The Illumina Infinium methylation assay for genome-wide methylation analyses

Abstract In this chapter, the author briefly covers the basic features of the HumanMethylation BeadChip array platform, such as its method of measuring DNA methylation, manufacturing arrays, and analyzing experimental data. The author subsequently introduces various recent large-scale DNA methylation studies in which the HumanMethylation BeadChip array platform has been used for methylome interrogation. Some of these illustrative studies have elucidated the molecular mechanisms underlying classical epigenetic phenomena (such as X chromosome inactivation and genomic imprinting) in humans, utilized DNA methylation profiles for disease diagnosis and subtype classification, or aimed to deepen our understanding of the implications of epigenetic variation among individuals in terms of traits and diseases. The author also discusses the next-generation sequencing-based approaches, which are increasingly being used in population epigenomic studies, and whether they are likely to supersede the array-based method soon.