Extended Data Fig. 1: IC subgroup distribution varies across stages of progression, ancestry and histology.

a) IC subgroup (left) and subtype (right) across stages of progression in ER+ samples. b) Inferred ancestry (primary samples, left or metastatic samples, right) across IC subgroups. c) IC subgroup (left) and subtype (right) across inferred ancestry in primary (top) and metastatic (bottom) stages. d) IC subgroup (left) and subtype (right) across inferred ancestry in primary (top) and metastatic (bottom) stages in ER+ samples. e) IC subtypes (left) and subgroups (right) across paired primary and metastatic samples with WES data. f) Graphical network representing primary/primary or primary/metastatic pairs; dots corresponding to a tumour biopsy colored by IC subgroup, the edge between two dots indicates whether the classification is stable (black) or changes (red) through metastasis. The surrounding color represents the PAM50 subtype (gray indicates missing data). g) IC subtype or subgroup consistency with PAM50 in pre-invasive DCIS (left), primary (middle), and metastatic (right) samples. h) ER early transcriptional signature according to subgroup. i) ER early signaling transcriptional signature in primary and metastatic tumours. j) Schematic overview of IC-specific amplification peaks and associated genes. ES, effect size. DCIS, ductal carcinoma in situ; LumA, luminal A; LumB, luminal B. The schematic in j was created with BioRender.com.