Fig. 3: Cyclic amplifications are early mutational processes in ER⁺ high-risk and HER2⁺ breast tumours.

a, Proportion (top) and number (bottom) of samples with at least one cyclic or complex non-cyclic amplification in primary or metastatic tumours. b, The density of SNVs occurring before amplification in primary (top) and metastatic (bottom) tumours. Boxplot represents median, 0.25 and 0.75 quantiles with whiskers at 1.5× the interquartile range. c, Illustration showing copy number (CN) and SVs linking together disjoint segments in ecDNA (top), ratio of read depth in the tumor versus normal sample (middle) and location of oncogenes in ecDNA (bottom) in a representative primary IC2 tumour. d, Ratio of sequencing coverage in digested versus parental UCD65 (IC2) cell line in the predicted ecDNA region (dashed red line) compared to 1,000 null regions. e, Proportion of tumours within each IC subtype that harbour cyclic, complex non-cyclic or linear amplification in IC-specific oncogenes. f, Schematic for the genesis of cyclic amplifications. TC-NER, transcription-coupled nucleotide-excision repair. g, The density of ER-induced R-loops in cyclic versus complex non-cyclic amplifications. h, The percentage of breakpoints that overlap ER-induced R-loops with (+) or without (−) E2 treatment. Error bars represent the standard deviation across three replicates. i, The distance of each oncogene to the nearest ER-induced R-loop. The schematic in f was created with BioRender.com.