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Your search keyword '"Gagneux, Sebastien"' showing total 5 results
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5 results on '"Gagneux, Sebastien"'

1. Author Correction: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Author

Ezewudo, Matthew, Borens, Amanda, Chiner-Oms, Álvaro, Miotto, Paolo, Chindelevitch, Leonid, Starks, Angela M, Hanna, Debra, Liwski, Richard, Zignol, Matteo, Gilpin, Christopher, Niemann, Stefan, Kohl, Thomas Andreas, Warren, Robin M, Crook, Derrick, Gagneux, Sebastien, Hoffner, Sven, Rodrigues, Camilla, Comas, Iñaki, Engelthaler, David M, Alland, David, Rigouts, Leen, Lange, Christoph, Dheda, Keertan, Hasan, Rumina, McNerney, Ruth, Cirillo, Daniela M, Schito, Marco, Rodwell, Timothy C, and Posey, James

Subjects
Microbiology, Biological Sciences, Infection, Good Health and Well Being
Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2020

2. Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

Author

Ezewudo, Matthew, Borens, Amanda, Chiner-Oms, Álvaro, Miotto, Paolo, Chindelevitch, Leonid, Starks, Angela M, Hanna, Debra, Liwski, Richard, Zignol, Matteo, Gilpin, Christopher, Niemann, Stefan, Kohl, Thomas Andreas, Warren, Robin M, Crook, Derrick, Gagneux, Sebastien, Hoffner, Sven, Rodrigues, Camilla, Comas, Iñaki, Engelthaler, David M, Alland, David, Rigouts, Leen, Lange, Christoph, Dheda, Keertan, Hasan, Rumina, McNerney, Ruth, Cirillo, Daniela M, Schito, Marco, Rodwell, Timothy C, and Posey, James

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Microbiology, Clinical Sciences, Human Genome, Tuberculosis, Antimicrobial Resistance, Rare Diseases, Biotechnology, Infectious Diseases, Aetiology, 2.1 Biological and endogenous factors, Infection, Good Health and Well Being, Antitubercular Agents, Bacterial Proteins, Drug Resistance, Multiple, Bacterial, Genome, Bacterial, Genotype, Humans, Knowledge Bases, Mutation, Mycobacterium tuberculosis, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Tuberculosis, Multidrug-Resistant, Whole Genome Sequencing
Abstract

Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) ( https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.

Published
2018

4. Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

Author

Otchere, Isaac Darko, Coscollá, Mireia, Sánchez-Busó, Leonor, Asante-Poku, Adwoa, Brites, Daniela, Loiseau, Chloe, Meehan, Conor, Osei-Wusu, Stephen, Forson, Audrey, Laryea, Clement, Yahayah, Abdallah Iddrisu, Baddoo, Akosua, Ansa, Gloria Akosua, Aboagye, Samuel Yaw, Asare, Prince, Borrell, Sonia, Gehre, Florian, Beckert, Patrick, Kohl, Thomas A., N’dira, Sanoussi, Beisel, Christian, Antonio, Martin, Niemann, Stefan, de Jong, Bouke C., Parkhill, Julian, Harris, Simon R., Gagneux, Sebastien, and Yeboah-Manu, Dorothy

Published
2018
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5. Tuberculosis in Swiss captive Asian elephants: microevolution of Mycobacterium tuberculosis characterized by multilocus variable-number tandem-repeat analysis and whole-genome sequencing

Author

Ghielmetti, Giovanni, primary, Coscolla, Mireia, additional, Ruetten, Maja, additional, Friedel, Ute, additional, Loiseau, Chloé, additional, Feldmann, Julia, additional, Steinmetz, Hanspeter W., additional, Stucki, David, additional, and Gagneux, Sebastien, additional

Published
2017
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