heterozygosity or missing rates between cases and controls were excluded. Duplicate samples, samples with a genotyping rate <95%, samples without gender information, or samples where the genotypic gender did not match the phenotype file gender were excluded. LD-based SNP pruning was used to determine a subset of SNPs in approximate linkage equilibrium. This subset of SNPs was used to identify related samples, which were subsequently removed (pi-hat >0.2). The software package EIGENSTRAT was used to detect population substructure by principal components analysis [29]. HapMap phase III release 2 genotypes were added into this analysis in order to determine population outliers. After removal of population outliers, new principal components were calculated. More detailed data on included subjects, genotyping methods, and quality control are available in Text S1 and Table S5.
