Microarray makers and users gathered for the four-day, all-you-can-eat Chips to Hits conference in San Diego last week.
Despite the widespread drop in air travel since September 11, this year’s annual conference proved to be the biggest so far, according to organizers. Over 1,350 attendees made their way to the event from as far away as Australia and Europe.
Not surprisingly, given the ascendance of proteomics in the past year, protein chips figured prominently on the agenda, spanning a whole day of talks and other scattered presentations. Another major area of discussion was the movement of microarray-based molecular diagnostic platforms from the research lab to the clinical marketplace. Additionally, there was ample discussion — and speculation — on how the new configuration of players in the research array market will shake out, and whether any of the emerging technologies presented at the conference would be able to take a bite out of Affymetrix’s growing market share.
Following is a selection of conference highlights:
DNA Diagnostics Panel Works On Untying Regulatory Knots
In a panel on molecular diagnostics, representatives from Motorola, Nanogen, the US Food and Drug Administration (FDA), the CDC, the National Cancer Institute, The Mayo Clinic, Philadelphia Childrens’ Hospital, and NeoGen Screening discussed the future of microarray-based molecular diagnostics.
The major obstacles, according to panel members, include the FDA regulatory process, the scarcity of genetic counselors who can explain the meaning of DNA diagnostic tests to patients and doctors; the ignorance of genetics among physicians; and the present state of the technology.
“The biggest barrier [to success in the diagnostic array arena] is regulatory,” proclaimed Dan Farkas, director of clinical diagnostics at Motorola Life Sciences. Motorola has recently launched its eSensor array platform, which is capable of detecting up to 36 SNPs on a chip using an electrochemical-based detection method. But neither the eSensor nor its rival, Nanogen’s NanoChip Workstation, has passed through the regulatory approval process. Both are being used experimentally by some diagnostics laboratories in “home brew” diagnostic tests.
Joseph Hackett, of the FDA’s Center for Devices and Radiological Health, expressed an eagerness to work with microarray companies to overcome these regulatory hurdles. He held up a knotted cord, saying it illustrated the result when the FDA regulatory process could get companies into a product quagmire. “If we work together, these knots will disappear,” Hackett said. When companies start making home brew screening tests, the FDA gives them a long list of questions, but encourages them to proceed. The agency has met with 22 manufacturers of arrays, diagnostics, and informatics, Hackett said.
An additional issue with diagnostics is reimbursement by public and private insurers. Farkas emphasized the need for molecular diagnostics companies to lobby for better reimbursement codes. European countries present additional reimbursement questions, and these issues need to be tackled before molecular diagnostics become commercially viable, he said.
Will big pharma step in and iron out some of these regulatory and reimbursement wrinkles? The panelists thought not: The financial incentives for molecular diagnostics are not big enough for big pharma.
For Protein Chips, It’s All on The Surface
Presenters unveiled a variety of novel protein and DNA chip surface chemistry solutions at a special session devoted to the subject. While most of these approaches have been aired before, Prolinx, of Bothell, Wash., introduced a new solution to the protein chip surface problem. The company’s new Versalinx chip is a glass slide covered with a thick forest of proprietary “polymer brushes” the company has licensed in. Two chemical conjugates, phenyldiboronic acid (PDBA) and salicylhydroxamic acid (SHA), make up the binding chemistry. The protein ligand is first conjugated to the PDBA, while the SHA has been pre-attached to the polymer brush surface. When the protein-PDBA complex is applied to the slide, the PDBA and SHA form a conjugate that the company said is stable under a wide range of pH conditions. A wash step removes the unconjugated PDBA-protein complexes, the company said.
The entire process from sample preparation to wash step takes as little as 70 minutes, according to the company.
This two-step process virtually eliminates non-specific binding, because the polymer brushes and the intermediate PDBA-SHA bond prevent the protein from sticking to the glass, said a Prolinx spokesperson. The company is selling the slide kits in four-packs and 20-packs.
