Clarifying the Criteria for Identifying Oncogenic Alterations in DepMap Cell Line Data

Q&A
1

Hello,

I am currently conducting research using the DepMap portal, particularly interested in the “Oncogenic Alterations” displayed on cell line pages, such as ACH-000328. I am seeking clarification on the methodology used to identify these specific oncogenic gene alterations.

In an effort to replicate this aspect of the data, I selected genes from the Mutations dataset where the ‘Likely LOF’ (Loss of Function) column is marked as TRUE. However, I’ve noticed that the list of genes I compiled greatly exceeds the number presented on the website’s page.

Could someone kindly provide insight into the additional conditions or filters that might be applied to determine the genes listed under “Oncogenic Alterations” on the DepMap portal? Understanding the precise criteria or methodology used in this process would be immensely helpful for my research.

Thank you in advance for your time and help.

2

Hi,

The “oncogenic alterations” on the cell line page only contains variants reported by OncoKB. For definition of specific columns in the mutation table, please refer to our documentation. Unfortunately, due to licensing issues, we are not allowed to directly redistribute OncoKB’s annotation in our mutation table, but you should be able to query OncoKB directly to get the information you need.

Thanks,
Simone