Vanderbilt University’s Vanderbilt-Ingram Cancer Center has entered into a translational medicine collaboration with Affymetrix, marking the 24th such deal for the array manufacturer. Vanderbilt will use Affy’s GeneChips in translational research projects studying cancer and HIV and AIDS.
Affymetrix has signed a number of translational medicine collaboration agreements over the past year. While the focus of each program is different — an agreement with the Peter MacCallum Cancer Center in Australia focuses on ovarian cancer, for example (see BAN 10/3/2006
) — the objective for the company is the same: provide large cancer centers with research tools with the long-term intent of using array technology clinically.
“We have now signed 24 of these translational medicine agreements,” Louisa Leung, associate director of market development at Affymetrix, told BioArray News in an e-mail last week.
“The program is paving the way for large-scale validation of genetic and genomic signatures to be rapidly adopted into widespread clinical use,” she wrote. Leung added that all candidates for Affymetrix’s translational medicine program must have a clinical intent.
Leung noted that translational research collaborators can commercialize the results of these studies via two routes: in the form of a diagnostic through the firm’s “Powered by Affymetrix” program, which includes partners such as Roche Diagnostics and Pathwork Diagnostics; or by providing regulatory-compliant commercial services.
Jeff Canter, a researcher at Vanderbilt University Medical Center, said that the immediate benefit for Vanderbilt will be expanded access to Affy’s microarray technology.
”This agreement with Affymetrix not only allows us to do studies of much greater size but has also opened up new chips for us to use, particularly the [Affymetrix Human Mitochondrial Resequencing Array 2.0], which will be used as a research tool to identify genetic variants that may make some patients more susceptible to adverse effects of certain drugs,” he wrote in an e-mail to BioArray News this week.
”The big change, as far as our approach to research, is that we are going for the complete mitochondrial genomic sequence as opposed to limited candidate and haplogroup-defining SNPs in that genome,” Canter wrote. “This is really big for us in mitochondrial genetic epidemiology because there will be no missing pieces to the mitochondrial genomic puzzle,” he added.
According to Canter, the MitoChip, which interrogates 16,500 bases of the human mitochondrial genome with three PCR reactions, will be helpful in Vanderbilt’s cancer and HIV/AIDS research.
”Our main research goal is to uncover the role the mitochondrial genome plays in important complex disorders,” he wrote. “We will be using arrays to identify specific mitochondrial variations that we will take into the lab for more detailed measurements of electron transport function and free radical damage,” Canter added.
Canter wrote that his group at Vanderbilt is “looking at a number of cancers and not really focusing on one.”
“This agreement with Affymetrix not only allows us to do studies of much greater size but has also opened up new chips for us to use.”
Shawn Levy, scientific director of the Microarray Shared Resource at the VICC, said that the agreement with Affy has paved the way for a variety of different clinical uses of array technology at Vanderbilt, but noted that Canter’s project was the most likely to show a rapid transition from research to the clinic.
All work will be done through the shared resource, which is currently outfitted with five fluidic stations and two fully loaded scanners with autoloaders, Levy said.
He also said that Vanderbilt is in the process of building a voluntary DNA databank that could house up to 1,500 human samples per week. Vanderbilt has been an early-access customer for all of Affy’s genotyping chips, and Levy said it’s possible that Vanderbilt researchers could conduct association studies using the databank in the future.
Despite Vanderbilt’s cozy relationship with Affymetrix, Levy said the university will continue to provide its researchers with access to technologies from a range of vendors. “Everyone should make an objective decision for each project on what technology is best,” Levy said.
Separately, Sigma-Aldrich said last week that Vanderbilt had joined its RNAi Partnership Program. Terms of the membership call for the Vanderbilt-Ingram Cancer Center to receive Sigma-Aldrich genomics products, including its TRC shRNA libraries for human and mouse genes.
Access to the shRNA library will help Vanderbilt researchers “prioritize genes identified from various proteomic and genomic screens," such as microarray experiments, Levy said in a statement last week.
“Obviously you could envision an experiment that uses arrays to identify targets for gene knockdowns,” Levy told BioArray News. “There are some projects that could use both agreements to their advantage, although these agreements are mutually exclusive and the timing here is coincidental,” he said.