Fig. 2: Polyclonal and monoclonal tumours are distinguished by Apc mutational profiling.

a, Fluorescence dissecting microscope view of a heterotypic tumour (top) and a homotypic tumour (bottom). b, Schematic of experimental approach. Tumours were either bulk- or micro-dissected before targeted amplicon sequencing. HEP, humane endpoint. c, Number of inactivating (nonsense-only) mutations in Apc for each bulk-sequenced tumour. Based on 56 homotypic, 88 uncoloured and 17 heterotypic tumours from 10 Apc^het + ENU mice. Two-sided Wilcoxon rank-sum tests. d, Sum of the VAFs of the inactivating Apc mutations for each tumour in the indicated bulk-dissected groups. n = 148 tumours. Two-sided Wilcoxon rank-sum tests. e,f, Confocal images of micro-dissected heterotypic tumours overlaid with detected high-impact Apc variants (e) and a large micro-dissected heterotypic tumour (f). Scale bars, 100 μm. g,h, Representative clonality plots showing mean VAF versus mean sequencing depth for variants shown for a homotypic (g) and an uncoloured (h) tumour. Dotted line represents minimum VAF threshold for variant calls. i, Arch diagram overlaid on a schematic of the APC protein to compare high-impact Apc mutations in monoclonal and polyclonal tumours. Arches begins at codon 580, representing the Cre-mediated recombination event of the transgenic Apc allele. n = 94 monoclonal tumours, 105 major and 105 minor clones. EB1, EB1-binding region; MCR, mutation cluster region; aa, amino acid. j, Non-parametric bootstrap analysis showing the probability of mutation in each of the pre-defined Apc bins for monoclonal tumours, and major and minor clones. Data are mean ± 95% confidence interval. n = 94 samples per group. Inset, magnified view of the Pre-Armadillo bin, highlighting the significant difference between monoclonal tumours and minor clones. k, Oncoprint of mutational patterns among the indicated groups. Percentages on the right denote fraction of samples with detected mutations in particular gene.

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