For this study, we tested 48 genes which had previously been tested individually on a custom addiction array. The array, developed by Dr. David Goldman, tested a total of 130 addiction candidate genes, selected from multiple functional systems and implicated in substance dependence phenotypes (primarily alcohol, cocaine and opiates). For the array genes, a genomic region containing 5 kb upstream and 1 kb downstream of each candidate gene was retrieved from NCBI (Human Genome Build 35.1) and genotype data from the African population, which is the most diverse, were obtained from HapMap Phase I Rel18 to re-construct haplotypes for each gene using SNPHAP (http://www.gene.cimr.cam.ac.uk/clayton/software/snphap.txt). A double classification tree search algorithm was applied to select minimum index SNPs representing maximum haplotype information and with frequency >0.6% for each gene. Probable functional SNPs (non-synonymous, splice site and putative functional SNPs from the literature) were forced in during the selection process. The performance of the initially selected SNP set was validated by the manufacturer and replacements made where necessary. In total, there were 1536 SNPs on this Illumina array, including 1350 SNPs from
