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NimbleGen to Add DNA Methylation Analysis to Portfolio in Q4 as Nascent Market Takes Shape

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After several years of providing global DNA methylation profiling arrays on a custom basis, NimbleGen Systems will round out its suite of catalog applications by launching catalog arrays for DNA methylation analysis by the end of this year, according to a company official.

Emile Nuwaysir, vice president of business development at NimbleGen, told BioArray News this week that the company has plans to add DNA methylation arrays to its catalog by the end of this year.

The company's actions come at a time when other early players in the DNA methylation array market, such as Agilent Technologies and Epigenomics, are laying the foundation for introducing their own DNA methylation arrays.

By introducing the new chips, NimbleGen will have established a presence across the spectrum of post-gene expression microarraying • in array comparative genomic hybridization, chromatin immunoprecipitation (ChIP)-on-chip analysis, comparative genome sequencing, and now, DNA methylation analysis.

According to Nuwaysir, the company's desire to develop its presence in the DNA methylation array market is very much tied to its experience with applications • like array CGH • that it launched last year (see BAN 2/23/2005).

"We see DNA methylation as a tremendous growth area, just as the areas of ChIP-chip, and [array] CGH have shown to be," Nuwaysir said.


"The old idea that genetic disease requires mutations is losing its exclusivity."

"It's a new application of arrays that expand the way that you can measure genomic variation. DNA methylation is just another layer of genomic variation that arrays can measure and that is critical to the biology people are studying," he added.

According to Nuwaysir, the company plans to offer two types of methylation array designs: a genome-wide tiling design, and then targeted tiling designs where content of interest, such as known promoters or the known CpG islands, is targeted, he explained.

NimbleGen will also continue to offer "custom content that is a function of what the researcher wants to study or the assay they've developed," Nuwaysir added.

He said that most of NimbleGen's customers will be able to get access to the new chips through the company's service lab in Iceland. Customers will also be able to buy chips "if they are a US government customer or they are located in territories where [NimbleGen] sells arrays," Nuwaysir said.

Nuwaysir also said that NimbleGen is well positioned to tackle the methylation market because he believes the DNA methylation analysis community is more established than some other emerging array application areas.

"If you look at a PubMed analysis of DNA methylation versus a PubMed analysis of ChIP-on-chip to get a measure of how much scientists have been studying DNA methylation versus other fields, DNA methylation goes back much longer and there's a much broader base of people doing these analyses," he said.

Customers have already been using NimbleGen's arrays for DNA methylation analysis and global methylation profiling for several years, and publications are "in the pipeline," Nuwaysir said.

John Greally, an associate professor in molecular genetics at Albert Einstein College of Medicine, told BioArray News this week that he has been using NimbleGen's arrays to study "epigenetic changes due to diet, and possible epigenetic changes predisposing [people] to type 2 diabetes." Specifically, Greally said that changing ideas about the roots of genetic diseases have fueled his interest in methylation analysis.

"The old idea that genetic disease requires mutations is losing its exclusivity • we now appreciate that a gene can be as effectively taken out of the game by inappropriate silencing, for which the hallmark is unusual cytosine methylation patterns," Greally said.

"This is most obvious for cancers, in which gene regulation is profoundly messed up. However, this epigenetic dysregulation is now being explored as a potential mediator of aging, type 2 diabetes, and other common disorders," he explained.

Greally added that researchers don't know where to look for methylation disturbances in the genome, making a high-throughput approach, as provided by microarray technology, "essential."

"There is overwhelming evidence that DNA methylation patterns affect phenotype and affect biology," Nuwaysir said. "So the community has needed a global methylation profiling tool like this for some time," he added.

The Developing Market

As NimbleGen prepares its entry to the methylation market, other early-bird companies are also developing chips for DNA methylation analysis.

Certain to join NimbleGen in the fray will be Agilent Technologies, which could roll out its first DNA methylation array, a content-specific array for studying CpG islands, as soon as next quarter.

Chris Hopkins, a senior scientist at Agilent, told BioArray News this month that the company is in the "early stages" of launching a methylation chip now (see BAN 6/20/2006).

"We have a microarray that we have designed for CpG islands and we are working with some experts in the field of DNA methylation, and we are working with their assay and our microarray to work on development of this technology," Hopkins said.

Agilent spokesperson Stu Matlow said this month that the company will provide more information on the methylation arrays in several weeks. Agilent already competes against NimbleGen in the array CGH and ChIP-on-chip markets.

One company that is also looking to expand its presence in the DNA methylation array market is Berlin-based Epigenomics, a molecular diagnostics company that offers its 50K DMH microarray for global methylation profiling to collaborators.

Epigenomics this week also became the latest diagnostics firm to sign an agreement with Affymetrix that will allow it to develop and market array-based in vitro diagnostic tests for oncology and other indications.

However, though the tests developed on the Affy platform will be on arrays, Epigenomics does not see a future in diagnostics for its methylation array.

Christoph Sachsenmaier, head of business development for Epigenomics' clinical solutions unit, told BioArray News this week that the 50K DMH microarray is custom produced by Affymetrix and so far has only been offered to its partners as a discovery tool.

"We use this in our collaborations with pharmas and biotechs as a discovery tool for biomarkers," Sachsenmaier said.

Though Epigenomics cannot sell the array, Sachsenmaier said the company plans to become an Affymetrix service provider and will eventually offer it as a service.

According to Tamas Rujan, project manager in clinical solutions at Epigenomics, the company's methylation chip is a compromise between offering genome-wide coverage and focusing on regions of interest.

"We are looking for CpG-dense regions and we have also tailored the chip for looking into the promoter and other regions of genes. We also have around 9,000 fragments that don't cover any regions that are annotated as genes or promoter regions in the genome," Rujan said.

Rujan said that the DMH chip is "mainly a discovery tool" and that Epigenomics does not plan to use it in the diagnostics field. "There are other technologies that can be used for analyzing methylation that are much more suitable for a diagnostic application, such as RT-PCR," he said. Instead the arrays will be intended for the research market.

Rujan added that Epigenomics will update its methylation array offering in the future by "going into other species such as rat or mouse, which would also support the drug development companies."

Similar to Epigenomics is Orion Genomics, a St. Louis biotech developing RT-PCR-based screening assays for ovarian and breast cancers. Jorge Leon, the company's acting chief scientific officer, told BioArray News in February that Orion offers a methylation array, called MethylScope, as an in-house discovery tool (see BAN 2/28/2006).

According to NimbleGen's Nuwaysir, MethylScope has been developed on the NimbleGen platform and the deal with Orion represents an interest in its arrays outside of academia.

Still, Leon said in February that Orion has no plans to offer MethylScope as an Orion product in the future.

• Justin Petrone ([email protected])

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