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

BACKGROUND: 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 ta...

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Detalles Bibliográficos
Autores principales: Meißner, Tobias, Fisch, Kathleen M, Gioia, Louis, Su, Andrew I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4494802/
https://www.ncbi.nlm.nih.gov/pubmed/25989980
http://dx.doi.org/10.1186/s12920-015-0095-z
Descripción
Sumario:BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: OncoRep is free and open-source (https://bitbucket.org/sulab/oncorep/), thereby offering a platform for future development and innovation by the community.