Haplotypes with copy number and single nucleotide polymorphisms in CYP2A6 locus are associated with smoking quantity in a Japanese population

Abstract

Smoking is a major public health problem, but the genetic factors associated with smoking behaviors are not fully elucidated. Here, we have conducted an integrated genome-wide association study to identify common copy number polymorphisms (CNPs) and single nucleotide polymorphisms (SNPs) associated with the number of cigarettes smoked per day (CPD) in Japanese smokers (N = 17,158). Our analysis identified a common CNP with a strong effect on CPD (rs8102683; P=3.8 x 10(-42)) in the 19q13 region, encompassing the CYP2A6 locus. After adjustment for the associated CNP, we found an additional associated SNP (rs11878604; P=9.7 x 10(-30)) located 30 kb downstream of the CYP2A6 gene. Imputation of the CYP2A6 locus revealed that haplotypes underlying the CNP and the SNP corresponded to classical, functional alleles of CYP2A6 gene that regulate nicotine metabolism and explained 2% of the phenotypic variance of CPD (ANOVA F-test P=9.5 x 10(-52)). These haplotypes were also associated with smoking-related diseases, including lung cancer, chronic obstructive pulmonary disease and arteriosclerosis obliterans.

Figure 1. Manhattan plot showing the significance of association for all CNPs and SNPs in the genome-wide CPD analysis.

The SNPs consist of both Illumina 610K chip and imputed HapMap SNPs. All CNPs and SNPs are plotted on the axis according to their positions on each chromosome against association with CPD on the axis (-value). SNPs and CNPs with -values are highlighted in green. A dark gray line shows the genome-wide significance level after Bonferroni's correction with a total of 2,312,503 SNPs and 4,256 CNPs.

Figure 2. Signal plots before conditioning (a), after conditioning on rs8102683 (b) and after conditioning on rs8102683 and rs11878604 (c).

SNPs and CNPs are plotted on the axis according to their positions on chromosome 19 (NCBI Build 37; hg19) against association with CPD on the left axis (-value). SNPs from the 1000 genomes imputation (phase I; 2011-11-23) are indicated with circles, SNPs genotyped on the Illumina 610K chip are indicated with triangles and CNPs genotyped with PlatinumCNV using the raw signal intensity data from the chip are indicated with diamonds. SNPs in the commonly deleted region (shown by the gray shaded area) are imputed as tri-allelic SNPs with deletions (see Materials and Methods for details). All SNP associations are assessed using allele dosages (the number difference between the A and B alleles; see Materials and Methods), and the CNP associations are assessed using the posterior mean copy number dosage . Recombination rates (cM/Mb) across the region are shown by the purple line plotted against the right axis. The most significant variant of the SNP or CNP for each panel is pink, and the surrounding SNPs and CNPs are color-coded to reflect the strength of LD with the top variant according to the Pearson's values.