GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE342nnn/GSE342177/primary200OKMethylation profilingHomo sapiensMethylation profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE342177GEOGSEfalseREMODEL: A modular framework for longitudinal ctDNA methylation profiling reveals treatment response and relapse-associated epigenetic remodelingCirculating tumour DNA (ctDNA) methylation profiling is a promising non-invasive tool for disease monitoring, but longitudinal interpretation is limited by variable sequencing coverage and the loss of clinically relevant signals. We developed REMODEL (Recovery-based Epigenetic Monitoring of Dynamic methylation for Longitudinal analysis), an integrated framework combining coverage-aware binning, count-based longitudinal statistics, and a novel Epigenetic Recovery Score (ERS) to quantify post-treatment methylation recovery. Applied to 17 serial plasma samples from two T-cell lymphoma patients (2,025 genomic bins), REMODEL distinguished durable remission, characterized by coordinated demethylation (86.4% of bins) and sustained positive ERS, from relapse, marked by widespread hypermethylation (64.9% of bins) and persistently negative ERS despite clinical remission. By integrating dynamic methylation detection with recovery modelling, REMODEL provides an interpretable framework for longitudinal ctDNA methylation analysis and minimal residual disease monitoring.2026/08/06GSE342177GSM9924550GSM9924541GSM9924552GSM9924551GSM9924540GSM9924539GSM9924543GSM9924554GSM9924542GSM9924553GSM9924545GSM9924544GSM9924547GSM9924546GSM9924538GSM9924549GSM992454834284342177Homo sapiens