Analysis of the clinical application value of cfDNA methylation and fragmentation in early diagnosis of esophageal cancer

IF 3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Genomics Pub Date : 2025-04-04 DOI:10.1016/j.ygeno.2025.111034

Xin Liu , Chen Liang , Lingwen Ding , Qian Zhang , Yi Liu , Wei Wang

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Abstract

Background

This study explores the clinical value of cfDNA methylation and fragmentation for the early diagnosis of esophageal cancer using liquid biopsy.

Methods

Whole genome bisulfite sequencing and low-pass whole genome sequencing were utilized to detect cfDNA biomarkers, comparing 30 esophageal cancer patients with 10 healthy controls.

Results

Significant differences in cfDNA methylation and fragmentation were observed between cancerous and non-cancerous samples (p < 0.05). A volcano plot identified 822 differentially methylated markers (817 upregulated, 5 downregulated), with SOX17, SOX1, ZNF382, ZNF667-AS1, and TFPI2 highly associated with esophageal cancer. Fragmentation markers (EDM, FSD, FSR, TFBS, CNV) showed 95 % specificity and sensitivity, with EDM demonstrating the best performance.

Conclusion

Our study highlights the clinical potential of cfDNA methylation and fragmentation biomarkers for the early diagnosis of esophageal cancer.

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cfDNA甲基化和片段化在食管癌早期诊断中的临床应用价值分析

本研究探讨cfDNA甲基化和片段化在食管癌液体活检早期诊断中的临床价值。方法采用亚硫酸氢盐全基因组测序和低通全基因组测序检测30例食管癌患者和10例健康对照者的cfDNA生物标志物。结果癌组和非癌组cfDNA甲基化和片段化差异显著(p <；0.05)。火山图鉴定出822个差异甲基化标记（817个上调，5个下调），其中SOX17、SOX1、ZNF382、ZNF667-AS1和TFPI2与食管癌高度相关。碎片标记（EDM、FSD、FSR、TFBS、CNV）的特异性和敏感性均为95%，其中EDM表现最佳。结论本研究强调了cfDNA甲基化和片段化生物标志物在食管癌早期诊断中的临床潜力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genomics 生物-生物工程与应用微生物

CiteScore

9.60

自引率

2.30%

发文量

260

审稿时长

60 days

期刊介绍： Genomics is a forum for describing the development of genome-scale technologies and their application to all areas of biological investigation. As a journal that has evolved with the field that carries its name, Genomics focuses on the development and application of cutting-edge methods, addressing fundamental questions with potential interest to a wide audience. Our aim is to publish the highest quality research and to provide authors with rapid, fair and accurate review and publication of manuscripts falling within our scope.