Method to detect genome doubling CNV is usually detected using either read depth or SNP VAF. However, neither of these methods can detect CNV in case of genome doubling (assuming genome doubling is a kind of genome scale CNV comparing to normal tissue which is diplod). We thought of other platform such as SNP array and we did not think they can detect genome doubling as well. Can any one share some comments on the method for such event? Thanks in advance.
In a tissue or cell line that used to be diploid and has undergone genome wide doubling, you expect more variants having observed allele frequencies that would also occur in tetraploid organism. That is, observed VAF distribution will have (possibly small) peaks at 0.25 and 0.75, in addition to the diploid peaks at 0, 0.5 and 1. Compare the distributions in the tissue or cell line of interest to those of the control, that is, known diploid. Also if it is a doubled male genome, the sex chromosomes will show a new peak at AF 0.5, that is, heterozygous X or Y variants. This is just an idea, I have never tried to look for such events.