The utility and perspectives of NGS-based methods in BSL-3 and BSL-4 laboratory – sequencing and analysis strategies
Identifieur interne : 000B42 ( Main/Exploration ); précédent : 000B41; suivant : 000B43The 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.
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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><idno type="wicri:Area/Pmc/Checkpoint">000686</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000686</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:29136087</idno><idno type="wicri:Area/PubMed/Corpus">000A88</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000A88</idno><idno type="wicri:Area/PubMed/Curation">000A88</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000A88</idno><idno type="wicri:Area/PubMed/Checkpoint">000734</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000734</idno><idno type="wicri:Area/Ncbi/Merge">001C45</idno><idno type="wicri:Area/Ncbi/Curation">001C45</idno><idno type="wicri:Area/Ncbi/Checkpoint">001C45</idno><idno type="wicri:doubleKey">2041-2649:2017:Wolkowicz T:the:utility:and</idno><idno type="wicri:Area/Main/Merge">000B45</idno><idno type="wicri:Area/Main/Curation">000B42</idno><idno type="wicri:Area/Main/Exploration">000B42</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><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Humans</term><term>Laboratories</term><term>Molecular Diagnostic Techniques</term><term>Nanopores</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Laboratoires</term><term>Nanopores</term><term>Séquençage nucléotidique à haut débit ()</term><term>Techniques de diagnostic moléculaire</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Humans</term><term>Laboratories</term><term>Molecular Diagnostic Techniques</term><term>Nanopores</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Humains</term><term>Laboratoires</term><term>Nanopores</term><term>Séquençage nucléotidique à haut débit</term><term>Techniques de diagnostic moléculaire</term></keywords></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. Clegg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drosten, C" uniqKey="Drosten C">C Drosten</name></author><author><name sortKey="Gottig, S" uniqKey="Gottig S">S Göttig</name></author><author><name sortKey="Schilling, S" uniqKey="Schilling S">S Schilling</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanchez, A" uniqKey="Sanchez A">A Sanchez</name></author><author><name sortKey="Ksiazek, Tg" uniqKey="Ksiazek T">TG Ksiazek</name></author><author><name sortKey="Rollin, Pe" uniqKey="Rollin P">PE Rollin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Panning, M" uniqKey="Panning M">M Panning</name></author><author><name sortKey="Laue, T" uniqKey="Laue T">T Laue</name></author><author><name sortKey="Olschlager, S" uniqKey="Olschlager S">S Olschlager</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Ashton, Pm" uniqKey="Ashton P">PM Ashton</name></author><author><name sortKey="Nair, S" uniqKey="Nair S">S Nair</name></author><author><name sortKey="Peters, Tm" uniqKey="Peters T">TM Peters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cummings, Ca" uniqKey="Cummings C">CA Cummings</name></author><author><name sortKey="Bormann Chung, Ca" uniqKey="Bormann Chung C">CA Bormann Chung</name></author><author><name sortKey="Fang, R" uniqKey="Fang R">R Fang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Girault, G" uniqKey="Girault G">G Girault</name></author><author><name sortKey="Blouin, Y" uniqKey="Blouin Y">Y Blouin</name></author><author><name sortKey="Vergnaud, G" uniqKey="Vergnaud G">G Vergnaud</name></author><author><name sortKey="Derzelle, S" uniqKey="Derzelle S">S. Derzelle</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gire, Sk" uniqKey="Gire S">SK Gire</name></author><author><name sortKey="Goba, A" uniqKey="Goba A">A Goba</name></author><author><name sortKey="Andersen, Kg" uniqKey="Andersen K">KG Andersen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Towner, Js" uniqKey="Towner J">JS Towner</name></author><author><name sortKey="Sealy, Tk" uniqKey="Sealy T">TK Sealy</name></author><author><name sortKey="Khristova, Ml" uniqKey="Khristova M">ML Khristova</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Delmont, To" uniqKey="Delmont T">TO Delmont</name></author><author><name sortKey="Prestat, E" uniqKey="Prestat E">E Prestat</name></author><author><name sortKey="Keegan, Kp" uniqKey="Keegan K">KP Keegan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Henderson, G" uniqKey="Henderson G">G Henderson</name></author><author><name sortKey="Cox, F" uniqKey="Cox F">F Cox</name></author><author><name sortKey="Kittelmann, S" uniqKey="Kittelmann S">S Kittelmann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Moore, Ra" uniqKey="Moore R">RA Moore</name></author><author><name sortKey="Warren, Rl" uniqKey="Warren R">RL Warren</name></author><author><name sortKey="Freeman, Jd" uniqKey="Freeman J">JD Freeman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cheval, J" uniqKey="Cheval J">J Cheval</name></author><author><name sortKey="Sauvage, V" uniqKey="Sauvage V">V Sauvage</name></author><author><name sortKey="Frangeul, L" uniqKey="Frangeul L">L Frangeul</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Frey, Kg" uniqKey="Frey K">KG Frey</name></author><author><name sortKey="Herrera Galeano, Je" uniqKey="Herrera Galeano J">JE Herrera-Galeano</name></author><author><name sortKey="Redden, Cl" uniqKey="Redden C">CL Redden</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Quick, J" uniqKey="Quick J">J