Cnv Data

Question

[RoyC]

Does anyone know where I can download copy number data (amplification/deletion) along with the Patient IDs?

I have tried using http://gdac.broadinstitute.org/runs/ but the CNV data I downloaded there does not have the TCGA IDs along with the amplification/deletion

I am trying to get all CNV data for a single tissue type. Thank you!

Answer 1

[Charles Warden]

If you mean a single cancer type, you can use the TCGA data portal:

https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp

For example, here are the copy number calls from the SNP chip data for breast cancer:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/cgcc/broad.mit.edu/genome_wide_snp_6/snp/

If the associated paper has already been published, there will probably also be a separate page with the associated data:

https://tcga-data.nci.nih.gov/docs/publications/

Again, here is the specific link for breast cancer:

https://tcga-data.nci.nih.gov/docs/publications/brca_2012/

Answer 2

[Ryan D]

This is a place that really suffers in the TCGA annotation. The file handles are different from the TCGA IDs and so you have to map each "barcode" back to the TCGA ID and determine if it is tumor/normal etc. I think that information comes as part of the download through the TCGA portal mentioned above. If not, I have a master "chemistry file" that has the mappings for all arrays run by TCGA as updated a few months ago.

It's also important to realize that the pipeline TCGA uses is best suited for identifying large deletions/duplication events in tumor or relative to other samples. As for common CNVs, you'll need to run something like Birdsuite to detect that on the Level 1 data from each array since the TCGA's GISTIC algorithm does not care about common CNVs/CNPs.

Answer 3

[smrutimayipanda]

CNV data with patient ID can be downloaded through R package TCGAbiolinks.