Understanding ecDNA Pipelines
Higher category: 【Bioinformatics】 Bioinformatics Analysis Index
1. Overview
2. CoRAL
3. Decoil
1. Overview
⑴ In cells with ecDNA, nuclear staining may reveal small dot-like structures, often called “double minutes “ (DMs), distinct from the linear chromosomes.
⑵ ecDNA is circular → Continuous replication, Discordant edge
Figure 1. Form of ecDNA
① Long-read seq & FISH: ecDNA ⇔ Hi-C: DNA-DNA interaction
② Concordant edges connect consecutive sequences with respect to the reference genome order, and discordant edges connect nonconsecutive genome segments.
⑶ Different scenarios of ecDNA composition per sample.
① Singleton: presence of a single ecDNA structure
② Co-occurrence: presence of different ecDNA species, without overlapping
③ Heterogeneity: presence of different ecDNA species, with overlapping
Figure 2. Different scenarios of ecDNA composition
⑷ ecDNA reconstruction is challenging, as different co-occurring ecDNA elements have overlapping genomic foodprints, making it difficult to attribute the overlapping features to each of the different circular elements.
⑸ Existing methods
① Simple circular amplicons: Circle-Map, ecc_finder
② Complex ecDNA: AmpliconArchitect, AmpliconReconstructor, CReSIL
③ De novo assembler: Shasta
④ Heuristic strategies return multiple small cycles that can later be recombined.
Figure 3. ecDNA heuristic analysis method
⑹ ecDNA structures are complex rearrangements, and currently, no guidelines or gold-standard data sets exist to assess the quality and performance of the reconstructions.
2. CoRAL
3. Decoil
Input: 2026.02.27 01:52