Genotypes for a total of 29 SNPs in the GAD1 (N = 12) and GAD2 (N = 17) genes were obtained as part of a large candidate gene study using an Illumina custom genotyping array designed in Dr. David Goldman's Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism. Detailed information of array design, genotyping and SNP selection are described elsewhere (Hodgkinson et al., 2008). In brief, for each gene selected, a genomic region including 5 kb upstream and 1 kb downstream was retrieved from NCBI Human Genome Build 35.1 and minimum index SNPs that represented maximum haplotype information for each gene were selected. The performance of the initially selected SNP set was validated by the manufacturer and replacements made where necessary. None of the selected 12 SNPs in GAD1 are coding SNPs, and two of them are at 5′ of the gene (around 1 kb and 3 kb upstream, respectively). One selected SNP in GAD2 is a coding SNP (rs2839673, locates in exon 6; A/G polymorphism codes for Glu/Gly) with a low minor allele frequency (0.01) in the present sample.
