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ABRF Meeting Spotlights Convergence And Multiplexing of Lab Technologies


Erin O’Leary-Jepsen and Marjorie Matocq are proof enough that there are still potential microarray customers to reach in the basic science research market.

O’Leary-Jepsen and Matocq were sitting in an auditorium last week as Jack Zhai, Applied Biosystems’ associate product manager for gene-expression analysis, led a workshop presenting the company’s Expression Analysis microarray platform, which is scheduled for availability some time in the next financial quarter (see BAN 2/4/2004).

But unlike many of the other attendees, who didn’t remain at the event much longer than it took to eat the complimentary box lunch the company provided, the two researchers from Idaho State University sat through Zhai’s hour-long presentation, which was a commercial portion of the annual meeting of the Association of Biomolecular Resource Facilities in Portland, Ore., last week. (The walkouts were not likely a reflection on Zhai’s presentation skills, but perhaps just a reminder that budgets in academia are tight, and free lunch is compelling.)

While Zhai did not give a price for the company’s new technology, Matocq, an assistant professor in the department of biological sciences, and O’Leary-Jepsen, manager of the school’s molecular research core facility, were in tune on a price they would not pay for this system, or for Affymetrix’s platform either.

“$250,000?” said Matocq. “Not today.”

The school has invested in ABI’s sequencing technology, and offers automated DNA sequencing and microsatellite analysis, as well as PCR, oligonucleotide synthesis, and other services, but not microarraying or microarray analysis. It services some 20 researchers and Matocq said the core lab is considering purchasing some form of microarray technology.

“Not so much for gene-expression analysis or sequencing, but for assessing environmental samples in a chip format,” she said.

Matocq apparently is not alone in looking beyond gene-expression profiling on microarrays. The meeting drew approximately 1,400 core laboratory financial decision-makers, and vendors to Portland’s convention center. And many of the attendees were exploring alternative uses of this technology.

“I think that it speaks to people wanting to make better use of the technology for a variety of applications,” said Andrew Brooks, the director of the Functional Genomics Center at the University of Rochester Medical Center and director of the Microarray Resource Center of the Academic Medicine Development Company, a research cooperative of 39 New York institutions.

Brooks listed alternative uses for microarrays, including Affymetrix’s work with alternative splicing analysis, Illumina’s bead-based approach, DNA-based arrays for diagnostics, and resequencing arrays, or tiling arrays, for comparative genomic hybridizations.

A Metamorphosis?

Change has been a constant in this technology, dating back to the late 1980s when Sir Edwin Southern was doing his pioneering work.

Southern told the conference that in those days, he thought the technology he was developing could be used to compare human genomes; it could be used as a way to find mutations in gene sequences, and to analyze messenger RNAs among mixed RNA populations.

“That, of course, is the major application [of the technology] today, but it wasn’t one at the time,” he said in addressing the conference (see related story, page 6).

Southern, who is preparing for an active career after retiring from Oxford University next year (see Lab Report, page 7) is evolving too. The microarray pioneer told the conference that his lab is developing tags to introduce as a labeling technology for mass spectrometry.

“We are getting interested in mass spectrometry, as are the rest of you; How can you not be interested in mass spectrometry?” said Southern.

The labs, and the association, are also feeling this convergence. During a meeting to discuss association business, members questioned how the organization might remain relevant in the future.

“[ABRF] is changing because we have to address the question of, basically, holistic biology,” said Preston Hensley, an executive board member of ABRF, and manager of protein and peptide chemistry at EMS Discovery, Pfizer global research and development.

He gave as an example the work of Marian Walhout, an assistant professor at the University of Massachusetts Medical School, who is studying the application of protein-DNA and protein-protein interaction mapping approaches to the understanding of transcriptional networks in C. elegans.

“Marian is saying let’s take the upstream sequence in every gene in C. elegans, all of the things she thinks binds to DNA, couples it to the activation domain and puts it in front of a reporter gene,” he said.

“She will discover vast new amounts of stuff and we will go and find out what these things do.”

He said this change of approach will lead to a consolidation among core labs.

“The isolated fee-for-service core lab, which is what ABRF is based on, is going to go out of business,” he said. “If you look at the Institute for Systems Biology, that is a gigantic version of what the future is going to be. There will be some medium level of that but core labs will work together. The distinction between pitcher and catcher is going to go away.”

Brooks of the University of Rochester also said small core labs are headed for oblivion, unless they adjust.

“Core labs that have the ability and the wherewithal to stay technologically current will continue to succeed and do well,” he said.

Part of that is focusing on making better use of technology to increase throughput, and better helping the researchers served.

This of course means buying the equipment.

“Capital investment needs to be part of the business plan, or else you are going to fail,” he said.



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