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dc.contributor.authorPaciello, Giuliaen_US
dc.contributor.authorAcquaviva, Andreaen_US
dc.contributor.authorPighi, Chiaraen_US
dc.contributor.authorFerrarini, Albertoen_US
dc.contributor.authorMacii, Enricoen_US
dc.contributor.authorZamo’, Albertoen_US
dc.contributor.authorFicarra, Elisaen_US
dc.date.accessioned2015-05-04T15:27:14Z
dc.date.issued2015en_US
dc.identifier.citationPaciello, Giulia, Andrea Acquaviva, Chiara Pighi, Alberto Ferrarini, Enrico Macii, Alberto Zamo’, and Elisa Ficarra. 2015. “VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool.” PLoS ONE 10 (3): e0118192. doi:10.1371/journal.pone.0118192. http://dx.doi.org/10.1371/journal.pone.0118192.en
dc.identifier.issn1932-6203en
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:15034899
dc.description.abstractIn this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that characterises the tissue of interest by recognizing the most abundant V(D)J rearrangement among the existing ones in the sample under study. The exact sequence of the clone identified is capable of accounting for the modifications introduced by the enzymatic processes. The proposed tool overcomes limitations of currently available lymphocyte rearrangements recognition methods, working on a single sequence at a time, that are not applicable to high-throughput sequencing data. In this work, VDJSeq-Solver has been applied to correctly detect the main clone and identify its sequence on five Mantle Cell Lymphoma samples; then the tool has been tested on twelve Diffuse Large B-Cell Lymphoma samples. In order to comply with the privacy, ethics and intellectual property policies of the University Hospital and the University of Verona, data is available upon request to supporto.utenti@ateneo.univr.it after signing a mandatory Materials Transfer Agreement. VDJSeq-Solver JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/VDJSeq-Solver/.en
dc.language.isoen_USen
dc.publisherPublic Library of Scienceen
dc.relation.isversionofdoi:10.1371/journal.pone.0118192en
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370828/pdf/en
dash.licenseLAAen_US
dc.titleVDJSeq-Solver: In Silico V(D)J Recombination Detection Toolen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalPLoS ONEen
dash.depositing.authorPighi, Chiaraen_US
dc.date.available2015-05-04T15:27:14Z
dc.identifier.doi10.1371/journal.pone.0118192*
dash.authorsorderedfalse
dash.contributor.affiliatedPighi, Chiara


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