OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials

Alida Palmisano, Yingdong Zhao, Ming Chung Li, Eric Polley, Richard M. Simon

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Trials involving genomic-driven treatment selection require the coordination of many teams interacting with a great variety of information. The need of better informatics support to manage this complex set of operations motivated the creation of OpenGeneMed. OpenGeneMed is a stand-alone and customizable version of GeneMed (Zhao et al. GeneMed: an informatics hub for the coordination of next-generation sequencing studies that support precision oncology clinical trials. Cancer Inform 2015;14(Suppl 2):45), a web-based interface developed for the National Cancer Institute 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 researchers as a communication hub. It automates the annotation of genomic variants identified by sequencing tumor DNA, classifies the actionable mutations according to customizable rules and facilitates quality control in reviewing variants. The system generates summarized reports with detected genomic alterations that a treatment review team can use for treatment assignment. OpenGeneMed allows collaboration to happen seamlessly along the clinical pipeline; it helps reduce errors made transferring data between groups and facilitates clear documentation along the pipeline. OpenGeneMed is distributed as a stand-alone virtual machine, ready for deployment and use from a web browser; its code is customizable to address specific needs of different clinical trials and research teams. Examples on how to change 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 efficient and successful for coordinating the application of next-generation sequencing in the NCI-MPACT trial.

Original languageEnglish (US)
Pages (from-to)723-734
Number of pages12
JournalBriefings in Bioinformatics
Volume18
Issue number5
DOIs
StatePublished - Sep 1 2017

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Precision Medicine
Informatics
Medicine
Pipelines
Oncology
Web browsers
Clinical Trials
National Cancer Institute (U.S.)
Quality control
Tumors
DNA
Documentation
Personnel
Neoplasms
Web Browser
Communication
Therapeutics
DNA Sequence Analysis
Quality Control
Research Personnel

Keywords

  • clinical trial management system
  • genomics
  • next-generation sequencing
  • open source software
  • precision medicine

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

Cite this

OpenGeneMed : a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials. / Palmisano, Alida; Zhao, Yingdong; Li, Ming Chung; Polley, Eric; Simon, Richard M.

In: Briefings in Bioinformatics, Vol. 18, No. 5, 01.09.2017, p. 723-734.

Research output: Contribution to journalArticle

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