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Development of autonomous intelligence acquisition system infrastructure from large scale transcriptome

Research Project

Project/Area Number 21H03549
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionNational Cancer Center Japan

Principal Investigator

Shiraishi Yuichi  国立研究開発法人国立がん研究センター, 研究所, 分野長 (70516880)

Co-Investigator(Kenkyū-buntansha) 飯田 直子  国立研究開発法人国立がん研究センター, 東病院, 研究員 (40360557)
吉見 昭秀  国立研究開発法人国立がん研究センター, 研究所, 分野長 (80609016)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2023: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2022: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2021: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywords大規模データ解析 / ゲノム変異 / クラウド / スプライシング / トランスクリプトーム / 公共データ / スプライシング異常
Outline of Research at the Start

ゲノム医療の実装等が進み、研究のみならず医療においても種々のオミクス解析が盛んに実行される中で、各種データの蓄積は加速度的に進んでいる。本研究課題においてはオミクスデータの有効性をさらに高めるべく、大規模トランスクリプトームデータを用いた新たな病的変異のスクリーニング基盤の開発を行う。本研究課題の遂行を通じて、大規模データから自律的に知識獲得を行うプラットフォームの一例を与えることで、今後のデータ駆動型科学・医療の推進に向けたデータ集取・解析基盤のあり方についての検討・提案を行うことを目指す。

Outline of Final Research Achievements

Using large-scale transcriptome data stored in public sequencing repositories, we developed and implemented algorithmic software to identify genomic mutations that cause various splicing abnormalities. These were applied to more than 300,000 transcriptome data in the Sequence Read Archive, and more than tens of thousands of splicing mutations were identified. In addition, we performed a detailed analysis of the biological significance of these splicing variants. As an example, we identified a gain-of-function splice-site generating mutation in the NOTCH1 gene and demonstrated through practical biological experiments that this mutation causes activity that can be suppressed by nucleic acid drugs.

Academic Significance and Societal Importance of the Research Achievements

今回開発したプラットフォームは、公共シークエンスレポジトリの蓄積されたデータを用いて実行することで、疾患に関連する変異および核酸医薬の創薬ターゲットとなる変異を自動的に検出可能となることを示した。これは、ゲノム医療における自律的な知識獲得の基盤となる実例となる。また、今後さらに蓄積が進むゲノムデータを効果的に活用するための実例となり、将来的にデータ駆動型の科学・医学を構築するための一つのモデルケースとなるだろう。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (25 results)

All 2024 2023 2022 2021 Other

All Journal Article (6 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 5 results,  Open Access: 6 results) Presentation (11 results) (of which Int'l Joint Research: 2 results,  Invited: 11 results) Book (3 results) Remarks (5 results)

  • [Journal Article] Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes2024

    • Author(s)
      Nakamura Wataru、Hirata Makoto、 Akira、Kawai、Noguchi Michio、Umezawa Akihiro、Ito Shuichi、Yoshida Teruhiko、Shiraishi Yuichi、NCBN Controls WGS Consortium et al
    • Journal Title

      npj Genomic Medicine

      Volume: 9 Issue: 1 Pages: 11-11

    • DOI

      10.1038/s41525-024-00394-z

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv2023

    • Author(s)
      Shiraishi Yuichi、Koya Junji、Chiba Kenichi、Okada Ai、Arai Yasuhito、Saito Yuki、Shibata Tatsuhiro、Kataoka Keisuke
    • Journal Title

      Nucleic Acids Research

      Volume: 51 Issue: 14 Pages: e74-e74

    • DOI

      10.1093/nar/gkad526

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phasing analysis of lung cancer genomes using a long read sequencer2022

    • Author(s)
      Sakamoto Yoshitaka、Miyake Shuhei、Oka Miho、Kanai Akinori、Kawai Yosuke、Nagasawa Satoi、Shiraishi Yuichi、Tokunaga Katsushi、Kohno Takashi、Seki Masahide、Suzuki Yutaka、Suzuki Ayako
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 3464-3464

    • DOI

      10.1038/s41467-022-31133-6

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data2022

    • Author(s)
      Shiraishi Yuichi、Okada Ai、Chiba Kenichi、Kawachi Asuka、Omori Ikuko、Mateos Ra?l Nicol?s、Iida Naoko、Yamauchi Hirofumi、Kosaki Kenjiro、Yoshimi Akihide
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 5357-5357

