Last week, Ed Southern complimented Agilent on its technology as he received the annual award of the Association of Biomolecular Research Managers at its meeting in Portland, Ore.
He said Agilent’s sponsorship of the award had nothing to do with his praise, and he wasn’t beyond tweaking the company on the pricing of its technology as he presented a lecture on his pioneering work on genomic analysis and walked through the current state of the art.
He cited Agilent’s in situ manufacturing process, which utilizes ink-jet printers, for allowing flexibility in creating arrays — as an advantage over pin-spotted arrays, and those produced by in situ photolithography techniques, which is Affymetrix’s microarray manufacturing technique.
“It’s hard to redesign the array under those two methods,” he said. “If you want to change it, you have a lot of work to do.”
Agilent licenses Southern’s technology through Oxford Gene Technology, the firm set up in 1995 to manage the intellectual property developed in Southern’s lab. The UK-based firm is perhaps best known for its courtroom success in defending its patent portfolio. It has earned licensing fees from Affymetrix through litigation, and now lists Amersham, as well as Germany’s Febit, as licensees.
Southern also mentioned the mirror-based microarray manufacturing technology used by Febit, and Madison, Wisc.-based NimbleGen Systems, as another example of a microarray manufacturing technology with re-design flexibility.
He praised long oligonucleotide probes as best for gene-expression analysis, while saying “you must use short probes” for point-mutation analysis.
“You have to make a careful choice of which you are going to use in the application, whether for expression analysis or [if] you are looking for mutations,” he said.
Southern said microarray technology is open to continued refinement.
“Array technology is far from being at the end of its developmental process,” he said. “When you have greater reproducibility, that is when you start seeing these in diagnostics. I think we have not yet gotten to the point where we have sufficient robustness, although we are getting closer.”
Users are looking for better quality arrays, and greater reproducibility, he said.
“You would like it to be cheaper. Message to our sponsors there,” he said with a smile to Agilent’s representatives.
People would like to see increased sensitivity too, he said.
“We are working on our lab to see a single molecule rather than taking this whole integrated signal from these spots,” he said.
And, hedging bets perhaps, his lab has developed some 40 tags for use in mass spectrometry analysis, he said.
“We thought this would be a good way of tagging things as an alternative for fluorescent tags and we have developed the chemistry for doing that,” he said. “Instead of using just two labels, we are able to make many, many more targets for certain applications and analyze them simultaneously in the mass spectrometer. It adds a further dimension to the analysis.”
Also, Southern gave details on the technology being commercialized by Oxamer, an early-stage technology and firm incubated by Oxford Gene Technology (see BAN 2/18/2004).
The technology, developed by Ryan Egeland, a former PhD student of Southern’s, deposits oligonucleotides on a substrate through an electrochemical process to produce features 40 microns in width, with sharp features, defined chemically, he said.