Representation of differences in CNA between patient tumors and xenografts. A, frequencies of genome copy number gains and losses plotted as a function of genome location in the patient tumors (left) and xenografts (right). Frequencies are based on GNL status and colors are calculated from the proportions of profiles without missing values. B, Frequency distributions plots of unchanged, positive and negative GNL differences. C, Frequency of CNA alterations distributed along chromosomes. Frequencies were calculated as the difference between patient tumor and xenograft GNLs. Negative frequencies represent DNA losses, while positive frequencies represent gains in xenografts. Only segments present in 10 or more pairs are shown (n = 992). D, Distribution of recurrent CNA gains (lower figure) and losses (upper figure) along chromosomes (frequency calculated for GNL differences occurring in at least 30% of pairs, n = 202 and 176, respectively). CAN, copy number alteration; FrAGL, Frequency of Amplicon, Gain and Loss; GNL, gain, normal, loss.