Posted 10/05/2007

EnGenCore opens with cutting edge
DNA-analyzing instruments

By Chris Horn

The University's newest research lab—the Environmental Genomics Core Facility—is now open for business, its gleaming array of DNA-analyzing instruments second to none in the Southeast.

The facility, dubbed EnGenCore by its staff, is located on the fourth floor of the Arnold School's Public Health Research Center and focuses on gene expression and gene discovery. The University research community has first priority in using the facility; EnGenCore is also open to outside users, and a sliding-scale fee for use is being established.

One of EnGenCore's biggest draws is a next-generation genome sequencing instrument capable of large-scale projects.

"The Roche Genome Sequencer FLX is our pride and joy," said Sean Norman, an environmental health sciences faculty member and interim director of EnGenCore. "It can sequence a bacterial genome in seven hours—one-hundred million bases. That would take several weeks if not months on a standard piece of equipment. We're the only lab in South Carolina with this instrument, one of only a handful in the world."

To handle the massive amounts of data that the genome sequencer generates, a Linux-based computer cluster with 64 2.2 GHz processors is set up with appropriate software for analysis. The genome sequencer, computer cluster, and other instruments were purchased through the legislature-funded Freshwater Environmental Initiative and upon the recommendation of the University's Environmental Research Initiatives Committee.

On the environmental front, scientists studying the state's rivers and other ecosystems will be able use the lab to determine the genetic effects of pollutants on organisms and explore other genetic issues in the environment. But the scope of scientific questions the facility can address extends much further.

Phil Buckhaults, a School of Medicine faculty member and scientist at the S.C. Cancer Center, has used EnGenCore to identify 100 new genes related to cancer development in the breast and colon.

"If you look at a dozen metastatic tumors and a dozen non-metastastic tumors and find the same gene in the metastatic tumors, you know that gene is responsible for metastasis," he said. "That would have taken many, many months the old-fashioned way—this machine did it overnight."

Discovering the new genes is an important scientific discovery—Buckhaults' findings have been published in a major journal—but the future implications are even more important, he said. "This methodology will revolutionize the way cancer patients are diagnosed and improve the information from which treatment decisions are made," Buckhaults said. "It will be a tremendous aid to oncologists as they look at the individual needs of each cancer patient."

Tara Sabo-Attwood, an environmental health sciences faculty member, is using another instrument in the facility—the Affymetrix microarray platform—to probe the entire human genome for changes in the expression of gene transcripts associated with toxicity of nanoparticles to better understand their potential human health impacts.

Norman has used the facility to complete the first-draft genome sequence of a sulfate-reducing bacterium. Identifying the genome composition will help scientists understand how the bacteria functions in natural ecosystems where it is involved in the biodegradation of pollutants and global biogeochemical cycles.

Other potential users of EnGenCore include pharmaceutical companies, biotechnology firms, hospital systems, and environmental consulting scientists.

Joe Jones, currently a scientist at Monterrey Bay Research Aquarium, has been named permanent director of EnGenCore and will start work in October. To learn more about the facility, go to www.sph.sc.edu/engencore or contact Norman at 803-777-0940.