Characterising copy number alterations


I have been using the Cell Model Passports Copy number alteration “CNV Driver gene data” ( dataset.

I am a bit confused and would like clarification with how the CNV scores are calculated ( 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


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 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 Perhaps they might be able to point you in the right direction?

Sorry I couldn’t offer any additional assistance.