Launched in 2016 by then-Vice President Biden, GDC now contains over 3.3 petabytes of data and serves more than 50,000 unique users every month.
The National Cancer Institute’s Genomic Data Commons (GDC) data, launched by then Vice President Joseph Biden in 2016 and hosted by the University of Chicago, has become one of the largest and most widely used resources in cancer genomics, with more than 3.3 petabytes of data from over 65 projects and more. From 84,000 anonymous patient cases, serving more than 50,000 unique users every month.
In new papers published on February 22 in Nature Communications And the Natural Genetics, The UChicago research team is sharing new details about the GDC, funded by the National Cancer Institute (NCI), via a sub-contract with the Frederick National Cancer Research Laboratory, currently operated by Leidos Biomedical Research, Inc. Describes the design and operation of the GDC. The other describes the pipelines used by the GDC to format the data provided to the GDC and to create the data sets used by the GDC research community.
The goal of the GDC is to provide the cancer research community with a data repository of uniformly processed genomic data and associated clinical data that enables data sharing and collaborative analysis in support of precision medicine.
Data production for what will become the GDC began in June 2015 using a private cloud. Just one year later, the GDC analyzed more than 50,000 primary sequence data entries. The GDC includes genomic, transcriptome, genomic, proteomic, clinical, and imaging data. The treatment pipelines described in the Nature paper produced more than 1,660 terabytes of data on more than twenty types of primary cancers. This data is stored in the GDC Data Portal, where it is available for viewing and download.
Besides the data portal, GDC also offers additional user resources, including GDC data analysis, visualization and exploration (DAVE) tools for interactive exploration of data by gene variant or specific change; GDC data submission portal for submitting data; GDC Data Transfer Tool (DTT) for downloading large genomic data sets; And GDC data format system, which allows users to operate the data submitted to GDC through coordinated processing lines.
“This data has a critical role to play,” said Robert Grossman, PhD, principal investigator at GDC and director of the Transition Data Science Center at UChicago. “As data accumulate, new signals will become easier to identify as important targets for understanding cancer biology. In addition, the infrastructure for sharing data can enrich research studies, providing new insight into the genetic diversity among individuals and how it might affect cancer outcomes.”
To read about the release of the GDC, visit uchicagomedicine.org.
The Genomic Data Commons project is federally funded by the National Cancer Institute and the National Institutes of Health from the following sources: Leidos Biomedical Research, Inc. Agreement 17X147 and F07 and F12 Task Orders under Main Contract 75N91019D00024 and Task Orders 75N91019F0129 and 75N91020F00003.
About the University of Chicago Medical and Biological Sciences
The University of Chicago Medicine, which dates back to 1927, is one of the nation’s premier academic health systems. It unifies the functions of the University of Chicago Medical Center, Pritzker School of Medicine, and the Department of Biological Sciences. Twelve Nobel Prize winners in Physiology or Medicine have joined the University of Chicago Medicine. Hyde Park’s main campus is home to the Care and Discovery Center, Bernard Mitchell Hospital, Comer Children’s Hospital and the Duchosoys Center for Advanced Medicine. It also has mobile facilities in Orlando Park, South Loop and River East as well as affiliations and partnerships that create a regional care network UChicago Medicine offers a full range of specialist care services for adults and children through more than 40 institutes and centers including the institute’s designated Comprehensive Cancer Center National Cancer. Along with Harvey-based Ingalls Memorial, UChicago Medicine has 1,296 licensed beds, nearly 1,300 treating physicians, more than 2,800 nurses and approximately 970 residents and fellows.
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Alison Caldwell, PhD
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