ECCsplorer: detection of extrachromosomal circular DNA (eccDNA) from NGS data
| Main Authors: | Mann, Ludwig, Seibt, Kathrin M., Weber, Beatrice, Schmidt, Thomas, Heitkam, Tony |
|---|---|
| Format: | Proceeding poster |
| Bahasa: | eng |
| Terbitan: |
, 2020
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/4017245 |
Daftar Isi:
- Extrachromosomal circular DNAs (eccDNAs) are ring-like DNA structures physically separated from the chromosomes. They have been reported in a broad range of eukaryotes ranging from around 100 bp to several mega base pairs in size. Most of their functions still remain unknown, however some are associated with stress, cancer or aging whilst certain carry gene copies or harbor repetitive DNAs. Here, we present the ECCsplorer, a bioinformatic pipeline to detect eccDNAs in any kind of organism or tissue using Next-generation sequencing (NGS). Amplified circular DNA serves as input for an easy and automated discovery of eccDNA candidates. The approach is based on two major procedures: Firstly, read mapping to the reference genome is followed by detection of exceptional read distributions including high coverage, discordant mapping and split reads. Secondly, we compare reference-free read clusters of the amplified eccDNA with control sample data determining specific enrichment. Both parts can be run separately or combined depending on the individual aim or data availability. To illustrate our approach we reanalyzed published Arabidopsis, and human eccDNA data. Observed eccDNA candidates can be further used in a wide field of investigations – from tracking of active transposable elements to therapy approaches in terms of cancer-related eccDNAs.