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

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:

1. preprocessing and analyzing RNA-Seq data in the n-of-1 setting,
2. extracting clinically relevant and actionable targets from complex data,
3. integrating drug databases, and
4. reporting results to clinicians in a timely and understandable manner.

To address these challenges, researchers from 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. OncoRep is free and open-source, thereby offering a platform for future development and innovation by the community.

Availability – OncoRep is distributed via Omics Pipe which handles the processing of the raw RNA-Seq data using distributed computing either on a local high performance cluster or on Amazon EC2. Installation and setup are documented online at http://pythonhosted.org/omics_pipe/.