By Kevin E. Noonan –

One of the characteristics of patent infringement litigation in the aftermath of the Supreme Court's decision in Markman v. Westview Instruments, Inc. (holding that claim construction was a matter of law to be reviewed de novo by the Federal Circuit; but see Teva Pharma. USA, Inc. v. Sandoz, Inc.) was that an inordinate proportion of claim construction decisions were overturned in whole or part.  Those proclivities have been attenuated in the years following the Cybor v. FAS Technologies* opinion, but the Court's recent decision in Malvern Panalytical Inc. v. TA Instruments-Waters LLC is reminiscent of those bygone days of Federal Circuit preeminence.

The case arose in patent infringement litigation when Malvern sued Waters for infringement of U.S. Patent Nos. 8,827,549 and 8,827,549.  The claims of each patent asserted by Malvern were directed to isothermal titration microcalorimeters, used to measure energy absorbed or released during chemical reactions between two compounds.  The claimed microcalorimeters comprise an automatic pipette assembly 220 illustrated in the opinion by this diagram:

The limitation at issue was another component, the pipette guiding mechanism that guides the pipette assembly "between and into at least two positions of operation."  Disclosed are two embodiments, one being "a pipette arm 520 that supports the pipette assembly 220, and an essentially vertical guide rod 530," illustrated by this Figure 5a:

The operation of this structure is described in the specification to be:

"The pipette arm 520 is moveably attached by a sleeve 540 to the guide rod 530, but its motion about the guide rod is restricted by a guide grove 550 in the guide rod 530 and a guide pin 560 that protrudes from the inner surface of the sleeve 540 and which fits into the guide groove 550" wherein the "movement of the pipette assembly 220 in the vertical direction is restricted to the angular positions of the positions of operation," and "rotational movement of the pipette assembly 220 between the angular positions only is permitted when the titration needle 260 is fully retracted from respective positions of operation."

The second embodiment of this claimed element is illustrated by this Figure 6:

In this embodiment, the guide groove in the guide rod 530 is replaced by a coaxial external guide sleeve 610 with corresponding guide paths 620 for the guide arm 520."

Claim 1 of the '549 patent and claim 9 of the '175 patent are set forth as representative:

1.  A micro titration calorimetry system comprising:
    an automatic pipette assembly comprising a titration needle arranged to be inserted into a sample cell for supplying titrant, a syringe for supplying titrant to the titration needle, a stirring paddle for stirring fluid in the sample cell, and a stirring motor for rotating the stirring paddle, and
    a pipette guiding mechanism arranged to restrict the movement of the pipette assembly along safe paths to ensure that the titration needle cannot be damaged during movement thereof between different positions of operation.

9.  A micro titration calorimetry system comprising:
    an automatic pipette assembly comprising a titration needle arranged to be inserted into a sample cell for supplying titrant, a syringe for supplying titrant to the titration needle, a stirring paddle for stirring fluid in the sample cell, and a stirring motor
    for rotating the stirring paddle, and
    a pipette guiding mechanism arranged to guide the pipette assembly between and into at least two positions of operation, wherein a first position of operation is a pipette washing position wherein the titration needle is inserted in a washing apparatus, and a second position of operation is a titration position wherein the titration needle is inserted into the sample cell for calorimetric measurements.

The opinion states as being "relevant to this appeal" prosecution of an unrelated patent, U.S. Patent No. 9,103,782 owned by Malvern.  In that case, applicants were able to overcome an anticipation rejection over U.S. Patent Application Publication No. 2010/0238968 based on common ownership.  Also relevant was a supplemental examination request under 35 U.S.C. § 257 that Malvern filed upon acquisition of the '175 patent.  As part of that effort, Malvern filed an Information Disclosure Statement including references cited against the '782 patent, including the '968 application (although as noted in the opinion Malvern did not characterize the references).  During supplemental examination, the Examiner cited an owner's manual for a prior art microcalorimeter disclosing a manually operated pipette guiding mechanism, which Malvern overcame by affidavit that this manual was the inventors' own work.

Turning to claim construction, the opinion recites the parties' proposed constructions of the term "pipette guiding mechanism," wherein Malvern argued the term meant a "mechanism that guides the pipette assembly," while Waters argued that it should mean a "mechanism that manually guides the pipette assembly"; the District Court adopted Waters' construction.  In ruling on this decision, the District Court characterized the phrase "pipette guiding mechanism" to be a "coined term" that required an examination of the intrinsic evidence to determine the "objective boundaries to the scope of the term," citing Iridescent Networks, Inc. v. AT&T Mobility, LLC, 933 F.3d 1345, 1353 (Fed. Cir. 2019).  In doing so, the District Court relied on statements on the meaning of the term made during prosecution of the '782 patent and that applicants had limited the meaning of the term to manual embodiments.  These arguments were attributed to Malvern as the common assignee of the '782, '549, and '175 patents and because statements made during prosecution of the '782 patent were incorporated into the intrinsic record during supplemental examination.  The parties consented to a stipulated judgment of infringement based on the disputed claim construction and this appeal followed.

