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Affy Says Its Next-Gen Array Platform Will Help High-Volume and Low-Throughput Users

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Affymetrix this week launched its next-generation microarray platform, the GeneTitan System, as well as a new “peg” microarray format that company officials claim will eventually replace the traditional cartridge-based format that Affy has popularized since its inception in the 1990s.
 
According to Affy, the GeneTitan is a fully automated instrument that offers array processing from hybridization to data analysis. The first application to run on the instrument is whole-genome expression profiling made available in the firm’s 24- and 96-peg array plate format. The whole-genome expression-profiling application is performed using Affy’s new HT 3' IVT Express Assay, which the company claims benefits from a streamlined protocol and the ability to work with less sample material.
 
While Affymetrix has introduced high-throughput, automated systems in the past, the company has made it clear that its path forward as a microarray vendor will now depend on the success of the GeneTitan System in reaching a variety of customers, from those involved in genome-wide association studies to lower-throughput academic labs.
 
However, several Affy customers contacted by BioArray News this week offered a variety of opinions on GeneTitan, with some hailing the system’s reduced operating time while others stating that they had never heard of it.
 
Company officials said the decision to develop GeneTitan is one outcome of Affymetrix’s ongoing “transition phase” that was sparked by weaker-than-expected interest from pharmaceutical and biotech customers and increased competition in the gene-expression and genotyping markets.
 
In recent quarters, the Santa Clara, Calif.-based company has disappointed investors by missing revenue forecasts, while at the same time promising to deliver to the market a low-cost, next-generation platform that will set the firm sailing into the 2010s (see BAN 7/29/2008). According to Affy President Kevin King, the GeneTitan is that platform.
 
“We are very deep into a transition phase of our business. It is going to take several more quarters for us to restore the growth that we’ve had historically in our business,” King told investors at UBS’ Global Healthcare Service Conference, held in New York last week.
 
King said that Affy’s three main priorities are reengineering its array platform — which resulted in the GeneTitan — entering new, high-growth markets, such as lower-multiplex genotyping, and improving profitability by streamlining its manufacturing resources. The new platform has been developed in line with this strategy.
 
“In 2007, we stepped back and decided that it was time to reengineer the platform,” King said. He said that Affy has “essentially been using the same technology since the early ‘90s,” but now sees “opportunities to make better contributions to that in terms of providing more and better content, more flexible array formats, as well as reducing hands-on time for our customers.”
 
At the core of Affy’s new platform is its instrumentation and peg array format. The system includes Affymetrix’s ArrayStation, launched in 2005, which fulfills automated sample-preparation and liquid-handling duties, while the GeneTitan provides all other array-processing steps.
 
King claimed at UBS that the use of the system would reduce array-processing time for operators from seven hours to 30 minutes.
 
Earlier this month, Affy Chief Financial Officer John Batty told investors at Morgan Stanley’s Global Healthcare Unplugged Conference in New York that Affy’s current installed base is “getting long in the tooth” and that the firm’s customers are looking to scale to larger studies while looking for ways to lower costs.
 
“It is really total lifecycle costs,” he said. “It is how many full-time employees are required to process samples, so we are automating all the front-end fluidics handling and the high-throughput scanning.”
 
Peg Array
 
The second component of Affy’s new platform roll-out is a change to its array format. The company is now making its gene-expression array content available in plates of peg array strips, which Affy claims will reduce the cost of its consumables and fuel the demand for whole-genome association studies.
 
“The new peg-array format provides for cost-effective and multi-sample formats,” King said. “Instead of the individual cartridges that we have had for the last 10 years, we can now put up to 100 samples on a standard industry plate. Customers can insert those into the GeneTitan system, walk away, and come back when the scanning is completed,” he said.
 
King estimated that the cost for Affy to make a peg array is about 60 percent less than a cartridge. Based on the lower manufacturing cost, King predicted that over the next two years, Affy would be able to reduce costs for its arrays across its portfolio by about 30 percent.
 

“This is an evolutionary step; it is not a remake.”

