Meißner Tobias, Fisch Kathleen M, Gioia Louis, Su Andrew I
Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, CA, USA.
BMC Med Genomics. 2015 May 21;8:24. doi: 10.1186/s12920-015-0095-z.
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.
乳腺癌包含多种具有不同生物学特征和临床行为的肿瘤实体，这使得个体化医疗成为为合适的患者提供合适药物的有力工具。RNA的下一代测序（RNA-Seq）是检测个体化治疗靶点的合适方法。出现的挑战包括：i）在单病例研究中对RNA-Seq数据进行预处理和分析；ii）从复杂数据中提取临床相关且可操作的靶点；iii）整合药物数据库；iv）及时且以易于理解的方式向临床医生报告结果。
为应对这些挑战，我们推出了OncoRep，这是一种基于RNA-Seq的针对乳腺癌患者的单病例研究报告工具。它报告分子分类、基因和通路改变、基因融合、临床可操作的突变以及药物推荐。它通过基于html的易于使用的交互式报告和PDF临床报告对数据进行可视化，为临床医生和肿瘤委员会提供了一个指导治疗决策过程的工具。
OncoRep是免费且开源的（https://bitbucket.org/sulab/oncorep/），从而为社区未来的开发和创新提供了一个平台。
