GABA system SNPs used in this study were drawn from genome-wide genotyping using the Illumina 660w Quad array, which in the MCTFR sample yielded a total of 527,829 viable SNP markers after quality control filtering. Quality control procedures for SNP markers and DNA samples have been previously described in detail (Miller et al., 2012). Briefly, the most common reasons for excluding markers were minor allele frequency less than 1%, more than two cross-family Mendelian inconsistencies, a call rate below 99%, and a significant deviation from Hardy-Weinberg equilibrium. For SNPs that remained in the analyses after quality control filtering, missing genotypes were replaced with the mean genotypic value for each SNP. The most common reason for excluding DNA samples from analyses was genotype call failure for more than 5000 SNPs.
