Thirty-three SNPs covering the CHRNA5-CHRNA3-CHRNB4 region were genotyped in the additional subjects by the Genome Center at Washington University1. These SNPs were genotyped using Illumina GoldenGate assay as part of a set of 1536 SNPs that included SNPs for checking population stratification and SNPs to follow up several genomic regions. Cleaning was performed using all 1536 SNPs. Four DNA samples had poor call rates (≤63% of the 1536 SNPs) and were dropped. All remaining DNA samples had call rates above 90% and were retained; 99.5% of DNA samples had call rates ≥95%. Twenty samples were included in duplicate. SNPs with more than 1 non-concordant duplicate sample genotype were dropped; the 33 SNPs reported here were 100% concordant. SNPs were also required to pass a call rate threshold of 98%. Self-reported race was verified using EIGENSTRAT [27]. An additional 42 SNPs were genotyped using Sequenom MassArray iPLEX technology2. These SNPs passed a call rate threshold of 95%. Map positions were obtained from the National Center for Biotechnology Information (NCBI) Human Reference Build 36.2 and dbSNP build 129.
