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

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
Creator	Kaiser, Laurent Huber, Michael Kufner, Verena Schmutz, Stefan Zagordi, Osvaldo Cordey, Samuel Fellay, Jacques Junier, Thomas Bachofen, Claudia Qi, Weihong Laubscher, Florian Barbié, Valérie Beuret, Christian Kubacki, Jakub Lebrand, Aitana Neuenschwander, Stefan Ramette, Alban
source	Medline; PMC
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.
has issue date	2019-08-28(xsd:dateTime)
bibo:doi	10.3390/genes10090655
bibo:pmid	31466373
has license	cc-by
sha1sum (hex)	3e8d0363f49f83917e0ddddf7b4322186da47dbc
schema:url	https://doi.org/10.3390/genes10090655
resource representing a document's title	Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
has PubMed Central identifier	PMC6770386
has PubMed identifier	31466373
schema:publication	Genes (Basel)
resource representing a document's body	covid:3e8d0363f49f83917e0ddddf7b4322186da47dbc#body_text
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