Using such information, we could classify samples into three groups, which we interpreted as corresponding to 0, 1 and > 1 genome doubling events in the clonal evolution of the cancer. These three groups had modal ploidy values of 1.75, 2.75, and 4.0, respectively (Fig. 6a), and also segregated into three clusters by ploidy and mean homologous copy-number imbalance (Fig. 6b). We interpreted this as evidence of SNCAs occurring with net losses, interspersed with the genome doublings. This process resulted in intermediate ploidy values for the doubled clones (2.2 – 3.4N), with pervasive imbalance of homologous chromosomes (Fig. 6b).
