Court Opinion

ID: 9916173
Source: CourtListenerOpinion
Date Created: 2024-01-09 16:01:29.516255+00
Date Added: 2024-06-11T13:24:20.677818
License: Public Domain

Case: 22-1410   Document: 52     Page: 1   Filed: 01/09/2024

   United States Court of Appeals
       for the Federal Circuit
                 ______________________

   PACIFIC BIOSCIENCES OF CALIFORNIA, INC.,
                   Appellant

                            v.

       PERSONAL GENOMICS TAIWAN, INC.,
                 Cross-Appellant
             ______________________

                  2022-1410, 2022-1554
                 ______________________

     Appeals from the United States Patent and Trademark
 Office, Patent Trial and Appeal Board in Nos. IPR2020-
 01163, IPR2020-01200.
                  ______________________

                Decided: January 9, 2024
                 ______________________

     EDWARD R. REINES, Weil, Gotshal & Manges LLP, Red-
 wood Shores, CA, argued for appellant. Also represented
 by DEREK C. WALTER.

    KEITH ORSO, Irell & Manella LLP, Los Angeles, CA, ar-
 gued for cross-appellant. Also represented by ALAN J.
 HEINRICH; MICHAEL RICHARD FLEMING, Washington, DC.
                 ______________________

   Before PROST, TARANTO, and HUGHES, Circuit Judges.
 TARANTO, Circuit Judge.
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 2                   PACIFIC BIOSCIENCES OF CALIFORNIA, INC. v.
                              PERSONAL GENOMICS TAIWAN, INC.

     Pacific Biosciences of California, Inc. (PacBio) filed two
 petitions with the Patent and Trademark Office under 35
 U.S.C. §§ 311–19, each one seeking an inter partes review
 of a group of claims of U.S. Patent No. 7,767,441, which is
 owned by Personal Genomics Taiwan, Inc. (PGI). The Pa-
 tent Trial and Appeal Board, acting for the PTO’s Director,
 instituted both IPRs, which overlapped in the claims chal-
 lenged but differed in the prior art invoked. The Board
 eventually issued final written decisions in the IPRs. In
 one of the IPRs, the Board rejected PacBio’s challenge to
 claims 1–2, 6–7, 10–22, 24, and 27–36. Pacific Biosciences
 of California, Inc. v. Personal Genomics Taiwan, Inc., No.
 IPR2020-01200, 2022 WL 214042 (P.T.A.B. Jan. 18, 2022)
 (’1200 Decision). In the other IPR, the Board agreed with
 PacBio’s challenge to claims 1–6, 9, and 43–58. Pacific Bi-
 osciences of California, Inc. v. Personal Genomics Taiwan,
 Inc., No. IPR2020-01163, 2022 WL 212276 (P.T.A.B. Jan.
 18, 2022) (’1163 Decision). Under those two decisions,
 claims 7, 10–22, 24, and 27–36 survive; claims 1–6, 9, and
 43–58 do not.
     Both parties appeal. Appellant PacBio principally
 challenges the Board’s construction of the claim phrase
 “identifying a single biomolecule,” while also briefly chal-
 lenging the Board’s finding that the prior art PacBio in-
 voked in the ’1200 IPR to meet this limitation does not
 teach it under the Board’s construction. Cross-appellant
 PGI, besides defending the Board’s construction of the dis-
 puted claim phrase, challenges the Board’s factual findings
 that the PacBio-invoked prior art in the ’1163 IPR teaches
 the disputed claim phrase. We affirm both decisions.
                                I
      U.S. Patent No. 7,767,441 describes and claims an “ap-
 paratus for identifying a single biomolecule” as well as
 methods of using or making that apparatus. ’441 patent,
 col. 26, line 11; see also id., col. 26, line 10 through col. 30,
 line 5. The patent describes an apparatus that uses many
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 “optical detection apparatuses” to “monitor a large number
 (e.g., in some embodiments, more than 10,000) of single bi-
 omolecules in parallel,” and thereby determines the iden-
 tity of many biomolecules in a sample “with high
 throughput.” Id., col. 3, lines 55–65; see also id., col. 4, lines
 11–16. The “optical detection apparatus” uses a “light de-
 tector” that is in close proximity to (e.g., “less than or equal
 to 100 micrometers” from) a “linker site” that is “treated to
 affix the biomolecule” to be identified. Id., col. 2, lines 30–
 44. The light detector can measure a signal from some
 light-emitting molecule—e.g., “a fluorophore attached to
 the biomolecule,” a “labeled probe,” or “labeled nucleo-
 tides”—and thereby identify the affixed biomolecule. Id.,
 col. 2, lines 43–62; see also id., col. 17, lines 58–62 (discuss-
 ing “chromophores”); id., col. 18, lines 18–21 (same).
     Claim 1 is representative for present purposes:
     1. An apparatus for identifying a single biomole-
     cule, comprising:
         a substrate having a light detector; and
         a linker site formed over the light detector,
         the linker site being treated to affix the bi-
         omolecule 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.
 Id., col. 26, lines 11–18.
     In the ’1200 IPR, PacBio challenged claims 1–2, 6–7,
 10–22, 24, and 27–36—all claiming the apparatus of claim
 1 or its use and many, though not all, focusing specifically
 on nucleic acids and determining their nucleotide se-
 quences—as unpatentable for anticipation or obviousness
 based principally on the Hassibi reference, a published
 United States patent application, U.S. Patent Application
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                             PERSONAL GENOMICS TAIWAN, INC.

