We selected two SNPs, rs279826 (intron 4) and rs279858 (exon 5, K132K) that capture the information of a long haplotype block of 109 Kb where previous associations have been reported with alcohol dependence and related traits. The two SNPs (rs279826 and rs279858) were genotyped by TaqMan using inventoried assays of primers and probes (Applied Biosystems, ABI, Foster City, CA). The PCR reactions were run in 5ul volume using ABI standard protocol 2.5ul of 2x Master Mix, 0.25ul of 20X primers and probes and 10–20 ng of genomic DNA. The cycling conditions for PCR consisted of 95°C for 10 min followed by 40 cycles of 92°C for 15 sec and 60°C for 1 min. The reactions and fluorescence scan were run on an ABI PRIZM 7900HT Sequence Analyzer. Allelic determination was done using SDS 2.1 (ABI). Probe sequences and allele information are publicly available online www.appliedbiosystems.com. We included twelve duplicates and no discrepancies were observed.
