A blood sample was collected by fingertip puncture and sent to the Alcohol Research Center at Indiana University for genotyping of ALDH2 (rs671, Lys487Glu) and ADH1B (rs1229984, Arg47His) loci. Genotyping was conducted by one of two methods (1) using enzymatic amplification of genomic DNA and allele-specific oligonucleotides (Crabb et al., 1989; Xu et al., 1988) or (2) isolating genomic DNA with the “HotSHOT” method (Truett et al., 2000) using TaqMan probes for allelic discrimination (Applied Biosystems, Foster City, CA; see Hendershot et al., 2009 for additional details). Approximately 30 samples were run using both methods when the laboratory was converting from genotyping by the first method to the second method to verify results matched across protocols. Quality control was maintained by several methods, including a) sample and data management to avoid entering mistakes, b) dedicated equipment and supplies for DNA preparation and robot-assist PCR preparation, and c) the inclusion of eight controls on each 96-well plate: two no template controls, two heterozygous samples, and two of each of the homozygous samples. From previously repeated genotyping results using banked samples, we found the SNP calling to be highly reliable (>99.9%). Any undetermined samples were repeated or sequenced until genotypes were obtained.