 Publication No. 2004/0197793 A1 (filed Jul. 24, 2003) (pub-
 lished Oct. 7, 2004) (Hassibi); J.A. 1638–1706. The Board
 issued a final written decision determining that PacBio
 had not shown any of the challenged claims to be unpatent-
 able. ’1200 Decision, at *21.
     In the ’1163 IPR, PacBio challenged claims 1–6, 9, and
 43–58—which refer to biomolecules generally, not to nu-
 cleic acids specifically—as unpatentable for anticipation or
 obviousness based principally on the Choumane reference,
 an international patent application, PCT Application Pub-
 lication No. WO 2007/045755 A1 (filed Oct. 17, 2006) (pub-
 lished Apr. 26, 2007) (Choumane); J.A. 5533–62. The
 Board issued a final written decision determining that Pac-
 Bio had proved all the challenged claims to be unpatenta-
 ble. ’1163 Decision, at *26.
     In reaching its decisions, the Board adopted a claim
 construction of the preamble phrase “identifying a single
 biomolecule,” setting forth reasoning that is materially
 identical in the two opinions. Compare ’1200 Decision, at
 *6–11, with ’1163 Decision, at *6–11. In a conclusion not
 challenged on appeal, the Board determined that the pre-
 amble phrase is a limitation on the claimed subject matter
 because it provides antecedent basis for references to “the
 biomolecule” in the body of the relevant claims. See ’1200
 Decision, at *7, *9 (claim 1); ’1163 Decision, at *7, *9
 (same). 1 In another conclusion not challenged on appeal,
 the Board determined that the full phrase “for identifying
 a single biomolecule” refers to a capability of the appa-
 ratus. See ’1200 Decision, at *9–10; ’1163 Decision, at *9–

     1    All independent claims either require the appa-
 ratus of claim 1 (claims 11, 12, 16, 30, 43), whether ex-
 pressly or indirectly, or have the same relevant preamble
 language tied to “the biomolecule” language in the body
 (claims 48, 53–55). See ’441 patent, col. 26, line 10 through
 col. 30, line 5.
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 10 (same); see ParkerVision, Inc. v. Qualcomm Inc., 903
 F.3d 1354, 1361–62 (Fed. Cir. 2018) (explaining that capa-
 bility is one meaning of “for” language).
     The claim-construction dispute central to the appeals
 before us involves the Board’s understanding that the
 “identifying a single biomolecule” phrase, in the context of
 the “[s]pecification of the ’441 patent,” “contemplates run-
 ning myriad optical detection apparatuses in parallel to de-
 tect a single or individual biomolecule in each such
 apparatus.” ’1200 Decision, at *8; ’1163 Decision, at *8.
 That construction requires that the apparatus have the ca-
 pability to characterize (determine the identity of) a bio-
 molecule by examining that biomolecule alone, with no
 copies created to form an ensemble for examination. In
 adopting that construction, the Board rejected PacBio’s ar-
 gument that an apparatus would come within this claim
 phrase if the apparatus, though not capable of characteriz-
 ing a biomolecule by examining it alone, had the capability
 to characterize a biomolecule by making copies, examining
 the resulting ensemble, and inferring the identity of the
 starter biomolecule. ’1200 Decision, at *8 (rejecting Pac-
 Bio’s construction as “inapposite when the challenged
 claims are read in light of the [s]pecification of the ’441 pa-
 tent”); ’1163 Decision, at *8 (same).
      In the ’1200 Decision, the Board found that PacBio
 failed to establish that this limitation was taught by the
 Hassibi reference—on which PacBio relied for this essen-
 tial point in the only ground raised in PacBio’s appeal to
 us. ’1200 Decision, at *12–17. That determination sufficed
 to reject PacBio’s challenge to the claims at issue in that
 IPR. Id. at *21.
       In the ’1163 Decision, the Board found, in contrast, that
 PacBio did establish that the “identifying a single biomole-
 cule” limitation was taught by the Choumane reference,
 i.e., that Choumane taught an apparatus with the capabil-
 ity required by the Board’s claim construction. ’1163
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                            PERSONAL GENOMICS TAIWAN, INC.

