Extended Data Fig. 6: Ecosystem characterisation in P2-TN1.
From: Spatial genomics maps the structure, nature and evolution of cancer clones
a, Haematoxylin and eosin (H&E) stained sections of the two primary breast cancers from case P2. b, Microregions selected for detailed analysis overlaid on BaSISS maps (regions relate to heatmaps in Fig. 3a; numbers relate to histological annotations in Supplementary Table 2). Microregions were not defined for P2-TN2 as a single clone was targeted and detected. c, Cell type contribution posterior density of the generalised linear mixed models (glmm) model with region specific random effect. Significant comparisons were controlled for FDR using the BH procedure. 19 clone territories (with dominant clone fraction > 0.1) were analysed. Fibroblasts and perivascular-like cells (PVL) could not be differentiated within this experiment and are reported as ‘fibroblasts’. d, Volcano plot of epithelial expression of the 91 oncology ISS panel genes in TN1 invasive regions. Significance was adjusted for multiple testing using BH procedure, only genes with FDR < 0.1 and fold change > 1.5 in both ways are coloured/labelled. DCIS = Ductal carcinoma in situ.
