OpenGeneMed
About OpenGeneMed
OpenGeneMed is an open and customizable version of the GeneMed system (Zhao et al, 2015). GeneMed is 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 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 for customization of existing features and addition of new modules to address the specific needs of different clinical trials and research teams. Examples of how to customize the code are provided in technical documentation that is 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.
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Palmisano A, Zhao Y, Li MC, Polley EC, Simon RM. OpenGeneMed: a portable, flexible and customizable informatics hub for the coordination of next-generation sequencing studies in support of precision medicine trials. Brief Bioinformatics. 2017;18(5):723-734. doi:10.1093/bib/bbw059 [PubMed Abstract]
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Disclaimer
This resource is intended for purely research purposes. It should not be used for emergencies or medical or professional advice.
OpenGeneMed was developed by Biometric Research Team (BRP): Alida Palmisano, Ming-Chung Li, Eric Polley, Yingdong Zhao, Richard Simon. We thank Henry Rivera for a preliminary implementation of the OpenGeneMed.
OpenGeneMed Screenshots
Please refer to the OpenGeneMed User Manual for more details and full description of all the software features.
Main modules defined in the default configuration of OpenGeneMed. Solid bold lines connect each team with
their main activity, i.e. the module for which they have the main input/edit responsibility. Dashed bold lines shows modules that the team can access in read-only mode: the information in these modules may be essential to perform their main activity, but the editing responsibility belongs to another group. Fine dotted lines indicate modules that are accessible to the team in editing mode but the access is granted only for emergency and unforeseen situations: in the everyday course of the study, those task should be carried out by other groups.
For more information, please refer to the User Manual.
Clinic Team, Patients, List. View of the current list of registered patients. Each record can be accessed, edited and delinked using the appropriate button on the right of each entry. The table has built-in features that allow to hide/show columns, view the records over different pages, sort the entries and search for specific content.
Lab Team, In study variants. Aggregate information about the variants of interest in the current study.
(1) the user can select to visualize only the approved variants, or all the ones that have been called.
(2) the pie chart (color coded for the pathways included in the study) shows the current variants found in samples uploaded in the system. The pie chart is dynamic and slices’ visibility can be toggled on/off.
(3) Dynamic bar chart with the same information and
(4) a table containing the same information for easy of query;
(5) visualize additional information about selected variants by clicking the appropriate button,
(6) additional table containing the specific information for the requested variants.
For more information, please refer to the User Manual.
Lab Team, Upload VCF file. Uploading a file requires to list the Patient ID, Sample Date and select the VCF file from a File explorer window. Once the information is entered, submitting the form will trigger the annotation procedure to start. The process may take between few seconds to few minutes (depending on the size and content of the uploaded file). A spinning icon is displayed while the annotation process in ongoing. Once completed, a message will appear and a link to the variant report is provided.
For more information, please refer to the User Manual.
Lab Team, Variants table. Variant call report for the selected sample.
(1) the Patient ID and the currently selected sample are shown at the top of the page;
(2) The table containing variant calls is a large interactive table with built-in features to hide/show columns, sort the entries and search for specific content;
(3) Some columns are hidden by default, and the complete list of columns is available in the top right corner of the table;
(4) A generic textual search filter is positioned on the top right corner of the table. The filter operates on the content of the entire table, not on specific columns;
(5) Sorting and Filters are provided for each separate column. Clicking on the column header sorts the entries in increasing/decreasing order.
(6) Each variant call should be reviewed by the Lab Team: clicking the icon in the ’Review’ column opens an additional page to review the entry;
(7) The table divides the content into pages (accessible from page numbers in the lower right corner of the table);
(8) The entire table can be saved into a CSV (comma separated value) format for access on a local machine and further off-line reviews;
(9) Once the review of the sample is complete, the Lab Team member should click the button at the top of the page to notify the Treatment Review Team that their action is required for this patient;
(10) The date and time of the current annotation result is displayed.
For more information, please refer to the User Manual.