The Illumina HiSeq 2000 sequencer, the supercomputer that analyzes the data it collects and the expertise of the doctor who runs the lab, is boosting local research in a number of ways — including increasing the efficiency of experiments and the amount of information derived from them.
Since CU’s BioFrontiers Institute opened last year, about 20 businesses and organizations have taken the university’s offer to use its sequencer, including OPX Biotechologies Inc. in Boulder and Thermo Fisher Scientific Inc. in the Lafayette.
Known as next-generation sequencing, the technology determines the chemical composition of genomes, which represent the complete genetic makeup of cells.
Most every cell in a body contains a complete copy of genomes — representing all the genes necessary to make up that organism.
“Sequencing data can be used in as many ways as someone can to think to use it,” said Jim Huntley, director of the Next-Generation Sequencing Facility at the BioFrontiers Institute.
“For example, if you wanted to come up with a bigger and better chickpea, you could use the genetic information from sequencing to determine which varieties are more drought resistant and use that information in breeding strategies to come up with healthier crops.”
Rather than altering the new version using GMO techniques, sequencing helps find a way to use the information that’s already there.
Uses for sequencing in the medical industry include potentially reducing the amount of time and increasing the amount of accuracy in determining treatment for serious diseases. With information from sequencing a tumor sample, for example, researchers could determine the best treatment for a particular individual upfront rather than relying on the trial-and-error process.
About two years ago, BioFrontiers recruited Huntley from Illumina because the Institute needed a niche expert to develop the sequencing capability for their own researchers, as well as to provide support for local startups and biotech companies.
Prior to setting up the lab, local sequencing projects tended to go overseas or to use microarray technology, which provides a narrower margin of data.
“Capital expenditure on rapidly evolving technologies used for research is a huge barrier for small- and mid-size businesses,” Huntley said. “Working with us gives these companies access to cutting-edge research equipment without substantial overhead.”
Partnering with biotech companies also helps support commercialization efforts while strengthening the biotech industry in Colorado.
“Our primary mission is to support the Boulder campus and the Anschutz Medical Campus as well as other research and biotech companies,” Huntley said.
Partners, as he calls the groups that utilize the Next-Generation Sequencing Facility, are in Colorado, New Mexico and Nebraska. “Our model is number 753, so there are at least that many in the world,” he said, referring to the number of sequencers like the one at CU.
Using a fee-for-service business model, the next-generation facility bases charges on the extent of data an organization is looking for. Costs range from $1,500 to $26,000 per project.
With a combined biotech and business background, Huntley built the institute’s business model. “A lot of time facilities struggle to remain solvent,” he said. “We’re not making money but we’re not losing it either. I’m pretty proud of that.”
To date, the Institute has worked with about 20 outside entities.
“Some of our partners use the data to do product development — to look at the response of cells to drugs in development — and some investigators and researchers are in renewable energy and biofuels,” Huntley said.
Travis Wolter, a scientist in the genomics group with OPX Biotechnologies in Boulder, works on projects with Huntley as one of the facility’s partners.
OPX develops and produces bio-based chemicals that compare with traditional petro-based chemicals.
“Using next-gen sequencing, we have been able to cut costs, improve data quality and implement changes even faster than we were with our microarray system,” Wolter said. “Traditional DNA sequencing requires preparing an individual sample and knowing the target you’re looking for in the sequence.”
Next-generation sequencing, on the other hand, measures the sequence in a sample without a target, therefore letting researchers look for unknowns rather than knowns.
“He provides genetic information that allows us to answer questions in a matter of weeks rather than months or years.”
Annaleen Vermeulen, senior scientist with Thermo Fisher Scientific Inc. in the Lafayette facility where it manufactures RNAi products, also has worked with Huntley.
She describes next-generation sequencing as expensive, but it’s more than the direct costs that make working with Huntley valuable.
“We propose to Jim to run an experiment, and he gives us feedback so we’re able to design the experiment more efficiently, making the project move more quickly,” Vermeulen said. “The commercial providers’ costs for standard applications were higher than Jim … (and they) were not willing to work with us to do custom applications.”