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High-dimensional data analysis platform realizing cancer genome medicine

Research Project

Project/Area Number 18H04123
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 62:Applied informatics and related fields
Research InstitutionNiigata University

Principal Investigator

Okuda Shujiro  新潟大学, 医歯学系, 教授 (00512310)

Co-Investigator(Kenkyū-buntansha) 赤澤 宏平  新潟大学, 医歯学総合病院, 教授 (10175771)
島田 能史  新潟大学, 医歯学系, 講師 (20706460)
永橋 昌幸  新潟大学, 医歯学総合病院, 研究准教授 (30743918)
若井 俊文  新潟大学, 医歯学系, 教授 (50372470)
市川 寛  新潟大学, 医歯学系, 助教 (50721875)
Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥45,760,000 (Direct Cost: ¥35,200,000、Indirect Cost: ¥10,560,000)
Fiscal Year 2020: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
Fiscal Year 2019: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Fiscal Year 2018: ¥29,900,000 (Direct Cost: ¥23,000,000、Indirect Cost: ¥6,900,000)
Keywordsがんゲノム / データベース / 精密医療
Outline of Final Research Achievements

Cancer is a disease caused by damage (mutation) to the DNA in a cell and the accumulation of mutations that are not repaired for many years. The development of very high-throughput DNA sequencers has made it possible to identify mutations at a relatively low cost. Therefore, it is important to integrate the data of cancer genome information and build a data analysis infrastructure. To date, we have created a database of genetic test results for more than 700 solid tumors, including colorectal cancer, gastric cancer, lung cancer, and breast cancer. In addition, we have developed a system that can analyze data under any conditions by combining clinical information and genome mutation information. Furthermore, as an application of this system to artificial intelligence, we have developed a technique for determining pathological conditions using pathological images.

Academic Significance and Societal Importance of the Research Achievements

ある程度以上の症例数が含まれるコホートなどになるとがんゲノムデータは非常に膨大な変異の情報となる。従来は、表計算ソフトなどを駆使し手作業でさまざまな解析を実施してきたが、このような大規模データになると手作業での解析は非常に困難であり、また、エラーを誘発する危険がある。我々が開発してきたデータ解析基盤は、この問題を解決し、がんゲノムデータ解析を効率化する事が可能になる。精密医療としてのがんゲノム医療が実際の患者に適用されているが、臨床データの解析においてエラーがなく信頼性の高い解析結果に基づいたエビデンスが得られる環境は、学術に関してのみならず社会的にも非常に大きな意義を持っていると考える。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (18 results)

All 2021 2020 2019 2018

All Journal Article (5 results) (of which Peer Reviewed: 4 results,  Open Access: 5 results) Presentation (13 results) (of which Int'l Joint Research: 3 results,  Invited: 7 results)

  • [Journal Article] Histopathological characteristics and artificial intelligence for predicting tumor mutational burden-high colorectal cancer2021

    • Author(s)
      Shimada Yoshifumi、Okuda Shujiro、Watanabe Yu、Tajima Yosuke、Nagahashi Masayuki、Ichikawa Hiroshi、Nakano Masato、Sakata Jun、Takii Yasumasa、Kawasaki Takashi、Homma Kei-ichi、Kamori Tomohiro、Oki Eiji、Ling Yiwei、Takeuchi Shiho、Wakai Toshifumi
    • Journal Title

      Journal of Gastroenterology

      Volume: - Issue: 6 Pages: 547-559

    • DOI

      10.1007/s00535-021-01789-w

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic profiling for diffuse type and genomically stable subtypes in gastric cancer2020

    • Author(s)
      Ling Yiwei、Watanabe Yu、Nagahashi Masayuki、Shimada Yoshifumi、Ichikawa Hiroshi、Wakai Toshifumi、Okuda Shujiro
    • Journal Title

      Computational and Structural Biotechnology Journal

      Volume: 18 Pages: 3301-3308

    • DOI

      10.1016/j.csbj.2020.10.021

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Knowledge base toward understanding actionable alterations and realizing precision oncology.2019

    • Author(s)
      Takeuchi S, Okuda S.
    • Journal Title

      Int J Clin Oncol.

