Independent replication of SNPs demonstrating evidence of significant association in the COGA sample was evaluated in the Study of Addiction: Genetics and Environment (SAGE) sample. SAGE is a case-control sample comprised of three complementary studies: COGA, the Family Study of Cocaine Dependence and the Collaborative Genetics Study of Nicotine Dependence (Bierut, 2010). There were 129 individuals from the 118 COGA families in the current study that overlapped with the SAGE sample, and were removed from the SAGE replication dataset. The remaining independent SAGE sample used for replication was limited to 2,647 individuals of European American descent. Factor analysis scores from Mplus were independently estimated for this study, as described above, based on DSM-IV dependence criteria for the 4 substances. Analyses were implemented in Plink and included age at interview and gender as covariates.
