Population Genetics Charlotte Alston NCG Mitochondrial Diagnostic Laboratory Newcastle upon Tyne

1. Population Genetics Charlotte Alston NCG Mitochondrial Diagnostic Laboratory Newcastle upon Tyne

2. Keywords: Population stratification Heterozygote advantage Random genetic drift Founder effect Penetrance Expressivity Tay Sachs Ellis-van-Creveld syndrome Huntington’s disease m.4300A>Gmt-tRNAIle Cystic Fibrosis

3. Describe the following terms with examples of how each factor can influence human disease. ►Population stratification ► Heterozygote advantage (include examples other than sickle cell) ► Random genetic drift ► Founder effect ► Penetrance ► Expressivity

4. Population Stratification Any of the reasons why allele frequencies deviate from the expected rates. Explains why allele frequencies differ when populations are compared to simple models of e.g. Hardy-Weinberg In genome wide association studies, population stratification can result in false positive or negative associations.

5. Population Stratification Hardy-Weinberg p2+2pq + q2 = 1 and p + q = 1 p = frequency of the dominant allele in the population q = frequency of the recessive allele in the population p2 = percentage of homozygous dominant individualsq2 = percentage of homozygous recessive individuals2pq = percentage of heterozygous individuals

6. Population Stratification Hardy-Weinberg p2+2pq + q2 = 1 and p + q = 1 Assumptions: No new mutations Stable gene pool (no migration of individuals in or out of the population) Random mating Describes a large population (no genetic drift) No selection can occur - for or against alleles

7. Population Stratification – Tay Sachs disease Carrier frequency for Ashkenazi Jewish: 1 in 25 Vs. Carrier frequency in non-Ashkenazi Jewish: 1 in 250 The allele frequency between both populations differs dramatically; mainly due to absence of random mating. Ashkenazi Jewish population tend to reside together and marry other members of the Ashkenazi Jewish community.

8. Random Genetic Drift Genetic drift operates randomly while natural selection functions non-randomly. By comparison, natural selection lowers the frequencies for alleles that cause unfavourable traits, and ignores those which are neutral. Random genetic drift refers to allele frequencies altering across successive generations without regard to fitness pressures imposed by the environment (i.e. no selection for or against) During meiotic segregation, the chance of transmitting a particular allele to the offspring is 50% and creates variation in successive generations and epitomises random genetic drift. In small populations, this random sampling can lead to chance allelic associations.

9. Random Genetic Drift Founders 3/8 alleles 5/12 alleles 4/10 alleles 5/20 alleles 6/24 alleles 7/28 alleles Random growth of a randomly breeding population with 10% growth/generation. Allele frequencies (red vs. blue) fluctuate due to both the random number of offspring from each individual and because of the randomness of meiosis.

10. Heterozygote Advantage Why are deleterious mutations not lost from the gene pool? “One of the important things to realise about heterozygote advantage is that it doesn't matter how disadvantageous the homozygous form is, as long as the heterozygote has an advantage over the other homozygote.” Heterozygote advantage refers to the heterozygote genotype having greater fitness than either of the homozygous genotypes Loss-of-function mutations tend to be recessive Dominant LOF mutations generally prevent the organism from reproducing therefore removes the mutation from the gene pool of the next generation

11. Heterozygote Advantage – Cystic Fibrosis Caused by mutations in the CFTR gene; affects chloride channels. Homozygous mutants have cystic fibrosis; enhanced sodium ion absorption; thick, sticky mucus in lungs → chest infections; pancreatic insufficiency. Avg life expectancy now 38yrs due to advances in intervention and screening programs. Historically, homozygotes would have died during childhood; before reproducing.

12. Heterozygote Advantage – Cystic Fibrosis Why haven't mutations in the CFTR gene been lost from the gene pool due to natural selection? Theories: 1967: CF heterozygotes had higher successful childbirth rate 1994: CF heterozygote mouse model proves to have selective advantage during cholera infection. Vibrio cholerae toxins open the transmembrane regulating ducts of small intestine. In wildtype individuals, excretion of chloride ions and water causes dehydration => fatal Carriers are resistant to this action; pump out half as much water during cholera infection => better hydrated => survival

13. Heterozygote Advantage – Tay Sachs disease Unknown as to whether Tay Sachs mutations are associated with heterozygote advantage… Carriers are hypothesised to be more resistant to tuberculosis; one (retrospective) study found death rates from TB were much lower in grandparents of children with two mutant TSD alleles vs. those who had no descendents with TSD. Cause or effect?One source of bias is the exclusion of carriers, “cases" are affected. Also could be explained by Ashkenazi Jews living in urban areas where TB was prevalent, resulting in greater selective pressures to evolve TB resistance. Possibly not heterozygote advantage, but a combination of founder effect, genetic drift, and immigration patterns.

