Most researchers who want to do microarray experiments on pathogens have to spot their own arrays, a feat that takes time, money, and technical expertise molecular biologists often lack.
Attempting to fill this need, the National Institute for Allergy and Infectious Diseases has awarded the Institute for Genomic Research a $25 million grant to establish a Pathogen Functional Genomics Resource Center.
First on the center’s agenda is developing microarrays for “a select group” of common pathogens, said Robert Fleischmann, the center’s administrative director.
“The NIAID was seeing a lot of RO1 grants in pathogen research asking for money to develop microarrays for various pathogens, and felt that it was a very expensive endeavor,” Fleischmann explained. “They wanted to see that the effort was centralized in a center that could handle that type of work.”
The center, which Fleischmann is co-directing with TIGR genomics researcher Scott Peterson, is to be housed in lab space in TIGR’s Rockville, Md., facility until 2003, when work is expected to be completed on a $12 million, 60,000-square-foot building that TIGR will begin constructing on its campus early next year.
To gear up for this effort, TIGR is now mounting a hiring campaign for the center, and expects to have a staff of up to 25 people, including hands-on lab personnel and software development engineers. The center is also planning to purchase two new arraying robots, as well as other equipment, and its directors are currently making the rounds of arraying equipment vendors.
In the first year, said Fleischmann, the center will develop arrays for three pathogens that have already been sequenced, and likely among these are strains of Staphylococcus, Mycobacterium tuberculosis, and Streptococcus pneumoniae. But he said that the final decision for which pathogen genomes to spot down will rest with the center’s scientific advisory committee, to which it is just now in the process of naming members.
In total, the center will provide 4,500 arrays to researchers in the first year; with 10 researchers on each of the three pathogens selected, and each researcher being able to obtain up to 150 arrays. The researchers will have to submit their requests for arrays to NIAID, Fleischmann said, and the institute will determine who gets the arrays.
Once accepted, a researcher will be able to order arrays through a password-accessible portal on the center’s website, http://pfgrc.tigr.org. Researchers will have to pay a small fee for arrays, which the center plans to distribute through a private company such as Research Genetics.
When told of these plans, pathogen researchers reacted with enthusiasm. This center “will be a big boon to pathogen research labs,” said Craig Cummings, a Stanfor postdoc who has spotted his own microbial arrays. “Pathogen microbiology labs will have an easy way to get microarrays without having to invest in facilities and people who have the expertise in microarrays.”
Initially, center personnel will make arrays by spotting down 250- to 500-base-pair amplicons, which a software program at TIGR identifies by looking at the annotated sequence and finding the middle of an open reading frame, then taking a few hundred base pairs on either side and designing a primer for it. But the center also is looking into developing oligonucleotides for the arrays, in conjunction with another private company. “This will bring down the cost, since we won’t have to make two primers for each open reading frame,” Fleischmann said.
While the initial beneficiaries of this new pathogen microarray facility will be researchers who have experience with microarrays, “ultimately, we also want to supply researchers with less experience, the have-nots,” said Fleischmann. “That was one of the major goals the NIH was trying to fulfill in putting this center together.”
To serve these newbies, the center plans to develop training sessions for microarray technology.
Cummings said the center can also provide pathogen microarray reseachers with standardization. “This whole microarray business is really short on standards. If there were widely distributed tools that worked really well, and that labs would be able to adapt as standard protocols for making arrays, using arrays, and storing the data, this would be an important advance for the field,” he said.
In addition to the microarraying facility, the center, which will spread out into 15,000 feet of the new TIGR facility, will also provide researchers with access to genotyping technology, clone sets, genomic DNA, and type strains.