Fig. 2: Copy number analysis reveals three tumour subclones with spatially restricted patterns in patient 1.

a Projection of spot clusters identified by inferCNV onto the tissue section. P1.background corresponds to the set of spots used as a reference for inferCNV, P1.1, P1.2, and P1.3 are three putative tumour subclones, P1.4 and P1.5 are probable tumour border clusters. Scale bar = 1 mm. b Heatmap generated by inferCNV showing inferred CNA profiles of Visium spots for five clusters. c High-confidence CNAs identified by Hidden Markov and Bayesian latent mixture modelling within inferCNV for the five clusters. d Adjacent tissue section showing areas collected for low pass whole genome sequencing (WGS). Colours of ellipses correspond to the colours of clusters in a. Scale bar = 1 mm. e IchorCNA CNA profiles for selected chromosomes confirming high-confidence CNAs predicted by inferCNV. See Supplementary Fig. S13 for the genome-wide view. Three tumour subclones and non-malignant tissue (P1.background) are shown with two or three replicates each, corresponding to tissue fragments in (d). f Representative tissue areas for the three subclones. Hematoxylin (blue) and eosin (red) staining (HnE) and histopathological expert annotation using QuPath⁶⁷ are shown, red corresponds to malignant cells, green corresponds to stroma. Location of these areas on the tissue is shown by rectangles in (a). Scale bar = 0.1 mm.