Hi,
I have been using the Cell Model Passports Copy number alteration “CNV Driver gene data” (https://cog.sanger.ac.uk/cmp/download/cnv_summary_20220509.zip) dataset.
I am a bit confused and would like clarification with how the CNV scores are calculated (https://depmap.sanger.ac.uk/documentation/datasets/copy-number/) as some of the values are 2 or 3 but it has been characterised as a “loss” when the ranking system says 2 = neutral and 3 = gain.
Thanks in advance for any help
Hello,
It looks like you are asking a question about a dataset produced by the Cancer Dependency Map at Sanger.
This forum is run largely to support users of https://depmap.org which is in conjunction with the Broad Institute Cancer Dependency Map. While people in these two projects (one at Sanger and one at the Broad Institute) do collaborate, I don’t know of anyone on the Broad side who is using this specific dataset that I could refer your question to.
(On the Broad side, we have a different copy-number calling pipeline which uses different scoring. As a result, I’m not sure if someone on this forum will be familiar with CNV scoring method that is being used at Sanger.)
The documentation you pointed to ends by citing A Landscape of Pharmacogenomic Interactions in Cancer, so that might have information, or alternatively, perhaps contacting depmap@sanger.ac.uk. Perhaps they might be able to point you in the right direction?
Sorry I couldn’t offer any additional assistance.
Thanks,
Phil
