To test the specificity of this most significant locus to alcohol dependence, the associations between this locus and 11 alcoholism or non-alcoholism disorders were tested in other 20 cohorts. These samples included case-control and family-based samples of European or African descent. We imputed this locus (Chr1: 31,425,179–31,732,987) using the same reference panel (i.e., 1,000 genome project and HapMap 3 panel) across all disease groups with the program IMPUTE2 (Howie et al., 2009), reference CEU panel for the samples of European descent and YRI panel for the samples of African descent, respectively, to make the genetic marker sets highly consistent across different samples. This program uses a Markov Chain Monte Carlo (MCMC) algorithm to derive full posterior probabilities, not “best-guess”, of genotypes of each SNP (burnin=10,000, iteration=10,000, k=100 and Ne=11,500). If the probability of one of the three genotypes of a SNP was over the threshold of 0.99, the genotypes of this SNP were expressed as a corresponding allele pair for the following association analysis; otherwise, they were treated as missing genotypes. For SNPs that were directly genotyped, we used the direct genotypes rather than the imputed data.
