Yes, a “single biomolecule” means one biomolecule

by Dennis Crouch

Pacific BioSciences v. Personal Genomics (Fed. Cir. 2024)

PacBio was partially successful in its IPR against Personal Genomics that resulted in cancellation of some claims of US7767441.  Both sides appealed with PacBio wanting all the claims cancelled, and Personal Genomics wanting restoration of its patent rights. The case focuses on preamble claim construction and interpreting the prior art.

Construing the Preamble: The claims were directed to “an apparatus for identifying a single biomolecule, comprising” three different elements. The preamble here has a purposive statement “for identifying a single biomolecule,” and a key question in the case is whether the preamble should be limiting. In the IPR, the patentee wanted a narrow construction – giving effect to the preamble – in order distinguish its invention from prior art apparently not capable of single-molecule identification.

The PTAB found the preamble as limiting and the Federal Circuit affirmed that holding on appeal. This is probably a case where the PTAB’s move to the Phillips v. AWH standard from Broadest-Reasonable-Interpretation during inter partes review.

The general presumption in patent claim construction is that the preamble is not limiting for obviousness purposes. But, the preamble can be given weight when it crosses some threshold of providing important meaning to the claimed invention.  Here, the preamble identified “a single biomolecule” and body of the claim referenced “the biomolecule.”  This antecedent basis for referencing the biomolecule was enough for the PTAB find the preamble limiting, and that construction was not appealed.

What was appealed was the actual construction of “a single biomolecule.”  Petitioner argued that the claims should cover identifying a biomolecule by making copies, examining the resulting ensemble, and inferring the identity of the original molecule. But the court rejected this, finding it inconsistent with the language of the claim as supported by the specification describing problems of such ensemble approaches.  Of interest, the court decided that the ordinary meaning of “identifying” should be applied and thus cited two dictionary definitions.

A final note on this preamble construction is that it could also be given no meaning because it appears simply state the purpose of the device (and thus not really limiting) rather than a structural limitation (that would be limiting).  On appeal, the Federal Circuit noted that this issue was not challenged on appeal, but that there is precedential to support the notion that the phrase “for identifying a single biomolecule” is a limitation on the capability of the machine rather than simply a statement of purpose.

Scope of the Prior Art: One of the key prior art references (Hassibi) described its detection sensitivity “as low as 0.1 attomoles,” which is >60,000 molecules.  Thus, the court was able to affirm that Hassibi does not meet the requirement of identifying a single biomolecule.

The patentee also argued that a second reference (Choumane), did not detect a single molecule.  The patentee’s expert conducted a number of calculations and testified that Choumane’s sensitivity required at least 78 biomolecules — i.e., more than one.  But, the text of Choumane disclosed “detection and observation of individual [biomolecules].”  On appeal, the Federal Circuit recognized that that the expert’s calculations might have merit, but that the Board had substantial evidence to support its conclusion that Choumane disclosed a single molecule detector.

[T]his type of calculation can be proper where based on the express disclosures of a
piece of prior art. In this case, however, the Board, considering the calculation, had sufficient reason, in light of the Choumane statement quoted above, to reject the inference about Choumane that PGI offered the calculation to support.

Id.  Although obviousness is a question of law, it must be supported by various factual findings, including a determination of the scope and content of the prior art.  This means that the Court gives deference to the PTAB — affirming its factual finding so long as there is enough evidence available that a reasonable fact finder could rule as the Board ruled.  See Shoes by Firebug LLC v. Stride Rite Children’s Group, LLC, 962 F.3d 1362, 1369 (Fed. Cir. 2020).

Edward Reines of Weil Gotshal argued for the patentee; Keith Orso of Irell & Manella argued for petitioner. The panel included judges Prost, Taranto, and Hughes, with Judge Taranto authoring the opinion.