We excluded 11 of the total 487 GWAS cases with alcohol dependence from further analyses. Of these, six DNA samples failed to genotype, and, in five subjects, the genome-wide IBS score was above 1.60, indicating possible cryptic relatedness. Of the 561,466 SNPs genotyped per individual, 99.6% passed quality control (QC). The final data set was comprised of 524,396 SNPs (511,701 autosomal and 12,695 sex-linked markers) in a total of 476 male cases and 1,358 male controls. The mean call rate of the final set of SNPs (cases and controls) was 99.76% (±0.45%).
