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WHI Imputation update

WHI Imputation update. Shuo Jiao. Status. WHIMS imputation is done 5,696 samples; 584,279 genotyped SNPs that overlaps with reference panel (Omni Express) Imputed to 28,097,484 SNPs; 2,760,266 Indels If we used the same R2 cutoff as implemented in GECCO 1KGP imputation

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WHI Imputation update

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  1. WHI Imputation update Shuo Jiao

  2. Status • WHIMS imputation is done • 5,696 samples; 584,279 genotyped SNPs that overlaps with reference panel (Omni Express) • Imputed to 28,097,484 SNPs; 2,760,266 Indels • If we used the same R2 cutoff as implemented in GECCO 1KGP imputation • MAF>0.01: Rsq>0.3 • 0.005<MAF<0.01: Rsq>0.5 • MAF<0.005: Rsq>0.99 There will be 8,482,425 SNPs that pass the cut-off. R2 maf<0.3 [0.3,0.9) >0.9 <0.1% 10,341,372(36.81%) 3,233,127(11.51%) 442,850(1.58%) 0.1-0.5% 2,224,714(7.92%) 2,173,405(7.74%) 249,285(0.89%) 0.5-1% 325,817(1.16%) 894,765(3.18%) 199,365(0.71%) 1-5% 262,162(0.93%) 1,281,792(4.56%) 1,055,033(3.75%) >5% 143,815(0.51%) 870,726(3.10%) 4,399,256(15.66%)

  3. Next steps • Imputation of Hipfx (550/610) and GARNET (Omni), which have already gone through QC and moved to HG19. • Should be finished by mid of May • The harmonization will happen at the same time as the imputation. After the imputation is done, it will take another week to create a harmonized imputed dataset.

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