Fig. 3

Copy number variants across BrM samples. Chromosomal map by GISTIC of CNV frequency and size by G-Score in a all BrM (n = 38 patients, m = 64 samples), b Basal (FFPE BrM n = 7, m = 8; frozen BrM n = 8, m = 9), c HER2-Enr (FFPE BrM n = 11, m = 11; frozen BrM n = 10, m = 10), d LumA (FFPE BrM n = 4, m = 4; frozen BrM n = 6, m = 6), and e LumB (FFPE BrM n = 7, m = 7; frozen BrM n = 4, m = 4). Gains/amplifications (red) are above the x axis, losses/deletions (blue) below the x axis, with significant (FDR < 0.10) variants colored and the chromosome arm region annotated; grey peaks indicate gains/amplifications with FDR < 0.25. Plots for PAM50 Normal and unassigned samples are not shown, f Heatmap of log2 copy number ratios in CR and PAM50 genes overlapping significantly amplified/deleted regions identified by GISTIC2 (FDR < 0.25) in FFPE BrM (n = 32 patients, m = 33 samples) and frozen BrM (n = 28, m = 29) by PAM50 inferred subtype. PAM50 Normals are not shown (FFPE BrM n = 1, m = 1; frozen BrM n = 1, m = 1) because no significantly amplified/deleted regions were identified by GISTIC2 among these samples. For cases where there was more than one GISTIC peak region associated with a given gene symbol and sample, the longest peak region was selected to be included in the heatmap. Clinical source refers to the location of the lesion assessed for clinical biomarkers (ER, PR and HER2) in that patient’s medical records used to assign the clinical subtype of the BrM