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Identification of functional variants by comprehensive analysis of coding variants for the implementation of genomic medicine

Research Project

Project/Area Number 19H03881
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 58020:Hygiene and public health-related: including laboratory approach
Research InstitutionThe University of Tokyo

Principal Investigator

TANIKAWA CHIZU  東京大学, 医科学研究所, 助教 (30422421)

Co-Investigator(Kenkyū-buntansha) 鎌谷 洋一郎  東京大学, 大学院新領域創成科学研究科, 教授 (00720880)
松田 浩一  東京大学, 大学院新領域創成科学研究科, 教授 (90401257)
Project Period (FY) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2021: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2020: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2019: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
KeywordsSNP / ゲノム医療
Outline of Research at the Start

近年の大規模なゲノム解析によって、様々な疾患感受性遺伝子が次々と明らかとなっているが、日本人での検証や機能的意義の解明、さらに医療応用がまだ十分に進んでいない。本研究では、約17万人の日本人症例を用いて、coding variantを対象とし、①117疾患、②58の血液生化学検査値、さらに③生命予後・死因について、網羅的ゲノム解析を実施することで、上記の問題点を克服しゲノム医療の実現へ向けた基盤情報を構築することを目指す。我々の研究成果は、ゲノム解析による疾患ハイリスク群の同定や個別化検査の実施などのゲノム医療の実現、さらには健康長寿社会の実現のための基盤情報となると期待される。

Outline of Final Research Achievements

Although recent large-scale genome analyses have successively revealed a variety of disease susceptibility genes, their validation and functional significance in the Japanese population as well as their medical application have yet to be fully developed. In this study, we attempted to conduct a comprehensive genome analysis of loss of functional polymorphisms with various diseases, blood and biochemical test values, life span, and cause of death using approximately 170,000 Japanese cases. Using the high-density Imputation reference panel constructed at McGill University based on the genome information of approximately 60,000 people, we obtained information on about 50,000 functional deletion polymorphisms. We are now preparing to release these data to the public database and are analyzing the relationship between genetic variations and more than 370 diseases.

Academic Significance and Societal Importance of the Research Achievements

coding variantの頻度については、人種差が知られているため、日本人を対象とした大規模な解析を実施することで、新規の疾患関連遺伝子の同定や疾患ハイリスク群のスクリーニングなどに寄与する。本研究の成果は、ゲノム医療の実現、さらには健康長寿社会の実現のための基盤情報となると期待される。Imputationデータが公開されれば、情報の利活用が可能となる。

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (17 results)

All 2022 2021 2020 2019 2018

All Journal Article (17 results) (of which Int'l Joint Research: 12 results,  Peer Reviewed: 17 results,  Open Access: 11 results)

  • [Journal Article] Large-scale integrated analysis of genetics and metabolomic data reveals potential links between lipids and colorectal cancer risk2022

    • Author(s)
      Shu Xiang、Kamatani Yoichiro、Matsuda Koichi、Matsuo Keitaro、Newcomb Polly A.、Oh Jae Hwan、Ose Jennifer、Oze Isao、Pai Rish K.、Pan Zhi-Zhong、Pharoah Paul D P.、Playdon Mary C.、Ren Ze-Fang、Schoen Robert E.、Shin Aesun、Shin Min-Ho、Shu Xiao-Ou、Sun Xiaohui、Tangen Catherine M.、Tanikawa Chizu、Zheng Wei
    • Journal Title

      Cancer Epidemiology, Biomarkers & Prevention

      Volume: - Issue: 6 Pages: 1216-1226

    • DOI

      10.1158/1055-9965.epi-21-1008

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Genetic susceptibility to hepatocellular carcinoma in chromosome 22q13.31, findings of a genome‐wide association study2021

    • Author(s)
      Wang Zhanwei、Iwasaki Motoki、Goto Atsushi、Suzuki Shiori、Matsuda Koichi、Tanikawa Chizu、Kamatani Yoichiro、Yu Herbert
    • Journal Title

      JGH Open

      Volume: 5 Issue: 12 Pages: 1363-1372

    • DOI

      10.1002/jgh3.12682

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Intracellular Accumulation of IFN-λ4 Induces ER Stress and Results in Anti-Cirrhotic but Pro-HCV Effects2021

