Plasma cell-free DNA methylation markers for detection and prognosis of gastric cancer: A case-control study.

Objective: Plasma cell-free DNA (cfDNA) methylation has shown potential in the detection and prognostic testing of multiple cancers. Here, we comprehensively investigate the performance of cfDNA methylation for gastric cancer (GC) detection and prognosis. Methods: GC-specific differentially methylated regions (DMRs) were identified by sequencing 56 GC tissues and 59 normal adjacent tissues (NATs). We then performed targeted bisulfite sequencing of cfDNA from 294 GC and 446 non-gastric cancer (NGC) plasma samples, identifying 179 DMRs that overlapped with those in tissue samples. The efficacy of plasma cfDNA methylation markers for GC detection and prognosis was evaluated. Results: Based on the 179 DMRs overlapping with those in tissue samples, the random forest (RF) model using 28 DMRs achieved an area under the curve (AUC) of 0.998 in the training cohort, whereas further refinement to the top 6 DMRs resulted in an AUC of 0.985. Consistent results were obtained in the validation cohort (28 DMR AUC: 0.985; 6 DMR AUC: 0.988). Support vector machine (SVM) and logistic regression (LR) models also demonstrated robust performance. Additionally, an 11-DMR signature was developed for prognostic prediction, successfully identifying high-risk GC patients with significantly shorter overall survival. Conclusions: Our study highlights the potential utility of cfDNA methylation markers for both the detection and prognostication of GC.