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

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 infectio...

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Autores principales: Junier, Thomas, Huber, Michael, Schmutz, Stefan, Kufner, Verena, Zagordi, Osvaldo, Neuenschwander, Stefan, Ramette, Alban, Kubacki, Jakub, Bachofen, Claudia, Qi, Weihong, Laubscher, Florian, Cordey, Samuel, Kaiser, Laurent, Beuret, Christian, Barbié, Valérie, Fellay, Jacques, Lebrand, Aitana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770386/
https://www.ncbi.nlm.nih.gov/pubmed/31466373
http://dx.doi.org/10.3390/genes10090655
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author Junier, Thomas
Huber, Michael
Schmutz, Stefan
Kufner, Verena
Zagordi, Osvaldo
Neuenschwander, Stefan
Ramette, Alban
Kubacki, Jakub
Bachofen, Claudia
Qi, Weihong
Laubscher, Florian
Cordey, Samuel
Kaiser, Laurent
Beuret, Christian
Barbié, Valérie
Fellay, Jacques
Lebrand, Aitana
author_facet Junier, Thomas
Huber, Michael
Schmutz, Stefan
Kufner, Verena
Zagordi, Osvaldo
Neuenschwander, Stefan
Ramette, Alban
Kubacki, Jakub
Bachofen, Claudia
Qi, Weihong
Laubscher, Florian
Cordey, Samuel
Kaiser, Laurent
Beuret, Christian
Barbié, Valérie
Fellay, Jacques
Lebrand, Aitana
author_sort Junier, Thomas
collection PubMed
description 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.
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spelling pubmed-67703862019-10-30 Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial Junier, Thomas Huber, Michael Schmutz, Stefan Kufner, Verena Zagordi, Osvaldo Neuenschwander, Stefan Ramette, Alban Kubacki, Jakub Bachofen, Claudia Qi, Weihong Laubscher, Florian Cordey, Samuel Kaiser, Laurent Beuret, Christian Barbié, Valérie Fellay, Jacques Lebrand, Aitana Genes (Basel) Article 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. MDPI 2019-08-28 /pmc/articles/PMC6770386/ /pubmed/31466373 http://dx.doi.org/10.3390/genes10090655 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Junier, Thomas
Huber, Michael
Schmutz, Stefan
Kufner, Verena
Zagordi, Osvaldo
Neuenschwander, Stefan
Ramette, Alban
Kubacki, Jakub
Bachofen, Claudia
Qi, Weihong
Laubscher, Florian
Cordey, Samuel
Kaiser, Laurent
Beuret, Christian
Barbié, Valérie
Fellay, Jacques
Lebrand, Aitana
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
title Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
title_full Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
title_fullStr Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
title_full_unstemmed Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
title_short Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial
title_sort viral metagenomics in the clinical realm: lessons learned from a swiss-wide ring trial
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770386/
https://www.ncbi.nlm.nih.gov/pubmed/31466373
http://dx.doi.org/10.3390/genes10090655
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