Plasma extrachromosomal circular DNA as a potential diagnostic biomarker for nodular thyroid disease

• Published in: Clinical and translational medicine Vol. 14; no. 6; pp. e1740 - n/a
• Main Authors: Zhou, Meng, Lv, Wei, Han, Peng, Sun, Kai, Hao, Ziqian, Gao, Ling, Xu, Yunyun, Xu, Zhe, Shao, Shanshan, Ma, Shizhan, Guo, Qingling, Zhang, Haiqing, Liu, Ke, Yang, Fan, Yuan, Zhongshang, Wu, Guojun, Yu, Changbin, Luo, Yonglun, Yao, Zhenyu, Zhao, Jiajun
• Format: Journal Article
• Language: English
• Published: Heidelberg John Wiley & Sons, Inc 01.06.2024; John Wiley and Sons Inc; Wiley
• Subjects: Biomarkers; Genes; Genomes; Letter to the Journal; Machine learning; Plasma; R&D; Research & development; Sample size; Thyroid cancer; Thyroid diseases
• ISSN: 2001-1326; 2001-1326
• DOI: 10.1002/ctm2.1740

The plasma eccDNA analysis in the PTC group showed longer fragments and higher Guanine-Cytosine (GC) content, with most eccDNA populations under 1000 bases, peaking at around 202 and 338 bases, a preference for high GC content areas in eccDNA formation (Figure S3A–C). To understand the distribution of eccDNA genomic locations in PTC patients, we aligned eccDNA sequences with the human genome and identified 450 gene-containing eccDNA (eccGenes) that were significantly prevalent in the PTC group (Figure S4A). Principal component analysis (PCA) highlighted distinct eccDNA gene region diversity associated with PTC (Figure 1G). By comparing 71 eccDNA locations identified in this study with the gene annotations of the human genome GRCh38.p13 in Ensembl (version 108), we found 18 locations showed no overlap with any known genes, while the remaining 53 locations overlapped with 71 known genes (Figure 4A and Table S2).