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Yale University Scores $1M NIH Grant For Affy System, Mulls Sequencing Buy

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Yale's Keck Biotechnology Resource Lab received a $1 million grant from the National Institutes of Health last week to purchase an Affymetrix high-throughput system for its microarray core facility.
 
The award — roughly double what other array labs have been getting from the NIH so far this year — is just the latest in a line of several lush grants the NIH has awarded the Yale microarray core in recent years.
 
According to Shrikant Mane, who heads Yale's Affymetrix GeneChip core and is responsible for all other array platforms offered at Yale, the Keck Lab has benefited for two reasons.
 
"First of all, Yale has unbelievable infrastructure," Mane told BioArray News last week. "Yale School of Medicine supports this technology immensely, so the NIH sees that as a tremendous support," he said. Secondly, he said, the Keck Lab does not only support researchers at Yale, but also supports researchers across the US.
 
According to the abstract for its most recent NIH grant, the Keck GeneChip facility has analyzed more than 4,000 samples from around 115 investigators at Yale and 22 other institutions since 2003 and has seen demand for its services increase by more than 50 percent in each of the last three years.
 
The core has also been raking in the NIH funding in recent years. In 2005 it received a $1.2 million grant as part of a larger five-year, $25 million NIH grant split between Yale and three other institutes to develop a neuroscience microarray consortium capable of serving researchers from across the NIH. The other neuroscience partners included Duke University, the Translational Genomics Research Institute, and the University of California, Los Angeles (see BAN 6/29/2005).
 

"The bottom line is that we were doing arrays in the first place because sequencing was so expensive."

Last year Mane received an additional $375,000 grant for administrative costs related to the neuroscience consortium. This year's grant, though, is not related to the consortium work, and it will enable Mane to purchase a GeneChip automation platform and MegAllele system, according to the grant abstract, which notes that the requested systems will allow the Keck Lab “to meet the anticipated increase in demand for existing services, to bring custom genotyping within reach of its users, and also … improve the reliability of the resulting data by reducing operator-to-operator variability.”
 
Adding Affy’s MegAllele genotyping technology will be just another arrow in the quiver for Mane's 5,000 square-foot lab. Since its inception six years ago, the lab has offered Yale University and other researchers access to in-house printed cDNA arrays, followed by Affy chips, and more recently, NimbleGen tiling arrays for copy number analysis.
 
Last year Mane installed an Illumina system for genotyping and gene expression purposes because he was enticed by Illumina's competitive pricing and the reputation of its genotyping technology. "You can select the SNP of your choice, and they had tag SNPs. It was also cost effective," he explained.
 
Mane said that he is also considering bringing a next-generation sequencer into the lab, and noted that his current relationship with Illumina makes the company’s Genome Analyzer a likely choice.
 
"Definitely the microarray field is evolving towards high-throughput sequencing, so Illumina fits in really well there," he said.
 
"The bottom line is that we were doing arrays in the first place because sequencing was so expensive. Now … sequencing is getting day by day cheaper," Mane said. "It is my impression that in a year or two they might even replace microarrays," he added.
 
Mane said that a sequencer could be useful in gene expression and genotyping studies and that his lab "definitely has interest from customers." He said that the neuroscience consortium already offers access to ABI 3730 and 3700 DNA analyzers through UCLA.
 
"This whole field is really changing at a rapid pace right now," Mane said. "I would like to purchase what is really needed at the time but at the same time try to keep our options open for the future."
 
Mane added that he is also considering Illumina's new digital microbead-based BeadXpress system and Sequenom’s MassArray for lower multiplex genotyping experiments.
 
"We need a SNP platform for low-throughput applications," he said. "Both Illumina and Sequenom are very well equipped for that. We are just evaluating all the technologies so we'll have to see in one month" what Yale's next purchase will be, Mane added.