Extended Data Fig. 4: Chromosomal aberrations in TKI-resistant clones.

a, Copy number profiles of early and late resistant PC9 clones. b, Copy number changes in each sample are shown on scatter plots where the y-axis is the copy number in the sample, and the x-axis is the copy number in the parental sample it was derived from. Genomic copy number segments are shown for both the minor allele (blue) and major allele (red). Size of points corresponds to the size of the copy-number segments. Points along the diagonal represent genomic segments that did not change in copy number between the parental and derived sample. Points above and below the diagonal represent copy-number gains and losses, respectively, relative to the parental sample (Right panels, two-sided Mann Whitney test). c, Late-evolving PC9 clones have increased SVs compared with early resistant clones. SVs were determined relative to parental cells using dRanger and BreakPointer. d, Circos plots depicting APOBEC mutations, copy number changes, kataegis/omikli mutation clusters and intra/inter-chromosomal interactions in PC9 resistant clones (all relative to parental cells).