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Large scale genome-wide association study in a Japanese population identified 45 novel susceptibility loci for 22 diseases

Kazuyoshi Ishigaki, Masato Akiyama, Masahiro Kanai, Atsushi Takahashi, Eiryo Kawakami, Hiroki Sugishita, Saori Sakaue, Nana Matoba, Siew-Kee Low, Yukinori Okada, Chikashi Terao, Tiffany Amariuta, Steven Gazal, Yuta Kochi, Momoko Horikoshi, Ken Suzuki, Kaoru Ito, Yukihide Momozawa, Makoto Hirata, Koichi Matsuda, Masashi Ikeda, Nakao Iwata, Shiro Ikegawa, Ikuyo Kou, Toshihiro Tanaka, Hidewaki Nakagawa, Akari Suzuki, Tomomitsu Hirota, Mayumi Tamari, Kazuaki Chayama, Daiki Miki, Masaki Mori, Satoshi Nagayama, Yataro Daigo, Yoshio Miki, Toyomasa Katagiri, Osamu Ogawa, Wataru Obara, Hidemi Ito, Teruhiko Yoshida, Issei Imoto, Takashi Takahashi, Chizu Tanikawa, Takao Suzuki, Nobuaki Sinozaki, Shiro Minami, Hiroki Yamaguchi, Satoshi Asai, Yasuo Takahashi, Ken Yamaji, Kazuhisa Takahashi, Tomoaki Fujioka, Ryo Takata, Hideki Yanai, Akihide Masumoto, Yukihiro Koretsune, Hiromu Kutsumi, Masahiko Higashiyama, Shigeo Murayama, Naoko Minegishi, Kichiya Suzuki, Kozo Tanno, Atsushi Shimizu, Taiki Yamaji, Motoki Iwasaki, Norie Sawada, Hirokazu Uemura, Keitaro Tanaka, Mariko Naito, Makoto Sasaki, Kenji Wakai, Shoichiro Tsugane, Masayuki Yamamoto, Kazuhiko Yamamoto, Yoshinori Murakami, Yusuke Nakamura, Soumya Raychaudhuri, Johji Inazawa, Toshimasa Yamauchi, Takashi Kadowaki, Michiaki Kubo, Yoichiro Kamatani
doi: https://doi.org/10.1101/795948
Kazuyoshi Ishigaki
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
2Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
3Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA
4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Masato Akiyama
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
5Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University. Fukuoka, Japan
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Masahiro Kanai
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
6Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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Atsushi Takahashi
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
7Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
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Eiryo Kawakami
8Healthcare and Medical Data Driven AI based Predictive Reasoning Development Unit, Medical Sciences Innovation Hub Program (MIH), RIKEN, Yokohama, Japan
9Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Hiroki Sugishita
9Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Saori Sakaue
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
10Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
11Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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Nana Matoba
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
12Department of Genetics & UNC Neuroscience Center, University of North Carolina at Chapel Hill, NC, USA
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Siew-Kee Low
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
13Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
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Yukinori Okada
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
10Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
14Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
15Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
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Chikashi Terao
16Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Tiffany Amariuta
2Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
3Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA
4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
6Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
17Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
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Steven Gazal
4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
18Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Yuta Kochi
19Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Momoko Horikoshi
20Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Ken Suzuki
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
10Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
20Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
21Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Kaoru Ito
22Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Yukihide Momozawa
23Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Makoto Hirata
24Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Koichi Matsuda
25Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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Masashi Ikeda
26Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
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Nakao Iwata
26Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
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Shiro Ikegawa
27Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Ikuyo Kou
27Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Toshihiro Tanaka
22Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
28Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Tokyo, Japan
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Hidewaki Nakagawa
29Laboratory for Genome Sequencing Analysis, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
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Akari Suzuki
19Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Tomomitsu Hirota
30Laboratory for Respiratory and Allergic Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Mayumi Tamari
30Laboratory for Respiratory and Allergic Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Kazuaki Chayama
31Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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Daiki Miki
31Department of Gastroenterology and Metabolism, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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Masaki Mori
32Department of Gastroenterological Surgery Graduate School of Medicine, Osaka University, Osaka, Japan
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Satoshi Nagayama
33Department of Gastroenterological Surgery, The Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo, Japan
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Yataro Daigo
34Department of Medical Oncology and Cancer Center, and Center for Advanced Medicine against Cancer, Shiga University of Medical Science, Shiga, Japan
35Center for Antibody and Vaccine Therapy, Research Hospital, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Yoshio Miki
36Department of Genetic Diagnosis, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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Toyomasa Katagiri
37Division of Genome Medicine, Institute for Genome Research, Tokushima University, Tokushima, Japan
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Osamu Ogawa
