414 24 10444 5 48716 document 10444 Coll2014_LinSpeSNPs_final.tab text/plain 4e9ad8b00bec62faf1b915a3fdd680fe7d7a09f1f8d7bfcec4420fd2d5e5b8a9 SHA256 500016 2021-03-23 15:39:54 https://datacompass.lshtm.ac.uk/id/eprint/414/1/Coll2014_LinSpeSNPs_final.tab 414 1 1 text/plain Text en public cc_by

Coll2014_LinSpeSNPs_final.tab

data indefinite Dataset archive 3 disk0/00/00/04/14 2017-04-28 09:55:10 2025-06-23 15:45:59 2017-04-28 09:55:10 data_collection show Coll Francesc 0000-0002-7882-2325 TRUE 6c2b7e9afcb260630b636d81fd3bfaf0 Mcnerney Ruth TRUE 742e523ff9b133b222c41fb882843cdb Guerra-Assunção José Afonso FALSE Glynn Judith R. 0000-0001-9325-4576 TRUE 780a51774911d12b019335185a7bde49 Perdigão João FALSE Viveiros Miguel FALSE Portugal Isabel FALSE Pain Arnab FALSE Martin Nigel FALSE Clark Taane G. 0000-0001-8985-9265 TRUE d6c0a9ae313d576cb0129f8b148489e7 Study consortium EPID EPNC ITCR ITPM Bacterial genetics Genetic variation Phylogenomics Dataset held for preservation purposes. The tab-delimited dataset may be obtained from http://pathogenseq.lshtm.ac.uk/downloads/Coll2014_LinSpeSNPs_final.csv. Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC samples into distinct lineages and families, using molecular genotypes (e.g. spoligotyping or MIRU-VNTR), regions of difference (RD) and single nucleotide polymorphisms (SNPs). However, these systems lack accuracy or resolution due to the limited genetic variation studied or small number of samples used in their construction. We identified ~90k SNP across a global strain collection of 1,590 genomes. The SNP-based phylogeny was consistent with the gold-standard RD classification system and revealed fine-scale diversity. Of the ~7k strain-specific SNPs identified, a minimum set of 61 markers are proposed to discriminate accurately and robustly known circulating strains. This SNP barcode may be used to classify clinical isolates and evaluate tools to control TB, including therapeutics and vaccines whose effectiveness may vary by strain-type. 2014 published London School of Hygiene & Tropical Medicine 10.17037/DATA.00000414 Dataset Study consortium Experiment public London, United Kingdom Bloomsbury Colleges PhD Studentship fund Fundação para a Ciência e Tecnologia Post-doctoral fellowship fund King Abdullah University of Science and Technology Wellcome Trust Dataset Quantitative en http://researchonline.lshtm.ac.uk/id/eprint/1911930 Bloomsbury Colleges PhD Studentship fund Fundação para a Ciência e Tecnologia Post-doctoral fellowship fund King Abdullah University of Science and Technology http://dx.doi.org/10.13039/501100004052 Wellcome Trust http://dx.doi.org/10.13039/100010269 2014