Pinpointing specific genetic makeup as a way of predicting and managing disease has long been a goal of medical science. With its Invader assay, Third Wave Technologies of Madison, Wis., is making great strides in the race to push healthcare into the molecular era.
The Invader assay, launched into clinical and research markets late last year, is one of a family of proprietary platform technologies from Third Wave. It is a linear signal-amplification system for direct detection and quantification of gene-specific sequences in complex mixtures of nucleic acids. The technology uses a fluorescence resonance energy transfer (FRET) detection format that allows it to analyze known nucleotide sequences in both DNA and RNA. It also can be configured for other detection formats.
(left to right) Scott Law, Ph.D., senior research scientist, is the lead scientist for any SNP special innovations required by pharma and genome companies; Karl Nichols, research scientist, works with customers on assay optimization; Monika De Arruda Indig, Ph.D., manager of the genetic variations group, oversees the discovery programs that involve setting up and screening SNPs for pharma and genome customers.
What makes the technology simpler and less expensive to use than other alternatives is that it’s PCR-free. It’s a much simpler chemistry. No special containment is needed, and assays may be run in standard microtiter plates. The cost is lower because it has a universal label rather than individual labels. The assay also integrates into the workflow of a research or clinical lab, essentially making it a “turn-key” operation, said Dr. Lance Fors, Third Wave founder and CEO.
Third Wave and the U.K.-based Sanger Centre, one of the world’s largest genome sequencing centers, are collaborating to build the first high-density single nucleotide polymorphism (SNP) map of a human chromosome and corresponding SNP test panel. The joint effort will focus on SNPs found on human chromosome 22, which were identified as part of the Sanger Centre’s completion of the chromosome 22 DNA sequence.
All of this puts Third Wave on the cutting edge of molecular research and disease management.
Lance Fors, CEO
“We are already making an impact on nucleic acid analysis,” Fors said from the company’s Madison, Wis., headquarters. “We are commercialized broadly into the research market. We have made over 1,000 products to date for research applications, which makes us a leading provider of assays for analyzing genetic variations. We are collaborating with the Sanger Centre, and (in January 2000) we announced a collaboration to produce assays for the known genetic variations that occur on chromosome 22.”
This year alone, Fors said, Third Wave will produce around 2,000 products for chromosome 22 research.
Third Wave recently merged with PE Biosystems, a division of Perkin Elmer, headquartered in Foster City, Calif., in a deal worth more than $300 million.
“Our merger with PE Biosystems opens up a big opportunity to combine our Invader chemistry with their instrumentation platforms and software to offer turnkey systems for high-volume clinical applications,” Fors said. “Our goal is to be the leading provider of genetic analysis products for research and clinical applications.”
Research into finding a new and better way to analyze DNA and RNA began in the early 1990s. A variety of methods and experiments were tried, with one resulting in the control working better than the experiment itself. In an effort to better understand their existing technology, Third Wave researchers experimented with (CFLP) cleavase fragment linked polymorph, which resulted in a reaction that was almost a thousand times more specific than previous technologies. This left the door open to possibilities that eventually yielded the Invader assay, Fors said.
“It’s all about paying attention to the unexpected,” Fors said. “It was a huge team effort, the efforts of different people paying attention to the unexpected.”
Invader technology can make DNA analysis quicker, easier and cheaper. “The beauty of this technology over PCR is that you’re not just using hybridization, but also a precise enzyme substrate reaction. It makes the assay more specific and easier to develop,” he said.
There are five key benefits to using the Invader assay, according to Fors. The first benefit is accuracy in test results.
“Invader has shown 99.7 percent accuracy, that’s phenomenal for routine high volume DNA analysis,” Fors said, referencing the research of Dr. David Bentley, the head of human genetics at the Sanger Centre.
“We’ve already received several hundred Invader chromosome 22 SNP assays and have set up an automated high-throughput system for genotyping using Invader assays,” Fors said. “Preliminary data shows that the Invader method is more accurate than PCR-based methods at detecting the less prevalent genetic variant for a given SNP.”
Secondly, Fors said, the cost per result is less with Invader technology. “Ongoing running costs are lower, and there are also very few moving parts and components.”
Breadth of menu is the third benefit, he said: “When you think about companies that are successful in the clinical arena, it’s because they have the broadest menus available. We can turn out products in a shorter time, at lower unit cost.”
Simplicity of operation is the fourth benefit, he said. “Invader is a simple chemistry that runs on existing hardware and this allows us to save the customer money,” he said. “The ease of use with existing instrumentation is important, the only things you need are two heat blocks, one to denature the DNA in sample and another to keep the temperature constant, and a florescent microtiter plate reader.”
The fifth benefit is that the Invader technology works today in a variety of arenas, he said. “If you’re really going to make a contribution to the field of nucleic acid analysis, then you need technology that’s robust enough to work in the research and clinical environment.”
Among those using the technology and touting its benefits is Brian Dawson, associate professor of pathology at the University of Texas Southwestern.
“There are advantages to using the Invader technology, such as it being less susceptible to contamination because there is no target amplification,” Dawson said. “The assays are very simple to do. The way it’s set up now, at the end of your run, you take the plate out, put it on the fluorometer and read the signal.”
He said the Invader technology also should be adaptable to real-time PCR type instruments as well.
“And it appears, if not cheaper than, it will be at least similar in price to PCR but without all the post-PCR manipulations we do now,” he added. “Plus, there’s no royalty paid to Roche when using its patented PCR technology.”
Invader technology is already a proven entity at Midwest Hemostasis and Thrombosis Laboratories in Muncie, Ind., said Dr. Douglas Triplett, medical director.
“We are already using Invader reagents for Factor V (Leiden) and are beginning to routinely use Invader reagents for the Factor II (prothrombin) application, eliminating the need for PCR-based tests for these important markers.”
Invader assays are “easier to run, require less lab space and equipment and are proving to be significantly less expensive than the PCR-based tests we used before, Triplett said. The MTHFR (methylene tetrahydrofolate reductase) test is a very important addition to our hemostasis screening panel.”
Triplett sees the technology as having tremendous potential. “I think we’re at the cusp of moving into the molecular era of medicine,” he said. “Our grandchildren or maybe our children may well know their genetic makeup and if they’re predisposed to disease.”
But with that technology comes a warning, he said. It may be opening Pandora’s Box.
“There are tremendous implications, negative and positive,” he said. “If (information about a person’s predisposition to disease) falls into the wrong hands, it can be negative. The government must work with insurance companies to ensure that everyone has an equal playing field, and that companies do not discriminate against someone who may have a disease.”
Coincidentally, on Feb. 8, President Clinton signed an executive order prohibiting federal agencies from using genetic information in hiring or promotion decisions, an order that affects about 2.8 million federal employees. Clinton said he hoped the order would help garner support for proposed legislation called the Genetic Nondiscrimination in Health Insurance and Employment Act of 1999. The act would extend federal employment protections to the private sector.
Triplett should be pleased to hear about the president’s action. Doctor-patient confidentiality must be protected, he said. “That information should be between me and my doctor. It should not go anywhere else.
“There must be universal laws that cut across state boundaries and cover all the population, guaranteeing privacy. It’s a major ethical issue that will probably be discussed over the next 20 years.”