38Department of Urology, Kyoto University Graduate School of Medicine, Kyoto, Japan
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Wataru Obara
39Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
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Hidemi Ito
40Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan
41Division of Descriptive Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Teruhiko Yoshida
42Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
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Issei Imoto
43Division of Molecular Genetics, Aichi Cancer Center Research Institute, Nagoya, Japan
44Risk Assessment Center, Aichi Caner Center Hospital, Nagoya, Japan
45Division of Cancer Genetics, Graduate School of Medicine, Nagoya University, Nagoya, Japan
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Takashi Takahashi
46Aichi Cancer Center, Nagoya, Japan
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Chizu Tanikawa
47Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
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Takao Suzuki
48Tokushukai Group, Tokyo, Japan
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Nobuaki Sinozaki
48Tokushukai Group, Tokyo, Japan
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Shiro Minami
49Department of Bioregulation, Nippon Medical School, Tokyo, Japan
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Hiroki Yamaguchi
50Department of Hematology, Nippon Medical School, Tokyo, Japan
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Satoshi Asai
51Division of Pharmacology, Department of Biomedical Science, Nihon University School of Medicine, Tokyo, Japan
52Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
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Yasuo Takahashi
52Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
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Ken Yamaji
53Department of Internal Medicine and Rheumatology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Kazuhisa Takahashi
54Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Tomoaki Fujioka
39Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
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Ryo Takata
39Department of Urology, Iwate Medical University School of Medicine, Iwate, Japan
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Hideki Yanai
55Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan
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56Aso Iizuka Hospital, Fukuoka, Japan
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57National Hospital Organization Osaka National Hospital, Osaka, Japan
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Hiromu Kutsumi
58Center for Clinical Research and Advanced Medicine, Shiga University of Medical Science, Shiga, Japan
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Masahiko Higashiyama
59Department of General Thoracic Surgery, Osaka International Cancer Institute, Osaka, Japan
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Shigeo Murayama
60Department of Neurology and Neuropathology (the Brain Bank for Aging Research), Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo, Japan
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Naoko Minegishi
61Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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Kichiya Suzuki
61Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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Kozo Tanno
62Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
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Atsushi Shimizu
62Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
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Taiki Yamaji
63Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
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Motoki Iwasaki
63Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
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Norie Sawada
63Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
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Hirokazu Uemura
64Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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Keitaro Tanaka
65Department of Preventive Medicine, Saga University Faculty of Medicine, Saga, Japan
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Mariko Naito
66Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
67Department of Oral Epidemiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Makoto Sasaki
62Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
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Kenji Wakai
66Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Shoichiro Tsugane
68Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
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Masayuki Yamamoto
61Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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Kazuhiko Yamamoto
19Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Yoshinori Murakami
69Division of Molecular Pathology, The Institute of Medical Sciences, The University of Tokyo, Tokyo, Japan
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Yusuke Nakamura
70Human Genome Center, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
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Soumya Raychaudhuri
2Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
3Center for Data Sciences, Harvard Medical School, Boston, MA 02115, USA
4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
6Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
17Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
71Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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  • For correspondence: soumya@broadinstitute.org yoichiro.kamatani@riken.jp
Johji Inazawa
72Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
73Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
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  • For correspondence: soumya@broadinstitute.org yoichiro.kamatani@riken.jp
Toshimasa Yamauchi
21Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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  • For correspondence: soumya@broadinstitute.org yoichiro.kamatani@riken.jp
Takashi Kadowaki
21Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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  • For correspondence: soumya@broadinstitute.org yoichiro.kamatani@riken.jp
Michiaki Kubo
74RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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  • For correspondence: soumya@broadinstitute.org yoichiro.kamatani@riken.jp
Yoichiro Kamatani
1Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
75Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
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  • For correspondence: soumya@broadinstitute.org yoichiro.kamatani@riken.jp
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INTRODUCTORY PARAGRAPH