So what’s the catch? The SHA-PDBA chemistry approach relies on the idea that a protein being captured will have four or five binding sites. If a protein has only one or two binding sites, it does not as strongly bind to the PDBA, and can be washed away more easily. Anyone looking to bind protein molecules with fewer binding sites, however, may want to look elsewhere. The company said it was developing a new chemistry for use on proteins with fewer binding sites and would make it available within four months.
Meanwhile, several other companies presented alternative approaches to surface chemistry for protein chips. Glaucus Proteomics of Bunnick, The Netherlands, presented its hydrogel coatings that contain a dextran-based “interlayer,” a layer that separates the hydrogel “trees” to which the proteins bind, from the substrate, in order to minimize non-specific binding. Zyomyx, of Hayward, Calif., discussed its non-specific binding strategy: a gold monolayer with a negatively charged surface.
To figure out which protein chip surface chemistry works best, scientists will clearly have to run head-to-head tests. And this may take some time, as protein chip technology is evolving rapidly.
Wanted: Hemophilia and Thrombosis Arrays
Microarrays are allowing scientists at the CDC’s molecular and hemostasis lab to spot a common genetically-linked cardiovascular condition, unstable plaque, which leads to heart attacks by causing the arteries to fill up more easily with plaque. The CDC researchers have so far found that a genotype PLA-1 is linked to stable plaque, while a distinct genotype, PLA-2, correlates with unstable plaque, and are conducting a prospective study of patients admitted to coronary facilities at Lenox Hill Hospital in New York. “We will attempt to use chip technology to scan entire genomes” of the study subjects, said Craig Hooper, the CDC scientist who gave the presentation.
The aim of the study is not only to uncover new information about the genetic etiology of cardiovascular disease, but to eventually enable doctors to detect unstable plaque and other cardiovascular disease-related conditions before the heart attack occurs, and to determine prognosis and improve risk assessment. The researchers hope to identify potential targets for pharmacologic intervention as well.
In addition to the Lenox Hill study, Hooper said researchers are looking into the possibility of developing microarrays that would be able to screen for Factor V Leiden and Factor VIII Leiden gene mutations, the two hemophilia-related genetic markers; as well as a screening chip for the clotting disorder thrombophilia. The Factor V Leiden test, according to Hooper, is the most commonly ordered DNA test in the US today, while a thrombophilia test is the second most common, given that thrombophilia is connected to cardiovascular disease. Hooper called for the development of chip technology to detect these disorders as a way to reduce the cost — which now can range into the hundreds or even thousands of dollars — and make the tests more widely available.
In Emerging Technologies, Xeotron Wins Best Poster
Xeotron, a Houston startup that is developing high-density microarrays in which oligos and peptide probes can be synthesized in situ, won the best poster award for the conference. The poster, “A flexible biochip technology,” describes the way the company can produce chips in a matter of hours by combining microfluidics, photosynthesis, and PhotoGenerated Reagent (PGR) chemistry to synthesize proteins on the chip. Xeotron scientist Xiaolian Gao described during a presentation the new peptide arrays the company is planning to introduce.
An additional conference highlight included a presentation by Ulf Landgren of Uppsala University in Sweden on padlock probes, nucleic acid loops that wrap around DNA and RNA molecules and can be used to detect specific sequences. These probes can also be multiplied using rolling circle amplification, and the probe-analyte complex can be spotted down on a chip for analysis of single nucleotide differences in DNA or RNA samples. Landgren presented a similar “proximity probe” that he said detected protein molecules in a much more sensitive way than traditional commercial protein tests.
Overall, delegates had mixed reviews of the conference. While some raved about novel technologies such as Xeotron’s, others complained that far too many sessions were little more than product demonstrations. But those who stayed for the final day — a full roster of academics presenting their microarray-related research — went away fully informed, if not saturated, by the multiplicity of microarray applications being developed in the laboratory and the marketplace.