TY - JOUR T1 - OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing JF - bioRxiv DO - 10.1101/008748 SP - 008748 AU - Tobias Meissner AU - Fisch Kathleen M. AU - Louis Gioia AU - Andrew I. Su Y1 - 2014/01/01 UR - http://biorxiv.org/content/early/2014/09/03/008748.abstract N2 - 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 action-able targets from complex data, iii) integrating drug databases, and iv) reporting results to clinicians in a timely and understandable manner. To address these challenges, we 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. ER -