In the PGC GWAMA, a logistic regression analysis was used to test the association between MDD and imputed SNP dosages under an additive model and adjusting for study indicators and five principal components (7). In the CHARGE GWAMA, a linear regression analysis was applied to test the association of depressive symptom score on imputed SNP dosages in the contributing studies adjusting for age and sex. Analyses were adjusted for principal components for most but not all cohorts in the CHARGE GWAMA. A P value based meta-analysis was applied in the CHARGE GWAMA (14). Effect size estimates were based on a dichotomous outcome in the PGC and on a continuous outcome in the CHARGE GWAMA. To combine these effect estimates, a P value based meta-analysis weighted by sample size with METAL was used. This method allows different weights for each study and takes into account the direction of effect at each SNP (33). To specify the direction of the effect, the PGC used the logistic regression coefficient beta and the CHARGE used z-scores. Weights were based on the number of the
