Comparative analysis of methodologies for detecting extrachromosomal circular DNA.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Extrachromosomal circular DNA (eccDNA) plays a key role in cancer development, influencing oncogene amplification, gene transcription, and tumor heterogeneity.
• Numerous computational pipelines and experimental techniques exist for eccDNA identification, but their comparative performance remains unevaluated.

Purpose of the Study:

• To systematically evaluate the detection efficiency and performance of various bioinformatics pipelines and experimental methods for identifying eccDNA.
• To provide guidance for researchers selecting optimal tools for eccDNA analysis.

Main Methods:

• Performance assessment of 7 short-read and long-read eccDNA analysis pipelines using simulated datasets, focusing on accuracy, identity, duplication rates, and computational demands.
• Comparative analysis of 7 experimental methods for eccDNA detection using 21 real sequencing datasets.

Main Results:

• Circle-Map and Circle_finder (bwa-mem-samblaster) demonstrated superior performance among short-read pipelines, though Circle_finder exhibited redundancy.
• CReSIL emerged as the most effective pipeline for long-read eccDNA detection at sequencing depths >10X.
• Long-read sequencing with Circle-Seq proved highly efficient for detecting copy number-amplified eccDNA longer than 10 kb.

Conclusions:

• The study highlights the strengths and weaknesses of different eccDNA detection methodologies.
• Findings offer crucial insights for researchers to select appropriate bioinformatics and experimental approaches for their specific eccDNA research needs.