These are exciting times for cancer research. The rapid evolution and decreasing cost of omics technologies provide unprecedented opportunities to improve individual patient diagnosis, prognosis, and treatment. To fully realize this goal, however, requires integrating and analyzing data from the laboratory and the clinic in a way that is meaningful and useful to health-care providers. This is no small challenge.
Researchers at Georgetown’s Innovation Center for Biomedical Informatics at the Lombardi Comprehensive Cancer Center are tackling this problem. Dr. Subha Madhavan, Director of Clinical Informatics there, described the Center’s still-evolving informatics infrastructure at our July 11 speaker series session. Dr. Madhavan’s group has developed the Georgetown Database of Cancer, or G-DOC, a web-based platform that supports basic and clinical research activities by hosting and integrating data related to clinical phenotypes (patient characteristics and outcomes) with biomedical data generated by a variety of high-throughput omics-based research technologies.
Partially funded through the NCI CBIIT In Silico Research Centers of Excellence program, G-DOC provides access to a variety of tools, both open source and proprietary, to efficiently manage and analyze petabytes of data. Data are organized by study in order to facilitate the investigation of individual disease states. Types of basic biological data that can be accessed through G-DOC and integrated with clinical data include expression, micro-RNA, copy-number alteration, transcriptomics, and metabolomics data. Available analytical tools include
• Pathway Studio (systems biology analysis and literature mining)
• JMol/Marvin (3-D structure and molecule visualization)
• JBrowse (genome visualization)
• Heatmap Viewer (visualization of copy-number data)
• Electronic Health Records (Aria, Amalga, Centricity)
• Clinical Research (REDCap)
• Ingenuity Variant Analysis (variants, pathways, Gene Ontology [GO], literature)
• Cytoscape (visualization networks, including pathways and interactions)
To view Dr. Madhavan’s slide presentation, visit: http://go.usa.gov/fxe
To view a video of her discussion, visit http://www.youtube.com/watch?v=Hkq8UBqXC2U
To access the G-DOC system, visit https://gdoc.georgetown.edu/gdoc/.
A key publication is Madhavan S, Gusev Y, Harris M, Tanenbaum DM, Gauba R, Bhuvaneshwar K, Shinohara A, Rosso K, Carabet LA, Song L, Riggins RB, Dakshanamurthy S, Wang Y, Byers SW, Clarke R, Weiner LM, G-DOC: a systems medicine platform for personalized oncology, Neoplasia 2011;13(9):771-783.
Kay Fleming, Ph.D. Scientific Writer
Mervi Heiskanen, Ph.D. Associate Director, Research Products and Programs
Juli Klemm, Ph.D. Associate Director, Research Products and Programs
Lisa Cole, MBA Director of Communications