A 5-year, $25 million National Institutes of Health grant awarded last week to the Neuroscience Microarray Consortium, a quartet of federally-subsidized academic and nonprofit labs that run microarray experiments for NIH researchers, could be a financial and practical boon to a few of the biggest biochip companies in the world.
Established in 2002 as part of the NIH Neuroscience Blueprint, a framework that supports neuroscience research done by NIH-affiliated investigators, the grant reflects increased usage of the consortium by NIH researchers, and the growing demand for array-gathered data among institute scientists.
According to one consortium participant, "eligible investigators" send RNA to the consortium, which performs all the labeling, hybridization, scanning, and data analysis for cost of reagents only. The grant pays for consumables and labor.
The $25 million award is the second for the consortium. The first grant, generated by the National Institute of Neurological Disorders and Stroke, raised $9 million over three years, "but based on demand and successful implementation of the program, the new project period is for five years," according to Thomas Miller, program director of extramural research programs at the NINDS.
Based on that demand, Miller said, the NIH decided that the consortium, which originally comprised labs at the Translational Genomics Institute, the University of California, Los Angeles, and Duke University, would take on a fourth partner at Yale University.
"I saw that grant and told the local sales people, 'Hey, talk to these people, they're using the wrong platforms,'" Dan Clutter, vice president of sales, NimbleGen.
Miller also said that the user group, which initially was limited to NINDS and the National Institute of Mental Health, would now be extended to all 15 institutes and centers that are part of the Neuroscience Blueprint — in all some 15,000 researchers.
Dietrich Stephan, director of the neurogenomics division at TGen, told BioArray News this week that the consortium has "a potential [user] group of 10,000 researchers across the country."
"About 10 percent of those people have either expressed interest or they are in the pipeline," according to Stephan.
"The effort has been very successful. To date we have 181 projects and we work with investigators all around the country, so it's a widely used resource," said Sarah Brautigam, a consortium coordinator and a TGen employee.
Brautigam said that researchers had focused on a variety of diseases, including Alzheimer's, epilepsy, autism, and others.
Of the $25 million subsidy, Stephan estimated that about one quarter of the money TGen is slated to receive would help pay for equipment, which are mostly arrays made by Affymetrix, Agilent, and GE Healthcare, along with Operon Technologies' oligonucleotides for a custom array service, which is offered at Duke University.
The most frequently run commercial platform is the Affymetrix gene chip, according to Pate Skene, the lead investigator at Duke University. "In the consortium as a whole, Affymetrix is the largest platform used. Agilent and CodeLink can also be done."
"We just put in a $1 million order to Affymetrix, so I would say 25 percent would go to support infrastructure, and the rest would go to support salaries and bioinformatics and stuff like that," Stephan added.
Rival companies saw the news as a new opportunity to market their products to the select labs.
"I saw that grant and told the local sales people, 'Hey, talk to these people, they're using the wrong platforms,'" said Dan Clutter, the vice president of sales at NimbleGen.
Clutter said that customers have been using NimbleGen's array comparative genomic hybridization platform for autism research and other neurological disorders.
Division of Labor
According to a decision made by officials at the National Institutes of Health some between 10,000 and 15,000 researchers at the 15 institutes and centers that make up the NIH's Neuroscience Blueprint framework for research on the nervous system will have access to the Neuroscience Microarray Consortium thanks to a $25 million, 5-year grant
According to the framework's website, the 15 institutes and centers that can now use the resource are:
Originally the consortium was only available to researchers from NINDS and NIMH.
TGen, which has the highest volume of users of the consortium according to Stephan, will receive $7.1 million of the total grant of $25 million, or around 28 percent of the total award. TGen, with its supercomputer provided by IBM, is handling the heavy bioinformatics work.
Asked about his group's award, Skene said, "We don't actually have the final award number but it's approximately $6.25 million," or 25 percent of the total funding.
According to Skene, Duke specializes in two services in the consortium: custom arrays printed with Operon oligos, and laser-capture micro-dissection.
"In terms of platforms we are focusing mainly on printed arrays which gives us the advantage of low cost, for people who need to do large numbers of samples or pilot studies," he said.
The remaining $11.65 million will be split between Yale and UCLA. UCLA has taken on the duties of SNP-genotyping, according to a statement by the consortium. It is still unclear how Yale, which was selected through a competitive reviewing process to be the fourth center, will fit into the consortium, according to fellow labs. Investigators at Yale did not return phone calls or e-mails by press time. According to last week's statement, the Yale lab is well-funded and equipped to handle the increasing load of the consortium.
The neuroscience faculty at Yale "command more than half of the university's biomedical research budget and occupy more than 60,000 square feet of well-equipped laboratory space," according to the statement.
Stephan said that the platform of choice at Yale was the GeneChip, but that the consortium may decide to offer an additional array platform there. "We'll probably add another platform at Yale, but we haven't decided yet," Stephan said.
5 AM World
In addition to Affymetrix, Agilent, Operon, and GE Healthcare, another company that may benefit from the refunding of the consortium is 5 AM Solutions, a five-person custom software shop that designed the portal and database that can be accessed by all researchers.
"5AM has worked with us to build the website, they've worked with us to build the sample submission process, the data upload, the data download, a way for us to report on work accomplished so that investigators can see the results of their experiments," explained Brautigam, the consortium's spokesperson.
According to Brent Gendleman, 5 AM's CEO, the company had developed a relationship with TGen through Stephan, who used to work in Washington, DC, where 5 AM was based, and encouraged them to relocate to Phoenix when he took on his position at TGen three years ago.
"We came out here specifically because of TGen," Gendleman said. Out of the initial $9 million grant, Gendleman said his company received "several hundred thousand dollars" to construct the electronic infrastructure that holds the consortium together.
"It's contractual, so where there's a need we address it," he explained. Therefore he was reluctant to guess on how much of the $25 million grant would go to IT support, but estimated that it may reach $500,000 over the 5-year period.
There is also the strong likelihood that the consortium will be funded again in 2010.
"This is one of the most successful programs in the NINDS portfolio, and they have recommended full funding with no administrative cuts which is unheard of in this NINDS climate," Stephan said
— Justin Petrone ([email protected])