    • Author(s)
      Onabajo Olusegun O.、Wang Fang、Lee Mei-Hsuan、Florez-Vargas Oscar、Obajemu Adeola、Tanikawa Chizu、Vargas Joselin M.、Liao Shu-Fen、Song Ci、Huang Yu-Han、Shen Chen-Yang、Banday A. Rouf、O’Brien Thomas R.、Hu Zhibin、Matsuda Koichi、Prokunina-Olsson Ludmila
    • Journal Title

      Frontiers in Immunology

      Volume: 12

    • DOI

      10.3389/fimmu.2021.692263

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Collagen XVII inhibits breast cancer cell proliferation and growth through deactivation of the AKT/mTOR signaling pathway2021

    • Author(s)
      Lothong Muttarin、Sakares Watchara、Rojsitthisak Pornchai、Tanikawa Chizu、Matsuda Koichi、Yodsurang Varalee
    • Journal Title

      PLOS ONE

      Volume: 16 Issue: 7 Pages: e0255179-e0255179

    • DOI

      10.1371/journal.pone.0255179

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The simplified Kyoto classification score is consistent with the ABC method of classification as a grading system for endoscopic gastritis2021

    • Author(s)
      Nishizawa Toshihiro、Toyoshima Osamu、Kondo Ryo、Sekiba Kazuma、Tsuji Yosuke、Ebinuma Hirotoshi、Suzuki Hidekazu、Tanikawa Chizu、Matsuda Koichi、Koike Kazuhiko
    • Journal Title

      Journal of Clinical Biochemistry and Nutrition

      Volume: 68 Issue: 1 Pages: 101-104

    • DOI

      10.3164/jcbn.20-41

    • NAID

      130007965311

    • ISSN
      0912-0009, 1880-5086
    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A single nucleotide polymorphism in <i>Prostate Stem Cell Antigen</i> is associated with endoscopic grading in Kyoto classification of gastritis2021

    • Author(s)
      Toyoshima Osamu、Nishizawa Toshihiro、Sekiba Kazuma、Matsuno Tatsuya、Kondo Ryo、Watanabe Hidenobu、Suzuki Hidekazu、Tanikawa Chizu、Koike Kazuhiko、Matsuda Koichi
    • Journal Title

      Journal of Clinical Biochemistry and Nutrition

      Volume: 68 Issue: 1 Pages: 73-77

    • DOI

      10.3164/jcbn.20-67

    • NAID

      130007965305

    • ISSN
      0912-0009, 1880-5086
    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Endoscopy-based Kyoto classification score of gastritis related to pathological topography of neutrophil activity2020

    • Author(s)
      Toyoshima Osamu、Nishizawa Toshihiro、Yoshida Shuntaro、Sakaguchi Yoshiki、Nakai Yousuke、Watanabe Hidenobu、Suzuki Hidekazu、Tanikawa Chizu、Matsuda Koichi、Koike Kazuhiko
    • Journal Title

      World Journal of Gastroenterology

      Volume: 26 Issue: 34 Pages: 5146-5155

    • DOI

      10.3748/wjg.v26.i34.5146

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Large-scale genome-wide association study in a Japanese population identifies novel susceptibility loci across different diseases2020

    • Author(s)
      Ishigaki K, Akiyama M, Kanai M, Takahashi A, Kawakami E, Sugishita H, Sakaue S, Matoba N, Low SK, Okada Y, Yamaji T, et al
    • Journal Title

      Nature Genetics

      Volume: 52 Issue: 7 Pages: 669-679

    • DOI

      10.1038/s41588-020-0640-3

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Claudin-2 deficiency associates with hypercalciuria in mice and human kidney stone disease2020

    • Author(s)
      Curry Joshua N.、Saurette Matthew、Askari Masomeh、Pei Lei、Filla Michael B.、Beggs Megan R.、Rowe Peter S.N.、Fields Timothy、Sommer Andre J.、Tanikawa Chizu、Kamatani Yoichiro、Evan Andrew P.、Totonchi Mehdi、Alexander R. Todd、Matsuda Koichi、Yu Alan S.L.
    • Journal Title

