2018 Fiscal Year Annual Research Report
Medical Sequence Classifier - a system for quick and accurate sequence-based diagnostics
| Project/Area Number |
17H07123
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| Research Institution | Tokai University |
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Principal Investigator |
クリュコフ キリル 東海大学, 医学部, 奨励研究員 (20806202)
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| Project Period (FY) |
2017-08-25 – 2019-03-31
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| Keywords | metagenome / sequence analysis / NGS |
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| Outline of Annual Research Achievements |
I developed an advanced sequence classifier for analyzing medical metagenomes.
My classifier was tested on a mock bacterial community and on pleural effusion samples from a patient with empyema (Mitsuhashi et al., 2017). It was applied to detecting bacterial pathogens in blood samples from sepsis patients (Watanabe et al., 2018). It also continues to be used for analysis of samples from empyema patients (Shiraishi et al., in preparation). Recently my classifier is also used at Kyoto University Hospital and Kansai Medical University for rapid identification of bacterial pathogens (Kai et al., 2019; Tanaka et al., 2019). A portable application of my classifier system was successfully tested in the field application in Zambia (Nakagawa et al., under review). Also my classifier was applied to detecting viral DNA in genome sequences (Kryukov et al., 2019).
My reference sequence database, called GenomeSync, currently contains 2,906 Gbp of sequence in 234,279 genomes, making it one of the largest reference genome resources. This database is specifically designed to facilitate metagenome analyses. As part of this project I developed a new advanced sequence compression method (Kryukov et al., 2019).
My sequence classifier 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. We expect that our system will be widely adopted for investigating infectious diseases using next generation sequencing.
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| Research Progress Status |
平成30年度が最終年度であるため、記入しない。
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| Strategy for Future Research Activity |
平成30年度が最終年度であるため、記入しない。
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[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
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Journal Title
JA Clinical Reports
Volume: 5
Pages: 24
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Detection of pathogenic bacteria in the blood from sepsis patients using 16S rRNA gene amplicon sequencing analysis2018
Author(s)
Nobuo Watanabe, Kirill Kryukov, So Nakagawa, Junko S. Takeuchi, Meiko Takeshita, Yukiko Kirimura, Satomi Mitsuhashi, Toru Ishihara, Hiromichi Aoki, Sadaki Inokuchi, Tadashi Imanishi, Shigeaki Inoue
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Journal Title
PLoS ONE
Volume: 13
Pages: e0202049
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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