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Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment

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dc.contributor Ministerio de Ciencia y Tecnología (España)
dc.contributor Comunidad de Madrid
dc.contributor Genetrix
dc.contributor Consejo Superior de Investigaciones Científicas (España)
dc.contributor Fundación Ramón Areces
dc.contributor European Commission
dc.contributor Instituto Nacional de Técnica Aeroespacial (España)
dc.contributor Ministerio de Educación y Ciencia (España)
dc.creator Martín, Verónica
dc.creator Perales, Celia
dc.creator Abia, David
dc.creator Ortiz, Ángel R.
dc.creator Domingo, Esteban
dc.creator Briones, Carlos
dc.date 2008-06-10T13:49:30Z
dc.date 2008-06-10T13:49:30Z
dc.date 2006-05-18
dc.date.accessioned 2017-01-31T01:38:38Z
dc.date.available 2017-01-31T01:38:38Z
dc.identifier BMC Genomics 2006, 7:117
dc.identifier 1471-2164
dc.identifier http://hdl.handle.net/10261/4958
dc.identifier.uri http://dspace.mediu.edu.my:8181/xmlui/handle/10261/4958
dc.description Article available at http://dx.doi.org/10.1186/1471-2164-7-117
dc.description [Background] The evolution of viral quasispecies can influence viral pathogenesis and the response to antiviral treatments. Mutant clouds in infected organisms represent the first stage in the genetic and antigenic diversification of RNA viruses, such as foot and mouth disease virus (FMDV), an important animal pathogen. Antigenic variants of FMDV have been classically diagnosed by immunological or RT-PCR-based methods. DNA microarrays are becoming increasingly useful for the analysis of gene expression and single nucleotide polymorphisms (SNPs). Recently, a FMDV microarray was described to detect simultaneously the seven FMDV serotypes. These results encourage the development of new oligonucleotide microarrays to probe the fine genetic and antigenic composition of FMDV for diagnosis, vaccine design, and to gain insight into the molecular epidemiology of this pathogen.
dc.description [Results] A FMDV microarray was designed and optimized to detect SNPs at a major antigenic site of the virus. A screening of point mutants of the genomic region encoding antigenic site A of FMDV C-S8c1 was achieved. The hybridization pattern of a mutant includes specific positive and negative signals as well as crosshybridization signals, which are of different intensity depending on the thermodynamic stability of each probe-target pair. Moreover, an array bioinformatic classification method was developed to evaluate the hybridization signals. This statistical analysis shows that the procedure allows a very accurate classification per variant genome.
dc.description [Conclusion] A specific approach based on a microarray platform aimed at distinguishing point mutants within an important determinant of antigenicity and host cell tropism, namely the G-H loop of capsid protein VP1, was developed. The procedure is of general applicability as a test for specificity and discriminatory power of microarray-based diagnostic procedures using multiple oligonucleotide probes.
dc.description Work supported by grants BMC 2001-1823-C02-01, CAM 08.2/0015/ 2001.1, PROFIT 2003 awarded to Genetrix S.L. (FIT 010000-2002-38), FIS2004-06414, BFU 2005-00863, GEN2001-4865-C13-10, GEN2001- 4856-C13-07, a CSIC contract I3P-PC2004L and an institutional grant from Fundación Ramón Areces. Work at Centro de Astrobiología was also supported by EU, INTA, MEC and CAM.
dc.description Peer reviewed
dc.format 570044 bytes
dc.format application/pdf
dc.language eng
dc.publisher BioMed Central
dc.relation Publisher’s version
dc.rights openAccess
dc.subject Foot-and-mouth disease virus
dc.subject Microarray
dc.title Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment
dc.type Artículo

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