Medical Genetics

1. Medical Genetics Fadel A. Sharif

2. Contact details Medical Laboratory Sciences Genetics Diagnosis lab fsharif@iugaza.edu

3. Grades First and Second Hour Exams 40% Final exam 60%

4. Topics 1: Patterns of Single-Gene Inheritance 2: Genetic Variation in Individuals 3: Genetic Variation in Populations 4: Gene Mapping 5: Principles of Clinical Cytogenetics 6: Clinical Cytogenetics: Disorders of the Autosomes and the Sex Chromosomes 7: Treatment of Genetic Diseases 8: Genetics and Cancer

5. Textbook: • Genetics in Medicine, 7th edition. Nussbaum, McInnes & Willard. W.B. Saunders Co. (2007). • Reference • Emery’s Elements of Medical Genetics, 13th edition, Turnpenny & Ellard. Churchill Livingstone. (2007).

6. Patterns of Single gene disorders

7. Objectives for this lecture • Gain familiarity with pedigrees & family history • Appreciate distinctions between major patterns of single gene inheritance • Autosomal dominant, autosomal recessive, sex-linked recessive, sex-linked dominant • Understand factors which complicate inheritance patterns

8. Terminology Genetics is concerned with variation and heredity in all living organisms Human genetics is the science of variation and heredity in humans Medical genetics deals with human genetic variation of significance in medical practice and research Cytogenetics: the study of chromosomes

9. Terminology Genomics: the study of genome, its organization and functions Population genetics: genetic variation in human populations and factors that affect allele frequencies Clinical genetics: application of genetics to diagnosis and patient care Genetic counseling: risk information, psychological and educational support to patients and/or their families

10. Terminology • Gene - The basic hereditary unit, initially defined by phenotype. By molecular definition, a DNA sequence required for production of a functional product, usually a protein, but may be an untranslated RNA. • Genotype - An individual’s genetic constitution, either collectively at all loci or more typically at a single locus. • Phenotype - Observable expression of genotype as a trait (morphological, clinical, biochemical, or molecular) or disease • Allele - One of the alternate versions of a gene present in a population. • Locus - Literally a “place” on a chromosome or DNA molecule. Used fairly interchangeably with “gene” and sometimes used to refer to a collection of closely spaced genes.

11. Wild-type (normal) allele: prevailing version, present in majority of individuals • Mutant allele: usually rare, differ from wild-type allele by mutation • Mutation: permanent change in nucleotide sequence or arrangement of DNA • Polymorphism: ≥ 2 relatively common (each > 1% in population) alleles at a locus in the population • Dominant trait - a trait that shows in a heterozygote • Recessive trait - a trait that is hidden in a heterozygote

12. Homozygous - Having two identical alleles at a particular locus, usually in reference to two normal alleles or two disease alleles. Heterozygous - Having two different alleles at a particular locus, usually in reference to one normal allele and one disease allele. Compound heterozygous- Having two different mutant alleles of the same gene, rather than one normal and one mutant.

13. Genotype: A A (Homozygous) Genotype: AB (Heterozygous) A B A A Gene Chromosome 6 Maternal copy Chromosome 6 Paternal copy DNA Basic terminology Single gene disorder - determined by the alleles at a single locus

14. Reminder • Autosomes • Chromosomes 1-22 • An individual inherits one chromosome from each parent • An individual therefore inherits a paternal copy and a maternal copy of an autosomal gene • Sex chromosomes • X and Y • A female inherits an X from their mother and an X from their father • A male inherits an X from their mother and the Y from their father

15. Single-gene traits are often called ‘Mendelian’ because like the garden peas studied by Gregor Mendel, they occur in fixed proportions among the offspring of specific types of mating.

16. Single-gene disorders are primarily disorders of the pediatric age range greater than 90% manifest before puberty only 1% occur after the end of the reproductive period

17. Obtaining a pedigree A three generation family history should be a standard component of medical practice. Family history of the patient is usually summarized in the form of a pedigree Points to remember: • ask whether relatives have a similar problem • ask if there were siblings who have died • inquire about miscarriages, neonatal deaths • be aware of siblings with different parents • ask about consanguinity • ask about ethnic origin of family branches

18. Pedigree terminology • Proband (propositus or index case): is the affected individual through whom a family with a genetic disorder is first brought to attention. • Consultand: the person who brings the family to attention by consulting a geneticist, may be an unaffected/affected relative of the proband • Brothers and sisters = sibs, and a family of sibs = sibship • Kindred = the entire family. Relatives are classified 1st degree, 2nd degree, etc. • Consanguineous = couples who have one or more ancestors in common • Isolated case = if only one affected member in the kindred (= sporadic case if disorder in propositus is determined to be due to new mutation)

