2.5. Detection of Full-Length Arm/Chromosome Section Aberrations
The topological approach of TAaCGH is designed to measure relative changes in copy number between a clone and its neighbors and, therefore, does not account for large-scale chromosome aberrations, such as full arm amplifications or deletions. To detect large-scale chromosome aberrations, we extended the topological method by measuring significant displacements of the center of masses of the point clouds. More specifically, the center of mass of the point cloud associated with each chromosome arm was calculated for each patient and averaged over all patients belonging to any given category. A p-value was assigned to the difference between the average value for the center of masses for both populations using the same permutation approach described above. We not only tested for significant differences between test and control, but also for significant displacements of the center of masses of the test population from the origin. This second test allowed us to drop those cases where the significant displacement was driven by the control population.