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Medical informatics infrastructure for personalized genomic medicine

Research Project

Project/Area Number 25280105
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionThe University of Tokyo

Principal Investigator

Satoru Miyano  東京大学, 医科学研究所, 教授 (50128104)

Co-Investigator(Kenkyū-buntansha) TOJO Arinobu  東京大学, 医科学研究所, 教授 (00211681)
FURUKAWA Yoichi  東京大学, 医科学研究所, 教授 (20272560)
Co-Investigator(Renkei-kenkyūsha) YAMAGUCHI Rui  東京大学, 医科学研究所, 准教授 (90380675)
IMOTO Seiya  東京大学, 医科学研究所, 教授 (10345027)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥13,780,000 (Direct Cost: ¥10,600,000、Indirect Cost: ¥3,180,000)
Fiscal Year 2015: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2014: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2013: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Keywordsメディカルインフォマティクス / 個別化ゲノム医療 / シリコン・シークエンサー / 消化器癌 / 血液腫瘍 / シリコンシークエンサー
Outline of Final Research Achievements

By utilizing the supercomputer at Human Genome Center (The University of Tokyo), we implemented a whole-genome based personalized cancer genomic medicine at the Research Hospital of the Institute of Medical Science. We employed NGS whole-genome analysis, whole-exome analysis, cancer panel, Sanger sequencing, and omics analysis including pathological data. In this process of implementation and clinical interpretation, we organized a tumor board for genomic medicine. We designed and constructed a system comprising an information infrastructure and sequencing facility of medical informatics including an application of cognitive computing technology (IBM Watson Genomic Analytics) based on biomedical big data and Clarity LIMS. In the practice of personalized cancer genomic medicine, we evaluated the usefulness of this system, and simultaneously identified challenging issues arising from whole-genome based personalized genomic medicine in addition to new discoveries in cancer research.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (45 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (6 results) Journal Article (16 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 16 results,  Open Access: 9 results,  Acknowledgement Compliant: 3 results) Presentation (21 results) (of which Int'l Joint Research: 2 results,  Invited: 14 results) Book (2 results)

  • [Int'l Joint Research] NIH/Duke University/Intermountain Healthcare(米国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] The Wellcome Trust/King's College(英国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] University of Queensland(Australia)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Universite Libre de Bruxelles/University of Leuven(Belgium)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] National University of Singapore/Duke-National University of Singapore(Singapore)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research]

    • Related Report
      2015 Annual Research Report
  • [Journal Article] A novel mouse model of intrahepatic cholangiocarcinoma induced by liver-specific Kras activation and Pten deletion2016

    • Author(s)
      Ikenoue T, Terakado Y, Nakagawa H, Hikiba Y, Fujii T, Matsubara D, Noguchi R, Zhu C, Yamamoto K, Kudo Y, Asaoka Y, Yamaguchi K, Ijichi H, Tateishi K, Fukushima N, Maeda S, Koike K, Furukawa Y
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 23899-23899

    • DOI

      10.1038/srep23899

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Molecular profiles of high-grade and low-grade pseudomyxoma peritonei.2015

    • Author(s)
      Noguchi R, Yano H, Gohda Y, Suda R, Igari T, Ohta Y, Yamashita N, Yamaguchi K, Terakado Y, Ikenoue T, Furukawa Y
    • Journal Title

      Cancer Med

      Volume: 4(12) Issue: 12 Pages: 1809-1816

    • DOI

      10.1002/cam4.542

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Attenuated familial adenomatous polyposis with desmoids by an APC mutation2015

    • Author(s)
      Ikenoue T, Yamaguchi K, Komura M, Imoto S, Yamaguchi R, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Miyano S, Furukawa Y
    • Journal Title

      Human Genome Variation

      Volume: 2 Issue: 1 Pages: 15011-15011

    • DOI

      10.1038/hgv.2015.11

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A novel APC mosaicism in a patient with familial adenomatous polyposis.2015

    • Author(s)
      Moriya Iwaizumi, Ken Sugimoto, et al.
    • Journal Title

      Hum Genome Var

      Volume: 10 Issue: 1 Pages: 15057-15057

    • DOI

      10.1038/hgv.2015.57

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Relationship between smoking and multiple colorectal cancers in patients with Japanese Lynch syndrome: a cross-sectional study conducted by the Japanese Society for Cancer of the Colon and Rectum.2015

    • Author(s)
      Tanakaya K, Furukawa Y, Nakamura Y, Hirata K, Tomita N, Tamura K, Sugano K, Ishioka C, Yoshida T, Ishida H, Watanabe T, Sugihara K.
    • Journal Title

      Jpn J Clin Oncol.

