Multi-cancer early detection via a DNA methylation multiplex ddPCR-based blood test

Abstract

Early cancer detection through minimally invasive methods is key for improving patient outcomes. We aimed to assess the performance of a novel blood-based test leveraging DNA methylation patterns for simultaneous detection of lung (LC), breast (BrC), colorectal (CRC), and prostate (PCa) cancer. Using The Cancer Genome Atlas (TCGA) methylation data, we identified shared hypermethylated gene promoters (ADCY4, MIR129-2, NID2, and MAGI2) among those four cancers. Validation was performed using online datasets, an in-house tissue set (N = 179), and plasma samples (N = 485) using droplet digital PCR (ddPCR). The test showed sensitivities of 81.82% (lung), 45% (breast), 69.23% (colorectal), and 44.14% (prostate), with 91.04% specificity. Overall, the PanCancer panel achieved 60.1% sensitivity and 87.4% specificity in detecting these four cancers. In early-stage cancers, sensitivities were slightly lower but followed a similar trend. Additionally, the test detected nine other cancer types in plasma. This proof-of-concept study demonstrates the feasibility of a single methylation-targeted blood test for multi-cancer detection, offering potential as an affordable and scalable screening tool for early cancer detection.

Keywords: DNA methylation; epigenetics; liquid biopsy; multi‐cancer detection; screening.