is it possible to extract zygosity of point mutations from DepMap data?

[Rydoggy1]

Hello,

For cell lines that carry a point mutation of interest in a given gene, is it possible to find out whether the mutation is homo or heterozygous in that cell line? If not possible through the portal, is there another way to obtain this information?

Thanks!

Ryan

[simz]

Hi Ryan,

Under the mutations tab, there is a dropdown that allows users to select mutation annotation fields they wish to see other than the defaults. In this case, you might be interested in GT and/or Allele Fraction. They should show up in the table after you check the corresponding fields here.

In addition to this view on the portal, we also always provide the full mutation file (OmicsSomaticMutations.csv) in the download page, which contains all annotations.

Hope this helps!
Simone

[Rydoggy1]

Hi Simone,

Thanks for the fast replay and helpful information! Two follow-up questions:

[Rydoggy1]

Correction to my last email. For AF ~0.75, would that suggest CN of >2 and 2 out of 3 or 3 out of 4 copies of a gene have the mutation?