      Volume: 45(3) Issue: 3 Pages: 307-310

    • DOI

      10.1093/jjco/hyu218

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Detection of APC mosaicism by next-generation sequencing in an FAP patient.2015

    • Author(s)
      Yamaguchi K, Komura M, Yamaguchi R, Imoto S, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Takahashi N, Ikenoue T, Hata K, Tsurita G, Shinozaki M, Suzuki Y, Sugano S, Miyano S, Furukawa Y
    • Journal Title

      J Hum Genet

      Volume: 60(5) Issue: 5 Pages: 227-231

    • DOI

      10.1038/jhg.2015.14

    • NAID

      40020462565

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Comparison of clinical features between suspected familial colorectal cancer type X and Lynch syndrome in Japanese patients with colorectal cancer:2015

    • Author(s)
      Yamaguchi T, Furukawa Y, Nakamura Y, Matsubara N, Ishikawa H, Arai M, Tomita N, Tamura K, Sugano K, Ishioka C, Yoshida T, Moriya Y, Ishida H, Watanabe T, Sugihara K;
    • Journal Title

      Jpn J Clin Oncol.

      Volume: 45(2) Issue: 2 Pages: 153-159

    • DOI

      10.1093/jjco/hyu190

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures2015

    • Author(s)
      Yuichi Shiraishi , Georg Tremmel, Satoru Miyano, Matthew Stephens
    • Journal Title

      PLoS Genetics

      Volume: 11(12) Issue: 12 Pages: e1005657-e1005657

    • DOI

      10.1371/journal.pgen.1005657

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Global implementation of genomic medicine: We are not alone2015

    • Author(s)
      Manolio TA, Abramowicz M, Al-Mulla F, Anderson W, (22名), Miyano S, Naparstek Y, O'Rourke PP, Patrinos GP, Rehm HL, Relling MV, Rennert G, Rodriguez LL, Roden DM, Shuldiner AR, Sinha S, Tan P, Ulfendahl M, Ward R, Williams MS, Wong JE, Green ED, Ginsburg GS
    • Journal Title

      Science Translational Medicine

      Volume: 7(290) Issue: 290

    • DOI

      10.1126/scitranslmed.aab0194

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Clearance of blasts from peripheral blood during induction chemotherapy using exponential decay model predicts complete remission and long-term survival in adult acute myeloid leukemia2015

    • Author(s)
      Konuma T, Kato S, Yuji K, Ohno N, Uchimaru K, Takahashi S, Tojo A.
    • Journal Title

      Int J Lab Hematol.

      Volume: - Issue: 3

    • DOI

      10.1111/ijlh.12302

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data2015

    • Author(s)
      Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 30(1) Pages: 116-118

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring the global structure of chromosomes from structural variations2015

    • Author(s)
      Yasuda T, Miyano S.
    • Journal Title

      BMC Genomics

      Volume: 16(suppl 2):S13

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations2014

    • Author(s)
      Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S.
    • Journal Title

      Bioinformatics

      Volume: 30(23) Pages: 3302-3309

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Overexpression of cohesion establishment factor DSCC1 through E2F in colorectal cancer.2014

    • Author(s)
      Yamaguchi K, Rui Yamaguchi R, Takahashi N, Ikenoue T, Fujii T, Shinozaki M, Tsurita G, Hata K, Niida A, Imoto S, Miyano S, Nakamura Y, Furukawa Y
    • Journal Title

      PLoS ONE

      Volume: 9 Issue: 1 Pages: e85750-e85750

    • DOI

      10.1371/journal.pone.0085750

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In vivo leukemogenic potential of an interleukin-7 receptor-α mutant in hematopoietic stem/progenitor cells.2013

