Abstract
Coffee is one of the most widely consumed beverages worldwide, and its role in human health has received much attention. Although genome-wide association studies (GWASs) have investigated genetic variants associated with coffee consumption in European populations, no such study has yet been conducted in an Asian population. Here, we conducted a GWAS to identify common genetic variations that affected coffee consumption in a Japanese population of 11,261 participants recruited as a part of the Japan Multi-Institutional Collaborative Cohort (J-MICC) study. Coffee consumption was collected using a self-administered questionnaire, and converted from categories to cups/day. In the discovery stage (n = 6,312), we found 2 independent loci (12q24.12–13 and 5q33.3) that met suggestive significance (P < 1 × 10−6). In the replication stage (n = 4,949), the lead variant for the 12q24.12–13 locus (rs2074356) was significantly associated with habitual coffee consumption (P = 2.2 × 10−6), whereas the lead variant for the 5q33.3 locus (rs1957553) was not (P = 0.53). A meta-analysis of the discovery and replication populations, and the combined analysis using all subjects, revealed that rs2074356 achieved genome-wide significance (P = 2.2 × 10−16 for a meta-analysis). These findings indicate that the 12q24.12-13 locus is associated with coffee consumption among a Japanese population.
Highlights
We analyzed the effects of common variants on coffee consumption from two study populations in the Japan Multi-Institutional Collaborative Cohort (J-MICC) study, namely 6,312 individuals for the discovery stage and 4,949 individuals for the replication stage
We investigated if additional loci associated with habitual coffee consumption might be suggested from our Japanese data using genome-wide association tests including both discovery and replication subjects (N = 11,261), with three sets of adjustment variables: (i) age and sex, (ii) age, sex, and smoking status, and (iii) age, sex, smoking status, and body mass index (BMI)
A meta-analysis of the discovery and replication populations, we discovered that 24 novel SNPs on a 12q24 locus had genome-wide significance with habitual coffee consumption
Summary
Revealed that rs2074356 achieved genome-wide significance (P = 2.2 × 10−16 for a meta-analysis) These findings indicate that the 12q24.12-13 locus is associated with coffee consumption among a Japanese population. Five genome-wide association studies (GWAS) have been carried out on coffee or caffeine consumption[13,14,15,16,17]. A GWAS revealed a significant association between PDSS2 and habitual coffee consumption[17] All these studies investigated subjects of European and/or African American ancestry, and no study has been conducted in an Asian population. We conducted a genome-wide association study to identify common genetic variations that affect coffee consumption in a Japanese population
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