The Experts below are selected from a list of 72789 Experts worldwide ranked by ideXlab platform
Gilles Vergnaud - One of the best experts on this subject based on the ideXlab platform.
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Comparison of Multiple-Locus Variable-Number Tandem-Repeat Analysis with Other PCR-Based Methods for Typing Brucella suis Isolates
Journal of clinical microbiology, 2007Co-Authors: David García-yoldi, Clara M Marin, Philippe Le Flèche, María Jesús De Miguel, Pilar M. Muñoz, José M. Blasco, Zeljko Cvetnic, Gilles Vergnaud, Ignacio López-goñiAbstract:Multiple-locus variable-number Tandem-Repeat analysis (MLVA), multiplex PCR, and PCR-restriction fragment length polymorphism analysis were compared for typing Brucella suis isolates. A perfect concordance was obtained among these molecular assays. However, MLVA was the only method to demonstrate brucellosis outbreaks and to confirm that wildlife is a reservoir for zoonotic brucellosis.
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high resolution on line identification of strains from the mycobacterium tuberculosis complex based on Tandem Repeat typing
BMC Microbiology, 2002Co-Authors: Philippe Le Fleche, Michel Fabre, Jeanlouis Koeck, Gilles VergnaudAbstract:Background Currently available reference methods for the molecular epidemiology of the Mycobacterium tuberculosis complex either lack sensitivity or are still too tedious and slow for routine application. Recently, Tandem Repeat typing has emerged as a potential alternative. This report contributes to the development of Tandem Repeat typing for M. tuberculosis by summarising the existing data, developing additional markers, and setting up a freely accessible, fast, and easy to use, internet-based service for strain identification.
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High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on Tandem Repeat typing
BMC Microbiology, 2002Co-Authors: Philippe Le Flèche, Michel Fabre, Jeanlouis Koeck, France Denoeud, Gilles VergnaudAbstract:Background Currently available reference methods for the molecular epidemiology of the Mycobacterium tuberculosis complex either lack sensitivity or are still too tedious and slow for routine application. Recently, Tandem Repeat typing has emerged as a potential alternative. This report contributes to the development of Tandem Repeat typing for M. tuberculosis by summarising the existing data, developing additional markers, and setting up a freely accessible, fast, and easy to use, internet-based service for strain identification. Results A collection of 21 VNTRs incorporating 13 previously described loci and 8 newly evaluated markers was used to genotype 90 strains from the M. tuberculosis complex ( M. tuberculosis (64 strains), M. bovis (9 strains including 4 BCG representatives), M. africanum (17 strains)). Eighty-four different genotypes are defined. Clustering analysis shows that the M. africanum strains fall into three main groups, one of which is closer to the M. tuberculosis strains, and an other one is closer to the M. bovis strains. The resulting data has been made freely accessible over the internet http://bacterial-genotyping.igmors.u-psud.fr/bnserver to allow direct strain identification queries. Conclusions Tandem-Repeat typing is a PCR-based assay which may prove to be a powerful complement to the existing epidemiological tools for the M. tuberculosis complex. The number of markers to type depends on the identification precision which is required, so that identification can be achieved quickly at low cost in terms of consumables, technical expertise and equipment.
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High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on Tandem Repeat typing.
BMC Microbiology, 2002Co-Authors: Philippe Le Flèche, Michel Fabre, Jeanlouis Koeck, France Denoeud, Gilles VergnaudAbstract:Currently available reference methods for the molecular epidemiology of the Mycobacterium tuberculosis complex either lack sensitivity or are still too tedious and slow for routine application. Recently, Tandem Repeat typing has emerged as a potential alternative. This report contributes to the development of Tandem Repeat typing for M. tuberculosis by summarising the existing data, developing additional markers, and setting up a freely accessible, fast, and easy to use, internet-based service for strain identification. A collection of 21 VNTRs incorporating 13 previously described loci and 8 newly evaluated markers was used to genotype 90 strains from the M. tuberculosis complex (M. tuberculosis (64 strains), M. bovis (9 strains including 4 BCG representatives), M. africanum (17 strains)). Eighty-four different genotypes are defined. Clustering analysis shows that the M. africanum strains fall into three main groups, one of which is closer to the M. tuberculosis strains, and an other one is closer to the M. bovis strains. The resulting data has been made freely accessible over the internet http://bacterial-genotyping.igmors.u-psud.fr/bnserver to allow direct strain identification queries. Tandem-Repeat typing is a PCR-based assay which may prove to be a powerful complement to the existing epidemiological tools for the M. tuberculosis complex. The number of markers to type depends on the identification precision which is required, so that identification can be achieved quickly at low cost in terms of consumables, technical expertise and equipment.
