Alcohol dependence is a phenotypically heterogeneous disorder which runs in families and which has a high genetic loading. Twin and adoption studies have shown that 40-60% of the inter-individual phenotypic variance is accounted for by genetic factors.3-5 In congruence with the observed phenotypic heterogeneity of alcohol dependence, vulnerability to alcohol dependence on the molecular level is thought to be mediated by many genetic loci of small to modest effects in Europeans.6-14 Despite strenuous efforts and numerous linkage and candidate gene studies, identification of the underlying susceptibility genes has proven difficult. Genome-wide association studies (GWAS) conducted in other complex disorders have been shown to be a successful tool in identifying underlying susceptibility genes (for all published GWAS see: http://www.genome.gov/26525384) and have already resulted in the identification of genetic susceptibility variants for psychiatric disorders such as nicotine addiction, schizophrenia and bipolar disorder15-24 which were mostly not detected through other diagnosis based discovery approaches. For alcohol dependence, only one GWAS using pooled DNA samples has been published to date, and it has proposed several new susceptibility loci for alcohol dependence. Their products are
