Skip to main content

OpenGeneMed: a flexible and customizable informatics hub for the coordination of Next-Generation Sequencing studies in support of oncology clinical trials

Thursday, September 17, 2015 — Poster Session II

12:00 p.m. – 1:30 p.m.
FAES Terrace


  • A Palmisano
  • H Rivera
  • MC Li
  • E Polley
  • Y Zhao
  • R Simon


We developed OpenGeneMed: an informatics system to support clinical trial research. OpenGeneMed is an open and customizable version of the GeneMed system (Zhao Y. et al, Cancer Informatics, 2015), a web-based interface developed for the Molecular Profiling based Assignment of Cancer Therapy (NCI-MPACT) clinical trial conducted at the NIH. OpenGeneMed streamlines clinical trial management and it can be used by clinicians, lab personnel, statisticians and other researchers as a communication hub. It automates the annotation of the genomic variants identified by sequencing, classifies the actionable mutations according to customizable rules, and facilitates quality control by the molecular characterization lab in the review of variants. OpenGeneMed collects baseline information of patients to determine eligibility for the panel of treatment regimens available. The system generates patient reports containing detected genomic alterations along with summarized information that can be used for treatment assignment by a supervising treatment review team. OpenGeneMed is distributed as a standalone virtual machine, ready for deployment and use from a web browser. OpenGeneMed code is modular which allows customization of existing features and addition of new modules to address the specific needs of different clinical trials and research teams. Examples on how to customize the code are provided in the technical documentation distributed with the virtual machine. In summary, OpenGeneMed offers an initial set of features inspired by our experience with GeneMed, a system that has been proven to be an efficient and successful informatics hub for coordinating the application of Next-Generation Sequencing in the NCI-MPACT trial.

Category: Cancer Biology