Given the positive evidence of the genetic comparability of these cohorts, we completed a GWA meta-analysis of 9.6 million imputed SNPs in 135,458 MDD and major depression cases and 344,901 controls (Fig. 1). There was no evidence of residual population stratification24 (LD score regression intercept 1.018, SE 0.009). We estimated hSNP2 to be 8.7% (SE 0.004, liability scale, assuming lifetime risk 0.15, Supplementary Table 3b and Supplementary Fig. 1), and note that this is about a quarter of h2 estimated from twin or family studies9. This fraction is somewhat lower than that of other complex traits18, and is plausibly due to etiological heterogeneity (and reflecting the mean rg <1 between cohorts).