      Volume: 24 Issue: 2 Pages: 123-130

    • DOI

      10.1007/s10147-018-1378-0

    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Journal Article] Next generation sequencing-based gene panel tests for the management of solid tumors.2018

    • Author(s)
      Nagahashi M, Shimada Y, Ichikawa H, Kameyama H, Takabe K, Okuda S, Wakai T.
    • Journal Title

      Cancer Sci.

      Volume: 110 Issue: 1 Pages: 6-15

    • DOI

      10.1111/cas.13837

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Novel gene fusions found in cervical cancer.2018

    • Author(s)
      Ling Y, Okuda S.
    • Journal Title

      EBioMedicine

      Volume: 38 Pages: 13-14

    • DOI

      10.1016/j.ebiom.2018.11.013

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 病理画像から遺伝子変異を予測する2020

    • Author(s)
      奥田修二郎
    • Organizer
      第9回生命医薬情報学連合大会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Mutational signatures and clinicopathological relationship extracted from clinical sequence data of 201 cases with colorectal cancer.2019

    • Author(s)
      Takeuchi, S., Ling, Y., Watanabe, Y., Shimada, Y., Wakai, T., Okuda, S.
    • Organizer
      ASHG2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Genome-wide analysis of mutational impact on post translational modification.2019

    • Author(s)
      Ling, Y., Yoshizaki, H., Okuda, S.
    • Organizer
      ISMB2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 固形癌における包括的ゲノム解析に基づくPrecision Medicine2019

    • Author(s)
      若井俊文、島田能史、永橋昌幸、市川寛、油座築、根本万里子、中野麻恵、廣瀬雄己、滝沢一泰、坂田純、亀山仁史、小林隆、棗田学、吉原弘祐、奥田修二郎
    • Organizer
      第57回日本癌治療学会学術集会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 次世代シークエンサーを用いた遺伝子検査とゲノム解析データベース構築2019

    • Author(s)
      永橋昌幸、若井俊文、島田能史、市川寛、羽入隆晃、滝沢一泰、石川卓、坂田純、小林隆、亀山仁史、竹内志穂、奥田修二郎
    • Organizer
      第78回日本癌学会学術総会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Precision Medicine実現に向けたバイオインフォマティクスの役割2019

    • Author(s)
      奥田修二郎
    • Organizer
      第57回日本癌治療学会学術集会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Precision medicine実現に向けたがんゲノムインフォマティクス2019

    • Author(s)
      奥田修二郎
    • Organizer
      第8回生命医薬情報学連合大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] プレシジョンメディスン実現に向けたがんゲノムインフォマティクスとマイクロバイオームへの応用2019

    • Author(s)
      奥田修二郎
    • Organizer
      第61回日本婦人科腫瘍学会・第18回日本婦人科がん分子標的研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Precision medicine を目指すがんゲノムインフォマティクス2019

    • Author(s)
      奥田修二郎
    • Organizer
      JPrOS2019/JES2019
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] がんプレシジョンメディシン実現に向けたバイオインフォマティクス:遺伝子変異と治療薬の知識ベース2018

    • Author(s)
      竹内志穂、凌一葦、渡邉由、若井俊文、奥田修二郎
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Computational approaches towards understanding human genome, proteome, and proteogenome data2018

    • Author(s)
      Shujiro Okuda
    • Organizer
      2018 Taiwan-Japan Joint Conference for Genomics and Proteogenomics and Annual Retreat of Taiwan Genomics and Genetics Society
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 新潟大学におけるがんゲノムプロジェクト2018

    • Author(s)
      奥田修二郎
    • Organizer
      第22回医療情報学会春季学術集会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] がんゲノム医療を加速するデータ解析システム2018

    • Author(s)
      奥田修二郎、渡辺由、凌一葦、竹内志穂
    • Organizer
      第78回新潟癌治療研究会
    • Related Report
      2018 Annual Research Report
    • Invited

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Published: 2018-04-23   Modified: 2022-01-27  

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