How to download a list of cases containing specific cnvs from TCGA?

Question

[bsb4390]

I am trying to obtain a list of all tcga cases for which there is a specific cnv (for example - brca2 gains). Using the GDC portal to access this data, I am able to get a list of all cases containing cnv's related to brca2, but I am unable to split this list into cases for which there is brca2 gain vs brca2 loss.

Does anyone know how to do this?

Answer 1

[Kevin Blighe]

The TCGA copy number data is arguably the most annoying because it has been processed and re-processed and made available on multiple domains across the World Wide Web. My 'go to' TCGA copy number data is that of the Broad Institute, which was processed by GISTIC 2.0. I give details of the link to this resource, here: C: How to extract the list of genes from TCGA CNV data

Once you download it, you can easily annotate it by following my code here: A: How to extract the list of genes from TCGA CNV data

I this way, you can have a reference dataset of somatic copy number gains/losses in all genes in all samples.

Kevin