Defining "deep" deletions and amplifications


I had previously used the CN calls from CCLE and earlier versions of DepMap (i.e. 18Q), where the scores were centered around 0. In those data, it was common to define “deep” deletions as < -1.28, while amplifications were set as > +0.75.

Given that the CN scores are now instead “relative copy number” (What is relative copy number/copy number ratio?), are there are any general recommendations for defining a “deep” deletion or amplification, analogous to previous versions of the data?

Thanks, and appreciate this awesome resource!

I should add that I am aware of the “+,-,0” scoring in the segment-level CN data, but I’m finding that this three-level scheme is very generous in defining a deletion or amplification (e.g., regions would previously have been defined as het loss or gain, rather than del/amp).