Ploidy vs. copy number in Sequenza

Question

[wclee47]

Hi,

I ran Sequenza for one tumor sample with the matched normal control. I obtained purity 0.9 and ploidy 3 for the tumor. When I saw the chromosome plots, I found that regions showing depth ratio close to 1 were set to copy number 3. In my understanding, copy numbers for depth ratio 1 should be 2 because normal control would have diploid. Is there a relation between copy number setting and ploidy?

Answer 1

[favero.francesco]

Yes, when the normalised depth ratio is equal to 1, it means that the segment have copy number equal to the ploidy sample.

It depends on the mechanism that have lead to the various rearrangements, but in a simple case, If ploidy is 3 it means that overall the chromosomes have 3 copies. In this cases you can inspect that the B-allele frequency is lower then in region with 2 or 4 copies and have a balanced number of alleles (if any AB, AABB)