It's relative simple to detect CNV with whole genome sequencing or whole exome sequencing, but how to do it with panel sequencing?
For example, to detect ERBB2 gene amplification (copy number gain) with a panel sequencing (i.e. a 100 genes panel), I can count the reads mapped into ERBB2 and other genes and calculate its relative gain/loss, but here comes the problems:
1, capturing has bias
2, PCR has bias
3, The gene region is too small, so this naive method is very instable.
a), any good way to do this?
b), how to design the panel? Shall I add some CONTROLs into the panel?
c), how to do normalization/correction so that the result will be stable?
Currently I do intra-sample normalization to normalize sequencing depth, and calcate the average value within different samples (with a same panel), then compare value of current sample to the average values. This method is expected to work, but the results show big difference with other clinical methods like FISH. Why?