Environmental Factor, August 2007, National Institute of Environmental Health Sciences
NIEHS Readies Molecular Genetics Core
By Eddy Ball
October 2007
Division of Intramural Research (DIR) investigators will soon have an in-house resource for genotyping and re-sequencing, according to Senior Investigator Douglas Bell, Ph.D., spokesman for the oversight committee of the new Molecular Genetics Core (MGC). Speaking on September 20 to a group of nearly 100 scientists gathered in Rodbell Auditorium, Bell said that he expects the MGC to begin processing requests as early as November 1 — the date the online requisition site is scheduled to be fully operational.
The MGC Steering Committee will be responsible for approving and prioritizing requests for services along a model currently used by the Microarray Core. Bell said that most routine requests should be approved quickly, but that large and expensive special projects may require more extensive committee consideration. “We anticipate a large demand for human single nucleotide polymorphism (SNP) genotyping. But because these projects often include large numbers of samples and require many genotypes per sample, we are not sure how many of these we can take on at once.”
According to Bell, the Core will eventually provide all knockout and transgenic mouse genotyping for DIR. Bell pointed to a survey indicating that 40 percent of DIR principal investigators have used genotyping of some kind and that “a significant number need it on a regular, even weekly basis.… Specifically, mouse genotyping is a huge need, there’s a need for rapid turnaround, and it’s proven to be very expensive when done by contract.” The MGC facility was made possible by the acquisition of high-throughput, automated equipment using robotics to perform most routine mouse genotyping runs in 48 hours. Larger, more complicated “special” projects will take longer, noted Core Director Lauranell Burch, Ph.D., but, because of sample bar coding, automation and the economies of scale, the MGC will still save the Institute considerable time and money.
While Burch expects most of her initial jobs to involve mouse tail molecular genetics, the core will also be able to process all kinds of human samples and samples from other organisms used in genotyping and re-sequencing, including Drosophila, C. Elegans, yeast and E. coli. The facility houses equipment capable of a broad range of services:
- Oracle-based Laboratory Information Management System project management with barcode interface.
- Mining of existing SNP databases using the SNPselector program
- Compilation of local SNP database resources for SNP projects
- Mouse tail genotyping
- SNP genotyping
- Gene re-sequencing
The audience was clearly receptive to the new service and eager to begin using the facility. Except for a few comments about redundant bar coding — labs that already use barcodes will still need to identify their samples with Core stickers — most of the scientists, including one especially impatient staff scientist, Dmitry Gordenin, Ph.D., couldn’t wait to get started.
A few scientists queried Burch about how the facility will handle the mass of data it will be generating when labs begin taking full advantage of the new resources. Several seemed to share the sentiments of Senior Scientist Darryl Zeldin, M.D., who predicted that demand would be “substantially higher” than the 20 strains each week that Burch and the committee are anticipating at startup. However, Bell said, “I believe that we can eventually handle genotyping on several hundred mouse strains per week.”
There will be a series of smaller meetings in October to work out more details about the Core. “This is really an experiment,” added Acting Scientific Director Perry Blackshear, M.D., D.Phil. “Nothing is fixed. If demand outstrips the supply, we’ll increase the Core as needed.”
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