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Genome Compiler Asks USPTO to Reexamine DNA2.0 Patent in Ongoing Legal Row

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Genome Compiler Corporation has asked the US Patent and Trademark Office to reexamine the legal document at the heart of an ongoing lawsuit filed against the company by competing gene synthesis firm DNA2.0 just over a year ago.

According to a request for reexamination filed with USPTO on Dec. 20, GCC is questioning the originality of the 69 claims listed in US Patent 7,805,252, awarded in September 2010 to DNA2.0 and describing "systems and methods for designing and ordering polynucleotides." The patent application includes a list of reference materials containing content that GCC argues "raise substantial questions of patentability" with respect to '252's claims.

Much of the fodder for the challenge comes from a July 2000 edition of a manual produced for the Vector NTI sequence design software — then owned by InforMax, now owned by Life Technologies — which was available at least one year prior to the earliest priority date of the '252 patent, according to the GCC. The company claims that this edition of the manual — which was not considered when the patent application was examined and ultimately granted — "either discloses or renders obvious the subject matter of each of claims 1 [through] 69, which primarily relate to the application of well-known software operations to common molecular biology techniques for designing and analyzing DNA and protein molecules."

For example, it describes a "graphical user interface and other features of a software product for arranging, constructing, organizing, and analyzing nucleic acid and amino acid sequences … [that] reflect substantially all of the individual software features claimed by the '252 patent, including … a molecular component database preferences, back translation display preferences, and design molecule, and feature display preferences."

BioInform reached out to both Genome Compiler and DNA2.0 for additional comment on the USPTO review application and what the move might mean for the ongoing litigation but did not receive responses as of press time. However, James Barta, a patent attorney who is not affiliated with the case, told BioInform via email that requesting a reexam is "somewhat standard practice in patent litigation" and that it’s usually done to "strengthen the position of one of the parties."

He also noted that while the re-examination is separate from the litigation, "if the Patent Office agrees with Genome Compiler, that decision could weigh heavily in the pending litigation;" for example, it could "weaken the position of DNA 2.0."

Furthermore, "as a general observation, the examination climate at the Patent Office is constantly changing," Barta said. There’s been "an increase in reliance on the ‘broadest reasonable interpretation’ standard which gives examiners significant leeway to broadly interpret claim language, which means that they can reject claims more easily."

That means that "even though the '252 patent [was] issued only a few years ago, the examiners — who may be different from the examiner that previously issued the patent — may be more willing to reject the claims now based on the prior art reference than if the same prior art reference had been considered years ago," he said.

DNA2.0 first filed suit against GCC on Dec. 19, 2012, alleging that the company's Genome Compiler software infringes on claims listed in US Patent 7,805,252, which protects DNA2.0's method of designing and ordering gene sequences through a drag-and-drop interface. The feuding firms offer similar software products that provide capabilities for designing custom gene sequences.

According to court documents submitted in the US District Court for the Northern District of California at the start of the suit, DNA 2.0 claimed that GCC provided technical support to its customers that enables them to use "certain functions" of the Genome Compiler software that infringe on the ''252 patent. The company also argued that GCC's software is "especially made and adapted for use" in a manner that infringes on its patent and concludes that the tool is "not suitable for substantial noninfringing uses."

In court documents dated June 17, GCC denied the bulk of the charges, asking the California courts to dismiss the case and for compensation to cover its costs and fees in this action including attorneys' fees and pre-judgment interest.

The defendant also lobbed a four-fold defense against the charges listed in the DNA2.0 suit. Among its arguments, it asserted that the claims of the '252 patent are "invalid on the grounds that the purported invention fails to meet the conditions of patentability" specified in 35 USC Section 101 — the part of US patent law that defines what counts as patentable material.

None of the claims listed in '252, according to GCC, "is tied to a particular machine or apparatus, and no claim is directed to a transformation of a particular article into a different state or thing. Rather, the '252 patent claims instructions for applying the basic concept of iconic representation to DNA sequences, which are implemented on a general purpose computer." GCC also challenged the originality of some claims in the patent pointing to what appears to be a similar system developed at the Massachusetts Institute of Technology and made public in 2004 — at least six years before DNA2.0 got its patent.

GCC further argued that DNA2.0's own words in the course of the suit sabotage its case. "DNA2.0 made statements during the prosecution of the '252 patent that limit the scope of the issued claims and bar DNA2.0's claim of infringement," the court docs state. For example, "in response to a rejection under 35 USC [Section] 101, DNA2.0 amended the claims to state 'a tangible computer readable storage medium' and explicitly limited its claims to tangible physical devices, such as compact discs."

It also claimed that its software does not violate '252 because it doesn't meet some of the stipulations that are listed in patent claims. "For example, the Genome Compiler software does not include 'instructions for displaying a plurality of icons [where] each respective icon … uniquely represent[s] … [and] depicts a directional property for the corresponding sequence element' as required by claim 1 of the '252 patent."

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