The Cancer Genome Atlas (TCGA) is an effort by the NCI to characterize cancers in depth, at the genomic level. One of the cancers in the TCGA is glioblastoma.
Even more interesting, in the context of the SPORE, is that NCI sees a strong connection between the TCGA and the SPOREs. One aspect of this is that the SPOREs are acting as a source of tissue samples - our group, under the leadership of Dr. Ken Aldape in Pathology, was the first center to provide glioblastoma tissues to the TCGA.
TCGA is analyzing tumors for:
- Broad Institute of MIT and Harvard, Cambridge, Mass.
Using the Affymetrix platform, this center will identify changes in expression and copy number alterations that occur in cancer.
- Harvard Medical School and Brigham and Women's Hospital, Boston, Mass.
Using the Agilent platform, this center will 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.
Using an Affymetrix Exon 1.0 array platform, this center will identify changes in the transcription profiles that occur in cancer.
- Memorial Sloan-Kettering Cancer Center, New York, N.Y.
Using Agilent arrays, this center will provide characterization of 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, Baltimore, Md.
This is a joint project with the University of Southern California/Norris Comprehensive Cancer Center, which will use Illumina GoldenGate Genotyping platform, to detect changes in methylation profiles associated with transcribed genes in cancer samples.
- Stanford University School of Medicine, Palo Alto, Calif.
Using Illumina HumanHap550 Genotyping BeadChip, this project will identify chromosome segments copy number variation found in cancer.
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, N.C.
Using an Agilent array platform, this center will identify changes in the transcription profiles that occur in cancer.
Join Us
Now the SPOREs are thinking about how to digest the data emerging from TCGA and designing the right back end studies. As part of that effort we hold TCGA/SPORE meetings every second Friday at 3pm in FC7.3035 - all welcome.
TCGA Knowledge Base
In today's meeting we discussed the state of the data available and how to translate specific biological questions into queries that can be applied to the current data. The new TCGA Knowledge Base was introduced. The TCGA-KB is an interface to access the raw TCGA data (e.g. CEL files) and the goal is to eventually add normalized data. Eventually a query interface will be added to the site.
Genboree
This is a group that is managing the sequencing effort for NCI - see at www.genboree.org. We will attempt to make contact to get access.
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