19. proband first degree second degree third degree fourth degree Pedigree terminology

21. Patterns of Single Gene Inheritance depend on 2 factors: • Whether the gene is on an autosome or a sex chromosome • Whether the phenotype is dominant or recessive Thus, there are 4 basic patterns of single gene inheritance • Autosomal Recessive • Autosomal Dominant • X-linked Recessive • X-linked Dominant

22. Activity Protein 1 Protein 2 Dominant and Recessive Mechanisms

23. Incomplete dominance: phenotype in hetrozygous is different from that seen in both homozygous genotypes and its severity is intermediate b/w them • Codominant alleles: if expression of each allele can be detected even in presence of the other

24. Dominant and Recessive Mechanisms continued • Loss of function • Usually recessive; mutation leads to inactive gene product but reduced activity level still sufficient • However, if reduced activity not sufficient (haploinsufficiency), the phenotype is deemed dominant • Gain of function • Novel action • Altered mRNA expression • Increased/decreased protein activity • ex: huntingtin mutations • Dominant negative • Abnormal function that interferes with normal allele ex: collagen mutations in osteogenesis imperfecta

25. Age of Onset and Other Factors Affecting Pedigree Patterns Age of Onset • Not all genetic disorders are congenital; many are not expressed until later in life, some at a characteristic age and others at variable ages • A genetic disorder is determined by genes, a congenital disease is that present at birth and may or may not be genetical • Many genetic disorders develop prenatally and thus are both genetic and congenital (e.g., osteogenesisimperfecta) • Some may be lethal in prenatal life • Others expressed as soon as the infant begins independent life • Others appear later, at a variety of ages (from birth to post-reproductive years)

26. Other Factors Affecting Pedigree Patterns • Small family size: the patient may be the only affected member  the inheritance pattern may not be immediately apparent • New mutation: is a frequent cause of AD and X-linked disease • Diagnostic difficulties: owing to absent or variable expression of the gene • Other genes and environmental factors: may affect gene expression • Persons of some genotypes may fail to survive to time of birth • Accurate info. about presence of disorder in relatives or about family relationships may be lacking

27. Genetic Heterogeneity • Genetic heterogeneity: includes a number of phenotyopes that are similar but are actually determined by different genotypes. May be due to allelic heterogeneity, locus heterogeneity, or both • Allelic heterogeneity: different mutations at the same locus • Locus heterogeneity: mutations at different loci • Recognition of genetic heterogeneity is an important aspect of clinical diagnosis and genetic counseling

28. Locus Heterogeneity • Pedigree analysis may be sufficient to demonstrate locus heterogeneity • Example-1, retinitis pigmentosa • A common cause of visual impairment due to photoreceptor degeneration associated with abnormal pigment distribution in retina. • Known to occur in AD, AR, and X-linked forms • Example-2, Ehndlers-Danlos syndrome, • Skin & other connective tissues may be excessively elastic or fragile, defect in collagen structure • May be AD, AR, or X-linked • At least 10 different loci involved

29. Allelic Heterogeneity • An important cause of clinical variation • Sometimes, different mutations at same locus  clinically indistinguishable or closely similar disorders • In other cases, different mutant alleles at same locus  very different clinical presentations • Example-1:RET gene (encodes a receptor tyrosine kinase) • Some mutations cause dominantly inherited failure of development of colonic ganglia  defective colonic motility and severe chronic constipation (Hirschsprung disease) • Other mutations in same gene  dominantly inherited cancer of thyroid and adrenal gland (multiple endocrine neoplasia) • A third group of RET mutations  both Hirschsprung disease and multiple endocrine neoplasia in the same individual

30. In fact, unless they have consanguineous parents, most people with autosomal recessive disorders are more likely to have compound rather than truly homozygous genotypes • Because different allelic combinations may have somewhat different clinical consequences, one must be aware of allelic heterogeneity as one possible explanation for variability among patients considered to have same disease

31. ALLELIC DISORDERS(Clinical heterogeneity)-This is an extreme example of how different mutations in the same gene can cause divergent phenotypes, in which there are actually two different diseases caused by the same gene.

