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Fig. 3 | Genome Medicine

Fig. 3

From: Integrative genomic and transcriptomic analyses illuminate the ontology of HER2-low breast carcinomas

Fig. 3

Copy number alterations across the HLBC-FPO cohort. A Heatmap of the copy number alteration (CNA) for the 59 genes comprised in the panel, reporting the log10 value of the fold change (FC), with a blue-to-red map describing gene loss-to-gain. Raw dendrogram groups patients by similar CNA, and column dendrogram groups co-occurrent CNAs. IHC class annotation on the right-hand side. B Validation of CNA results by FISH. Clockwise, CCND1, FGFR1, MET, and KRAS gene amplification (green signals: gene; red signals: centromeric probes). White bar: 5-Ī¼m in size. C Boxplot of the ERBB2 gene FC distribution (sequencing data) for the IHC-based cohorts. HLBCs-2 showed a significantly higher number of ERBB2 copies compared to HLBCs-1, with the highest values identified in the HLBC-2E cohort, in line with the FISH equivocal subtyping (HLBC-1 vs HLBC-2N P = 0.01, HLBC-1 vs HLBC-2E P < 0.01, unpaired T-test)

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