Extended Data Fig. 5: Characterization of chromosome and gene-level copy number alterations in LUAD tumors that developed BM within 5 years compared to LUAD that did not develop BM within 5 years of follow-up.

a, GISTIC analysis results with significantly amplified (red) and deleted (blue) chromosome regions depicted as peaks extending beyond the green significance cutoff (q < 0.25). b, Heatmap comparing gene-level copy number data between LUAD with and without 5-year BMs along with associated mean difference (yes vs. no BM) and Wilcoxon’s rank sum test p-values. c, Chromosome-level and gene-level CN alterations as genomic correlates of nomogram risk scores (prognostic in univariable Cox proportional hazards models but not independent of nomogram scores in multivariable analyses). Correlates of increased BM risk include amplifications of EGFR, 8q23.2, MCL1, MYC, MDM2, CCND1, and FGFR3 as well as deletions of ACTG2. Correlates of a lower BM risk were BLM and 21q21.2 deletions. *Multivariable models include each amplification or deletion together with nomogram risk scores.