{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T02:47:22Z","timestamp":1791082042196,"version":"4.1.0"},"reference-count":25,"publisher":"Wiley","issue":"9","license":[{"start":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T00:00:00Z","timestamp":1774828800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T00:00:00Z","timestamp":1774828800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100022538","name":"Kinghorn Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100022538","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Clinical Laboratory Analysis"],"published-print":{"date-parts":[[2026,5]]},"abstract":"ABSTRACT<\/jats:title>\n \n Background<\/jats:title>\n Tissue\u2010specific cell\u2010free DNA (cfDNA) offers promise as a minimally invasive biomarker of organ injury. However, current methods for cfDNA tissue\u2010of\u2010origin analysis often depend on genome\u2010wide sequencing approaches, limiting their clinical scalability.<\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n We developed a streamlined workflow for translating publicly available DNA methylation datasets into PCR\u2010compatible biomarker assays, using kidney\u2010derived cfDNA as a model. DNA methylation microarray data were mined to identify kidney\u2010specific hypermethylated regions, and candidate biomarkers were screened in silico and experimentally. A digital PCR assay targeting a\n PAX2<\/jats:italic>\n \u2010associated DMR was evaluated for analytical performance and assessed in a small exploratory clinical cohort (healthy controls\n n<\/jats:italic>\n \u2009=\u20099; transplant recipients\n n<\/jats:italic>\n \u2009=\u20095 pre\u2010transplant,\n n<\/jats:italic>\n \u2009=\u20097 at 24\u2009h,\n n<\/jats:italic>\n \u2009=\u20092 at day 7).\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n The selected\n PAX2<\/jats:italic>\n methylation marker demonstrated high analytical specificity for kidney tissue and was not detected in healthy donor plasma or pre\u2010transplant samples. In contrast, the marker was robustly detected in post\u2010transplant plasma samples, consistent with acute kidney injury due to ischemia\u2013reperfusion.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n This proof\u2010of\u2010concept study outlines a scalable method for developing PCR\u2010based tissue\u2010specific cfDNA biomarkers. Our kidney\u2010specific assay demonstrates the potential for rapid, cost\u2010effective organ injury monitoring and could be adapted for other tissue types. This strategy may support future diagnostic applications in nephrology, oncology, and transplant medicine.<\/jats:p>\n <\/jats:sec>","DOI":"10.1002\/jcla.70210","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T12:01:48Z","timestamp":1774872108000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["From\n DNA<\/scp>\n Methylation Microarray to Digital\n PCR<\/scp>\n : A Stepwise Strategy for Tissue Specific\n cfDNA<\/scp>\n Biomarker Development"],"prefix":"10.1002","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3073-3593","authenticated-orcid":false,"given":"David H.","family":"Murray","sequence":"first","affiliation":[{"name":"Garvan Institute of Medical Research Darlinghurst New South Wales Australia"},{"name":"School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine University of Newcastle Callaghan New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicky","family":"Boulter","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research Darlinghurst New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanon","family":"Ranjit","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research Darlinghurst New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2456-9544","authenticated-orcid":false,"given":"Natasha M.","family":"Rogers","sequence":"additional","affiliation":[{"name":"Centre for Transplant and Renal Research Westmead Institute for Medical Research Westmead New South Wales Australia"},{"name":"Faculty of Medicine and Health University of Sydney Sydney New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Kummerfeld","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research Darlinghurst New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason P.","family":"Ross","sequence":"additional","affiliation":[{"name":"CSIRO Health & Biosecurity Westmead New South Wales Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodney J.","family":"Scott","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine University of Newcastle Callaghan New South Wales Australia"},{"name":"Priority Research Centre for Cancer Research, Innovation and Translation Hunter Medical Research Institute New Lambton New South Wales Australia"},{"name":"Division of Molecular Medicine, Pathology North John Hunter Hospital New Lambton New South Wales 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