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Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting

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Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting. / de Vries, Jutte J C; Brown, Julianne R; Couto, Natacha; Beer, Martin; Le Mercier, Philippe; Sidorov, Igor; Papa, Anna; Fischer, Nicole; Oude Munnink, Bas B; Rodriquez, Christophe; Zaheri, Maryam; Sayiner, Arzu; Hönemann, Mario; Cataluna, Alba Perez; Carbo, Ellen C; Bachofen, Claudia; Kubacki, Jakub; Schmitz, Dennis; Tsioka, Katerina; Matamoros, Sébastien; Höper, Dirk; Hernandez, Marta; Puchhammer-Stöckl, Elisabeth; Lebrand, Aitana; Huber, Michael; Simmonds, Peter; Claas, Eric C J; López-Labrador, F Xavier; ESCV Network on Next-Generation Sequencing.

In: J CLIN VIROL, Vol. 138, 104812, 05.2021.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

de Vries, JJC, Brown, JR, Couto, N, Beer, M, Le Mercier, P, Sidorov, I, Papa, A, Fischer, N, Oude Munnink, BB, Rodriquez, C, Zaheri, M, Sayiner, A, Hönemann, M, Cataluna, AP, Carbo, EC, Bachofen, C, Kubacki, J, Schmitz, D, Tsioka, K, Matamoros, S, Höper, D, Hernandez, M, Puchhammer-Stöckl, E, Lebrand, A, Huber, M, Simmonds, P, Claas, ECJ, López-Labrador, FX & ESCV Network on Next-Generation Sequencing 2021, 'Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting', J CLIN VIROL, vol. 138, 104812. https://doi.org/10.1016/j.jcv.2021.104812

APA

de Vries, J. J. C., Brown, J. R., Couto, N., Beer, M., Le Mercier, P., Sidorov, I., Papa, A., Fischer, N., Oude Munnink, B. B., Rodriquez, C., Zaheri, M., Sayiner, A., Hönemann, M., Cataluna, A. P., Carbo, E. C., Bachofen, C., Kubacki, J., Schmitz, D., Tsioka, K., ... ESCV Network on Next-Generation Sequencing (2021). Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting. J CLIN VIROL, 138, [104812]. https://doi.org/10.1016/j.jcv.2021.104812

Vancouver

de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I et al. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting. J CLIN VIROL. 2021 May;138. 104812. https://doi.org/10.1016/j.jcv.2021.104812

Bibtex

@article{010522abaa2044f4bb94c9d7a0610e1e,
title = "Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting",
abstract = "Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.",
keywords = "Computational Biology, High-Throughput Nucleotide Sequencing, Humans, Metagenome, Metagenomics, Sensitivity and Specificity, Viruses/genetics",
author = "{de Vries}, {Jutte J C} and Brown, {Julianne R} and Natacha Couto and Martin Beer and {Le Mercier}, Philippe and Igor Sidorov and Anna Papa and Nicole Fischer and {Oude Munnink}, {Bas B} and Christophe Rodriquez and Maryam Zaheri and Arzu Sayiner and Mario H{\"o}nemann and Cataluna, {Alba Perez} and Carbo, {Ellen C} and Claudia Bachofen and Jakub Kubacki and Dennis Schmitz and Katerina Tsioka and S{\'e}bastien Matamoros and Dirk H{\"o}per and Marta Hernandez and Elisabeth Puchhammer-St{\"o}ckl and Aitana Lebrand and Michael Huber and Peter Simmonds and Claas, {Eric C J} and L{\'o}pez-Labrador, {F Xavier} and {ESCV Network on Next-Generation Sequencing}",
note = "Copyright {\textcopyright} 2021 The Authors. Published by Elsevier B.V. All rights reserved.",
year = "2021",
month = may,
doi = "10.1016/j.jcv.2021.104812",
language = "English",
volume = "138",
journal = "J CLIN VIROL",
issn = "1386-6532",
publisher = "Elsevier",

}

RIS

TY - JOUR

T1 - Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II:bioinformatic analysis and reporting

AU - de Vries, Jutte J C

AU - Brown, Julianne R

AU - Couto, Natacha

AU - Beer, Martin

AU - Le Mercier, Philippe

AU - Sidorov, Igor

AU - Papa, Anna

AU - Fischer, Nicole

AU - Oude Munnink, Bas B

AU - Rodriquez, Christophe

AU - Zaheri, Maryam

AU - Sayiner, Arzu

AU - Hönemann, Mario

AU - Cataluna, Alba Perez

AU - Carbo, Ellen C

AU - Bachofen, Claudia

AU - Kubacki, Jakub

AU - Schmitz, Dennis

AU - Tsioka, Katerina

AU - Matamoros, Sébastien

AU - Höper, Dirk

AU - Hernandez, Marta

AU - Puchhammer-Stöckl, Elisabeth

AU - Lebrand, Aitana

AU - Huber, Michael

AU - Simmonds, Peter

AU - Claas, Eric C J

AU - López-Labrador, F Xavier

AU - ESCV Network on Next-Generation Sequencing

N1 - Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.

PY - 2021/5

Y1 - 2021/5

N2 - Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

AB - Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

KW - Computational Biology

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Metagenome

KW - Metagenomics

KW - Sensitivity and Specificity

KW - Viruses/genetics

U2 - 10.1016/j.jcv.2021.104812

DO - 10.1016/j.jcv.2021.104812

M3 - SCORING: Journal article

C2 - 33819811

VL - 138

JO - J CLIN VIROL

JF - J CLIN VIROL

SN - 1386-6532

M1 - 104812

ER -