Illumina HumanMethylation BeadChip for Genome-Wide DNA Methylation Profiling: Advantages and Limitations

  • Kazuhiko Nakabayashi
Reference work entry


HumanMethylation BeadChip is an array platform for highly multiplexed measurement of DNA methylation at individual CpG locus in the human genome based on Illumina’s bead technology. It measures the DNA methylation level of individual CpG site by quantitative genotyping of C/T polymorphisms generated in bisulfite-converted and amplified genomic DNA. The current version, HumanMethylationEPIC, measures the DNA methylation level of >850,000 CpG sites, while the previous versions, HumanMethylation450 (HM450) and HumanMethylation27 (HM27), measured that of >480,000 and >27,000 CpG sites, respectively. HumanMethylation BeadChip requires only 4 days to produce methylome profiles of human samples using 250–500 ng of genomic DNA as a starting material. Because of its time and cost efficiency, high sample output, and overall quantitative accuracy and reproducibility, HM450 has become the most widely used means of large-scale methylation profiling of human samples in recent years. However, it is important to consider potential confounders originating in the technical limitations of HumanMethylation BeadChip such as cross-reactive probes, SNP-affected probes, within-array bias (Infinium I and II bias), and between-array bias (batch effects) especially when subtle methylation differences need to be detected by statistical tests between large numbers of cases and controls. Many integrated analysis packages have been developed by the epigenetics research community as computational solutions for technical and biological confounders associated with HumanMethylation BeadChip data. Considering the substantial increase of the coverage of regulatory regions along with the advantages inherited from HM450, EPIC is expected to maintain its popularity as a platform for epigenome-wide association studies for the foreseeable future.


DNA methylation Bisulfite conversion Methylome Infinium assay Array Epigenome-wide association study Genomic imprinting Data normalization Batch effects SNP genotyping 

List of Abbreviations






Dideoxynucleotide triphosphate




Epigenome-wide association study


Next-generation sequencing




Single-nucleotide polymorphism


Untranslated region


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© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Division of Developmental Genomics, Department of Maternal-Fetal BiologyNational Research Institute for Child Health and DevelopmentTokyoJapan

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