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Hierarchical Bayesian method for analyzing high polymorphic HLA genome sequence

Research Project

Project/Area Number 15H02775
Research Category

Grant-in-Aid for Scientific Research (B)

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

Principal Investigator

Imoto Seiya  東京大学, 医科学研究所, 教授 (10345027)

Co-Investigator(Kenkyū-buntansha) 水野 晋一  九州大学, 先端医療イノベーションセンター, 特任准教授 (40569430)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥15,340,000 (Direct Cost: ¥11,800,000、Indirect Cost: ¥3,540,000)
Fiscal Year 2017: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2016: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2015: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywordsベイズモデル / HLA遺伝子型 / がんゲノム / マルコフ連鎖モンテカルロ / 免疫ゲノム / 階層ベイズモデル / HLA / シークエンスデータ
Outline of Final Research Achievements

Although human leukocyte antigen (HLA) genotyping based on amplicon, whole exome sequence (WES), and RNA sequence data has been achieved in recent years, accurate genotyping from whole genome sequence (WGS) data remains a challenge due to the low depth. We developed a Bayesian model, called ALPHLARD, that collects reads potentially generated from HLA genes and accurately determines a pair of HLA types for each of HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes at 6-digit resolution. Furthermore, ALPHLARD can detect rare germline variants not stored in HLA databases and call somatic mutations from paired normal and tumor sequence data. We illustrate the capability of ALPHLARD using 253 WES data and 25 WGS data from Illumina platforms and showed its high accuracy, 98.8% for WES data and 98.5% for WGS data at 4-digit resolution. We applied ALPHLARD to 2834 WGS data of PCAWG and showed somatic mutation landscape of HLA genes.

Report

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

    (17 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (6 results) Journal Article (4 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 4 results,  Open Access: 3 results) Presentation (5 results) (of which Int'l Joint Research: 3 results,  Invited: 4 results) Book (2 results)

  • [Int'l Joint Research] Seoul National University(韓国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Peking University(China)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] MD Anderson Cancer Center(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] ソウル大学(韓国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] 北京大学(中国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] シカゴ大学(米国)

    • Related Report
      2016 Annual Research 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] Identification of an immunogenic neo-epitope encoded by mouse sarcoma using CXCR3 ligand mRNAs as sensors2017

    • Author(s)
      Fujii K, Miyahara Y, Harada N, Muraoka D, Komura M, Yamaguchi R, Yagita H, Nakamura J, Sugino S, Okumura S, Imoto S, Miyano S, Shiku H
    • Journal Title

      OncoImmunology

      Volume: 印刷中 Issue: 5 Pages: e1306617-e1306617

    • DOI

      10.1080/2162402x.2017.1306617

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Characterization of T-cell receptor repertoire in inflamed tissues of patients with crohn's disease through deep sequencing2016

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

      Inflamm Bowel Dis

      Volume: 22(6) Issue: 6 Pages: 1275-1285

    • DOI

      10.1097/mib.0000000000000752

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] がん免疫ゲノムの計算科学的解析2017

    • Author(s)
      井元清哉
    • Organizer
      日本人類遺伝学会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Immuno-Genomic Landscape of PanCancer2017

    • Author(s)
      Seiya Imoto
    • Organizer
      The 13th ICGC Scientific Workshop
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Computational Methods for Cancer Immunogenomics2016

    • Author(s)
      井元清哉
    • Organizer
      The 25th KOGO Annual Conference
    • Place of Presentation
      ソウル、韓国
    • Year and Date
      2016-09-05
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] がんゲノムビッグデータ解析から生命科学・医療へ2015

    • Author(s)
      井元清哉
    • Organizer
      第9回スーパーコンピュータ「京」と創薬・医療の産学連携セミナー
    • Place of Presentation
      ステーションコンファレンス東京501(東京都千代田区)
    • Year and Date
      2015-12-18
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Bayesian Method for HLA Genotyping from Whole-Genome Sequencing Data2015

    • Author(s)
      Shuto Hayashi, Rui Yamaguchi, Shinichi Mizuno, Mitsuhiro Komura, Satoru Miyano, Hidewaki Nakagawa, Seiya Imoto
    • Organizer
      2015 International Workshop on Bioinformatics and Systems Biology
    • Place of Presentation
      Boston, USA
    • Year and Date
      2015-07-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [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] 実験医学 がん免疫療法×ゲノミクスで変わるがん治療2017

    • Author(s)
      井元清哉、山口類、水野晋一、中川英刀
    • Total Pages
      137
    • Publisher
      羊土社
    • Related Report
      2016 Annual Research Report

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Published: 2015-04-16   Modified: 2022-08-30  

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