    • Author(s)
      Yokoyama K, Tojo A, et al.
    • Journal Title

      Blood

      Volume: 122 Issue: 26 Pages: 4259-4263

    • DOI

      10.1182/blood-2012-08-451278

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Genetic alterations in Japanese extrahepatic biliary tract cancer

    • Author(s)
      Noguchi R, Yamaguchi K, Ikenoue T, Terakado Y, Ohta Y, Yamashita N, Kainuma O, Yokoi S, Maru Y, Nagase H, Furukawa Y. Genetic alterations in Japanese extrahepatic biliary tract cancer
    • Journal Title

      Oncology Letters

      Volume: 印刷中

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] コグニティブ・コンピューティングの造血器腫瘍臨床シーケンスへの試験的導入2016

    • Author(s)
      横山和明、遊佐 希、伊藤美香、小林真之、小川弥穂、竹田玲奈、武井智美、越智清純、川俣豊隆、小沼貴晶、加藤せい子、清水英悟、小山尚彦、大野伸広、高橋聡、内丸薫、山口 類、井元清哉、古川洋一、宮野 悟、東條有伸
    • Organizer
      第78回日本血液学会学術集会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-10-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] WASPの一アミノ酸変異に起因するX連鎖重症好中球減少症の本邦第一例2016

    • Author(s)
      小林真之、横山和明、遊佐 希、川俣豊隆、大野伸広、清水英悟、山口 類、井元清哉、古川洋一、宮野 悟、東條有伸
    • Organizer
      第78回日本血液学会学術集会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-10-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] MYD88 L265P Mutated Splenic Marginal Zone Lymphoma associated with Cold Agglutinin Disease2016

    • Author(s)
      越智清純、横山和明、遊佐 希、伊藤美香、小林真之、小川弥穂、竹田玲奈、武井智美、川俣豊隆、福山朋房、大野伸広、高橋聡、山口 類、内丸薫、井元清哉、古川洋一、宮野 悟、東條有伸
    • Organizer
      第78回日本血液学会学術集会
    • Place of Presentation
      パシフィコ横浜(神奈川県横浜市)
    • Year and Date
      2016-10-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Cancer Genomes and Clinical Sequence2015

    • Author(s)
      Satoru Miyano
    • Organizer
      Princess Al Jawhara Center for Molecular Medicine: The 9th Scientific Conference
    • Place of Presentation
      Arabic Gulf University, Manama, Bahrain
    • Year and Date
      2015-11-28
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Cancer Clinical Whole Genome Sequencing2015

    • Author(s)
      Satoru Miyano
    • Organizer
      Global Genomic Medicine 2015: Implementing Genomic Medicine into Practice
    • Place of Presentation
      Biopolis, Singapore
    • Year and Date
      2015-11-06
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ゲノムとビッグデータ―がん研究の視点から―2015

    • Author(s)
      宮野 悟
    • Organizer
      日本人類遺伝学会第60回大会
    • Place of Presentation
      京王プラザホテル(東京都新宿区)
    • Year and Date
      2015-10-15
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 東大医科学研究所における臨床シークエンス体制2015

    • Author(s)
      宮野 悟
    • Organizer
      日本人類遺伝学会第60回大会[キアゲン・ランチョンせみなー]
    • Place of Presentation
      京王プラザホテル(東京都新宿区)
    • Year and Date
      2015-10-15
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Understanding Cancer Heterogeneity with Supercomputers2015

    • Author(s)
      Satoru Miyano
    • Organizer
      The Third BMIRC International Symposium
    • Place of Presentation
      池のおく園(福岡県田川市)
    • Year and Date
      2015-03-05
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] がんゲノムとその未来2015

    • Author(s)
      宮野 悟
    • Organizer
      NPO健康医療開発機構第8回シンポジウム
    • Place of Presentation
      学士会館(東京都千代田区)
    • Year and Date
      2015-03-01
    • Related Report
      2014 Annual Research Report
  • [Presentation] 体質を知って、予防する。遺伝性のがんについて2015

