CNVkit background(Noise)

Question

[kwanghoon]

Hi, I did Tumor-Normal CNVkit analysis using WES data.

Tumor data was generated from FFPE DNA, Normal was from blood DNA.

I can see many background(Noise)... Is this because of FFPE tumor data?

Thank you.

Answer 1

[Eric T.]

Yes, this is noisy. You might be able to bring down the noise by using a larger pool of normal samples to build the reference profile (instead of T/N pairing), and maybe exclude problematic genomic regions if you know what they are.