Starting with the dbGaP data, additional quality control measures were applied to both the samples and the SNPs. Samples having genotypes for at least 98% of the SNPs were considered for inclusion in analyses. These samples were rigorously checked for cryptic relatedness, population stratification, and related issues. Thirteen additional samples were removed from further analyses due to poor sample quality (n=4) or cryptic relatedness among subjects (n=9). 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. The final European American (EA) sample included 847 alcohol dependent cases and 552 controls (n=1,399 individuals). The African American (AA) sample contained 345 cases and 140 controls (n=485 individuals). The remaining 21 individuals did not cluster with either of the two samples and were not analyzed.
