Fig. 5

Pre and post-chemotherapy changes in individual cases. Patient 1—MSK-0745. a Clinical course of Patient 1 with no response to therapy, rapid recurrence and death. b Inferred phylogenetic tree showing acquired amplification of E2F3 and JUN in the post-treatment clones. c Graph of total genomic copy number showing focal copy number amplifications in segments containing JUN and E2F3 in the resistant tumor. Patient 2—DFCI-12. d Clinical course with no response to chemotherapy and recurrence and death at 605 and 646 days after initial biopsy, respectively. e Phylogenetic analysis demonstrating FBXW7 LOH in the pre-treatment tumor with subsequent additional FBXW7 E111* event detected in the post-treatment tumor. f Pre- and post- treatment cancer cell fractions (CCFs) of inferred tumor subclones. The subclone containing the FBXW7 E111* mutation had post-treatment CCF of 0.94 but was not detected in the pre-treatment tumor (CCF 0). The size of each subclone cloud represents the uncertainty in the inferred subclone’s pre- and post-treatment CCFs. Patient 3—FCCC-022. g Clinical course demonstrating poor response to neoadjuvant chemotherapy, recurrence at 258 days and death at 614 days. h Phylogenetic analysis demonstrating a gain in PD-L1/2 in the resistant sample, and that the resistant clone arose out of a pre-existing clone. i Pre- and post- treatment CCFs of inferred tumor subclones, with pre-treatment CCF on the x-axis and post-treatment CCF on the y-axis. A subclone with CCF 0.09 in the pre-treatment sample had CCF 1.0 in the post-treatment sample. The size of each subclone cloud represents the uncertainty in the inferred subclone’s pre- and post-treatment CCFs