Queries regarding GISTIC output for Pancancer Atlas

[Hannan Wong]

Hi cBioPortal group,

Firstly, thanks for putting together such an extensive and updated database! I have a rather basic question regarding the data_cna.txt values from any TCGA study from the TCGA PanCancer Atlas dataset. What was the input into GISTIC? Was it the ASCAT2 files from GDC portal? If not, could you point me in the right direction? Thanks!

Warmest regards,

Hannan wong

[Benjamin Gross]

Hi Hannan,

Thank you for your email.

The data_cna.txt files for TCGA PanCancer Atlas studies in cBioPortal represent GISTIC2.0 thresholded gene‑level copy number calls. These calls were generated from segmentation data derived from Affymetrix SNP6.0 array copy‑number profiles (in this case I believe CBS-based segmentation was used). The harmonized segmented data were then analyzed with GISTIC2.0 to identify recurrent amplifications and deletions across a cohort, and these results form the basis of the data_cna.txt thresholded calls you see in PanCancer Atlas and cBioPortal. 

Here is a link with more information:

Best,

-Benjamin

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