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user manual User Manual

Developed by: Alida Palmisano, Ming-Chung Li, Eric Polley, Yingdong Zhao*, Richard Simon*

OpenGeneMed is an informatics system to support clinical trial research.

OpenGeneMed is an open and customizable version of the GeneMed system (Zhao et al, 2015), a web-based interface developed for the Molecular Profiling based Assignment of Cancer Therapy (NCI-MPACT) clinical trial coordinated by 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.

*corresponding author

Acknowledgment: we thank Henry Rivera for a preliminary implementation of the OpenGeneMed.

Screenshots from OpenGeneMed

Please refer to the User Manual for more details and full description of all the software features.

OpenGeneMed groups
Groups available in the default setup

OpenGeneMed workflow
A typical workflow

OpenGeneMed admin tab
Admin tab

OpenGeneMed study coordinator
Study coordinator: customizable eligibility questions

OpenGeneMed clinic team
Clinic team: patient overview

OpenGeneMed biostatisticians
Biostatistician Team: study statistics

OpenGeneMed upload
Upload VCF for annotation

OpenGeneMed annotation
Table with annotation information

Last updated on August, 2016