Extended Data Fig. 7: DCIS clone specific histologies.
From: Spatial genomics maps the structure, nature and evolution of cancer clones
a, BaSISS clone map of P1-D3, a sample that contains Ductal carcinoma in Situ (DCIS), stroma and normal glandular regions. The most prevalent genetic clone colour is projected as a coloured field on DAPI images (reported if cancer cell fraction > 25% and inferred local cell density > 300 cells/mm2). Scale bar = 5 mm. Inlaid, H&E stained image (from a serial tissue section) details the histological transition from normal to DCIS morphology, consistent with the clone field transition in the BASISS map (scale bar = 1 mm). b, Heatmap of cancer cell fractions (CCF) derived from LCM WGS of six regions of P1-D1/P1-D2 with cartoon of predicted clone composition indicating inference of monoclonal and polyclonal growth patterns. c, Example of a clone interface within a single sub-lobular space in P1-D1. Clone fields (top left); spatial BaSISS mutation signals (top right); characteristic histological features on H&E (bottom left) with zoom image of clone interface (scale bar = 100 um) (bottom right). d, Histological, genetic and transcriptional features of three lobules (identified on the clone map of P1-D2; left, scale bar = 5 mm) are shown: H&E staining (top) scale bar = 1 mm; BaSISS clone fields projected on DAPI with frequency plots of the local, mean cancer (coloured areas) and non-cancer (white) corresponding to horizontal dashed line (middle); and ISS gene expression signals reporting CCND1 and KRT8 that exhibit clone specific spatial patterns. e, Clone maps of P1-D1/P1-D2 (as presented in Fig. 4a) but microregions are coloured according to histological grade. f, Histopathological annotations for each microregion presented alongside the same clone composition heatmap as shown in Fig. 4b.
