A simple simulation was performed to obtain P-values for the probability that an observed configuration of homologous copy-numbers could be produced from a serial process of independent gains and losses. Genome-wide homologous copy-numbers are summarized at chromosome-arm resolution as integer gains/losses (total of 78 states). We then fix the total number of gains/losses N for the sample, and calculate rates for each arm, which are normalized to probabilities. Simulation of the sample is performed by independently sampling N gains and losses from these probabilities. This was repeated 1000 times for each sample, keeping track of the number of times M that the extent of even high homologous copy-number present in the observed sample was attained or exceeded. The P-value is then: P = M/1000, if M > 0, otherwise P < 0.001.
