Computational protocol: Population Structure among Mycobacterium tuberculosis Isolates from Pulmonary Tuberculosis Patients in Colombia

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Protocol publication

[…] IS6110-RFLP, spoligotyping, and 24-locus MIRU-VNTRs results were analyzed using the BioNumerics software version 6.6 (Applied Maths. Sint-Martens-Latem, Belgium) to establish the relationships between different isolates of M. tuberculosis. Patterns of IS6110-RFLP were digitized and similarities were calculated using the Dice coefficient. MIRU-VNTR and spoligotyping data were entered as character type and analyzed using the categorical coefficient. Similarity trees and dendrograms were calculated using the unweighted pair group method with arithmetic averages (UPGMA). A cluster was defined as two or more M. tuberculosis isolates with identical patterns. The MIRU-VNTR allelic diversity (h) at a given locus was calculated as h = 1−∑ xi2 [(n/n−1)], where xi is the frequency of the ith allele at the locus and n is the number of isolates , . To determine the discriminatory power (DP) of each genotyping method or a combination thereof, the Hunter-Gaston Discriminatory Index (HGDI) was calculated .Minimum spanning trees (MST) were created using the Bionumerics software (Version 6.60) to explore the evolutionary relationship among spoligotyping and 24-locus MIRU-VNTR isolates. Spoligoforest trees were drawn to determine the parent-to-descendant spoligotypes in the group of isolates studied using the Fruchterman-Reingold algorithm and a hierarchical layout using the SpolTools software [http://www.emi.unsw.edu.au/spolTools, ], and reshaped and colored using the GraphViz software [http://www.graphviz.org]. […]

Pipeline specifications

Software tools BioNumerics, Graphviz
Application Population genetic analysis
Organisms Mycobacterium tuberculosis, Homo sapiens, Osphranter robustus, Human immunodeficiency virus 2
Diseases Tuberculosis, Tuberculosis, Pulmonary