CVE

CVE facilitates prioritization and analysis of variants from tumour exomes to support precision oncology research.

Key Features:

• Integration with Oncotator: Uses the Oncotator Variant Annotation tool to summarize variant-centric information aggregated from 14 publicly available resources relevant to cancer research.
• Variant exploration and prioritization: Performs exploration and prioritization of variants from individual or multiple tumour exomes using known germline and cancer-specific mutation annotations, DNA repair gene lists, and functional prediction scores.
• Druggability assessment: Assesses druggability of identified variants by integrating data from the Drug Gene Interaction Database to identify drug–gene interactions and potential resistance mechanisms.
• Tissue-specific network analysis: Enables exploratory analysis of tissue-specific networks to contextualize variant effects within specific biological tissues.
• Modular and extendable design: Provides a modular architecture that supports extensions such as incorporation of tumour-specific co-expression networks.
• Implementation: Implemented as an R package.

Scientific Applications:

• Individual Patient Analysis: Supports analysis of individual patient genetic data to identify actionable variants for personalized treatment considerations.
• Cohort-Wide Studies: Facilitates prioritization of variants across patient cohorts to identify recurrent drivers and resistance mechanisms.
• Molecular Tumour Boards: Provides comprehensive variant analyses to inform decision-making in molecular tumour boards.

Methodology:

Annotation via Oncotator summarizing 14 public resources; variant prioritization using known germline and cancer-specific mutation annotations, DNA repair gene lists, and functional prediction scores; druggability assessment through integration with the Drug Gene Interaction Database; tissue-specific network analyses and optional tumour-specific co-expression network incorporation; implemented as an R package.