 5 A’s of Down syndrome ◦ Advanced maternal age ◦ Atresia (duodenal) ◦ Atrioventricular septal defect ◦ Alzheimer disease (early onset) ◦ AML (5  Trisomy 21 Accounts for about 10% of all cases of intellectual disability in the U.S. With interventional care (including surgical): ◦ 80% will survive to age 10 ◦ 50% will survive to age 50 Males are usually sterile; females can reproduce but 40% fail to ovulate Females with Down syndrome have a 50% risk of producing trisomic offspring (through production of n+1 gametes) BUT the risk of spontaneous abortion is the same as in other females (so overall risk is lower) ◦ SO…Most cases of trisomy 21 are regarded as de  Mechanism of Trisomy 21 95% of cases are caused by nondisjunction, usually in the mother and usually in Meiosis I Mosaicism is possible – the extra chromosome 21 can be lost from some cells during mitosis in early embryogenesis (Often results in a milder phenotype) Up to 40% of the genes on chromosome 21 currently have no known purpose Candidate genes: Important region seems to be 21q21 to 21q22.3 ◦ Looking for “dosage-sensitive genes” – causing problems when present in too many copies ◦ DYRK1A: candidate gene for intellectual disability; causes learning and memory problems in mice when it is overexpressed ◦ DSCR1 (Down syndrome critical region gene 1): overexpressed in the brains of Down syndrome fetuses; plays a role in CNS development ◦ APP: amyloid beta precursor protein; associated with some cases of Alzheimer’s disease  Trisomy 18 (Edwards syndrome) Major clinical characteristics ◦ SGA (due to prenatal growth deficiency) ◦ Characteristic facial features ◦ Distinctive hand abnormality ◦ Small ears and mouth ◦ Short sternum ◦ Congenital heart defects (especially VSDs) ◦ Omphalocele ◦ Diaphragmatic hernia More severe developmental difficulties than children with Down syndrome, including an inability to walk independently Second most common autosomal trisomy resulting in live births  Trisomy 13 (Patau syndrome) Karyotype: 47, XY, +13 Extremely distinctive characteristics ◦ Oral-facial clefts ◦ Microphthalmia ◦ Postaxial polydactyly ◦ CNS, heart, and renal abnormalities Third most common autosomal trisomy resulting in live births  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome. When do most structural abnormalities occur? Unequal crossing over due to improper synapsis (random) Toxic agent exposure that causes increased breakage and rejoining of chromosomes  Two major types of structural abnormalities Balanced: no gain or loss of genetic material in the chromosome rearrangement ◦ Usually does not cause problems in the carrier of the abnormality – but may be inherited by offspring and cause serious problems ◦ Translocations, isochromosomes, inversions Unbalanced: causes a gain or loss of genetic material ◦ Typically always problematic in the carrier of the abnormality AND their offspring ◦ Deletions, ring chromosomes, subtelomeric rearrangements, duplications  Translocations Exchange of genetic material between two non- homologous chromosomes Balanced translocations are among the most common chromosomal abnormalities (as high as 1 in 500) Reciprocal translocations ◦ Breaks occur in two different chromosomes and there is a mutual exchange ◦ Leads to derivative (der) chromosomes ◦ The carrier of the translocation is usually normal  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome.  Robertsonian translocations The short arms of two nonhomologous chromosomes are lost, and the remaining long arms fuse to form a single new chromosome Occurs only in the acrocentric chromosomes (13, 14, 15, 21, and 22) A carrier who has this translocation is normal, but the karyotype will have only 45 chromosomes  Familial Down syndrome Accounts for up to 5% of all Down syndrome cases Robertsonian translocation of 14q and 21q No correlation with increased maternal age The presence of a Robertsonian translocation in one parent does correlate to the risk of Down syndrome in a Mendelian fashion Typical carrier karyotype: – 45, XY, der(14;21) (q10,q10) Mechanism of Familial Down Syndrome  Familial Down Syndrome without a Robertsonian translocation isochromos ome  Learning objectives 1.Describe the anatomy of a chromosome with respect to landmarks and genetic notation conventions. 2.Describe how karyotyping, FISH, and CGH are used in cytogenetic analysis. 3.Describe how nondisjunction during meiosis can lead to different forms of aneuploidy. 4.Recognize major elements of the phenotypes associated with trisomy 21, trisomy 18, and trisomy 13. 5.Differentiate between balanced and unbalanced chromosomal structural abnormalities. 6.Describe how Robertsonian translocations and isochromosomes occur, and their potential role in familial Down syndrome. 7.Recognize major elements of the phenotypes associated with deletion syndromes such as Cri du chat and WAGR syndrome.  Deletions Chromosome breaks with loss of genetic material Terminal deletion: includes tip of chromosome Interstitial deletion: two internal breaks that join with a loss of material in between Autosomal deletion syndromes are the most common group of clinically significant chromosome structural abnormalities  Cri-du-chat syndrome Also known as 5p deletion syndrome Distinctive cry in infants – becomes less obvious after 2 years of age Deletion of the distal short arm of chromosome 5 – Length of the deletion can vary Frequency is 1 in 50,000 live births Phenotype: intellectual disability, microcephaly, and characteristic facial appearance – Some patients have milder mental effects depending on the size of the deletion  Cri-du-chat syndrome In 80% of cases the chromosome with the deletion can be traced back to the father The deleted region can contain many genes – CTNND2 (delta-catenin) ◦ Important protein in the process of neuronal migration during embryogenesis ◦ Also important for proper functioning of synapses in the developed brain – TERT (telomerase reverse transcriptase) ◦ Involved in regulation and replacement of the ends of chromosomes (telomeres)  Microdeletion syndromes Only detectable after the development of high-resolution banding, FISH, and CGH Example: 70% of Prader-Willi/Angelman patients have microdeletions in 15q ◦ Typically a consistent 4 Mb deletion ◦ Determined by low-copy repeat sequences at the boundaries of the deletion which promote unequal crossing-over, leading to the deletion Contiguous gene syndrome ◦ Syndrome resulting from deletion of adjacent genes on a chromosome, each causing a different facet of the syndrome ◦ WAGR syndrome (11p deletions) ◦ Wilms’ tumor (tumor of the kidney) ◦ Aniridia ◦ Genitourinary abnormalities ◦ Intellectual disability (Mental Retardation)  Generalizations of chromosomal structural abnormalities 1. Most result in developmental delay or intellectual disability – As many as 1/3 of all human genes play some role in CNS development 2. Most involve alterations of facial morphogenesis that produce characteristic facial features 3. Most produce growth delays 4. Most exhibit accompanying congenital malformations (pleiotropic effects)