To assess the significance of the overlap between CNAs and annotated regions (namely chromatin fragile sites 16 and recurrent somatic copy number altered regions in cancer 68 we randomly generated a set of 2,000 matched control regions for each CNA. Control regions were generated so that they had the same size as the CNA, did not overlap with telomeres or centromeres, and did not overlap the original CNA. Overlaps were determined between the CNA and the annotated regions and between the matched control regions and the annotated regions to calculate an empirical P-value.
