Nick repair step preserves cancer-relevant methylation signals in cell-free DNA libraries

Researchers have posted a preprint on bioRxiv describing cf-Cabernet, a modified library preparation workflow aimed at improving the accuracy of DNA methylation profiling from cell-free DNA (cfDNA). The protocol introduces a nick-repair step before standard end-repair, targeting a specific artefact in which DNA polymerases initiate synthesis from single-strand breaks and overwrite endogenous methylated cytosines with unmethylated nucleotides.

The authors argue this damage pattern is distinct from the well-characterised terminal jagged-end effect and disproportionately affects cfDNA and formalin-fixed, paraffin-embedded (FFPE) DNA — two sample types central to liquid biopsy and archival cancer research. Without correction, they say, affected reads systematically lose genuine methylation signal, potentially confounding analyses that rely on methylation patterns for cancer type classification or minimal residual disease detection.

The preprint reports that applying nick repair prior to end repair preserves endogenous methylation information across the affected positions. The work is relevant to researchers developing or benchmarking cfDNA methylation assays, and to those working on multi-cancer early-detection methods that use methylome signatures. As a preprint, the findings have not yet been peer-reviewed.