Richard F. Selden - One of the best experts on this subject based on the ideXlab platform.
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Fully integrated, fully automated generation of short Tandem Repeat profiles
Investigative genetics, 2013Co-Authors: Eugene Sern Ting Tan, Rosemary S. Turingan, Catherine Hogan, Sameer Vasantgadkar, Luke Palombo, James W. Schumm, Richard F. SeldenAbstract:Background The generation of short Tandem Repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short Tandem Repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short Tandem Repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings.
Anthony J. Hannan - One of the best experts on this subject based on the ideXlab platform.
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Huntington's Disease and other Tandem Repeat Disorders
2013Co-Authors: Kenneth Myer, Anthony J. Hannan, Julie C. Stout, Nellie Georgiou-karistianis, Anita M.y. Goh, Martin B. Delatycki, Andrew Churchyard, Danny M. HattersAbstract:Huntington's Disease (HD) is the most common of at least nine Tandem Repeat disorders caused by expansion of CAG/glutamine Tandem Repeats in different genes/proteins. Many of the other neurodegenerative diseases are spinocerebellar ataxias and are likely to exhibit shared mechanisms. Furthermore, various other neurological and psychiatric disorders, such as Friedreich ataxia and Fragile X syndrome are caused by Tandem Repeat expansions in other genes. The meeting will include an integrated mixture of basic and clinical research, with the aim to promote a better understanding of these neurological disorders.
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Tandem Repeat Polymorphisms - Tandem Repeat Polymorphisms
Advances in Experimental Medicine and Biology, 2012Co-Authors: Anthony J. HannanAbstract:Tandem repetitive DNA elements (Tandem Repeats), including microsatellites and simple sequence Repeats, are extremely common throughout the genomes of a wide range of species. Tandem Repeat expansions have been found to cause a range of monogenic diseases, such as Huntington’s disease, various ataxias and other neurological diseases. The human genome contains hundreds of thousands of distinct Tandem Repeats, many of which appear to have evolved to regulate specific aspects of gene expression, RNA function and protein function. Tandem Repeat polymorphisms (TRPs) provide a unique source of genetic variability that has an extended digital distribution, asopposed to theusual binary natureofsinglenucleotidepolymorphisms. In this chapter I will review studies in which Tandem Repeats have been implicated in a multitude of molecular and cellular processes associated with the development, behavior and evolution of a variety of animal species, including mammals. Recent data suggesting that these repetitive sequences can increase the ‘evolvability’ of genomes provides further evidence that TRPs not only have functional consequences but also provide a rich source of genetic diversity that can facilitate evolutionary processes. I propose that a readily mutable subclass of Tandem Repeats may provide an important template for stochastic genetic variation, which could in turn generate diversity in epigenetics, development and organismal function, thus impacting upon evolution. Furthermore, the distinctive characteristics of TRPs also uniquely position them as contributors to complex polygenic disorders. Ultimately, there is much to be gained from systematic analysis of the ‘Repeatome’, defined as the entire set of Tandem Repeats and other repetitive DNA in a genome, as well as their transcribed and translated expression products. Applying such approaches not only to the human genome but to other species will yield new insights into the genetic regulation of a wide range of biological processes in healthy and diseased states.
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Tandem Repeat Polymorphisms - Tandem Repeat polymorphisms: Mediators of genetic plasticity, modulators of biological diversity and dynamic sources of disease susceptibility.
