Development of DNA Methylation Assays

DNA methylation is an important epigenetic modification involved in gene regulation, development, aging, and disease. Accurate methylation analysis requires high-throughput technologies capable of detecting methylation at single-base resolution across diverse sample types.

Illumina's Infinium® BeadArray™ platform has become a widely adopted solution for genome-wide DNA methylation profiling. The technology has evolved from the HumanMethylation450 (450K) array to the MethylationEPIC v1.0 (850K), and most recently to the MethylationEPIC v2.0 (935K) BeadChip.

The latest EPIC v2.0 (935K) array analyzes approximately 935,000 CpG sites, offering expanded coverage of enhancers, CpG islands, CTCF binding sites, CNV-associated regions, and disease-related genomic loci. Built on the GRCh38 (hg38) reference genome with updated annotations, it provides a powerful platform for epigenome-wide association studies (EWAS), biomarker discovery, and precision medicine research.

Human DNA Methylation Assay (935K)

N2Jenomics Lab Pvt. Ltd. offers genome-wide DNA methylation profiling using the Illumina Infinium MethylationEPIC v2.0 (935K) BeadChip. Our optimized workflow supports high-quality methylation analysis from a variety of sample types, including FFPE tissues, fresh samples, and circulating cell-free DNA (cfDNA).

With rigorous quality control and experienced technical support, we deliver reliable data for epigenetics, biomarker discovery, disease research, and translational studies.

Advantages of Our DNA Methylation Assay (935K)

• Comprehensive Genome Coverage

The EPIC v2.0 array profiles approximately 935,000 CpG sites, providing enhanced coverage of:

• - Enhancers and super-enhancers

• - CpG islands
• - CTCF binding regions
• - CNV-associated loci
• - Cancer-related genomic regions
• - Updated GRCh38 (hg38) genome annotation

It also incorporates epigenomic features identified through ATAC-Seq and ChIP-Seq, enabling deeper analysis of gene regulation.

• Optimized for Disease Research

The array includes expanded coverage of genomic regions associated with:

• - Cancer epigenetics
• - Differentially methylated regions (DMRs)
• - Chromatin accessibility
• - Biomarker discovery
• - Precision medicine applications

• Reliable & Validated Platform

Built on Illumina's proven Infinium technology, the platform delivers reproducible, high-quality methylation data and is widely used in large-scale epigenetic studies.

• Broad Sample Compatibility

The assay supports multiple sample types, including:

• - FFPE tissue
• - Fresh and frozen tissue
• - Whole blood
• - Plasma-derived cfDNA
• - Saliva
• - Buccal swabs

Its compatibility with archived FFPE specimens makes it particularly valuable for cancer and retrospective clinical research.

Applications

Suitable for:

• • Epigenome-wide association studies (EWAS)
• • DNA methylation profiling
• • Cancer epigenetics
• • Biomarker discovery
• • Aging research
• • Precision medicine
• • Disease mechanism studies

• Data Analysis

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• Sample Requirements

• Sample Type	Requirements
  Human/Animal Genomic DNA	≥2 µg DNA; concentration ≥20 ng/µL (Qubit); free of RNA and protein contamination.
  Fresh Frozen Tissue	10–30 mg tissue; store at -20°C or -80°C until shipment.
  Cultured Cells	≥2 × 10⁶ cells; wash once with PBS, centrifuge at 600 × g for 5 minutes, discard supernatant, and retain the cell pellet.
  Whole Blood	0.5–2 mL peripheral blood or buffy coat collected in a suitable tube; avoid anticoagulants that may interfere with downstream analysis.
  FFPE DNA	≥1 µg DNA; concentration ≥20 ng/µL (Qubit); DNA fragment size preferably >500 bp.
  FFPE Tissue Sections	≥15 sections, 4–10 µm thick; tissue area ≥1 cm² per slide; tumor content ≥30%; ship in a 1.5 or 2.0 mL tube.
  Plasma/Serum cfDNA	≥15 ng cfDNA with minimal genomic DNA contamination; mononucleosomal cfDNA ≥50%.
  Plasma/Serum Samples	Submit 1–4 mL of plasma or serum for cfDNA extraction.

1. Which CpG sites from the 850K array are retained in the 935K array?

The EPIC v2.0 (935K) array retains most high-value CpG sites from previous Illumina methylation arrays, including regions associated with CpG islands, enhancers, open chromatin, DNase I hypersensitive sites, miRNA promoters, and over 85% of the probes from the HumanMethylation450 array.

2. What new features does the 935K array include?

The 935K array expands genome coverage with additional CpG sites in:

• • Cancer-associated differentially methylated regions (DMRs)

• • Enhancers and super-enhancers
• • ATAC-Seq-defined accessible chromatin regions
• • CpG islands
• • CNV-related genomic regions
• • Cancer-associated genomic loci

3. Can 850K and 935K methylation data be analyzed together?

Yes. Data generated from both platforms can be integrated by focusing on the CpG sites shared between the two arrays.

4. Which sample types are supported?

The EPIC v2.0 (935K) array supports a wide range of sample types, including genomic DNA, FFPE tissue, fresh or frozen tissue, whole blood, plasma-derived cfDNA, saliva, and buccal swabs.

5. Is there a minimum number of samples required?

No. The platform is suitable for both small and large-scale studies, with no fixed minimum sample requirement.

6. What are the major applications of the 935K methylation array?

The assay is widely used for:

• • Cancer epigenetics
• • Biomarker discovery
• • Epigenome-wide association studies (EWAS)
• • Precision medicine
• • Aging and longevity research
• • Developmental biology
• • Complex disease research
• • Environmental epigenetics
• • Liquid biopsy and cfDNA methylation profiling