Extended Data Fig. 9: Genetic mechanisms of immune escape in IC subgroups.

a) Proportion of primary and metastatic samples in each ER+ High-risk subtype with genetic immune escape (GIE) alterations, where values correspond to the number of pathways altered (left). Proportion of samples with alterations in each pathway stratified by IC subtype and disease stage (right). b) Proportion of primary ER+ High-risk samples with co-amplification of IDO1 with FGFR1 or ZNF703 by IC subgroup. c) Proportion of IC6 tumours with immune enriched (IE or IE/F) or immune depleted (D or F) TME subtypes stratified by the co-amplification of IDO1 with FGFR1 or ZNF703 in METABRIC and TCGA. d) Proportion of ER+ Typical IDC and ILC with GIE (left). Odds ratio and p-value from Fisher’s exact test. Proportion of pathways altered in IDC and ILC with GIE (right). e) Number of alteration in immune escape pathways for primary and metastatic samples, normalized by number of samples with alterations. f) Odds ratio for the frequency of GIE pathway alterations, comparing metastatic to primary samples. Background shading indicates FDR adjusted p-values (Fisher’s exact test). The color of the dot represents the direction and magnitude of the odds ratio while the dot size indicates the number of samples with a GIE in each pathway (y-axis). LOH, loss-of-heterozygosity.