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Jul 17

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G-DOC: Enabling Systems Medicine Through Innovations in Informatics

G-DOC chart

Components of the Georgetown Database of Cancer

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)

G-DOC remains under continuing development and is moving into the Amazon Cloud environment.

 

 

Notes:

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.

 

 

Authors : NCIP Staff Blog Post Graphic

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

 

 

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Permanent link to this article: http://ncip.nci.nih.gov/blog/g-doc-enabling-systems-medicine-through-innovations-in-informatics/

3 comments

  1. JS Stuart

    I missed Dr Madhavan’s talk. Thank you for this recap. Do you have these for previous speaker series sessions?

    1. ncip.nci.nih.gov

      All of the presentations so far are listed as pdf/Powerpoint files on the Speaker Series wiki page (https://wiki.nci.nih.gov/display/CBIITSpeakers/CBIIT+Speaker+Series+Presentations+and+Resources), and as voiceover/screencasts on the NCI Events Youtube channel (http://www.youtube.com/playlist?list=PLFAF53BE7B120386E&feature=plcp). Hope this helps.

      Lisa Cole

      1. JS Stuart

        Thank you!

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