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Epidemiology

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

European Journal of Clinical Nutrition volume 75, pages 480–488 (2021)Cite this article

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Abstract

Background/objective

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.

Methods

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.

Results

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.

Conclusion

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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Acknowledgements

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.

Author information

Authors and Affiliations

  1. Department of Food Science and Human Nutrition, Ryukoku University, Otsu, Japan

    Taro Suzuki & Yukio Doi

  2. Department of Public Health, Shiga University of Medical Science, Otsu, Japan

    Yasuyuki Nakamura, Katsuyuki Miura, Naoyuki Takashima, Yoshikuni Kita, Yoshikuni Kita & Katsuyuki Miura

  3. Yamashina Racto Clinic and Medical Examination Center, Kyoto, Japan

    Yasuyuki Nakamura

  4. Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan

    Keitaro Matsuo, Isao Oze & Keitaro Matsuo

  5. Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan

    Akira Narita

  6. Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Shiwa-gun, Iwate, Japan

    Atsushi Shimizu

  7. Department of Nutrition, Faculty of Wellness, Shigakkan University, Obu, Japan

    Nahomi Imaeda

  8. Department of Health and Nutrition, School of Health and Human Life, Nagoya Bunri University, Inazawa, Japan

    Chiho Goto

  9. Division of Bioethics and Healthcare Law, Center for Public Health Sciences, The National Cancer Center Japan, Tokyo, Japan

    Kenji Matsui

  10. Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan

    Masahiro Nakatochi

  11. Department of Public Health, Faculty of Medicine, Kindai University Osaka-Sayama, Osaka, Japan

    Naoyuki Takashima

  12. Laboratory of Public Health, School of Food and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan

    Kiyonori Kuriki & Kiyonori Kuriki

  13. Department of Preventive Medicine, Faculty of Medicine, Saga University, Saga, Japan

    Chisato Shimanoe, Keitaro Tanaka & Keitaro Tanaka

  14. Department of Comprehensive General Internal Medicine, Kyushu University Graduate School, Faculty of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan

    Hiroaki Ikezaki & Hiroaki Ikezaki

  15. Department of General Internal Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan

    Hiroaki Ikezaki & Masayuki Murata

  16. Department of International Island and Community Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan

    Rie Ibusuki, Toshiro Takezaki & Toshiro Takezaki

  17. Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan

    Yuriko Koyanagi & Hidemi Ito

  18. Department of Epidemiology for Community Health and Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan

    Daisuke Matsui, Teruhide Koyama & Ritei Uehara

  19. Cancer Prevention Center, Chiba Cancer Center Research Institute, Chiba, Japan

    Haruo Mikami, Yohko Nakamura & Haruo Mikami

  20. Department of Public Health, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan

    Sadao Suzuki, Takeshi Nishiyama & Sadao Suzuki

  21. Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan

    Sakurako Katsuura-Kamano, Kokichi Arisawa & Kokichi Arisawa

  22. Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan

    Kenji Takeuchi, Takashi Tamura, Rieko Okada, Yoko Kubo, Kenji Wakai, Kenji Wakai, Kenji Takeuchi & Asahi Hishida

  23. Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan

    Yukihide Momozawa & Michiaki Kubo

  24. Faculty of Nursing Science, Tsuruga Nursing University, Tsuruga, Japan

    Yoshikuni Kita & Yoshikuni Kita

  25. Division of Cancer Genetics, Chiba Cancer Center Research Institute, 666-2 Nitona-Cho, Chuo-Ku, Chiba, 260-8717, Japan

    Hiroki Nagase

  26. Cancer Prevention and Control Division, Kanagawa Cancer Center Research Institute, 2-3-2 Nakao, Asahi-ku, Yokohama, Kanagawa, 241-8515, Japan

    Hiroto Narimatsu

  27. School of Health of Innovation, Kanagawa University of Human Services, 3-25-10, Research Gate Building 2-A,Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-0821, Japan

    Hiroto Narimatsu

  28. Center for Epidemiologic Research in Asia, Shiga University of Medical Science, Seta-tsukinowa-cho, Otsu, Shiga, 520-2192, Japan

    Katsuyuki Miura

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  1. Taro Suzuki
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for the J-MICC Research Group

  • Kenji Wakai
  • , Kenji Takeuchi
  • , Haruo Mikami
  • , Hiroki Nagase
  • , Hiroto Narimatsu
  • , Kiyonori Kuriki
  • , Sadao Suzuki
  • , Keitaro Matsuo
  • , Asahi Hishida
  • , Yoshikuni Kita
  • , Katsuyuki Miura
  • , Ritei Uehara
  • , Kokichi Arisawa
  • , Hiroaki Ikezaki
  • , Keitaro Tanaka
  •  & Toshiro Takezaki

Contributions

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 75, 480–488 (2021). https://doi.org/10.1038/s41430-020-00702-7

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