Extended Data Fig. 6: Elevated replication stress in TNBC, ER+ High-risk and HER2+ tumours.

a-b) Replication stress signature stratified by IC subgroup (left) or by histology within ER+ Typical-risk subgroup IDC and ILC (right) in the TCGA (a) and METABRIC (b) datasets. FDR adjusted p-values are reported. c-d) Replication stress signature stratified by IC subtypes in TCGA (c) and METABRIC (d) datasets. e) Pareto projection of METABRIC tumors, colored by replication stress. f) Replication stress signature in HER2+ tumors; IC1, IC6, and IC9 subtypes of ER+ High-risk; and TNBC IC10 stratified by presence of ecDNA. ER+ High IC2 was excluded due to lack of sample size (n = 2 for ecDNA+ IC2). g-h) cGAS/STING signature stratified by IC subgroup (left) or by histology within ER+ Typical-risk subgroup IDC and ILC (right) in the TCGA (g) and METABRIC (h) datasets. FDR adjusted p-values are reported. In a-d, effect sizes (ES) and FDR-adjusted p-values from Mann-Whitney Rank Sum test are shown. In f, ES and p-values from linear regression correcting for cohort are shown. Additionally, the amplicon copy number was corrected for amplicon-driven HER2+ and ER+ Typical tumors.