TCGA Copy Number Portal (TCGA)

This portal is designed to facilitate the use and understanding of high resolution copy number data amassed from cancer samples in the TCGA. All data in this portal were generated at the Broad Institute TCGA Genome Characterization Center. This portal is modeled after Tumorscape which contains copy number data from non-TCGA projects (Beroukhim et al., 2010).


Gene-Centric GISTIC Analyses

Genes (including miRNAs) can be individually queried by Gene Symbol here. The available data include:

  1. A summary statement of the significance of copy number alterations affecting that gene or transcript.
  2. For amplifications and deletions separately, a table representing the results of GISTIC analyses pertaining to that gene across the entire dataset and within cancer types that are well-represented in the dataset.
  3. Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region.

More details on available analyses    More details on gene-centric analyses    Explore data by gene now


Cancer-Centric GISTIC Analyses

Cancer types can be individually queried here. The available data include:

  1. A summary statement of the number of specimens analyzed.
  2. For amplifications and deletions separately, a table representing the results of GISTIC analyses pertaining to that cancer type. The significantly aberrant peak regions of the genome are listed.
  3. Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region.

More details on available analyses    More details on cancer-centric analyses    Explore data by cancer type now


New User?

Only curators need to register and log in when using the portal. They must request curator privileges in order to manage the data and analyses tools TCGA provides.


Terms of Access   Register


Tutorials / Manuals

Tutorials, analysis descriptions and other documentation is available at:
HELP > DOCUMENTS


News / Events

Jun 7, 2015: If you publish using the results found on this portal, please cite: Zack et al. Pan-cancer patterns of somatic copy number alteration. Nature Genetics (2013). 

Jun 1, 2015: Today the results of two new analysis sets of the complete set of TCGA SNP 6.0 array experiments, consisting of 10844 patient tumor samples across 33 cancer types, have been published on the portal. This final data set has expanded by 274 patient samples and contains two new cancer types, Thymoma (123 patients) and Testicular germ cell tumors (150 patients). The two analysis sets differ in the method used to discriminate individual regions. One analysis set uses "arm-level peel-off" which helps specifically locate strong drivers on a chromosome arm with a potential cost of decreased sensitivity to other drivers on the arm. The other analysis set uses standard arbitrated peel-off and trades in increased sensitivity for detecting multiple drivers for less specificity.