Fusion genes and abnormal methylation modifications are critical pathogenic factors in various cancers. Compared to gold-standard detection methods such as fluorescence in situ hybridization (FISH) and bisulfite sequencing, nanopore sequencing offers megabase-level read lengths and the ability to directly analyze DNA/RNA for structural variants and modification types. This technology holds broad application prospects in tumor molecular subtyping, prognosis assessment, treatment guidance, minimal residual disease detection, and clonal evolution monitoring.