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Figure 2 | Breast Cancer Research

Figure 2

From: Integrative analyses identify modulators of response to neoadjuvant aromatase inhibitors in patients with early breast cancer

Figure 2

Grouped and pairwise analysis of matched pre- and post-aromatase inhibitor (AI) therapy copy number profiles. (A) Frequency plot of copy-number gains and losses (top) or amplifications (bottom) in 19 matched pre- and post-letrozole-treated breast cancer samples. The proportion of tumors in which each bacterial artificial chromosome (BAC) clone is gained (green bars) or lost (red bars) is plotted (y-axis) for each BAC clone according to its genomic position (x-axis). No significant differences were identified between the two components. (B) Hierarchical cluster analysis performed with array comparative genomic hybridization (aCGH) categorical states (that is, gains, losses and amplifications) using the Euclidean distance metric and Ward's algorithm of 19 matched pre- and post-letrozole treatment samples from estrogen receptor (ER)-positive breast carcinomas. Matched samples from each patient preferentially cluster together, and have similar patterns of copy number aberrations. In some cases, small regions show differential copy number states between matched samples (green squares), but these are private events. The heatmap displays each case along the x-axis and the genomic position along the y-axis. Amp, amplification; Gain, copy number gain; Loss, copy number loss; NC, no copy number change. (C) Genome plots of pre- and post-letrozole samples from two patients. The genomic position is plotted along the x-axis and circular binary segmentation (cbs)-smoothed log2 ratio on the y-axis; amplifications are shown in bright green, gains in dark green, losses in dark red and normal copy number in black. Red stars denote amplicons present in only one sample of a matched pair.

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