Journal Article

GUIDE: a prospective cohort study for blood-based early detection of gastrointestinal cancers using targeted DNA methylation and fragmentomics sequencing

Cheng, Jian-Wen, Zhou, Jian, Qi, Zhi-Peng, Li, Qing, Lu, Pin-Xiang, Wang, Wen-Quan, Yang, Xin-Rong, Liu, Rui, Zhang, Shi-Yu, Guo, Wei, Huang, Ao, Yan, Bin, He, Qi-Ye, Jin, Gang, Goel, Ajay, Guo, De-Zhen, Zhong, Yun-Shi, Fan, Jia, Xiong, Zhi-Guo, Liu, Liang, He, Meng-Jiang, Lin, Guo-Yong, Qiu, Shuang-Jian, Sun, Hui-Chuan, Su, Zhi-Xi, He, Dong-Li, Feng, Zhen, Li, Quan-Lin, Guo, Qi

2025

Overview

Background Gastrointestinal (GI) cancers are among the most prevalent and lethal malignancies worldwide. Early, non-invasive detection is essential for timely intervention and improved survival. To address this clinical need, we developed GutSeer, a blood-based assay combining DNA methylation and fragmentomics for multi-GI cancer detection. Methods Genome-wide methylome profiling identified 1,656 markers specific to five major GI cancers and their tissue origins. Based on these findings, we designed GutSeer, a targeted bisulfite sequencing panel, which was trained and validated using plasma samples from 1,057 cancer patients and 1,415 non-cancer controls. The locked model was blindly tested in an independent cohort of 846 participants, encompassing both inpatient and outpatient settings across five hospitals. Results In the validation cohort, GutSeer achieved an area under the curve (AUC) of 0.950 [95% Confidence Interval (CI): 0.937–0.962] for cancer detection, with 82.8% sensitivity (95% CI: 79.5–86.0) and 95.8% specificity (95% CI: 94.3–97.2). It detected 92.2% of colorectal, 75.5% of esophageal, 65.3% of gastric, 92.9% of liver, and 88.6% of pancreatic cancers. The independent test cohort included 198 early-stage cancers (stage I/II, 66.4%) and 63 advanced precancerous lesions. GutSeer maintained robust performance, with 81.5% sensitivity (95% CI: 77.1–85.9) for GI cancers and 94.4% specificity (95% CI: 92.4–96.5). It also demonstrated the ability to detect advanced precancerous lesions in the colorectum, esophagus, and stomach as a single, non-invasive blood test. Conclusions By integrating DNA methylation and fragmentomics into a compact panel, GutSeer outperformed genome-wide sequencing in both accuracy and clinical applicability. Its high sensitivity for early-stage GI cancers and practicality as a non-invasive assay highlights its potential to revolutionize early cancer detection and improve patient outcomes. Trial registration ClinicalTrials.gov identifier: NCT05431621.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Accuracy / Aged / Biomarkers, Tumor - genetics / Biomedical and Life Sciences / Biomedicine / Biopsy / Bisulfite / Blood / Cancer / Cancer Research / Cell-free DNA (cfDNA) / Cohort analysis / Diagnosis / DNA / DNA Methylation / DNA sequencing / Early Detection of Cancer - methods / Female / Fragmentomics / Gastrointestinal cancer / Gastrointestinal Neoplasms - blood / Gastrointestinal Neoplasms - diagnosis / Gastrointestinal Neoplasms - genetics / Genetic aspects / Genomes / Genomics / Humans / Invasiveness / Liver cancer / Male / Malignancy / Medical diagnosis / Methylation / Middle Aged / Multi-cancer early detection (MCED) / Multi-dimensional features / Oncology / Oncology, Experimental / Pancreatic cancer / Patients / Plasma / Prospective Studies / ROC Curve / Sequence Analysis, DNA - methods / Sulfites / Whole genome sequencing