Clinical Genetics in Medical Practice PDF

Clinical Genetics in Medical Practice Dr Cristina Dias Clinical Senior Lecturer Medical and Molecular Genetics  Learning Objectives (Part I) Students should be able to: 1. Construct a pedigree 2. Identify inheritance pattern(s) from a pedigree 3. Assess genetic risk  Wh...

Clinical Genetics in Medical Practice Dr Cristina Dias Clinical Senior Lecturer Medical and Molecular Genetics  Learning Objectives (Part I) Students should be able to: 1. Construct a pedigree 2. Identify inheritance pattern(s) from a pedigree 3. Assess genetic risk  What is Medical Genetics? Application of genetic knowledge to medical practice Diagnosis of genetic disorders Interpret specialised laboratory testing Provide patient and family counselling Study the causes and natural history of genetic disorders Contribute/facilitate patient management Rare disease clinical trials and treatments  Dominant A Recessive a Alleles Gregor Mendel 1822-1884 1st law: Law of segregation – each individual has two forms (alleles) of each characteristic and only one of these is transmitted to each offspring 2nd law: Law of independent assortment – genes at different loci segregate independently (note that this does not apply if two loci closely linked) Law of segregation Molecular genetics timeline Mersha, T.B. Eur J Hum Genet, 2024 Genome Sequencing Number of human genomes sequenced per year Source: MIT Technology Review Single gene (Mendelian) disorders Caused by mutations in a single gene Classical (coding) definition: a pathogenic (heritable) alteration in the gene affecting the structure or function of a protein 23,000 -25,000 genes >12,000 single gene disorders are known Genetic jargon Locus: Position/location of a gene on a chromosome Allele/allelic: Different form of a gene at a locus Genotype: An individual’s genetic constitution at a specified locus (or loci) Phenotype: The clinical effect of an expressed gene or genes Heterozygote: An individual with different alleles at a specified locus Hemizygous: The presence of only a single copy of chromosome or gene e.g. the X chromosome in males Example Chromosome 7 Phenotype/disease: ? Allele 1 Allele 2 CFTR Locus Wild type p.Phe508del 7q31 Genotype: p.Phe508del heterozygote  Autosomal genes - located on autosomes (Ch 1–22) X-linked and Y-linked genes are located on the X and Y chromosomes respectively X-linked conditions are sometimes said to be sex-linked or show sex- linked inheritance Heterogeneity Monogenic Phenotypic heterogeneity Genetic heterogeneity  Recognise, understand and use standard pedigree symbols Bennet et al, JGC, 2008 Case 1 Anna 02/10/82 Anna is a consultand seeking medical advice because of her family history of Myotonic Dystrophy Case 1 Anna 02/10/82 Anna is the consultand seeking medical advice because of her family Key Myotonic dystrophy History of Myotonic Dystrophy What is the inheritance pattern of Myotonic Dystrophy? Ø Autosomal dominant Ø Anticipation Affected What is the inheritance pattern of Myotonic Dystrophy? Ø Autosomal dominant Ø Anticipation Affected Autosomal dominant conditions Caused by a mutation in a single autosomal gene Affected individuals are heterozygous for the mutation One normal (wild) type and one mutant copy of the gene Autosomal dominant conditions Autosomal dominant conditions Transmitted from generation to generation Ø vertical inheritance Males and females are usually affected equally Affected parent can transmit the disorder to sons or daughters 1 in 2 (50%) risk of an affected parent transmitting the condition Key feature: male to male transmission  Autosomal dominant conditions Two important characteristics of autosomal dominant conditions to remember: 1. Variable (reduced) penetrance 2. Variable expression  Reduced Penetrance The proportion of carriers who manifest phenotypic signs of the condition ØNot all individuals who inherit a dominant disease mutation necessarily show signs of the condition i.e. penetrance is a statistic – usually expressed as a % Penetrance - example: Cherubism Autosomal dominant disorder 100% penetrance in males 50 – 75% penetrance in females 2:1 male predominance Marked fullness of the jaws  Case 2: Marfan syndrome ©Scion Publishing Ltd Case 2: Marfan syndrome Tall stature, long limbs Chest abnormalities, scoliosis ©Scion Publishing Ltd Arachnodactyly (long fingers) Dislocated lens (ectopia lentis) Risk of aortic aneurism Abraham Lincoln Variable expression/Expressivity Extent of clinical manifestation Variable within and between families  Autosomal dominant conditions Inherited - from an affected parent - from an apparently unaffected mosaic parent De novo - new mutation in a gamete (sporadic event) or shortly after fertilisation - during early development: mosaicism Examples: Achondroplasia Marfan syndrome Neurofibromatosis type 1 and type 2 Acuna-Hidalgo et al, Gen Biol 2016 Germline mosaicism Achondroplasia Point mutation FGFR3 Two children affected with achondroplasia, but normal healthy parents Non-paternity excluded 2 independent de-novo mutations unlikely ØGermline mosaicism: a parent carries a small proportion of gametes (germline cells) that harbour the same mutation (Examples: Osteogenesis imperfecta, Duchenne muscular dystrophy) Autosomal Recessive Pedigree Cystic Fibrosis Autosomal Recessive Pedigree Consanguinity increases the risk of recessive disorders in the offspring  Autosomal Recessive Conditions Males and females can equally be affected Generally only members of a single sibship, or cousins are affected (unless multiple consanguinity in the family) The probability that a future sibling of an affected individual will also be affected is 1 in 4 The probability that a future sibling will be a carrier is 1 in 2 The probability that an existing unaffected sibling is a carrier is 2 in 3 (the denominator changes as we have excluded the affected individual from our calculation) Autosomal Recessive Conditions Unaffected Affected 2 out of 3 are carriers 1 in 4 is affected i.e unaffected sibs have (½ x ½ = ¼ ) a 2/3 carrier risk Compound heterozygosity Compound heterozygosity: different mutations in the same gene (different alleles) Example: CFTR p.Gly542X / p.Phe508del (2 commonest Caucasian CF alleles) Homozygosity: Same allele on both chromosomes Example: Sickle cell anaemia, HbS p.E6V/E6V Compound heterozygosity Someone who has different allelic mutations at the same locus Ø compound heterozygote β-thalassaemia Sickle-cell anaemia Chromosome 11 Chromosome 11 Compound heterozygote Compound heterozygosity: clinical example ? Tay-Sachs disease: beta-hexosaminidase A deficiency > GM2 ganglioside accumulation 2 mutations in HEXA identified: - 1278insTATC (p.Tyr427fs) - p.Arg170Gln Parents, Scenario 1: Parents, Scenario 2: Mother: p.Tyr427fs, p.Arg170Gln Mother: p.Arg170Gln Father: no variant Father: p.Tyr427fs cis trans X linked inheritance Carrier female Unaffected 1 in 4 offspring affected ½ daughters are carriers ½ sons unaffected, not a carrier X linked pedigree  X-linked recessive disorders Only males related via the female line are usually affected Women usually asymptomatic* 1 in 2 chance that each son born to a carrier female will be affected 1 in 2 chance that each daughter will be a carrier All the daughters of an affected male will be carriers Sons of affected male are not affected (no male to male transmission) X-linked recessive disorders NHS Genomics Education Program Females can be affected with X-linked recessive disorders Non-random inactivation leading to chance expression in certain tissues e.g. expression of mutant allele in: - heart in Duchenne muscular dystrophy carriers - kidney in X-linked Alport’s disease - brain in Fragile X syndrome (learning disability) Turner syndrome 45,X  X inactivation Example: Tortoiseshell cat: X-linked gene Black/tan alleles Gendrel & Heard, Dev, 2011  X inactivation Only one X used per cell in 46 XX, 47 XXY Ø Dosage compensation One X in each cell is switched off before blastocyst implants in female embryos All women are mosaics, expressing either their maternal or paternal X but not both in any one of their cells Random X inactivation INACTIVE ACTIVE One X chromosome per cell is inactivated by methylation All daughter cells have the same X chromosome inactivated (i.e. they are a clone of cells with the same pattern of X inactivation) Puck & Willard. N Engl J Med. 1998; 338(5): 325-8  X-linked Dominant disorders Males and females affected (females < males) Affected females can show a mosaic pattern of involvement in tissues such as skin Example: Rett Syndrome The condition may be lethal in males 50% offspring risk to males and females of affected mothers All daughters of affected males inherit the condition No sons of affected male inherit the condition www.rettsyndrome.org Part I summary Introduced basic genetic nomenclature Reviewed the principles of Mendelian inheritance Revised pedigree symbols for drawing family trees Observed different patterns of inheritance in a pedigree Discussed basic phenomena that can help to describe or influence the severity of a disorder  Learning Objectives (Part II) Identify indications for genetic