Quick</name></author><author><name sortKey="Grubaugh, Nd" uniqKey="Grubaugh N">ND Grubaugh</name></author><author><name sortKey="Pullan, St" uniqKey="Pullan S">ST Pullan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Gunther, S" uniqKey="Gunther S">S Gunther</name></author><author><name sortKey="Asper, M" uniqKey="Asper M">M Asper</name></author><author><name sortKey="Roser, C" uniqKey="Roser C">C Roser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Grard, G" uniqKey="Grard G">G Grard</name></author><author><name sortKey="Biek, R" uniqKey="Biek R">R Biek</name></author><author><name sortKey="Muyembe Tamfum, J J" uniqKey="Muyembe Tamfum J">J-J Muyembe Tamfum</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kobinger, Gp" uniqKey="Kobinger G">GP Kobinger</name></author><author><name sortKey="Leung, A" uniqKey="Leung A">A Leung</name></author><author><name sortKey="Neufeld, J" uniqKey="Neufeld J">J Neufeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Matranga, Cb" uniqKey="Matranga C">CB Matranga</name></author><author><name sortKey="Andersen, Kg" uniqKey="Andersen K">KG Andersen</name></author><author><name sortKey="Winnicki, S" uniqKey="Winnicki S">S Winnicki</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pareek, Cs" uniqKey="Pareek C">CS Pareek</name></author><author><name sortKey="Smoczynski, R" uniqKey="Smoczynski R">R Smoczynski</name></author><author><name sortKey="Tretyn, A" uniqKey="Tretyn A">A. Tretyn</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feng, Y" uniqKey="Feng Y">Y Feng</name></author><author><name sortKey="Zhang, Y" uniqKey="Zhang Y">Y Zhang</name></author><author><name sortKey="Ying, C" uniqKey="Ying C">C Ying</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Castro Wallace, Sl" uniqKey="Castro Wallace S">SL Castro-Wallace</name></author><author><name sortKey="Chiu, Cy" uniqKey="Chiu C">CY Chiu</name></author><author><name sortKey="John, Kk" uniqKey="John K">KK John</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mcintyre, Abr" uniqKey="Mcintyre A">ABR McIntyre</name></author><author><name sortKey="Rizzardi, L" uniqKey="Rizzardi L">L Rizzardi</name></author><author><name sortKey="Yu, Am" uniqKey="Yu A">AM Yu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, Ss" uniqKey="Johnson S">SS Johnson</name></author><author><name sortKey="Zaikova, E" uniqKey="Zaikova E">E Zaikova</name></author><author><name sortKey="Goerlitz, Ds" uniqKey="Goerlitz D">DS Goerlitz</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hoenen, T" uniqKey="Hoenen T">T. Hoenen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Coltart, Cem" uniqKey="Coltart C">CEM Coltart</name></author><author><name sortKey="Lindsey, B" uniqKey="Lindsey B">B Lindsey</name></author><author><name sortKey="Ghinai, I" uniqKey="Ghinai I">I Ghinai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cao, Md" uniqKey="Cao M">MD Cao</name></author><author><name sortKey="Nguyen, Sh" uniqKey="Nguyen S">SH Nguyen</name></author><author><name sortKey="Ganesamoorthy, D" uniqKey="Ganesamoorthy D">D Ganesamoorthy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bolisetty, Mt" uniqKey="Bolisetty M">MT Bolisetty</name></author><author><name sortKey="Rajadinakaran, G" uniqKey="Rajadinakaran G">G Rajadinakaran</name></author><author><name sortKey="Graveley, Br" uniqKey="Graveley B">BR. Graveley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Larsen, Mv" uniqKey="Larsen M">MV Larsen</name></author><author><name sortKey="Cosentino, S" uniqKey="Cosentino S">S Cosentino</name></author><author><name sortKey="Lukjancenko, O" uniqKey="Lukjancenko O">O Lukjancenko</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giardine, B" uniqKey="Giardine B">B Giardine</name></author><author><name sortKey="Riemer, C" uniqKey="Riemer C">C Riemer</name></author><author><name sortKey="Hardison, Rc" uniqKey="Hardison R">RC Hardison</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mazzocco, G" uniqKey="Mazzocco G">G Mazzocco</name></author><author><name sortKey="Wr Blewski, P" uniqKey="Wr Blewski P">P Wróblewski</name></author><author><name sortKey="Lermo, M" uniqKey="Lermo M">M Lermo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Judge, K" uniqKey="Judge K">K Judge</name></author><author><name sortKey="Hunt, M" uniqKey="Hunt M">M Hunt</name></author><author><name sortKey="Reuter, S" uniqKey="Reuter S">S Reuter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mullis, K" uniqKey="Mullis K">K Mullis</name></author><author><name sortKey="Faloona, F" uniqKey="Faloona F">F Faloona</name></author><author><name sortKey="Scharf, S" uniqKey="Scharf S">S Scharf</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nadon, C" uniqKey="Nadon C">C Nadon</name></author><author><name sortKey="Van Walle, I" uniqKey="Van Walle I">I Van Walle</name></author><author><name sortKey="Gerner Smidt, P" uniqKey="Gerner Smidt P">P Gerner-Smidt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanger, F" uniqKey="Sanger F">F Sanger</name></author><author><name sortKey="Nicklen, S" uniqKey="Nicklen S">S Nicklen</name></author><author><name sortKey="Coulson, Ar" uniqKey="Coulson A">AR. Coulson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ronaghi, M" uniqKey="Ronaghi M">M Ronaghi</name></author><author><name sortKey="Uhlen, M" uniqKey="Uhlen M">M Uhlén</name></author><author><name sortKey="Nyren, P" uniqKey="Nyren P">P. Nyrén</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Canard, B" uniqKey="Canard B">B Canard</name></author><author><name sortKey="Sarfati, Rs" uniqKey="Sarfati R">RS. 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