{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE328nnn/GSE328835/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Other"],"species":["Homo sapiens"],"gds_type":["Other"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE328835"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Identification of a G-quadruplex-forming cell-free DNA fragment as a biomarker for the precise diagnosis of hepatocellular carcinoma[cfDNA]","description":"Early detection of hepatocellular carcinoma (HCC) remains challenging, as the currently recommended surveillance strategy based on ultrasound combined with alpha-fetoprotein (AFP) is limited by suboptimal sensitivity and accessibility. Cell-free DNA (cfDNA) provides a minimally invasive avenue for cancer detection. However, most existing cfDNA-based approaches either perform unreliably in low-input samples or require analytically complex workflows. Here, we systematically profiled serum cfDNA from individuals with HCC and without HCC and identified a high-abundance tumor-associated single cfDNA fragment at the FAM230F genomic region. Integrative analysis of liver assay for transposase-accessible chromatin with sequencing (ATAC-seq) revealed consistent tumor-specific chromatin accessibility at this locus, suggesting a tumor-derived origin. Structural characterization further demonstrated enrichment of G-quadruplex (G4) features within the target sequence, which may increase resistance to serum nuclease degradation and promote its preferential retention in circulation. Based on these properties, we established a qPCR-based detection workflow with clinical accessibility. In a validation cohort independent of the discovery cohort, a ΔCt cutoff of 2 was selected by maximizing the Youden index within the same cohort. The assay showed a sensitivity of 94.5% and a specificity of 90.5% for distinguishing HCC from non-HCC. Collectively, our study identifies FAM230F as a structurally stable tumor-associated cfDNA fragment and establishes a simple and scalable qPCR-based assay for HCC detection, providing a practical framework for translating cfDNA fragment analysis into clinical biomarkers.","dates":{"publication":"2026/09/09"},"accession":"GSE328835","cross_references":{"GSM":["GSM9690536","GSM9690535","GSM9690534","GSM9690533","GSM9690539","GSM9690538","GSM9690537","GSM9690543","GSM9690542","GSM9690541","GSM9690540","GSM9690525","GSM9690524","GSM9690523","GSM9690522","GSM9690529","GSM9690528","GSM9690527","GSM9690526","GSM9690532","GSM9690531","GSM9690530","GSM9690519","GSM9690514","GSM9690513","GSM9690512","GSM9690555","GSM9690511","GSM9690518","GSM9690517","GSM9690516","GSM9690515","GSM9690521","GSM9690520","GSM9690509","GSM9690508","GSM9690547","GSM9690503","GSM9690502","GSM9690546","GSM9690501","GSM9690545","GSM9690544","GSM9690500","GSM9690507","GSM9690506","GSM9690505","GSM9690549","GSM9690504","GSM9690548","GSM9690550","GSM9690510","GSM9690554","GSM9690553","GSM9690552","GSM9690551"],"GPL":["24676"],"GSE":["328835"],"taxon":["Homo sapiens"],"PMID":["[42729963]"]}}