Figure 3

Individual sample comparator. The individual sample comparison tool allows for sets of patients to be explored. It shows disruptions at the gene or sub chromosome level and shows the complexity of gene disruptions between patients and normal/disease pairs. Using the cancer comparison (Figure 1) and genome focused (Figure 2) views, regions or genes of interest can be mined from hundreds of samples and then smaller sets of samples can be visually compared. In this instance on the right hand side are cancer samples, and on the left hand side are the matched normal tissues. The visualization displays the level of rearrangement at the chosen loci. The rearrangements can be complex and involve multiple crossovers or translations across different loci. To accommodate such complexity a nested layout procedure is used, where the main x-axis shows the scaffold chromosome, and the graph that is drawn directly from this shows represents how the rearrangement has resulted in connections between new non-contiguous portions of the chromosome (the thickness of the connecting curves gives an indication as to the portion of reads that show this level of structural variation). For complex multi-site rearrangements this branching procedure is repeated using nested graphs. The amount of disruption, and degree of gene fusion or similar, can then be visually compared. Color coding is used to show different chromosomes, and coverage information is displayed below the x-axis. The system is interactive so selecting on different loci will allow for further exploration filters can also be applied to change the patients being viewed.