LDSC was used in two ways: 1) to identify genetic correlations and SNP-based heritability within each of the depression cohorts and phenotypes (Table S5); and 2) to identify genetic correlation with other traits based on the primary meta-analysis (MDD-META). Heritability in the primary MDD-META analysis was 11.3% (z= 29.63, sample prevalence 28.6%, population prevalence 20%), while heritability in the secondary analyses of self-reported depression (SR-depression, see online methods) and PHQ-2 were 7.8% (z=28.74, sample prevalence 27.1%, population prevalence 20%) and 5.5% (z=14.0), respectively. Genetic correlation between depression phenotypes ranged from 0.59 to 1.21, with lower rg identified between measures of depressive symptoms and case-control phenotypes (Figure 2 Upper). Some of the genetic correlations from the LD score regression were greater than one; genetic correlation from LDSC does not bound to one,13 and the instances with values higher than one occurred when testing in the same sample with similar phenotype (rg 1.07, SE=0.0343) between MDD and SR-Depression within MVP), or between the somewhat smaller FinnGen sample and the large PGC/UKB broad depression (rg 1.21, SE=0.25) and 23andMe (rg=1.07, SE=0.21) samples. LD-intercept
