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dc.contributor.authorRoyo Sánchez-Palencia, José Luis
dc.contributor.authorPascual Pons, Mariona
dc.contributor.authorLupiañez, Arantxa
dc.contributor.authorSanchez Lopez, Isabel
dc.contributor.authorFibla Palazón, Joan
dc.date.accessioned2016-02-02T19:08:03Z
dc.date.available2016-02-02T19:08:03Z
dc.date.issued2015
dc.identifier.issn0890-8508
dc.identifier.urihttp://hdl.handle.net/10459.1/49428
dc.description.abstractCopy number variant (CNV) regions have been proven to have a significant impact on gene expression. Some of them have been also found to be associated to different human diseases. CNV genotyping is often prone to error and cross-validation with independent methods is frequently required. The platform of choice depends on whether it is a genome-wide discovery screening or a candidate CNV study, the cohort size and the number of CNVs included in the assay and, finally, the budget available. Here we illustrate a affordable approach to determine the CNV genotype using matrix-assisted laser desorption/ ionization mass spectrometry (MALDI-MS) and based on the quantitative determination of single nucleotide duplicated mismatches (SNDM) mapping the CNV region and a paralogue genomic region that is used as a two-copy reference. We have genotyped nsv436327, a common CNV mapping SIRPB1 intron 1 that has been associated to human personality behavior. SIRP cluster region was subjected to several ancestral duplication events what makes SIRPB1 CNV genotyping technically challenging. We designed three sets of primer pairs that amplified paralogue regions inside and outside the CNV, containing three SNDMs. Post-PCR extension analyses of sequencing oligonucleotides mapping immediately upstream each SNDM allowed us to quantify using MALDI-MS the proportion of PCR products derived from the CNV region versus the external reference. In contrast to other approaches, setting up this genotyping method requires an affordable investment.
dc.format.mimetypeapplication/pdf
dc.language.isoeng
dc.publisherElsevier
dc.relation.isformatofReproducció del document publicat a: https://doi.org/10.1016/j.mcp.2015.07.009
dc.relation.ispartofMolecular and Cellular Probes, 2015, vol. 29, núm. 6, p. 517-521
dc.rights(c) Elsevier, 2015
dc.subjectSIRPB1
dc.subjectcnv
dc.subjectMALDI-TOF
dc.subjectgenotyping-by-sequencing
dc.subject.classificationGens
dc.subject.otherGenes
dc.titleGenotyping of common SIRPB1 copy number variant using Paralogue Ratio Test coupled to MALDI-MS quantification
dc.typeinfo:eu-repo/semantics/article
dc.date.updated2016-02-02T19:08:04Z
dc.identifier.idgrec023182
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.rights.accessRightsinfo:eu-repo/semantics/restrictedAccess
dc.identifier.doihttps://doi.org/10.1016/j.mcp.2015.07.009
dc.date.embargoEndDate10000-01-01


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