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dc.contributor.authorMock, Aen
dc.contributor.authorMurphy, Sen
dc.contributor.authorMorris, Jen
dc.contributor.authorMarass, Fen
dc.contributor.authorRosenfeld, Nitzanen
dc.contributor.authorMassie, Charlesen
dc.date.accessioned2017-05-26T06:02:23Z
dc.date.available2017-05-26T06:02:23Z
dc.date.issued2017-05-25en
dc.identifier.citationBMC Medical Genomics. 2017 May 25;10(1):37
dc.identifier.issn1755-8794
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/264441
dc.description.abstractBACKGROUND: An increasing number of precision oncology programmes are being launched world-wide. To support this development, we present the Cancer Variant Explorer (CVE), an R package with an interactive Shiny web browser interface. RESULTS: Leveraging Oncotator and the Drug Gene Interaction Database, CVE offers exploration of variants within single or multiple tumour exomes to identify drivers, resistance mechanisms and to assess druggability. We present example applications including the analysis of an individual patient and a cohort-wide study, and provide a first extension of CVE by adding a tumour-specific co-expression network. CONCLUSIONS: The CVE package allows interactive variant prioritisation to expedite the analysis of cancer sequencing studies. Our framework also includes the prioritisation of druggable targets, allows exploratory analysis of tissue specific networks and is extendable for specific applications by virtue of its modular design. We encourage the use of CVE within translational research studies and molecular tumour boards. The CVE package is available via Bioconductor ( http://bioconductor.org/packages/CVE/).
dc.description.sponsorshipAM was supported by the National Institute for Health Research, Biomedical Research Centre (NIHR Cambridge BRC) and the German National Academic Foundation (Studienstiftung des deutschen Volkes). We would like also to acknowledge the support of The University of Cambridge, Cancer Research UK Cambridge Centre and Hutchison Whampoa Limited. The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement n. 337905. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
dc.languageengen
dc.publisherBioMed Central
dc.subjectCancer variant exploreren
dc.subjectMelanomaen
dc.subjectPrioritizationen
dc.subjectPersonalized oncologyen
dc.subjectWGCNAen
dc.subjectCo-expression networken
dc.subjectTCGAen
dc.subjectMolecular tumor boarden
dc.titleCVE: an R package for interactive variant prioritisation in precision oncologyen
dc.typeArticle
dc.date.updated2017-05-26T06:02:23Z
dc.language.rfc3066en
dc.rights.holderThe Author(s)
prism.issueIdentifier37en
prism.publicationDate2017en
prism.publicationNameBMC Medical Genomicsen
prism.volume10en
dc.identifier.doi10.17863/CAM.9919
dcterms.dateAccepted2017-04-20en
rioxxterms.versionofrecord10.1186/s12920-017-0261-6en
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/en
rioxxterms.licenseref.startdate2017-05-25en
dc.contributor.orcidRosenfeld, Nitzan [0000-0002-2825-4788]
dc.contributor.orcidMassie, Charles [0000-0003-2314-4843]
dc.identifier.eissn1755-8794
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idEuropean Research Council (337905)
pubs.funder-project-idCancer Research UK (C14303_do not transfer)


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