Determining Copy Number Alterations for Genes/, as boolean, in DepMap Public 22Q2

Q&A
1

I am using “DepMap Public 22Q2 Primary Files”. I have a list of a few hundred genes. For each gene I want to determine whether it has a copy number deletion or not. Also, for each gene I want to determine whether it has a copy number amplification or not.

Could you please advise how to get this information?

I was looking at CCLE_gene_cn.csv. But this seems to contain floating point values, I do not understand how to interpret those how they relate to copy number deletions/amplifications. Also not sure if this is even the right file to look at.

2

Hello,

We currently don’t have a specific threshold recommendation for determining amp/del using relative copy number data, but perhaps the discussion in this thread could be helpful.

And in case you are interested in absolute copy number calls instead of relative to classify CNAs, we currently have data generated by the ABSOLUTE algorithm on the CCLE lines. You can find the file called CCLE_ABSOLUTE_combined_20181227 in the “CCLE 2019” data set on the download page.

Simone