TY - JOUR
T1 - Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing data sets
AU - Brinkmann, Annika
AU - Andrusch, Andreas
AU - Belka, Ariane
AU - Wylezich, Claudia
AU - Höper, Dirk
AU - Pohlmann, Anne
AU - Petersen, Thomas Nordahl
AU - Lucas, Pierrick
AU - Blanchard, Yannick
AU - Papa, Anna
AU - Melidou, Angeliki
AU - Oude Munnink, Bas B.
AU - Matthijnssens, Jelle
AU - Deboutte, Ward
AU - Ellis, Richard J.
AU - Hansmann, Florian
AU - Baumgärtner, Wolfgang
AU - van der Vries, Erhard
AU - Osterhaus, Albert
AU - Camma, Cesare
AU - Mangone, Iolanda
AU - Lorusso, Alessio
AU - Marcacci, Maurilia
AU - Nunes, Alexandra
AU - Pinto, Miguel
AU - Borges, Vítor
AU - Kroneman, Annelies
AU - Schmitz, Dennis
AU - Corman, Victor Max
AU - Drosten, Christian
AU - Jones, Terry C.
AU - Hendriksen, Rene S.
AU - Aarestrup, Frank M.
AU - Koopmans, Marion
AU - Beer, Martin
AU - Nitsche, Andreas
N1 - Publisher Copyright:
© 2019 Brinkmann et al.
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - External quality assessment
KW - High-throughput sequencing
KW - Next-generation sequencing
KW - Proficiency testing
KW - Virus diagnostics
UR - http://www.scopus.com/inward/record.url?scp=85069938556&partnerID=8YFLogxK
U2 - 10.1128/JCM.00466-19
DO - 10.1128/JCM.00466-19
M3 - Article
C2 - 31167846
AN - SCOPUS:85069938556
SN - 0095-1137
VL - 57
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
IS - 8
M1 - e00466-19
ER -