A principal component-based analysis was performed in PLINK (Purcell et al., 2007) to cluster these samples along with HapMap reference samples (CEU, YRI, CHB, and JPT) to assign the study subjects to groups of predominantly European and African ancestry. We conducted analyses on the European American (EA) subsample (N=1399) in the interest of reducing genetic and etiological heterogeneity. The somewhat restricted nature of inclusion criteria necessarily limits both case and control sample sizes. Futhermore, exclusion of depressed controls (N=144) and cases whose depression met bereavement exclusion criteria (N=26) resulted in a final GWAS sample size of N=467 comorbid cases (N=287 males and N=180 females) and N=407 unaffected controls (N=132 males and N=275 females). Of the 467 cases, N=181 met criteria for an independent depressive episode – one experienced outside the context of drug or alcohol use – while N=286 reported moderate to heavy alcohol or drug use during the time they experienced depressive symptoms.
