Federal Circuit Affirms IPR Invalidation of Columbia University Next-Generation Sequencing Patents

On July 17, 2015, in Trustees of Columbia University in the City of New York v. Illumina , the Federal Circuit affirmed inter partes review (IPR) decisions invalidating all challenged claims in three Columbia University patents related to Next-Generation DNA sequencing. In particular, the three patents (U.S. Patent Nos. 7,713,698 (the “’698 patent”) (Appeal No. 2014-1547), 8,088,575 (the “’575 patent”) (Appeal No. 2014-1548), and 7,790,869 (the “’869 patent”) (Appeal No. 2014-1550) are directed towards synthetic nucleotide analogs that comprise the following features: (1) a deaza substitution in the base component of the nucleotide; (2)  a label attached to the base component (as opposed to the sugar component); and (3) a removable cap at the 3’OH position of the sugar component of the nucleotide. The nucleotide analogs are useful in automated sequencing-by-synthesis methods.

 In a nonprecedential opinion, the Federal Circuit found that that the Patent Trial and Appeal Board (PTAB) had not erred in finding all of the challenged claims either anticipated or obvious in view of seven prior art references. Most of the references are listed on the face of at least one of the patents, and thus (at least as a formal matter) were considered by the patent examiner during prosecution of the patents. In particular, the primary reference relied upon by the PTAB (Roger Tsien et al., WO 91/06678 (May 16, 1991) (“Tsien”)) was before the patent examiner. In a nutshell, the Federal Circuit agreed with the PTAB that the references disclosed all of the elements of the claimed inventions and provided a motivation to combine the elements, with a reasonable expectation of success.

 One of the issues on appeal was whether the PTAB had erred by not explicitly determining the level of skill in the art. The Federal Circuit held that under certain circumstances a failure to determine the level of skill, or an incorrect determination of the level of skill, can be a reversible error, but not always, particularly “where the prior art itself reflects an appropriate level and a need for testimony is not shown.” In this case, the Federal Circuit found that it was not necessary for the PTAB to explicitly define the relevant level of skill in the art.

 Interestingly, in making its arguments regarding level of skill in the art, Columbia actually argued against its own interests, as explicitly pointed out by the Federal Circuit. In particular, Illumina’s expert testified that one of skill in the relevant art would be knowledgeable with respect to molecular biology, while Columbia argued that one of skill in the art of DNA sequencing technology would be skilled in both molecular biology and chemistry. As pointed out by the Federal Circuit, the higher the level of skill in the art, the more likely it is that the invention would have been obvious to the skilled artisan. Thus, by arguing that the PHOSITA is skilled in both molecular biology and chemistry, Columbia was actually arguing that the PHOSITA has a higher level of skill, which would tend to make the invention more obvious. The Federal Circuit concluded that PTAB had not erred in finding that the invention would have been obvious to one skilled in molecular biology, and that it would have been even more obvious to one having skill in both molecular biology and chemistry.

The Federal Circuit also identified another instance in which Columbia made arguments that went against its own interest. Columbia argued that other companies had copied its invention from a grant application filed by the inventors, and that this “copying by others” was an objective indication that the invention was nonobvious. But Columbia also argued that these other companies had thought that they would be able to patent invention, which the Federal Circuit found was inconsistent with them having copied the invention. After all, how could they have thought that they could patent the invention if they had knowingly copied it from someone else’s grant application?

The Federal Circuit found that the near-simultaneous invention by others was a secondary consideration weighing “modestly in favor of obviousness.” In particular, two other entities were found to have independently come up with the invention prior to publication of the Columbia patent applications, i.e., prior to public disclosure of the invention. Columbia argued that this independent inventive activity did not constitute “prior art,” but the Federal Circuit criticized Columbia’s argument as reflecting “confusion over the difference between simultaneous invention on the one hand and anticipation and obviousness on the other.”

These IPRs arose out of an ongoing patent infringement litigation between Intelligent Bio-Systems Inc. (IBS, Columbia’s exclusive licensee) and Illumina, in which both sides have asserted that the other infringes patents relating to Next-Generation DNA Sequencing technologies.  Both sides have successfully invalidated some of their opponent’s patents using the IPR process. In Trustees of Columbia University in the City of New York v. Illumina the Federal Circuit has affirmed the PTAB's invalidation of the IBS/Columbia patents.  We are still waiting to hear the outcome of Illumina’s appeal of the PTAB’s decisions invalidating a number of patent claims it has asserted against IBS (the parties’ briefs have already been filed in that case).