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NimbleGen to Debut Trio of New Microarray-Based Services in March

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San Diego — NimbleGen, a Madison, Wis.-based custom array provider, will launch several new products and services in the coming weeks, according to a company official.

Dan Clutter, the firm’s vice president of sales, said at the Clinical Genomics conference here last week that NimbleGen will release comparative genomic hybridization (CGH) arrays, a comparative genomic re-sequencing (CGR) service, and an array re-use service for its chromatin immunoprecipitation-based (ChIP) arrays.

The new products and services are currently available to the company’s clients in an early-access phase before they are formally launched, although Clutter said that anyone who desired early access to the services was welcome to approach NimbleGen.

Clutter said that the CGH arrays will give users that previously were using bacterial artificial chromosome and fluorescent in situ hybridization arrays the extra ante in determining “breakpoint analysis” — the location where [breaks and combinations] in the genome occurred.

“We are the only company that can offer high-density (up to 390,000 features), long oligo (up to 100 nucleotides) arrays,” Clutter said in an e-mail about its CGH offering.

“[With] our large number of features combined with the length of oligonucleotide probes we use, we can cover a lot of genomic territory on a single array,” he said.

Clutter went on to explain that the next new offering, the CGR service, is “a technique we invented that allows us to compare prokaryote genomes and rapidly map all of the mutations — SNPs, deletions, hypervariable regions — between them.”

Clutter added that the new service would be useful for “focused array-based sequencing to determine the SNP changes and deletions on the portions that are different. This drops the time and cost of genome sequencing dramatically.”

Finally, Clutter predicted that array re-use, the third service being offered by NimbleGen, would be nothing short of a “paradigm shift” for the microarray industry.

The technology allows for arrays to be hybridized with a sample, and then have the sample stripped away, leaving the oligos on the array intact. The array can then be rehybridized with another sample.

“We have validated the buffer systems and stripping protocols for the ChIP-chip assays and are in the process of moving all of our array applications to the new buffer conditions. Our expectation is that it will lower the cost of our services to the point where a sample can be processed through our services for about the same cost as an array from Affymetrix,” Clutter said.

Clutter said that for NimbleGen’s US government and Icelandic customers — who receive their arrays directly — the array re-use technology will “make the cost of our arrays equal or less than the cost of a spotted array.”

On the Road to Commercial Viability

The new services and products follow on the heels of a series of moves the company made last year to become more commercially viable.

In December 2004, NimbleGen named the Berlin-based German Resource Center for Genome Research as its exclusive distributor in the German and Austrian markets (See BAN 12/15/2004).

The broadened marketplace gave NimbleGen more opportunities to provide customers with its ChIP-chip technology, launched in June 2004, which several of the attendees at the Clinical Genomics conference acknowledged had been very useful in their research.

Clutter said that ChIP-chip has been very successful because it “can cover up to 40 Mb of genome on a single array.”

“This is enough space to map out all known human promoter regions on a single array or the entire human or mouse genomes on a multi-array set,” he said. “Coupling in array re-use, this allows whole-genome scans for under $10,000.”

The VP said that it would take nine of NimbleGen’s competitors’ arrays to equal the extent of the genome available on one of its ChIP arrays.

NimbleGen also launched an ENCODE service in November 2004, based on content generated by the Encyclopedia of DNA Elements Project Consortium (See BAN 11/17/04).

The ENCODE array contains more than 384,000 unique 50-mer probes selected from 30 Mb of human sequence data specified by the consortium, and NimbleGen was one of two microarray providers to launch an ENCODE service, the other being microarray market leader Affymetrix.

Yet at the same time that NimbleGen was competing with Affy, it was releasing its technology under Affy’s name. An agreement with Affy signed in June 2004 gave the company distribution and commercialization rights to NimbleGen’s NimbleExpress custom array, which is based on its maskless array synthesis technology.

Clutter explained that “NimbleGen wanted to have Affy’s endorsement of [the company’s] quality and reproducibility.”

“Affy is a distributor of our product. They sell our technology in their GeneChip format to their customers. Customers buy Affymetrix because of their quality and reproducibility. [However], they do not own us and it is not an exclusive distribution agreement,” Clutter said.

To top off 2004, NimbleGen raised $12.75 million in a series F private financing in November, and the fresh round of funding brought NimbleGen’s total private funding to approximately $41 million - money NimbleGen CEO Stan Rose told BioArray News at the time was part of a “fundamental transition from being primarily a technology-development organization to a much more commercially oriented company.” (See BAN 12/01/2004)

“I think the opportunities for us go way beyond expression analysis in all the organisms for which there are not catalog arrays — and that was really our thinking a year ago,” Rose said in November.

Now that the company’s plans appear to have come to fruition, Clutter said that he did not anticipate any new financing campaigns in the near future. He would not disclose how the company was faring financially, but said he did not forsee a need to raise more funds in the near future.

“We are a privately held company and don’t publicly disclose our finances. That being said, our revenues doubled last year and will more than double this year. I don’t expect us to raise any more funds unless our board decides that it is strategically important to do so,” Clutter said.

“We have had these applications in house and have been working on them for basically two years. Now we are focused on getting the products out in product form.”

— JP

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