biostudies-literatureUnknown13(1)Velut YThe standard of care for the follow-up of kidney allograft recipients combines non-invasive but non-specific biomarkers and kidney biopsies for the gold standard histology-based diagnosis, limited by the sampling bias, haemorrhagic risk, and low cost-effectiveness. We hypothesized that a targeted epigenetic analysis of cell-free DNA (cfDNA) would combine non-invasiveness and specificity for the diagnosis of kidney allograft rejection. We developed an in silico pipeline to identify 9 specific methylation signatures of epithelial or endothelial cell types in glomerular and tubular kidney compartments. Methylation-specific digital Polymerase Chain Reaction (dPCR) were designed and validated for these markers and combined in a 10-plex dPCR. In a retrospective cohort of 170 plasma cfDNA from adBiomarker research118https://www.ebi.ac.uk/biostudies/studies/S-EPMC12465476biostudies-literatureEpigenetic signatures on plasma cell-free DNA to detect kidney allograft rejection in a non-invasive way: development of a 10-plex digital PCR assay.PMC12465476Heneine JChoukroun GBersez TRabant MFerlicot SAnglicheau DSnanoudj RVuiblet VGnanalingam SVerkarre Vde Nattes TParier BBuob DVelut YMaujean CBoyer PPoulet GMoniot CGalichon PAudenet FfalseEpigenetic signatures on plasma cell-free DNA to detect kidney allograft rejection in a non-invasive way: development of a 10-plex digital PCR assay.The standard of care for the follow-up of kidney allograft recipients combines non-invasive but non-specific biomarkers and kidney biopsies for the gold standard histology-based diagnosis, limited by the sampling bias, haemorrhagic risk, and low cost-effectiveness. We hypothesized that a targeted epigenetic analysis of cell-free DNA (cfDNA) would combine non-invasiveness and specificity for the diagnosis of kidney allograft rejection. We developed an in silico pipeline to identify 9 specific methylation signatures of epithelial or endothelial cell types in glomerular and tubular kidney compartments. Methylation-specific digital Polymerase Chain Reaction (dPCR) were designed and validated for these markers and combined in a 10-plex dPCR. In a retrospective cohort of 170 plasma cfDNA from ad2025-01-01T00:00:00Z2025 Sep2026-07-15T06:48:48.996Z2026-06-30T03:23:39.082ZS-EPMC124654764101385510.1186/s40364-025-00834-7