diffMONT: predicting methylation-specific PCR biomarkers based on nanopore sequencing data for clinical application.

DNA methylation serves as a key biomarker in clinical diagnostics, especially in cancer detection. With methylation-specific PCR (MSP), a widely used approach, patient samples can be screened fast and efficiently for differential methylation. During MSP, methylated regions are selectively amplified with specific primers. With nanopore sequencing, knowledge about DNA methylation is generated during direct DNA sequencing without needing pretreatment of the DNA. Multiple methods, mainly developed for whole-genome bisulfite sequencing (WGBS) data, exist to predict differentially methylated regions (DMRs) in the genome. However, the predicted DMRs are often very large and not sufficiently discriminating to generate meaningful results in MSP, creating a gap between theoretical cancer marker research and practical application, as no tool currently provides methylation difference predictions tailored for PCR-based diagnostics.