 Decision, at *12–16. The Board added, id. at *22, that this
 limitation was also taught by a second reference that Pac-
 Bio invoked for obviousness in combination with
 Choumane, namely, a published patent application, U.S.
 Patent Application Publication No. 2002/0182716 A1 (filed
 Feb. 12, 2002) (published Dec. 5, 2002) (Weisbuch); J.A.
 5563–80. The Board found the requisite proof as to the
 other limitations of the challenged claims, by Choumane
 alone or in the specified combinations for obviousness, but
 those findings are not at issue on appeal. The Board there-
 fore found that PacBio had shown unpatentability of the
 claims challenged in the ’1163 IPR. ’1163 Decision, at *26.
     The Board issued both of its final written decisions on
 January 18, 2022. PacBio filed a timely notice of appeal
 from the ’1200 Decision on January 24, 2022, and PGI filed
 a timely notice of appeal from the ’1163 Decision on March
 18, 2022. The appeals are authorized by 35 U.S.C.
 §§ 141(c) and 319, and we have statutory jurisdiction under
 28 U.S.C. § 1295(a)(4)(A). PGI’s pending infringement suit
 against PacBio under the ’441 patent supports constitu-
 tional standing. See PacBio’s Opening Brief at 1.
                              II
                              A
     PacBio’s appeal principally challenges the Board’s con-
 struction of the “identifying a single biomolecule” claim
 limitation. We review this construction, which rests on in-
 trinsic evidence, without deference. Polaris Innovations
 Ltd. v. Brent, 48 F.4th 1365, 1372 (Fed. Cir. 2022). We af-
 firm the Board’s construction of “identifying a single bio-
 molecule” as requiring an apparatus capable of
 ascertaining the identity of one single, individual biomole-
 cule by examining only that biomolecule.
     It is undisputed before us that the claim language at
 issue—“for identifying a single biomolecule”—refers to a
 capability of an apparatus. What is disputed is the
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 meaning of “identifying a single biomolecule.” That phrase
 has an ordinary meaning on its face and in context. The
 language refers to (a) ascertaining the identity of a biomol-
 ecule, i.e., what that biomolecule is, and (b) doing so by ex-
 amining just that one biomolecule, not others (even copies).
 It is that capability the apparatus must have, no matter
 what other capabilities it has or how the apparatus may be
 used in a particular instance.
      The proper construction in this case is determined by
 the ordinary meaning of the claim language understood in
 the context of the patent document. See World Class Tech-
 nology Corp. v. Ormco Corp., 769 F.3d 1120, 1123 (Fed. Cir.
 2014); Phillips v. AWH Corp., 415 F.3d 1303, 1312–17 (Fed.
 Cir. 2005) (en banc). The ascertainment of the identity of
 a molecule is the ordinary meaning in this context of ‘iden-
 tify,’ as the aim of the invention is to ascertain the identity,
 e.g., the nucleotide sequence, of the single biomolecule. See
 BRYAN A. GARNER, GARNER’S MODERN AMERICAN USAGE
 435 (3d ed. 2009) (defining “identify” as “(2) to ascertain or
 demonstrate what something . . . is”); RANDOM HOUSE
 WEBSTER’S UNABRIDGED DICTIONARY 950 (2d ed. 2001) (de-
 fining “identify” as “1. to recognize or establish as being a
 particular . . . thing; verify the identity of”). That aspect of
 the claim meaning is not in genuine dispute. Only the
 above-stated second part of the meaning is disputed.
      We agree with the Board that this identifying-by-ex-
 amining-one-alone meaning is the ordinary meaning of the
 phrase in context. The striking feature of the phrase is its
 inclusion of the word “single.” There 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 mol-
 ecule with just that one molecule in view.
     The ’441 patent’s specification confirms this under-
 standing by repeatedly stressing that this “single biomole-
 cule” capability is critical to the invention. It states that it
 is describing “a bioassay system for identifying a single
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 8                  PACIFIC BIOSCIENCES OF CALIFORNIA, INC. v.
                             PERSONAL GENOMICS TAIWAN, INC.

