Copy number variation

Hello,

I’m trying to get a copy number mutational signature.
I saw that I used ABSOLUTE method in 2018. Is it the same way you use it now?
If it’s different, I wonder what you use.
And can I get a file like the 2018 CCEL_ABSOLUTE_combined as the current sample?

Hi,

We are no longer using ABSOLUTE on current depmap data. For absolute copy number calling, we are currently using PureCN instead, and we are hoping to release the data on the public portal soon. The format of PureCN data will be similar (segments + gene-level), but the columns won’t be the same.

Stay tuned!
Simone

i am very interested in the PureCN absolute copy numbers! there are ABSOLUTE estimates for a subset of the cell lines i am interested in, but not all. will the PureCN estimates be made available for all CCLE cell lines and roughly when can we expect them? thank you!

Hello!

We are planning to release PureCN calls to the public portal in 24Q2. Please stay tuned!

Best,
Simone