Methylation Array Analysis
Introduction to Methylation Array Analysis
Methylation arrays enable quantitative interrogation of selected methylation sites across the genome, offering high-throughput capabilities that minimize the cost per sample. Array-based methylation studies can provide valuable insights into the regulation of gene expression. DNA methylation allows cells to suppress expression of viral and nonhost DNA elements, and facilitates response to environmental stimuli. Aberrant DNA methylation (hyper- or hypomethylation) and its impact on gene expression have been implicated in many biological processes and diseases.
Advantages of Methylation Arrays
Methylation microarrays combine comprehensive coverage and high-throughput capabilities. Advantages include:
- Comprehensive genome-wide coverage of content categories requested by methylation experts such as:
- CpG islands
- Non-CpG and differentially methylated sites
- Enhancers
- Open chromatin
- Transcription factor binding sites
- miRNA promoter regions
- Assay reproducibility
- > 98% reproducibility between technical replicates for all Illumina Infinium methylation arrays
- User-friendly, streamlined workflow and simple analysis
- Many methylation arrays are validated for use with FFPE samples
Illumina Methylation Arrays
The Infinium Methylation Assay allows you to interrogate CpG sites at single-nucleotide resolution, providing highly robust measurements of DNA methylation. Choose from one of our curated genome-wide arrays, or design your own microarray for targeted applications.
MethylationEPIC v2.0
This array is ideal for cancer research, tumor profiling, and various cell biology experiments. It offers comprehensive, expert-selected coverage, including 99% of RefSeq genes, 95% of CpG islands, high coverage of enhancer regions, and other content categories. With > 90% of the original content from the Infinium HumanMethylation450K covered, the MethylationEPIC v2.0 supports the next generation of epigenetics research.
Infinium Methylation Screening Array
Ultra-scalable methylation array optimized for population health research. Ideal for studies >1,000 samples, up to millions of samples.
Mouse Methylation BeadChip
The Mouse Methylation BeadChip can be used in EWAS and other experiments probing the methylome in healthy and diseased tissues of model organisms. Much like the MethylationEPIC v2.0, the Mouse Methylation BeadChip offers genome-wide coverage, with probes targeted to CpG islands, enhancer regions, transcription start sites, and other important regions of the methylome.
HTS iSelect Methyl Custom BeadChip
Custom Methylation Beadchips provide the ultimate flexibility and cost-savings for targeted research and commercial applications. Custom beadchips can be designed with between 3,000 and 100,000 markers for a variety of applications. The 24-sample beadchip enables low per sample and processing costs while maintaining the same robust methylation measurements provided by the Infinium assay.
DNA methylation for human disease research
This eBook introduces DNA methylation and its applications for the study of human diseases and other phenotypes. It will also cover epigenome-wide association studies, including considerations for study design, sample types, and data analysis.
Download eBookMethylation Array Workflow
Our methylation arrays follow a streamlined workflow, enabling processing of up to 96 samples simultaneously from low sample input (as little as 250 ng).
Offering quantitative measurement at the single-CpG-site level, these methylation microarrays offer powerful resolution for understanding epigenetic changes.
Click on the below to view products for each workflow step.
MethylationEPIC v2.0
Robust methylation profiling microarray with extensive coverage of CpG islands, genes, and enhancers and FFPE compatibility.
Infinium Methylation Screening Array
Ultra-scalable methylation array optimized for population health research. Ideal for studies >1,000 samples, up to millions of samples.
Infinium Mouse Methylation BeadChip
Features > 285k markers across the methylome for high resolution epigenetic analyses of diverse murine strains.
Infinium Custom Methylation Kit
Create made-to-order, high-throughput assays to fit your specific needs. The flexibility and features of this array make it a powerful tool for a wide range of epigenetic applications.
iScan System
Supports high-throughput BeadChip processing, scanning hundreds to thousands of samples quickly and accurately.
Infinium Automation Option Packages
Illumina genotyping automation options for Infinium, GoldenGate, and DASL Assays streamline workflow and reduce errors. Illumina robot control software, together with liquid-handling automation, enables seamless automation of sample preparation into the iScan System workflow.
DRAGEN Array Methylation QC
Cloud-based high-throughput and quantitative reporting for Infinium methylation microarrays.
GenomeStudio Software Methylation Module
Visualize Infinium controls to ensure quality processing and perform basic analysis on DNA methylation beadchip data.
Featured Webinars
Exploring the Genetics of Neuropsychiatric Disease
Dr. Kristen Brennand discusses how integrating methylation array data with DNA and RNA sequencing data from stem cells can help identify disease-associated genes and pathways.
View WebinarDNA Methylation Classifiers for Brain Tumors and Sarcomas
Dr. Matija Snuderl discusses his team's research into the use of machine learning and epigenetic signatures to improve the accuracy of solid tumor classifications, especially for brain tumors and sarcomas.
View WebinarScientists Discuss Methylation Array Research
Methylome and Clinical Outcomes
Dr. Kathleen C. Barnes describes her work as a genetic epidemiologist, how COVID-19 impacted her research plans, and how methylation arrays add another dimension to the study of infectious diseases.
Read InterviewThe Genetic Basis of Oral Cancer
Researchers use methylation arrays together with RNA-Seq and other next-generation sequencing methods to identify genetic alterations associated with a deadly oral cancer.
Read InterviewEpigenetics Studies Uncover Obesity-Driven Methylation Signatures
Dr. Samani at University of Leicester uses methylation arrays to identify cell signaling disruption linked with high BMI.
Read InterviewRelated Solutions
Complex Disease Studies
Methylation array studies enable researchers to understand the functional mechanisms at work in complex disease. Illumina offers complementary solutions for researchers studying these disorders. Learn more about complex disease research.
Epigenetics and Cancer
Illumina array and sequencing solutions are ideal for detecting altered methylation patterns and epigenetic changes that provide insight into tumorigenic pathways and cancer progression. Learn more about cancer epigenetics.
Publications
DNA methylation-based classification of central nervous system tumours.
Nature 555 469-74 2018
Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders.
Genetics in Medicine 23 1065-74 2021
Host methylation predicts SARS-CoV-2 infection and clinical outcome.
Commun Med 1(1):42 124-29 2021
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Additional Resources
Methylation Sequencing
Methylation sequencing approaches offer higher density and flexibility in assessing epigenome changes.
Methylation Array Data Analysis Tips
Explore advanced approaches for analyzing Illumina methylation array data.
Methylation Field Guide
Explore a variety of methods used to detect cytosine modifications, including methylation arrays and sequencing approaches.