The Federal Circuit vacated the stipulated judgment in an opinion by Judge Prost, joined by Judges Hughes and Cunningham.  The panel agreed with Malvern that the term "pipette guiding mechanism" encompassed both manual and automated embodiments based on the intrinsic evidence, specifically the plain meaning of the claims, the specification, and the prosecution history.  Regarding the claim language, the panel considered the plain meaning of the words individually, citing Littelfuse, Inc. v. Mersen USA EP Corp., 29 F.4th 1376, 1381 (Fed. Cir. 2022), and 3M Innovative Props. Co. v. Tredegar Corp., 725 F.3d 1315, 1329 (Fed. Cir. 2013), and found no basis for limiting the pipette guide mechanism to only manual embodiments ("Instead, the broad claim language supports the conclusion that the 'pipette guiding mechanism' encompasses both manual and automatic embodiments.")  Interpreting the claim broadly is consistent, in the panel's view, with how the Court construed the claims in Hill-Rom Services, Inc. v. Stryker Corp., 755 F.3d 1367 (Fed. Cir. 2014), wherein broad claim language supported broad claim interpretation.  And the Court found that the remaining language of the claims similarly supported this interpretation.  According to the opinion, while "[t]he claims clarify and restrict what the guiding mechanism does, . . . they provide no language suggesting the restriction to manual embodiments Waters advocates."

The specification supports this interpretation according to the Court, based on disclosure of two embodiments neither of which is limited to manual pipette guiding mechanisms.  "In fact," the Court says, "the specification states nothing about whether the guiding mechanism is manual or automatic," and cites Hill-Rom Services, Inc. v. Stryker Corp., 755 F.3d 1367, 1373 (Fed. Cir. 2014), for the principle that "[t]here are no magic words that must be used, but to deviate from the plain and ordinary meaning of a claim term to one of skill in the art, the patentee must, with some language, indicate a clear intent to do so in the patent" and, as in Hill-Rom, "there is no such language here."  The Court dismissed Waters' arguments to the contrary because they were based on portions of the disclosure that "say nothing about whether the guiding mechanism is manually or automatically operated."  Nor was the Court persuaded by the fact that other components were described as automatic (and thus not describing the pipette guiding mechanism as being automatic implied the term should be limited to manual embodiments).

Finally, regarding the prosecution history, the Court was not persuaded to Waters' construction by the supplemental examination of the '175 patent, wherein the inventors testified that a manual for a prior art microcalorimeter comprising a manual pipette guide mechanism was their own work and thus not prior art.  Waters argued that this testimony should be interpreted to mean the claimed microcalorimeters of the '175 patent were themselves limited to manual embodiments of the pipette guide mechanisms.  (In a footnote the panel explains that they found the statements to be "too vague or ambiguous to qualify as a disavowal of claim scope.")

Turning to the "coined term" issue which provided one basis for the district court's decision, the opinion notes the District Court's reliance on Indacon, Inc. v. Facebook, Inc., 824 F.3d 1352,  1357–58 (Fed. Cir. 2016), in construing the claims.  While recognizing that their Indacon decision involved the question of construing a claim that did not have an established meaning in the art, the panel maintained that what the District Court had needed to do was "answer the question of what plain and ordinary meaning a term has in the context of a patent," which the District Court here did not do, in the Federal Circuit's opinion.

Finally, the panel considered what weight (if any) to give the prosecution history of the '782 patent.  The Court concluded that the '782 prosecution was not relevant to claim construction of the '175 and '549 patents-in-suit merely because that history had been submitted in an IDS during the supplemental examination of the '175 patent.  The Court relied on its precedent in Goldenberg v. Cytogen, Inc., 373 F.3d 1158, 1167 (Fed. Cir. 2004), that "[i]n the absence of an incorporation into the intrinsic evidence, this court's precedent takes a narrow view on when a related patent or its prosecution history is available to construe the claims of a patent at issue and draws a distinct line between patents that have a familial relationship and those that do not."  And the opinion further asserts that citing the prosecution history in an IDS is at most an admission that "'references in the disclosure may be material to prosecution of the pending claims,' but [] "does not admit materiality," citing Abbott Labs. v. Baxter Pharm. Prods., Inc., 334 F.3d 1274, 1279 (Fed. Cir. 2003) (emphasis added).  The Court concluded here that there was no such admission by Malvern's "bare listing" of the IDS.  And even if considered to be so, the opinion further states that this disclosure was insufficient to amount to disclaimer of automatic pipette guiding mechanisms, because the applicant of the '782 patent had abandoned arguments having to do with scope of claims reciting pipette guiding mechanisms.  Reaching this conclusion was supported by their decision in Ecolab, Inc. v. FMC Corp., 569 F.3d 1335, 1343 (Fed. Cir. 2009), in the Court' view.

For these reasons the panel vacated the District Court's claim construction and remanded, where questions of infringement and claim invalidity will be assessed under the Federal Circuit's construction of the "pipette guiding mechanism" term.  The Court also awarded costs to Malvern.

* In his dissent from this en banc decision upon which de novo review of claim construction by the Federal Circuit was established until partially overturned by the Supreme Court in Teva Pharma v. Sandoz, Judge Rader cited statistics that in 1997, the Federal Circuit reversed 53% of the cases decided (27% reversed completely, 26% reversed in part) and for 246 cases decided by the Federal Circuit after Markman, 141 explicitly reviewed the District Court's claim construction, and reversed, in whole or part, in 54 of these cases (about 38%).  He identified eight problem areas caused by Markman: multiple trials, bias towards summary judgment, new evidence, the "learning curve problem," and a propensity for every decision to be appealed to the CAFC for de novo review.

Malvern Panalytical Inc. v. TA Instruments-Waters LLC (Fed. Cir. 2023)
Panel: Circuit Judges Prosy, Hughes, and Cunningham
Opinion by Circuit Judge Prost

By Kevin E. Noonan –

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.