GWAS was performed with stratification by ancestry group and study. Strata were only analyzed if they had a minimum of 50 cases and 50 controls, or alternatively 200 participants total. Where noted (Supplementary Table 2), small studies of similar composition were jointly genotyped so they could be analyzed together as a single unit. For GWAS, the association between each SNP and PTSD was tested under an additive genetic model, using a regression model appropriate to the data structure. The statistical model, covariates, and analysis software used to analyze each study is detailed in Supplementary Table 30. In brief, studies of unrelated individuals with continuous (case/control) measures of PTSD were analyzed using PLINK 1.988 using a linear (logistic) regression model that included 5 PCs as covariates. For studies that retained related individuals, analyses were performed using methods that account for relatedness. QIMR was analyzed using GEMMA89 v0.96, including the first five PCs as covariates. RCOG was analyzed using the generalized disequilibrium test90. UKBB was analyzed using BOLT-LMM91 including 6 PCs, and batch and center indicator variables as covariates. VETS was analyzed
