At the individual level, samples were removed if the genotyping call rate was <0.98, the absolute value of the heterozygosity F statistic was >0.20, or there was an inconsistency between genetic sex and reported sex. Furthermore, pairwise identity by descent (IBD) analysis was used to identify cryptic relatedness between individuals, and one individual was removed at random from any pair related at the approximate level of first cousins (pi-hat>0.2). Principal component analyses were performed using EIGENSOFT (Price et al. 2006) separately for each sub-population, (Supplementary Methods; Supplementary Figure 2 and 3) and PC plots were inspected to ensure that for every cluster of cases there was a cluster of controls in the same PC space. PCs are visualized separately by sex in order to ensure no subpopulation structure within each sex. After quality control, the total sample comprised 4,038 males and 5,832 females. The numbers of post-QC SNPs and individuals are listed in Supplementary Table 1.
