A subset of the replication sample (n=931, including 672 cases and 259 controls) of AAs were also genotyped by the Illumina Omni1-Quad platform at CIDR (690 subjects) or the Yale Keck center (241 subjects) for our ongoing GWAS study of alcohol, cocaine, opioid, and nicotine dependence. Genotype information from these subjects were used to control for the potential population stratification in association test in AAs (The prioritized SNP rs17664708 was not included on the Illumina Omni1-Quad chip). After QC (SNP call rate ≥ 95%, sample call rate ≥ 97%, MAF ≥ 0.005 in controls, HWE P ≥ value 0.00001 in controls), 2745 AIMs across the whole genome and 188 SNPs located at NRG1 were extracted to estimate the global and local ancestry in this subset of AA samples, respectively.
