While our results indicate an overall strong rg between PTSD and MDD (rg = 0.85, s.e. = 0.008, P < 2 × 10−16), the correlation between PTSD and MDD varied significantly across PTSD subsets, with the most homogeneously assessed subset, MVP, showing the lowest correlation, and the biobank subset being most strongly associated (Supplementary Table 24). Further, to evaluate if specific genetic regions differ substantially from genome-wide estimates, we used LAVA53 to estimate the local h2SNP and rg of PTSD and MDD across the genome, as partitioned into 2,495 approximately independent regions (Supplementary Table 25). Local h2SNP was significant (P < 0.05/2,495) for both PTSD and MDD in 141 regions. Of these, local rg was significant (P < 0.05/141) in 40 regions, all in the positive effect direction, where the mean local rg was 0.57 (s.d. = 0.24). In addition, we assessed the local rg between PTSD and MDD specifically for the 76 autosomal GWS EA loci (Supplementary Table 26). While LAVA identified 20 significantly correlated loci (rg < 6.58 × 10−4), there was also evidence for PTSD loci lacking evidence for correlation with MDD (Supplementary Figs. 9 and 10 showcase 6 selected loci with low and high rg).
