eccDNA Atlas: a comprehensive resource of eccDNA catalog.

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology
• Cancer Research

Background:

• Extrachromosomal circular DNA (eccDNA) are crucial in tumorigenesis and immune responses, but data is fragmented.
• Existing whole-genome sequencing (WGS) data is underutilized for eccDNA identification.
• A centralized resource is needed for eccDNA analysis.

Purpose of the Study:

• To develop a user-friendly database, eccDNA Atlas, for integrated eccDNA analysis.
• To consolidate eccDNA information from diverse sources, including literature and WGS data.
• To provide comprehensive annotation and analysis tools for eccDNA research.

Main Methods:

• Manual curation of eccDNAs from scientific literature.
• Prediction of eccDNAs using AmpliconArchitect on WGS data.
• Development of a web-based portal for data browsing, searching, and analysis.

Main Results:

• eccDNA Atlas hosts 629,987 eccDNAs and 8,221 ecDNAs from literature, plus 1,105 predicted eccDNAs.
• Data covers 66 diseases, 57 tissues, and 319 cell lines.
• Includes detailed annotations and analysis utilities for oncogenes, enhancers, SNPs, and more.

Conclusions:

• eccDNA Atlas offers a high-quality, integrated resource for eccDNA research.
• The database facilitates exploration of eccDNA characteristics and functions.
• Serves as a vital tool for advancing eccDNA-related scientific investigations.