Resequencing of Nicotinic Acetylcholine Receptor Genes and Association of Common and Rare Variants with the Fagerström Test for Nicotine Dependence

Abstract

Common single-nucleotide polymorphisms (SNPs) at nicotinic acetylcholine receptor (nAChR) subunit genes have previously been associated with measures of nicotine dependence. We investigated the contribution of common SNPs and rare single-nucleotide variants (SNVs) in nAChR genes to Fagerström test for nicotine dependence (FTND) scores in treatment-seeking smokers. Exons of 10 genes were resequenced with next-generation sequencing technology in 448 European-American participants of a smoking cessation trial, and CHRNB2 and CHRNA4 were resequenced by Sanger technology to improve sequence coverage. A total of 214 SNP/SNVs were identified, of which 19.2% were excluded from analyses because of reduced completion rate, 73.9% had minor allele frequencies <5%, and 48.1% were novel relative to dbSNP build 129. We tested associations of 173 SNP/SNVs with the FTND score using data obtained from 430 individuals (18 were excluded because of reduced completion rate) using linear regression for common, the cohort allelic sum test and the weighted sum statistic for rare, and the multivariate distance matrix regression method for both common and rare SNP/SNVs. Association testing with common SNPs with adjustment for correlated tests within each gene identified a significant association with two CHRNB2 SNPs, eg, the minor allele of rs2072660 increased the mean FTND score by 0.6 Units (P=0.01). We observed a significant evidence for association with the FTND score of common and rare SNP/SNVs at CHRNA5 and CHRNB2, and of rare SNVs at CHRNA4. Both common and/or rare SNP/SNVs from multiple nAChR subunit genes are associated with the FTND score in this sample of treatment-seeking smokers.

CHRNA5/A3/B4 Variant rs3743078 and Nicotine-Related Phenotypes: Indirect Effects Through Nicotine Craving

“…Thus, the FTND score ranged from 0 to 8. The mean FTND (3.4) was within the range of mean scores (2.8-4.6) from 15 general population studies in Europe and the United States (Fagerström & Furberg, 2008) and lower than scores reported in clinical samples (Wessel et al, 2010).…”

“…Although rs16969968 is considered robustly associated with CPD based on meta-analyses in populations of European origin (Furberg et al, 2010;Liu et al, 2010;Saccone et al, 2010), some of the individual data sets within the meta-analyses did not show a significant association between rs16969968 and CPD (e.g., Figure 1 in Saccone et al, 2010). Although previous studies showed an association between rs16969968 and FTND (reviewed in Ware et al, 2012), other studies did not find evidence for this association (Sherva et al, 2010;Wessel et al, 2010); evidence for this association is less robust than for CPD. As additional evidence accumulates from diverse populations with different genetic backgrounds and motivations for smoking, the relationship between rs16969968 and smoking phenotypes may become better understood.…”

Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses

“…[24][25][26][27][28] These studies come to similar conclusions: that it is not a single variant acting alone that is causal, but rather sets of variants. 24,25,28 The sets they identified are rare variants that overlap with functional annotations such being missense or nonsynonymous variants.…”

“…24,25,28 The sets they identified are rare variants that overlap with functional annotations such being missense or nonsynonymous variants. Several of these previous studies focused only on exons, [24][25][26]29 and therefore would have missed 22 out of 27 (81.5%) of the single locus top findings and 23 out of 33 (69.6%) variant set top findings. To our knowledge, none of these previous investigations examined the role regulatory variant sets may play in smoking.…”

Translational Research in Nicotine Dependence

“…For example, SNPs in CHRNA6 and CHRNB3, the genes encoding the a6 and b3 subunits, have been associated with nicotine dependence, subjective response to nicotine, and self-reported number of unsuccessful quit attempts (Bierut et al 2007;Greenbaum et al 2006;Saccone et al 2007;Zeiger et al 2008;Hoft et al 2009). Additional studies have implicated the gene encoding for the a4 subunit, CHRNA4, in various smoking phenotypes (Breitling et al 2009;Wessel et al 2010;Han et al 2011;Xie et al 2011). Furthermore, polymorphisms in the CHRNA4 gene have been significantly associated with abstinence rates while on nicotine replacement therapy (Hutchison et al 2007) or varenicline (King et al 2012), suggesting a potential role for CHRNA4 as a target for therapeutic intervention.…”