Account for WGD

[teng-gao]

Ideally, we should account for WGD (baseline is 4 copies) when analyzing hyperploid tumors (e.g. TNBC5), which should lead to better model fit and prediction stability

[DarioS]

Isn't the baseline usually at three copies because of fitness? I have a cancer with 70% of samples with whole genome duplication and genome ploidy from PURPLE is rarely near four but often close to three, so I am looking forward to this enhancement!

Whereas chromosome losses are rarely tolerated in diploid cells, they occur frequently in tetraploid cells and can promote cancer formation.

[teng-gao]

Isn't the baseline usually at three copies because of fitness? I have a cancer with 70% of samples with whole genome duplication and genome ploidy from PURPLE is rarely near four but often close to three, so I am looking forward to this enhancement!

Right, although tumors that have ploidy near 3 should be ok unless no diploid regions are available anywhere on the genome. The issue only arises when the lowest (in copy number) balanced segments are 4 copies.

[DarioS]

I noticed that non-WGD samples have near-perfect agreement to whole genome sequencing (PURPLE) but not WGD.

It seems implausible that all of a sample's arms would be lost or gained rather than a mix. Sample IDs ending in Bulk are WGS.