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DNA2.0 Sues Genome Compiler, Alleging Infringement of DNA Design Software


Gene synthesis firm DNA2.0 has filed suit against bioinformatics company Genome Compiler Corporation for allegedly infringing a patent related to GeneDesigner, DNA2.0's software for designing custom gene sequences.

In a complaint filed in December in the US District Court for the Northern District of California, Menlo Park, Calif.-based DNA2.0 claimed that GCC's Genome Compiler software infringes 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.

According to a court document dated Dec. 19, 2012, DNA2.0 GCC “knowingly and actively encourages and intends its customers to practice one or more of the claims of the ‘252 patent” when using Genome Compiler.

The companies offer similar products. GCC’s Genome Compiler software allows customers to upload the parts needed to design DNA sequences as well as rearrange the order of the parts in order to change the design of their sequences. Similarly, DNA2.0’s Gene Designer provides its clients with tools to design custom gene sequences and also lets them order the sequences directly through the software.

DNA2.0 alleges that GCC provides 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 argues that GCC’s software is “especially made and adapted for use” in a manner that infringes its patent and concludes that the tool is “not suitable for substantial noninfringing uses.”

It also argued that its business has suffered and will continue to suffer “substantial damage” because of the patent infringement. DNA2.0 relies on revenue from orders for custom sequences made using GeneDesigner.

The company has asked the court to prevent GCC and any persons associated with the company from engaging in activities that it believes directly or indirectly infringe on the ‘252 patent while the case is pending and afterwards without written authorization from DNA2.0.

It is also asking the court to direct GCC to compensate DNA2.0 for damages related to patent infringement as well as the costs of the suit and an assessment of interest, though the actual compensation amount was not disclosed in the court document.

DNA2.0 has also asked the court to order GCC to turn over all software and code that infringe on the ‘252 patent as well as account for all “gains, profits, advantages, and unjust enrichments derived from its violations of the law.”

DNA2.0 declined to comment on the ongoing litigation. Omri Amirav-Drory, Genome Compiler’s founder and CEO, told BioInform that his company has yet to be served with the suit.

He noted that Genome Compiler has been discussing a collaboration with DNA2.0 “for several months” and speculated that the lawsuit was “just another negotiation move” but he did not elaborate.

The two companies have worked together on at least one project in the past. Employees from DNA2.0 and GCC were involved in the development of the Synthetic Biology Open Language — a standardized framework for describing and exchanging biological parts, modules, and systems — which they both planned to integrate into their respective software packages (BI 12/16/2011).

The Heart of the Matter

Christopher Holman, a law professor at the University of Missouri, Kansas City, School of Law, said the case is a reflection of a much broader legal issue — where the boundaries of patentable subject matter lie.

“The boundary is you can’t patent abstract ideas [but] the uncertainty is we don’t know what that means,” he told BioInform. As a result, there is “a lot of flux” on the subject and someone could successfully argue that DNA2.0’s claim “crosses that boundary.”

In the case of DNA2.0, it might look to some like the company has patented an abstract idea but there are those who might disagree, said Holman, who has consulted for DNA2.0 in the past but is not involved with the suit.

He added that DNA2.0 could make a case that its claim is valid since it was issued a patent.

Clearly, when the patent was granted in 2010, the US Patent and Trademark Office believed that DNA2.0's patent was valid. However, Holman noted, several recent US Supreme Court decisions — for example Bilski v. Kappos and Mayo Collaborative Services v. Prometheus Laboratories — have raised questions about once-accepted criteria for patentable subject matter.

In Bilski v. Kappos, the Supreme Court rejected a patent for a method of “optimizing a fixed bill system for energy markets” on the grounds that it is an unpatentable abstract idea. And in Mayo Collaborative Services v. Prometheus Laboratories, the Court invalidated Prometheus Labs' diagnostic patents, ruling that they covered "well-understood, routine, conventional" methods to correlate biological processes with treatment decisions and therefore were not patent eligible.

If the DNA2.0 case goes to trial, given the uncertainty about patentable subject matter, the courts could decide in favor of either the plaintiff or the defendant, Holman said.

In court, DNA2.0 could argue that its particular process isn’t abstract at all but “more tangible and real world,” he said.

And it would have in its favor the fact that the patent was issued, he said. “There is a legal presumption that an issued patent is valid … it would be up to someone else to prove that the patent office was wrong and should not have issued the patent.”

Genome Compiler, on the other hand, could argue that the patent should be invalidated because the subject matter isn’t a patentable idea or because “it preempts all uses of the abstract idea,” Holman said. The company could also argue that the patent does not cover its particular process, he said.

“We have to see what specific arguments will be raised,” but “a reasonable person can see it coming out either way,” he said.

James Cuticchia, an attorney with AJC Legal Services who is not affiliated with the case, expressed sentiments similar to Holman’s.

“Legal battles such as these are going to be fought at the level of a software patent fight,” he told BioInform in an email.

Assuming the case goes to trial, “it will be up to DNA2.0 to show that its patent is not overly broad” — a tactic that he expects GCC to use when it responds to the suit.

“It is always a push-pull with the USPTO in having claims granted which are not overly broad or so narrow as to be insignificant,” he said.

“This certainly isn’t Apple v. Samsung” but if this lawsuit proceeds, “the process will show much to the bioinformatics community intellectual property and patent laws,” he said.