    • Author(s)
      古川 洋一
    • Organizer
      NPO健康医療開発機構第8回シンポジウム
    • Place of Presentation
      学士会館(東京都千代田区)
    • Year and Date
      2015-03-01
    • Related Report
      2014 Annual Research Report
  • [Presentation] がん研究とスーパーコンピュータ、そして臨床シークエンス2014

    • Author(s)
      宮野 悟
    • Organizer
      ゲノム創薬・医療フォーラム第1回シンポジウム
    • Place of Presentation
      東大医科研(東京都港区)
    • Year and Date
      2014-09-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 臨床シークエンス情報インフラストラクチャー2014

    • Author(s)
      宮野 悟
    • Organizer
      日本人類遺伝学会第59回大会
    • Place of Presentation
      タワーホール船堀(東京都江戸川区)
    • Year and Date
      2014-09-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Supercomputers for Cancer Research and Cancer Big Data2014

    • Author(s)
      Satoru iyano
    • Organizer
      The 3rd SNU International Bioinformatics Workshop 2014
    • Place of Presentation
      ソウル(韓国)
    • Year and Date
      2014-06-23
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Informatics Infrastructure for Clinical Whole Genome Sequencing2014

    • Author(s)
      Satoru Miyano
    • Organizer
      The 41st IMSUT Founding Commemorative Symposium
    • Place of Presentation
      東大医科研(東京都港区)
    • Year and Date
      2014-05-30
    • Related Report
      2014 Annual Research Report
  • [Presentation] Personalized Genomic Medicine at Institute of Medical Science of University of Tokyo

    • Author(s)
      Satoru Miyano
    • Organizer
      Dagstuhl Seminar on Genomic Privacy
    • Place of Presentation
      Schloss Dagstuhl, Germany
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] New initiative for the implementation of Genomic Medicine in Japan

    • Author(s)
      Naoko Okamura, Michiaki Kubo, Satoru Miyano
    • Organizer
      NIH NHGRI Genomic Medicine Meeting VI “GLOBAL LEADERS IN GENOMIC MEDICINE”
    • Place of Presentation
      National Academy of Sciences, Washington, DC 20001, USA
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole Genome Sequencing and Supercomputer for Personalized Genomic Medicine

    • Author(s)
      Satoru Miyano
    • Organizer
      JST Big Data Workshop
    • Place of Presentation
      梅田、大阪
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] DNAビッグデータの新世界より

    • Author(s)
      宮野 悟
    • Organizer
      JDSF BIG DATA DAY 2014セミナー
    • Place of Presentation
      株式会社ビットアイル <セミナールーム> 東京都品川区東品川2-2-28 タチバナビル1F
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 臨床シークエンス情報基盤

    • Author(s)
      宮野 悟
    • Organizer
      ゲノムテクノロジー第164 委員会 第42 回研究会「クリニカルシークエンス」
    • Place of Presentation
      秋葉原UDX ギャラリーネクスト、東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] DNAの新世界―未来の健康と医療はここに

    • Author(s)
      宮野 悟
    • Organizer
      第九回「知創薬コンソーシアム」
    • Place of Presentation
      浜松町貿易センタービル39F、東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ヒトゲノム解読から10年、黒船来航から160年~日本は夢物語、米国では明日の問題~

    • Author(s)
      宮野 悟
    • Organizer
      NPO健康医療開発機構セミナー
    • Place of Presentation
      学士会館、神田神保町、東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] 実験医学 Vol.34-No.5 「ビッグデータ 変革する生命科学・医療」激増するオミクスデータ・医療データとどう向き合い、どう活用すべきか?2016

    • Author(s)
      永井良三,宮野 悟,大江和彦/編
    • Total Pages
      223
    • Publisher
      羊土社
    • Related Report
      2015 Annual Research Report
  • [Book] 変わる遺伝子医療-私のゲノムを知るとき2014

    • Author(s)
      古川洋一
    • Total Pages
      189
    • Publisher
      ポプラ社
    • Related Report
      2013 Annual Research Report

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Published: 2013-05-21   Modified: 2022-01-31  

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