CVE: an R package for interactive variant prioritisation in precision oncology

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Precision oncology programs are expanding globally.
• There is a need for tools to analyze complex cancer genomic data.
• The Cancer Variant Explorer (CVE) was developed to address this need.

Purpose of the Study:

• To introduce the Cancer Variant Explorer (CVE), an R package and Shiny web application.
• To facilitate the exploration of genetic variants in cancer.
• To support precision oncology initiatives by enabling variant prioritization.

Main Methods:

• Developed CVE as an R package with an interactive Shiny web browser interface.
• Integrated Oncotator and the Drug Gene Interaction Database for variant annotation and druggability assessment.
• Included functionality for analyzing single or multiple tumor exomes and co-expression networks.

Main Results:

• CVE enables interactive exploration of cancer variants to identify drivers and resistance mechanisms.
• The tool assesses the druggability of identified variants.
• Demonstrated applications include individual patient analysis and cohort-wide studies.

Conclusions:

• The CVE package expedites the analysis of cancer sequencing studies through interactive variant prioritization.
• It facilitates the identification of druggable targets and exploratory analysis of tissue-specific networks.
• CVE is designed for translational research, molecular tumor boards, and is available via Bioconductor.