ArticleComputational and structural biotechnology journal2026
Global Hypomethylation in Cell-Free DNA Enables Noninvasive Colorectal Cancer Screening: Results from a Retrospective Validation Study.
Article in Computational and structural biotechnology journal, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Global DNA hypomethylation is a defining hallmark of colorectal cancer (CRC) but is poorly captured by existing cell-free DNA (cfDNA) technologies, which typically interrogate only a fraction of CpG sites and are biased toward CpG islands. Asima Rev is a rapid, label-free, whole-genome electrical impedance cfDNA assay previously characterized across 216 clinical samples spanning 15 cancer types, from which a diagnostic threshold was established. The assay differentiates healthy individuals from those with cancer by measuring cfDNA aggregation patterns associated with methylation state, enabling functional detection of genome-wide hypomethylation. In this study, this prespecified threshold (adjusted to the present electrode geometry via cell constant normalization) is applied without modification to an independently collected cohort of 46 treatment-naïve patients with CRC and 33 controls, constituting a disease-specific retrospective validation of the assay. Only 4 samples overlapped between the 2 cohorts; all remaining samples were independently collected, processed, and analyzed. Asima Rev achieved 95.65% sensitivity (95% confidence interval, 85.47% to 99.23%) and 93.94% specificity (95% confidence interval, 80.39% to 98.92%), with longitudinal monitoring in 6 patients fully concordant with clinical outcomes. Interrogation of 11 public methylation array datasets showed that whole-array analyses underestimate global changes. Restricting analyses to OpenSea regions, where cfDNA is enriched, however, revealed patterns consistent with Asima Rev and a significant 5.8% global hypomethylation in CRC tissue compared to adjacent normal tissue. Hypomethylation was not observed in immune cell genomic DNA, a major contributor to cfDNA, supporting a predominantly tumor-derived contribution to the observed cfDNA signal. Together, these results demonstrate that Asima Rev captures a cfDNA signal consistent with true global methylation loss and outperforms locus-specific assays by measuring structural consequences of pan-genomic epigenetic alterations.
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