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Small Core Labs Say Affy’s GeneTitan Is Better Suited for Larger Facilities, Oct 10, 2008

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Affymetrix may have launched its next-generation microarray platform, the GeneTitan System, with core laboratories big and small in mind, but a week after the system hit the market, larger labs appeared to embrace the new system while smaller cores stated that they are satisfied with their current set-ups.
 
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 using Affy’s new HT 3' IVT Express Assay, which the company said offers a streamlined protocol and the ability to work with less sample material (see BAN 9/30/2008).
 
According to Affy, the new system, as well its new, lower-cost “peg” microarray format, will eventually replace the traditional cartridge-based format that Affy has popularized since its inception in the 1990s. Affy’s first peg-formatted products are plates for expression profiling in human, mouse, and rat. Affy said it plans to add SNP-genotyping products in the peg array format to its menu next year.
 
Doug Farrell, Affy’s head of investor relations, last month told investors at Morgan Stanley Global Healthcare Unplugged Conference in New York 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 (see BAN 9/30/2008).
 
CEO Kevin King last month told investors at UBS’ Global Healthcare Service Conference that the new peg array platform would enable Affy to offer customers “cost-effective and multi-sample formats.“ According to King, Affy can now put up to 100 samples on a standard industry plate, and “customers can insert those into the GeneTitan system, walk away, and come back when the scanning is completed.” He estimated that that the cost for Affy to make a peg array is about 60 percent less than a cartridge, and 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 (see BAN 9/30/2008).
 
Such overtures have been welcomed by some Affy customers. “There’s always been an issue with the cartridge format of not being scalable in a high-throughput genomics environment,” Dietrich Stephan, head of the neurobehavioral research unit at the Translational Genomics Research Institute in Phoenix, told BioArray News last week.
 
“It takes a lot of full-time personnel time to run a cartridge format. The new format would reduce manpower by about 25 percent,” he said, though he added that smaller labs may not see this same benefit. Even though Affy is has said that the GeneTitan is also for lower-throughput users, “I think this is for larger projects in a genome-scale environment,” he said.
 
Stephan said that TGen would “absolutely consider” bringing a system in house. “We are using a robotics system to do 96-well format labeling but we still have to do cartridges by hand. But if this can do labeling, hybridization, and scanning, then, yes, I would absolutely consider a switch to that platform,” he said.
 

“At this time, when funds are tight, we would like to better utilize the current equipment rather than duplicate it with similar stuff.”

He also said that he is interested in Affy’s new genotyping products and “when one becomes available, we would immediately look at it, because it would reduce cost all around, which is more critical in a for-profit environment than a research environment.”
 
Shawn Levy, director of the Vanderbilt Microarray Shared Resource in Nashville, Tenn., was similarly enthusiastic about GeneTitan. He said that the VMSR is scheduled to have one installed within the next few weeks. “If you do a reasonable volume of human and mouse expression, it’s an instrument that will pay for itself very quickly. You are looking at half the cost for arrays and reagents, and half the time for personnel,” he said.
 
“We run thousands of arrays per year. If we cut our cost in half, it doesn't take a few years to recover the cost of this instrument. In less than three years it could pay for itself,” said Levy. “We've been running in batches of 96 for 18 months now. For us it makes a lot of sense.”
 
The VMSR runs eight Affy fluidics stations and three scanners with autoloaders, and Levy said that the GeneTitan “should basically take the place of the eight fluidic stations in terms of throughput per day and two scanners in terms of throughput per day.” He added that the GeneTitan would be a “pretty attractive” offering to investigators setting up a new core facility.
 
At the same time, Levy said that he has been lobbying Affy to increase the flexibility of the instrument so that it can handle more diverse projects. “I am continuing to push Affy so they change the design so you can run any multiple of 24 up to 96, and make it like Legos, so you can do 24, 48, 72, or 96 samples at a time,” he said.
 
“You should be able to have the instrument do 24 human, 24 mouse, 24 yeast, and 24 fly in a single run,” said Levy. “That would open up the market to a much broader group of investigators that saves them a lot of full-time employee time and, most importantly, their cost per sample gets cut in half.”
 
Strapped for Cash
 
While larger cores have warmed to the idea of bringing the GeneTitan in house, smaller labs are skeptical. Moreover, given the current funding environment, conservative core directors may have to choose between buying a second-generation sequencing instrument and another Affy platform, though Affy has not disclosed pricing for the GeneTitan.
 
“This is a problem that every core has across the nation: funding for new equipment,” said Chris Barker, director of the genomics core at the University of California San Francisco’s Gladstone Institute. Barker said last week that his “small core” was “very hesitant” to adopt GeneTitan. “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” (see BAN 9/30/2008).
 
“We also have an eye on sequencing. We know that next-gen sequencing is doing well,” said Barker. “The question is when it will be cost effective against arrays, and it’s a difficult calculus to balance new array platforms versus sequencing as demand changes as well.”
 
Sridar Chittur, director of the Center for Functional Genomics’ microarray core facility at the University of Albany, this week said that his core was unlikely to buy a GeneTitan since it would require an investment in more capital equipment. “At this time, when funds are tight, we would like to better utilize the current equipment rather than duplicate it with similar stuff,” he said.
 
Chittur told BioArray News this week that UAlbany’s current Affy set-up is one Affy scanner and two fluidics stations. He said that, while time consuming, his instrumentation gives him the flexibility to handle a variety of projects. “As a core lab, we run experiments for PIs that range anywhere from two-array comparisons to 200-array comparisons,” Chittur said. “If I need to run more samples, I would rather just buy a couple of extra fluidics stations than a whole new system.”
 
Agnes Viale, manager of the Genomics Core Laboratory at Memorial Sloan-Kettering Cancer Center in New York, said that she did not plan to acquire a GeneTitan system for similar reasons.
 
“Despite the fact that we have quite a large throughput for an academic core, 1,500 arrays per year and between 500 and 1,000 SNP arrays per year, I still see my core as a ‘boutique core’ in that we have a lot of different projects and array types, from zebrafish to human,” Viale told BioArray News this week.
 
“We have different labeling methods, and a different preexisting dataset to use for analysis. For all these reasons, I do not foresee a complete switch to the GeneTitan at this time,” she said. However, Viale said that she would consider adopting the GeneTitan “if a large project of 2,000 or more samples came along.”
 
Shrikant Mane, principal investigator at Yale University’s Neuroscience Microarray Center, said this week that he is reluctant to invest in a GeneTitan system solely for gene expression, citing a decline in demand in his lab for Affy arrays over the past year.
 
“GeneTitan may be good for a lab which is processing hundreds of gene-expression samples at a time, but due to the cost and throughput considerations, we may not like to adopt this platform at this stage,” he said. Mane added though that he would consider adopting GeneTitan once Affy introduces genotyping products in the peg array format.
 
“I think this system will only benefit larger labs, especially those who are processing large numbers of gene expression samples,” he said.
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