Pagano Lorenzo, Lagrotteria Davide, Facconi Alessandro, Saraceno Claudia, Longobardi Antonio, Bellini Sonia, Ingannato Assunta, Bagnoli Silvia, Ducci Tommaso, Mingrino Alessandra, Laganà Valentina, Paparazzo Ersilia, Borroni Barbara, Maletta Raffaele, Nacmias Benedetta, Montesanto Alberto, Ghidoni Roberta
Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy.
Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende, Italy.
Int J Mol Sci. 2025 Apr 28;26(9):4198. doi: 10.3390/ijms26094198.
DNA methylation is a critical epigenetic mechanism involved in numerous physiological processes. Alterations in DNA methylation patterns are associated with various brain disorders, including dementias such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). Investigating these alterations is essential for understanding the pathogenesis and progression of these disorders. Among the various methods for detecting DNA methylation, DNA sequencing is one of the most widely employed. Specifically, two main sequencing approaches are commonly used for DNA methylation analysis: bisulfite sequencing and single-molecule long-read sequencing. In this review, we compared the performances of CpG methylation detection obtained using two popular sequencing platforms, Illumina for bisulfite sequencing and Oxford Nanopore (ON) for long-read sequencing. Our comparison considers several factors, including accuracy, efficiency, genomic regions, costs, wet-lab protocols, and bioinformatics pipelines. We provide insights into the strengths and limitations of both methods with a particular focus on their application in research on AD and FTD.
DNA甲基化是一种关键的表观遗传机制，参与众多生理过程。DNA甲基化模式的改变与各种脑部疾病相关，包括痴呆症，如阿尔茨海默病（AD）和额颞叶痴呆（FTD）。研究这些改变对于理解这些疾病的发病机制和进展至关重要。在检测DNA甲基化的各种方法中，DNA测序是应用最广泛的方法之一。具体而言，两种主要的测序方法通常用于DNA甲基化分析：亚硫酸氢盐测序和单分子长读长测序。在本综述中，我们比较了使用两种流行的测序平台（用于亚硫酸氢盐测序的Illumina和用于长读长测序的牛津纳米孔（ON））进行CpG甲基化检测的性能。我们的比较考虑了几个因素，包括准确性、效率、基因组区域、成本、湿实验室方案和生物信息学流程。我们深入探讨了这两种方法的优缺点，特别关注它们在AD和FTD研究中的应用。
