Candidate genes for addiction, including the ADH genes on chromosome 4 and the aldehyde dehydrogenase genes ALDH1A1, ALDH1A3 and ALDH2, were selected by a panel of expert members of the NIDA Genetics Consortium for their putative biological significance in addiction (Saccone et al., 2007). The set of SNPs selected to cover candidate genes was derived from Phase II of the HapMap Project. The number of SNPs genotyped was reduced using linkage disequilibrium (LD) binning using the method described in (Carlson et al., 2004). Briefly, SNPs were grouped into “LD bins” in which at least one tag SNP satisfied r2 ≥ 0.8 with every other SNP in the bin. The candidate gene SNP set included tag SNPs for any LD bin that intersected the physical footprint of a candidate gene. Coverage of additional alcohol metabolizing genes (ALDH1L1, ALDH1L2, ALDH1A2, ALDH3B1, ALDH5A1, ALDH6A1, and ALDH18A1) was attained through the genome-wide component of the study (Bierut et al., 2007). Since these genes were not initially targeted in the candidate gene component of the study, SNP coverage is generally sparser. Because this study is
