Nanopore sequencing has emerged as a transformative tool in the study of central nervous system (CNS) disorders, offering unique advantages in analyzing complex genomic regions and epigenetic modifications. One significant application is highlighted in the study by Chybowska, which utilizes Oxford Nanopore sequencing to extend a blood- and brain-based epigenome-wide association study (EWAS) of smoking. The research involved a large cohort of 46 individuals, analyzing approximately 4-21 million sites to develop 'mCigarette', an epigenetic biomarker for smoking. This study underscores the potential of nanopore sequencing in providing deeper insights into the epigenetic landscape associated with lifestyle factors and their impact on CNS health (ref: Chybowska doi.org/10.1038/s41467-025-58357-6/). Furthermore, the study's methodology, which integrates both conventional Illumina EPIC array data and long-read sequencing, demonstrates the robustness of nanopore technology in validating findings across different platforms, enhancing the reliability of the results. In another pivotal study, Chelban investigated the role of FGF14 GAA repeat expansions in multiple system atrophy, employing long-read Oxford Nanopore sequencing to confirm the presence and size of repeat expansions. This research revealed a high concordance (Pearson's r = 0.99, P < 0.0001) between the results obtained from nanopore sequencing and traditional PCR methods, highlighting the accuracy and efficiency of nanopore technology in genetic diagnostics. The findings suggest that these repeat expansions may significantly impact disease progression and survival, indicating a critical area for further research in the genetic underpinnings of CNS disorders. The integration of nanopore sequencing in both studies illustrates its versatility and potential to uncover novel biomarkers and genetic variations that could inform therapeutic strategies in CNS diseases.