Subjects in our three cohorts, Yale-Penn 1-3, were recruited from five eastern US sites to participate in studies of the genetics of drug (opioid or cocaine) or alcohol dependence (see Supplementary Table 1 for the specific relationship between the samples used in the present study and our previous study (2)). These samples contain unrelated individuals and a small proportion of small nuclear families (SNFs) originally collected for linkage studies. All participants provided written informed consent as approved by the institutional review board at each site. Certificates of confidentiality were issued by the National Institute on Drug Abuse and the National Institute on Alcohol Abuse and Alcoholism.