32. Autosomal Recessive Pedigree illustrating recessive inheritance

33. Representative Autosomal Recessive Disorders Disease Frequency Chromosome Cystic fibrosis 1/2,500 7q -Thalassemia High 16p -Thalassemia High 11p Sickle cell anemia High 11p Myeloperoxidase deficiency 1/2,000 17q Phenylketonuria 1/10,000 12q Gaucher disease 1/1,000 1q Tay-Sachs disease 1/4,000 15q Hurler syndrome 1/100,000 22p Glycogen storage disease Ia (von Gierke disease) 1/100,000 17q Wilson disease 1/50,000 13q Hereditary hemochromatosis 1/1,000 6p 1-Antitrypsin deficiency 1/7,000 14q Oculocutaneous albinism 1/20,000 11q Alcaptonuria <1/100,000 3q Metachromatic leukodystrophy 1/100,000 22q

34. Cystic fibrosis (CF) - an autosomal recessive disease • Diseased homozygotes: 1/2000 • Carriers (heterozygotes): 1/22 • Caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) on chromosome 7q31 • Clinical symptoms include pancreatic insufficiency and pulmonary infections

35. Lung abscess • Chronic bronchitis • Bronchiectasis • Honeycomb lung Secondary biliary cirrhosis Malabsorption Chronic pancreatitis Meconium ileus (newborn) Abnormal sweat electrolytes Obstructed vas deferens (sterility) Multiorgan System Manifestations of CF

36. CFTR function Regulates the flow of chloride ions across the cell membrane

38. maternal l A a a n r e A AA Aa 1/4 unaffected non-carrier t a p a Aa aa 1/2 unaffected carrier 1/4 affected

41. maternal l A a a n r A AA Aa e t X a p a Aa aa 1. Probability of Carrier = 2/3 2. Probability of Mate Carrier: q2 =1/2,000 q = (1/2,000)1/2 q =0.022 (use p 1) heterozygote freq. = 2pq  2q = (2)(0.022) = 0.044 = 4.4%  1/23 3. Put it together: P(Carrier) x P(Transmit Affected Allele) x P(Mate’s Carrier) x P(Transmit Affected Allele) (2/3) x (1/2) x (1/23) x (1/2) = 0.008 = 0.8%

42. Maternal A a Aa aa a 1/4 1/4 Paternal AA A Aa 1/4 1/4 Aa Aa unaffected non-carrier unaffected carrier affected What is the probability that this pending pregnancy will be affected? Cystic Fibrosis 1/4 aa 1/2 1/4 Note also that 2/3 of the normal siblings of a recessive child are heterozygous: Aa/(AA+Aa)=1/2/3/4

43. Consanguinity Phenylketonuria (PKU) • Refers to a relationship by descent from a common ancestor (inbreeding) • A concern in autosomal recessive disorders. • If a rare disease (due to infrequent alleles), the disease will occur more commonly in individuals whose parents are related. 2nd cousin mating

44. Studies of the offspring of incestuous matings indicate that everyone carries at least 8-10 mutant alleles from well-known autosomal recessive disorders However, the offspring of first cousin marriages are only at twice the risk of abnormal offspring compared to the general population

45. A1 Calculating the inbreeding coefficient (F) for a child of a first cousin mating Measure of consanguinity is relevant because the risk of a child being homozygous for a rare allele is proportional to how related the parents are pedigree Coefficient of inbreeding (F) -probability that an individual has received both alleles at a locus from an ancestral source = proportion of loci identical by descent from the common ancestor

46. A1 Inbreeding coefficient (F) of the proband is 1/16; he has a 6% chance of being homozygous by descent for any locus pedigree Path diagram 1/2 1/2 1/2 1/2 1/2 1/2 (F) = 1/16

48. Rare recessive disorders in genetic isolates • Genetic isolates: groups in which the frequency of rare recessive genes is quite different from that in the general population • Although such populations are not consanguineous, the chance of mating with another carrier of a particular recessive condition may be as high as observed in cousin marriages • E.g., Tay-Sachs disease (GM2 gangliosidosis) a lysosomal storage disease

49. Tay-Sachs Disease lysosomal storage disease Tay-Sachs Disease normal GM2 ganglioside GM2 ganglioside hexosaminidase A hexosaminidase A degradation products GM2 ganglioside accumulates in the lysosomes removal/ recycling of sphingolipid components Neurodegeneration

50. Tay-Sachs: the clinical picture • Infants with Tay-Sachs appear normal until about 3 to 6 months of age • Motor development plateaus by 8-10 months • loss of all voluntary movement by 2 yrs • Visual deterioration begins within the first year, "cherry red spot" at the macula (retina). • Worsening seizures • difficulty swallowing • vegetative, unresponsive state • Patients almost always die by 2 to 4 years of age. • There is no cure, and no effective treatment.