End-repair causes methylation underestimation in cell-free DNA sequencing libraries
Abstract
Cell-free DNA methylation sequencing provides insight into tissue of origin and chromatin structure. In some workflows, generating libraries includes end-repair. Using matched single-stranded and double-stranded libraries prepared from the same cfDNA extracts, we show that end-repair in double-stranded DNA libraries reduces globally inferred CpG methylation leading to decreased tissue of origin accuracy. Trimming read termini partially mitigates this bias but decreases coverage and removes fragmentomic information compared to single-stranded DNA libraries, which forego end-repair.
Fields of Study & Subjects
Cancer Genomics and Diagnostics
Epigenetics and DNA Methylation
Genomic variations and chromosomal abnormalities
Publication details
- Journal / source
- The Journal of Liquid Biopsy
- Volume
- 11
- Pages
- 100455–100455
- Publication date
- 3 January 2026
- Language
- EN