Role of rare and low-frequency variants in gene-alcohol interactions on plasma lipid levels

Wang, Z.; Chen, H.; Bartz, T.M.; Bielak, L.F.; Chasman, D.I.; Feitosa, M.F.; Franceschini, N.; Guo, X.Q.; Lim, E.; Noordam, R.; Richard, M.A.; Wang, H.M.; Cade, B.; Cupples, L.A.; Vries, P.S. de; Giulanini, F.; Lee, J.; Lemaitre, R.N.; Martin, L.W.; Reiner, A.P.; Rich, S.S.; Schreiner, P.J.; Sidney, S.; Sitlani, C.M.; Smith, J.A.; Dijk, K.W. van; Yao, J.; Zhao, W.; Fornage, M.; Kardia, S.L.R.; Kooperberg, C.; Liu, C.T.; Mook-Kanamori, D.O.; Province, M.A.; Psaty, B.M.; Redline, S.; Ridker, P.M.; Rotter, J.I.; Boerwinkle, E.; Morrison, A.C.; CHARGE Gene Lifestyle Interactions

doi:doi:10.1161/CIRCGEN.119.002772

Background: Alcohol intake influences plasma lipid levels, and such effects may be moderated by genetic variants. We aimed to characterize the role of aggregated rare and low-frequency protein-coding variants in gene by alcohol consumption interactions associated with fasting plasma lipid levels. Methods: In the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, fasting plasma triglycerides and high- and low-density lipoprotein cholesterol were measured in 34 153 individuals with European ancestry from 5 discovery studies and 32 277 individuals from 6 replication studies. Rare and low-frequency functional protein-coding variants (minor allele frequency, <= 5%) measured by an exome array were aggregated by genes and evaluated by a gene-environment interaction test and a joint test of genetic main and gene-environment interaction effects. Two dichotomous self-reported alcohol consumption variables, current drinker, defined as any recurrent drinking behavior, and...Show moreBackground: Alcohol intake influences plasma lipid levels, and such effects may be moderated by genetic variants. We aimed to characterize the role of aggregated rare and low-frequency protein-coding variants in gene by alcohol consumption interactions associated with fasting plasma lipid levels. Methods: In the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, fasting plasma triglycerides and high- and low-density lipoprotein cholesterol were measured in 34 153 individuals with European ancestry from 5 discovery studies and 32 277 individuals from 6 replication studies. Rare and low-frequency functional protein-coding variants (minor allele frequency, <= 5%) measured by an exome array were aggregated by genes and evaluated by a gene-environment interaction test and a joint test of genetic main and gene-environment interaction effects. Two dichotomous self-reported alcohol consumption variables, current drinker, defined as any recurrent drinking behavior, and regular drinker, defined as the subset of current drinkers who consume at least 2 drinks per week, were considered. Results: We discovered and replicated 21 gene-lipid associations at 13 known lipid loci through the joint test. Eight loci (PCSK9,LPA,LPL,LIPG,ANGPTL4,APOB,APOC3, andCD300LG) remained significant after conditioning on the common index single-nucleotide polymorphism identified by previous genome-wide association studies, suggesting an independent role for rare and low-frequency variants at these loci. One significant gene-alcohol interaction on triglycerides in a novel locus was significantly discovered (P=6.65x10(-6)for the interaction test) and replicated at nominal significance level (P=0.013) inSMC5. Conclusions: In conclusion, this study applied new gene-based statistical approaches and suggested that rare and low-frequency genetic variants interacted with alcohol consumption on lipid levels.Show less

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Role of rare and low-frequency variants in gene-alcohol interactions on plasma lipid levels