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Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases
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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
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