The genotype data from each subsample first underwent separate standard quality control (QC) procedures (not reported here), before undergoing two additional, more stringent rounds of QC for this project (see Supplementary Table 1). In each subsample, we removed SNPs with a MAF <0.01, with a Hardy-Weinberg equilibrium (HWE) test p-value<.001, and a call rate <95% (i.e. missing genotype calls > 5%). We further removed individuals with an overall call rate <95%. Note that the QIMR subsample consisted of data from three genotype platforms - SNP and individual call rates were checked separately for data from each platform prior to this study. After combining the data from all subsamples we performed another round of QC on the total sample, again checking for Hardy-Weinberg equilibrium and SNP call rate. Our final sample included 12,859 individuals and 269,616 SNPs that were genotyped in at least 95% of individuals in the sample.
