NIST Industrial Impact

Company: GeneTrace Systems, Inc., Menlo Park, California
Business: Genetic analysis technology developer
Number of Employees: 20 

The goal is among the most sought-after in science: To design a fully automated process for deciphering the genetic code that is rapid, reliable, and inexpensive. And a small start-up company from California did it--with a much needed assist from NIST's Advanced Technology Program.

The resulting system combines a potpourri of advanced technologies: new chemistries, robots, instruments, and software. GeneTrace Systems, Inc., describes its prototype technology as a synergistic combination of automated DNA probing, sequencing, and sizing reactions with laser-based "time of flight" mass spectrometry, which identifies particles by their mass as calculated from their speed under certain conditions. The fully automated process is hundreds of times faster than conventional DNA sequencing methods. An analysis can be done in 5 seconds that ordinarily takes 3 hours, says Christopher Becker, the company co-founder and president. In fact, GeneTrace has separated and identified DNA fragments in less than a millisecond.

That speed, combined with greatly reduced labor costs due to full automation, could make genetic information much more accessible, offering the potential for genetic screening tests, for example, that are as affordable as simple blood tests.

"Knowledge is power," says Becker, adding, "The more you know and the better your tools are, the more you can do for people." He envisions the technology leading to comprehensive understanding of DNA that eventually will enable scientists to engineer highly effective, yet affordable, drugs and to design rapid, inexpensive tests for diagnostic and identification purposes.

Becker began work on rapid DNA sequencing in 1990 when he led the surface chemistry group at SRI International. DNA sequencing is the standard technique for determining the precise order in which four chemical bases appear in a strand of genetic material--the "code" that constitutes genes and provides instructions for cellular activity. GeneTrace was spun off from SRI in 1994 by Becker and a colleague, Joseph Monforte, a nucleic acid specialist, to bring "high throughput" sequencing technology to market.

"My partner Joe and I sort of looked at each other and said, 'Hey, we can make a business out of this,'" Becker recalls. The pair figured the ATP competition offered a way to turn a concept into a practical tool. The award enabled them to form a research team, which combined expertise in physics, microbiology, chemistry, engineering, instrumentation, robotics, and software, to build a robust automated system that was faster and cheaper than the current state of the sequencing art. "I think its fair to say that if it had not been for ATP funding, this company would not exist," Becker says. "To automate all this is not trivial--it takes a lot of work and effort."

The most common DNA sequencing method today is separation of fragments in an electrically charged gel ("gel electrophoresis"), which is expensive and time consuming because it requires several handling steps and costly reagents.

Some DNA sequencing had previously been attempted using mass spectrometry, in which gaseous ions (charged particles) are separated and identified by their mass. This method is rapid and can be automated, but until now it could analyze only tiny bits of genetic material containing only one type of base. A key problem was fragmentation of the fragile DNA during one phase of the analysis process. GeneTrace formulated a matrix compound that permits the material to be processed without breaking up, enabling the analysis of longer segments containing different bases. The matrix is just one of the company's innovations: Eight patents are pending related to the rapid sequencing technology, which was engineered as a system rather than merely a collection of components. Special methods and reagents were developed, for example, so chemical reactions and protocols could be automated and optimized.

GeneTrace's software-controlled process is initiated by a robotics system that mixes a small amount of DNA in solution with the matrix compound and places tiny samples on a flat plate to dry and form crystals. The samples then are placed in a vacuum chamber and hit with a quick pulse of ultraviolet laser light to elicit a puff of the matrix entraining the DNA, which accelerates toward a detector in an electric field. The gaseous ions separate by size, with the lighter ones traveling the fastest--up to 3 kilometers per second. The particles are identified by their mass as calculated based on their speed in hitting the detector. These hits set off a particle multiplier for amplification of the signal. The data are processed by proprietary software that identifies bases with greater than 98 percent accuracy. About 1,000 samples can be processed in an hour.

In addition to its speed and accuracy, the GeneTrace system eliminates gel waste, the need for dyes (used in gel separation to label certain molecules), and the human error sometimes involved in conventional sample preparation and data analysis. The new technology can sequence pieces of DNA that are 100 bases long--far shorter than the "read length" possible using gels but adequate to provide unique identification for applications such as clinical diagnostics and gene expression.

GeneTrace signed an agreement in 1996 with Incyte Pharmaceuticals, Inc., which licensed the mass spectrometry technology. Incyte also acquired a stake in GeneTrace, and the two companies are collaborating to develop applications. This alliance will demonstrate the use of the new system for studying differential gene expression patterns, a research technique used in drug development. In addition, Incyte plans to use the technology to help build its genetic database, a research tool for subscribing drug companies. According to Marian Marra, director of R&D Ventures for Incyte, GeneTrace technology will help "rapidly screen thousands of genes at a time in order to study gene function in multiple biological samples." In January 1997, the two companies announced that they had achieved highly accurate sequencing of a large number of DNA samples while using fully automated base-identifying software.

Several other companies are using GeneTrace technology for pilot projects focusing on gene discovery, gene expression, and genotyping, among other topics. Meanwhile, GeneTrace is using the remaining ATP funds to improve the rapid sequencing system by developing new assays and refining the automation, Becker says.

Becker says the GeneTrace system might lead to genetic screening tests for as little as a few dollars (they are $300 to $5,000 now) as well as highly effective new drugs and other benefits accruing from expanded knowledge of genetics. "I think the public should look forward to some major advances in medicine," he says.

September 1997