Pacific Biosciences of California, Inc. v. Personal Genomics Taiwan, Inc. (Fed. Cir. 2024)

Kevin Noonan Ph.D.
McDonnell Boehnen Hulbert & Berghoff LLP
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The importance of claim construction, and how construing the same term facing a challenge based on different prior art in separate inter partes review proceedings can result in contrary findings on invalidity, was illustrated by the Federal Circuit's decision recently in Pacific Biosciences of California, Inc. v. Personal Genomics Taiwan, Inc.

The case arose in Pacific Bioscience's IPR challenges to different combinations of claims* of U.S. Patent No. 7,767,441, owned by Personal Genomics Taiwan (PGI). Claim 1, challenged in both IPRs, is representative:

1. An apparatus for identifying a single biomolecule, comprising:
a substrate having a light detector; and
a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site;
wherein the linker site is proximate to the light detector and is spaced apart from the light detector by a distance of less than or equal to 100 micrometers.

The two instituted IPRs were directed to claims 1, 2, 6, 7, 10–22, 24, and 27–36 ("the '1200 IPR") and claims 1–6, 9, and 43–58 ("the '1163 IPR"). Pacific Biosciences (PacBio) asserted U.S. Patent Application Publication No. 2004/0197793 A1 in the '1200 IPR, on anticipation and obviousness grounds, and International Publication No. WO 2007/045755 A1 in the '1163 IPR, also asserting anticipation or obviousness against the challenged claims. The Board held in separate Final Written Decisions that PacBio failed to establish invalidity of the challenged claims in the '1200 IPR on either ground, but that the claims challenged in the '1163 IPR were invalid as being anticipated by the '755 published PCT application. (The opinion notes that the FWD in the '1163 IPR also found invalidity on obviousness grounds that was not at issue in the appeal assessed below.) As discussed in the Federal Circuit's opinion, both these determinations relied on the Board's construction of the term "identifying a single biomolecule" to have its plain and ordinary meaning encompassing identification of a single molecule and not multiple copies of the same molecule. This appeal followed by each of the losing parties on each of the IPRs.

The Federal Circuit affirmed the Board's determinations in each IPR, in an opinion by Judge Taranto, joined by Judges Prost and Hughes. The opinion first addresses the Board's construction of the phrase "identifying a single biomolecule," which was given its plain and ordinary meaning of identifying a single biomolecule and not an amplified or multiplicity of the same biomolecule, or as stated in the opinion "requiring an apparatus capable of ascertaining the identity of one single, individual biomolecule by examining only that biomolecule." The panel held that the plain and ordinary meaning, both on its face and in the context of the claims and specification supported the Board's construction that as a feature of the claimed apparatus the language recites "(a) ascertaining the identity of a biomolecule, i.e., what that biomolecule is, and (b) doing so by examining just that one biomolecule, not others (even copies)." The Federal Circuit, reviewing the Board's construction without deference (because it was based solely on intrinsic evidence), nevertheless resorted to two dictionary definitions of "identify" to affirm the Board's construction with regard to the first portion of the definition, and the panel relied on the context of the claim to decide conformity with the second portion. The "striking feature" the court stated that provided this context was the word "single," the panel stating that "[t]here is no apparent reason for the inclusion of the word 'single' in the phrase except to indicate that the capability required is to identify a molecule with just that one molecule in view." The Federal Circuit was also persuaded by statements in the specification that the capability to identify singe biomolecules was "critical" to the invention, and that the "single molecule" feature avoided recognized problems in detecting "a population-level signal from an ensemble or cluster of amplified or copied biomolecules." Finally, regarding claim construction the opinion uses comparisons with the language in other claims in the '441 patent that related to detecting more than one biomolecule to limit claim 1 to identifying a single biomolecule.

