We first performed GWAS of PTSD in American veterans of European (EUR) and African (AFR) ancestry, basing diagnosis on a validated VA EHR algorithm23 that had excellent discriminative ability for lifetime PTSD cases vs. controls as determined by chart review (0.90 sensitivity, 0.97 specificity, 0.87 positive predictive value, and 0.90 negative predictive value), and substantial agreement with gold-standard Clinician-Administered PTSD Scale (CAPS) interview (90.2% agreement and κ = 0.75 (95% CI: 0.62, 0.88))17. GWAS analyses were carried out (on two tranches of data genotyped on the same array platform at two different times) on SNP dosages imputed from 1000 Genomes Phase 3 using logistic regression for case-control traits and linear regression for continuous traits in PLINK 2.024, separately by ancestry, adjusting for age, sex, and the first 10 principal components of ancestry. Meta-analysis by tranche (and later by ancestral group) was performed using METAL25. Combat exposure information was available for only a subset (51.2%) of the sample (Supplementary Table 1), and GWAS of that subset yielded no genome-wide significant (GWS) findings (Supplementary Table 2 shows findings at P < 10−6).
