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MUS2046 Genetics in Medicine Finding disease genes Cathryn Lewis Professor of Genetic Epidemiology and Statistics

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Introduction to genetics: 1 DNA structure

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www.onlineeducation.net/dna Introduction to genetics: 2 DNA sequence

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What makes us different? These differences control our hair colour, our height, and the diseases we will get Introduction to genetics: 3 DNA differences

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Complex disease: contributions from genetic and environmental factors Gene4 Env4 Env3 Env2 Env4 Disease Env1 Gene8 Gene7 Gene6 Gene5 Gene4 Gene3 Gene2 Gene1 Examples: asthma, breast cancer, heart disease, autism, arthritis, migraine, obesity, diabetes, stroke Most diseases that have a major economic, social and health burden

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Complex Diseases Raised risk in families But increase in risk may be slight compared with population risk Can be measured by the sibling relative risk No clear mode of inheritance Multiple genes Environmental effects Gene-gene, gene-environment interactions Examples Inflammatory bowel disease, multiple sclerosis, depression, asthma, rheumatoid arthritis, diabetes, heart disease,.... Most diseases that have a considerable public health impact

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Genetic Association Study A genetic association study tests whether the presence of a specific genetic variant correlates with a trait of interest (such as risk of disease) A SNP has two alleles: C, T Each individual has a genotype at this SNP CC, CT or TT

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Genetic variation: Single nucleotide polymorphism (SNP) Alleles A and C are present in the population Genotype : carried by an individual, on paternal and maternal inherited chromosomes....TGGACCTGCA........TGGACATGCA........TGGACCTGCA........TGGACATGCA........TGGACATGCA........TGGACCTGCA.... Genotype: AA ACCC

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Genetic Association Study A genetic association study tests whether the presence of a specific genetic variant correlates with a trait of interest (e.g. presence/absence of disease)

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Identifying SNPs that increase risk of disease Cases affected with disease Controls not affected with disease Genotype SNP with A, C alleles: AAACCC More AC and CC genotypes in cases than in controls Indicates that carrying C allele increases risk of disease

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Case control studies Compare frequency of SNP alleles or genotypes in a series of cases and controls Cases Diagnosed with disease Ascertainment - through hospital or community? Define criteria for inclusion in study Controls Unaffected with disease (supernormal controls) Randomly ascertained (e.g. blood donors) Both types of controls are valid Important to match cases and controls on genetic ancestry if not, genetic differences between cases and controls may reflect their ancestry, not their disease status

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Association of PTPN22 mutation with rheumatoid arthritis (RA) Steer et al., Arthritis Rheum, 2005 RA is a complex disease with a sibling relative risk of approximately 3, and a strong HLA effect PTPN22 encodes a protein tyrosine phosphatase which interacts with the negative regulatory kinase Csk to inhibit T cell signalling and activation The R620W mutation was shown in other studies to increase risk of RA Association study of R620W performed in London RA patients 302 RA cases (hospital-ascertained) and 374 controls, all of European ancestry

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Association of PTPN22 mutation with RA Significant difference in allele frequency (p=3 x 10 -5 ) 17.2 (3.8-77.8) 1.7 (1.2 2.5) 1Odds ratio (95% CI) 15.9%12 4% 72 24% 218 72% Cases (n=302) 8.4%1 0.3% 61 16% 312 83% Controls (n=374) Freq. of T allele TTCTCC Odds ratio of CT genotype compared to CC genotype = 312 x 72 / (218 x 61)

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Association of PTPN22 mutation with RA 17.2 (3.8-77.8) 2.05 (1.47- 2.88) 1Allelic Odds ratio (95% CI) 15.9%12 4% 96 16% 508 84% Cases (n=302) 8.4%1 0.3% 63 8% 685 92% Controls (n=374) Freq. of T alleleTTTC Odds ratios for genotypes CC, CT, TT are 1, r, r 2 Here, OR for CC 1 (baseline), OR for CT=2.05, OR for TT = 4.02

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Rheumatoid arthritis: contributions from genetic and environmental factors STAT4 TRAF1 PTPN22 Gene4 ? Sex Age Env4 Rheumatoid arthritis Smoking HLA TNFAIP3 CD40 CTLA4 Other genes Now over 100 genes identified that are associated with rheumatoid arthrtis

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Genome-wide association studies (GWAS) SNP chips from Illumina and Affymetrix will genotype up to 1 million SNPs across the genome Capture most of the variation across the genome

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WTCCC (2007) Nature 447: 661-78

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Steps in WGA study Design study Collect samples Define phenotypes Type DNA on whole-genome panel Quality Control (QC) SNP-by-SNP analysis Interpret results Replicate, perform meta-analysis

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GWAS analysis methods SNP-by-SNP analysis against phenotype Analysis of genotype counts Regression analysis of quantitative trait Logistic regression of case-control status on SNP genotype, ancestry covariates, phenotypic covariates, environmental factors.... Problems of multiple testing with 500K SNPs

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25000 p-values