Illumina and RainDance Technologies have both debuted new products for analyzing DNA methylation.
While the firms' platforms are different, each company believes its can offer customers a more comprehensive approach to methylation analysis than has existed in the past.
Illumina last month began shipping its Infinium HumanMethylation450 BeadChips. According to the firm, the arrays enable users to interrogate more than 450,000 methylation sites per sample, including coverage of all designable RefSeq genes, including promoter, 5', and 3' regions, without bias against those lacking islands of CpG sites.
Additional content on the array includes CpG islands and shores; CpG sites outside of CpG islands, non-CpG methylated sites identified in human stem cells; differentially methylated sites identified in tumor versus normal in multiple forms of cancer and across several tissue types; CpG islands outside of coding regions; microRNA promoter regions; and disease-associated regions identified through genome-wide association studies, Illumina said.
Customers can process the 12-sample arrays on the company's iScan or HiScanSQ systems. The assay requires 500 nanograms of bisulfite-converted DNA per sample. According to San Diego-based Illumina, the assay contains 90 percent of the content of its previous offering, a kit that enables customers to assay approximately 27,000 CpG sites per sample and was marketed as a "genome-wide" methylation array product when it was launched three years ago (BAN 11/20/2007).
Carsten Rosenow, Illumina's associate director of global market development for genotyping, told BioArray News recently that the firm's previous methylation array has been "very successful," and that there has been "a lot of interest to go to a whole-genome methylation array."
He argued that the broad coverage of the 450K will give it an advantage over other methylation arrays sold by rivals such as Agilent Technologies and Roche NimbleGen.
"To the best of my knowledge this is the only array that actually types and looks at individual CPG sites, the individual bases," Rosenow said. "The others only look at CPG islands, so [the new array] is the closest to a sequencing solution that you can get."
Rosenow said potential customers include cancer researchers and those who study how methylation affects other diseases.
"It all goes back to the idea of missing heritability," Rosenow said. "People think that methylation and epigenetics in general plays a role in some of the diseases being studied. Cancer research is a big area of interest."
One of Illumina's closest competitors is Santa Clara, Calif.-based Agilent. The firm's Human DNA Methylation Microarray is designed to interrogate more than 27,000 known CpG islands and two additional groups of methylated DNA.
The array is specifically designed to analyze methylated DNA derived from affinity-based isolation methods such as methylated DNA immunoprecipitation, according to the company.
Madison, Wis.-based Roche NimbleGen is another rival. The company sells a number of whole-genome and targeted designs for methylation studies. The company sells 2.1-million feature whole-genome tiling sets, as well as a 385K Promoter Plus CpG Island Array that includes all annotated CpG islands and RefSeq gene promoter regions, and a 385K Targeted Tiling Array that offers fine tiling of select biologically significant areas.
RainDance's Alternative
While a number of array-based options for methylation research are now available, all of them lack the coverage necessary for successful studies, according to RainDance CEO Roopom Banerjee.
"Our understanding of the current array technologies is they tend to cover specific SNPs or specific regions of the genome against known methylation regions," Banerjee told BioArray News recently. "We have yet to see a true, whole methylome-type product. We have seen whole genome, we have seen whole exome, but we have not seen whole methylome."
RainDance recently launched an alternative for researchers interested in studying methylation on its RDT 1000 platform. The technology relies on its RainStorm microdroplet-based technology to conduct PCR-based sequence enrichment, which runs captured sequences on next-generation sequencers.
Banerjee said the offering, which is now commercially available, is the "first single-molecule quantitative approach to doing methylated, bisulfate treated DNA with single-base resolution."
According to Banerjee, single-molecule quantitation is "something that arrays just can't do." He said that arrays "have never had the sensitivity of PCR and so one of the reasons PCR still exists and is the gold standard" is because of that limitation. He added that SNP-based approaches, such as Illumina's, report individual methylated variations, but "do not correlate necessarily to specific genes."
RainDance "designs its amplicons and primers to cover specific genes and specific regions of interest that will go well beyond individual base-level changes," Banerjee said. He said the firm's offering is focused on researchers who want to "understand the functional genes that are affected by methylation" so that they can correlate those changes to disease.
According to Banerjee, one of the reasons any one dominant application for studying methylation has not yet emerged is because of ongoing cleavages in the scientific community. "There is still in the scientific community a diverse group of perspectives on what to cover across the methylome," he said.
"Is it CPG islands, is it upstream, downstream regulators, or untranslated regions of certain genes? The science is continuing to evolve in terms of what is important and what is not, so the array companies have had a challenge in trying to standardize methylation products," Banerjee added.
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