 biomolecule at a detecting unit.” ’441 patent, col. 2, lines
 30–31. In such a bioassay system, the specification indi-
 cates, “[e]ach optical detection apparatus may sense the ex-
 istence of a fluorophore on the single molecule by detecting
 photons emitted from the fluorophore.” Id., col. 3, lines 59–
 61. When the patent illustrates optical detection apparat-
 uses “identifying a single biomolecule,” it depicts examina-
 tion of one individual biomolecule, not an ensemble or
 cluster consisting of multiple biomolecules. See id., figs. 2
 & 6–8.
      Significantly, in explaining the claimed bioassay sys-
 tem’s single-molecule sensitivity, the specification differen-
 tiates, on one hand, “identifying a single biomolecule” by
 examining that individual biomolecule from, on the other,
 detecting a population-level signal from an ensemble or
 cluster of amplified or copied biomolecules. It indicates
 that the latter process involves problems that the former
 avoids. In particular, the patent requires that the claimed
 apparatus be capable of the former functionality, explain-
 ing that the claimed “devices should be capable of sequenc-
 ing single molecules to avoid the known difficulty of
 asynchrony in both the amplification (e.g., drift between
 the sequences of ideally clonal templates) and sequencing
 (e.g., dephasing of the stepwise sequencing reactions
 amongst the sequencing templates) steps of clustered se-
 quencing methods.” Id., col. 1, line 67 through col. 2, line
 6. Avoiding those problems was accomplished by an appa-
 ratus with single-molecule detection sensitivity, enabling
 single-molecule examination for identification, confirming
 the proper understanding of the claim language here in dis-
 pute.
     Other claims of the patent—method claims that call for
 particular uses of the claim 1 apparatus—provide support
 for this claim construction. Method claim 26 depends on
 claim 16, which claims a method (using a claim 1 appa-
 ratus) of “performing nucleic acid sequencing” of “one nu-
 cleic acid molecule,” but adds the limitation “wherein the
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 nucleic acid is amplified.” ’441 patent, col. 27, lines 20–21
 (claim 26); id., col. 26, lines 59–64 (claim 16). Claim 30
 claims a method (using a claim 1 apparatus) of “detecting”
 “one or more biomolecule.” Id., col. 27, lines 30–34. Those
 claims thus call for using the claim 1 apparatus for ex-
 pressly described multiple-molecule examinations, includ-
 ing where amplification of a starter molecule produces the
 group examined, implicitly requiring a capability to do so.
 Dependent claims often add capabilities to those stated in
 the independent claim (where there is no inconsistency),
 and here the language used underscores what is not re-
 quired by the claim 1 phrase itself.
     We reject PacBio’s contention that the Board’s (and
 our) reading “conflates identifying a single molecule with
 detecting a single molecule.” PacBio’s Reply and Re-
 sponse Brief at 2. We need not deny that, in some contexts,
 one might say that a molecule can be identified by following
 processes for making copies, examining the resulting en-
 semble, and inferring the identity of the starting molecule.
 But the ’441 patent recognizes the problems with such pro-
 cesses and seeks to avoid those problems by claiming an
 apparatus capable of identification by single-molecule ex-
 amination. Such a claim does not “conflat[e]” identification
 with detection but instead uses a detection requirement to
 specify a particular identification capability.
     For those reasons, we affirm the Board’s construction
 of the claim language in dispute, understood as we have
 explained it.
                              B
     Both PacBio and PGI challenge the Board’s factual
 findings regarding the prior art. PacBio challenges the
 Board’s finding in the ’1200 IPR that Hassibi does not dis-
 close “identifying a single biomolecule” under the claim
 construction we are affirming. PGI challenges the Board’s
 finding in the ’1163 IPR that Choumane does disclose
 “identifying a single biomolecule” under that construction.
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 We conclude that both findings are supported by substan-
 tial evidence, and we therefore affirm them. See Shoes by
 Firebug LLC v. Stride Rite Children’s Group, LLC, 962
 F.3d 1362, 1369 (Fed. Cir. 2020) (explaining that we review
 Board findings regarding the content of prior art for sub-
 stantial-evidence support). 2
                              1
     In the ’1200 IPR, the critical disclosure in Hassibi is
 that the principal embodiment of the described and
 claimed invention uses an assay—a bioluminescence re-
 generative cycle (BRC) assay—that Hassibi describes as
 having “a sensitivity of detection as low as 0.1 attomoles.”
 J.A. 1670–71 ¶¶ 16–17; see also J.A. 1704, Claim 24
 (“wherein sensitivity of detection is at least 0.1 attomol”).
 This is a minimum-detection limit of greater than 60,000
 molecules. J.A. 3800, lines 1–4 (testimony of PacBio ex-
 pert). This assay is referred to repeatedly in Hassibi for
 detection purposes, and in other places, Hassibi discloses
 an even higher minimum sensitivity. J.A. 1696 ¶ 325 (re-
 porting a sensitivity of “1 amol to 100 amol”). The Board
 credited the testimony of Dr. Harris (PGI’s expert) and
 Hassibi itself in finding that nothing in Hassibi or else-
 where in the record rebuts this evidence by demonstrating
 that Hassibi, instead, discloses the capacity to ascertain
 the identity of one individual biomolecule using either a
 more sensitive BRC assay or a different assay. ’1200 Deci-
 sion, at *15–17. This evidence provides substantial-evi-
 dence support for the Board’s finding that Hassibi does not
 disclose “identifying a single biomolecule.”

