Fig. 3
Multi-region copy number profiling in FFPE breast cancer tissue sections. a Scheme of regions within individual FFPE breast cancer sections from which gDNA was extracted. S, small regions of ~3 mm2. L, large regions of ~7 mm2. For each L region, gDNA was split in two technical replicates, L1 and L2. F, remaining tissue in the section. b Scans (×10 magnification) of 35 hematoxylin–eosin-stained tissue sections from primary (T) and metastatic (M) breast cancers, and corresponding copy number profiles (100 kb resolution), for F, L, and S regions. Black circles: L region from which L1 and L2 replicates were obtained. Black arrowheads: amplification of the RAD51B gene in patient KI2 and of the HER2 gene in patient KI7. In all the profiles, chr1 is on the left and chr22 on the right. c Pearson’s correlation (ρ) between the fraction of the genome either amplified or deleted in all the L1–L2 replicates shown in b. d Hierarchical clustering of copy number profiles for F, L, and R regions, in patient KI13. e Same as d, but for patient KI14. f Ranking of 712 cancer-associated genes in COSMIC15 based on the number of samples in which they were found amplified (AMP). Gene names refer to a subset of 31 COSMIC genes that were found to be frequently amplified or deleted in 560 breast cancers16. g Same as f, but for genes deleted (DEL) in the samples shown in b. h Hierarchical clustering of 712 COSMIC genes (rows) based on their amplification (red) or deletion (blue) status in the 133 samples shown in b (columns). Gene names indicate 14 out of 31 genes that were previously found to be either amplified or deleted in breast cancer16. For each gene, the rectangles on the right indicate whether it is amplified (no boundary) or deleted (black boundary) in at least one sample (F, L, R) in the corresponding KI patient. In all cases, KI refers to the ID of samples from Karolinska Institute, as described in Supplementary Table 2. All the source data for this figure are provided as a Source Data file
