Journal article
Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets
Robert Koch-Institut1
University of Veterinary Medicine Hannover, Foundation2
Utrecht University3
Artemis One Health Research Institute4
Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise5
National Institute of Health Dr. Ricardo Jorge6
National Institute of Public Health and the Environment7
Charité – Universitätsmedizin Berlin8
Friedrich-Loeffler-Institute9
National Food Institute, Technical University of Denmark10
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark11
Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail12
Aristotle University of Thessaloniki13
Erasmus University Medical Center14
KU Leuven15
Animal & Plant Health Agency16
...and 6 moreQuality management and independent assessment of high-throughput sequencing-based virus diagnostics have not yet been established as a mandatory approach for ensuring comparable results. 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 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 dataset of Illumina HiSeq sequences was provided to 13 different European institutes for bioinformatics analysis towards the identification of 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 dataset.
The identification of slightly mutated and highly divergent virus genomes has been identified as being 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 harmonization, comparability, and reproducibility of results.
Similar to what is established for conventional laboratory tests like PCR, there is a need for the establishment of international proficiency testing for bioinformatics pipelines and interpretation of such results.
Language: | English |
---|---|
Publisher: | American Society for Microbiology |
Year: | 2019 |
Pages: | e00466-19-e00466-19 |
ISSN: | 1098660x , 00951137 and 1070633x |
Types: | Journal article |
DOI: | 10.1128/JCM.00466-19 |
ORCIDs: | 0000-0002-9556-4698 , 0000-0002-3605-0136 , Petersen, Thomas Nordahl , Hendriksen, Rene S. and Aarestrup, Frank Møller |
External quality assessment High-throughput sequencing Proficiency testing Virus diagnostics next-generation sequencing
Computational Biology Computer Simulation Data Analysis Europe Genome, Viral High-Throughput Nucleotide Sequencing Humans Intersectoral Collaboration Laboratory Proficiency Testing Reproducibility of Results Sequence Analysis, DNA Viruses external quality assessment high-throughput sequencing proficiency testing virus diagnostics