cfNOMe- A single assay for comprehensive epigenetic analyses of cell-free DNA

Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We presentcfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single assay using non-disruptive enzymatic cytosine conversion and a custom bioinformatic pipeline. We show that enzymatic cytosine conversion better preserves cfDNA fragmentation information than does bisulfite conversion. Whereas previously separate experiments were required to study either epigenetic marking,cfNOMedelivers reliable results for both, enabling more comprehensive and inexpensive epigenetic cfDNA profiling.cfNOMehas the potential to advance biomarker discovery and diagnostic usage in diseases with systemic perturbations of cfDNA composition.