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By Donna Young
Washington Editor
A ruling last Friday by a three-judge panel from the U.S. Court of Appeals for the Federal Circuit, which affirmed the government's rejection of a patent application filed by two Amgen Inc. scientists, could not only impede gene patenting, but could make all medical-related patents more difficult to obtain.
The case, known as In re Kubin, involved claims directed to the cDNA encoding the human natural killer cell activation inducing ligand (NAIL) protein.
Natural killer cells express a number of surface molecules which, when stimulated, can activate cytotoxic mechanisms. NAIL is a specific receptor protein on the cell surface that plays a role in activating the natural killer cells.
For the cells to become active, they need to be triggered. The inventors involved in the patent application, Marek Kubin and Raymond Goodwin, discovered the trigger and cloned the gene that codes for the trigger protein.
Prior to the filing of the Kubin patent, which is owned by Thousand Oaks, Calif.-based Amgen, other scientists also had been working on the killer cells and had identified the receptor protein but had not fully characterized it.
While an earlier scientist had partially characterized the protein and had created an antibody against it, he did not know the amino acid sequence or the gene that was later claimed by Kubin in the Amgen patent application.
When the U.S. Patent and Trademark Office (PTO) examiner evaluated the Kubin patent application, the examiner determined that because the protein was already known and there were reliable methods in place for working on such a discovery, that any scientist in that area could have identified the amino acid sequence and conducted all of the same experiments as Kubin to arrive at the same conclusion with the cloned gene.
Therefore, the PTO examiner determined that Kubin did not do anything that other scientists could or would have inevitably done in due course. And so the PTO rejected Kubin's patent on the grounds of obviousness.
Amgen appealed the PTO's decision to the Court of Appeals for the Federal Circuit.
Hans Sauer, associate general counsel for intellectual property at the Biotechnology Industry Organization, said the patent office's decision, as well as the Federal Court's decision, were wrong because they failed to follow controlling legal authority in the court's 1995 ruling in a patent rejection case known as In re Deuel.
The Deuel case, Sauer said, "already disposed" of the questions raised in the Kubin case.
The Deuel case also involved a protein that had been described in a scientific publication and was partially characterized. Sauer noted that the Deuel case involved even more prior art than did the Kubin case.
In the Federal Circuit's 1995 ruling, the court said the PTO was incorrect and said that genomic inventions should be treated as chemicals "because DNA is a chemical, albeit a complex one," Sauer explained.
"So the court said because the genetic code doesn't really have this one-on-one clear correspondence between amino acids and proteins and nucleotide triplets in cDNA, there also is no clear informational link between the protein and the nucleotide," he said. "So looking at it as a whole, the court said there is really nothing that makes the gene obvious in light of the protein."
As in the 1995 Deuel case, there was a prior art protein in the Kubin case and what was claimed was the gene, Sauer noted.
"There was no prior art gene that you could have directly compared," he said. Therefore, Sauer said, the court's ruling in Kubin should have been the same as it was with Deuel.
But, he said, the Federal Circuit determined that a 2007 ruling by the Supreme Court in KSR International v. Teleflex Inc. voided the Deuel decision.
KSR, a Canadian-based designer of gas pedals for General Motors, used other patented designs to make an adjustable pedal with electronic signals. Limerick, Pa.-based Teleflex filed a patent infringement suit.
KSR argued that Teleflex's patents were invalid because the combination of the two features was obvious.
"Basically, the Federal Circuit said that when the Supreme Court looked at KSR, they wiped out Deuel and that is because the Supreme Court said that something that is obvious to try can also be obvious," Sauer explained.
The high court also ruled in KSR that if an inventor has a combination invention using existing machine components put together in some new way, then that combination would have been obvious to try, he added.
But, Sauer argued, the Federal Circuit "kind of took that a bit far in the Kubin case."
What was obvious to try in the Kubin case was to use the methods for getting from the protein to the gene, he noted.
However, Sauer contended, Kubin was not claiming the method for getting from the protein to the gene, but was claiming the gene itself.
Kubin also did not claim a new combination of old elements, he added.
"He discovered the gene, which was not a combination of old elements that he put together in some new way," Sauer contended.
Obvious to try, he asserted, should not apply to new genes that are discovered.
"So we really wonder whether the federal circuit was truly correct in applying this 'obvious to try' reasoning that features so prominently in this decision to the invention of Dr. Kubin," Sauer said.
The reason the decision is disappointing and unsatisfactory in its legal reasoning, he said, "is that the court doesn't seem to have considered at all the implications of this case for life sciences innovation."
"There is no limit in this case and no guidance for where it stops and what is not made obvious by this case," Sauer warned.
Under the Federal Circuit's ruling, he said, "we don't really know where the obviousness" in the chain of discovery stops "because a motivated scientists who had a starting point and reliable tools to go down that chain, who is to say that the patent office wouldn't reach a determination that the scientist would have gotten there eventually."
The burden is now on the patent applicant to show that something really was not obvious, unexpectedly difficult to achieve or did not go according to plan, Sauer said.
If taken to its logical conclusion, the Federal Circuit's decision "is quite disconcerting because it would make many biotech inventions that we now think are legitimate inventions obvious and make it much harder to get a patent for what today are legitimate discoveries of patentable inventions."
In addition, he said, patent applications that were allowed under the reasoning of the Deuel case could potentially now be deemed questionable, Sauer said.
The really troubling concern of the court's decision, he said, is that "the method that you use for discovering something makes the thing that you discover itself obvious, and that just seems wrong, in biotech as in any other technology."
Mike Stimson, a partner with Irvine, Calif.-based law firm Howrey LLP, said that while the court's ruling was "not terribly surprising," the real question is "was it really justified."
The Federal Circuit's reliance on KSR, which the court determined overruled Deuel, is "somewhat controversial because the KSR decision really was talking about the obviousness of one structure over another structure," he said. "It wasn't talking about the obviousness of making a new structure using a known method. So that really is a departure from the holding in KSR," Stimson contended.
The Federal Circuit's three-judge panel took the KSR ruling "certainly beyond what the Supreme Court actually said," he said. "I do believe that it is a pretty broad jump."
Unless this decision is overturned by a review of the full Federal Circuit court or the Supreme Court, "I think that it will seriously reduce the number of DNA patents out there," Stimson said.
He said he hoped Amgen decides to pursue the case further so that the issue can be "fleshed out a little bit better."
"I would like to see more of an explanation as to why KSR should be used to overturn" earlier rulings, such as the Deuel and other cases.
However, he said, the court's ruling may have a broader implication for biotech.
"The language in the opinion really made it clear that they are going to be focusing on the methods about how you could get to the products that you are claiming," Stimson said. "Biotech is full of methods that are well known and used by many people in the art. I would question whether this opinion could actually go beyond DNA patents to touch any kind of new protein or drug that is made using conventional methods." | 
