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UK-GWAS cases (n = 1045) HumanOmniExpress (733202 SNPs)

UK-GWAS cases (n = 1045) HumanOmniExpress (733202 SNPs). NBS Controls (n = 2501) Human1.2M-DuoCustom (900580 SNPs). 1958 BC Controls (n = 2699) Human1.2M-DuoCustom (899696 SNPs). US-GWAS cases (n = 1311) Illumina 550/610/660w BeadChips (548809 SNPs). US-GWAS controls

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UK-GWAS cases (n = 1045) HumanOmniExpress (733202 SNPs)

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  1. UK-GWAS cases (n = 1045) HumanOmniExpress (733202 SNPs) NBS Controls (n = 2501) Human1.2M-DuoCustom (900580 SNPs) 1958 BC Controls (n = 2699) Human1.2M-DuoCustom (899696 SNPs) US-GWAS cases (n = 1311) Illumina 550/610/660w BeadChips (548809 SNPs) US-GWAS controls (n = 3424) Illumina 550/610/660w BeadChips (548809 SNPs) • Samples excluded: • 3 low call rate (< 97%) • 1 abnormal X chr homo rate (> .2 and < .8) • 24 outlying hetero rate (< .33 or > .36 2 sfs) • 14 closely-related (IBD > .185) • 62 divergent ancestry cases (top 2 principal components not within controls’ min/max.) • Samples excluded: • 9 low call rate (< 97%) • 14 abnormal X chr homo rate (> .2 and < .8) • 64 outlying hetero rate (< .31 or > .33 2 sfs) • 7 closely-related (IBD > .185) • 1 divergent ancestry case (top 2 principal components not within controls’ min/max. ) • 4082 of 455569 SNPs excluded: • 0 low call rate (< 95% cases/controls) • 3426 case v control call rates (P ≤ 10-5) • 14 low MAF (< 1% cases/controls) • 642 failed HWE (P ≤ 10-5 controls) • 32641 of 548809 SNPs excluded: • 7301 low call rate (< 95% cases/controls) • 5632 case v control call rates (P ≤ 10-5) • 18397 low MAF (< 1% cases/controls) • 1311 failed HWE (P ≤ 10-5 controls) Meta-analysis of 683365 SNPs (284369 common across all case and control series) Transorce Study: 944 cases, 5197 controls NCI Study: 1271 cases, 3369 controls

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