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CCG Welcomes a New Genomic Data Analysis Network

October 20, 2016, by Jean Claude Zenklusen, Ph.D.

Jean C. Zenklusen, M.S., Ph.D.

Jean Claude Zenklusen, Ph.D.

As NCI’s Center for Cancer Genomics (CCG) shifts its focus from The Cancer Genome Atlas (TCGA) project to new programs and collaborations, our strategy is to maintain the efficient workflow that made TCGA a success while adding key functionalities and expertise. The new members of our Genomic Data Analysis Network (GDAN), four of whom are first-time NIH grant recipients, each bring unique knowledge to the network, creating an exciting blend of scientific capabilities. This team, expanded from seven to thirteen centers, will deliver actionable insights from CCG’s genomic and clinical data to the entire cancer research community.

There are three types of centers in the GDAN, each designed to contribute to a different facet of genomic analysis: Processing, Specialized, and Visualization.

Processing

One processing center, the Broad Institute of MIT and Harvard, will do all of the initial processing of the data. After receiving sequencing data from Genome Characterization Centers that have been aligned by the Genomic Data Commons (GDC), the processing center will run an automated analysis of the data using Firehose, a genomic data analysis pipeline. This first-pass produces standard displays of the data, such as DNA mutation plots and maps of changes in the number of copies of genes in the genome, called copy number alterations. Because the output is automated, these data represent a starting point for further analysis.

Specialized

The network’s eleven specialized centers are comprised of foremost experts in their fields who will work with the processed data to illuminate particular patterns in the data, and integrate the data, forming a more complete picture.

The network has one specialized center for each modality of analysis. For example, the new reverse phase protein array (RPPA) center is run by Rehan Akbani, Ph.D., of MD Anderson Cancer Center, a first-time grant recipient who is part of a renowned center for RPPA analysis. Similarly, Peter Laird, Ph.D., of the Van Andel Research Institute, will be in charge of the methylation specialized center. His group is recognized for performing deep analyses of the methylation data, which are far beyond what the network’s processing center can provide.

The network also contains three new centers focused on integrating different types of genomic data and one center focused on identifying potential therapeutically actionable opportunities in DNA mutation data.

Visualization

The network’s single visualization center, led by first-time grant recipient Jingchun Zhu, Ph.D., of University of California Santa Cruz, will enable the research community to interact with and manipulate the CCG data. This group developed UCSC Xena, an interactive interface for visualizing genomics data, and will continue to refine their platform as the network’s visualization center.

GDAN Awardees

Processing Genomic Data Center
Principal Investigator Project Title Institution
Gad Getz, Ph.D. Global Infrastructure for Collaborative High-throughput Cancer Genomics Analysis Broad Institute, Inc.
Visualization Genomic Data Center
Principal Investigator Project Title Institution
Jingchun Zhu, Ph.D. Visualization hub for genomics data exploration and translational discovery University of California Santa Cruz
Specialized Genomic Data Centers
Principal Investigator Project Title Institution
Li Ding, Ph.D. Deep Discovery and Clinical Interpretation of Germline and Somatic Cancer Drivers Washington University
John N. Weinstein, M.D., Ph.D. Batch effects in molecular profiling data on cancers: detection, quantitation, interpretation, and correction MD Anderson Cancer Center
Rameen Beroukhim, M.D., Ph.D. Center for the comprehensive analysis of somatic copy-number alterations in cancer Broad Institute, Inc.
Steven John Jones, Ph.D. Integrative miRNA data analysis for clinical cancer genomics British Columbia Cancer Agency
Olivier Elemento, Ph.D. The joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor Profiles Weill Medical College of Cornell University
Paul T. Spellman, Ph.D. OHSU Center for Specialized Data Analysis as part of the GDAN Oregon Health & Science University 
Joshua Stuart, Ph.D. UCSC-Buck Specialized Genomic Data Analysis Center for the Genomic Data Analysis Network University of California Santa Cruz  
Benjamin Raphael, Ph.D. Pathway and Network Integration of Cancer Genomics and Clinical Data Princeton University
Rehan Akbani, Ph.D. Integrated analysis of protein expression data from the Reverse Phase Protein Array (RPPA) platform MD Anderson Cancer Center  
Peter W. Laird, Ph.D. Integrative Cancer Epigenomic Data Analysis Center (ICE-DAC) Van Andel Research Institute
Katherine Hoadley, Ph.D. RNA sequencing analysis of Cancer University of North Carolina Chapel Hill

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