Extended Data Fig. 2: Genomic features of primary IC subgroups.
From: Complex rearrangements fuel ER+ and HER2+ breast tumours
a) IC group-level copy number profile with SV burden overlay in DCIS. b) Fraction of genome altered by subgroup across pre-invasive, primary invasive and metastatic tumours. Boxplot represents median, 0.25 and 0.75 quantiles with whiskers at 1.5x interquartile range. c) Alteration burden in metastatic tumours split based on treatment prior to biopsy. The sample size is indicated at the top of each bar. d) Fraction genome altered, fraction LOH, and number of damaging SVs in IC10 and IC4ER- subtypes. e) Proportion of IC10 and IC4ER- tumours with alterations in genes involved in three key pathways: cell cycle, DNA damage response (DDR), and ubiquitination. f) Alteration burden distribution in metastatic samples across metastatic sites. The sample size for each group is at the top of each bar. g-h) Activity of each of the six rearrangement signatures across the IC subgroups (g) or the ER+ High-risk subtypes (h) in primary tumours. i) Copy number and SV profiles of primary (left) and metastatic (right) samples, each representative of either a TNBC -enriched, ER+ Typical -enriched, ER+ High/HER2 + -enriched, or mixed profile in the center of the Pareto front. j) Proportion that each complex SV event contributes to the total complex SV burden stratified by subgroup. DEL, deletion; LOH, loss-of-heterozygosity; FDR, false discovery rate; BFB, bridge-fusion breakage; CPXDM, complex double minute; DM, double minute; INVDUP, inverted-duplication; TIC, templated insertion chain; TRA, translocation.