Advances in experimental medicine and biology, 2012Co-Authors: Anthony J. HannanAbstract:Tandem repetitive DNA elements (Tandem Repeats), including microsatellites and simple sequence Repeats, are extremely common throughout the genomes of a wide range of species. Tandem Repeat expansions have been found to cause a range of monogenic diseases, such as Huntington’s disease, various ataxias and other neurological diseases. The human genome contains hundreds of thousands of distinct Tandem Repeats, many of which appear to have evolved to regulate specific aspects of gene expression, RNA function and protein function. Tandem Repeat polymorphisms (TRPs) provide a unique source of genetic variability that has an extended digital distribution, asopposed to theusual binary natureofsinglenucleotidepolymorphisms. In this chapter I will review studies in which Tandem Repeats have been implicated in a multitude of molecular and cellular processes associated with the development, behavior and evolution of a variety of animal species, including mammals. Recent data suggesting that these repetitive sequences can increase the ‘evolvability’ of genomes provides further evidence that TRPs not only have functional consequences but also provide a rich source of genetic diversity that can facilitate evolutionary processes. I propose that a readily mutable subclass of Tandem Repeats may provide an important template for stochastic genetic variation, which could in turn generate diversity in epigenetics, development and organismal function, thus impacting upon evolution. Furthermore, the distinctive characteristics of TRPs also uniquely position them as contributors to complex polygenic disorders. Ultimately, there is much to be gained from systematic analysis of the ‘Repeatome’, defined as the entire set of Tandem Repeats and other repetitive DNA in a genome, as well as their transcribed and translated expression products. Applying such approaches not only to the human genome but to other species will yield new insights into the genetic regulation of a wide range of biological processes in healthy and diseased states.
Philippe Le Flèche - One of the best experts on this subject based on the ideXlab platform.
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Comparison of Multiple-Locus Variable-Number Tandem-Repeat Analysis with Other PCR-Based Methods for Typing Brucella suis Isolates
Journal of clinical microbiology, 2007Co-Authors: David García-yoldi, Clara M Marin, Philippe Le Flèche, María Jesús De Miguel, Pilar M. Muñoz, José M. Blasco, Zeljko Cvetnic, Gilles Vergnaud, Ignacio López-goñiAbstract:Multiple-locus variable-number Tandem-Repeat analysis (MLVA), multiplex PCR, and PCR-restriction fragment length polymorphism analysis were compared for typing Brucella suis isolates. A perfect concordance was obtained among these molecular assays. However, MLVA was the only method to demonstrate brucellosis outbreaks and to confirm that wildlife is a reservoir for zoonotic brucellosis.
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High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on Tandem Repeat typing
BMC Microbiology, 2002Co-Authors: Philippe Le Flèche, Michel Fabre, Jeanlouis Koeck, France Denoeud, Gilles VergnaudAbstract:Background Currently available reference methods for the molecular epidemiology of the Mycobacterium tuberculosis complex either lack sensitivity or are still too tedious and slow for routine application. Recently, Tandem Repeat typing has emerged as a potential alternative. This report contributes to the development of Tandem Repeat typing for M. tuberculosis by summarising the existing data, developing additional markers, and setting up a freely accessible, fast, and easy to use, internet-based service for strain identification. Results A collection of 21 VNTRs incorporating 13 previously described loci and 8 newly evaluated markers was used to genotype 90 strains from the M. tuberculosis complex ( M. tuberculosis (64 strains), M. bovis (9 strains including 4 BCG representatives), M. africanum (17 strains)). Eighty-four different genotypes are defined. Clustering analysis shows that the M. africanum strains fall into three main groups, one of which is closer to the M. tuberculosis strains, and an other one is closer to the M. bovis strains. The resulting data has been made freely accessible over the internet http://bacterial-genotyping.igmors.u-psud.fr/bnserver to allow direct strain identification queries. Conclusions Tandem-Repeat typing is a PCR-based assay which may prove to be a powerful complement to the existing epidemiological tools for the M. tuberculosis complex. The number of markers to type depends on the identification precision which is required, so that identification can be achieved quickly at low cost in terms of consumables, technical expertise and equipment.
