QC procedures were performed sequentially on each of the 19 data subsets as follows: monomorphic SNPs and SNPs with missingness >0.05 were removed, and individuals with missingness >0.02 were removed. Individuals with heterozygosity >|0.2| and individuals failing sex checks were removed. SNPs with missingness >0.02 were removed (a more stringent SNP missingness filter was applied after individual level filters). SNPs with differential missingness between cases and controls >0.02 were removed. SNPs failing Hardy–Weinberg equilibrium: controls (P<1 × 10−6) and cases (P<1 × 10−10) were removed. All analyses were performed using second-generation PLINK.18
