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Development of statistical methods for large scale somatic mutation data mining

Research Project

Project/Area Number 15K00398
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionThe University of Tokyo

Principal Investigator

Yuichi Shiraishi  東京大学, 医科学研究所, 助教 (70516880)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsがんゲノム / 機械学習 / パターンマイニング / 可視化 / 統計手法 / 変異シグナチャー / スプライシング / 統計モデル / トピックモデル / 最適化
Outline of Final Research Achievements

We have developed a novel statistical method for extracting characteristic pattern from somatic mutation data (Shiraishi et al., 2015, https://github.com/friend1ws/pmsignature). Assuming the independence on each factor of mutation signatures and reducing the number of parameters, more robust and interpretable estimates can be obtained. Additionally, the proposed model has close relationships with the “mixed-membership models,” that have been intensively utilized in statistical machine learning and statistical genetics community. Furthermore, we have applied this approach to the set of splicing associated variants and identified several novel patterns (Shiraishi et al., BioRxiv, 2017).

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (19 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (3 results) Journal Article (4 results) (of which Int'l Joint Research: 2 results,  Open Access: 3 results,  Peer Reviewed: 2 results,  Acknowledgement Compliant: 1 results) Presentation (6 results) (of which Int'l Joint Research: 1 results) Remarks (6 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
      2017 Annual Research Report
  • [Int'l Joint Research] スイス連邦工科大学チューリッヒ校(スイス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] The University of Chicago(米国)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types2018

    • Author(s)
      PCAWG Transcriptome Core Group
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/183889

    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Journal Article] A comprehensive characterization of cis-acting splicing-associated variants in human cancer2017

    • Author(s)
      Yuichi Shiraishi, Keisuke Kataoka, Kenichi Chiba, Ai Okada, Yasunori Kogure, Hiroko Tanaka, Seishi Ogawa, Satoru Miyano
    • Journal Title

      bioRxiv

      Volume: -

    • DOI

      10.1101/162560

    • Related Report
      2017 Annual Research Report
    • Open Access
  • [Journal Article] A framework for generating interactive reports for cancer genome analysis2017

    • Author(s)
      Ai Okada, Kenichi Chiba, Hiroko Tanaka, Satoru Miyano, Yuichi Shiraishi
    • Journal Title

      The Journal of Open Source Software

      Volume: 2(20) Issue: 20 Pages: 457-457

    • DOI

      10.21105/joss.00457

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures2015

    • Author(s)
      Yuichi Shiraishi , Georg Tremmel, Satoru Miyano, Matthew Stephens
    • Journal Title

      PLoS Genetics

      Volume: 11(12) Issue: 12 Pages: e1005657-e1005657

    • DOI

      10.1371/journal.pgen.1005657

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] The landscape of splicing associated variants revealed bylarge scale whole exome and transcriptome analysis2017

    • Author(s)
      白石 友一、片岡 圭亮、千葉 健一、岡田 愛、田中 洋子、小川 誠司、宮野 悟
    • Organizer
      第77回日本癌学会学術総会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Genomon-SVを使った大規模エキソーム解析で明らかになった構造変異の全体像2016

    • Author(s)
      白石友一
    • Organizer
      第75回日本癌学会学術総会
    • Place of Presentation
      横浜
    • Year and Date
      2016-10-06
    • Related Report
      2016 Research-status Report
  • [Presentation] 大規模がんゲノム変異データマイニングのための統計学的手法2016

    • Author(s)
      白石友一
    • Organizer
      第五回生命医薬情報学連合大会
    • Place of Presentation
      東京
    • Year and Date
      2016-09-29
    • Related Report
      2016 Research-status Report
  • [Presentation] 大規模がんゲノム変異データマイニングのための統計学的手法2016

    • Author(s)
      白石友一
    • Organizer
      2016年度統計関連学会連合大会
    • Place of Presentation
      金沢
    • Year and Date
      2016-09-04
    • Related Report
      2016 Research-status Report
  • [Presentation] がんゲノムにおける変異シグナチャーを検出する新たな統計的手法について2015

    • Author(s)
      白石友一
    • Organizer
      第74回日本癌学会総会
    • Place of Presentation
      名古屋国際会議場(愛知県名古屋市)
    • Year and Date
      2015-10-08
    • Related Report
      2015 Research-status Report
  • [Presentation] Extraction of Latent Probabilistic Mutational Signature in Cancer Genomes2015

    • Author(s)
      Yuichi Shiraishi
    • Organizer
      RECOMB-Seq/CCB-2015
    • Place of Presentation
      ワルシャワ、ポーランド
    • Year and Date
      2015-04-10
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Remarks] SAVNet’s documentation

    • URL

      http://savnet.readthedocs.io/en/latest/

    • Related Report
      2017 Annual Research Report
  • [Remarks] paplot documentation

    • URL

      http://paplot-doc.readthedocs.io/en/latest/

    • Related Report
      2017 Annual Research Report
  • [Remarks] pmsignature

    • URL

      https://github.com/friend1ws/pmsignature

    • Related Report
      2016 Research-status Report
  • [Remarks] pmsignature_shiny

    • URL

      https://friend1ws.shinyapps.io/pmsignature_shiny/

    • Related Report
      2016 Research-status Report
  • [Remarks] R package for pmsignature

    • URL

      https://github.com/friend1ws/pmsignature

    • Related Report
      2015 Research-status Report
  • [Remarks] pmsignature shiny

    • URL

      https://friend1ws.shinyapps.io/pmsignature_shiny/

    • Related Report
      2015 Research-status Report

URL: 

Published: 2015-04-16   Modified: 2022-05-30  

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