      Journal of Clinical Investigation

      Volume: 130 Issue: 4 Pages: 1948-1960

    • DOI

      10.1172/jci127750

    • Related Report
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of a novel uterine leiomyoma GWAS locus in a Japanese population2020

    • Author(s)
      Sakai Kensuke、Tanikawa Chizu、Hirasawa Akira、Terao Chikashi、Kamatani Yoichiro、Takahashi Atsushi、Momozawa Yukihide、Hirata Makoto、Kubo Michiaki、Matsuda Koichi
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 1024-1024

    • DOI

      10.1038/s41598-020-58066-8

    • NAID

      120006872359

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of Novel Loci and New Risk Variant in Known Loci for Colorectal Cancer Risk in East Asians2019

    • Author(s)
      Lu Yingchang、Tanikawa Chizu、Matsuo Keitaro、Kamatani Yoichiro、Matsuda Koichi、Zheng Wei
    • Journal Title

      Cancer Epidemiology Biomarkers & Prevention

      Volume: 29 Issue: 2 Pages: 477-486

    • DOI

      10.1158/1055-9965.epi-19-0755

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of two novel breast cancer loci through large-scale genome-wide association study in the Japanese population2019

    • Author(s)
      Low Siew-Kee、Chin Yoon Ming、Ito Hidemi、Matsuo Keitaro、et al.
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 17332-17332

    • DOI

      10.1038/s41598-019-53654-9

    • NAID

      120006875665

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Genetic variants of calcium and vitamin D metabolism in kidney stone disease2019

    • Author(s)
      Howles Sarah A.、Wiberg Akira、Goldsworthy Michelle、Bayliss Asha L.、Gluck Anna K.、Ng Michael、Grout Emily、Tanikawa Chizu、Kamatani Yoichiro、Terao Chikashi、Takahashi Atsushi、Kubo Michiaki、Matsuda Koichi、Thakker Rajesh V.、Turney Benjamin W.、Furniss Dominic
    • Journal Title

      Nature Communications

      Volume: 10 Issue: 1

    • DOI

      10.1038/s41467-019-13145-x

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] INKA2, a novel p53 target that interacts with the serine/threonine kinase PAK4.2019

    • Author(s)
      Liu, Y.Y., Tanikawa, C., Ueda, K., and Matsuda, K.
    • Journal Title

      International journal of oncology

      Volume: 54 Pages: 1907-1920

    • DOI

      10.3892/ijo.2019.4786

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Novel Risk Loci Identified in a Genome-Wide Association Study of Urolithiasis in a Japanese Population2019

    • Author(s)
      Tanikawa Chizu、...、Ogishima Soichi、...、Matsuda Koichi
    • Journal Title

      Journal of the American Society of Nephrology

      Volume: 印刷中 Issue: 5 Pages: 855-864

    • DOI

      10.1681/asn.2018090942

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Polymorphic Variant in p19Arf Confers Resistance to Chemically Induced Skin Tumors by Activating the p53 Pathway2019

    • Author(s)
      Saito M, Okumura K, Isogai E, Araki K, Tanikawa C, Matsuda K, Kamijo T, Kominami R, Wakabayashi Y.
    • Journal Title

      Journal of Investigative Dermatology

      Volume: in press Issue: 7 Pages: 30032-6

    • DOI

      10.1016/j.jid.2018.12.027

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Large-Scale Genome-Wide Association Study of East Asians Identifies Loci Associated With Risk for Colorectal Cancer.2018

    • Author(s)
      Lu Y, Kweon SS, Tanikawa C, Jia WH, Xiang YB, Cai Q, Zeng C, Schmit SL, Shin A, Matsuo K, Jee SH, Kim DH, Kim J, Wen W, Shi J, Guo X, Li B, Wang N, Zhang B, Li X, Shin MH, Li HL, Ren Z, Oh JH, Oze I, Ahn YO, Jung KJ, Conti DV, Schumacher FR, Rennert G, Je
    • Journal Title

      Gastroenterology

      Volume: 156 Issue: 5 Pages: 1455-1466

    • DOI

      10.1053/j.gastro.2018.11.066

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research

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Published: 2019-04-18   Modified: 2023-01-30  

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