Extended Data Fig. 5: Single-cell genome sequencing of SP cells from Pre-tumour mice reveals an intermediate evolutionary genomic state.

a, Hierarchal, copy number clustering heatmaps of SP single cells sequenced from 7 Pre-tumour mice. Colour code for lineage (L), ploidy (P), and chromosome copy number are provided. Sample annotation and number of single-cells sequenced are provided. b, Bar-plot quantification of percent SP cells sequenced that were polyploid across Pre-tumour mice analysed. c, Breakpoint based phylogenetic tree of single SP cells (n = 171) sequenced from Pre-mouse P1. Colour codes for ploidy, lineage, and copy number information are provided. Phylogenetic distance is based on statistical considerations of breakpoint similarity/dissimilarity (Methods). Clone track denotes lineage that underwent genome doubling (purple). Clonal relationship between diploid and polyploid single cells is computed with a FDR not exceeding a threshold value of t = 0.01. d, Genome-wide copy number profiles of representative single cells of highly rearranged diploid Pre-SP cells (top panel) and its genetically traced polyploid counterpart (top panel) from Pre-Tumour Sample P3. Black arrows denote distinguishing copy number alterations and their breakpoint positions used in inferring phylogenetic relationships.