Figure 3

CGH profiles of one FFPE tumor with post hybridization wash at different temperatures. CGH profiles with post-hybridization wash steps 6 and 7 at 65°C (A) or at 68°C (B) of averaged duplicates of one FFPE primary breast tumor, hybridized according to our optimized protocol for automated array-CGH. Chromosomes (X-axis, alternate shading per chromosome) versus the log2 ratios (Y-axis). At 68°C, dynamic range increased and standard deviation of the triplicate spot measurements decreased compared with 65°C, therefore 68°C was used in our optimal protocol. As can be seen in panel B, the dynamic range and the signal-to-noise are adequate to detect and to distinguish homozygous and heterozygous loss (chromosome 11p), one single-copy number gain (e.g. chromosome 7p), multiple-copy numbers gain (chromosome 1q), and unchanged chromosome copy numbers (e.g. chromosome 10). Red lines in both panel represents the segmentation calls as calculated by CGH-segmentation.