Could cfDNA Improve Gallbladder Cancer Diagnosis?

GALLBLADDER cancer (GBC) diagnosis could be enhanced by analysing circulating cell-free DNA (cfDNA), according to a proof-of-concept study that identified distinct fragmentomics features capable of distinguishing GBC from people with gallstones and healthy controls.

GBC is a rare but highly lethal biliary tract cancer that is often detected at an advanced stage because symptoms are non-specific and reliable non-invasive diagnostic biomarkers are lacking.

Researchers found that individuals with GBC had characteristic cfDNA alterations that differentiated them from non-cancer groups, highlighting the potential of blood-based sequencing approaches as a non-invasive diagnostic tool. The findings also suggested that archived plasma samples could be successfully used for cfDNA sequencing, potentially expanding opportunities for biomarker research.

Why Gallbladder Cancer Diagnosis Remains Challenging

Gallstones affect 10-20% of adults globally and as many as 30-40% of people in some South American countries, including Chile. Although gallstones are present in more than 90% of GBC cases in high-risk areas, fewer than 1% of individuals with gallstones develop gallbladder cancer.

Existing biomarkers, including carbohydrate antigen 19-9 and carcinoembryonic antigen, lack sufficient sensitivity for diagnostic use. Differentiating benign from malignant gallbladder disease using imaging alone remains challenging, particularly in the presence of chronic cholecystitis, xanthogranulomatous cholecystitis, and porcelain gallbladder. Together, these limitations have contributed to GBC often being diagnosed at a late stage, with a five-year survival rate of 19%.

cfDNA Fragmentomics Identified Distinct Cancer Signatures

Researchers analysed cfDNA extracted from archived plasma samples from 67 individuals enrolled in two case-control studies in China and Chile. Low-coverage whole-genome sequencing and computational analyses were then used to assess fragmentomics features and develop a classification model, with findings compared with external datasets from related hepatopancreatobiliary diseases.

Compared with healthy controls and individuals with gallstones, patients with GBC showed significant differences in fragment lengths, end motif patterns, estimated tumour fractions, detectable copy number alterations, and transcription factor binding site accessibility (p<0.05). Collectively, these features distinguished GBC from the combined non-cancer group with an AUC of 0.852. Many of the observed alterations were also consistent with tissue genomics data and findings from liver cancer, pancreatic cancer, and non-GBC biliary tract cancer.

Potential Clinical Role Requires Further Validation

The investigators concluded that cfDNA profiling captured biologically meaningful alterations consistent with tissue-based genomic findings, supporting its potential for biological characterisation and non-invasive gallbladder cancer diagnosis.

As a pilot study, the findings provide proof of concept rather than definitive clinical evidence. However, the results suggested that cfDNA fragmentomics could complement existing diagnostic approaches, support risk stratification and help guide clinical decision-making or optimise cholecystectomy waitlists in populations at high risk of GBC.

Reference

Daniels M et al. A pilot study of plasma cell-free DNA fragmentomics in gallbladder cancer. JHEP Rep. 2026;DOI:10.1016/j.jhepr.2026.101955.

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