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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Published on: April 4, 2016
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eccDNAdb: a database of extrachromosomal circular DNA profiles in human cancers
Li Peng1,2, Nan Zhou3,4, Chao-Yang Zhang5
1Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. pengli9@mail.sysu.edu.cn.
Oncogene
|April 7, 2022
Summary
Extrachromosomal circular DNA (eccDNA) is crucial in cancer. This study developed eccDNAdb, the first integrated database of eccDNAs, aiding cancer research and therapy development.
Area of Science:
- Genomics and Bioinformatics
- Cancer Research
- Molecular Biology
Background:
- Extrachromosomal circular DNA (eccDNA) elements are DNA molecules independent of chromosomes.
- eccDNA is prevalent in cancers and plays a role in oncogene amplification and tumor progression.
Purpose of the Study:
- To develop the first integrated database of eccDNAs (eccDNAdb).
- To analyze the role of eccDNAs in human cancers using integrated data.
Main Methods:
- Whole-genome sequencing (WGS) data from cancer samples were analyzed bioinformatically.
- eccDNAs were also collected through manual literature curation.
- Gene expression, clinical, and chromatin accessibility data were integrated into eccDNAdb.
Main Results:
- eccDNAdb contains 1270 eccDNAs from 480 samples across 42 cancer types.
- A total of 54,901 eccDNA-associated genes are annotated in the database.
- The database integrates WGS data from 3395 tumor samples across 57 cancer types.
Conclusions:
- eccDNAdb is the first comprehensive database for eccDNA research.
- It facilitates the study of eccDNA biological functions and clinical relevance in cancers.
- The database is freely accessible and expected to advance novel cancer therapies.