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High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on Tandem Repeat typing.
BMC Microbiology, 2002Co-Authors: Philippe Le Flèche, Michel Fabre, Jeanlouis Koeck, France Denoeud, Gilles VergnaudAbstract:Currently available reference methods for the molecular epidemiology of the Mycobacterium tuberculosis complex either lack sensitivity or are still too tedious and slow for routine application. Recently, Tandem Repeat typing has emerged as a potential alternative. This report contributes to the development of Tandem Repeat typing for M. tuberculosis by summarising the existing data, developing additional markers, and setting up a freely accessible, fast, and easy to use, internet-based service for strain identification. A collection of 21 VNTRs incorporating 13 previously described loci and 8 newly evaluated markers was used to genotype 90 strains from the M. tuberculosis complex (M. tuberculosis (64 strains), M. bovis (9 strains including 4 BCG representatives), M. africanum (17 strains)). Eighty-four different genotypes are defined. Clustering analysis shows that the M. africanum strains fall into three main groups, one of which is closer to the M. tuberculosis strains, and an other one is closer to the M. bovis strains. The resulting data has been made freely accessible over the internet http://bacterial-genotyping.igmors.u-psud.fr/bnserver to allow direct strain identification queries. Tandem-Repeat typing is a PCR-based assay which may prove to be a powerful complement to the existing epidemiological tools for the M. tuberculosis complex. The number of markers to type depends on the identification precision which is required, so that identification can be achieved quickly at low cost in terms of consumables, technical expertise and equipment.
Peter Gill - One of the best experts on this subject based on the ideXlab platform.
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Highly discriminating heptaplex short Tandem Repeat PCR system for forensic identification.
BioTechniques, 1995Co-Authors: A. Urquhart, N. Oldroyd, C. P. Kimpton, Peter GillAbstract:: We describe a highly discriminating multiplex short Tandem Repeat PCR human identification system that gives a matching probability for Caucasians of European ancestry of 2.94 x 10(-8) or 5.66 x 10(-10) when used in combination with a previously described system. The system produces discrimination equal to or greater than four single locus probes (restriction fragment length polymorphism [RFLP] typing of variable nucleotide Tandem Repeat [VNTR] loci). The test is robust and reproducible and works with 1-10 ng of template DNA, using fluorescent detection of PCR products from either 4 or 6 short Tandem Repeat loci and the X-Y homologous gene amelogenin, giving simultaneous sex diagnosis.
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variation in short Tandem Repeat sequences a survey of twelve microsatellite loci for use as forensic identification markers
International Journal of Legal Medicine, 1994Co-Authors: A. Urquhart, C. P. Kimpton, T. J. Downes, Peter GillAbstract:Alleles at 12 Short Tandem Repeat loci have been sequenced to investigate candidate loci for a multiplex Short Tandem Repeat system for forensic identification, and for single-locus amplification of Short Tandem Repeat loci. Variation from the consensus sequence was found at 6 loci, while one locus, D21S11, was found to be complex in sequence. The presence of non-consensus alleles does not rule out loci for inclusion as forensic identification markers, but size differences between alleles of 1 base pair require very precise sizing. We suggest criteria for the suitability of Short Tandem Repeat loci as forensic identification markers, and propose a universal allele nomenclature for simple and compound Short Tandem Repeats. The effect of the Repeat unit sequence of the evolution of Short Tandem Repeats is discussed.
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automated dna profiling employing multiplex amplification of short Tandem Repeat loci
Genome Research, 1993Co-Authors: C. P. Kimpton, Peter Gill, A. Urquhart, A Walton, Emma S Millican, Maia AdamsAbstract:Short Tandem Repeat (STR) loci are a class of polymorphic markers which occur throughout the human genome and which consist of simple Tandemly Repeated sequences 1–6bp in length. Their abundance, hypervariability and amenability to amplification by the polymerase chain reaction (PCR) make them ideal markers for use in the identification of individuals.
