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Multiple loci VNTR analysis

January 01, 1970

Multiple loci VNTR analysis (MLVA) is a method employed for the genetic analysis of particular microorganisms, such as pathogenic bacteria, that takes advantage of the polymorphism of tandemly repeated DNA sequences. A "VNTR" is a "variable-number tandem repeat". This method is well known in forensic science since it is the basis of DNA fingerprinting in humans. When applied to bacteria, it contributes to forensic microbiology through which the source of a particular strain might eventually be traced back, making it a useful technique for outbreak surveillance.

Tandem (top) versus interspersed (bottom) repeated nucleic acid sequence

In a typical MLVA, a number of well-selected and characterised (in terms of mutation rate and diversity) loci are amplified by polymerase chain reaction (PCR), so that the size of each locus can be measured, usually by electrophoresis of the amplification products together with reference DNA fragments (a so-called DNA size marker). Different electrophoresis equipment can be used depending on the required size estimate accuracy, and the local laboratory set-up, from basic agarose gel electrophoresis up to the more sophisticated and high-throughput capillary electrophoresis devices.[1] From this size estimate, the number of repeat units at each locus can be deduced. The resulting information is a code which can be easily compared to reference databases once the assay has been harmonised and standardised.[2][3]

MLVA has become a major first line typing tool in a number of pathogens where such an harmonisation could be achieved, including Mycobacterium tuberculosis,[4] Bacillus anthracis,[5] Brucella.[6][7]

Some MLVA-associated web sites edit

Software for analysis of MLVA data edit

  • GeneMapper A commercial software for normalisation and size calling of peaks from a certain brand of capillary electrophoresis machines.
  • BioNumerics A commercial bioinformatics solution to store and analyze a large panel of biological data, including MLVA, and more generally character datasets. Normalisation, size calling, size correction, assignment of number of repeats and cluster analysis on MLVA data can be performed.

References edit

  1. ^ Vergnaud G, Pourcel C (2009). "Multiple locus variable number of tandem repeats analysis". Molecular Epidemiology of Microorganisms. Methods Mol. Biol. Vol. 551. pp. 141–58. doi:10.1007/978-1-60327-999-4_12. ISBN 978-1-60327-998-7. PMID 19521873.
  2. ^ Grissa I, Bouchon P, Pourcel C, Vergnaud G (2008). "On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing". Biochimie. 90 (4): 660–8. doi:10.1016/j.biochi.2007.07.014. PMID 17822824.
  3. ^ Nadon CA, Trees E, Ng LK, Møller Nielsen E, Reimer A, Maxwell N, Kubota KA, Gerner-Smidt P, the MLVA Harmonization Working Group (2013). "Development and application of MLVA methods as a tool for inter-laboratory surveillance". Euro Surveill. 18 (35): 20565. doi:10.2807/1560-7917.es2013.18.35.20565. PMC 5667538. PMID 24008231.
  4. ^ Blouin Y, Hauck Y, Soler C, Fabre M, Vong R, Dehan C, Cazajous G, Massoure PL, Kraemer P, Jenkins A, Garnotel E, Pourcel C, Vergnaud G (2012). "Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade". PLOS ONE. 7 (12): e52841. doi:10.1371/journal.pone.0052841. PMC 3531362. PMID 23300794.
  5. ^ Thierry S, Tourterel C, Le Flèche P, Derzelle S, Dekhil N, Mendy C, Colaneri C, Vergnaud G, Madani N (2014). "Genotyping of French Bacillus anthracis strains based on 31-loci multi locus VNTR analysis: epidemiology, marker evaluation, and update of the internet genotype database". PLOS ONE. 9 (6): e95131. doi:10.1371/journal.pone.0095131. PMC 4046976. PMID 24901417.
  6. ^ Scholz HC, Vergnaud G (2013). "Molecular characterisation of Brucella species". Rev. Sci. Tech. 32 (1): 149–62. doi:10.20506/rst.32.1.2189. PMID 23837373.
  7. ^ Lindstedt BA, Torpdahl M, Vergnaud G, Le Hello S, Weill FX, Tietze E, Malorny B, Prendergast DM, Ní Ghallchoir E, Lista RF, Schouls LM, Söderlund R, Börjesson S, Åkerström S (2013). "Use of multilocus variable-number tandem repeat analysis (MLVA) in eight European countries, 2012". Euro Surveill. 18 (4): 20385. doi:10.2807/ese.18.04.20385-en. hdl:11250/219465. PMID 23369388.

