Extended Data Figure 5. Prognostic impact of the CIN signature.

a, Volcano plot showing differentially expressed genes between CIN-high and CIN-low MDA-MB-231 cells. Red data points denote genes subsequently used for determining the CIN signature. b–e, Enrichment plots for all differentially expressed genes (a) or those on Chromosome 1 (d–e). Circos plot (c) showing genomic location (outer circle), log₂-fold expression of genes significantly differentially expressed in metastases compared to primary tumors (middle circles), and the log₁₀(p value, inner circle) for genomic amplifications (red) or deletions (blue) in metastases relative to primary tumors. n = 2 (CIN-low), 3 (CIN-high), 11 (primary tumors), 28 (metastases). Significance tested using two-sided Wald test (a), one-sided Weighted Smirnov-Kolmogorov test (b, d, e), and one-sided hypergeometric test (c) all corrected for multiple testing. f–g, DMFS of breast cancer patients stratified by lymph node status, grade, and receptor status, from a meta-analysis (f, n = 664 patients) or a validation cohort (g, n = 171 patients) divided based on their average expression of the CIN gene expression. Significance tested using two-sided log-rank test.