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Development of methods for comprehensive characterization of somatic variants causing transcription aberrations and their application to genomic medicine

Research Project

Project/Area Number 18H03327
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

Yuichi Shiraishi  国立研究開発法人国立がん研究センター, 研究所, ユニット長 (70516880)

Co-Investigator(Kenkyū-buntansha) 片岡 圭亮  国立研究開発法人国立がん研究センター, 研究所, 分野長 (90631383)
Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2020: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2019: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2018: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Keywordsゲノム / 統計科学 / がん / トランスクリプトーム / スプライシング / 大規模データ解析 / ゲノム変異 / がんゲノム / クラウド / 機械学習 / 後天的変異
Outline of Final Research Achievements

We have summarized the research results of SAVNet, which we had been developing, and contributed to The Pan-Cancer Analysis of Whole Genomes project led by the International Cancer Genome Consortium. In addition, by applying SAVNet to data on rare diseases, we have succeeded in discovering several novel genetic mutations. In order to utilize large-scale transcriptome data in public databases such as Sequence Read Archive, we have developed an algorithm and software to identify splicing-related variants from transcriptome data alone. In addition, we developed an information analysis infrastructure for large-scale transcriptomes by integrating technologies such as container virtualization and cloud computing.

Academic Significance and Societal Importance of the Research Achievements

ゲノムシークエンス技術の革新により、様々な疾患の新規原因遺伝子変異が同定され、さらに、個人のゲノムのシークエンスを行い、診断、治療に役立てる「ゲノム医療」の試みが進んでいる。一方で、特に、非エキソン領域における変異の機能的意義付けが困難であり、未だにゲノムデータが有するポテンシャルを人類は十分に活かしきれていない。本研究の目的は、ゲノム変異における最も重要なクラスの一つである、スプライシングの異常を引き起こす変異に着目し、当該変異を同定するための方法論の開発を進め、大規模データ解析を通じたデータベース化を行い、ゲノム医療に役立つ基盤技術・リソースの開発を行うものである。

Report

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

    (19 results)

All 2020 2019 2018 Other

All Int'l Joint Research (2 results) Journal Article (3 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 3 results,  Open Access: 3 results) Presentation (9 results) (of which Int'l Joint Research: 1 results,  Invited: 5 results) Book (1 results) Remarks (4 results)

  • [Int'l Joint Research] カリフォルニア大学 サンタクルーズ校(米国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] チューリッヒ工科大学(スイス)

    • Related Report
      2019 Annual Research Report
  • [Journal Article] Genomic basis for RNA alterations in cancer2020

    • Author(s)
      PCAWG Transcriptome Core Group et al.
    • Journal Title

      Nature

      Volume: 578 Issue: 7793 Pages: 129-136

    • DOI

      10.1038/s41586-020-1970-0

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Effectiveness of integrated interpretation of exome and corresponding transcriptome data for detecting splicing variants of genes associated with autosomal recessive disorders2019

    • Author(s)
      Yamada Mamiko、Suzuki Hisato、Shiraishi Yuichi、Kosaki Kenjiro
    • Journal Title

      Molecular Genetics and Metabolism Reports

      Volume: 21 Pages: 100531-100531

    • DOI

      10.1016/j.ymgmr.2019.100531

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A comprehensive characterization of cis-acting splicing-associated variants in human cancer.2018

    • Author(s)
      Shiraishi Y, Kataoka K, Chiba K, Okada A, Kogure Y, Tanaka H, Ogawa S, Miyano S.
    • Journal Title

      Genome Res.

      Volume: 28 Issue: 8 Pages: 1111-1125

    • DOI

      10.1101/gr.231951.117

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] An atlas of intron retention associated variants collected by cloud-based transcriptome analysis platform2020

    • Author(s)
      Yuichi Shiraishi
    • Organizer
      3rd International Caparica Conference in Splicing 2020
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Detecting genomic variants causing abnormal splicing using only transcriptome data2020

    • Author(s)
      Naoko Iida, Kenichi Chiba, Raul Mateos, Yuichi Shiraishi
    • Organizer
      79th Annual Meeting of the Japanese Cancer Association
    • Related Report
      2020 Annual Research Report
  • [Presentation] Splicing Junction Variant-based Naive Bayes Classifier as a Tool for Hot Spot Mutation Status Prediction in Pancancer2020

    • Author(s)
      Raul Mateos, Naoko Iida, Kenichi Chiba, Ai Okada, Yuichi Shiraishi
    • Organizer
      79th Annual Meeting of the Japanese Cancer Association
    • Related Report
      2020 Annual Research Report
  • [Presentation] 大規模トランスクリプトーム解析の情報基盤2020

    • Author(s)
      白石 友一
    • Organizer
      第2回日本メディカルAI学会学術集会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 大規模トランスクリプトーム解析の情報基盤2019

    • Author(s)
      白石 友一
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] がんゲノム・トランスクリプトームの統合解析2018

    • Author(s)
      白石友一
    • Organizer
      2018年度統計関連学会連合大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] がんゲノムにおけるスプライシング変異の網羅的な検出2018

    • Author(s)
      白石友一
    • Organizer
      生命医薬情報学連合大会(IIBMP2018)
    • Related Report
      2018 Annual Research Report
  • [Presentation] がんゲノムにおけるスプライシング変異の網羅的な検出2018

    • Author(s)
      白石友一
    • Organizer
      第91回日本生化学会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Systematic Identification of Splicing Associated Variants toward Precision Medicine2018

    • Author(s)
      白石友一
    • Organizer
      第49回高松宮妃癌研究基金国際シンポジウム
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Book] 「がんゲノムにおけるスプライシング変異の検出」、医学のあゆみ 2675巻 5号2020

    • Author(s)
      白石友一
    • Total Pages
      7
    • Publisher
      医歯薬出版
    • Related Report
      2020 Annual Research Report
  • [Remarks] SAVNet 0.4.0 documentation

    • URL

      https://savnet.readthedocs.io/en/latest/index.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] Intron retention associated variant detection

    • URL

      https://github.com/friend1ws/iravnet

    • Related Report
      2019 Annual Research Report
  • [Remarks] SAVNet github page

    • URL

      https://github.com/friend1ws/SAVNet

    • Related Report
      2018 Annual Research Report
  • [Remarks] SAVNet documentation

    • URL

      https://savnet.readthedocs.io/en/latest/index.html

    • Related Report
      2018 Annual Research Report

URL: 

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

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