Figure 3

Whole genome tiling path array CGH karyogram of an oral low grade dysplasia which subsequently progressed to cancer. Whole genome tiling path array CGH karyogram of an oral low grade dysplasia which subsequently progressed to cancer (Oral51). Each dark blue dot on the karyogram represents the average signal ratio for an individual BAC clone from the array. Clones were plotted vertically against known chromosomal position. Log2 signal intensity ratios for each clone were plotted horizontally, with colored vertical lines denoting log2 signal ratios from -1 to 1. Where the signal intensity ratio equals zero (purple line), equivalent DNA copy number between the sample and the reference DNA was inferred. Alternatively, DNA copy number increases were inferred where log2 > 0 (red line) and losses were inferred where log2 < 0 (green line). Numerous whole chromosome, whole arm, and segmental changes are apparent. Examples of these alterations were magnified and are represented in orange boxes. High level segmental amplicons for chromosome 2 and 4 are depicted in this manner. Lower copy number segmental (chromosome 8) and whole arm (chromosome 12) gains are similarly shown. The magnified image for Chromosome 9 shows a complex genomic rearrangement that includes multiple segmental losses and a high level segmental amplification event.