Personal Cancer Genome Reporter (PCGR)

Personal Cancer Genome Reporter annotates and prioritizes somatic single nucleotide variants (SNVs), insertions/deletions (InDels), and copy number aberrations in individual tumor genomes to support clinical interpretation of diagnostic, prognostic, and therapeutic biomarkers in precision oncology.

Key Features:

• Comprehensive annotation: Extends beyond Ensembl's Variant Effect Predictor (VEP) to include oncology-relevant, up-to-date annotations for somatic SNVs, InDels, and copy number aberrations.
• Integration with knowledge resources: Integrates an extensive set of tumor biology and therapeutic biomarker knowledge resources at both gene and variant levels.
• Tiered reporting system: Generates tiered reports that prioritize and highlight the most clinically relevant findings from individual cancer genomes.

Scientific Applications:

• Clinical genome interpretation and decision support: Supports clinical interpretation of tumor genomes for diagnosis, prognosis, and therapy selection based on annotated biomarkers.
• Research variant prioritization: Enables systematic analysis and prioritization of somatic variants for translational and cancer genomics research.
• Biomarker-driven therapeutic insights: Integrates tumor biology and therapeutic biomarker data to translate genomic findings into actionable treatment hypotheses.

Methodology:

PCGR extends Ensembl Variant Effect Predictor (VEP) annotations and is implemented using Python and R, with the software packaged for distribution via Docker.