Fig. 1: ENiClust identifies the IC subtypes.

a, Schematic of the study design. BC, breast cancer; HTAN, Human Tumor Atlas Network; sWGS, shallow WGS; TCGA, The Cancer Genome Atlas; PCAWG, Pan-Cancer Analysis of Whole Genomes. b, Schematic of the ENiClust IC classifier. WES, whole-exome sequencing. c, Kaplan–Meier curves of distant relapse-free (DRF) survival of the ER⁺ typical-risk and ER⁺ high-risk classes detected by the four IC subtype classifiers. Shaded area represents 95% confidence interval. HR, hazard ratio. d, Difference in distant relapse-free survival probability (top) or delta in Cox proportional hazard ratio (bottom) between ER⁺ typical-risk and ER⁺ high-risk classes detected by the four different IC classifiers. Error bars represent the difference in 95% confidence intervals between ER⁺ typical-risk and ER⁺ high-risk in each model. e, Differential pattern of relapse across the ICs, illustrated by the cumulative (black) and annual (red) risk of relapse over time. f, IC subgroup (left) and subtype (right) distributions across disease stages. P, primary; M, metastatic. The schematics in a,b were created with BioRender.com.