| Literature DB >> 31209399 |
Conor J Meehan1, Galo A Goig2, Thomas A Kohl3,4, Lennert Verboven5, Anzaan Dippenaar6, Matthew Ezewudo7, Maha R Farhat8,9, Jennifer L Guthrie10, Kris Laukens11, Paolo Miotto12, Boatema Ofori-Anyinam13,14, Viola Dreyer3,4, Philip Supply15,16, Anita Suresh17, Christian Utpatel3,4, Dick van Soolingen18, Yang Zhou19, Philip M Ashton20, Daniela Brites21,22, Andrea M Cabibbe12, Bouke C de Jong1, Margaretha de Vos5, Fabrizio Menardo21,22, Sebastien Gagneux21,22, Qian Gao23, Tim H Heupink5, Qingyun Liu23, Chloé Loiseau21,22, Leen Rigouts1, Timothy C Rodwell17, Elisa Tagliani12, Timothy M Walker24, Robin M Warren6, Yanlin Zhao19, Matteo Zignol25, Marco Schito7, Jennifer Gardy10, Daniela M Cirillo12, Stefan Niemann3,4, Inaki Comas26, Annelies Van Rie27.
Abstract
Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.Entities:
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Year: 2019 PMID： 31209399 DOI： 10.1038/s41579-019-0214-5
Source DB: PubMed Journal: Nat Rev Microbiol ISSN： 1740-1526 Impact factor: 60.633