#34 · Epigenomics

Jagged-end correction for cfDNA methylation profiling preserves duplex integrity

The dominant thread is methylation-informed analysis of cell-free DNA, where correction of technical error is treated as a prerequisite for biological interpretation. JEEPERS detects and corrects jagged-end-induced methylation errors in cfDNA sequencing while preserving duplex integrity, enabling joint mutation-methylation analysis. What is new here is explicit error correction at the sequencing level. Adjacent items extend methylation resources in complementary directions: CellMethMarker provides 347,514 de novo and 2.2M literature-derived cell- and tissue-type markers for deconvolution, a genome-wide DNA methylation framework reports a harmonized compendium of over 90 tissues and cell types alongside Wreath for variant effect prediction, and XenoMix quantifies mouse DNA contamination in PDX methylation microarray data via human-mouse sequence homology. FiberBrowser and FiberHMM convert single-molecule footprinting data into per-molecule chromatin states, a related single-molecule theme rather than cfDNA methylation itself.