A genome-wide association study in the Japanese population identifies the 12q24 locus for habitual coffee consumption: The J-MICC Study

• Published in: Scientific reports Vol. 8; no. 1; pp. 1493 - 11
• Main Authors: Nakagawa-Senda, Hiroko, Hachiya, Tsuyoshi, Shimizu, Atsushi, Hosono, Satoyo, Oze, Isao, Watanabe, Miki, Matsuo, Keitaro, Ito, Hidemi, Hara, Megumi, Nishida, Yuichiro, Endoh, Kaori, Kuriki, Kiyonori, Katsuura-Kamano, Sakurako, Arisawa, Kokichi, Nindita, Yora, Ibusuki, Rie, Suzuki, Sadao, Hosono, Akihiro, Mikami, Haruo, Nakamura, Yohko, Takashima, Naoyuki, Nakamura, Yasuyuki, Kuriyama, Nagato, Ozaki, Etsuko, Furusyo, Norihiro, Ikezaki, Hiroaki, Nakatochi, Masahiro, Sasakabe, Tae, Kawai, Sayo, Okada, Rieko, Hishida, Asahi, Naito, Mariko, Wakai, Kenji, Momozawa, Yukihide, Kubo, Michiaki, Tanaka, Hideo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 24.01.2018; Nature Publishing Group
• Subjects: 38/22; 45/23; 45/43; 631/208/205/2138; 631/67/2324; Asian Continental Ancestry Group - genetics; Beverages; Chromosome 12; Chromosomes, Human, Pair 12 - genetics; Coffee; Coffee - adverse effects; Cohort Studies; Female; Gene Expression Regulation - drug effects; Genetic diversity; Genetic variance; Genome-wide association studies; Genome-Wide Association Study; Genomes; Health risk assessment; Humanities and Social Sciences; Humans; Male; Middle Aged; multidisciplinary; Polymorphism, Single Nucleotide; Population; Population studies; Replication; Risk Factors; Science; Science (multidisciplinary); Surveys and Questionnaires
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-018-19914-w

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.