Medical informatics infrastructure for personalized genomic medicine

• Project/Area Number: 25280105
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: The 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: ¥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.

Research Products

• [Int'l Joint Research] NIH/Duke University/Intermountain Healthcare(USA)
• [Int'l Joint Research] The Wellcome Trust/King's College(UK)
• [Int'l Joint Research] University of Queensland(Australia)
• [Int'l Joint Research] Universite Libre de Bruxelles/University of Leuven(Belgium)
• [Int'l Joint Research] National University of Singapore/Duke-National University of Singapore(Singapore)
• [Int'l Joint Research]
• [Journal Article] Smyd5 plays pivotal roles in both primitive and definitive hematopoiesis during zebrafish embryogenesis. (2016)
  • 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: Scientific Report Volume: 印刷中 Pages: 1-11
  • DOI: 10.1038/srep23899
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] A simple model-based approach to inferring and visualizing cancer mutation signatures (2016)
  • Author(s): Yuichi Shiraishi , Georg Tremmel, Satoru Miyano, Matthew Stephens
  • Journal Title: PLoS Genetics Volume: 11(12)
  • DOI: 10.1371/journal.pgen.1005657
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [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 Medicine Volume: 4(12) Pages: 1809-1816
  • DOI: 10.1002/cam4.542
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Attenuated familial adenomatous polyposis with desmoids by an APC mutation (2015)
  • 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 Pages: 15011-15011
  • DOI: 10.1038/hgv.2015.11
  • 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 Variation Volume: 10 Pages: 15057-15057
  • DOI: 10.1038/hgv.2015.57
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [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: Japanese Journal of Clinical Oncology Volume: 45(3) Pages: 307-310
  • DOI: 10.1093/jjco/hyu218
  • 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: Journal of Human Genetics Volume: 60(5) Pages: 227-231
  • DOI: 10.1038/jhg.2015.14
  • NAID: 40020462565
  • 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: a cross-sectional study conducted by the Japanese Society for Cancer of the Colon and Rectum (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: Japanese Journal of Clinical Oncology Volume: 45(2) Pages: 153-159
  • DOI: 10.1093/jjco/hyu190
  • Peer Reviewed / Open Access
• [Journal Article] Global implementation of genomic medicine: We are not alone (2015)
  • 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)
  • DOI: 10.1126/scitranslmed.aab0194
  • 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 leukemia. (2015)
  • Author(s): Konuma T, Kato S, Yuji K, Ohno N, Uchimaru K, Takahashi S, Tojo A.
  • Journal Title: Int J Lab Hematol Volume: -
  • DOI: 10.1111/ijlh.12302
  • Peer Reviewed
• [Journal Article] Genomon ITDetector: A tool for somatic internal tandem duplication detection from cancer genome sequencing data (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Inferring the global structure of chromosomes from structural variations (2015)
  • Author(s): Yasuda T, Miyano S.
  • Journal Title: BMC Genomics Volume: 16(suppl 2):S13
  • Peer Reviewed
• [Journal Article] HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations (2014)
  • 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
  • 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
  • DOI: 10.1371/journal.pone.0085750
  • Peer Reviewed
• [Journal Article] In vivo leukemogenic potential of an interleukin 7 receptor α chain mutant in hematopoietic stem and progenitor cells (2013)
  • Author(s): Yokoyama K, Tojo A, et al.
  • Journal Title: Blood Volume: 122 Pages: 4259-4263
  • DOI: 10.1182/blood-2012-08-451278
  • 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
  • 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
• [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
• [Presentation] MYD88 L265P Mutated Splenic Marginal Zone Lymphoma associated with Cold Agglutinin Disease (2016)
  • 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
• [Presentation] Cancer Genomes and Clinical Sequence (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Cancer Clinical Whole Genome Sequencing (2015)
  • 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
  • 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
  • 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
  • Invited
• [Presentation] Understanding Cancer Heterogeneity with Supercomputers (2015)
  • 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
  • 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
• [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
• [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
  • 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
• [Presentation] Supercomputers for Cancer Research and Cancer Big Data (2014)
  • 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
  • Invited
• [Presentation] Informatics Infrastructure for Clinical Whole Genome Sequencing (2014)
  • 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
• [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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
• [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