We excluded SNPs with call rates of <95%. We also excluded SNPs that deviated from Hardy-Weinberg equilibrium in controls at P < 1 × 10−7, on the basis of a stratified 1-degrre-of-freedom test in which the deviations were summed across strata67. We also excluded SNPs for which the genotypes were discrepant in more than 2% of duplicate samples across all COGS consortia. The final analyses were based on data from 199,961 SNPs.
