Hierarchical clustering of log transformed qPCR copy number (CN) values for chr17 genes in association with relevant breast cancer subtypes.

<p><b>A:</b> clustering of all 14 genes was informative in 376 cases and revealed 4 main CN patterns, out of which high CN for the HER2-related genes form the HER2 cluster and are predominantly found in HER2-positive (Luminal-HER2 and HER2-enriched) tumors; gains for the HER2 gene itself (ERBB2) mostly occur in parallel with STARD3. Luminal A and B, as well as TNBC are evenly represented in the non-HER2 clusters. <b>B:</b> If analyzing CN for the 4 HER2-related genes only, 36 of 93 tumors (38.7%) have non-continuous gains for these genes (complex pattern, red cluster) while the rest exhibit continuous gains in at least two genes, predominantly STARD3 and ERBB2 (gains, green cluster). <b>C:</b> Clustering of the non-HER2-related gene CN, i.e., 10 of 14 genes excluding STARD3, ERBB2, PSMD3 and THRA, yields 3 main clusters with equal representation of all subtypes (distribution of HER2-positive tumors and TNBC is shown). Cluster legend: natural log 0.69 corresponds to 2 copies; log 1.38 to 4 copies.