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Comprehensive analysis of microsatellites polymorphism in the human population

Research Project

Project/Area Number 18K19426
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 48:Biomedical structure and function and related fields
Research InstitutionThe University of Tokyo (2019-2021)
Kyoto University (2018)

Principal Investigator

Fujimoto Akihiro  東京大学, 大学院医学系研究科(医学部), 教授 (30525853)

Project Period (FY) 2018-06-29 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2020: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2019: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2018: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywordsマイクロサテライト / 人類の集団史 / 集団史 / 集団の歴史 / 人類進化
Outline of Final Research Achievements

Microsatellites have been widely used as genetic markers in population genetics and genealogy studies due to their high mutation rate and rich patterns of repeat length among individuals. However, few studies have been analyzed the genome-wide pattern of microsatellites due to methodological difficulties. To reveal the landscape of the polymorphism in microsatellites at the whole genome level, we analyzed 9 million microsatellites in approximately 4,000 whole-genome sequencing (WGS) data of four public datasets (HGDP, SGDP, ICGC, KPGP) across the various ethnic groups. We analyzed the genetic differentiation among human populations. The principal component analysis (PCA) of microsatellites showed the efficiency of microsatellites for genetic studies. Our analysis provides a comprehensive picture of microsatellite polymorphisms along with the detection method, as well as the efficiency in population genetic studies.

Academic Significance and Societal Importance of the Research Achievements

近年のゲノム解析技術の進展により、DNA多型解析アレイや全ゲノムシークエンスを用いて大量のSNP情報を得ることができる。この情報を用いて、人類の集団史を推定することができる。例えば、集団間の遺伝的関係性の推定や、過去の集団の大きさの変遷が推定されている。しかし、SNP情報を用いた研究では、極めて近い集団の関係性や最近の集団サイズの変遷を正確に推定することが難しい。本研究では、突然変異率が高いマイクロサテライトを用いることで、近縁な集団間の遺伝的関係性や最近の集団史の情報を得ることを目的とした。本研究は、マイクロサテライトを用いた集団解析のための方法論を提供する。

Report

(5 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (7 results)

All 2021 2020 2019

All Journal Article (7 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 7 results,  Open Access: 6 results)

  • [Journal Article] Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression2021

    • Author(s)
      Ashouri Saeideh、Wong Jing Hao、Nakagawa Hidewaki、Shimada Mihoko、Tokunaga Katsushi、Fujimoto Akihiro
    • Journal Title

      Human Genetics

      Volume: 140 Issue: 8 Pages: 1201-1216

    • DOI

      10.1007/s00439-021-02291-2

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Whole genome sequencing with long-reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer.2021

    • Author(s)
      Fujimoto A, Wong JH, Yoshii Y, Akiyama S, Tanaka A, Yagi H, Shigemizu D, Nakagawa H, Mizokami M, and Shimada M.
    • Journal Title

      Genome Medicine

      Volume: 13 Issue: 1 Pages: 65-65

    • DOI

      10.1186/s13073-021-00883-1

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations.2020

    • Author(s)
      Fujita M, Yamaguchi R, Hasegawa T, Shimada S, Arihiro K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H.
    • Journal Title

      EBioMedicine

      Volume: 53 Pages: 102659-102659

    • DOI

      10.1016/j.ebiom.2020.102659

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Comprehensive Analysis of Indels in Whole-genome Microsatellite Regions and Microsatellite Instability across 21 Cancer Types2020

    • Author(s)
      Fujimoto A*, Fujita M, Hasegawa T, Wong JH, Maejima K, Oku-Sasaki A, Nakano K, Shiraishi Y, Miyano S, Yamamoto G, Akagi K, Imoto S, and Nakagawa H
    • Journal Title

      Genome Research

      Volume: 30 Issue: 3 Pages: 334-34

    • DOI

      10.1101/gr.255026.119

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Pan-cancer analysis of whole genomes2020

    • Author(s)
      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
    • Journal Title

      Nature

      Volume: 578 Issue: 7793 Pages: 82-93

    • DOI

      10.1038/s41586-020-1969-6

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA2019

    • Author(s)
      Mizuno Kei、Akamatsu Shusuke、Sumiyoshi Takayuki、Wong Jing Hao、Fujita Masashi et al.
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 15017-15017

    • DOI

      10.1038/s41598-019-51459-4

    • NAID

      120006734882

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population.2019

    • Author(s)
      Wong JH, Shigemizu D, Yoshii Y, Akiyama S, Tanaka A, Nakagawa H, Narumiya S, Fujimoto A
    • Journal Title

      Genome Medicine

      Volume: 11 Issue: 1 Pages: 44-44

    • DOI

      10.1186/s13073-019-0656-4

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access

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Published: 2018-07-25   Modified: 2023-01-30  

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