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Structural analysis of the whole genome data from BioBank Japan

Research Project

Project/Area Number 26860228
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Human genetics
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Kamatani Yoichiro  国立研究開発法人理化学研究所, 統合生命医科学研究センター, チームリーダー (00720880)

Research Collaborator SESE Jun  国立研究開発法人産業技術総合研究所, 人工知能研究センター・機械学習研究チーム, チーム長
KOIDO Masaru  国立研究開発法人理化学研究所, 統合生命医科学研究センター, 客員研究員
KANAI Masahiro  国立研究開発法人理化学研究所, 統合生命医科学研究センター, 研修生
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywords機械学習 / ゲノム / 遺伝統計学 / 全ゲノム解析 / エピスタシス / ポリジェニックモデル
Outline of Final Research Achievements

We used BioBank Japan data and applied machine learning technique to detect genetic factors associated with disease occurrence. By using Random Forest (RF), LASSO, Elastic Net, Support Vector Machine (SVM), Extremely Randomized Trees (ERT), and mixed Random Forest (mixed RF), we identified that LASSO and Elastic Net outperformed other methods. This results indicates the importance of regularization in the genetic association model.
In parallel, we applied LD score regression method or Popcorn method to see the differences of genetic background for the complex disease between Japanese and European populations from the view point of polygenic architecture. We revealed that higher heritability for atopic dermatitis and lower for bipolar disorder in Japanese compared with European population. Further studies would clarify the actual genetic regions responsible for these differences.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (3 results)

All 2016 2015 2014

All Presentation (3 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results)

  • [Presentation] Trans-ethnic comparison of partitioned heritability reveals shared cell-type specific enrichment between East Asian and European GWAS2016

    • Author(s)
      金井正弘、秋山雅人、岡田随象、池田匡志、岩田仲生、久保充明、鎌谷洋一郎
    • Organizer
      American Society of Human Genetics Annual Meeting 2016
    • Place of Presentation
      バンクーバー、カナダ
    • Year and Date
      2016-10-18
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Statistical analyses used for gene mapping of human diseases2015

    • Author(s)
      鎌谷 洋一郎
    • Organizer
      Tokyo Workshop on Statistically Sound Data Mining
    • Place of Presentation
      産業技術総合研究所 臨海副都心センター/東京都江東区
    • Year and Date
      2015-02-16
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] missing heritabilityと、遺伝率推定における仮定について2014

    • Author(s)
      鎌谷 洋一郎
    • Organizer
      生命医薬情報学連合大会
    • Place of Presentation
      仙台国際センター/仙台市
    • Year and Date
      2014-10-02
    • Related Report
      2014 Research-status Report
    • Invited

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Published: 2014-04-04   Modified: 2018-03-22  

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