A multi‐centre, prospective trial of a methylation‐based liquid biopsy for early detection of liver cancer in high‐risk populations

Abstract Background and aims Existing imaging and serum‐marker assays miss many early liver cancers, especially in high‐risk chronic liver disease carriers. We aimed to create a highly accurate, non‐invasive, methylation‐based liquid biopsy for early detection. Methods We used a comprehensive, multi‐platform, multi‐cohort strategy for marker discovery, starting with methylation profiling of hepatocellular carcinoma samples from TCGA and in‐house cohorts. From 30 initial candidates, nine highly liver‐specific methylation markers were shortlisted, and three optimal cfDNA markers (RNF135, CHFR, PAX5) were selected to develop a robust diagnostic model, tuned in a training set ( N = 280) and locked in an internal testing set ( N = 124). The model was then validated in a prospective, large‐scale trial conducted at four geographically distinct Chinese centres. Results The clinical trial included 1097 participants from two groups, (i) a diagnosing group ( N = 646) that prospectively enrolled individuals without prior diagnostic results and represented a real‐world high‐risk population, and (ii) a diagnosed group recruited after pathology confirmation. Overall, the model achieved 94.43% (95% confidence interval, 92.12–96.09%) sensitivity and 95.16% (92.78–96.78%) specificity for liver cancer, with stage‐I sensitivity of 93.10% (89.78–95.40%). Within the diagnosing group, overall sensitivity was 93.99% (91.28–95.90%), and for the 267 stage‐I cases, it reached 92.88% (89.15–95.39%). As for specificity, it remained high across confounders: 92.78% (85.84–96.46%) in cirrhosis, 91.74% (85.46–95.45%) in other‐cancer interference samples. Besides, the model outperformed the traditional liver cancer biomarker AFP and showed changes in methylation signals before and after surgery, suggesting a possible role in perioperative monitoring. Each centre independently reported sensitivities and specificities exceeding 90%, demonstrating robust geographic performance. Conclusions Using a systematic marker‐discovery pipeline and a multi‐centre prospective cohort, we developed a methylation‐based liquid biopsy that reliably detects early liver cancer in high‐risk populations. Clinical trial number Chictr.org identifier: ChiCTR2400092883. Key points Three cfDNA methylation markers, RNF135, CHFR and PAX5, were identified for liver cancer liquid biopsy. A three‐marker diagnostic model based on qMSP was established for highly accurate non‐invasive detection of liver cancer. The LC‐HMC model achieved 94.43% sensitivity and 95.16% specificity in the clinical trial. The model detected stage‐I liver cancer with a sensitivity of 93.10%.