{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE317nnn/GSE317007/"]},"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=GSE317007"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"FLARE: a Long-Read Nanopore Fragmentomics Pipeline Integrating Copy Number, Methylation, and End-Motif Analysis for Liquid Biopsy","description":"Cell-free DNA (cfDNA) fragmentation patterns encode biologically and clinically relevant information beyond fragment length, reflecting nuclease activity, chromatin organization, and tissue of origin. Fragmentomics has therefore emerged as a promising strategy to enhance circulating tumor DNA (ctDNA) detection, particularly in cancers with low tumor fractions. However, most existing approaches are optimized for short-read sequencing, limiting their applicability to third-generation platforms. Here, we present FLARE (Fragmentation and Long-read Analysis of Regulatory Epigenetics), an integrated and scalable fragmentomics pipeline specifically optimized for Oxford Nanopore long-read sequencing. FLARE preserves native cfDNA fragment ends and enables the simultaneous analysis of copy number alterations, tumor fraction estimation, methylation-derived signals, fragment length distributions, and 5′ end-motif profiles.","dates":{"publication":"2026/04/01"},"accession":"GSE317007","cross_references":{"GSM":["GSM9463741","GSM9463740","GSM9463732","GSM9463731","GSM9463742","GSM9463734","GSM9463733","GSM9463736","GSM9463735","GSM9463738","GSM9463737","GSM9463739"],"GPL":["26167"],"GSE":["317007"],"taxon":["Homo sapiens"],"PMID":["[41908150]"]}}