Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient. Next generation sequencing of RNA (RNA-Seq) is a suitable method to detect targets for individualized treatment. Challenges that arise are:
i) preprocessing and analyzing RNA-Seq data in the n-of-1 setting,
ii) extracting clinically relevant and actionable targets from complex data,
iii) integrating drug databases, and
iv) reporting results to clinicians in a timely and understandable manner.
To address these challenges, researchers at the Scripps Research Institute present OncoRep, an RNA-Seq based n-of-1 reporting tool for breast cancer patients. It reports molecular classification, altered genes and pathways, gene fusions, clinically actionable mutations and drug recommendations. It visualizes the data in an approachable html-based interactive report and a PDF clinical report, providing the clinician and tumor board with a tool to guide the treatment decision making process.
Availability – OncoRep is free and open-source: https://bitbucket.org/sulab/oncorep/