      2  Because we affirm the Board’s finding about the
 teaching of Choumane, we need not address PGI’s chal-
 lenge to the Board’s finding about the teaching of Weis-
 buch.
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                               2
     The critical disclosure in Choumane is that the claimed
 invention can include “very small openings . . . of a dimen-
 sion less than the wavelength of light emitted by chromo-
 phores,” where “[t]hese openings delimit very small
 observation volumes . . . for the detection and observation
 of individual chromophores.” J.A. 5551, lines 20–24 (em-
 phasis added). The Board reasonably understood this to
 disclose the capacity to identify one individual biomolecule,
 given that a single chromophore is often used to tag a single
 biomolecule. ’1163 Decision, at *15–16; J.A. 5360 ¶ 61; ’441
 patent, col. 3, lines 59–61. Added support is found in
 Choumane’s description of “a biosensor with ultrasensitive
 detection” for detecting “biological probes,” not merely
 chromophores in isolation. J.A. 5538, lines 3–6.
      PGI’s principal challenge to the Board’s finding relies
 on a calculation, starting from (and perhaps extending a
 bit beyond) analysis supplied by its expert witness, that
 Choumane’s disclosures do not disclose a detection sensi-
 tivity of less than 78 biomolecules. PGI’s Principal and Re-
 sponse Brief at 68–73 (citing J.A. 7605–06 ¶ 86). Although
 PacBio seems to suggest otherwise, this type of calculation
 can be proper where based on the express disclosures of a
 piece of prior art. See Perfect Web Technologies, Inc. v. In-
 foUSA, Inc., 587 F.3d 1324, 1329 (Fed. Cir. 2009) (“We
 therefore hold that while an analysis of obviousness always
 depends on evidence that supports the required Graham
 factual findings, it also may include recourse to logic, judg-
 ment, and common sense available to the person of ordi-
 nary skill that do not necessarily require explication in any
 reference or expert opinion.”). 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 calcu-
 lation to support.
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      PacBio’s expert provided rebuttal testimony stating
 that Choumane teaches “improv[ing] collection efficiency
 by a factor of 400,” which, PacBio’s expert ultimately con-
 cluded, allows a sensitivity increase over the prior art suf-
 ficient to disclose single-biomolecule detection capability.
 J.A. 7427–28 ¶ 6; see also J.A. 7428 ¶ 7 (calculating that
 Choumane discloses “a minimum detection of 0.975 chro-
 mophores (i.e. single molecule detection)”); cf. J.A. 7428–29
 ¶ 8 (calculating that combining Choumane’s disclosures
 with Weisbuch’s results in “a minimum detection of 0.25
 chromophores”). In contrast, PGI’s expert stated that
 when Choumane expressly discloses improving sensitivity
 over the prior art only by “several tens of times,” J.A. 5537,
 line 3, it means only about “30 or 40 or 50” times better,
 J.A. 7334, line 2, which, PGI has argued, is not sufficient
 for single-biomolecule detection sensitivity. See PGI’s Re-
 ply Brief at 25 n.4 (“Substituting a 40-fold improvement for
 [PacBio’s expert’s] 400-fold improvement would increase
 sensitivity . . . [to] about 9.5 chromophores.”). Where the
 overall evidence reasonably allows the Board’s factual find-
 ing on a point, we do not “reweigh the evidence” to reject
 that finding. Regents of the University of California v.
 Broad Institute, Inc., 903 F.3d 1286, 1294 (Fed. Cir. 2018).
 Here, on the evidence before it, the Board could reasonably
 credit PacBio’s expert, ’1163 Decision, at *16, and rely on
 the “detection and observation of individual chromophores”
 language of Choumane, J.A. 5551, line 24, for its finding
 about Choumane’s teaching.
                              III
     We find none of PacBio’s and PGI’s remaining argu-
 ments persuasive. The Board’s final written decisions in
 the ’1200 IPR and the ’1163 IPR are affirmed.
      The parties shall bear their own costs.
                         AFFIRMED