ArticleJournal of clinical laboratory analysis2026
From DNA Methylation Microarray to Digital PCR: A Stepwise Strategy for Tissue Specific cfDNA Biomarker Development.
Article in Journal of clinical laboratory analysis, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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7 authors.
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Abstract
backgroundTissue-specific cell-free DNA (cfDNA) offers promise as a minimally invasive biomarker of organ injury. However, current methods for cfDNA tissue-of-origin analysis often depend on genome-wide sequencing approaches, limiting their clinical scalability.
methodsWe developed a streamlined workflow for translating publicly available DNA methylation datasets into PCR-compatible biomarker assays, using kidney-derived cfDNA as a model. DNA methylation microarray data were mined to identify kidney-specific hypermethylated regions, and candidate biomarkers were screened in silico and experimentally. A digital PCR assay targeting a PAX2-associated DMR was evaluated for analytical performance and assessed in a small exploratory clinical cohort (healthy controls n = 9; transplant recipients n = 5 pre-transplant, n = 7 at 24 h, n = 2 at day 7).
resultsThe selected PAX2 methylation marker demonstrated high analytical specificity for kidney tissue and was not detected in healthy donor plasma or pre-transplant samples. In contrast, the marker was robustly detected in post-transplant plasma samples, consistent with acute kidney injury due to ischemia-reperfusion.
conclusionThis proof-of-concept study outlines a scalable method for developing PCR-based tissue-specific cfDNA biomarkers. Our kidney-specific assay demonstrates the potential for rapid, cost-effective organ injury monitoring and could be adapted for other tissue types. This strategy may support future diagnostic applications in nephrology, oncology, and transplant medicine.
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