January 01, 1970
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This article needs additional citations for verification Please help improve this article by adding citations to reliable sources Unsourced material may be challenged and removed Find sources Multiple loci VNTR analysis news newspapers books scholar JSTOR February 2012 Learn how and when to remove this message Multiple loci VNTR analysis MLVA is a method employed for the genetic analysis of particular microorganisms such as pathogenic bacteria that takes advantage of the polymorphism of tandemly repeated DNA sequences A VNTR is a variable number tandem repeat This method is well known in forensic science since it is the basis of DNA fingerprinting in humans When applied to bacteria it contributes to forensic microbiology through which the source of a particular strain might eventually be traced back making it a useful technique for outbreak surveillance Tandem top versus interspersed bottom repeated nucleic acid sequence In a typical MLVA a number of well selected and characterised in terms of mutation rate and diversity loci are amplified by polymerase chain reaction PCR so that the size of each locus can be measured usually by electrophoresis of the amplification products together with reference DNA fragments a so called DNA size marker Different electrophoresis equipment can be used depending on the required size estimate accuracy and the local laboratory set up from basic agarose gel electrophoresis up to the more sophisticated and high throughput capillary electrophoresis devices 1 From this size estimate the number of repeat units at each locus can be deduced The resulting information is a code which can be easily compared to reference databases once the assay has been harmonised and standardised 2 3 MLVA has become a major first line typing tool in a number of pathogens where such an harmonisation could be achieved including Mycobacterium tuberculosis 4 Bacillus anthracis 5 Brucella 6 7 Some MLVA associated web sites edithttps web archive org web 20141225151444 http tandemrepeat u psud fr http minisatellites u psud fr http mlva u psud fr http www mlva eu http www umcutrecht nl subsite MLVA http miru vntrplus org http www pasteur fr recherche genopole PF8 mlva http mlva net https web archive org web 20130927082141 http microgeno org Software for analysis of MLVA data editGeneMapper A commercial software for normalisation and size calling of peaks from a certain brand of capillary electrophoresis machines BioNumerics A commercial bioinformatics solution to store and analyze a large panel of biological data including MLVA and more generally character datasets Normalisation size calling size correction assignment of number of repeats and cluster analysis on MLVA data can be performed References edit Vergnaud G Pourcel C 2009 Multiple locus variable number of tandem repeats analysis Molecular Epidemiology of Microorganisms Methods Mol Biol Vol 551 pp 141 58 doi 10 1007 978 1 60327 999 4 12 ISBN 978 1 60327 998 7 PMID 19521873 Grissa I Bouchon P Pourcel C Vergnaud G 2008 On line resources for bacterial micro evolution studies using MLVA or CRISPR typing Biochimie 90 4 660 8 doi 10 1016 j biochi 2007 07 014 PMID 17822824 Nadon CA Trees E Ng LK Moller Nielsen E Reimer A Maxwell N Kubota KA Gerner Smidt P the MLVA Harmonization Working Group 2013 Development and application of MLVA methods as a tool for inter laboratory surveillance Euro Surveill 18 35 20565 doi 10 2807 1560 7917 es2013 18 35 20565 PMC 5667538 PMID 24008231 Blouin Y Hauck Y Soler C Fabre M Vong R Dehan C Cazajous G Massoure PL Kraemer P Jenkins A Garnotel E Pourcel C Vergnaud G 2012 Significance of the identification in the Horn of Africa of an exceptionally deep branching Mycobacterium tuberculosis clade PLOS ONE 7 12 e52841 doi 10 1371 journal pone 0052841 PMC 3531362 PMID 23300794 Thierry S Tourterel C Le Fleche P Derzelle S Dekhil N Mendy C Colaneri C Vergnaud G Madani N 2014 Genotyping of French Bacillus anthracis strains based on 31 loci multi locus VNTR analysis epidemiology marker evaluation and update of the internet genotype database PLOS ONE 9 6 e95131 doi 10 1371 journal pone 0095131 PMC 4046976 PMID 24901417 Scholz HC Vergnaud G 2013 Molecular characterisation of Brucella species Rev Sci Tech 32 1 149 62 doi 10 20506 rst 32 1 2189 PMID 23837373 Lindstedt BA Torpdahl M Vergnaud G Le Hello S Weill FX Tietze E Malorny B Prendergast DM Ni Ghallchoir E Lista RF Schouls LM Soderlund R Borjesson S Akerstrom S 2013 Use of multilocus variable number tandem repeat analysis MLVA in eight European countries 2012 Euro Surveill 18 4 20385 doi 10 2807 ese 18 04 20385 en hdl 11250 219465 PMID 23369388 Retrieved from https en wikipedia org w index php title Multiple loci VNTR analysis amp oldid 1195773517, wikipedia, wiki, book, books, library,

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