Abstract
BackgroundThe CHRNA5/A3/B4 gene locus is associated with nicotine dependence and other smoking related disorders. While the non-synonymous CHRNA5 variant rs16969968 appears to be the main risk factor, linkage disequilibrium (LD) bins in the gene cluster carry frequent variants that regulate expression. Pairwise LD and haplotype analyses had identified at least three haplotype tagging SNPs including rs16969968 as main genetic risk factors. Searching for variants with evidence of regulatory functions, we have reported interactions between CHRNA5 and CHRNA3 enhancer variants (tagged by rs880395 and rs1948, respectively) and rs16969968, forming 3-SNP haplotypes and diplotypes that may more accurately reflect the cluster’s combined effects on nicotine dependence (Barrie et al., Hum Mutat 38:112–9, 2017). Here we address further contributions by variants affecting CHRNB4, a possibly limiting component of nicotinic receptors.ResultsWe identify an LD bin (tagged by rs4887074) associated with expression of CHRNB4. Additive logistic regression models indicate that rs4887074 is associated with nicotine dependence and modulates the effect of rs16969968 in GWAS datasets (COGEND, UW-TTURC, SAGE). 4-SNP haplotype and diplotype analyses (rs880395-rs16969968-rs1948 -rs4887074) yield nicotine dependence risk values that further differentiate those obtained with the 3-SNP model. Moreover, both the main G allele of rs16969968 and the minor G allele of rs4887074 (associated with reduced expression of CHRNB4), residing predominantly on common haplotypes that are protective, represent significant allele-specific variance QTLs, indicating that they interact with each other.ConclusionsThese results indicate rs4887074 is associated with CHRNB4 expression, and along with two regulatory variants of CHRNA3 and CHRNA5, modulates the effect of rs16969968 on nicotine dependence risk. Assignable to individuals because of strong LD structures, 4-SNP haplotypes and diplotypes serve to assess the combined genetic influence of this multi-gene cluster on complex traits, accounting for complex LD relationships and tissue-specific genetic effects (CHRNA5/3) relevant to the traits analyzed. The 4-SNP haplotypes account at least in part for previous tagging SNPs, including the highly GWAS-significant rs6495308, located in a distinct pair-wise LD bin but included in protective 4-SNP haplotypes. Our approach refines and integrates the cluster’s overall genetic influence, an important variable when integrating the genetics of multiple genomic loci.
Highlights
The CHRNA5/A3/B4 gene locus is associated with nicotine dependence and other smoking related disorders
Pre-selection of candidate variants across the CHRNA5CHRNA3-CHRNB4 gene cluster To identify putative causal variants, we followed the criteria outlined previously [11] to select variants for CHRNA5/A3/B4: 1. Clinical associations/gene expression (GWAS/eQTL hits): To select genetic variants associated with clinical phenotypes, SNPs derived from NHGRIEBI Genome wide association study (GWAS) Catalog and Genome-Wide Repository of Associations Between SNPs and Phenotypes (GRASP) were preselected with p < 10− 5 and p < 0.05 for GWAS and GRASP, respectively
Candidate variants across the CHRNA5-CHRNA3-CHRNB4 gene cluster identified as eQTLs or GWAS hits The broad search of genomics data on the gene cluster identified 44 candidate SNPs showing evidence for potential function that coalesce into 4 groups representing distinct linkage disequilibrium (LD) bins (Fig 1)
Summary
The CHRNA5/A3/B4 gene locus is associated with nicotine dependence and other smoking related disorders. While the non-synonymous CHRNA5 variant rs16969968 appears to be the main risk factor, linkage disequilibrium (LD) bins in the gene cluster carry frequent variants that regulate expression. The CHRNA5-CHRNA3-CHRNB4 gene cluster on chromosome 15 encodes the α5, α3 and β4 subunits of nicotinic acetylcholine receptors (nAChR). Genetic variants in this cluster, in particular the non-synonymous (ns) SNP of CHRNA5, rs16969968, yields the strongest genome-wide association with nicotine dependence and smoking related disease such as lung cancer [1,2,3,4]. Derived 3-SNP haplotypes served to estimate the combined genetic influence of the gene locus [10]; the presence of additional LD bins suggested as yet undetected multi-SNP haplotypes
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
