PCGR - Personal Cancer Genome Reporter

PCGR interprets individual tumor genomes to prioritize somatic single nucleotide variants (SNVs), insertions/deletions (InDels), and copy number aberrations in the context of diagnostic, prognostic, and therapeutic biomarkers for precision oncology.

Key Features:

• Comprehensive Annotation: Extends basic gene and variant annotations from Ensembl's Variant Effect Predictor (VEP) with oncology-relevant updates.
• Integration of Knowledge Resources: Integrates a wide array of knowledge resources related to tumor biology and therapeutic biomarkers at both gene and variant levels.
• Tiered Reporting System: Generates tiered reports that prioritize and highlight clinically significant findings.
• Somatic Variant Interpretation: Interprets somatic single nucleotide variants (SNVs), insertions/deletions (InDels), and copy number aberrations within tumor genomes.
• Biomarker Identification and Prioritization: Supports identification and prioritization of diagnostic, prognostic, and therapeutic biomarkers.

Scientific Applications:

• Somatic Variant Analysis: Interpretation of somatic SNVs, InDels, and copy number aberrations for tumor genome characterization.
• Biomarker Discovery and Clinical Actionability: Identification and prioritization of diagnostic, prognostic, and therapeutic biomarkers to inform personalized treatment strategies.

Methodology:

PCGR is implemented in Python and R, extends Ensembl's Variant Effect Predictor (VEP) annotations with oncology-specific updates, and is packaged using Docker.