Hi!

I am recently working on CNV calling with a complex genomic background. This tumor sample has estimated ploidy 2.67 (by PureCN), purity near 100% (by PureCN). I am using PureCN and CNVkit default parameters with Panel of Normal 80 samples to perform CNV calling. The germline allele frequency plot is shown as below:

The negative control's germline allele frequency plot looks normal:

In tumor sample, the segmentation of the CNV events looks messy in chromosome 1 (as an example)

The log2CopyRatio of NRAS gene is 1.3, while for NTRK1 is 0.8.

It looks all good in control sample

Are there any suggestions to distinguish whether these two genes are both gain or only gain of NRAS? Previously we had a similar sample with ploidy = 3 purity 100%, when Copy number = 3, 4, 5, we called them gain, however, they are all validated as copy-neutral events. Do you have any ideas how to get rid of the false positive gains?

Thank you so much! Best, Julia