tests Understand the concept of genetic risk Undertake simple risk calculation to estimate the risk of a family member being affected by genetic disease  Genetic Consultation Diagnostic Clinical assessment Investigations Counselling: explain the condition, prognosis, treatment options Implications for the proband and for family members Pre-symptomatic testing (Predictive) Individual at risk, based on family history Usually adult onset conditions Genetic Counselling Genetic Counselling: A process of communication of the nature of a genetic disorder between counsellor and family Risks of transmission / inheritance / penetrance Future pregnancies To the consultand, on the basis of family history Choices and options available: Non-directive counselling Non-judgemental Support in making an informed decision: allow time to consider, reflect and plan Diagnosis of a genetic condition Clinical based on clinical (dysmorphic) features Genetic tests Classical chromosome analysis (karyotype) Molecular cytogenetics (array CGH, SNP array) Single gene testing Next Generation Sequencing (NGS) Methylation analysis (imprinting disorders) Clinical Diagnosis  Differential diagnosis with non-genetic conditions Teratogens Foetal Alcohol Syndrome Foetal Anticonvulsant Syndrome http://kidstoadopt.org/adoption-resources/medical- http://www.fact-uk.co.uk/ conditions/about-fetal-alcohol-syndrome/  Unknown genetic aetiology Example: VATER (VACTERL) Association Vertebral Anal Atresia Cardiac Tracheo-oesophageal atresia/fistula Renal abnormalities Limb (radial ray defect) Karyotype Standard karyotype Chromosome painting  Karyotype Classical genetic test Multiple problems (structural abnormality/developmental delay) Often unusual combination, unless recognised syndrome Largely replaced by array CGH / SNP array  Chromosome rearrangements A. Number - Aneuploidies (chromosome number not divisible by 23) - Polyploidies (multiple sets of 23 chromosomes) B. Structure Balanced (translocations) 1 in 500 healthy individuals Unbalanced Deletions Duplications Inversions Translocations Often associated with problems A. Aneuploidy Sex chromosome aneuploidy Turner Syndrome (45,X) Peripheral oedema at birth Short stature Primary amenorrhoea (streak ovaries) Usually normal intelligence B. Structural chromosome abnormalities Deletion Duplication Inversion Chromosome translocation  Fluorescent in Situ Hybridisation (FISH) Targeted probe Largely replaced by molecular cytogenetics Del22q11 del22q11.2 syndrome/ DiGeorge/ velocardiofacial syndrome Congenital heart disease (CHD) Cleft lip and/or palate Absent thymus Absent parathyroid glands Dysmorphic features Learning difficulties  Comparative Genomic Hybridisation Array (aCGH) and SNP arrays Powerful tool for identifying very small genomic imbalances Imbalances may affect individual’s health or development May confer increased susceptibility to certain conditions: Autism spectrum disorder Psychiatric disease Congenital abnormalities  Resolution over time karyotyping array CGH whole genome sequencing resolution From: Stephenson et al J R Soc Interface. Sep 8. 2010  Single gene testing For diagnosis/confirmation of genetic disorders Facilitate management Accurate recurrence risk Reproductive options Prenatal diagnosis (PND) Pre-implantation genetic diagnosis (PGD) Test (carrier or pre-symptomatic) for at risk relatives Example: Duchenne & Becker Muscular Dystrophy http://astronlife.wordpress.com/astron- http://my-beckers- articles/duchenne-muscular-dystrophy-dmd/ story.blogspot.co.uk/2012/07/theprogressionofmuscula rdystrophy.html  Genetic diagnosis Confirmation of clinical diagnosis Reduces need for other investigations In some cases may be the only diagnostic test May help prognostication Recurrence risk Informed choice in future pregnancies Pre-symptomatic testing Gene based therapies – rare (may increase in future) Risk assessment Risk assessment Key aspect of genetic counselling is to provide: Risk figure for an adult onset condition Offspring risk Family members’ risk Accurate estimation of risk requires: Confirmation of the diagnosis Accurate family tree ® information about the pattern of inheritance Genetic tests help refine the risk Options for informed choice in future pregnancy Management Autosomal dominant inheritance Autosomal dominant polycystic kidney disease (AD PKD) Dominant mutant allele is A What is risk to offspring (recurrence risk)? Aa aa I 1 2 II ? 