RUN-ONCO: A Highly Extensible Software Platform for Cancer Precision Medicine

Abstract

Precision medicine is a strategy to personalize disease identification and medical care decisions through genetics. The rapid development of -omics technologies e.g., DNA and RNA sequencing, which reveal specific gene mutations in a patient's tumor or profiling of gene expressions for drug responses helps oncologists find effective treatments for individual patients based on their genetics. Hence, besides the clinical records, -omics data become essential for personalized diagnosis and treatments. In this paper, a web-based standalone software platform for cancer precision medicine, called RUN-ONCO, is proposed aiming to help oncologists and researchers manage and make use of the available clinical and -omics data easily and efficiently. The platform allows the management of clinical records, biospecimens, and -omics data and enables various integrative data analyses together with public databases such as STRING and OncoKB. With the increasing number of published methods for various -omics data analyses together with the availability of numerous javascript libraries for data visualization, RUN-ONCO has also been designed to be highly extensible with plugins for both visualizations and analysis methods. A demo version of RUN-ONCO is available online at http://cucpbioinfo.cp.eng.chula.ac.th:6002 and the source code for local deployment is at https://gitlab.com/peyrone/run-onco.