Fig. 4

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) from patients in the combination arm. 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). a Untreated tumors from good response (GR) tumors (n = 19, top plot) show a higher frequency of alterations genome wide, in comparison with no response (NR) (n = 10, bottom plot). Loci significantly associated to different responses are marked with asterisk. b, c Aberrations disappear during treatment for patients responding (top) to the therapy, while for the NR (bottom), several copy number changes are kept