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WHI Imputation

WHI Imputation. Target GWAS data. WHIMS +, ~5,000-6,000 samples, Illumina Omni express GRANET, ~5,000 samples, Illumina Omni Hipfx , ~4,000-5,000 samples, Illumina 550k-610k SHARE, ~12,000 samples, Affy 6 (already imputed)

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WHI Imputation

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  1. WHI Imputation

  2. Target GWAS data • WHIMS +, ~5,000-6,000 samples, Illumina Omni express • GRANET, ~5,000 samples, Illumina Omni • Hipfx, ~4,000-5,000 samples, Illumina 550k-610k • SHARE, ~12,000 samples, Affy 6 (already imputed) • GECCO, ~4,000 samples, Illumina 550K, 550K duo, 610K, 300K (already imputed) • WHI NCI GWAS, ~1000 samples, not cleaned and will not be included in the current batch of imputations

  3. Reference Panel • Reference Panel: 1000G Phase I Integrated Release Version 2 Haplotypes; downloaded from MACH website • 1092 samples (AFR 246;AMR 181;ASN 286; EUR 379). We used all population because it has been shown to increase the imputation quality of the rare variants. • 36,648,992 SNPs; 3,660,720 indels

  4. Imputation steps • Convert the GWAS data from HG18 to 19 • Matched the strand in GWAS data with 1000 genomes reference panel (forward strand) • Phased each study separately using Beagle • Impute each study using minimac. Will break chromosomes small chunks to facilitate the imputation process; there will be overlapping between neighbouringchunks, which improves accuracy near the edges

  5. Expected output • The imputation program will output the imputed dosage and the imputation quality measure R2 for each SNP. • Previously in imputation of GECCO data, we determined the R2 cutoff by MAF categories to filter SNPs • For MAF>0.01: R2>0.3 • For 0.005<MAF<0.01: R2>0.5 • For MAF<0.005: R2>0.99 • Around 9M SNPs and 1.2M indels left after the filtering • Comparison of SNPs that pass the filtering for Hapmap and 1000 genomes imputation

  6. Timeline • It will take approximately one half month to finish the imputation for each study • So the imputation should be done by the end of May 2013 assuming we get access to GWAS data in a timely manner.

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