226 SNPs covering the 16 CHRN genes were analyzed in this study. Initial genotyping was carried out by Perlegen Sciences using custom arrays as previously detailed (Bierut et al., 2007; Saccone et al., 2007a), leading to 119 CHRN SNPs passing quality control (QC) measures including reliability of genotype calls and Hardy-Weinberg equilibrium (HWE) > 0.01. Additional genotyping was then performed by the Center for Inherited Disease Research (CIDR) using Illumina Golden Gate technology (http://www.illumina.com/downloads/GOLDENGATEASSAY.pdf). These additional SNPs were selected for the following purposes. First, SNPs with poor or marginal genotype call rates (<98%) in our initial data were selected for regenotyping; these included some of the 119 SNPs and also SNPs that had already been attempted but did not meet the prior QC requirements. Second, SNPs were selected using our custom tag SNP programs which use r2 bin tagging (Carlson et al., 2004) to enhance coverage of the CHRN genes. Third, we chose additional SNPs to fine-map the strong association signals already seen in the CHRNA5-CHRNA3-CHRNB4 and CHRNB3-CHRNA6 clusters. Prior to analysis, all SNPs were required to have call rates
