For the second stage, forty-two promising SNPs from the GWAS were tested for association with theta EROs in a set of 262 genetically informative, multiplex alcohol dependence pedigrees (N = 1,095 individuals). The ethnic composition of the sample based on self-reporting is predominantly European-American (78.5%; N = 862) and African-American (13.9%; N = 153). Both linkage [Reich et al, 1998; Williams et al., 1999; Foroud et al., 2000; Jones et al., 2004] and family-based association analyses [Edenberg et al., 2004; Wang et al. 2004; Edenberg and Foroud, 2006; Jones et al., 2006a; Dick et al., 2007] have been performed previously in these families. Although some members of these families, primarily probands, were included among the GWAS case-controls, overlapping individuals were removed from this family-based sample using the program PEDSYS, and thus the results from each association test are independent.
