In each individual cohort, association testing was based on an additive logistic regression model using PLINK11. As covariates we used a subset of the first 20 principal components (PCA), derived within each cohort. By default, we included the first 4 PCAs and thereafter every PCA that was nominally significantly associated (p<0.05) to case-control status. PCAs in trios were only used to remove extreme ancestry outliers. We conducted a meta-analysis of the results (including the 9 cohorts comprising African-American and Latino participants) using a standard error inverse-weighted fixed effects model. For chrX, gene dosages in males were scored 0 or 2, in females, 0/1/2. We summarised the associations as number of independently associated index SNPs. Index SNPs were LD independent and had r2 < 0.1 within 3 Mb windows. We recorded the left and rightmost variant with r2<0.1 to an index SNP to define an associated clump. To define loci, we added a 50kb window on each side of the LD clump and combined overlapping LD-clumps into a single locus.
