I Genomic Characterization Data

The seven Cancer Genomic Characterization Centers (CGCCs) produce data from transcription, chromosomal copy number, loss of heterozygosity (LOH), methylation, and microRNA expression analyses.

Transcription data are available from the following platforms:

• Affymetrix Human Genome HTS U133A 2.0 Array
• Affymetrix GeneChip® Human Exon 1.0 ST Array
• Agilent 244K Array

Chromosomal copy number and LOH data are available from the following platforms:

• Agilent 244K Array
• Illumina Infinium 550K BeadChip
• Affymetrix 500K SNPChip

Technology Development

Three analyses are being performed by the CGCCs as a part of TCGA Technology Development. These analyses employ nascent, innovative technologies that increase the ability to detect a broader range of genomic alterations.

Methylation analysis data are available from the following platform:

• Illumina GoldenGate® BeadArray, after identification of differentially expressed transcripts with Agilent 44K Array

MicroRNA expression data are available from the following platform:

• Agilent customized microRNA Array

RNA expression data from Polony Massive Analysis of Gene Expression (PMAGE) are available.

Analysis

For most platforms, data will be available in the following three forms:

1. Raw Data: Individual data files generated by each platform (in file formats such as: .cel, genepix, .snp).
2. Normalized Data: Data obtained after computational analysis which removes intra-experimental background and allows for comparison of data within the experiment.
3. Interpreted Data: Analysis that identifies genes and/or regions of interest within an experiment.