Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2019 |
| Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | http://hdl.handle.net/10400.18/6623 |
Resumo: | Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31167846/ |
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Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data SetsExternal Quality AssessmentHigh-throughput SequencingNext-generation SequencingProficiency TestingVirus DiagnosticsFree PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31167846/Quality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. The sensitivity and specificity of viral high-throughput sequence data analysis are highly affected by bioinformatics processing using publicly available and custom tools and databases and thus differ widely between individuals and institutions. Here we present the results of the COMPARE [Collaborative Management Platform for Detection and Analyses of (Re-)emerging and Foodborne Outbreaks in Europe] in silico virus proficiency test. An artificial, simulated in silico data set of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis to identify viral pathogens in high-throughput sequence data. Comparison of the participants' analyses shows that the use of different tools, programs, and databases for bioinformatics analyses can impact the correct identification of viral sequences from a simple data set. The identification of slightly mutated and highly divergent virus genomes has been shown to be most challenging. Furthermore, the interpretation of the results, together with a fictitious case report, by the participants showed that in addition to the bioinformatics analysis, the virological evaluation of the results can be important in clinical settings. External quality assessment and proficiency testing should become an important part of validating high-throughput sequencing-based virus diagnostics and could improve the harmonization, comparability, and reproducibility of results. There is a need for the establishment of international proficiency testing, like that established for conventional laboratory tests such as PCR, for bioinformatics pipelines and the interpretation of such results.This study was supported by EU Horizon 2020 funding for COMPARE Europe (grant agreement 643476).American Society for MicrobiologyRepositório Científico do Instituto Nacional de SaúdeBrinkmann, AnnikaAndrusch, AndreasBelka, ArianeWylezich, ClaudiaHöper, DirkPohlmann, AnneNordahl Petersen, ThomasLucas, PierrickBlanchard, YannickPapa, AnnaMelidou, AngelikiOude Munnink, Bas B.Matthijnssens, JelleDeboutte, WardEllis, Richard J.Hansmann, FlorianBaumgärtner, Wolfgangvan der Vries, ErhardOsterhaus, AlbertCamma, CesareMangone, IolandaLorusso, AlessioMarcacci, MauriliaNunes, AlexandraPinto, MiguelBorges, VítorKroneman, AnneliesSchmitz, DennisCorman, Victor MaxDrosten, ChristianJones, Terry C.Hendriksen, Rene S.Aarestrup, Frank M.Koopmans, MarionBeer, MartinNitsche, Andreas2020-05-08T18:32:38Z2019-07-262019-07-26T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.18/6623engJ Clin Microbiol. 2019 Jul 26;57(8):e00466-19. doi: 10.1128/JCM.00466-19. Print 2019 Aug0095-113710.1128/JCM.00466-19info:eu-repo/semantics/embargoedAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-20T15:41:46Zoai:repositorio.insa.pt:10400.18/6623Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:41:42.627787Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.fl_str_mv |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| title |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| spellingShingle |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets Brinkmann, Annika External Quality Assessment High-throughput Sequencing Next-generation Sequencing Proficiency Testing Virus Diagnostics |
| title_short |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| title_full |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| title_fullStr |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| title_full_unstemmed |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| title_sort |
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets |
| author |
Brinkmann, Annika |
| author_facet |
Brinkmann, Annika Andrusch, Andreas Belka, Ariane Wylezich, Claudia Höper, Dirk Pohlmann, Anne Nordahl Petersen, Thomas Lucas, Pierrick Blanchard, Yannick Papa, Anna Melidou, Angeliki Oude Munnink, Bas B. Matthijnssens, Jelle Deboutte, Ward Ellis, Richard J. Hansmann, Florian Baumgärtner, Wolfgang van der Vries, Erhard Osterhaus, Albert Camma, Cesare Mangone, Iolanda Lorusso, Alessio Marcacci, Maurilia Nunes, Alexandra Pinto, Miguel Borges, Vítor Kroneman, Annelies Schmitz, Dennis Corman, Victor Max Drosten, Christian Jones, Terry C. Hendriksen, Rene S. Aarestrup, Frank M. Koopmans, Marion Beer, Martin Nitsche, Andreas |
| author_role |
author |
| author2 |
Andrusch, Andreas Belka, Ariane Wylezich, Claudia Höper, Dirk Pohlmann, Anne Nordahl Petersen, Thomas Lucas, Pierrick Blanchard, Yannick Papa, Anna Melidou, Angeliki Oude Munnink, Bas B. Matthijnssens, Jelle Deboutte, Ward Ellis, Richard J. Hansmann, Florian Baumgärtner, Wolfgang van der Vries, Erhard Osterhaus, Albert Camma, Cesare Mangone, Iolanda Lorusso, Alessio Marcacci, Maurilia Nunes, Alexandra Pinto, Miguel Borges, Vítor Kroneman, Annelies Schmitz, Dennis Corman, Victor Max Drosten, Christian Jones, Terry C. Hendriksen, Rene S. Aarestrup, Frank M. Koopmans, Marion Beer, Martin Nitsche, Andreas |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Repositório Científico do Instituto Nacional de Saúde |
| dc.contributor.author.fl_str_mv |
Brinkmann, Annika Andrusch, Andreas Belka, Ariane Wylezich, Claudia Höper, Dirk Pohlmann, Anne Nordahl Petersen, Thomas Lucas, Pierrick Blanchard, Yannick Papa, Anna Melidou, Angeliki Oude Munnink, Bas B. Matthijnssens, Jelle Deboutte, Ward Ellis, Richard J. Hansmann, Florian Baumgärtner, Wolfgang van der Vries, Erhard Osterhaus, Albert Camma, Cesare Mangone, Iolanda Lorusso, Alessio Marcacci, Maurilia Nunes, Alexandra Pinto, Miguel Borges, Vítor Kroneman, Annelies Schmitz, Dennis Corman, Victor Max Drosten, Christian Jones, Terry C. Hendriksen, Rene S. Aarestrup, Frank M. Koopmans, Marion Beer, Martin Nitsche, Andreas |
| dc.subject.por.fl_str_mv |
External Quality Assessment High-throughput Sequencing Next-generation Sequencing Proficiency Testing Virus Diagnostics |
| topic |
External Quality Assessment High-throughput Sequencing Next-generation Sequencing Proficiency Testing Virus Diagnostics |
| description |
Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31167846/ |
| publishDate |
2019 |
| dc.date.none.fl_str_mv |
2019-07-26 2019-07-26T00:00:00Z 2020-05-08T18:32:38Z |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
| status_str |
publishedVersion |
| dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.18/6623 |
| url |
http://hdl.handle.net/10400.18/6623 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
J Clin Microbiol. 2019 Jul 26;57(8):e00466-19. doi: 10.1128/JCM.00466-19. Print 2019 Aug 0095-1137 10.1128/JCM.00466-19 |
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info:eu-repo/semantics/embargoedAccess |
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embargoedAccess |
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application/pdf |
| dc.publisher.none.fl_str_mv |
American Society for Microbiology |
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American Society for Microbiology |
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reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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