Three human breast cancer cell lines are represented by panels a-b (SK-BR-3), panels c-d (MCF-7), and panels e-f (ZR-75-30). The X-axis in all six panels is the physical position of SNPs along chromosome 17. The vertical lines just above the X-axis of each panel represent heterozygous (green) and homozygous (red) genotype calls. The Y-axis in all six panels is the estimated copy number. The points are derived from the kernel smoothing step and the solid horizontal lines are derived from the regression tree. Black colored lines indicate total copy number, the blue colored lines indicate the allele with the higher copy number estimate and the purple colored lines indicate the allele with the lower copy estimate. The vertical black line proximal to 40 Mb indicates the location of the HER2/neu gene. The panels on the left (panels a, c, and e) show an enlarged view of the genomic region harboring HER2/neu while the panels on the right (panels b, d, and f) show a larger view of the chromosome.