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

HUMAN EPIC v2.0 INFINIUM METHYLATION BEADCHIP

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 SamplesArray pricingArray pricing with FFPE restore
6 (internal customers only)$425/sample$525/sample
14 - 92 (internal customers only)$405/sample$505/sample
94 - 5000$375/sample$475/sample

MOUSE INFINIUM METHYLATION BEADCHIP

The  Illumina Infinium Mouse Methylation Beadarray features more than 275,000 markers across the methylome. This allows high-resolution epigenetic analyses of diverse murine strains, which is useful 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


A list of all CpG sites is available for download.  Need help understanding this information? See Illumina’s  CpG loci identification tech note for more information.

Number of SamplesArray pricingArray pricing with FFPE restore
22 - 93 samples (internal customers only)$370/sample$470/sample
94 - 5000$320/sample$420/sample

Full service pricing for all Illumina arrays includes:

  • 100% and 0% methylation controls (1 of each per plate)
  • Bisulfite Conversion
  • Full data release, which includes: raw intensity data, GenomeStudio Project, Methylation Profile, Samples Table, Analysis using minfi including code used, minfi output including PLINK and README docs explaining the data in each directory


For more information on these services, please contact  Roxann Ashworth [410-614-0702].

Sample Requirements

  • 50 ul of genomic DNA at a concentration of 30-50 ng/ul in 1xTE (10mM Tris, 1mM EDTA, pH8) or water.
    * Uniform Volumes are required.
    * Whole Genome Amplified (WGA) samples will not work
    * Highly fragmented (FFPE or degraded) samples may be used, but will need the restore process, which adds $100/sample to the cost.


Targeted Methylation Analysis

Validate your Illumina array results or investigate your favorite epigenetic regions for human and rodents.

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. A video describing the process is available on  YouTube.

Custom Pyrosequening Assays

Custom regions can be amplified, or one of the 30,000 human and rodent predesigned kits can be ordered from Qiagen. Primers  ordered through us receive a slight discount and free shipping. Assay design assistance is available for all projects being run in our facility.

Pricing

$15.00/sample

For more information, contact Roxann Ashworth.

PCR & Bisulfite Conversion support available. Scroll down for more information.

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.

Ancillary Services

PCR Support

If you don’t have the lab equipment and/or the time to run your own samples, we are here for you! We provide a full range of services for your pyrosequencing projects.

Full Service: includes bisulfite conversion of DNA samples (if needed), PCR of samples, amplification confirmation of the PCR by agarose gel electrophoresis and submission for Pyrosequencing. Please contact  Alejandra Gutierrez for more information.

Pricing: PCR support pricing is sample number dependent. Please contact Dr. Gutierrez.

Sample Requirements

Pyrosequencing (methylation analysis): 40 ng at 5 ng/ul to 10 ng/µl of bisulfite converted DNA per amplicon. If submitting genomic DNA for bisulfite conversion, we recommend converting a minimum of 100ng.

Pyrosequencing (SNP analysis, mutation detection, sequencing): 40 ng at 5 ng/µl to 10 ng/µl per amplicon.


Bisulfite Conversion

 Bisulfite conversion of isolated DNA is offered using Zymo Research Corporation EZ DNA Methylation Kit or Qiagen EpiTect Bisulfite Kits.

Converted DNA is suitable for PCR, endonuclease digestion, sequencing, microarrays, and Illumina Infinium and Golden Gate Methylation Assays.

  • EpiTect Bisulfite conversion: $18/sample. (Recommended for Pyrosequencing.)
  • EZ DNA Methylation conversion pricing is sample number dependent. (Recommended for Illumina and included in array prices listed above.)

Please contact Dr. Gutierrez for pricing and ordering.