Enhanced cfDNA methylation profiling by detection and correction of jagged ends

Analysis of cell-free DNA (cfDNA) methylation can enable noninvasive disease detection by leveraging tissue-specific epigenetic differences between malignant and nonmalignant cells. However, such analyses can be confounded by the repair of jagged DNA fragment ends during double-stranded sequencing library preparation, which introduces spurious methylation signals into cfDNA molecules. Here we present JEEPERS, a framework to detect and correct jagged-end-induced methylation errors while preserving duplex integrity and native methylation patterns. We showed high fidelity for measuring tumor burden and demonstrated allele-specific methylation differences at recurrent somatic mutations, revealing a link between adjacent CpG methylation and EGFR/TP53 driver and resistance mutations. We further demonstrated enhanced diagnostic performance across liquid biopsy applications, including tumor-type-specific methylation profiles, hemimethylation profiling, epigenetic-clock-based age estimation and cell type deconvolution. By faithfully correcting end-repair errors, JEEPERS provides a versatile framework for integrating mutations and methylation features in cfDNA at high resolution, enabling more precise molecular profiling and disease monitoring. The computational tool JEEPERS detects and corrects jagged-end-induced errors in cell-free DNA methylation analysis, demonstrating improved performance in multiple applications, such as cancer detection and monitoring.