Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_B438BB51FAF9
Type
Article: article from journal or magazin.
Collection
Publications
Title
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.
Journal
Genes
Author(s)
Junier T., Huber M., Schmutz S., Kufner V., Zagordi O., Neuenschwander S., Ramette A., Kubacki J., Bachofen C., Qi W., Laubscher F., Cordey S., Kaiser L., Beuret C., Barbié V., Fellay J., Lebrand A.
ISSN
2073-4425 (Electronic)
ISSN-L
2073-4425
Publication state
Published
Issued date
28/08/2019
Peer-reviewed
Oui
Volume
10
Number
9
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
Shotgun metagenomics using next generation sequencing (NGS) is a promising technique to analyze both DNA and RNA microbial material from patient samples. Mostly used in a research setting, it is now increasingly being used in the clinical realm as well, notably to support diagnosis of viral infections, thereby calling for quality control and the implementation of ring trials (RT) to benchmark pipelines and ensure comparable results. The Swiss NGS clinical virology community therefore decided to conduct a RT in 2018, in order to benchmark current metagenomic workflows used at Swiss clinical virology laboratories, and thereby contribute to the definition of common best practices. The RT consisted of two parts (increments), in order to disentangle the variability arising from the experimental compared to the bioinformatics parts of the laboratory pipeline. In addition, the RT was also designed to assess the impact of databases compared to bioinformatics algorithms on the final results, by asking participants to perform the bioinformatics analysis with a common database, in addition to using their own in-house database. Five laboratories participated in the RT (seven pipelines were tested). We observed that the algorithms had a stronger impact on the overall performance than the choice of the reference database. Our results also suggest that differences in sample preparation can lead to significant differences in the performance, and that laboratories should aim for at least 5-10 Mio reads per sample and use depth of coverage in addition to other interpretation metrics such as the percent of coverage. Performance was generally lower when increasing the number of viruses per sample. The lessons learned from this pilot study will be useful for the development of larger-scale RTs to serve as regular quality control tests for laboratories performing NGS analyses of viruses in a clinical setting.
Keywords
Clinical Laboratory Services/standards, Genome, Human, Genome, Viral, Humans, Laboratory Proficiency Testing/methods, Metagenome, Metagenomics/methods, Metagenomics/standards, Sequence Analysis/methods, Sequence Analysis/standards, Switzerland, EQA, external quality assessment, quality control, ring trial, viral metagenomics
Pubmed
Web of science
Open Access
Yes
Create date
17/09/2019 16:43
Last modification date
14/01/2021 11:36
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