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:

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.

rna-seq

Availability – OncoRep is free and open-source: https://bitbucket.org/sulab/oncorep/

Meißner T, Fisch KM, Gioia L, Su AI. (2015) OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing. BMC Med Genomics 8(1):24. [abstract]

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