SNPs and GWAS Xiaole Shirley Liu STAT 115215

SNPs and GWAS Xiaole Shirley Liu STAT 115/215, BIO/BST 282

Polymorphism • Polymorphism: sites/genes with “common” variation • Locus (location) vs alleles (variations) • Minor allele frequency >= 1%, otherwise called rare variant and not polymorphic • Single Nucleotide Polymorphism – Come from DNA-replication mistake individual germ line cell, then transmitted – ~90% of human genetic variation • Copy number variations – May or may not be genetic 2 STAT 115

SNP Characteristics: Linkage Disequilibrium • Hardy-Weinberg equilibrium – In a population with genotypes AA, aa, and Aa, if p = freq(A), q =freq(a), the frequency of AA, aa and Aa will be p 2, q 2, and 2 pq respectively at equilibrium. – Similarly with two loci, each two alleles Aa, Bb 3 0. 26 ab. STAT 115

SNP Characteristics: Linkage Disequilibrium • LD: If Alleles occur together more often than can be accounted for by chance, then indicate two alleles are physically close on the DNA • Haplotype block: a cluster of linked SNPs • Haplotype boundary: blocks of sequence with strong LD within blocks and no LD between blocks, reflect recombination hotspots 4 STAT 115

Haplotype • Association studies using haplotype is more accurate than using individual SNPs • Haplotype size distribution 5 STAT 115

SNP Profiling • [C/T] [A/G] T X C [A/C] [T/A] – 24 possible haplotype, although often a few common ones explain 90% variations • Tagging (non-redundant) SNPs that capture most variations in haplotypes – reference SNP ID number: rs 12345678 • SNP arrays covering whole genome • Now WES or WGS • Geno-type 2 alleles 6 STAT 115

Association Studies • Association between genetic markers and phenotype – E. g. Cystic Fibrosis ~70% of Cystic Fibrosis patients have a deletion of 3 base pairs resulting in the loss of a phenylalanine amino acid at position 508 of the CFTR gene • Especially, find disease genes, SNP / haplotype markers, for susceptibility prediction and diagnosis 7

Influences individual decisions on life styles, prevention, screening, and treatment 8

Warfarin and CYP 2 C 9: SNPs in Pharmacogenomics • Warfarin anticoagulant drug; CYP 2 C 9 gene metabolizes warfarin. • A patient requiring low dosage warfarin compared to normal population, has an odd ratio of 6. 21 for having 1 variant allele • Subgroup of patients who are poor metabolisers of warfarin are potentially at higher risk of bleeding Break Aithal et al. , 1999, Lancet.

Genome-Wide Association Studies • Quality Control – Unusual similarity between individual – Wrong sex – Trio has non-Mendelian inheritance – Genotyping quality • Two strategies: – Family-based association studies – Population-based case-control association studies 10

Family-based Association Studies Look at allele transmission in unrelated families and one affected child in each Like coin toss, likelihood of fair coin A A a 11 a 0 0

TDT: Transmission Disequilibrium Test • Only heterozygote parents matters, calculate observed over expected • Could also compare allele frequency between affected vs unaffected children in the same family 12

Case Control Studies • SNP/haplotype marker frequency in sample of affected cases compared to that in age /sex /population-matched sample of unaffected controls 13

From Genotyping to Allele Counts 14

Test Significant Associations • Expected: – (24 + 278) * (24 + 86) / (24 + 278 + 86 + 296) = 49 – (278+296) * (86+296) / (24 + 278 + 86 + 296) = 321 • 2 = 27. 5, 1 df, p < 0. 001 15

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Association of Alleles and Genotypes of rs 1333049 with Myocardial Infarction C N (%) G N (%) Cases 2, 132 (55. 4) 1, 716 (44. 6) Controls 2, 783 (47. 4) 3, 089 (52. 6) 2 (1 df) P-value 55. 1 1. 2 x 10 -13 Allelic Odds Ratio = 1. 38 • • OR = 1, no disease association OR > 1, allele C increase risk of disease OR < 1, allele C decrease risk of disease Adjusting for multiple hypotheses testing? Break Samani N et al, N Engl J Med 2007; 357: 443 -453.

Reproducibility of Association Studies • Most reported associations have not been consistently reproduced • Hirschhorn et al, Genetics in Medicine, 2002, review of association studies – 603 associations of polymorphisms and disease – 166 studied in at least three populations – Only 6 seen in > 75% studies 18

Size Matters Visscher, AJHG 2012 19

Unusual Pvalue distributions • Pvalue QQ plot 20 • ? ?

Population Stratification • Population stratification – e. g. some SNP unique to ethnic group – Need to make sure sample groups match – Hidden environmental structure ● ● 21 Two populations have different disease frequency, and different allele frequency. Association picks up the fact they are different populations!

Genotyping Principal Components (PCs) Can Model Population Stratification • Li et al. , Science 2008

IBD: Identity By Descent Test • If two individuals share common ancestor, they will share many SNPs / haplotype blocks on their genome (identical by state: IBS) • IBD are IBS by definition; IBS not necessarily IBD 23

IBD: Identity By Descent Test • Pairwise IBD probability between samples • Probability two individuals share 0 (Z 0), 1 (Z 1), and 2 (Z 2) haplotypes across the genome. • Remove IDBs 24

Detection Power of GWAS 25

Manolio et al. , Clin Invest 2008

Summary • SNP, LD, haplotypes and tagging SNPs • GWAS: – Family based association studies: TDT transmitted allele to affected child – Case control studies: X-sq (allele frequency difference in case and controls) and OR • Increase reproducibility by size and reduce population stratification and IBD 27 STAT 115

Acknowledgement • • • 28 Francisco Ubeda Jun Liu Tim Niu Bo Li Cheng Li Jim Stankovich Teri Manolio David Evans Guodong Wu Stefano Mont Wei Wang Soumya Raychaudhuri • • • Kenneth Kidd Judith Kidd Glenys Thomson Joel Hirschhorn Greg Gibson Spencer Muse Jim Stankovich Teri Manolio Benjamin Neale Enrico Petretto