Fig. 2

Structural variant (SV) view of AmpliconArchitect (AA) reconstructions. The SV View of reconstructed amplicon structures shows a simple cycles; b heterogeneity with amplicons containing Epidermal Growth Factor Receptor (EGFR) VIII deletion, as well as the intact EGFR; and c SV view and Cycle view of the complex medulloblastoma multi-chromosomal amplification. d A model for extrachromosomal DNA (ecDNA)-mediated focal amplification. e AA amplified intervals compared against 12,162 amplified TCGA intervals shows significant overlap. The interval sizes (mean 1.74 Mb) and copy numbers (mean 3.16 copies) are exponentially distributed, with no clear distinction between homogenously staining region (HSR) and ecDNA amplicons (Supplementary Data 4). f Amplicons containing multiple genomic regions from the same chromosome (MultiCluster) or multiple chromosomes (MultiChrom) are significantly larger in size (p-value < 0.016, Wilcoxon Rank-Sum test) than amplicons containing intervals from a single chromosomal region (Clustered). However, the size distribution of individual intervals in clustered amplicons is similar to the size distribution of intervals in MultiChrom or MultiCluster amplicons (Supplementary Data 4). g Heatmap of negative log p-values (Bonferroni-corrected Poisson Binomial) showing enrichment of 59 oncogenes in amplifications in 33 cancer types. Source data are provided in a Source Data file