CNV calling with complex genomic background
0
0
Entering edit mode
8 days ago
雨辰 • 0

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: Tumor Sample

The negative control's germline allele frequency plot looks normal: GM24385

In tumor sample, the segmentation of the CNV events looks messy in chromosome 1 (as an example) 03-chr1

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

It looks all good in control sample GM24385-chr1

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

CNV • 115 views
ADD COMMENT

Login before adding your answer.

Traffic: 3741 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6