Fig. 5

Frequency plots of genome-wide copy number aberrations (CNAs) in tumors at the time of diagnosis (a), after 12 weeks of treatment (b), and at the time of surgery (c) for patients treated with chemotherapy alone. The y-axis indicates frequency (%) of tumors with gains (red) and deletions (green) sorted by genomic positions (x-axis) across all chromosomes (annotated at top of the plots). Higher frequency of copy number changes is observed in untreated good response (GR) tumors (a, top) compared to no response (NR) tumors (a, bottom). During treatment (weeks 12 and 25), the GR tumors shrink and CNA frequency profiles lose their aberrations (b, c, top). Tumors not responding to treatment keep their aberrations during treatment (bottom)