Concordance of variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses of Mycobacterium tuberculosis strains

Concordance of variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP)... Variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses were compared to determine whether VNTR analysis was effective for population genetic analysis of Mycobacterium tuberculosis strains. A total of 682 strains, 510 Beijing genotype and 172 non-Beijing genotype strains, were studied. The number of repeats was investigated for 24 VNTR loci: the 15 loci of “optimized miru”, the 8 loci of “Beijing option”, and 1 locus for “JATA12”. Six loci (miru31, Mtub4, QUB4156c, QUB3232, VNTR3820, and VNTR4120) showed significantly different median numbers of repeats in strains belonging to different lineages defined by LSP ( P < 0.01, Mann–Whitney U test). When a minimum-spanning tree (MST) was reconstructed using these 6 loci, most strains clustered in the expected branches in the MST branches. However, topology of the MST was not congruent with the evolutional hypothesis of M . tuberculosis , indicating that MST analysis using VNTR data should not use for phylogeny of the organism. When the standardized index of association (s I A ) was calculated using data for the 6 VNTR loci, the value of s I A was significantly different from zero (Monte Carlo simulation with 10,000 resamplings) in every lineage, indicating the linkage disequilibrium in different lineage strains of M . tuberculosis . These results were consistent with the hypothesis that clonal evolution of lineages of the organism has occurred. Therefore, the 6 loci identified in this study would be effective for M. tuberculosis population genetic analysis due to their significantly different median numbers of repeat and linkage disequilibrium though VNTR data was not effective for phylogeny of the organism. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Infection, Genetics and Evolution Elsevier

Concordance of variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses of Mycobacterium tuberculosis strains

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Publisher
Elsevier
Copyright
Copyright © 2010 Elsevier B.V.
ISSN
1567-1348
DOI
10.1016/j.meegid.2010.05.013
Publisher site
See Article on Publisher Site

Abstract

Variable-number tandem repeat (VNTR) and large sequence polymorphism (LSP) analyses were compared to determine whether VNTR analysis was effective for population genetic analysis of Mycobacterium tuberculosis strains. A total of 682 strains, 510 Beijing genotype and 172 non-Beijing genotype strains, were studied. The number of repeats was investigated for 24 VNTR loci: the 15 loci of “optimized miru”, the 8 loci of “Beijing option”, and 1 locus for “JATA12”. Six loci (miru31, Mtub4, QUB4156c, QUB3232, VNTR3820, and VNTR4120) showed significantly different median numbers of repeats in strains belonging to different lineages defined by LSP ( P < 0.01, Mann–Whitney U test). When a minimum-spanning tree (MST) was reconstructed using these 6 loci, most strains clustered in the expected branches in the MST branches. However, topology of the MST was not congruent with the evolutional hypothesis of M . tuberculosis , indicating that MST analysis using VNTR data should not use for phylogeny of the organism. When the standardized index of association (s I A ) was calculated using data for the 6 VNTR loci, the value of s I A was significantly different from zero (Monte Carlo simulation with 10,000 resamplings) in every lineage, indicating the linkage disequilibrium in different lineage strains of M . tuberculosis . These results were consistent with the hypothesis that clonal evolution of lineages of the organism has occurred. Therefore, the 6 loci identified in this study would be effective for M. tuberculosis population genetic analysis due to their significantly different median numbers of repeat and linkage disequilibrium though VNTR data was not effective for phylogeny of the organism.

Journal

Infection, Genetics and EvolutionElsevier

Published: Oct 1, 2010

References

  • Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis
    Estoup, A.; Jarne, P.; Cornuet, J.-M.
  • Population genomics: linkage disequilibrium holds the key
    Goldstein, D.B.; Weale, M.E.
  • Molecular methods for Mycobacterium tuberculosis strain typing: a users guide
    Kanduma, E.; McHugh, T.D.; Gillespie, S.H.
  • Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences
    Lovett, S.T.
  • Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area
    Supply, P.; Warren, R.M.; Banuls, A.L.; Lesjean, S.; van der Spuy, G.D.; Lewis, L.A.; Tibayrenc, M.; van Helden, P.D.; Locht, C.
  • Allelic diversity of variable number of tandem repeats provides phylogenetic clues regarding the Mycobacterium tuberculosis Beijing family
    Wada, T.; Iwamoto, T.
  • Improved differentiation of Mycobacterium tuberculosis strains, including many Beijing genotype strains, using a new combination of variable number of tandem repeats loci
    Yokoyama, E.; Kishida, K.; Uchimura, M.; Ichinohe, S.

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