Figure 1

Comparative genomic analysis of claudin-low and basal breast cancers. A) Frequency plots of DNA copy number alterations in claudin-low samples (N = 28) and basal samples (N = 61). Frequencies (vertical axis, from 0 to 100%) are plotted as a function of chromosome location (from 1pter on the left to 22qter on the right). Vertical lines indicate chromosome boundaries. Positive and negative values indicate frequencies of tumors showing copy number increase and decrease, respectively, with gains (in red), amplifications (dark red), losses (in green) and deletions (dark green). Bottom: supervised analysis comparing the genomic profiles of CL versus basal cases. The difference was assessed with the Fisher’s exact test. The blue line indicates the limit of significance (p = 0.05). B) Genomic patterns of CL and basal tumors using Hicks’ classification [56]. The difference between the subtypes was assessed with the Pearson's Chi-squared test.