By Matthew Willett

Nucleic acid amplification and detection technology that can detect both pathogens and single nucleotide ploymorphisms is at stake in a patent infringement lawsuit brought by ID Biomedical Corp. against Third Wave Technologies Inc.

Vancouver-based ID incorporates the technology in its Cycling Probe gene identification system, which is useful in a gamut of applications that run from genomics to diagnostics, and includes development of vaccines and immunotherapeutics.

ID claims the same underlying intellectual property is used by Third Wave in its Invader signal amplification platform. The suit seeks an injunction prohibiting Third Wave from selling Invader products or services, and prohibiting the sale of any product, kit or reagent that enables an end user to perform an Invader assay. The suit also seeks damages for alleged past infringements.

"I think we have a strong patent, and I think it goes to the heart of their Invader technology. That's what we put in the suit," said Todd Patrick, ID's chief operating officer.

Representatives of Madison, Wis.-based Third Wave did not return phone calls Friday.

ID licensed U.S. patent 5,403,711 - the patent it claims is infringed - from the University of Iowa in 1993. Since then, said Patrick, it has licensed the technology to PE Biosytems, now Applied Biosciences, of Foster City, Calif.; Mitsubishi Chemical, of Tokyo; and Alexon Trend Inc., a subsidiary of Sybron Chemicals, of Birmingham, N.J.

He added that his company is currently in talks to further license the technology, which he noted differs materially from older DNA analysis platforms incorporating polymerase chain reaction technology.

"Under the broad patent, we developed a technology called Cycling Probe that uses signal amplification based on the broad concept of using the target as a catalyst for the reaction as opposed to amplifying the DNA like PCR does," Patrick said. "We use the target DNA as a catalyst for the reaction, so as a probe comes in and attaches to the target, then an enzyme comes and clips that probe. The process repeats itself, cycling."

Invader technology, according to Third Wave's SEC registration for a proposed initial public offering, makes use of two short strands of synthetic DNA, called Invader probes and Primary probes, that bind, or hybridize, to the target. The primary probe contains a short portion that does not bind to the target, and together the probes form a structure recognized by Third Wave's patented Clevase enzyme.

When the Clevase enzyme encounters the hybridized structure, it cuts the unbound flap, which hybridizes to a third probe, called the signal probe. When the Cleavase enzyme recognizes that structure and acts on it, the resultant separate portion of the signal probe emits a detectable fluorescent signal.

The high-frequency process is said by Third Wave to produce tens of millions of detectable signals per target when the target is present.

Third Wave has had its hands full of late, with the IPO, the intellectual property dispute with ID and a proposed merger with PE Biosystems that fell through in May due to antitrust concerns at the Justice Department. The all-stock transaction valued Third Wave at $330 million when it was disclosed in January.

Third Wave itself filed suit against ID in August, seeking a declaration that several ID patents are invalid and that Third Wave products and processes do not infringe on ID patents. That suit remains unresolved.

In August, Third Wave also announced its intentions to take its stock public with hopes of garnering about $100 million through the sale. That filing came close on the heels of a $48 million private placement.

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