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2019-07-26Zeitschriftenartikel DOI: 10.25646/6290
Proficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Sets
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.accessioned2019-09-20T09:54:18Z
dc.date.available2019-09-20T09:54:18Z
dc.date.issued2019-07-26none
dc.identifier.other10.1128/JCM.00466-19
dc.identifier.urihttp://edoc.rki.de/176904/6304
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.ger
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectexternal quality assessmenteng
dc.subjecthigh-throughput sequencingeng
dc.subjectnext-generation sequencingeng
dc.subjectproficiency testingeng
dc.subjectvirus diagnosticseng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleProficiency Testing of Virus Diagnostics Based on Bioinformatics Analysis of Simulated In Silico High-Throughput Sequencing Data Setsnone
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:0257-176904/6304-0
dc.identifier.doihttp://dx.doi.org/10.25646/6290
dc.type.versionpublishedVersionnone
local.edoc.container-titleJournal of Clinical Microbiologynone
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://jcm.asm.org/content/57/8/e00466-19/article-infonone
local.edoc.container-publisher-nameAmerican Society for Microbiology (ASM)none
local.edoc.container-volume57none
local.edoc.container-issue8none
local.edoc.container-reportyear2019none
local.edoc.container-year2019none
local.edoc.container-firstpage1none
local.edoc.container-lastpage12none
local.edoc.rki-departmentZentrum für Biologische Gefahren und Spezielle Pathogenenone
dc.description.versionPeer Reviewednone

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