Turning to the Board's factual predicates for its decisions on validity (challenged by both appellants), the panel held that the Board's conclusions in each case were supported by substantial evidence. For the '1200 IPR, the "principal embodiment" disclosed in the cited art was using an assay having a sensitivity that permitted detection of biomolecules in amounts "as low as 0.1 attomoles." This corresponds to detecting more than 60,000 molecules (according to PacBio's expert), and other portions of the prior art reference recited even higher amounts ("1 amol to 100 amol"). "This evidence," according to the opinion, "provides substantial-evidence support for the Board's finding that [the asserted prior art] does not disclose 'identifying a single biomolecule.'" For the '1163 IPR, the "critical disclosure" was the capacity of the prior art apparatus to include openings in the detector sufficiently small to detect "individual chromophores" (emphasis in opinion). In the Court's opinion, this disclosure provided substantial evidence supporting the Board's determination that the prior art was capable of detecting a single biomolecule, because such biomolecules were typically tagged with a single chromophore. The panel found that the Board had sufficient basis for rejecting a contrary opinion from PGI's expert (that the sensitivity of the prior art detector was no less than 78 biomolecules) that included rebuttal evidence from PacBio that the disclosed improvement in detection provided by the cited prior art ("a factor of 400") could result in a sensitivity improvement permitted single biomolecule detection. While the panel recognized that PacBio's expert asserted a lower estimate of improved sensitivity ("30 or 40 or 50 times better"), "[w]here the overall evidence reasonably allows the Board's factual finding on a point, we do not 'reweigh the evidence' to reject that finding," citing Regents of the University of California v. Broad Institute, Inc., 903 F.3d 1286, 1294 (Fed. Cir. 2018). Accordingly, the Federal Circuit affirmed the Board's decisions in these IPRs.

Pacific Biosciences of California, Inc. v. Personal Genomics Taiwan, Inc. (Fed. Cir. 2024)
Panel: Circuit Judges Prost, Taranto, and Hughes
Opinion by Circuit Judge Taranto

* The challenged claims of the '441 patent:

'1200 IPR

'1163 IPR

1. An apparatus for identifying a single biomolecule, comprising:

a substrate having a light detector; and

a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site;

wherein the linker site is proximate to the light detector and is spaced apart from the light detector by a distance of less than or equal to 100 micrometers.

2. The apparatus of claim 1, further comprising a blind sheet formed over the substrate, the blind sheet including a pinhole having a diameter, wherein the linker site is formed proximate to the pinhole.

6. The apparatus of claim 2, further comprising a microlens formed between the substrate and the blind sheet.

7. The apparatus of claim 1, wherein the distance is less than or equal to 25 micrometers.

10. An optical detection system, comprising at least 10,000 apparatuses as recited in claim 1.

11. A method of sequencing a plurality of nucleic acid molecules, the method comprising the steps of:

affixing a plurality of nucleic acid molecules to the linker sites of the optical detection system of claim 10; and

performing nucleic acid sequencing of the nucleic acid molecules in parallel on the optical detection system.

12. A method of detecting a plurality of biomolecules, the method comprising the steps of:

affixing a plurality of biomolecules to the linker sites of the optical detection system of claim 10; and

detecting the biomolecules on the optical detection system in parallel.

13. An optical detection system, comprising at least 250,000 apparatuses as recited in claim 1.

14. An optical detection system, comprising at least 2,000,000 apparatuses as recited in claim 1.

15. An optical detection system, comprising at least 10,000,000 apparatuses as recited in claim 1.

16. A method of sequencing a nucleic acid, comprising the steps of:

affixing one nucleic acid molecule to the linker site of the apparatus of claim 1; and

performing nucleic acid sequencing of the nucleic acid molecule on the apparatus.

17. The method of claim 16, wherein the nucleic acid is affixed to the linker site by binding to a polymerase molecule affixed to the linker site.

18. The method of claim 16, wherein the nucleic acid sequencing comprises the step of adding labeled nucleotides to the apparatus.

19. The method of claim 18, wherein the nucleotides are labeled fluorescently.

20. The method of claim 19, wherein the nucleotides are labeled fluorescently on their terminal phosphate.

21. The method of claim 16, wherein the nucleic acid sequencing is base extension sequencing and includes the step of adding blocked and labeled nucleotides to the apparatus.

22. The method of claim 21, wherein the nucleotides are labeled fluorescently.

24. The method of claim 22, wherein the nucleotides have distinct fluorescent labels and are added simultaneously.

27. The method of claim 16, wherein the sequence of the nucleic acid is unknown.

28. The method of claim 16, wherein the nucleic acid is detected with a label excited by Förster resonance energy transfer (FRET).

29. The method of claim 16, wherein the nucleic acid is detected with a label by time-resolved fluorescence technology.

30. A method of detecting a biomolecule, comprising the steps of:

affixing one or more biomolecule to the linker site of the apparatus of claim 1; and

detecting the biomolecule on the apparatus.

31. The method of claim 30, wherein the biomolecule comprises a label.

32. The method of claim 31, wherein the label is fluorescent.

33. The method of claim 32, wherein the biomolecule comprises a moiety chosen from a polypeptide, antibody, lipid, vitamin, low molecular weight organic molecule, and polysaccharide.

