We used logistic regression to test the association of MDD diagnosis with imputed SNP dosages under an additive model. This test has correct type 1 error with imputed data.51 Covariates included study indicators and five principal components reflecting ancestry. For the MDD replication samples, the top SNP in each region was tested for association, and fixed-effect meta-analysis was used for the replication samples, and for the combination of PGC discovery and replication data.
