Understanding the TCGA Data Types

The TCGA dataset is unique in that the tumor samples were assayed using a standard set of platforms and pipelines in order to produce a comprehensive dataset including:

• DNA sequencing of tumor samples and matched-normals (typically blood samples) in order to detect somatic mutations;
• SNP array based DNA copy-number and genotyping analysis of tumor samples and matched-normals;
• DNA methylation of tumor samples;
• messenger RNA (mRNA) expression analysis of the tumor samples to capture the gene expression profile;
• micro-RNA (miRNA) expression profiling of the tumor samples;

In addition, protein expression for a significant fraction (~20%) of all tumor samples was obtained using RPPA (reverse phase protein array).

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