Global Hypomethylation in Cell-free DNA Enables Non-invasive Colorectal Cancer Screening: Results from a Retrospective Validation Study

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. We developed Asima Rev, an electrical-impedance cfDNA assay that can differentiate healthy individuals from those with cancer by measuring cfDNA aggregation patterns associated with methylation state, enabling functional detection of genome-wide hypomethylation. In a cohort of 46 treatment-naive CRC patients and 33 controls, Asima Rev achieved 96% sensitivity and 94% specificity, with longitudinal monitoring in six patients fully concordant with clinical outcomes. Interrogation of 11 public methylation array datasets showed that whole array analyses underestimate global changes. However, restricting analyses to OpenSea regions, where cfDNA is enriched, 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 (gDNA), 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.