14. Founder Effect A disease-associated mutation which is present in higher than expected frequency caused by a single mutational event which has been transmitted through an isolated (or once isolated) population Opposed to the mutation arising independently multiple times

15. Founder Effect Tay-Sachs disease (TSD) Autosomal recessive lysosomal storage disorder HEXA gene on chromosome 15 encodes the alpha-subunit of the lysosomal enzyme beta-N-acetylhexosaminidase A Classical TSD - paediatric onset (~6mnths) Degenerative condition Symptoms: cherry red macula; developmental regression; paralysis; dementia; blindness. There is no treatment, and average life expectancy is 2-3 years

16. Founder Effect Tay-Sachs disease (TSD) in Ashkenazi Jewish Carrier frequency: 1 in 25; ~ 1 in 200 in non-Jewish populations TATC insertion in exon 11 causing a PTC → Nonsense mediated decay of mRNA transcript The high incidence of the c.1278insTATC mutation is hypothesised to be due to random genetic drift, which further amplified a high frequency mutation present in an early founder population

17. Founder Effect Ellis-van-Creveld syndrome in Amish populations Caused by mutations in EVC gene. Symptoms: polydactyly, congenital heart defects (60% of affected individuals have an atrial septal defect => common atrium) and numerous bone malformations. Small Amish population migrated to Pennsylvania in 1744, two founder members were carriers of Ellis–van Creveld syndrome. The colony and their descendants were relatively insular on grounds of religion; the inbreeding resulted in greater prevalence of Ellis-van Creveld syndrome amongst the Amish vs. the general population.

18. Founder Effect Huntington’s disease in Tasmania Incidence of HD is fairly evenly distributed throughout Australia Exception being Tasmania, with an unusually high frequency of HD in one large clan of English descent. Tracked back 9 generations to a single ancestor with HD who emigrated from Somerset.

19. Penetrance Penetrance is defined as the percentage of individuals with a given genotype who exhibit the phenotype associated with that genotype. The likelihood of a phenotype being present or absent Affected vs unaffected Expressivity The scale of a gene’s expression or the severity of a phenotype Affected, but how badly

20. Penetrance vs Expressivity

21. Penetrance in human disease - Huntington’s disease CAG triplet repeat disorder; Exon 1 of IT15 gene. Normal alleles are ≤26 CAG repeats CAG allele sizes of >40 are fully penetrant - all patients will develop HD CAG allele sizes 36–39 repeats have reduced penetrance. - quoted as 67% penetrance rate by age 70 years. Intermediate alleles 27–35 CAG repeats not associated with HD - meiotically unstable in sperm → resulting in paternal expansion and affected offspring.

22. Penetrance in human disease – Maternally inherited cardiomyopathy Homoplasmic m.4300A>G mtDNA mutation in MTTI Associated with maternally inherited cardiomyopathy; variable penetrance in two large families Heteroplasmy (wt and mt mtDNA molecules) typically explains variation in expression associated with mtDNA mutations but as m.4300A>G is homoplasmic, a nuclear defect must explain penetrance.

23. Penetrance in human disease – Maternally inherited cardiomyopathy Transnuclear cardiomyocyte studies have shown both mtDNA and nuclear DNA are required to cause biochemical defect.

24. Expressivity Different degrees of expression may be due to: Allelic variants – e.g. p.Arg117His & 5T variant in CF associated with milder phenotype, but associated with CBAVD in males Environment effect – e.g. exposure to aminoglycoside antibiotics in conjunction with the otherwise neutral m.1555A>G mtDNA variant can cause sensorineural deafness

25. References Huang HY, Lee WC.A triple combination strategy corrects population stratification bias and saves genotyping cost.J Clin Epidemiol. 2010 Nov 12. [Epub ahead of print] Quarrell OW, Rigby AS, Barron L, Crow Y, Dalton A, Dennis N, Fryer AE, Heydon F, Kinning E, Lashwood A, Losekoot M, Margerison L, McDonnell S, Morrison PJ, Norman A, Peterson M, Raymond FL, Simpson S, Thompson E, Warner J. 2007. Reduced penetrance alleles for Huntington’s disease: A multi-centre direct observational study. J Med Genet 44:e68. Nahhas F, Garbern J, Feely S, Feldman GL. An intergenerational contraction of a fully penetrant Huntington disease allele to a reduced penetrance allele: interpretation of results and significance for risk assessment and genetic counseling. Am J Med Genet A. 2009 Feb 15;149A(4):732-6. Griffiths AJF, Miller JH, Suzuki DT, et al. An Introduction to Genetic Analysis. 7th edition. New York: W. H. Freeman; 2000. Gabriel SE, Brigman KN, Koller BH, Boucher RC, Stutts MJ. Cystic fibrosis heterozygote resistance to cholera toxin in the cystic fibrosis mouse model. Science. 1994 Oct 7;266(5182):107-9. Davidson MM, Walker WF, Hernandez-Rosa E, Nesti C. Evidence for nuclear modifier gene in mitochondrial cardiomyopathy. J Mol Cell Cardiol. 2009 Jun;46(6):936-42. Epub 2009 Feb 21. Pridmore SA. The large Huntington's disease family of Tasmania. Med J Aust. 1990 Nov 19;153(10):593-5. NH Barton; DEG Briggs, JA Eisen, DB Goldstein, NH Patel. Evolution pp 414-415. ISBN 978-087969684-9