The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
Identifieur interne : 001292 ( Pmc/Curation ); précédent : 001291; suivant : 001293The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
Auteurs : Tomasz Wołkowicz [Pologne]Source :
- Briefings in Functional Genomics [ 2041-2649 ] ; 2017.
Abstract
Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like
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DOI: 10.1093/bfgp/elx033
PubMed: 29136087
PubMed Central: 7109780
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies</title><author><name sortKey="Wolkowicz, Tomasz" sort="Wolkowicz, Tomasz" uniqKey="Wolkowicz T" first="Tomasz" last="Wołkowicz">Tomasz Wołkowicz</name><affiliation wicri:level="1"><nlm:aff id="aff1">National Institute of Public Health – NIH, Poland</nlm:aff><country xml:lang="fr">Pologne</country><wicri:regionArea>National Institute of Public Health – NIH</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">29136087</idno><idno type="pmc">7109780</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7109780</idno><idno type="RBID">PMC:7109780</idno><idno type="doi">10.1093/bfgp/elx033</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">001292</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001292</idno><idno type="wicri:Area/Pmc/Curation">001292</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001292</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies</title><author><name sortKey="Wolkowicz, Tomasz" sort="Wolkowicz, Tomasz" uniqKey="Wolkowicz T" first="Tomasz" last="Wołkowicz">Tomasz Wołkowicz</name><affiliation wicri:level="1"><nlm:aff id="aff1">National Institute of Public Health – NIH, Poland</nlm:aff><country xml:lang="fr">Pologne</country><wicri:regionArea>National Institute of Public Health – NIH</wicri:regionArea></affiliation></author></analytic><series><title level="j">Briefings in Functional Genomics</title><idno type="ISSN">2041-2649</idno><idno type="eISSN">2041-2657</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like <italic>Bacillus anthracis</italic>, <italic>Francisella tularensis</italic>, <italic>Yersinia pestis</italic>, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e.g. library preparation). Nowadays there is a possibility to implement pocket size MinION - real time whole genome sequencer into BSL-3 and 4 laboratory for rapid and precise diagnostic purposes.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Johansson, A" uniqKey="Johansson A">A Johansson</name></author><author><name sortKey="Ibrahim, A" uniqKey="Ibrahim A">A Ibrahim</name></author><author><name sortKey="Gorangsson, I" uniqKey="Gorangsson I">I Gorangsson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tomaso, H" uniqKey="Tomaso H">H Tomaso</name></author><author><name sortKey="Scholz, Hc" uniqKey="Scholz H">HC Scholz</name></author><author><name sortKey="Naubauer, H" uniqKey="Naubauer H">H Naubauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jackson, Pj" uniqKey="Jackson P">PJ Jackson</name></author><author><name sortKey="Hugh Jones, Me" uniqKey="Hugh Jones M">ME Hugh-Jones</name></author><author><name sortKey="Adair, Dm" uniqKey="Adair D">DM Adair</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gierczy Ski, R" uniqKey="Gierczy Ski R">R Gierczyński</name></author><author><name sortKey="Zasada, Aa" uniqKey="Zasada A">AA Zasada</name></author><author><name sortKey="Raddadi, N" uniqKey="Raddadi N">N Raddadi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhou, D" uniqKey="Zhou D">D Zhou</name></author><author><name sortKey="Han, Y" uniqKey="Han Y">Y Han</name></author><author><name sortKey="Dai, E" uniqKey="Dai E">E Dai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Demby, Ah" uniqKey="Demby A">AH Demby</name></author><author><name sortKey="Chamberlain, J" uniqKey="Chamberlain J">J Chamberlain</name></author><author><name sortKey="Brown, Dw" uniqKey="Brown D">DW Brown</name></author><author><name sortKey="Clegg, Cs" uniqKey="Clegg C">CS. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Brief Funct Genomics</journal-id><journal-id journal-id-type="iso-abbrev">Brief Funct Genomics</journal-id><journal-id journal-id-type="publisher-id">bfgp</journal-id><journal-title-group><journal-title>Briefings in Functional Genomics</journal-title></journal-title-group><issn pub-type="ppub">2041-2649</issn><issn pub-type="epub">2041-2657</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">29136087</article-id><article-id pub-id-type="pmc">7109780</article-id><article-id pub-id-type="doi">10.1093/bfgp/elx033</article-id><article-id pub-id-type="publisher-id">elx033</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review Paper</subject></subj-group></article-categories><title-group><article-title>The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wołkowicz</surname><given-names>Tomasz</given-names></name><pmc-comment>twolkowicz@pzh.gov.pl </pmc-comment>
<xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"></xref></contrib></contrib-group><aff id="aff1">National Institute of Public Health – NIH, Poland</aff><author-notes><corresp id="cor1">Corresponding author: Tomasz Wołkowicz, National Institute of Public Health – National Institute of Hygiene, Chocimska 24 str., 00-791 Warsaw, Poland. Tel. +48 22 54 21 263; E-mail: <email>twolkowicz@pzh.gov.pl</email></corresp></author-notes><pub-date pub-type="collection"><month>11</month><year>2018</year></pub-date><pub-date pub-type="epub" iso-8601-date="2017-11-10"><day>10</day><month>11</month><year>2017</year></pub-date><pub-date pub-type="pmc-release"><day>10</day><month>11</month><year>2018</year></pub-date><pmc-comment> PMC Release delay is 12 months and
0 days and was based on the
<volume>17</volume><issue>6</issue><fpage>471</fpage><lpage>476</lpage><permissions><copyright-statement>© The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com</copyright-statement><copyright-year>2017</copyright-year><license license-type="oup-standard" xlink:href="https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"><license-p>This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (<ext-link ext-link-type="uri" xlink:href="https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model">https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model</ext-link>)</license-p></license><license><license-p>This article is made available via the PMC Open Access Subset for unrestricted re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the COVID-19 pandemic or until permissions are revoked in writing. Upon expiration of these permissions, PMC is granted a perpetual license to make this article available via PMC and Europe PMC, consistent with existing copyright protections.</license-p></license></permissions><self-uri xlink:href="elx033.pdf"></self-uri><abstract><title>Abstract</title><p>Modern diagnostics is in general based on molecular biology methods. Nowadays sequencing-based methods, especially whole genome sequencing, are becoming increasingly important. Implementation of such methods into routine diagnostic of highly dangerous pathogens, like <italic>Bacillus anthracis</italic>, <italic>Francisella tularensis</italic>, <italic>Yersinia pestis</italic>, Ebola virus, MERS, Lassa virus etc. would be very helpful. The best diagnostic strategy would be the metagenomic sequencing directly from the clinical sample. Implementation of majority of currently available WGS platforms inside the BSL-3 or 4 laboratory is impractical because of the size of the equipment and time consuming wet lab part (e.g. library preparation). Nowadays there is a possibility to implement pocket size MinION - real time whole genome sequencer into BSL-3 and 4 laboratory for rapid and precise diagnostic purposes.</p></abstract><kwd-group kwd-group-type="author"><kwd>Whole genome sequencing</kwd><kwd>molecular diagnostics</kwd><kwd>BSL-3</kwd><kwd>BSL-4</kwd></kwd-group><funding-group><award-group award-type="grant"><funding-source><named-content content-type="funder-name">Narodowe Centrum Nauki</named-content><named-content content-type="funder-identifier">10.13039/501100004281</named-content></funding-source><award-id>2015/17/N/NZ6/03517</award-id></award-group></funding-group><counts><page-count count="6"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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