Title |
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
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Published in |
BMC Medical Genomics, May 2015
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DOI | 10.1186/s12920-015-0095-z |
Pubmed ID | |
Authors |
Tobias Meißner, Kathleen M Fisch, Louis Gioia, Andrew I Su |
Abstract |
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, 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 ( https://bitbucket.org/sulab/oncorep/ ), thereby offering a platform for future development and innovation by the community. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United Kingdom | 3 | 21% |
United States | 2 | 14% |
France | 1 | 7% |
Germany | 1 | 7% |
Australia | 1 | 7% |
Unknown | 6 | 43% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 7 | 50% |
Members of the public | 6 | 43% |
Science communicators (journalists, bloggers, editors) | 1 | 7% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Belgium | 2 | 3% |
Ireland | 1 | 1% |
Germany | 1 | 1% |
United Kingdom | 1 | 1% |
United States | 1 | 1% |
Unknown | 65 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 15 | 21% |
Student > Ph. D. Student | 11 | 15% |
Student > Master | 11 | 15% |
Professor > Associate Professor | 6 | 8% |
Student > Bachelor | 6 | 8% |
Other | 10 | 14% |
Unknown | 12 | 17% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 18 | 25% |
Medicine and Dentistry | 12 | 17% |
Biochemistry, Genetics and Molecular Biology | 8 | 11% |
Computer Science | 7 | 10% |
Engineering | 4 | 6% |
Other | 8 | 11% |
Unknown | 14 | 20% |