Where doubling happens across TCGA tumours, how far genomes drift from the tetraploid baseline afterwards, and what that does to expression. Pictures and figures below are placeholders — the real ones are on their way in.
Whole-genome doubling is common in cancer, and the cells that undergo it do not remain at the doubled state. Ploidy falls afterwards and settles at values that differ by cancer type.
Working from a cohort of roughly 10,000 TCGA patient samples across 23 cancer types, I called copy number at the arm level and modelled differential expression continuously against ploidy, alongside survival analysis, gene set enrichment, and deconvolution of bulk expression into cell-type fractions.
A simulated dataset was used to check the pipeline's calls against a known ground truth before trusting it on real tumours. Mostly R, some Python, on a dataset large enough that pipeline design mattered as much as the statistics did.