Human DNA Methylation Microarray Service for 935K & 270K EWAS Profiling
Human DNA methylation microarrays provide a cost-effective, high-throughput way to measure DNA methylation at hundreds of thousands of CpG sites across the human genome. By converting genomic DNA with bisulfite treatment and detecting methylation-dependent probe signals on Illumina Infinium arrays, this service helps researchers identify differentially methylated positions and regions associated with disease, development, aging, environmental exposure, and therapeutic response.
CD Genomics supports both 935K and 270K human methylation array projects to match different study goals and sample scales.
935K Human Methylation Array — Recommended for broad methylome discovery, cancer epigenetics, FFPE-compatible studies, regulatory-region analysis, and CNV-aware methylation interpretation.
270K Human Methylation Array — Suitable for cost-efficient EWAS, population screening, environmental exposure research, aging studies, and large-cohort methylation profiling.
At CD Genomics, we offer two human DNA methylation microarray platforms based on Illumina's Infinium technology. Each service is optimized for a different research focus—from comprehensive genome-wide methylation analysis to cost-effective screening of phenotype-linked CpG sites. Whether you're investigating cancer epigenetics or conducting large-scale population studies, our flexible options ensure you get the best-fit solution.
Service Comparison: CD Genomics Methylation Array Platforms
In general, 935K is the better choice for discovery-oriented, oncology, FFPE, and complex disease studies, while 270K is better suited for large-scale EWAS, population health, aging, exposure, and screening-focused projects.
All platforms utilize Illumina's gold-standard Type I + Type II probe chemistry, ensuring high sensitivity, consistent results, and full compatibility with FFPE samples.
Applications
Research Applications for DNA Methylation Microarrays
CD Genomics' Human DNA Methylation Microarray service is purpose-built for high-throughput epigenetic studies. Whether you're mapping methylation across large cohorts or exploring disease mechanisms, our platform offers unmatched scale, accuracy, and flexibility.
Genome-Wide Methylation Mapping
Quickly generate high-resolution methylation profiles across hundreds of thousands of CpG sites to identify epigenetic patterns in tissues, conditions, or populations.
Multi-Omics Integration
Combine DNA methylation data with transcriptome, miRNA, or proteome datasets to uncover regulatory networks and deepen insights into gene expression control.
Disease Association Studies (EWAS)
Detect statistically significant methylation changes linked to disease states, environmental exposures, or clinical phenotypes using cohort-based or case-control designs.
Cancer Epigenetics Research
Characterise tumour-specific methylation differences between normal and malignant tissues, across cancer subtypes, or at different disease stages to uncover regulatory drivers.
Developmental & Environmental Epigenetics
Track dynamic methylation changes across developmental stages or under environmental stimuli to understand how epigenetic mechanisms shape adaptation and growth.
Biomarker Discovery & Drug Screening (Research Use Only)
Identify candidate epigenetic biomarkers for early-stage drug research or assess methylation-based indicators of drug response and treatment efficacy.
Workflow
CD Genomics' End-to-End Workflow for Human DNA Methylation Microarray Analysis
At CD Genomics, we prioritize efficiency and reliability across every step of our DNA methylation microarray service. From project planning to data delivery, our streamlined workflow ensures high-quality results that help researchers move faster toward discovery.
Consultation and Project Design
Requirement Discussion
Experimental Plan Customization
Sample Preparation and Submission
Support for Multiple Human Sample Types
DNA Quality Control and Bisulfite Conversion
DNA Purity Assessment
Bisulfite Treatment
Microarray Hybridization and Scanning
Illumina Infinium 935K/270K Arrays
8–48 Samples per Chip
Illumina iScan System
Single-Base Resolution Methylation Detection
Data Analysis and Report Generation
Quality Control
Methylation Level Analysis
Differential Methylation Detection
Standardized Report Delivery
Deliverables
Clear Data Deliverables for EWAS and Methylation Interpretation
Our deliverables are designed to help researchers move from raw array output to interpretable methylation results, including QC summaries, normalized β-values, differential methylation results, annotations, and optional advanced visualizations.
✅ Standard Deliverables
Our standard deliverables provide everything needed for basic methylation data interpretation and visualization:
Raw IDAT Files
Direct output from the Illumina scanner, ready for downstream analysis or archive.
