To demonstrate that Decoil can resolve structurally distinct ecDNA elements with an overlapping genomic footprint, we generated 33 in silico mixtures, by pair-wise combination of three neuroblastoma cell lines at different ratios, namely, CHP212, STA-NB-10DM, and TR14, each containing a structurally distinct ecDNA element harboring a MYCN gene (see section “Evaluate amplicon's breakpoint recovery in ecDNA mixtures” in the Methods) (Fig. 3C,E). The gene discussed is MYCN; the disease is neuroblastoma.