Examples of putative breakpoints in the areas of frequent genomic rearrangements in breast cancer. Breakpoints on chromosome 17 (A and B), in two HER2+ genomes, cutting through gene BCAS3, which is often rearranged and fused to other genomic sequences; specimens T111 (A) and T333 (B). A breakpoints within the CCND1 gene on chromosome 11 in ER+ tumor; specimen T147 (C). A breakpoints within the PVT1 oncogene at the edge of the amplicon containing the MYC oncogene in a triple negative breast tumor; specimen T199 (D). Each panel shows data points for log 2 ratios of fluorescence between labeled tumor DNA and the differentially labeled normal human reference. Shaded areas identify aberrations called by the ADM-2 algorithm, and the genes are indicated with blue boxes (bottom).