March 3, 2012
Instead of sequencing (and paying for, managing, storing, and analyzing) everything, target enrichment blazes through samples like a combine, harvesting for regions of interest. Even as sequencing costs drop towards that “$1,000 genome” level, enriching for select targets makes a lot of sense, especially if you only want to look at a subset of the genome like interesting methylated regions.
A SureSelect Thing for Genome-Wide DNA Methylation Analysis
Three years ago, researchers from Cold Spring Harbor Laboratory, the University of Southern California, Albert Einstein College of Medicine, and Agilent used custom microarrays to capture DNA fragments associated with methylation prior to sequencing. In concert with bisulfite conversion, this created a powerful high definition, targeted DNA methylation analysis approach. As effective as they were, target enrichment techniques have continued to evolve, and the most recent methods have exchanged the array capture step with in-solution, liquid hybridization that can be done in a single tube. But the innovation hasn’t stopped there.
Enter SureSelectXT Human Methyl-Seq
Agilent’s latest baby, the SureSelectXT Human Methyl-Seq kit wraps all of these advantages together in one package:
- In-solution hybridization protocols,
- Probes targeting all of the most relevant regulatory regions
- Single base resolution of bisulfite sequencing
It’s the first complete DNA methylation discovery platform using target enrichment.
As Agilent R&D scientist Doug Roberts, Ph.D. explains, “In solution hybridization is much more efficient than on array capture with more favorable kinetics. The procedure is also more amenable to scale-up and automation.”
Epigenetics researchers will be salivating over SureSelect’s ability to tease out tiny methylation differences in genomes, like in differentially methylated regions (DMRs). “Since other techniques depend on the methylation status (MeDIP) or CpG density (RRBS), it is difficult to get a common comprehensive set of DMRs in different test conditions. SureSelect Methyl-Seq probes are designed based on the primary DNA sequence and are not limited to regions of high or low CpG density or affected by the inherent methylation state of the sample. This allows for comprehensive targeting of all types of regulatory regions.” Says Roberts.
The system covers over 3.7 million individual CpG sequences found in:
- CpG islands
- Cancer, tissue-specific DMRs
- GENCODe promoters
- CpG Islands, shores and shelves ±4kb
- DNAseI hypersensitive sites
- Ensemble Regulatory Features
The kits come stocked with reagents for library prep and target enrichment, so all in all, it’s a pretty slick way to get your genome-scale DNA methylation analysis done.