Family-based association analyses were performed using PDT (78) as implemented in the program UNPHASED (version 2.404) (31). Individuals were considered affected if they were alcohol dependent on the basis of meeting both DSM-IIIR criteria for alcohol dependence (24) and Feighner criteria for definite alcoholism (25); there were 876 affected and 915 unaffected by this definition. Because of the possibility of shared genetic vulnerability between dependence on alcohol and dependence on other illicit drugs, a secondary analysis was done in which all individuals who were alcohol dependent were considered affected (876), individuals not dependent on either alcohol or illicit drugs were considered unaffected (835), and individuals who were not alcohol dependent but were dependent on illicit drugs were considered unknown (203). We report results using the PDTaverage option, which weighs each family equally in computing the overall test statistic. Linkage disequilibrium between the indel and SNPs previously genotyped in these families (17) was evaluated using HAPLOVIEW (32).
