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Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases
Open accessPublished version of a preprint
Abstract
The overwhelming majority of participants in current genetic studies are of European ancestry. To elucidate disease biology in the East Asian population, we conducted a genome-wide association study (GWAS) with 212,453 Japanese individuals across 42 diseases. We detected 320 independent signals in 276 loci for 27 diseases, with 25 novel loci (P < 9.58 × 10-9). East Asian-specific missense variants were identified as candidate causal variants for three novel loci, and we successfully replicated two of them by analyzing independent Japanese cohorts; p.R220W of ATG16L2 (associated with coronary artery disease) and p.V326A of POT1 (associated with lung cancer). We further investigated enrichment of heritability within 2,868 annotations of genome-wide transcription factor occupancy, and identified 378 significant enrichments across nine diseases (false discovery rate < 0.05) (for example, NKX3-1 for prostate cancer). This large-scale GWAS in a Japanese population provides insights into the etiology of complex diseases and highlights the importance of performing GWAS in non-European populations.
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“BBJ is a registry of over 200,000 Japanese patients including information about 47 diseases and 59 quantitative traits (Supplemental Table 1) [29, 30].”
From Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations (2022) · cites this paper as [30]
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Metadata
- Authors
- Ishigaki, K., Akiyama, M., Kanai, M., Takahashi, A., Kawakami, E., Sugishita, H., Sakaue, S., Matoba, N., Low, S.-K., Okada, Y., Terao, C., Amariuta, T., Gazal, S., Kochi, Y., Horikoshi, M., Suzuki, K., Ito, K., Koyama, S., Ozaki, K., Niida, S., Sakata, Y., Sakata, Y., Kohno, T., Shiraishi, K., Momozawa, Y., Hirata, M., Matsuda, K., Ikeda, M., Iwata, N., Ikegawa, S., Kou, I., Tanaka, T., Nakagawa, H., Suzuki, A., Hirota, T., Tamari, M., Chayama, K., Miki, D., Mori, M., Nagayama, S., Daigo, Y., Miki, Y., Katagiri, T., Ogawa, O., Obara, W., Ito, H., Yoshida, T., Imoto, I., Takahashi, T., Tanikawa, C., Suzuki, T., Sinozaki, N., Minami, S., Yamaguchi, H., Asai, S., Takahashi, Y., Yamaji, K., Takahashi, K., Fujioka, T., Takata, R., Yanai, H., Masumoto, A., Koretsune, Y., Kutsumi, H., Higashiyama, M., Murayama, S., Minegishi, N., Suzuki, K., Tanno, K., Shimizu, A., Yamaji, T., Iwasaki, M., Sawada, N., Uemura, H., Tanaka, K., Naito, M., Sasaki, M., Wakai, K., Tsugane, S., Yamamoto, M., Yamamoto, K., Murakami, Y., Nakamura, Y., Raychaudhuri, S., Inazawa, J., Yamauchi, T., Kadowaki, T., Kubo, M., & Kamatani, Y.
