Extended Data Figure 7 : Array CGH analysis of primary tumour–metastasis pairs.

From: Early dissemination seeds metastasis in breast cancer

Extended Data Figure 7

a, Number of aberrations detected by array comparative genomic hybridization in primary tumours and matched lung metastases. Dot plot with median; statistical analysis by Mann–Whitney U-test. b, Heatmap of copy number states for the 28 primary tumours and 44 matched metastases across chromosomes 1–19 and X. Light, medium and dark yellow or blue colours indicate weak, intermediate and strong amplification (yellow) or deletion (blue) amplitudes, respectively (thresholds at ± 0.1, ± 0.2, ± 0.3). c, Prototype aberrations (top) constructed from segmented array CGH profiles (bottom) of the primary tumour (PT) and the matched metastases (Met 1–3) of mouse 3769 (phylogenetic tree and phylogenetic paths displayed in Fig. 4h, i). Prototypes (top) are organized in stacked rows per chromosome and numbered according to chromosome and positional order of their first change point, for example, 1.2 denotes the second prototype of chromosome 1. These prototype aberrations are then used to construct the phylogenetic paths (for example, Fig. 4i) and trees. For better visibility, small focal aberrations were enlarged to have a minimal extension of 300 probes. Yellow, amplification (+1); blue, deletion (−1). Corresponding segmentation profiles of the normalized and wavy-pattern-corrected array CGH data (grey dots) are indicated by red lines (bottom). For segmentation and prototype construction, see Methods. d, Table for calculating the relative time points of dissemination (Fig. 4j). PT ab, number of aberrations in the primary tumour; Mk ab, number of aberrations in the matched metastases (k = 1, 2, 3); PT–Mk cab, number of common aberrations between primary tumours and metastases; PT–Mk pcab, proportion of common aberrations relative to the primary tumour, that is, pcab = cab/PT ab.