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Medical Sequence Classifier - a system for quick and accurate sequence-based diagnostics

Research Project

Project/Area Number 17H07123
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Life / Health / Medical informatics
Research InstitutionTokai University

Principal Investigator

KRYUKOV Kirill  東海大学, 医学部, 奨励研究員 (20806202)

Project Period (FY) 2017-08-25 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2018: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
KeywordsMetagenome / NGS sequencing / classification / diagnostics / DNA / sequence / metagenome / sequence analysis / NGS / metagenomics / medical metagenomics / 生体生命情報学
Outline of Final Research Achievements

Rapid and accurate diagnostics of infectious disease pathogen is important for successful treatment outcome. In this project I developed a highly efficient sequence classifier system. This system can be applied to medical metagenomic sequence samples in order to detect pathogens contained in those samples. I also developed the GenomeSync database that is used by the classifier as a reference. My system for investigating medical metagenomes has shown utility in research studies, field trips and tests on medical samples. The results have been described in peer-reviewed literature. I expect that my classifier system will be widely adopted for investigating infectious diseases using next generation sequencing.

Academic Significance and Societal Importance of the Research Achievements

Our society is increasingly threatened by pandemics and spread of drug-resistant pathogens. My sequence classifier will help in achieving rapid response to these threats, by providing fast and accurate sequence based diagnostics.

Report

(3 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • Research Products

    (19 results)

All 2019 2018 2017 Other

All Journal Article (6 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 6 results,  Open Access: 6 results) Presentation (11 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results) Remarks (2 results)

  • [Journal Article] Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION nanopore sequencer2019

    • Author(s)
      Shinichi Kai, Yoshiyuki Matsuo, So Nakagawa, Kirill Kryukov, Shino Matsukawa, Hiromasa Tanaka, Teppei Iwai, Tadashi Imanishi, Kiichi Hirota
    • Journal Title

      FEBS Open Bio

      Volume: 9 Issue: 3 Pages: 548-557

    • DOI

      10.1002/2211-5463.12590

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Systematic survey of non-retroviral virus-like elements in eukaryotic genomes.2019

    • Author(s)
      Kryukov K, Ueda MT, Imanishi T, Nakagawa S.
    • Journal Title

      Virus Research

      Volume: 262 Pages: 30-36

    • DOI

      10.1016/j.virusres.2018.02.002

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Real-time diagnostic analysis of MinION-based metagenomic sequencing in clinical microbiology evaluation: a case report2019

    • Author(s)
      Hiromasa Tanaka, Yoshiyuki Matsuo, So Nakagawa, Kenichiro Nishi, Akihisa Okamoto, Shinichi Kai, Teppei Iwai, Yoshiteru Tabata, Takeshi Tajima, Yuji Komatsu, Motohiko Satoh, Kirill Kryukov, Tadashi Imanishi, Kiichi Hirota
    • Journal Title

      JA Clinical Reports

      Volume: 5 Issue: 1 Pages: 24-24

    • DOI

      10.1186/s40981-019-0244-z

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences2019

    • Author(s)
      Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi
    • Journal Title

      Bioinformatics

      Volume: in press Issue: 19 Pages: 3826-3828

    • DOI

      10.1093/bioinformatics/btz144

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Detection of pathogenic bacteria in the blood from sepsis patients using 16S rRNA gene amplicon sequencing analysis.2018

    • Author(s)
      Watanabe N, Kryukov K, Nakagawa S, Takeuchi JS, Takeshita M, Kirimura Y, Mitsuhashi S, Ishihara T, Aoki H, Inokuchi S, Imanishi T, Inoue S
    • Journal Title

      PLoS One

      Volume: 13 Issue: 8 Pages: e0202049-e0202049

    • DOI

      10.1371/journal.pone.0202049

    • NAID

      120006826803

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer2017

    • Author(s)
      Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S. Takeuchi, Yoshiki Shiraishi, Koichiro Asano, Tadashi Imanishi
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 5657-5657

    • DOI

      10.1038/s41598-017-05772-5

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] NAF - data compression for next generation of genome databases2019

    • Author(s)
      Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi
    • Organizer
      Society of Genome Microbiology, Japan
    • Related Report
      2018 Annual Research Report
  • [Presentation] Classifying metagenomic reads using GenomeSync and Genome Search Toolkit2018

    • Author(s)
      Kirill Kryukov, Tadashi Imanishi
    • Organizer
      The 91st Annual Meeting of Japanese Society for Bacteriology
    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
  • [Presentation] Phylogenetic trees explain mysteries of complete genomes2018

    • Author(s)
      Kirill Kryukov
    • Organizer
      Neighbor-Joining Symposium in National Institute of Genetics, Mishima
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Non-retroviral virus-like elements in eukaryotic genomes2018

    • Author(s)
      Kirill Kryukov, Mahoko Takahashi Ueda, Tadashi Imanishi, So Nakagawa
    • Organizer
      SMBE2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] GenomeSync - an automatically synchronizing local database of genome sequences2018

    • Author(s)
      Kirill Kryukov, Tadashi Imanishi
    • Organizer
      Molecular Biology Soeicty of Japan
    • Related Report
      2018 Annual Research Report
  • [Presentation] GenomeSync - a comprehensive auto-updating genome database and its applications2017

    • Author(s)
      Kirill Kryukov
    • Organizer
      NIG Biological Symposium
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] A portable system for rapid bacterial composition analysis using MinION and laptop computer2017

    • Author(s)
      Satomi Mitsuhashi, So Nakagawa, Kirill Kryukov, Tadashi Imanishi
    • Organizer
      London Calling 2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] GenomeSync - an automatically synchronizing local database of genome sequences2017

    • Author(s)
      Kirill Kryukov, Tadashi Imanishi
    • Organizer
      NGS Field Meeting
    • Related Report
      2017 Annual Research Report
  • [Presentation] Detecting human contamination in genome assemblies2017

    • Author(s)
      Kirill Kryukov, Tadashi Imanishi
    • Organizer
      12th International Workshop on Advanced Genomics
    • Related Report
      2017 Annual Research Report
  • [Presentation] A portable system for rapid bacterial composition analysis using MinION and laptop computer2017

    • Author(s)
      Satomi Mitsuhashi, Nana Asami, So Nakagawa, Kirill Kryukov, Tadashi Imanishi
    • Organizer
      Second Technology Seminar on the MinION sequencing
    • Related Report
      2017 Annual Research Report
  • [Presentation] Methods and databases for analyzing medical metagenomes2017

    • Author(s)
      Kirill Kryukov
    • Organizer
      AMED-JGRID Symposium
    • Related Report
      2017 Annual Research Report
  • [Remarks] GenomeSync database

    • URL

      http://genomesync.org/

    • Related Report
      2017 Annual Research Report
  • [Remarks] pEVE database

    • URL

      http://peve.med.u-tokai.ac.jp/

    • Related Report
      2017 Annual Research Report

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Published: 2017-08-25   Modified: 2020-03-30  

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