34. The method of claim 33, wherein the biomolecule is affixed to the linker site of the apparatus by a linking molecule.

35. The method of claim 34, wherein the linking molecule comprises a capture molecule.

36. The method of claim 35, wherein the capture molecule is a protein.

1. An apparatus for identifying a single biomolecule, comprising:

a substrate having a light detector; and

a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site;

wherein the linker site is proximate to the light detector and is spaced apart from the light detector by a distance of less than or equal to 100 micrometers.

2. The apparatus of claim 1, further comprising a blind sheet formed over the substrate, the blind sheet including a pinhole having a diameter, wherein the linker site is formed proximate to the pinhole.

3. The apparatus of claim 2, wherein the pinhole has a diameter of less than or equal to 1,000 nanometers.

4. The apparatus of claim 2, wherein the pinhole has a diameter of less than or equal to 200 nanometers.

5. The apparatus of claim 2, further comprising a filter layer formed between the substrate and the blind sheet.

6. The apparatus of claim 2, further comprising a microlens formed between the substrate and the blind sheet.

9. The apparatus of claim 1, wherein the light detector collects light from the biomolecule within a solid angle, the solid angle being greater than or equal to 0.8 SI steridian.

43. A method of providing biomolecule analysis service, comprising the steps of:

providing a sample comprising a biomolecule from a service requester to a service provider;

the service requester receiving analytical results from the service provider, wherein the results are produced using the apparatus of claim 1.

44. The method of claim 43, wherein the method is performed for remunerative consideration.

45. The method of claim 44, wherein the service requester and the service provider are mediated by a vendor.

46. The method of claim 43, wherein the analytical results are produced in another country.

47. The method of claim 43, wherein the analytical results are produced in a country other than the United States of America.

48. An apparatus for identifying a single biomolecule, comprising:

a substrate having a light detector;

a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site; and

an excitation light source formed over the substrate;

wherein the linker site is proximate to the light detector and is spaced apart from the light detector by a distance of less than or equal to 100 micrometers.

49. The apparatus of claim 48, wherein the excitation light source includes a light emitting layer, the light emitting layer emitting excitation light to the linker site along a horizontal direction parallel to a surface of the light detector.

50. The apparatus of claim 49, further comprising a filter layer formed between the substrate and the light emitting layer.

51. The apparatus of claim 48, wherein the excitation light source is chosen from a light emitting diode (LED), an organic light emitting diode (OLED), a polymer light emitting diode (PLED), and a laser diode (LD).

52. The apparatus of claim 48, wherein the excitation light source provides excitation light of a first wavelength range not overlapping with a second wavelength range of light emitted from the biomolecule.

53. An apparatus for identifying a single biomolecule, comprising:

a substrate having a light detector; and

a linker site formed over the light detector, the linker site being treated to affix the biomolecule to the linker site;

wherein the light detector collects light emitted from the biomolecule within a solid angle of greater than or equal to 0.8 SI steridian.

54. An apparatus for identifying a single biomolecule, comprising:

a substrate having a light detector;

a linker site formed over the light detector, the linker site being treated to affix the biomolecule to it; and

an excitation light source formed over the substrate;

wherein the light detector collects light emitted from the biomolecule within a solid angle of greater than or equal to 0.8 SI steridian.

55. A method for manufacturing an apparatus for identifying a single biomolecule, comprising:

forming a light detector and a control circuit on a substrate;

forming a blind sheet having a pinhole over the substrate; and

forming a linker site over the light detector and proximate to the pinhole, the linker site being treated to affix the biomolecule to the linker site, wherein the linker site is proximate to the light detector and is spaced apart from the light detector by a distance of less than or equal to 100 micrometers.

56. The method of claim 55, further comprising forming a filter layer between the substrate and the blind sheet.

57. The method of claim 56, wherein forming the blind sheet comprises:

forming an opaque layer on the filter layer;

forming a photoresist layer on the opaque layer;

patterning the photoresist layer to expose a portion of the opaque layer;

etching the opaque layer using the patterned photoresist layer as a mask until the filter layer is exposed; and

removing the photoresist layer.

58. The method of claim 57, wherein the opaque layer comprises metal.

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DISCLAIMER: Because of the generality of this update, the information provided herein may not be applicable in all situations and should not be acted upon without specific legal advice based on particular situations.

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