Methylation Data Analysis and Interpretation

DNA methylation, a covalent modification, fundamentally shapes mammalian gene regulation and cellular identity. This review examines methylation's biochemical underpinnings, genomic distribution patterns, and analytical approaches. We highlight three distinctive aspects that separate methylation from other epigenetic marks: its remarkable stability as a silencing mechanism, its capacity to maintain distinct states independently of DNA sequence, and its effectiveness as a quantitative trait linking genotype to disease risk. We also explore the phenomenon of methylation clocks and their biological significance. The review addresses technical considerations across major assay types—both array-based technologies and sequencing approaches—with emphasis on data normalization, quality control, cell proportion inference, and the specialized statistical models required for next-generation sequencing analysis.