- Affiliations
- Broad Institute (US)
- Kyushu University (JP)
- National Cerebral and Cardiovascular Center (JP)
- Chiba University (JP)
- RIKEN Center for Integrative Medical Sciences (JP)
- University of North Carolina at Chapel Hill (US)
- Tokyo Medical and Dental University (JP)
- Medical Genome Center, National Center for Geriatrics and Gerontology (JP)
- Tohoku University (JP)
- National Cancer Center Research Institute (JP)
- Institute of Medical Science, The University of Tokyo (JP)
- The University of Tokyo (JP)
- Fujita Health University (JP)
- Hiroshima University (JP)
- The Cancer Institute Hospital (JP)
- Shiga University of Medical Science (JP)
- Japanese Foundation For Cancer Research (JP)
- Tokushima University (JP)
- Kyoto University (JP)
- Iwate Medical University (JP)
- Aichi Cancer Center (JP)
- Nippon Medical School (JP)
- Nihon University (JP)
- Juntendo University (JP)
- Japan Anti Tuberculosis Association (JP)
- Aso Iizuka Hospital (JP)
- Osaka National Hospital (JP)
- Osaka International Cancer Institute (JP)
- Tokyo Metropolitan Institute of Gerontology (JP)
- National Cancer Centre Japan (JP)
- University of Hyogo (JP)
- Saga University (JP)
- Nagoya University (JP)
- Corresponding author
- Raychaudhuri, Soumya
- Inazawa, Johji
- Yamauchi, Toshimasa
- Kadowaki, Takashi
- Kubo, Michiaki
- Kamatani, Yoichiro
- ORCID
- Ishigaki, Kazuyoshi
- Akiyama, Masato
- Kanai, Masahiro
- Takahashi, Atsushi
- Kawakami, Eiryo
- Sugishita, Hiroki
- Sakaue, Saori
- Matoba, Nana
- Low, Siew-Kee
- Okada, Yukinori
- Terao, Chikashi
- Amariuta, Tiffany
- Gazal, Steven
- Kochi, Yuta
- Horikoshi, Momoko
- Suzuki, Ken
- Ito, Kaoru
- Koyama, Satoshi
- Ozaki, Kouichi
- Niida, Shumpei
- Sakata, Yasushi
- Sakata, Yasuhiko
- Kohno, Takashi
- Shiraishi, Kouya
- Momozawa, Yukihide
- Hirata, Makoto
- Matsuda, Koichi
- Ikeda, Masashi
- Iwata, Nakao
- Ikegawa, Shiro
- Kou, Ikuyo
- Tanaka, Toshihiro
- Nakagawa, Hidewaki
- Suzuki, Akari
- Hirota, Tomomitsu
- Tamari, Mayumi
- Chayama, Kazuaki
- Miki, Daiki
- Mori, Masaki
- Nagayama, Satoshi
- Daigo, Yataro
- Miki, Yoshio
- Katagiri, Toyomasa
- Ogawa, Osamu
- Obara, Wataru
- Ito, Hidemi
- Imoto, Issei
- Takahashi, Takashi
- Suzuki, Takao
- Yamaguchi, Hiroki
- Asai, Satoshi
- Takahashi, Yasuo
- Yamaji, Ken
- Takahashi, Kazuhisa
- Takata, Ryo
- Yanai, Hideki
- Murayama, Shigeo
- Minegishi, Naoko
- Suzuki, Kichiya
- Tanno, Kozo
- Shimizu, Atsushi
- Yamaji, Taiki
- Iwasaki, Motoki
- Sawada, Norie
- Uemura, Hirokazu
- Tanaka, Keitaro
- Naito, Mariko
- Sasaki, Makoto
- Wakai, Kenji
- Tsugane, Shoichiro
- Yamamoto, Masayuki
- Yamamoto, Kazuhiko
- Murakami, Yoshinori
- Nakamura, Yusuke
- Raychaudhuri, Soumya
- Inazawa, Johji
- Yamauchi, Toshimasa
- Kadowaki, Takashi
- Kubo, Michiaki
- Kamatani, Yoichiro
- Venue
- Nature Genetics
- Published
- 2020-06-08
- Volume
- 52
- Issue
- 7
- Pages
- 669-679
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC7968075
- OpenAlex
- W3033304694
- Cited by
- 508
- References
- 65
- Citations by year
- 2026: 56 · 2025: 72 · 2024: 120 · 2023: 100 · 2022: 81 · 2021: 63 · 2020: 15
- FWCI
- 38.26
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
- Funders
- Japan Agency for Medical Research and Development (JP20dk0207045, JP18kk0205009, JP19ek0210081, JP16ck0106096, JP17km0305001, JP19km0105001, JP19km0105002, JP17km0305002)
- National Cancer Center Research and Development Fund
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- disease susceptibility loci, Japanese population, novel genetic loci, missense mutations, ATG16L2, POT1, coronary artery disease, lung cancer, transcription factor occupancy, heritability enrichment, NKX3.1, prostate cancer, complex diseases, non-European populations
- MeSH terms
- Female, Humans, Japan, Male, Sex Factors, Transcription Factors, Genetic Variation, Cohort Studies, Genetic Predisposition to Disease, Inheritance Patterns, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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