    • DOI

      10.1038/s41467-022-32887-9

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multi-omics analysis defines highly refractory RAS burdened immature subgroup of infant acute lymphoblastic leukemia2022

    • Author(s)
      Tomoya Isobe, Masatoshi Takagi, Aiko Sato-Otsubo, et al. (57人中28番目)
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 4501-4501

    • DOI

      10.1038/s41467-022-32266-4

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data2021

    • Author(s)
      Yuichi Shirishi et al.,
    • Journal Title

      bioRxiv

      Volume: NA

    • DOI

      10.1101/2021.10.05.463278

    • Related Report
      2021 Annual Research Report
    • Open Access
  • [Presentation] 大規模公共データを用いたスプライスサイト生成変異の網羅的探索2024

    • Author(s)
      白石 友一
    • Organizer
      計算疾患システム生物学シンポジウム
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Systematic discovery of splice-site creating variants from massive publicly available transcriptome sequencing data2023

    • Author(s)
      Yuichi Shiraishi
    • Organizer
      CSHL Genome Informatics Meetings
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 完全がんゲノム配列の再構成に向けたロングリードシークエンス解析基盤の開発2023

    • Author(s)
      白石友一
    • Organizer
      令和4年度国際がん研究シンポジウム「WGS, Long-read and Beyond」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] Integrated whole genome and transcriptome analysis platform applied to adolescent and young adult cancers2022

    • Author(s)
      白石友一
    • Organizer
      第81回 日本癌学会学術総会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 高精度に構造異常を検出するための解析基盤2022

    • Author(s)
      白石友一
    • Organizer
      日本メディカルAI学会 ToMMo 共催企画サテライトシンポジウム「コホート・バイオバンクとビッグデータ解析の可能性」
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 知識発見を加速するゲノム解析プラットフォームについて2022

    • Author(s)
      白石友一
    • Organizer
      和3年度国際がん研究シンポジウム「全ゲノム解析が変革するがん研究・がん医療」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 大規模公共トランスクリプトームレポジトリからの自律的知識獲得システム基盤2022

    • Author(s)
      白石友一
    • Organizer
      2021年度国立遺伝学研究所研究会「ゲノム医科学とバイオインフォマティクスの接点と集学研究」
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 知識発見を加速するオミクス解析基盤2022

    • Author(s)
      白石友一
    • Organizer
      大阪大学医学系研究科バイオインフォマティクスセミナー
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] クラウドを使ったゲノム解析基盤2022

    • Author(s)
      白石友一
    • Organizer
      第11回マルチNGSオミクス解析研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Systematic identification of intron retention associated variants from massive publicly available transcriptome sequencing data2021

    • Author(s)
      Yuichi Shiraishi
    • Organizer
      International Conference on Genomics (IGC-16)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Massive in-silico screening of intron retention causing variants using publicly available transcriptome sequencing data2021

    • Author(s)
      Yuichi Shiraishi
    • Organizer
      nternational Caparica Conference in splicing 2021 (splicing2021)
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] 実験医学増刊 41 (7)2023

    • Author(s)
      白石友一、岡田愛、河野隆志
    • Total Pages
      6
    • Publisher
      羊土社
    • Related Report
      2022 Annual Research Report
  • [Book] 医学のあゆみ 283 (9)2022

    • Author(s)
      白石友一、岡田愛
    • Total Pages
      8
    • Publisher
      医歯薬出版
    • Related Report
      2022 Annual Research Report
  • [Book] 実験医学2022

    • Author(s)
      白石友一
    • Total Pages
      5
    • Publisher
      クラウドを使ったゲノム解析環境の構築
    • Related Report
      2021 Annual Research Report
  • [Remarks] SSCV DB

    • URL

      https://sscvdb.io/

    • Related Report
      2023 Annual Research Report
  • [Remarks] juncmut software

    • URL

      https://github.com/ncc-gap/juncmut

    • Related Report
      2023 Annual Research Report
  • [Remarks] IRAVNet software page

    • URL

      https://github.com/friend1ws/iravnet

    • Related Report
      2022 Annual Research Report
  • [Remarks] IRAV DB

    • URL

      https://iravdb.io/

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
  • [Remarks] IRAVNet

    • URL

      https://github.com/friend1ws/iravnet

    • Related Report
      2021 Annual Research Report

URL: 

Published: 2021-04-28   Modified: 2025-01-30  

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