At Morgan Stanley, Doug Farrell, Affy’s head of investor relations, said that the lower cost of the peg array strips will “be the currency going forward” for Affy, “not just for high-volume projects, but towards lower-throughput users,” such as academic labs.
 
Farrell added that the new expression products will contain the same content as Affy’s existing menu of expression chips. “This is an evolutionary step; it is not a remake,” Farrell said. “The assays will be the same. The proof of principle is already done; that will be available with the initial sales cycle,” he said.
 
Farrell added that Affy sees data comparison issues as “very important” and that the company has not yet disclosed comparability results between its older and newer formats, but that it intends to do so soon.
 
Batty said the core configuration for the GeneTitan will be 96 samples on a plate, though the company plans to configure its products, depending on the focus of the researcher, in strips of 24, 48, or 96.
 
Last week, Affy rolled out its first peg-formatted products, the GeneChip HT HG-U133+ PM array plate, which offers the same content as its Human Genome U133 Plus 2.0 array cartridge; the GeneChip HT MG-430 PM array plate, which offers the same content as its Mouse Genome 430 2.0 array cartridge; and the GeneChip HT RG-230 PM array plate, which offers the same content as its Rat Genome 230 2.0 array cartridge.
 
On top of the new expression products, Affy intends to offer SNP-genotyping products in the peg array format next year. Unlike the recently launched array plates, the newer chips will contain new content generated in an internal screen of 1,300 individuals.
 
“All of the products that are on the market today are largely based on the Human HapMap 2 project that looked at 270 individuals, which is hardly representative of the diversity that exists on the planet,” King said.
 
“Those products that are on the market today have done a good job of helping people to understand common sequence variation, which has led us to understand common diseases, whether it be Alzheimer’s or diabetes or what have you,” he said.
 
King said that Affy’s new database of human variation will be the source of its “competitive advantage” for its future genotyping products.
 
King did not discuss what impact the switch to the GeneTitan system would have on Affy’s customers. An Affymetrix spokesperson told BioArray News this week that the company will “continue to give our existing customers every support for their current platform” and will “work with them to enable them to transition to the new platform whenever they are ready to switch.”
 
Customers’ Take
 
While Affy is touting its new GeneTitan system and peg array format as its “currency going forward,” customers have so far provided diverse responses to its appearance in the market.
 
Shawn Levy, assistant professor of biomedical informatics and director of the Vanderbilt Microarray Shared Resource in Nashville, Tenn., said in a statement issued by Affymetrix this week that the new array plates “offer a scalable solution using some of the industry's most widely cited gene-expression array content.
 
"The GeneTitan System's 24- and 96-array plate formats and the new automated array processing capabilities enable us to scale from low- to high-throughput projects more efficiently than before, with minimal user intervention," Levy said.
 
But Chris Barker, director of the genomics core at the University of California San Francisco’s Gladstone Institute, said that, as a “relatively small facility,” the core would be “very hesitant” to adopt the peg array format.
 
“We are not making big plans to run to that platform,” Barker told BioArray News this week. “The peg format, based on the old system, requires one to run all 96 of the same array at once,” he said. “If you have the higher volume it makes sense, especially for those doing SNP arrays. We are moving into that direction, but we are not there yet,” he said.
 
“I think this platform is focused more towards biotechnology companies, pharmaceutical companies, people that are doing large-scale studies,” Barker added.
 
Barker also speculated that Affy might have a difficult time getting other smaller core labs to switch to the new platform. “This is a problem that every core has across the nation: funding for new equipment,” he said. “Unless there is a substantial reason for us to do it, where the costs per assay come down dramatically, then it may not make sense for us to do that.”
 
Meantime, several long-time Affy users contacted by BioArray News said they were unfamiliar with Affy’s new platform.
 
“Honestly, I have not heard a single word about a peg-array format or a GeneTitan instrument,” said Herbert Auer, manager of the Functional Genomics Core at the Institute for Research in Biomedicine in Barcelona, Spain.
 
“Last week I was at [Cambridge Healthtech Institute’s] Data-Driven Discovery Summit in Providence, RI, and nobody there mentioned a single word about it either.”

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