This may not be a pure bioinformatics question although I got this problem while trying detecting CNV on a old (over 3 years) FFPE samples. What I observed is very noisy CNV backgroud almost acorss all these old FFPE samples.
I did some research and articles shows that this is typical to old FFPE sample are is caused by de-crosslinking during DNA extraction (Pauline Robbe and Haile S). However, I did not get the logics why de-crosslinging on the old FFPE sample could cause such noisy CNV background. Can anyone share some insights? Really appreciated.