Description: Extrachromosomal circular DNA (eccDNA) is evolving as a valuable biomarker while little is known about its presence in urine. Here we report the discovery and analysis of urinary cell free eccDNAs (ucf-eccDNA) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq. Millions of unique ucf-eccDNAs are identified and comprehensively characterized. The ucf-eccDNAs are GC rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of genomic distribution of ucf-eccDNAs shows that eccDNAs are found in all chromosomes but enriched in chromosomes 17, 19 and 20 with high density of protein-coding genes, CpG islands, SINE and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomolgy and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than healthy controls. Moreover, eccDNA with miRNA genes are highly enriched in the CKD ucf-eccDNA.

Data type: Raw sequence reads

Sample scope: Other

Relevance: Medical

Release date: 2022-03-16

Last updated: 2022-03-16

Data size: 241.46GB