Because rs1229984 is not on most GWAS arrays, is relatively uncommon (< 5% minor allele frequency) in populations of European and African descent, and the accuracy of imputation is poor, the association with alcohol dependence has not been detected in several recent genome-wide association studies11, 23–24, including studies in which these subjects were included in this sample11, 24. For example, this SNP was imputed from the GWAS data using BEAGLE25. Though over 98% of the genotyped GG samples are correctly assigned, only 68% of the AG heterozygote and AA homozygote genotypes are accurately imputed. As a result, testing this association required direct genotyping of this SNP.
