Mock Andreas, Murphy Suzanne, Morris James, Marass Francesco, Rosenfeld Nitzan, Massie Charlie
Cancer Research UK Cambridge Centre, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK.
BMC Med Genomics. 2017 May 25;10(1):37. doi: 10.1186/s12920-017-0261-6.
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.
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.
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/ ).
全球范围内越来越多的精准肿瘤学项目正在启动。为支持这一发展，我们推出了癌症变异体浏览器（CVE），这是一个带有交互式Shiny网络浏览器界面的R包。
利用Oncotator和药物基因相互作用数据库，CVE可对单个或多个肿瘤外显子组内的变异体进行探索，以识别驱动因素、耐药机制并评估药物可及性。我们展示了示例应用，包括对单个患者的分析和全队列研究，并通过添加肿瘤特异性共表达网络对CVE进行了首次扩展。
CVE包允许交互式变异体优先级排序，以加快癌症测序研究的分析。我们的框架还包括可药物化靶点的优先级排序，允许对组织特异性网络进行探索性分析，并且由于其模块化设计，可针对特定应用进行扩展。我们鼓励在转化研究和分子肿瘤学委员会中使用CVE。CVE包可通过生物导体（http://bioconductor.org/packages/CVE/）获取。
