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Agilent Leads Effort as Array, Microfluidic Tools Shops Compete for US Pathogen-Detection Cash

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Competition between microfluidic- and array-based technologies that can detect the presence of biological and chemical threats has increased in recent months.

Agilent has released a microfluidic-based pathogen detector, while rival companies plan this year on providing government sponsors with array-based threat-detecting prototypes.

The firm has been busy recently marketing its automated lab-on-chip platform [ALP] 5100 bioanalyzer — most prominently to the US Departments of Homeland Security and Defense — as a rapid pathogen-detection system.

The Palo Alto, Calif.-based company announced earlier this month that the Midwest Research Institute, an independent proving ground for novel technologies and applications, has found that the product can effectively perform ultra-high throughput screenings.(See sidebar, p. 5)

The announcement, made Feb. 2, follows on the heels of similar tests performed by the US Environmental Protection Agency and the US Army, both of which tested the technology for its reliability in detecting pathogens in the field. Agilent has also scheduled a series of e-seminars on biodefense and pathogen detection throughout the first half of 2005.

“ALP enables more high-throughput screening of changes in DNA,” explained Christine Maehr, a spokesperson for Agilent. “So if you are looking to identify something based on DNA, like anthrax, the typical turnaround for earlier tests was something like 24 hours. With [the ALP] you can do it in 30 minutes for a quick print screening.”

Had ALP been composed of Agilent’s microarray technology, the company would have been among the first to develop an array-based biodefense product. Yet Agilent has decided to forego pursuing microarrays in biodefense. Instead, ALP uses microfluidic technology to identify biological and chemical threats, and, according to Maehr, Agilent has decided that microfluidics offers a better vehicle than microarrays for pathogen detection.

“That was never something, even after [the terrorist attacks on] Sept. 11, 2001, that Agilent as a company pursued,” Maehr said of using microarrays for pathogen detection.

Maehr attributed the decision to several factors, including the speed of the technology in identifying pathogens, the cost of using the technology, and the scope of pathogens the technology can detect.

“It depends on what you are trying to do,” she said. “If you want to identify something rapidly and cheaply, then the ALP is going to win out [over microarray-based detectors].” Lab chips usually run in the ballpark of a couple bucks, while individual microarrays can cost a few hundred, she noted.

Maehr argued that because ALP can do chemical as well as biological pathogen detection it was a better bet for the biodefense and homeland security industries.

“There are a lot more chemical weapons out there than there are biological,” she said

Room for Arrays?

How will rival microarray companies fair if Agilent believes that chemical reactions trump microarray-based technologies for identifying bio and chemical threat agents?

CombiMatrix, for one, is currently funded by the US Department of Defense to develop a microarray that will compete with Agilent’s ALP. This product is scheduled to be released in 2006, and the US government has agreed to fund CombiMatrix with an $8 million grant over 2005 and 2006 to help bring the project to fruition, according to Bret Undem, vice president of the Mulkiteo,Wash.-based company.

“We are developing a prototype unit for [the Department of Defense] that can also do electrochemical detection,” Undem said.

Because the chip CombiMatrix is developing is equipped with the tools for detecting biological and chemical-based toxins, viruses, and bacteria, and can run approximately 12,000 individual assays simultaneously, Undem said it will be a competitive technology when it is released.

According to David Danley (see Lab Report, p. 7), director of CombiMatrix’s homeland security and defense program, the trend in bio and chemical threat detection is toward integrated systems that offer more than one service. Danley predicted that microfluidic and microarray applications would eventually be “married” and available on one integrated chip.

“I think the user community wants to get rid of redundant systems or systems that are incompatible,” he said. “In the military, particularly when you’ve got to deploy something to the field, to have three or four different instruments to detect biothreat agents is just not logistically sound. The users would like to have one format, one system that does everything,” Danley said.

Danley said the chip CombiMatrix is developing can test for chemical, biological, viral, bacterial, and toxic agents.

Undem argued that because microarrays tend to be more specific and sensitive than the microfluidic technology used by Agilent’s ALP and Caliper’s 90 lab-on-chip, it will make an integrated chip more attractive for users in the biodefense and homeland security industries.

Undem added that the market for microarray-based biodefense tools is still wide open and hinted that it probably won’t materialize until 2006 when many similar technologies developed by companies such as Affymetrix — which is also funded by the US government — and CombiMatrix hit the market.

Affymetrix announced plans for a microarray-based offering in October 2004, but the company has not said when it plans to release it, nor has it revealed a name for the technology. The microarray market leader said its test would be able to “detect hundreds of top-priority bacterial and viral biological threats, such as anthrax and plague.”

Funded by a $2.1 million grant from the National Institute of Allergy and Infectious Diseases, Affy touted the assay as “the quickest, most comprehensive single test yet for biodefense.”

Saying its product could simultaneously detect dozens of bacterial and viral species and antibiotic-resistance genes, Affy said the test would enable users to “detect an attack where multiple pathogens are used.”

The company claims another advantage of its test is that it will enable medical personnel to treat victims of biological attacks in a more sensitive and efficient manner by recognizing genetic responses to biological agents, strains, or organisms that a less sensitive test would fail to register.

However, despite the possibilities presented in an October 2004 press release, Affy said its chip has yet to see a release date. At that time, Affymetrix said that its prototype test would be ready “in three months” — which was last month.

A spokesperson for the company told BioArray News last week that the test was still in the research-and-design stage, and that she was unsure of when it would become available.

CombiMatrix’s Danley speculated that in addition to Affymetrix and his firm, “there are a lot of companies that are working on this technology.”

Danley said the budding industry’s primary client is the US government, but he couldn’t “hazard a guess” on the amount of funding the Department of Defense and the Department of Homeland Security had set aside to fund the creation of pathogen detectors. However, he “would assume tens of millions of dollars will be invested in this technology, trying to bring it to fruition, and when they see it coming to fruition there will be quite a bit of funding available.”

— JP

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