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


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

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