The overwhelming majority of participants in current genetic studies are of European ancestry1–3, limiting our genetic understanding of complex disease in non-European populations. To address this, we aimed to elucidate polygenic disease biology in the East Asian population by conducting a genome-wide association study (GWAS) with 212,453 Japanese individuals across 42 diseases. We detected 383 independent signals in 331 loci for 30 diseases, among which 45 loci were novel (P < 5 × 10−8). Compared with known variants, novel variants have lower frequency in European populations but comparable frequency in East Asian populations, suggesting the advantage of this study in discovering these novel variants. Three novel signals were in linkage disequilibrium (r2 > 0.6) with missense variants which are monomorphic in European populations (1000 Genomes Project) including rs11235604(p.R220W of ATG16L2, a autophagy-related gene) associated with coronary artery disease. We further investigated enrichment of heritability within 2,868 annotations of genome-wide transcription factor occupancy, andidentified 378 significant enrichments across nine diseases (FDR < 0.05) (e.g. NF-κB for immune-related diseases). This large-scale GWAS in a Japanese population provides insights into the etiology of common complex diseases and highlights the importance of performing GWAS in non-European populations.

Footnotes

  • http://jenger.riken.jp/en/result

  • https://humandbs.biosciencedbc.jp/en/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Large scale genome-wide association study in a Japanese population identified 45 novel susceptibility loci for 22 diseases
Kazuyoshi Ishigaki, Masato Akiyama, Masahiro Kanai, Atsushi Takahashi, Eiryo Kawakami, Hiroki Sugishita, Saori Sakaue, Nana Matoba, Siew-Kee Low, Yukinori Okada, Chikashi Terao, Tiffany Amariuta, Steven Gazal, Yuta Kochi, Momoko Horikoshi, Ken Suzuki, Kaoru Ito, Yukihide Momozawa, Makoto Hirata, Koichi Matsuda, Masashi Ikeda, Nakao Iwata, Shiro Ikegawa, Ikuyo Kou, Toshihiro Tanaka, Hidewaki Nakagawa, Akari Suzuki, Tomomitsu Hirota, Mayumi Tamari, Kazuaki Chayama, Daiki Miki, Masaki Mori, Satoshi Nagayama, Yataro Daigo, Yoshio Miki, Toyomasa Katagiri, Osamu Ogawa, Wataru Obara, Hidemi Ito, Teruhiko Yoshida, Issei Imoto, Takashi Takahashi, Chizu Tanikawa, Takao Suzuki, Nobuaki Sinozaki, Shiro Minami, Hiroki Yamaguchi, Satoshi Asai, Yasuo Takahashi, Ken Yamaji, Kazuhisa Takahashi, Tomoaki Fujioka, Ryo Takata, Hideki Yanai, Akihide Masumoto, Yukihiro Koretsune, Hiromu Kutsumi, Masahiko Higashiyama, Shigeo Murayama, Naoko Minegishi, Kichiya Suzuki, Kozo Tanno, Atsushi Shimizu, Taiki Yamaji, Motoki Iwasaki, Norie Sawada, Hirokazu Uemura, Keitaro Tanaka, Mariko Naito, Makoto Sasaki, Kenji Wakai, Shoichiro Tsugane, Masayuki Yamamoto, Kazuhiko Yamamoto, Yoshinori Murakami, Yusuke Nakamura, Soumya Raychaudhuri, Johji Inazawa, Toshimasa Yamauchi, Takashi Kadowaki, Michiaki Kubo, Yoichiro Kamatani
bioRxiv 795948; doi: https://doi.org/10.1101/795948
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Large scale genome-wide association study in a Japanese population identified 45 novel susceptibility loci for 22 diseases
Kazuyoshi Ishigaki, Masato Akiyama, Masahiro Kanai, Atsushi Takahashi, Eiryo Kawakami, Hiroki Sugishita, Saori Sakaue, Nana Matoba, Siew-Kee Low, Yukinori Okada, Chikashi Terao, Tiffany Amariuta, Steven Gazal, Yuta Kochi, Momoko Horikoshi, Ken Suzuki, Kaoru Ito, Yukihide Momozawa, Makoto Hirata, Koichi Matsuda, Masashi Ikeda, Nakao Iwata, Shiro Ikegawa, Ikuyo Kou, Toshihiro Tanaka, Hidewaki Nakagawa, Akari Suzuki, Tomomitsu Hirota, Mayumi Tamari, Kazuaki Chayama, Daiki Miki, Masaki Mori, Satoshi Nagayama, Yataro Daigo, Yoshio Miki, Toyomasa Katagiri, Osamu Ogawa, Wataru Obara, Hidemi Ito, Teruhiko Yoshida, Issei Imoto, Takashi Takahashi, Chizu Tanikawa, Takao Suzuki, Nobuaki Sinozaki, Shiro Minami, Hiroki Yamaguchi, Satoshi Asai, Yasuo Takahashi, Ken Yamaji, Kazuhisa Takahashi, Tomoaki Fujioka, Ryo Takata, Hideki Yanai, Akihide Masumoto, Yukihiro Koretsune, Hiromu Kutsumi, Masahiko Higashiyama, Shigeo Murayama, Naoko Minegishi, Kichiya Suzuki, Kozo Tanno, Atsushi Shimizu, Taiki Yamaji, Motoki Iwasaki, Norie Sawada, Hirokazu Uemura, Keitaro Tanaka, Mariko Naito, Makoto Sasaki, Kenji Wakai, Shoichiro Tsugane, Masayuki Yamamoto, Kazuhiko Yamamoto, Yoshinori Murakami, Yusuke Nakamura, Soumya Raychaudhuri, Johji Inazawa, Toshimasa Yamauchi, Takashi Kadowaki, Michiaki Kubo, Yoichiro Kamatani
bioRxiv 795948; doi: https://doi.org/10.1101/795948

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