OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing

Area of Science:

• Genomics
• Oncology
• Bioinformatics

Background:

• Breast cancer exhibits diverse biological features and clinical behaviors, necessitating individualized medicine.
• Next-generation sequencing of RNA (RNA-Seq) is crucial for identifying therapeutic targets in precision oncology.
• Challenges include n-of-1 RNA-Seq data analysis, extracting actionable targets, integrating drug databases, and timely reporting.

Purpose of the Study:

• To present OncoRep, an RNA-Seq based n-of-1 reporting tool for breast cancer.
• To address the challenges in analyzing individual patient RNA-Seq data for clinical decision-making.

Main Methods:

• OncoRep utilizes RNA-Seq data for n-of-1 analysis in breast cancer.
• The tool preprocesses and analyzes complex RNA-Seq data to identify clinically relevant targets.
• It integrates drug databases and generates interactive reports for clinicians.

Main Results:

• OncoRep provides molecular classification, identifies altered genes and pathways, and detects gene fusions.
• The tool reports clinically actionable mutations and suggests drug recommendations.
• Results are presented in an interactive HTML report and a PDF clinical report.

Conclusions:

• OncoRep offers a comprehensive solution for RNA-Seq based n-of-1 reporting in breast cancer.
• The tool supports clinicians and tumor boards in treatment decision-making.
• OncoRep is freely available as an open-source platform for community development.