Repository logo
 
Publication

Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets

2019-07-26Journal article Restricted access
Simple item page
dc.contributor.authorBrinkmann, Annika
dc.contributor.authorAndrusch, Andreas
dc.contributor.authorBelka, Ariane
dc.contributor.authorWylezich, Claudia
dc.contributor.authorHöper, Dirk
dc.contributor.authorPohlmann, Anne
dc.contributor.authorNordahl Petersen, Thomas
dc.contributor.authorLucas, Pierrick
dc.contributor.authorBlanchard, Yannick
dc.contributor.authorPapa, Anna
dc.contributor.authorMelidou, Angeliki
dc.contributor.authorOude Munnink, Bas B.
dc.contributor.authorMatthijnssens, Jelle
dc.contributor.authorDeboutte, Ward
dc.contributor.authorEllis, Richard J.
dc.contributor.authorHansmann, Florian
dc.contributor.authorBaumgärtner, Wolfgang
dc.contributor.authorvan der Vries, Erhard
dc.contributor.authorOsterhaus, Albert
dc.contributor.authorCamma, Cesare
dc.contributor.authorMangone, Iolanda
dc.contributor.authorLorusso, Alessio
dc.contributor.authorMarcacci, Maurilia
dc.contributor.authorNunes, Alexandra
dc.contributor.authorPinto, Miguel
dc.contributor.authorBorges, Vítor
dc.contributor.authorKroneman, Annelies
dc.contributor.authorSchmitz, Dennis
dc.contributor.authorCorman, Victor Max
dc.contributor.authorDrosten, Christian
dc.contributor.authorJones, Terry C.
dc.contributor.authorHendriksen, Rene S.
dc.contributor.authorAarestrup, Frank M.
dc.contributor.authorKoopmans, Marion
dc.contributor.authorBeer, Martin
dc.contributor.authorNitsche, Andreas
dc.date.accessioned2020-05-08T18:32:38Z
dc.date.available2020-05-08T18:32:38Z
dc.date.issued2019-07-26
dc.descriptionFree PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31167846/
dc.description.abstractQuality 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.pt_PT
dc.description.sponsorshipThis study was supported by EU Horizon 2020 funding for COMPARE Europe (grant agreement 643476).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationJ Clin Microbiol. 2019 Jul 26;57(8):e00466-19. doi: 10.1128/JCM.00466-19. Print 2019 Augpt_PT
dc.identifier.doi10.1128/JCM.00466-19pt_PT
dc.identifier.issn0095-1137
dc.identifier.urihttp://hdl.handle.net/10400.18/6623
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherAmerican Society for Microbiologypt_PT
dc.relationCOllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe
dc.relation.publisherversionhttps://jcm.asm.org/content/57/8/e00466-19pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/pt_PT
dc.subjectExternal Quality Assessmentpt_PT
dc.subjectHigh-throughput Sequencingpt_PT
dc.subjectNext-generation Sequencingpt_PT
dc.subjectProficiency Testingpt_PT
dc.subjectVirus Diagnosticspt_PT
dc.titleProficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Setspt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleCOllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe
oaire.awardURIinfo:eu-repo/grantAgreement/EC/H2020/643476/EU
oaire.citation.issue8pt_PT
oaire.citation.startPagee00466-19pt_PT
oaire.citation.titleJournal of Clinical Microbiologypt_PT
oaire.citation.volume57pt_PT
oaire.fundingStreamH2020
project.funder.identifierhttp://doi.org/10.13039/501100008530
project.funder.nameEuropean Commission
rcaap.embargofctDe acordo com política editorial da revista.pt_PT
rcaap.rightsembargoedAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublication0ed12fe3-c5b4-449d-bc04-80dac4f120ea
relation.isProjectOfPublication.latestForDiscovery0ed12fe3-c5b4-449d-bc04-80dac4f120ea

Files

Original bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
Journal of Clinical Microbiology-2019-Brinkmann-e00466-19.full.pdf
Size:
978.57 KB
Format:
Adobe Portable Document Format
Download

Collections

DDI - Artigos em revistas internacionais