Single variant analysis (GWAS within each of the 19 data subsets) was performed using an additive model in PLINK, with the first 10 PCs as covariates, on dosage data. Fixed-effects meta-analysis was accomplished using METAL23, 24 with inverse variance weighting. Plotting was performed in R.25 Analyses were completed with both study-specific PCs and with PCs computed within each ancestry group (‘generic’ PCs for AA, EA, LA and separately the two South African data sets), with similar results. Final results in Manhattan, QQ plot, top hits tables and Supplementary Information online use study-specific PCs.
