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Development of rapid diagnosis methods based on pathogen genome and their validation using clinical sample

Research Project

Project/Area Number 15H05272
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section海外学術
Research Field Parasitology (including sanitary zoology)
Research InstitutionHokkaido University

Principal Investigator

Yamagishi Junya  北海道大学, 人獣共通感染症リサーチセンター, 准教授 (80535328)

Co-Investigator(Kenkyū-buntansha) 鈴木 穣  東京大学, 大学院新領域創成科学研究科, 教授 (40323646)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥16,120,000 (Direct Cost: ¥12,400,000、Indirect Cost: ¥3,720,000)
Fiscal Year 2017: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2016: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2015: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Keywords感染症 / ゲノム / 次世代シーケンサー / 網羅的診断 / 感染症迅速診断 / ナノポアシーケンサー / 非特異的病原体検出 / メタゲノム / MinION / diagnosis-by-sequencing / ウイルス / 原虫 / マラリア / デングウイルス / 迅速診断 / 遺伝子型
Outline of Final Research Achievements

To develop novel system for rapid diagnosis of infectious diseases based on pathogen genome, we had attempted to integrate 1) MinION, a rapid real-time portable next generation sequencer available in the market recently, and isothermal amplification system such as 2) Loop-mediated Isothermal Amplification (LAMP) method and 3) non- or semi-specific multiple displacement amplification (MDA) method in this study. The whole system including sequencing and library preparation is totally portable; therefore, it is executable in any place in standalone. We had proved the concept of the system at the lab then successfully demonstrated that it is feasible even at clinical site including Indonesia where various infectious are endemic.

Academic Significance and Societal Importance of the Research Achievements

MinIONは小型迅速であるだけでなく省電力でもあり、ノートPCのUSBから電力の供給が可能である。そこで、今回開発した乾燥LAMP法あるいはMDA法を応用した非特異的検体処理法と組み合わせることで、遺伝子解析システム一式のポータビリティーと汎用性が革新的に向上することが予想される("どこでも・なんでもシーケンス"の実現)。これら特徴を病原体の一次診断に用いることで、途上国において遺伝子型判定に基づく先進医療の提供が可能になるだけでなく、日本を含む先進国においても感染症の国境を越えた移動とそのアウトブレイクに対する対策を提供できる。

Report

(4 results)
  • 2018 Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (6 results)

All 2019 2018 2017 2016

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

  • [Journal Article] East/Central/South African Genotype in a Chikungunya Outbreak, Dhaka, Bangladesh, 20172019

    • Author(s)
      Rahman Mizanur、Yamagishi Junya、Rahim Rummana、Hasan Abu、Sobhan Abu
    • Journal Title

      Emerging Infectious Diseases

      Volume: 25 Issue: 2 Pages: 370-372

    • DOI

      10.3201/eid2502.180188

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum with MinION nanopore sequencer.2018

    • Author(s)
      Kazuo Imai, Norihito Tarumoto, Lucky Ronald Runtuwene, Jun Sakai, Kyoko Hayashida, Yuki Eshita, Ryuichiro Maeda, Josef Tuda, Hideaki Ohno, Takashi Murakami, Shigefumi Maesaki, Yutaka Suzuki, Junya Yamagishi, Takuya Maeda.
    • Journal Title

      Malaria J

      Volume: 29 Issue: 1 Pages: 217-217

    • DOI

      10.1186/s12936-018-2362-x

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum2018

    • Author(s)
      Runtuwene Lucky R.、Tuda Josef S. B.、Mongan Arthur E.、Makalowski Wojciech、Frith Martin C.、Imwong Mallika、Srisutham Suttipat、Nguyen Thi Lan Anh、Tuan Nghia Nguyen、Eshita Yuki、Maeda Ryuichiro、Yamagishi Junya、Suzuki Yutaka
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 8286-8286

    • DOI

      10.1038/s41598-018-26334-3

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Serotyping dengue virus with isothermal amplification and a portable sequencer2017

    • Author(s)
      Yamagishi Junya、Runtuwene Lucky R.、Hayashida Kyoko、Mongan Arthur E.、Thi Lan Anh Nguyen、Thuy Linh Nguyen、Nhat Cam Nguyen、Limkittikul Kriengsak、Sirivichayakul Chukiat、Sathirapongsasuti Nuankanya、Frith Martin、Makalowski Wojciech、Eshita Yuki、Sugano Sumio、Suzuki Yutaka
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 3510-3510

    • DOI

      10.1038/s41598-017-03734-5

    • NAID

      120006337766

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION? nanopore sequencer2017

    • Author(s)
      Imai Kazuo、Tarumoto Norihito、Misawa Kazuhisa、Runtuwene Lucky Ronald、Sakai Jun、Hayashida Kyoko、Eshita Yuki、Maeda Ryuichiro、Tuda Josef、Murakami Takashi、Maesaki Shigefumi、Suzuki Yutaka、Yamagishi Junya、Maeda Takuya
    • Journal Title

      BMC Infectious Diseases

      Volume: 17 Issue: 1 Pages: 621-621

    • DOI

      10.1186/s12879-017-2718-9

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Book] 今すぐ始める! メタゲノム解析 実験プロトコール: 8.歯垢検体の保存・管理と細菌叢のメタ16S解析【佐藤行人,山岸潤也,山下理宇,篠﨑夏子,長﨑正朗】2016

    • Author(s)
      服部 正平
    • Total Pages
      231
    • Publisher
      羊土社
    • ISBN
      9784758101974
    • Related Report
      2016 Annual Research Report

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Published: 2015-04-16   Modified: 2020-03-30  

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