Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence
Hancock, D. B., Reginsson, G. W., Gaddis, N. C., Chen, X., Saccone, N. L., Lutz, S. M., Qaiser, B., Sherva, R., Steinberg, S., Zink, F., Stacey, S. N., Glasheen, C., Chen, J., Gu, F., Frederiksen, B. N., Loukola, A., Gudbjartsson, D. F., Brueske, I., Landi, M-T., ... Stefansson, K. (2015). Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence. Translational Psychiatry, 5, Article e651. https://doi.org/10.1038/tp.2015.149
We conducted a 1000 Genomes-imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerstrom Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry samples. We followed up novel variants in 7469 ever smokers from five independent European-ancestry samples. We identified genome-wide significant association in the alpha-4 nicotinic receptor subunit (CHRNA4) gene on chromosome 20q13: lowest P = 8.0 x 10(-9) across all the samples for rs2273500-C (frequency = 0.15; odds ratio = 1.12 and 95% confidence interval = 1.08-1.17 for severe vs mild dependence). rs2273500-C, a splice site acceptor variant resulting in an alternate CHRNA4 transcript predicted to be targeted for nonsense-mediated decay, was associated with decreased CHRNA4 expression in physiologically normal human brains (lowest P = 7.3 x 10(-4)). Importantly, rs2273500-C was associated with increased lung cancer risk (N = 28 998, odds ratio = 1.06 and 95% confidence interval = 1.00-1.12), likely through its effect on smoking, as rs2273500-C was no longer associated with lung cancer after adjustment for smoking. Using criteria for smoking behavior that encompass more than the single 'cigarettes per day' item, we identified a common CHRNA4 variant with important regulatory properties that contributes to nicotine dependence and smoking-related consequences.