• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

全ゲノム・トランスクリプトームのシステム的統合解析による肝癌の非コード領域の理解

Publicly Offered Research

Project AreaIntegrative Systems Understanding of Cancer for Advanced Diagnosis, Therapy and Prevention
Project/Area Number 25134717
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

中川 英刀  独立行政法人理化学研究所, 統合生命医科学研究センター, チームリーダー (50361621)

Project Period (FY) 2013-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywordsゲノム / がん / トランスクリプトーム / 非コード領域
Outline of Annual Research Achievements

肝癌270症例の全ゲノムシークエンス(WGS)と、対応する凍結標本のうち高品質のRNAが抽出できた200症例以上のRNA-Seqを完了した。WGS解析によって体細胞点突然変異 (SNV)、挿入・欠失(indel)、構造異常(SV)、コピー数変化(CNA)をそれぞれ独自の解析パイプラインにて検出した。特に、非コード領域に注目し、データベースにて登録されている非コードRNA、プロモーター領域、3'および 5'-UTR領域中で、変異が集積している領域を多数同定した。その中には、すでに報告されているTERET遺伝子の上流プロモーター領域の変異が含まれていた。また、全ゲノムを500 baseの領域に区切り(bin)その中に含まれる体細胞変異の個数を集計し、周辺の前後500kb、合計1 Mbの背景的変異率を計算し、背景変異率に比べて有意に変異率が高い500kbのbin領域を100箇所以上同定し、更なるフィルタリングを行い、87箇所に変異が集積するゲノム部位を同定した。その中には、TP53、CTNNB1、およびALB遺伝子領域が含まれていた。そのうち32箇所は、遺伝子間領域にあり、周囲の遺伝子との発現との関連が見られるものもあった。3%以上の肝がんで変異が検出された領域については、Sanger法によって、体細胞変異の確認を行った。また、transcription factorとの結合が予測される領域もあり、EMSA法やluciferase法による実験も行い、その機能的意義についても確認ができた。

Research Progress Status

26年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

26年度が最終年度であるため、記入しない。

Report

(2 results)
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (14 results)

All 2015 2014 2013

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 2 results) Presentation (12 results) (of which Invited: 12 results)

  • [Journal Article] Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity2015

    • Author(s)
      Fujimoto A, Furuta M, Shiraishi Y, Shigemizu D, Abe T, Boroevich KA, Nakano K, Yamamoto Y, Tanaka H, Shibuya T, Shibata T, Kubo M, Chayama K, Miyano S, Tsunoda T, Nakagawa H, 他
    • Journal Title

      Nature Communications

      Volume: 6 Issue: 1 Pages: 6120-6120

    • DOI

      10.1038/ncomms7120

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers2014

    • Author(s)
      Shiraishi Y, Fujimoto A, Furuta M, Chayama K, Tsunoda T, Miyano S, and Nakagawa H, 他
    • Journal Title

      PLoS One

      Volume: 9 Issue: 12 Pages: e114263-e114263

    • DOI

      10.1371/journal.pone.0114263

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Rearrangements and non-coding mutations detected in liver cancers by whole genome sequencing2015

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      10th ICGC Scientific Workshop
    • Place of Presentation
      Verona, Italy
    • Year and Date
      2015-02-15 – 2015-02-17
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Decoding liver cancer genome by whole genome sequencing2014

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      14th Japanese-German Cancer Workshop
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2014-11-14 – 2014-11-16
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequence analysis of liver cancers reveals non-coding alterations and impact of chronic inflammation on mutational landscape2014

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      9th ICGC Scientific Workshop
    • Place of Presentation
      北京、中国
    • Year and Date
      2014-05-17 – 2014-05-20
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Decoding liver cancer genome toward personalized medicine2014

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      11th Asian Clinical Oncology Society Meeting
    • Place of Presentation
      Taipei, Taiwan
    • Year and Date
      2014-05-02 – 2014-05-03
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Whole genome pictures of live cancers and personalized medicine2014

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      AACR 2014, Major Symposium
    • Place of Presentation
      San Diego, USA
    • Year and Date
      2014-04-06 – 2014-04-09
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequencing analysis for liver cancer genome2013

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      4th Institute for Refractory Cancer Research International Symposium
    • Place of Presentation
      Seoul, Korea
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole genome signatures of liver cancer and personalized medicine2013

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      12th Roche Round Asia Oncology Forum
    • Place of Presentation
      Seoul, Korea
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequencing analysis of cancer and its interpretation2013

    • Author(s)
      中川 英刀
    • Organizer
      第72回日本癌学会総会
    • Place of Presentation
      横浜
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequencing analysis of liver cancer, forwarding to personalized medicine2013

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      BGI 8th International Conference on Genomics
    • Place of Presentation
      Shenzen, China
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequencing analysis of liver cancer, forwarding to personalized medicine2013

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      20th Yonsei Cancer Research Annual International Symposium
    • Place of Presentation
      Seoul, Korea
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Whole genome sequencing analysis of liver cancer and personalized cancer medicine2013

    • Author(s)
      Hidewaki Nakagawa
    • Organizer
      Genomic Research Asia
    • Place of Presentation
      Singapore
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] がんの全ゲノムシークエンス解析による個別化医療2013

    • Author(s)
      中川 英刀
    • Organizer
      第58回 日本人類遺伝学会
    • Place of Presentation
      仙台
    • Related Report
      2013 Annual Research Report
    • Invited

URL: 

Published: 2013-05-15   Modified: 2019-07-29  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi