The COGA GWAS dataset was used to evaluate the gene rankings. It contains 1205 cases and 700 controls [23]. All cases met DSM-IV criteria for alcohol dependence. Controls were defined as individuals who have consumed alcohol, but did not meet any definition of alcohol dependence or alcohol abuse, nor did they meet any DSM-IIIR or DSM-IV definition of abuse or dependence for other drugs (except nicotine). The Illumina human 1M chipset was used for genotyping. Only DNA samples achieving a call rate of > 95% were included. A total of 1,041,465 SNP markers were used for case-control analyses. We conducted population stratification and association analyses using PLINK, a highly flexible, fast, and user-friendly package for GWAS analysis [46]. In our analyses we included only SNPs if their genome-wide failure rate did not exceed 0.05. SNPs were further excluded if minor allele frequency was less than 0.01. After these data filtering processes, 958,380 SNPs were used for further analyses. Then, we mapped these SNPs to non-pseudogenes in the NCBI Entrez Gene database. Specifically, a SNP belongs to a gene if it locates in the region within 10 kb upstream to 10 kb downstream of the gene.
