CVE: an R package for interactive variant prioritisation in precision oncology
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BMC Medical Genomics
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Mock, A., Murphy, S., Morris, J., Marass, F., Rosenfeld, N., & Massie, C. (2017). CVE: an R package for interactive variant prioritisation in precision oncology. BMC Medical Genomics, 10 (37)https://doi.org/10.1186/s12920-017-0261-6
BACKGROUND: 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/).
Cancer variant explorer, Melanoma, Prioritization, Personalized oncology, WGCNA, Co-expression network, TCGA, Molecular tumor board
AM 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.
European Research Council (337905)
Cancer Research UK (C14303_do not transfer)
External DOI: https://doi.org/10.1186/s12920-017-0261-6
This record's URL: https://www.repository.cam.ac.uk/handle/1810/264441
Rights Holder: The Author(s)