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Developments of methods for T-cell receptor sequence data analysis and understanding of diversities in the immune cells

Research Project

Project/Area Number 15K00399
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

Yamaguchi Rui  東京大学, 医科学研究所, 准教授 (90380675)

Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords免疫細胞シークエンスデータ解析 / 免疫細胞受容体レパトア解析 / T細胞受容体 / B細胞受容体 / バイオインフォマティクス / 免疫細胞集団シークエンス / 適応免疫 / 免疫細胞集団シークエンスデータ情報処理分野
Outline of Final Research Achievements

We have developed methodologies and tools for analyzing Next Generation Sequencing data sets from T-cell or B-cell receptors that characterize diversities of those immune cells. The tools are accurate and efficient for analyzing vast amount of data sets. By applying the tools to data sets from various diseases, e.g., cancers, Crohn’s disease, and GVHD after hematopoietic stem cell transplantations, we succeeded to extract novel information representing relationships between those diseases and immune environments. We also could find new exon candidates in those receptor sequences. Furthermore, we proceeded with developments of dynamic models to estimate and predict variations of structure of immune-cell groups from time-course data sets.

Report

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

    (11 results)

All 2018 2017 2016 2015 Other

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

  • [Int'l Joint Research] シカゴ大学医学部(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] シカゴ大学/医学部(米国)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] シカゴ大学/医学部(米国)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Characterization of the B-cell receptor repertoires in peanut allergic subjects undergoing oral immunotherapy2018

    • Author(s)
      Kiyotani K, Mai TH, Yamaguchi R, Yew PY, Kulis M, Orgel K, Imoto S, Miyano S, Burks AW, Nakamura Y
    • Journal Title

      J Hum Genet

      Volume: 63(2) Issue: 2 Pages: 239-248

    • DOI

      10.1038/s10038-017-0364-0

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clinical significance of T cell clonality and expression levels of immune-related genes in endometrial cancer2017

    • Author(s)
      Ikeda Y, Kiyotani K, Yew PY, Sato S, Imai Y, Yamaguchi R, Miyano S, Fujiwara K, Hasegawa K, Nakamura Y
    • Journal Title

      Oncol Rep

      Volume: 37(5) Issue: 5 Pages: 2603-2610

    • DOI

      10.3892/or.2017.5536

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Characterization of T cell repertoire in tumor tissues and blood in advanced colorectal cancers through deep T cell receptor sequencing2016

    • Author(s)
      Tamura K, Hazama S, Yamaguchi R, Imoto S, Takenouchi H, Inoue Y, Kanekiyo S, Shindo Y, Satoru Miyano S, Nakamura Y, Kiyotani K
    • Journal Title

      Oncology Letters

      Volume: 印刷中 Issue: 6 Pages: 3643-3649

    • DOI

      10.3892/ol.2016.4465

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Characterization of T Cell Receptor Repertoire in Inflamed Tissues of Crohn’s Disease through Deep Sequencing2016

    • Author(s)
      Chapman CG, Yamaguchi R, Tamura K, Weidner J, Imoto S, Kwon J, Marino SR, Miyano S, Nakamura Y, Kiyotani K
    • Journal Title

      Inflammatory Bowel Diseases

      Volume: 印刷中

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Quantitative characterization of T-cell repertoire in allogeneic hematopoietic stem cell transplant recipients2015

    • Author(s)
      Yew PY, Alachkar H, Yamaguchi R, Kiyotani K, Fang H, Yap KL, Liu HT, Wickrema A, Artz A, van Besien K, Imoto S, Miyano S, Bishop MR, Stock W, Nakamura Y
    • Journal Title

      Bone Marrow Transplantation

      Volume: 50 Issue: 9 Pages: 1227-1234

    • DOI

      10.1038/bmt.2015.133

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 大腸癌患者におけるペプチドワクチン特異的T細胞のTCRシークエンス解析2017

    • Author(s)
      清谷 一馬、田村 賢司、山口 類、井元 清哉、竹之内 寛子、宮野悟、硲 彰一、中村 祐輔
    • Organizer
      日本癌学会学術総会
    • Place of Presentation
      神奈川県横浜市
    • Related Report
      2016 Research-status Report
  • [Book] 遺伝統計学と疾患ゲノムデータ解析(第2章-6: T細胞受容体レパトア解析)2018

    • Author(s)
      井元清哉、長谷川嵩矩、山口類
    • Total Pages
      272
    • Publisher
      メディカルドゥ
    • ISBN
      9784944157631
    • Related Report
      2017 Annual Research Report
  • [Book] Chapter2: A TCR sequence data analysis pipeline: Tcrip. In Immunopharmacogenomics. Nakamura, Y. (Ed.)2015

    • Author(s)
      Yamaguchi R, Imoto S, Miyano S
    • Total Pages
      17
    • Publisher
      Springer Japan
    • Related Report
      2015 Research-status Report

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Published: 2015-04-16   Modified: 2019-03-29  

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