As above, PGS were calculated from the all-ancestries meta-analysis using the p-value P+CT method implemented in PRSice v243 For C+T, the LD estimation was based on the 1000 Genomes Project phase 3 samples (N=503) with European ancestry to match the discovery sample. We fixed the LD r2 threshold at 0.1 and we assessed p-value thresholds (1, 0.5, 0.1, 0.05, 0.005, 5e-3, 5e-4, 5e-5, 5e-6, 5e-7, 5e-8), reporting results for the optimal threshold in each data set. The rl2 was calculated on the liability scale, using an MDD lifetime prevalence estimate of 0.15, by taking the difference of the R2liability of the regression of PGS on the case status with the first ten PCs as covariates, and the R2liability of the null model including the first 10 PCs alone. The confidence intervals for the rl2 were calculated using bootstrapping with 100 iterations.
