The pair-wise option of Tagger (de Bakker et al., 2005) (implemented in Haploview: Barrett et al., 2005) with a threshold of r2≥0.8 for most genes was used to select a custom set of 1536 SNPs. The set, selected on the basis of relevance for heroin dependence, provided coverage of 72 candidate genes (see Supplementary Table 1), 47 additional SNPs for which association was previously reported, and 30 ancestry-informative markers (AIMs). The set of 30 ancestry-informative markers (AIMs), distributed physically across the genome, was selected from SNPs for which the greatest allele frequency differences were found between populations with European and East Asian ancestry in Hapmap2 data for use in principal components analyses (AIMs are indicated as such in Supplementary Table 2).
