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Neurodegenerative diseases such as Alzheimer’s disease (AD) are difficult to diagnose early, often resulting in irreversible brain damage before treatment begins. This study presents a novel diagnostic approach using neuron-derived cell-free DNA (cfDNA) in blood plasma as a minimally invasive biomarker for early disease detection. By analyzing Differential Methylation Regions (DMRs), researchers identified biomarkers that accurately distinguish neuronal cfDNA and achieved 100% identification of AD patients using a 5% detection threshold. The method also differentiated patients with mild cognitive impairment (MCI) who later progressed to AD, demonstrating strong prognostic potential. Compared to existing protein-based assays, this cfDNA approach offers greater accuracy, convenience, and promise for earlier diagnosis, monitoring, and personalized treatment of neurodegenerative diseases.