1 Therefore 1 in 2 risk (A or a) that child II.1 will inherit mutation II.1 can inherit allele A or a with equal probability from I.1 Incomplete penetrance Sporadic - often unilateral and unifocal, mutation negative on blood DNA Eg. Retinoblastoma Familial - autosomal dominant, with incomplete penetrance Incomplete penetrance Consider the childhood tumour syndrome - retinoblastoma A treatable dominant condition with a penetrance of 0.8 (4/5) i.e. 80% of all heterozygotes will develop life threatening eye tumours ? Risk of child being affected = probability of inheriting mutant allele x penetrance = 1/2 x 4/5 = 4/10 or 0.4 Variable expression Neurofibromatosis type I (NF1) - the various phenotypic abnormalities which characterise the condition are very variable ©Scion Publishing Ltd X-linked inheritance Carrier female Unaffected 1 in 4 offspring affected ½ daughters are carriers ½ sons unaffected, not a carrier X-linked inheritance (Ocular albinism) Obligate carrier Carrier risk of the consultand is ½ Risk of passing the gene on is ½ Probability of having male offspring approx. 1/2 Risk of having an affected child + ½ x ½ x ½ = 1/8 Autosomal recessive inheritance Unaffected Affected 2 out of 3 are carriers 1 in 4 is affected i.e unaffected sibs have (½ x ½ = ¼ ) a 2/3 carrier risk AR inheritance: example What’s the risk of cystic fibrosis to the couples’ offspring? Affected No family history What’s the risk of cystic fibrosis to the couples’ offspring? Affected No family history Hardy-Weinberg Principle 1908 GW Hardy (Cambridge mathematician) W. Weinberg (German physician) Simple model helps to explain gene frequencies in a population and therefore useful for calculating risks of autosomal recessive disorders Consider the simple case where there are just 2 alleles A and a Frequency A = p Frequency a = q (NB – these frequencies represent the proportion of chromosomes which harbour the allele, NOT the number of people who carry the allele) The Hardy-Weinberg ratios explained Genotype AA Aa aa Frequency: p2 2pq q2 Can be explained by ‘Punnett square’ Female gametes A a Totals: freq p q AA p2 Male AA Aa Gametes A p p2 pq Aa 2pq a q Aa aa aa q2 pq q2  HW Main learning points 1 HW equilibrium for application to autosomal recessive inheritance Allele frequencies at a locus add up to one: p + q = 1 The genotype frequencies sum up to one: p2 + 2pq + q2 = 1 p = frequency of the wild type allele; q = frequency of the recessive allele Allele frequency for a recessive allele can be calculated from the disease incidence = q2, such that the frequency of the recessive allele = square root of q2 = q NOTE: Carrier frequency 2pq is not the same as the recessive allele frequency q Carrier frequency = 2pq NB. this approximates to 2q when q is small (most cases)  HW main learning point 2 Why does carrier frequency approximate to 2q? Carrier frequency =2pq p2 + 2pq + q2 = 1 When q is very small (very low incidence), p is close to 1. Multiplying 2pq when p=~1 is ~2x1xq = 2q  HW example in clinical practice Therefore - For cystic fibrosis: Incidence 1 in 2500 If we assume in HW equilibrium: q2 = 1/2500 √2500=50, therefore q = 1/50 = 0.02 (p = 1-0.02 = 0.98) Carrier frequency = 2pq i.e. 2 x 1/50 (approx) = 1/25 (4%) 2 x 0.98 x 0.02 = 0.0392  CF preconception counselling What’s the risk of cystic fibrosis to the couple’s offspring? No family history Affected Carrier risk 2/3 Population carrier risk 1/25 Offspring risk = probability both parents carriers x ¼ risk offspring is affected Offspring risk = 2/3 x 1/25 x ¼ = 2/300 = 1/150  Genetic diagnosis Confirmation of clinical diagnosis Reduces need for other investigations In some cases may be the only diagnostic test May help prognostication Recurrence risk Informed choice in future pregnancies Pre-symptomatic testing Gene based therapies – rare (may increase in future) Summary of Part II 1. It is important to establish/confirm a genetic diagnosis - To facilitate management, treatment - Reduce number of diagnostic investigations - Assess recurrence risk - Options in future pregnancies - Prognostication 2. Tests for chromosomal abnormalities detect rearrangements at different level resolutions 3. Roles of different genetic tests 4. Risk calculation based on Hardy-Weinberg principle Thank you Slides: courtesy of Dr Dragana Josifova (and Dr. Charlotte Barker) Questions: [email protected] Genomics Education England: www.genomicseducation.hee.nhs.uk British Society for Genetic Medicine: www.bsgm.org.uk/membership/ Unique: Understanding Rare Chromosome and Gene Disorders: www.rarechromo.org/  Opportunities in clinical genetics Special study modules Standalone projects Medical elective Research placements Career (after 4y adult medicine or paediatrics)