CCG Welcomes a New Genomic Data Analysis Network
, by Jean Claude Zenklusen, Ph.D.
Jean Claude Zenklusen, Ph.D., Director of The Cancer Genome Atlas
As NCI’s Center for Cancer Genomics (CCG) shifts its focus from The Cancer Genome Atlas (TCGA) project to new research, 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
| Principal Investigator | Project Title | Institution |
|---|---|---|
| Gad Getz, Ph.D. | Global Infrastructure for Collaborative High-throughput Cancer Genomics Analysis | Broad Institute, Inc. |
| Principal Investigator | Project Title | Institution |
|---|---|---|
| Jingchun Zhu, Ph.D. | Visualization hub for genomics data exploration and translational discovery | University of California Santa Cruz |