SNPs were genotyped using the Illumina Golden Gate custom genotyping method by the Microarray Core of the Genome Sequencing Center at Washington University (Director, Dr. Seth Crosby). For the Golden Gate data, clustering was performed using the default algorithm in BeadStudio (Illumina; San Diego, California) and manually reviewed by two technicians. Using the filter function in Bead Studio, we removed SNPs with a call frequency of less than 95% (N=3) and SNPs for which Hardy-Weinberg equilibrium (HWE) was rejected (p<0.05; N=2). Thus, genotyping results for 56 nicotinic receptor SNPs and 200 population SNPs were used in this study. No genotyping results were obtained for 102 samples, leaving 1479 heavy smokers and 1419 light smokers for analyses.
