OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations

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• dc.contributor.author Mularoni, Lorisca
• dc.contributor.author Sabarinathan, Radhakrishnanca
• dc.contributor.author Déu Pons, Jordica
• dc.contributor.author González-Pérez, Abelca
• dc.contributor.author López Bigas, Núriaca
• dc.date.accessioned 2016-11-28T16:33:21Z
• dc.date.available 2016-11-28T16:33:21Z
• dc.date.issued 2016ca
• dc.description.abstract Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here we present OncodriveFML, a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis. We describe the method and illustrate its usefulness to identify protein-coding genes, promoters, untranslated regions, intronic splice regions, and lncRNAs-containing driver mutations in several malignancies.
• dc.description.sponsorship We acknowledge funding from the Spanish Ministry of Economy and Competitiveness (SAF2015-66084-R, MINECO/FEDER, UE), the Marató de TV3 Foundation, and the Spanish National Institute of Bioinformatics (INB). R.S. is supported by an EMBO Long-Term Fellowship (ALTF 568-2014) co-funded by the European Commission (EMBOCOFUND2012, GA-2012-600394) support from Marie Curie Actions. A.G.-P. is supported by a Ramón y Cajal contract (RYC-2013-14554).
• dc.format.mimetype application/pdfca
• dc.identifier.citation Mularoni L, Sabarinathan R, Déu Pons J, González-Pérez A, López Bigas N. OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations. Genome Biology. 2016;17:128. DOI: 10.1186/s13059-016-0994-0ca
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-016-0994-0
• dc.identifier.issn 1474-760Xca
• dc.identifier.uri http://hdl.handle.net/10230/27626
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Biology. 2016;17:128
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/600394
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2015-66084-R
• dc.rights © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Cancer drivers
• dc.subject.keyword Non-coding regions
• dc.subject.keyword Local functional mutations bias
• dc.subject.keyword Non-coding drivers
• dc.title OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutationsca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca