To further determine a genetic contribution of the CHRNA5/A3/B4 cluster to the three smoking-related phenotypes, we performed a gene-gene interaction analysis for the total and male samples as we did previously for nAChR genes alpha 4 (CHRNA4) and beta 2 (CHRNB2) [34] and GABA-B receptor subunits 1 (GABAB1) and 2 (GABAB2) [35]. By using the generalized multifactor dimensionality reduction (GMDR) approach [36], we performed the interaction analysis for all possible combinations of two to six SNPs within CHRNA5/A3/B4 for SI and SC in both the total and the male sample. Among these gene-gene interaction analyses, a significant result emerged only in the male sample for SI, with the best interaction model consisting of SNPs rs7163730 in LOC123688, rs6495308 in CHRNA3 and rs7166158, rs8043123, and rs11072793 from the downstream region of CHRNB4; the corresponding P value was 0.011 (Table 5). Because of the limitation of the current GMDR version, which cannot handle ordinal phenotypes such as SQ, we could not carry out gene-gene interaction analysis on this particular phenotype in our samples. However, we did perform interaction analysis on SQ by employing a cumulative logit model, which revealed no significant interactions of SNPs located in this genomic region in affecting SQ.
