Supplementary Table 3 summarizes the numbers of cases and controls in PGC29 and the six additional cohorts. The most direct and important way to evaluate the comparability of these cohorts for a GWA meta-analysis is using SNP genotype data. 22,24 We used LD score (LDSC) regression (described below) to estimate hSNP2 for each cohort (Supplementary Table 3 and Supplementary Fig. 1), and rg for all pairwise combinations of the cohorts (Supplementary Table 3b), and to demonstrate no evidence of sample overlap. We used leave-one-sample-out genetic risk scores (GRS) finding significant differences in case-control GRS distributions of the left-out-sample for all-but-one PGC29 samples (Supplementary Table 4). For full details of the cohort comparability analyses including GRS analyses see the Supplementary Note. In GRS analyses the discovery sample is the GWA sample that provides the allelic-weightings for each SNP used to generate a sum score for each individual in the independent target sample.
