DNA methylation analysis of the SDC2, SEPT9 and VIM genes in fecal DNA for colorectal cancer diagnosis

Sep 21, 2026

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Background Colorectal cancer is among the most common cancers worldwide, and DNA methylation sites may provide a new gene signature for diagnosis. This study systematically identified a methylation gene panel for colorectal cancer diagnosis using both tissue and fecal samples. Methods 181 fecal and 50 tumor tissue samples from 83 patients and 98 healthy subjects were analyzed by quantitative bisulfite next-generation sequencing, with site screening and model construction/validation using separate datasets. Results Tissue cancer samples showed markedly higher methylation than fecal controls, and a 29-locus panel enabled strong logistic regression performance with high sensitivity and specificity. Conclusions Key methylation sites in feces support effective colorectal cancer diagnosis via a validated panel-based model.

LanguageEnglish

CategoryResearch & Report

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Reading Time28 min

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Abstract

Background

Methods

Results

Conclusions

Background

Clinical rationale for fecal DNA methylation

Liu et al. BMC Cancer (2024) 24:1205 [https://doi.org/10.1186/s12885-024-12990-4](https://doi.org/10.1186/s12885-024-12990-4) BMC Cancer RESEARCH Open Access DNA methylation analysis of the SDC2, SEPT9 and VIM genes in fecal DNA for colorectal cancer diagnosis Yue Liu1, Hongbo Ming1, Lizhi Xu1, Lizhen Li1, Qi Liu1, Jinyin Zhao1, Cundi Zhong2* and Hongzhi Li 1* Abstract Background Colorectal cancer is one of the most common cancers worldwide. DNA methylation sites may serve as a new gene signature for colorectal cancer diagnosis. The search for representative DNA methylation sites is urgently needed. This study aimed to systematically identify a methylation gene panel for colorectal cancer diagnosis via tissue and fecal samples. Methods A total of 181 fecal and 50 tumor tissue samples were collected. They were obtained from 83 colorectal cancer patients and 98 healthy subjects. These samples were evaluated for DNA methylation of 9 target genes via quantitative bisulfite next-generation sequencing. We employed the rank-sum test to screen the colorectal cancerspecific methylation sites in the tissue and fecal cohorts. A data model was subsequently constructed and validated via the dedicated validation dataset. Results Compared with the fecal and negative control samples, the colorectal cancer tissue samples presented significantly higher methylation rates for all the selected gene sites. The methylation rates of the tissue and preoperative fecal samples showed the same high and low rates at the same sites. After screening, a panel of 29 loci in the SDC2, SEPT9, and VIM genes proved to be reliable biomarkers for colorectal cancer diagnosis in fecal samples. Logistic regression models were then constructed and validated using this panel. The sensitivity of the model was 91.43%(95% CI = [89 . 69, 93 . 17]), the specificity was 100%(95% CI = [100,100]), and the AUC value is 99 . 31%(95% CI = [99,99 . 62]) . The diagnostic accuracy of the model for stage I and stage II colorectal cancer was 100%(11/11) and 91 . 3%(21/23), respectively. Overall, this study confirms that the gene locus panel and the model can be used to diagnose colorectal cancer effectively through feces. Conclusions Our study identified a set of key methylation sites for colorectal cancer diagnosis from fecal samples, highlighting the importance of using tissue and fecal samples to accurately assess DNA methylation levels to screen for methylation sites, and developing an effective diagnostic model for colorectal cancer. Keywords Colorectal cancer, Targeted sequencing, DNA methylation analysis, Logistic regression †Yue Liu and Hongbo Ming contributed equally to this work and should be considered co-first authors. *Correspondence: Cundi Zhong [zhongcundi@dmu.edu.cn](zhongcundi@dmu.edu.cn)[ ](zhongcundi@dmu.edu.cn)Hongzhi Li[lihzh@gentalker.com](lihzh@gentalker.com) Full list of author information is available at the end of the article © The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit [http://creativecommons.o

FAQs

What was the purpose of this study?

To systematically identify a methylation gene panel for colorectal cancer diagnosis using tissue and fecal samples, and to build and validate a diagnostic model based on the selected loci.

How were the samples collected and analyzed?

The study collected 181 fecal and 50 tumor tissue samples from 83 colorectal cancer patients and 98 healthy subjects, then measured DNA methylation of nine target genes using quantitative bisulfite next-generation sequencing.

What diagnostic performance did the final model achieve using the fecal panel?

A 29-locus panel produced a logistic regression model with high sensitivity (91.43%) and perfect specificity (100%), with an AUC value around 99.31%, and diagnostic accuracy for early stages reported as 100% for stage I and 91.3% for stage II.

Sep 21, 2026

Uploaded by Rowan