Extended Data Fig. 4: Cyclic amplifications preferentially amplify IC-specific oncogenes.

a) Proportion or number of samples with at least one cyclic or complex non-cyclic amplification in primary GEL tumours. b) Proportion or number of samples with at least one cyclic or complex non-cyclic amplification in HER2+ primary tumors stratified by ER positivity. c) Proportion or number of primary samples with at least one cyclic amplification according to JaBbA. d) Proportion of samples where AmpliconArchitect called a cyclic amplification but JaBbA called an alternative type of alteration. Colors indicate which alteration JaBbA called. e) Proportion of HER2+ primary tumours that harbor cyclic or linear amplification in ER+ High-risk-specific oncogenes (left), and the SV types (right). f) Proportion or number of samples with at least one cyclic or complex non-cyclic amplification in DCIS lesions. Left panel: DCIS cohort stratified by subgroup, right panel: DCIS cohort and additional samples from GEL stratified by sequencing method. g) Proportion of cyclic amplifications, stratified by subgroup, that amplify IC-specific or alternative oncogenes in primary tumours, both the discovery and replication (GEL) cohorts. The number of amplifications in each category are included on each bar. h) Number ecDNA involving more than one IC-specific oncogene. i) Number of oncogenes per megabase involved in ecDNA in each subgroup. Boxplot represents median, 0.25 and 0.75 quantiles with whiskers at 1.5x interquartile range. j) Ratio of oncogenes amplified on ecDNA compared vs. oncogenes in the IC-specific cytoband per megabase. k) Proportion of ER+ Typical-risk ecDNA that incorporate each oncogene. l) Proportion of each archetype in ER+ High-risk, ER+ Typical and ER+ Typical containing ecDNA tumours.