β-value Matrix
Normalized methylation values (0–1) for each CpG probe across all samples, enabling statistical and comparative analysis.
Quality Control Summary Report
Includes detection p-values, probe performance, and sample-wise QC metrics; ensures data reliability with typical detection rates >98%.
Differentially Methylated Sites (DMS) List
Identifies statistically significant CpG sites between groups, with annotations for gene region and CpG context.
🔍 Advanced Modules (Optional Add-ons)
Available as customizable bioinformatics services for deeper biological insights and publication-ready figures:
Differentially Methylated Regions (DMRs)
Aggregated regions of consistent methylation change; ideal for identifying epigenetic regulatory hotspots.
Methylation–Expression Correlation Analysis
Integrated analysis of methylation and transcriptome data to explore regulatory relationships (requires RNA-seq input).
Multi-Dimensional Visualization Suite
Includes hierarchical clustering heatmaps, volcano plots, PCA, and genomic track visualization (e.g., UCSC Genome Browser formats).
Sample Requirements
Sample Requirements & Submission Guidelines
To ensure accurate, high-quality results from your DNA methylation microarray, please prepare samples according to the following standards:
Sample Type
Key Requirements
Storage & Shipping
Recommended DNA Concentration
Notes
Cell Samples
≥5×10⁶ cells
Flash-freeze in liquid nitrogen; store at −80°C; ship on dry ice
N/A
Fresh or cultured cells accepted
Tissue Samples
≥100 mg tissue or slices
Flash-freeze in liquid nitrogen; store at −80°C; ship on dry ice
N/A
Avoid repeated freeze–thaw cycles
DNA Samples
High-purity genomic DNA
−20°C for short-term; −80°C for long-term; ship on ice packs
≥50 ng/μL; ≥500 ng total
Must be free of RNA/protein; TE buffer or nuclease-free water
✅ Label all samples clearly and seal packaging tightly to avoid degradation or contamination during transit. 📬 For unusual sample types or special conditions, feel free to consult our expert team.
Advantages
Why CD Genomics Is Your Trusted Partner in DNA Methylation Microarray Services
At CD Genomics, we don't just deliver data—we deliver discovery.
Platform selection support
Guidance on whether 935K or 270K better fits your sample type, cohort size, and research goal.
End-to-end project handling
Support from DNA QC and bisulfite conversion to array scanning and report delivery.
EWAS-ready bioinformatics
QC, normalization, β-value matrix generation, DMS/DMR analysis, annotation, and visualization.
Flexible service scope
Choose array processing only, standard analysis, or advanced downstream bioinformatics.
Batch-aware project design
Practical planning for multi-group, multi-batch, or large-cohort methylation studies.
Method Comparison
DNA Methylation Microarray vs WGBS vs RRBS: Which Method Should You Choose?
DNA methylation microarrays are often preferred for human EWAS, biomarker screening, and large-cohort studies because they provide standardized CpG coverage, scalable sample processing, and analysis-ready β-value outputs. Compared with WGBS, microarrays are more cost-effective for large human sample sets. Compared with RRBS, they offer more standardized probe-based coverage across known regulatory, disease-associated, and phenotype-linked CpG sites.
RRBS: CpG-rich region profiling, smaller-scale discovery, budget-limited sequencing projects
Publications
Publications
Selected publications from researchers utilizing CD Genomics' DNA methylation analysis services for advanced epigenetic research.
Nkongolo, Kabwe, and Paul Michael. "Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel." Genome (2024). https://doi.org/10.1139/gen-2024-0019
Eileen, Lindsey, and Maria Peterson. "High-Fat Diets Fed during Pregnancy Cause Changes to Pancreatic Tissue DNA Methylation and Protein Expression in the Offspring: A Multi-Omics Approach." International Journal of Molecular Sciences (2024). https://doi.org/10.3390/ijms25137317
Gretarsson, Kristjan H., et al. "Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch." Science Advances (2024). https://www.science.org/doi/10.1126/sciadv.adp0975
Negi, Chander K., et al. "Triphenyl Phosphate Alters Methyltransferase Expression and Induces Genome-Wide Aberrant DNA Methylation in Zebrafish Larvae." Chemical Research in Toxicology (2024). https://doi.org/10.1021/acs.chemrestox.4c00223
