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PolyTB: a genomic variation map for Mycobacterium tuberculosis.

Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG - Tuberculosis (Edinb) (2014)

Bottom Line: The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies.Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies.Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800).

View Article: PubMed Central - PubMed

Affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK. Electronic address: francesc.coll@lshtm.ac.uk.

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Related in: MedlinePlus

SNP-based neighbour-joining phylogenetic tree of 140 isolates belonging to four different locations (Phylogenetic view) A neighbour phylogenetic tree based on pre-calculated SNP distances is built in real time for the set of 140 isolates from Shanghai (China), Hamburg (Germany), Karonga (Malawi) and Kampala (Uganda). Spoligotype lineages and locations are colour-coded as bar charts around the tree (outer bar representing locations and the inner one spoligotypes) to enable the visual identification of correlations between spoligotype/location and phylogenetic clustering. A table summarising all colour codes will be shown at the left hand side of the page.
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fig5: SNP-based neighbour-joining phylogenetic tree of 140 isolates belonging to four different locations (Phylogenetic view) A neighbour phylogenetic tree based on pre-calculated SNP distances is built in real time for the set of 140 isolates from Shanghai (China), Hamburg (Germany), Karonga (Malawi) and Kampala (Uganda). Spoligotype lineages and locations are colour-coded as bar charts around the tree (outer bar representing locations and the inner one spoligotypes) to enable the visual identification of correlations between spoligotype/location and phylogenetic clustering. A table summarising all colour codes will be shown at the left hand side of the page.

Mentions: The phylogenetic view allows the user to construct phylogenies for a subset of isolates using whole-genome spanning SNPs. Spoligotypes are included to investigate whether clustering based on SNPs correlates with a strain-type. Figure 5 shows the resulting SNP-based neighbour-joining phylogenetic tree constructed for 140 isolates belonging to four different locations. Other PHYLYP distance-based methods (Fitch-Margoliash, UPGMA and Least Squares) are available too. Lineages and locations are shown as colour-coded bar charts around the tree to highlight the correlation between lineage and location with phylogenetic clustering. The aim of the phylogenetic view is to assess the genetic relatedness of isolates within and across populations as well as comparing genetic clustering with spoligotype and geographical assignation.


PolyTB: a genomic variation map for Mycobacterium tuberculosis.

Coll F, Preston M, Guerra-Assunção JA, Hill-Cawthorn G, Harris D, Perdigão J, Viveiros M, Portugal I, Drobniewski F, Gagneux S, Glynn JR, Pain A, Parkhill J, McNerney R, Martin N, Clark TG - Tuberculosis (Edinb) (2014)

SNP-based neighbour-joining phylogenetic tree of 140 isolates belonging to four different locations (Phylogenetic view) A neighbour phylogenetic tree based on pre-calculated SNP distances is built in real time for the set of 140 isolates from Shanghai (China), Hamburg (Germany), Karonga (Malawi) and Kampala (Uganda). Spoligotype lineages and locations are colour-coded as bar charts around the tree (outer bar representing locations and the inner one spoligotypes) to enable the visual identification of correlations between spoligotype/location and phylogenetic clustering. A table summarising all colour codes will be shown at the left hand side of the page.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4066953&req=5

fig5: SNP-based neighbour-joining phylogenetic tree of 140 isolates belonging to four different locations (Phylogenetic view) A neighbour phylogenetic tree based on pre-calculated SNP distances is built in real time for the set of 140 isolates from Shanghai (China), Hamburg (Germany), Karonga (Malawi) and Kampala (Uganda). Spoligotype lineages and locations are colour-coded as bar charts around the tree (outer bar representing locations and the inner one spoligotypes) to enable the visual identification of correlations between spoligotype/location and phylogenetic clustering. A table summarising all colour codes will be shown at the left hand side of the page.
Mentions: The phylogenetic view allows the user to construct phylogenies for a subset of isolates using whole-genome spanning SNPs. Spoligotypes are included to investigate whether clustering based on SNPs correlates with a strain-type. Figure 5 shows the resulting SNP-based neighbour-joining phylogenetic tree constructed for 140 isolates belonging to four different locations. Other PHYLYP distance-based methods (Fitch-Margoliash, UPGMA and Least Squares) are available too. Lineages and locations are shown as colour-coded bar charts around the tree to highlight the correlation between lineage and location with phylogenetic clustering. The aim of the phylogenetic view is to assess the genetic relatedness of isolates within and across populations as well as comparing genetic clustering with spoligotype and geographical assignation.

Bottom Line: The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies.Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies.Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800).

View Article: PubMed Central - PubMed

Affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK. Electronic address: francesc.coll@lshtm.ac.uk.

Show MeSH
Related in: MedlinePlus