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A Genome Characterization Center (GCC) is a TCGA center that uses high-throughput technologies to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the GSCs.

Overview

Genomics is a fast-moving field with novel technologies and platforms that help characterize the genome being made available to the research community on a continual basis. Genome Characterization Centers (GCCs) are responsible for characterizing all of the genomic changes found in the tumors studied as part of the TCGA program. The GCCs will use multiple platforms to provide data to the cancer research community on changes in miRNA and gene expression, single nucleotide polymorphisms and copy number changes. The GCCs will also be working to validate specific regions of interest through targeted sequencing.

See TCGA website for details on characterization focuses.

Data Submissions to the DCC

GCCs transfer the files of experimental results of characterization assays in data archives to the DCC.

GCC data for the TCGA project is also known as Array-Based Data.

GCC Results Files

For GCCs, each TCGA result file has a Data Type and corresponding Data Level. A TCGA result file is any file that is listed in the SDRF file under column header ending in "File" (such as "Derived Array Data Matrix File").

To determine the Data Level of a file, look under its corresponding "Comment [TCGA Data Level]" column. Similarly, to determine the Data Type of a file, look under the "Comment [TCGA Data Type]" column of the SDRF file. If you follow a row of data from its Extract Name and onwards, you can see how a data file progresses through the Data Levels as protocols (or procedures) are applied.

The figure below is an excerpt of an SDRF file. In this section of the file, the data files (under "Derived Array Data Matrix File") are text (.txt) files, the Data Level (under "Comment [TCGA Data Level]") is Level 2 and the data type (under "Comment [TCGA Data Type]") is DNA-Methylation.

excerpt from and SDRF file

For more information, see SDRF.

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