We tested 6 SNPs in GABRA2 (major and minor alleles, respectively, shown in parentheses, along with minor allele frequencies): rs497068 (T-C; 0.42), rs279871 (A-G; 0.43), rs279867 (T-G; 0.43), rs279858 (A-G; 0.43), rs279845 (T-A; 0.45), and rs279836 (T-A; 0.43). These SNPs were selected for being among the most significantly associated with alcohol dependence in previous COGA analyses (Edenberg, Dick et al. 2004). The SNPs are highly correlated with each other, with r2 values ranging from 0.82 to 0.99, mean = 0.89; accordingly we expect consistency of results across SNPs. Genotyping was performed at the Genome Technology Access Center at Washington University School of Medicine in St. Louis (http://gtac.wustl.edu/) using an Illumina GoldenGate custom array as part of a larger set of 384 SNPs. All 6 SNPs had a genotyping rate greater than 98% and were in Hardy-Weinberg equilibrium. Because of the relatively few number of SNPs genotyped, we used both PLINK and PREST to examine IBD relationship.
