Subjects were genotyped for the synonymous variant rs1051730 in exon 5 of CHRNA3 and the non-synonymous variant rs16969968 in CHRNA5, the candidate SNPs the most likely to be causal in the 15q region associated with lung cancer in the three published GWAS (3-5). DNA was extracted from lymphocytes and the two variants were genotyped with the TaqMan allele discrimination assay (Applied Biosystems, Foster City, CA). The genotype frequencies were consistent with Hardy Weinberg equilibrium in each ethnic group (p>0.05). Concordance rate across the ∼10% blinded duplicate samples genotyped with the study samples was 100%. The genotyping call rate was 99%. The frequency of the T allele for rs1051730 was 0.34 in European Americans, 0.19 in Native Hawaiians and 0.03 in Japanese Americans. The corresponding frequencies of the A allele for rs16969968 were 0.34, 0.20 and 0.03.
