Methylation Analysis
Beyond the nucleotide sequence of DNA are heritable patterns of non-sequence information involving the attachment of methyl groups to bases. These epigenetic modifications are important in the regulation of gene expression and contribute to developmental programming and cell differentiation.
The AGRF offers rapid and accurate techniques to analyse methylation patterns using various platforms for many applications: from whole genome methylation to quantitative customized analysis.
Services include:
- Whole genome methylation screen:
illumina Infinium HumanMethylation450 Beadchip - Gene and promoter methylation discovery:
Sequenom EpiTYPER on the MassARRAY - Targeted sites and methylation validations:
Qiagen PyroMark pyrosequencing - Discovery: Applied Biosystems sanger sequencing
Methylation Analysis: Sample Submission Requirements
For sample submission requirements for Methylation Analysis using other AGRF platforms, please contact us.
illumina
Screen a whole human genome’s methylation pattern to identify variable genomic regions that may be contributing to gene expression variation or the phenotypic outcome.
This 12 sample BeadChip features:
- Single CpG site resolution for over 450,000 CpG sites encompassing 99% of RefSeq genes
- CpG sites outside of CpG islands and DNAse hypersensitive sites
- Covers 96% of CpG islands with multiple sites in the island, the ‘shores’ and the ‘shelves’
- Incorporates miRNA promoter regions
Infinium HumanMethylation450 Beadchip Data Sheet (PDF)
For non-human whole genome methylation, consider a next generation sequencing approach. Contact nextgensequencing@agrf.org.au for more information.
Methylation Analysis Service Process using the illumina Platform
Sequenom
The EpiTYPER system provides an overview for methylation discovery in known genes over larger base regions. The EpiTYPER can also be quantitative for most CpG sites.
The benefits of using the Sequenom platform are:
- Rapid, automated discovery of multiple methylated CpG positions in regions of 200-600 bp
- Simplified assay design
- Quantitative assessment on the degree of methylation
- Simple identification of hypomethylation and hypermethylation
- Detection of methylation levels as low as 5% in sample mixtures
- High precision, reproducibility and throughput on an established MassARRAY system
DNA Methylation Analysis Product Preview Note (PDF)
Methylation Analysis Service Process using the Sequenom Platform
Qiagen
PyroMark sequencing is used for a high resolution result by targeting known sites for methylation quantification on specific CpG’s
The benefits of using the Qiagen platform include:
- Ability to measure specific CpG site methylation levels, even in close proximity
- Simple and flexible design giving the highest percentage of customisable targets
- Suitable for smaller sample batches
- Accurate quantification – results within 1-3%
- Bisulphate conversion quality indication which measures non-CpG cytosine’s converted to thymine’s
DNA Methylation Analysis Data Sheet (PDF)
Methylation Analysis Service Process using the Qiagen Platform
Applied Biosystems
Sanger sequencing is a readily accessible and known technology that can provide an overview for discovery of methylation sites.
A specialist methylation PCR and sequencing service is offered by AGRF Perth. Other benefits of using this service are:
- Ability to screen long targeted regions up to 800bp
- Economical and familiar analysis options
