Methylation Analysis
The GRCF offers genome-wide and targeted methylation analysis for your project.
We support methylation projects with PCR and Bisulfite conversion services as well.
Whole Genome Arrays for Human and Mouse
Human EPIC 2.0 Infinium Methylation Array
The Infinium MethylationEPIC v2.0 BeadChip targets 935,000 methylation sites in biologically significant regions of the human methylome and is backwards compatible with v1.0. Multiple samples, from many different sources, including FFPE, can be analyzed in parallel to deliver high-throughput power while minimizing the cost per sample.
This chip provides a pan-enhancer and coding region view of the methylome for epigenome-wide association studies. It covers the following content areas:
- Expanded coverage of CpG islands
- Non-CpG methylated sites identified in human stem cells
- Differentially methylated sites identified in tumor vs. normal
- FANTOM5 enhancers
- ENCODE open chromatin and enhancers
- DNase hypersensitive sites
- miRNA promoter regions
- Enchancers and super-enhancers identified by ChIP-Seq in cancer & cell line samples
- Differentially accessible chromatin regions identified in primary human cancers using ATAC-Seq
- Enhanced exon coverage for more accurate CNV detection
- >450 common cancer driver mutations
- >85% of the 450K and EPIC v1.0 BeadChip content is retained.
A list of all CpG sites is available for download from the Illumina website (Open EPIC-8v2-0_A1.csv once download is complete). Need help understanding this information? See Illumina’s CpG loci identification tech note for more information.
| Number of Samples | Array pricing | With FFPE Restore |
|---|---|---|
| 6 (internal customers only) | $430/sample | $530/sample |
| 14 – 92 | $395/sample | $495/sample |
| 94 – 2000 | $365/sample | $465/sample |
**All FFPE samples must be restored.
Human Methylation Screening Array (MSA)
This array provides highly informative content for common disease in human populations. It features ~270K unique methylation sites selected from methylation array studies, sequencing studies and databases, and provides comprehensive coverage of DNA methylation sites implicated in genetic diseases, environmental exposures, aging and development. It also provides coverage of emerging functional genomics markers, including cell-type specific methylation, intermediate methylation and correlated regions of systemic inter-individual variation (CoRSIVs).
| Number of Samples | Array pricing | With FFPE Restore |
|---|---|---|
| 24-94 | $260/sample | $360/sample |
| 96-2,000 | $240/sample | $340/sample |
**All FFPE samples must be restored.
Mouse Infinium Methylation Array
Featuring more than 275,000 markers across the methylome, this array allows high-resolution epigenetic analyses of diverse murine strains.
Use this array for epigenome-wide association studies, xenograft experiments, preclinical research, toxicology, embryology and other applications. Coverage includes:
- 28,847 transcription start sites
- miRNAPromotor transcription start sites
- Noncoding RNA transcription start sites
- Enhancers
- Imprinted loci
- 16,000 CpG islands
- Hypermethylated regions in cancer
- 25,000 highly conserved human EPIC array probesStrain-specific SNP probes from 18 mouse strains
| Number of Samples | Array pricing | Array pricing with FFPE restore |
|---|---|---|
| 22 – 93 samples (internal customers only) | $355/sample | $455/sample |
| 94 – 5000 | $320/sample | $420/sample |
**All FFPE samples must be restored.
Targeted Methylation Analysis
Illumina iSelect Methyl Custom Chips
The Infinium HTS iSelect Methyl Custom BeadChip allows researchers and commercial customers to create made-to-order, high-throughput assays to fit their specific needs. The flexibility and features of the Infinium HTS iSelect Methyl Custom BeadChip make it a powerful tool for a wide range of epigenetic applications.
For more information, contact us.
Analysis via Pyrosequencing
Specific regions of methylation can be assayed via sequencing on the Pyromark Q48 system from Qiagen, using their advanced methylation reagents. This is not high throughput/next generation sequencing. Bisulfite converted DNA is PCR amplified with a biotinylated primer pair. The non-biotinylated strand is sequenced in the Pyromark system.
Customers may choose to do their own PCRs and bring them to us for sequencing or they may opt for our full pyrosequencing service which includes bisulfite conversion and PCR of customer samples plus seven methylation controls, in addition to the pyrosequencing reactions. Full details can be found on our pyrosequencing page.
A video describing the pyrosequencing process is available on YouTube.
Hours
7:00 am to 4:30 pm
Location
600 N. Wolfe Street
Blalock Building, Room 1004
Baltimore, MD 21287 USA
my green lab Certified: Level “Green”