Clonal evolution for samples with no common CNV

Question

[sal.mith]

Hi, I am trying to derive clonal evolution plots for a series of samples collected before, during and after treatment using SciClone. However, it returns a message indicating that as no common CNV were present between samples, it was not able to generate the plots.

Are we able to design plots for samples that have evolved that they do not match the ancestor/previous samples? If so, what softwares can be used?

Thank you Salmith

Answer 1

[Chris Miller]

You're going to have to provide more information, starting with exactly what the error message was.

I strongly suspect that the message was "ERROR: no sites are copy number neutral and have adequate depth in all samples", which means you need to look at your inputs carefully. Did your points meet the minimum depth threshold that you set? Were your copy number regions expressed in absolute terms (2 = CN neutral)? If not, did you set the "cnCallsAreLog2" parameter correctly?