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

BMC Medical Genomics

Andrew I Su¹  Louis Gioia¹  Kathleen M Fisch¹  Tobias Meißner¹ 

[1] Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla 92037, CA, USA

关键词: n-of-1 reporting;    RNA-Seq;    Individualized medicine;    Breast cancer;   

Others  :  1210997
DOI  :  10.1186/s12920-015-0095-z

 received in 2014-12-31, accepted in 2015-04-30,  发布年份 2015

【 摘 要 】

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/ webcite), thereby offering a platform for future development and innovation by the community.

【 授权许可】

   
2015 Meißner et al.; licensee BioMed Central.

【 图 表 】

Fig. 1.

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