A genome-wide association study on fish consumption in a Japanese population—the Japan Multi-Institutional Collaborative Cohort study



Although benefits of fish consumption for health are well known, a significant percentage of individuals dislike eating fish. Fish consumption may be influenced by genetic factors in addition to environmental factors. We conducted a genome-wide association study (GWAS) to find genetic variations that affect fish consumption in a Japanese population.


We performed a two-stage GWAS on fish consumption using 13,739 discovery samples from the Japan Multi-Institutional Collaborative Cohort study, and 2845 replication samples from the other population. We used a semi-quantitative food frequency questionnaire to estimate food intake. Association of the imputed variants with fish consumption was analyzed by separate linear regression models per variant, with adjustments for age, sex, energy intake, principal component analysis components 1–10, and alcohol intake (g/day). We also performed conditional analysis.


We found 27 single nucleotide polymorphisms (SNPs) located in 12q24 and 14q32.12 that were associated with fish consumption. The 19 SNPs were located at 11 genes including six lead SNPs at the BRAP, ACAD10, ALDH2, NAA25, and HECTD4 regions on 12q24.12-13, and CCDC197 region on 14q32.12. In replication samples, all five SNPs located on chromosome 12 were replicated successfully, but the one on chromosome 14 was not. Conditional analyses revealed that the five lead variants in chromosome 12 were in fact the same signal.


We found that new SNPs in the 12q24 locus were related to fish intake in two Japanese populations. The associations between SNPs on chromosome 12 and fish intake were strongly confounded by drinking status.

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Fig. 1: A quantile–quantile plot (black) of genome-wide association tests.
Fig. 2: Genome-wide association signals.


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We would like to thank all the staff at the Laboratory for Genotyping Development, Center for the Integrative Medical Sciences, RIKEN, and the staff of the BioBank Japan project. This study was supported by a Grants-in-Aid for Scientific Research for Priority Areas of Cancer (No. 17015018) and Innovative Areas (No. 221S0001), and by JSPS KAKENHI Grants (No. 16H06277) from the Japanese Ministry of Education, Culture, Sports, Science and Technology. This work was also supported in part by a Grant-in-Aid from the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant B Numbers 24390165, 20390184, 17390186. This study was supported in part by funding for the BioBank Japan Project from the Japan Agency for Medical Research and development from April 2015, and the Ministry of Education, Culture, Sports, Science and Technology from April 2003 to March 2015.

J-MICC Research Group

Kenji Wakai22, Kenji Takeuchi22, Haruo Mikami19, Hiroki Nagase25, Hiroto Narimatsu26,27, Kiyonori Kuriki12, Sadao Suzuki20, Keitaro Matsuo4, Asahi Hishida22, Yoshikuni Kita2,24, Katsuyuki Miura2,28, Ritei Uehara18, Kokichi Arisawa21, Hiroaki Ikezaki14, Keitaro Tanaka13, Toshiro Takezaki16.

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TS, YaN, YoKi, and KW: designed the research; KeMa, KaMi, NT, KK, CS, KeTa, HiIk, MM, RI, ToT, YuK, HiIt, DM, TK, HM, YoN, SS, TN, SKK, KA, KenT, TaTa, RO, YoKu, YM, MK, YoKi, and KW: conducted the research; TS, YaN, KeMa, IO, AN, AS, NI, CG, and MN: analyzed data and performed statistical analysis; TS, YaN, KeMa, IO, and YD: wrote the manuscript and had primary responsibility for final content; and all authors: read and approved the final manuscript.

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Correspondence to Yasuyuki Nakamura.

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Suzuki, T., Nakamura, Y., Matsuo, K. et al. A genome-wide association study on fish consumption in a Japanese population—the Japan Multi-Institutional Collaborative Cohort study. Eur J Clin Nutr (2020). https://doi.org/10.1038/s41430-020-00702-7

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