Of the 909,622 SNP probes, 874,517 (HPFS), 879,071 (NHS) and 841,820 (ARIC) passed quality control analysis by the Broad Institute and the GENEVA Coordinating Center (excluding SNPs with missing call rate ≥ 5% or plate association P < 1×10−10)9. We further excluded SNPs with missing rate ≥ 2%, > 1 discordance in the duplicated samples, Hardy-Weinberg equilibrium P < 1×10−3 or minor allele frequency < 0.01. A total of 687,398 (27,578), 665,163 (24,108) and 593,521 (23,664) autosomal (X-chromosome) SNPs were retained for the HPFS, NHS and ARIC cohorts, respectively, 565,040 (21,858) of which were in common across the three cohorts.
