The genotypic data set of 731 444 SNPs was carefully examined to ensure high quality standards (Turner et al. 2011). In this QC, each SNP was first examined for genotypic completeness. A genotype call score threshold of 0.15 was used, as recommended by Illumina Technical Support, which led to the removal of 1.7% of SNPs from further analysis. For those cases (n = 162, 0.33%) in which duplication or deletion was observed, the entire chromosome harboring this copy number variant was removed from further analysis. Inconsistencies (a non-missing, but different, genotype on the two arrays) of the 544 276 overlapping SNPs on the Illumina Human 1M-Duo and the Illumina Human OmniExpress arrays were tested using the 51 twice-genotyped subjects. We found 571 SNPs with more than one discrepancy and removed those SNPs in all 2322 subjects. Deviations from Hardy-Weinberg equilibrium (HWE) were evaluated using 442 genotyped founders, and SNPs that failed the HWE test at p < 10−6 were removed. SNPs with minor allele frequency less than 0.01 were removed. In total, 634 627 autosomal SNPs were analyzed for association.
