All alcohol-dependent cases and controls in the GWAS sample (N = 1,884) are genetically unrelated. Cases (N = 1,192) were diagnosed for DSM-IV alcohol dependence at each clinical assessment if assessed multiple times. Controls (N = 692) were chosen for the GWAS if considered unaffected during their entire lifetimes according to any of the four alcohol dependence criteria. To avoid pleiotropic genetic components that contribute to multiple substance abuse phenotypes, controls for the GWAS also did not meet diagnostic criteria for other illicit substance abuse or dependence. Furthermore, controls were required to be 25 years or older and to have consumed alcohol at some point in their lives to ensure that their unaffected status was not due to lack of exposure to alcohol. Based on the results of a multidimensional (MDS) analysis of genomewide IBS differences, GWAS samples predominantly clustered among two subgroups characterized as being of either European (74.3%; N = 1,399) or African ancestry (25.7%; N = 485) (refer to the section on GWAS genotyping for more detail). Twenty-one individuals did not cluster with either of the two
