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.
“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]
Online Methods (Subjects; page unavailable) describes BBJ as having recruited approximately 200,000 patients in Japan with at least one of 47 diseases. It does not substantiate the more precise claim of over 200,000 patients or the claim that BBJ includes information on 59 quantitative traits; a search for that trait count found no supporting passage. (LLM, conf=0.86)
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Self-citationMetagenome-genome-wide association studies reveal human genetic impact on the oral microbiome
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Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma
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Insights from complex trait fine-mapping across diverse populationsPreprint
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Self-citationGenome-wide risk prediction of common diseases across ancestries in one million people
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Self-citationEye-brain connections revealed by multimodal retinal and brain imaging genetics
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Genomic Risk Factors for Cervical Cancer
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Sequential immunotherapy: towards cures for autoimmunity
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Eight novel susceptibility loci and putative causal variants in atopic dermatitis
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Self-citationQuantifying the contribution of Neanderthal introgression to the heritability of complex traits
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A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases
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Sex differences in the oral microbiome, host traits, and their causal relationships
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Hypertension genetics past, present and future applications
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Development and Validation of a Polygenic Risk Score for Stroke in the Chinese Population
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Insulin‐like growth factor‐1 and site‐specific cancers: A Mendelian randomization study
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Genetics of chronic respiratory disease
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Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes
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Plasma Proteomics to Identify Drug Targets for Ischemic Heart Disease
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Epigenetic and integrative cross-omics analyses of cerebral white matter hyperintensities on MRI
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Genetic insights into ossification of the posterior longitudinal ligament of the spine
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Atlas of Circulating Immune Cells in Kawasaki Disease
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Graves Disease and Inflammatory Bowel Disease: A Bidirectional Mendelian Randomization
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10 Years of GWAS discovery in endometrial cancer: Aetiology, function and translation
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Peroxisome proliferator-activated receptor α as a novel therapeutic target for schizophrenia
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The role of ATG16L2 in autophagy and disease
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The Propagation of Racial Disparities in Cardiovascular Genomics Research
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Self-citationYeung, S. L. A., Borges, M. C., Wong, T. H. T., Lawlor, D. A., & Schooling, C. M. (2022) · International Journal of Epidemiology · doi:10.1093/ije/dyac212 · Cited by 35 · see citing works
Dissecting the genetic heterogeneity of gastric cancer
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Beyond GWAS: from simple associations to functional insights
Ishigaki, K. (2021) · Seminars in Immunopathology · doi:10.1007/s00281-021-00894-5 · Cited by 34 · see citing works
Self-citationZhao, J. V., Liu, F., Schooling, C. M., Li, J., Gu, D., & Lu, X. (2022) · Diabetologia · doi:10.1007/s00125-021-05645-7 · Cited by 34 · see citing works
Advances and Applications of Polygenic Scores for Coronary Artery Disease
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The Population-Specific Impact of Neandertal Introgression on Human Disease
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Graves’ Disease and Rheumatoid Arthritis: A Bidirectional Mendelian Randomization Study
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IL6 genetic perturbation mimicking IL-6 inhibition is associated with lower cardiometabolic risk
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Temprano‐Sagrera, G., Sitlani, C. M., Bone, W. P., Martín‐Bórnez, M., Voight, B. F., Morrison, A. C., Damrauer, S. M., de Vries, P. S., Smith, N. L., Sabater‐Lleal, M., et al. (2022) · Journal of Thrombosis and Haemostasis · doi:10.1111/jth.15698 · Cited by 30 · see citing works
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Rheumatoid arthritis and osteoporosis: shared genetic effect, pleiotropy and causality
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Self-citationKoel, M., Võsa, U., Jõeloo, M., Läll, K., Pujol‐Gualdo, N., Laivuori, H. M., Lemmelä, S. M., Daly, M. J., FinnGen, Palta, P., et al. (2023) · Human Molecular Genetics · doi:10.1093/hmg/ddad043 · Cited by 27 · see citing works
FHL5 Controls Vascular Disease–Associated Gene Programs in Smooth Muscle Cells
Wong, D., Auguste, G. E., Cardenas, C. L. L., Turner, A. W., Chen, Y., Song, Y., Ma, L., Perry, R. N., Aherrahrou, R., Kuppusamy, M., et al. (2023) · Circulation Research · doi:10.1161/circresaha.122.321692 · Cited by 28 · see citing works
Construction and Application of Polygenic Risk Scores in Autoimmune Diseases
Khunsriraksakul, C., Markus, H., Olsen, N. J., Carrel, L., Jiang, B., & Liu, D. J. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.889296 · Cited by 28 · see citing works
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Koller, D., Wendt, F. R., Pathak, G. A., De Lillo, A., De Angelis, F., Cabrera-Mendoza, B., Tucci, S., & Polimanti, R. (2022) · BMC Biology · doi:10.1186/s12915-022-01449-2 · Cited by 27 · see citing works
“Leveraging data generated from large-scale GWAS conducted in Biobank Japan (BBJ) [29, 30], we analyzed the genetic background of individuals of East Asian descent (EAS).”
BackgroundMethodInfluentialJCS/JCC/JSPCCS 2024 Guideline on Genetic Testing and Counseling in Cardiovascular Disease
Imai, Y., Kusano, K., Aiba, T., Ako, J., Asano, Y., Harada‐Shiba, M., Kataoka, M., Kosho, T., Kubo, T., Matsumura, T., et al. (2024) · Circulation Journal · doi:10.1253/circj.cj-23-0926 · Cited by 31 · see citing works
Self-citationUpdate on the genetics of allergic diseases
Lawson, L. P., Parameswaran, S., Panganiban, R. A. M., Constantine, G. M., Weirauch, M. T., & Kottyan, L. C. (2025) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2025.03.012 · Cited by 27 · see citing works
MicroRNAs in Kawasaki disease: An update on diagnosis, therapy and monitoring
Xiong, Y., Xu, J., Zhang, D., Shu-qin, W., Li, Z., Zhang, J., Xia, Z., Xia, P., Cai, X., Tang, X., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1016575 · Cited by 27 · see citing works
Ben, S., Ding, Z., Xin, J., Li, F., Cheng, Y., Chen, S., Fan, L., Zhang, Q., Li, S., Du, M., et al. (2024) · Advanced Science · doi:10.1002/advs.202402954 · Cited by 26 · see citing works
Genome-Wide Meta-Analysis Identifies Two Novel Risk Loci for Epilepsy
Song, M., Liu, J., Yang, Y., Lv, L., Li, W., & Luo, X. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.722592 · Cited by 26 · see citing works
XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis
Xiao, J., Cai, M., Hu, X., Wan, X., Chen, G., & Yang, C. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac029 · Cited by 23 · see citing works
Wang, Z., Lu, J., & Hu, J. (2023) · Liver International · doi:10.1111/liv.15566 · Cited by 26 · see citing works
- 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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