PeSV-Fisher: identification of somatic and non-somatic structural variants using nextgeneration sequencing data

Escaramís, Geòrgia; Tornador Antolin, Cristian, 1979-; Bassaganyas Bars, Laia, 1985-; Rabionet, Raquel; Tubio, José M. C.; Martínez Fundichely, Alexander, 1978-; Cáceres Aguilar, Mario; Gut, Marta; Ossowski, Stephan; Estivill, Xavier, 1955-

PeSV-Fisher: identification of somatic and non-somatic structural variants using nextgeneration sequencing data

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dc.contributor.author Escaramís, Geòrgiaca
dc.contributor.author Tornador Antolin, Cristian, 1979-ca
dc.contributor.author Bassaganyas Bars, Laia, 1985-ca
dc.contributor.author Rabionet, Raquelca
dc.contributor.author Tubio, José M. C.ca
dc.contributor.author Martínez Fundichely, Alexander, 1978-ca
dc.contributor.author Cáceres Aguilar, Marioca
dc.contributor.author Gut, Martaca
dc.contributor.author Ossowski, Stephanca
dc.contributor.author Estivill, Xavier, 1955-ca
dc.date.accessioned 2015-07-24T10:10:21Z
dc.date.available 2015-07-24T10:10:21Z
dc.date.issued 2013ca
dc.description.abstract Next-generation sequencing technologies expedited research to develop efficient computational tools for the identification of structural variants (SVs) and their use to study human diseases. As deeper data is obtained, the existence of higher complexity SVs in some genomes becomes more evident, but the detection and definition of most of these complex rearrangements is still in its infancy. The full characterization of SVs is a key aspect for discovering their biological implications. Here we present a pipeline (PeSV-Fisher) for the detection of deletions, gains, intra- and inter-chromosomal translocations, and inversions, at very reasonable computational costs. We further provide comprehensive information on co-localization of SVs in the genome, a crucial aspect for studying their biological consequences. The algorithm uses a combination of methods based on paired-reads and read-depth strategies. PeSV-Fisher has been designed with the aim to facilitate identification of somatic variation, and, as such, it is capable of analysing two or more samples simultaneously, producing a list of non-shared variants between samples. We tested PeSV-Fisher on available sequencing data, and compared its behaviour to that of frequently deployed tools (BreakDancer and VariationHunter). We have also tested this algorithm on our own sequencing data, obtained from a tumour and a normal blood sample of a patient with chronic lymphocytic leukaemia, on which we have also validated the results by targeted re-sequencing of different kinds of predictions. This allowed us to determine confidence parameters that influence the reliability of breakpoint predictions.
dc.description.sponsorship This work was supported by AGAUR (Generalitat de Catalunya, 2009 SGR 1502) (X.E.); CIBERESP (Instituto de Salud Carlos III) (G.E.); ESGI (European Commission, 262055_ESGI) (R.R., X.E.), ENGAGE (European Commission, ENGAGE_201413), TECHGENE (European Commission, TECHGENE_223143), and GEUVADIS (European Commission, 261123_GEUVADIS) (X.E.); NOVADIS (Ministerio de Ciencia y Technologia, SAF2008-00357) (X.E.); Galicia Government Xunta de Galicia (Spain) through the project number 10PXIB918057 (J.M.C.T.); MAEC-AEC1 Predoctoral Fellowship (Ministerio de Asuntos Exteriores y Cooperación, Spain) (A.M.F.); and Ramón y Cajal position and grant BFU2007-60930 (Ministerio de Educación y Ciencia) (M.C.).
dc.format.mimetype application/pdfca
dc.identifier.citation Escaramís G, Tornador C, Bassaganyas L, Rabionet R, Tubio JM,/nMartínez-Fundichely A et al. PeSV-Fisher: identification of somatic and non-somatic structural variants using next generation sequencing data. PLoS One. 2013 May 21;8(5):e63377. DOI: 10.1371/journal.pone.0063377ca
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0063377
dc.identifier.issn 1932-6203ca
dc.identifier.uri http://hdl.handle.net/10230/24641
dc.language.iso engca
dc.publisher Public Library of Science (PLoS)ca
dc.relation.ispartof PLoS One. 2013 May 21;8(5):e63377
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/262055
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/201413
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/223143
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/261123
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2008-00357
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BFU2007-60930
dc.rights © 2013 Escaramís et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits/nunrestricted use, distribution, and reproduction in any medium, provided the original author and source are creditedca
dc.rights.accessRights info:eu-repo/semantics/openAccessca
dc.rights.uri http://creativecommons.org/licenses/by/3.0/
dc.subject.other Genètica -- Bases de dades
dc.subject.other Genòmica
dc.subject.other ADN -- Anàlisi
dc.title PeSV-Fisher: identification of somatic and non-somatic structural variants using nextgeneration sequencing dataca
dc.type info:eu-repo/semantics/articleca
dc.type.version info:eu-repo/semantics/publishedVersionca

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