For PGC cohorts, GWAS were conducted within each cohort using an additive logistic regression model in PLINK v1.9099, covarying for PCs 1–5 and any others as required. Association analyses of the X chromosome were conducted in males and females separately using the same procedures, with males coded as 0 or 2 for 0 or 1 copies of the reference allele. Results from males and females were then meta-analyzed within each cohort. For external cohorts, GWAS were conducted by the collaborating research teams using comparable procedures (Supplementary Note). To control test statistic inflation at SNPs with low minor allele frequency (MAF) in small cohorts, SNPs were retained only if cohort MAF was > 1% and minor allele count was > 10 in either cases or controls (whichever had smaller n). There was no evidence of stratification artifacts or uncontrolled inflation of test statistics in the results from any cohort (λGC = 0.97–1.05) (Supplementary Table 1). Meta-analysis of GWAS summary statistics was conducted using an inverse variance-weighted fixed effects model in METAL (version 2011-03-25)100 across 57 cohorts for the autosomes (41,917 BD
