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Cancer Genome Atlas Pilot Project Outlines Research for Participating Labs

NEW YORK (GenomeWeb News) — The National Cancer Institute and the National Human Genome Research Institute today disclosed additional information about the Cancer Genome Atlas Pilot Project.
 
According to the organizers, awards have been made to seven institutions in five states to establish Cancer Genome Characterization Centers. These centers, which will work as a network, will be charged to use genome -analysis technologies “to identify major changes in the genomes of the cancers chosen for TCGA pilot program.”
 
The Broad Institute of MIT and Harvard will use the Affymetrix platform to identify changes in expression and copy number alterations that occur in cancer; Harvard Medical School and Brigham and Women's Hospital will use the Agilent platform to characterize tumor samples for alterations in chromosome segments copy number. This center will also develop new technologies to analyze expression profiles.
 
Lawrence Berkeley National Laboratory, Berkeley, Calif., will use the Affymetrix Exon 1.0 array platform to identify changes in the transcription profiles that occur in cancer; Memorial Sloan-Kettering Cancer Center in New York will use Agilent arrays to characterize chromosome segment gains and losses. This center will also develop new approaches to detect novel genetic rearrangements.
 
The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins
 University, a joint project with the University of Southern California/Norris Comprehensive Cancer Center, will detect changes in methylation profiles associated with transcribed genes in cancer samples.
 
Stanford University School of Medicine will use high-throughput whole-genome genotyping technology to identify chromosome segments copy number variation found in cancer; and the University of North Carolina Lineberger Comprehensive Cancer Center in Chapel Hill, NC, will use an Agilent array platform to identify changes in the transcription profiles that occur in cancer.
 
Additionally, SRA International of Fairfax, Va., will develop the Data Coordinating Center, which will track data produced by components of TCGA, “ensuring that this data meets quality standards set for the project, and make TCGA data publicly accessible through databases supported by NCI's Cancer Biomedical Informatics Grid and the National Library of Medicine's National Center for Biotechnology Information.
 
The DCC will also establish public data resources that scientists can use in their research.

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