Development of diagnostic method for comprehensive viral detection using not so random primer sets
Project/Area Number |
25670271
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Research Category |
Grant-in-Aid for Challenging Exploratory Research
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Allocation Type | Multi-year Fund |
Research Field |
Laboratory medicine
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Research Institution | Osaka University |
Principal Investigator |
NAKAMURA SHOTA 大阪大学, 微生物病研究所, 助教 (90432434)
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Project Period (FY) |
2013-04-01 – 2015-03-31
|
Project Status |
Completed (Fiscal Year 2014)
|
Budget Amount *help |
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
|
Keywords | 感染症 / メタゲノム / 応用ゲノム科学 / 臨床検査学 / 微生物学 / ウイルス学 / バイオインフォマティクス |
Outline of Final Research Achievements |
Unbiased next-generation sequencing approaches enable a diagnostic method for comprehensive pathogen detection. This method employs a single common protocol without specific treatment for each pathogen, which consists of the amplification of DNA/RNA in clinical specimens by a random primer set, metagenomic shotgun sequencing, and identification of pathogenic genes. Our previous studies have revealed that a large amount of human genomic DNA in clinical specimens decreases the sensitivity for pathogen detection. Therefore, we tried to develop the subtraction method for human-derived sequences using not so random primer sets. Using the newly designed primer sets, we were able to subtract the human sequences and amplify the target viral sequences from the specimen of influenza A infection. However, undesirable environmental bacterial sequences were obtained coincidentally. Further study on improving the sensitivity by redesign of the primer sets and protocols needs to be considered.
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Report
(3 results)
Research Products
(10 results)
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[Journal Article] Emergence of infectious malignant thrombocytopenia in Japanese macaques (Macaca fuscata) by SRV-4 after transmission to a novel host.2015
Author(s)
Okamoto M, Miyazawa T, Morikawa S, Ono F, Nakamura S, Sato E, Yoshida T, Yoshikawa R, Sakai K, Mizutani T, Nagata N, Takano J, Okabayashi S, Hamano M, Fujimoto K, Nakaya T, Iida T, Horii T, Miyabe-Nishiwaki T, Watanabe A, Kaneko A, Saito A, Matsui A, Hayakawa T, Suzuki J, Akari H, Matsuzawa T, Hirai H.
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Journal Title
Sci Rep.
Volume: 5
Pages: 8850
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes.2014
Author(s)
Miyamoto M, Motooka D, Gotoh K, Imai T, Yoshitake K, Goto N, Iida T, Yasunaga T, Horii T, Arakawa K, Kasahara M, Nakamura S.
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Journal Title
BMC Genomics
Volume: 15
Pages: 699
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Comprehensive metagenomic approach for detecting causative microorganisms in culture-negative infective endocarditis.2014
Author(s)
Imai A, Gotoh K, Asano Y, Yamada N, Motooka D, Fukushima M, Kanzaki M, Ohtani T, Sakata Y, Nishi H, Toda K, Sawa Y, Komuro I, Horii T, Iida T, Nakamura S, Takashima S.
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Journal Title
Int J Cardiol
Volume: 172
Pages: 288-9
DOI
Related Report
Peer Reviewed
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[Journal Article] Virus purification and enrichment by hydroxyapatite chromatography on a chip2014
Author(s)
Niimi, M., Masuda, T., Kaihatsu, K., Kato, N., Nakamura, S., Nakaya, T., and Arai, F.
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Journal Title
Sensors and Actuators B: Chemical
Volume: 201
Pages: 185-190
Related Report
Peer Reviewed
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[Journal Article] Allergic bronchopulmonary mycosis due to co-infection with Aspergillus fumigatus and Schizophyllum commune2014
Author(s)
Seki, M., Ohno, H., Gotoh, K., Motooka, D., Nakamura, S., Iida, T., Miyazaki, Y., and Tomono, K.
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Journal Title
ID Cases
Volume: 1
Pages: 5-8
Related Report
Peer Reviewed
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[Journal Article] Severe respiratory failure due to co-infection with human metapneumovirus and Streptococcus pneumoniae2014
Author(s)
Seki, M., Yoshida, H., Gotoh, K., Hamada, N., Motooka, D., Nakamura, S., Yamamoto, N., Hamaguchi, S., Akeda, Y., Watanabe, H., Iida, T., and Tomono, K.
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Journal Title
Respiratory Medicine Case Reports
Volume: 12
Pages: 13-15
Related Report
Peer Reviewed
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