Plasma Cell-Free DNA Methylation Analysis Is Highly Sensitive to Detecting Hepatocellular Carcinoma

Chen Kui, Li Zhihao, Kirsh BO. Plasma Cell-free DNA Methylomes for Hepatocellular Carcinoma Detection and Monitoring After Liver Resection or Transplantation. Ann Surg. December 2025.

This study evaluated a tumor-agnostic, plasma cell-free DNA (cfDNA) methylation–based approach (cfMeDIP-seq) for the detection of hepatocellular carcinoma (HCC) and for monitoring recurrence after curative-intent liver resection or transplantation. 

The investigators analyzed 236 cfDNA samples from 89 HCC patients and 35 healthy controls, applying machine-learning models to genome-wide methylation profiles to derive an HCC methylation score (HMS) reflecting the probability of tumor-derived cfDNA. In the discovery cohort, the classifier achieved 97% sensitivity and 99% specificity for HCC detection, with similarly high accuracy in an independent validation cohort. 

Importantly, assay performance was independent of conventional clinicopathologic variables, underlying liver disease etiology, cirrhosis status, or serum AFP levels, supporting its robustness as a tumor-agnostic diagnostic tool.

Beyond baseline detection, the study demonstrated the clinical utility of longitudinal HMS monitoring after surgery. Following resection or transplantation, HMS values declined markedly within the first postoperative months, consistent with clearance of tumor burden. Over time, HMS trajectories diverged between patients who developed recurrence and those who remained disease-free. Rising HMS levels were strongly associated with recurrence, often preceding radiographic or clinical diagnosis by several weeks. A baseline HMS greater than 0.9 was independently associated with a significantly increased risk of recurrence (hazard ratio 3.43), although longitudinal percentage changes in HMS appeared to be more informative than single baseline thresholds for postoperative surveillance.

Overall, the findings indicate that cfMeDIP-seq–based methylome profiling enables highly sensitive, noninvasive detection of HCC and an accurate biomarker of cell free DNA, now possible for HCC. By overcoming limitations of imaging, AFP, and tumor-informed genomic assays, this approach has potential to refine postoperative surveillance, guide earlier therapeutic intervention, and improve risk stratification in both resection and transplant populations. While larger prospective studies are needed for validation, the results support cfDNA methylation analysis as a promising adjunct in the clinical management of HCC.