This problem had been bothered me for a long time. Because some tumor samples can not find a normal sample to compare with. But you still want to analyze the CNV, what can we do about this?
My thoughts is to find some "stable genes" as control. Then comparing the target fragment with these control genes to get the CNV information. It's kind of the similar with beta-actin in the qPCR experiment. If this is a possible solution?
But the problem is:
1) How to evaluate some genes are "stable" across the samples?
2) Maybe we should make sure that the control genes are only one copy in each sample to make the comparison easier.
I hope that I can get some suggestions related to this issue. Thanks in advance.