Peter Mac joins Affymetrix translational medicine program

Melbourne's Peter MacCallum Cancer Centre has entered into a five-year collaboration with Affymetrix to use the company's GeneChip microarray technology for translational research projects. Kate McDonald reports.

As part of Affymetrix's Translational Medicine Program, Peter Mac will aim to develop define and molecular signatures for improving patient care. As initial disease targets, Peter Mac researchers will use the Affymetrix technology to determine and validate genomic signatures of ovarian cancer and unknown primary carcinoma.

As part of the collaboration, Peter Mac joins key research institutes and other major cancer centres throughout the world, including the Karolinksa Institute, Institut Curie, the MD Anderson Cancer Center at the University of Texas, the School of Clinical Medicine at Cambridge University and the Broad Insitute of MIT and Harvard.

Peter Mac's director of research, Professor David Bowtell, said one of the benefits of the collaboration was the ability to move from the research setting into clinical applications.

"It's really a collaboration designed to take things we are finding in a basic research setting closer to the clinical setting," Bowtell said. "Particularly research projects where there's likely to be a clinical outcome, [such as] prediction of response to treatment or diagnosis of difficult diagnostic cases. Those sorts of things are of mutual interest to us and Affymetrix."

He said involvement in the Translational Medicine Program would allow Peter Mac to collaborate more closely with other international cancer centres. "It puts you in a community of people who are also trying to bring genomics to cancer medicine and that's part of the appeal of being in the program."

Another appeal was the development of new technology and the introduction of microarray technology into the clinical setting. "Affymetrix is constantly developing new applications in its photolithography systems, so it helps us to be an early test-bed for those. And Affymetrix is keen to see the technology applied and taken to the next stage, so it helps them as well."

Bren Collinson, managing director of Millennium Science, the Australian supplier of Affymetrix products, said his company had recommended Peter Mac for the program. "We've already supplied them with the instrumentation - they've been an Affymetrix user for some years," Collinson said.

"We'll continue to provide them with the arrays and reagents that they require and also an enhanced level of technical support through our in-house applications scientists."

Collinson said the translational medicine initiative was based on Affymetrix's desire to see its microarray technology developed into a molecular diagnostic platform that can be used in the clinical setting.

"Right now it's just being used in research," he said. "Everyone's talking about moving microarrays into the diagnostic market but there are very few platforms that are easy to move in there, because the diagnostic market of course requires a far higher degree of control.

"The Affymetrix microarray is manufactured, rather than just made on the hop. It is a process very similar to manufacturing semi-conductor chips, using photolithography, which means chip to chip variability is extremely low."

Variability and contamination has always been an issue in using microarrays in the clinical setting, he said.

"Particularly with the slide-based spotted array with people using home-made arrays - the big facilities would have a robot that would spot oligos on the glass slide but you do get a lot of variation.

"With Affymetrix chips, the oligos themselves are synthesised in situ on the glass slide using the photolithographic process, so base by base they are made one by one and you get a very consistent response.

"The biological variations you get between two samples are far greater than any variation you will see chip to chip."

Contamination is another issue that precludes home-made chips from the diagnostic setting, he said.

"The fact that the Affymetrix chip is enclosed in a sealed cartridge means that you don't have people sticking their thumb on it - people do that. There is also the problem of aerial contamination of the chip. With Affymetrix controls, the only thing that goes on that chip is the sample.

"The various buffers and hybridisation reagents are injected via the port on the back of the chip. The only way of introducing anything is by a sealed receptor through the port so you don't get any issues of contamination.

"Those two points are really the major reason why the Affymetrix platform was the first to receive FDA registration as an in vitro diagnostic device (IVD). And that's also why they have partnerships with Roche Diagnostics, bioMerieux and other large diagnostic companies to develop specific microarray-based tests."

Collinson said Affymetrix was keen to see this developed on a broader basis. "By working with academic groups rather than pharma companies you are more likely to see these things develop on a broad base, quickly."