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BMC Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z.

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

Author information

1
Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA. meissner.t@googlemail.com.
2
Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA. kathleenfisch@gmail.com.
3
Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA. lhgioia@scripps.edu.
4
Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA. asu@scripps.edu.

Abstract

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.

PMID:
25989980
PMCID:
PMC4494802
DOI:
10.1186/s12920-015-0095-z
[Indexed for MEDLINE]
Free PMC Article

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