an estimate of SNP-based heritability. Pre-computed LD Scores were used, estimated from the European-ancestry samples in the 1000 Genomes Project43. To obtain heritability estimates on the liability scale, sample and population prevalence estimates were used. Sample prevalence estimates were calculated as the proportion of cases in each subset. Population prevalence estimates were derived from the literature48–50. Prevalence estimates used in GCTA-GREML and LDSC are given in Supplementary Table 1. Genetic correlations between meta-analyzed depression subgroups and 200 health-related traits were calculated using bivariate LDSR51, implemented in the LD Hub software52. Traits derived from non-Caucasian or mixed ethnicity samples were removed prior to analysis. False discovery rate (FDR) correction was applied across the 800 tests to correct for multiple testing53.
