WGS CN data and functional partial deletions

Hello,

I have a question regarding the new CN data released with the DepMap release 24Q2. It appears that functional partial gene deletions are not detected in the WGS/WES derived CN data (OmicsAbsoluteCNGene.csv).

For example, the cell line NCI-H1650 has a partial deletion of the PTEN gene that is described as a functional deletion [reference]. The CN call for PTEN based on WGS resulted in an absolute copy number of 1 (with ploidy 2.20) and the functional deletion is therefore not detected with the standard CN annotation. However, when looking at the segmented data (OmicsAbsoluteCNSegmentsProfile.csv), a segment (chr10:87963620-87979619) which partially covers the PTEN coding sequence has a copy number of 0 (figure).

Do you have some thoughts on why the difference occurs and the best approach to identify these partial deletions?

Many thanks!

Daphne

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