July 24, 2008
UI and ISU establish shared DNA sequencing instrumentation
The University of Iowa and Iowa State University are pooling their resources to significantly enhance both institutions' genetic research capabilities.
The two institutions have each purchased a massively parallel DNA sequencer -- an instrument capable of deciphering DNA sequences at the rate of millions to billions of bases in a single run. The two machines -- each with unique advantages -- will be available on a fee-for-service basis to researchers at both universities and to other institutions and private companies. Together, the two instruments represent the state-of-the-art in DNA sequencing technology.
The initiative was spearheaded by Michael Apicella, M.D., professor and head of microbiology and senior associate dean for scientific affairs in the UI Roy J. and Lucille A. Carver College of Medicine; Stephen Howell, Ph.D., professor of genetics, development and cell biology and director of the Plant Sciences Institute at Iowa State; Paul McCray, M.D., the Roy J. Carver Chair in Pulmonary Research and UI professor of pediatrics; and Patrick Schnable, Ph.D., professor of agronomy and genetics, development and cell biology and associate director of the Plant Sciences Institute at Iowa State.
"The range of capabilities represented by these new instruments could not have been developed by the two institutions working alone," Howell noted. "The cooperative spirit generated through this interaction will help Iowa scientists stay at the forefront of this rapidly evolving field, and help us maintain our leadership in areas ranging from the medical to agricultural sciences."
"These machines can sequence extensive tracts of DNA to look for genetic differences associated with human diseases," said Apicella. "I can see this technology having a significant impact in the clinical realm in the next four to five years.
"These instruments also make us competitive for major federal funding related to new genome sequencing initiatives, including the NIH's 'microbiome' project, aimed at investigating human microbial flora diversity," he added.
The new sequencers use an approach called single molecule detection with amplification whereby hundreds of thousands of DNA fragments are sequenced concurrently to generate hundreds of millions to billions of bases of sequence information per sequencing run. At the same time, this highly sensitive technology also permits the detection of rare sequence variants that previously were not detected using traditional capillary-based sequencing approaches.
The UI-based sequencer is a Roche 454, which cost around $500,000. The instrument will be part of the UI DNA facility, which is directed by Kevin Knudtson, Ph.D. Sixty percent of the cost was covered by funding from the Office for the Vice President for Research and the UI Carver College of Medicine, and the remaining 40 percent was raised from Carver College of Medicine departments and faculty members interested in taking advantage of the research opportunities the instruments provide.
The Roche 454 instrument is a so-called "long-read" machine, capable of sequencing relatively long DNA fragments of 200 to 500 bases. This instrument will be especially useful for sequencing new genomes from scratch.
The Iowa State sequencer is an Illumina Genome Analyzer II with a price tag of more than $535,000. The instrument will be part of the DNA Facility of the Office of Biotechnology, which is managed by Gary Polking, Ph.D. The cost was shared by Iowa State's Plant Sciences Institute, the Office of Biotechnology's DNA Facility, the Office of the Vice President for Research and Economic Development, the Center for Integrated Animal Genomics, the Department of Animal Science, the Department of Agronomy, the Agricultural Experiment Station, the College of Agriculture and Life Sciences, the College of Liberal Arts and Sciences, and the College of Engineering.
The Illumina is a "short-read" instrument that can sequence relatively short DNA fragments of 18 to 36 bases. The instrument is capable of sequencing many more fragments per run, producing in excess of a billion bases of sequence data, compared to the long-read machine, which generates around 100 million base pairs of sequence. The Illumina sequencer is well suited for genome-wide applications, studies that analyze mutations and sequence variations associated with genetic diseases in humans and beneficial crop traits in plants. It includes ChIP-seq, digital gene expression tag profiling, whole genome and candidate gene re-sequencing, and small RNA identification and profiling.
"Sharing the two instruments will allow researchers at both universities to conduct research projects that might not have been economically feasible without this dual access," Polking said. "University of Iowa researchers who send DNA or RNA samples to our facility in Ames will pay the same rates as Iowa State researchers. We have been contacted by several UI and Iowa State researchers who are very excited about having access to both instruments."
"It doesn't matter that each institution only has one machine on site because this will function as one single facility," Apicella said. "Researchers from either institution now have access to two machines, which have different capabilities and will be useful for different projects. We really are sharing resources at every level."
Apicella added that additional infrastructure already is in place to take advantage of the sequencing power provided by the machines, including bioinformatics expertise and fiber optic cables between the two institutions to transfer the huge amounts of data generated by the machines.
NOTE TO REPORTERS: For information about researchers and projects that will use the massively parallel DNA sequencers, contact Jennifer Brown, firstname.lastname@example.org, at UI, or Mike Krapfl, email@example.com, at ISU.
STORY SOURCE: University of Iowa Health Science Relations, 5135 Westlawn, Iowa City, Iowa 52242-1178