Family based association analyses were performed using the Pedigree Disequilibrium test (PDT) (Martin et al., 2000) as implemented in the program UNPHASED (version 2.404) (Dudbridge, 2003). Affected individuals were defined as those meeting criteria for DSM-IV alcohol dependence. The PDT utilizes data from all available trios in a family, as well as discordant sibships. We report results using the PDTaverage option, which weights each family equally in computing the overall test statistic. Analysis was also performed classifying as affected only those DSM-IV alcohol dependence cases who also met criteria for early onset, defined as with the case control sample, as onset by age 22 or younger. After examining results in the family sample, five additional SNPs (cSNPs or SNPs in 3′ UTRs) from regions with evidence for replication were selected for genotyping in the family sample.
