Fig. 1: WGD is a dynamic mutational process.

a, Overview of the MSK SPECTRUM cohort and specimen collection workflow, including numbers of patients, sites and samples processed by various means. H&E, haematoxylin and eosin; IF, immunofluorescence. b, Study design for analysing cellular ploidy and WGD in single cells using scWGS with the DLP+ protocol. The plot shows the classification of WGD multiplicity in cancer cells (0, 1 or 2 WGDs) using the fraction of the genome with major copy number (CN) ≥ 2 versus the mean allele CN difference; n = 30,260 cells. BAF, B-allele frequency; TCN, total copy number. c, Top, age at diagnosis, mutation signature, BRCA1/BRCA2 mutation status, and WGD class. Middle, distribution of cell ploidy of individual cells for each tumour, coloured by the number of WGDs. Bottom, percentage of WGDs, number of cells per patient, and fraction of cells in the minority WGD multiplicity state. Bottom right, illustrations of cell classifications. d, Heatmaps of total copy number (left) and allelic imbalance (right) for patient OV-045, with predicted WGD multiplicity and site of resection for each cell annotated. The 1×WGD population was downsampled from 1,857 to 200 cells for visualization, and the full 0×WGD and 2×WGD populations, numbering 18 and 44 cells, respectively, are shown. A-Hom, homozygous for haplotype A; A-gained, allelic imbalance with more copies of haplotype A (analogous for haplotype B); Balanced, equal copies of the two haplotypes.