Circulating Cell-Free DNA as a Liquid Biopsy Biomarker for Early Detection of Hepatocellular Carcinoma in Chronic Hepatitis B Patients in South West Nigeria

Hepatocellular carcinoma arising from chronic hepatitis B infection carries a dismal prognosis in Nigeria due to late-stage presentation, and liquid biopsy using circulating cell-free DNA offers a potentially transformative early detection strategy. This study investigates circulating cell-free DNA quantity, fragmentation patterns, and methylation-based tissue-of-origin signatures as liquid biopsy biomarkers for early hepatocellular carcinoma detection in chronic HBV patients in Oyo, Osun, and Ondo States, South West Nigeria. A prospective case-control design was employed, recruiting 80 HCC patients at diagnosis, 80 chronic HBV patients without HCC, and 60 healthy controls. Plasma cfDNA was extracted and quantified by droplet digital PCR. Fragment size profiling was performed by paired-end sequencing, exploiting nucleosomal positioning differences between HCC and non-tumour derived cfDNA. Tissue-of-origin deconvolution used a 3000-CpG tissue methylation reference atlas to estimate hepatocyte-derived cfDNA fractions. Serum alpha-fetoprotein and des-gamma-carboxyprothrombin were measured as conventional comparators. Clinical diagnostic performance of cfDNA markers versus AFP was compared by ROC analysis. This study generates original evidence for cfDNA liquid biopsy in HCC within a chronic HBV-burdened West African population and proposes a novel methylation biomarker panel. Keywords: circulating cell-free DNA, liquid biopsy, hepatocellular carcinoma, hepatitis B, South West Nigeria.