학술논문
OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Document Type
Clinical report
Source
BMC Medical Genomics. May 21, 2015, Vol. 8 Issue 1
Subject
Language
English
ISSN
1755-8794
Abstract
Author(s): Tobias Meissner[sup.1] , Kathleen M Fisch[sup.1] , Louis Gioia[sup.1] and Andrew I Su[sup.1] Background Breast cancer is the leading cause of cancer among females making up 23 % of [...]
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. Keywords: Breast cancer, Individualized medicine, RNA-Seq, n-of-1 reporting
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. Keywords: Breast cancer, Individualized medicine, RNA-Seq, n-of-1 reporting