Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences

Abstract

ABSTRACTExtrachromosomal circular DNA (eccDNA) of chromosomal origin is found in a range of eukaryotic species and cell type including cancer where eccDNA with oncogenes appear to drive tumorigenesis. Most studies of eccDNA employ short-read sequencing to identify for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA identification. An alternative is the long-read sequencing technologies that can potentially be used to construct complete eccDNA. We present a software suite, Construction-based Rolling-circle amplification for eccDNA Sequence Identification and Location (CReSIL) 2.0, to identify and characterize eccDNA from long-read sequences. CReSIL’s performance in the identification of eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL’s capability in many of the long-read sequencing datasets. This includes datasets enriched for eccDNA as well as whole genome datasets from many cells that contained large eccDNA. CReSIL suite software will be a versatile tool to deeply investigate eccDNA in biological samples.