GWAS analysis was carried out in the MVP cohorts by logistic regression for MDD and SR-Depression and by linear regression for PHQ2 within each ancestry group and tranche using PLINK 2.0 on dosage data, covarying for age, sex, and the first 10 PCs. A similar GWAS was performed using linear regression in the UK Biobank samples, also using age, sex, and the first 10 PCs for PHQ2.
