What should I consider when choosing a suitable method for DNA methylation analysis?

The primary consideration when selecting a DNA methylation analysis method is ensuring it provides an unbiased solution to the research question. Another consideration is the research goals. For example, if the goal is to discover new epigenetic changes across the genome, a whole-genome bisulfite sequencing (WGBS) approach might be appropriate. The availability of bioinformatics software for data analysis is also essential. Cost is another consideration when selecting a DNA methylation analysis method. Methylation-sensitive high-resolution melting (MS-HRM) is more cost-effective compared to WGBS. Additionally, depending on the experiment, different levels of sensitivity and specificity may be required. Some methods, like quantitative real-time PCR (qPCR) or digital PCR (dPCR), offer high sensitivity but may lack specificity. Another consideration is certain DNA methylation analysis methods may require specialized equipment and reagents. The quality and quantity of DNA extracted from samples play a crucial role in determining the appropriate method. For instance, DNA obtained from Formalin-Fixed Paraffin-Embedded (FFPE) tissues may be degraded and require specialized techniques.