Filed October 25, 2018
`
`
`On behalf of:
`
`Patent Owner The Regents of the University of California
`By: Kerry S. Taylor
`
`Ryan E. Melnick
`
`Maria V. Stout
`
`KNOBBE, MARTENS, OLSON & BEAR, LLP
`
`2040 Main Street, 14th Floor
`
`Irvine, CA 92614
`
`Tel.: (949) 760-0404 Fax: (949) 760-9502
`
`Email: BoxUC@knobbe.com
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`__________________________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`__________________________________
`
`THERMO FISHER SCIENTIFIC, INC.
`
`Petitioner
`
`v.
`
`THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
`
`Patent Owner
`
`__________________________________
`
`IPR2018-01347
`U.S. Patent 9,085,799
`__________________________________
`
`PATENT OWNER PRELIMINARY RESPONSE TO PETITION
`
`
`
`
`
`On behalf of:
`
`Patent Owner The Regents of the University of California
`By: Kerry S. Taylor
`
`Ryan E. Melnick
`
`Maria V. Stout
`
`KNOBBE, MARTENS, OLSON & BEAR, LLP
`
`2040 Main Street, 14th Floor
`
`Irvine, CA 92614
`
`Tel.: (949) 760-0404 Fax: (949) 760-9502
`
`Email: BoxUC@knobbe.com
`
`
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`__________________________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`__________________________________
`
`THERMO FISHER SCIENTIFIC, INC.
`
`Petitioner
`
`v.
`
`THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
`
`Patent Owner
`
`__________________________________
`
`IPR2018-01347
`U.S. Patent 9,085,799
`__________________________________
`
`PATENT OWNER PRELIMINARY RESPONSE TO PETITION
`
`
`
`
`TABLE OF CONTENTS
`
`Page No.
`
`I. INTRODUCTION .................................................................................................. 1
`II. THE PERSON OF ORDINARY SKILL .............................................................. 4
`III. CLAIM CONSTRUCTION ................................................................................. 4
`A.
`“greater than 4 fold increase in fluorescence emission” ....................... 5
`B.
`“in the absence of the polymer” ............................................................ 6
`C.
`“multichromophore system” ................................................................. 7
`D.
`“sample” ................................................................................................ 8
`E.
`“water soluble conjugated polymer” and “polymer” ............................ 9
`IV. CLAIMS 1, 3, 4, 6, AND 7 ARE ENTITLED TO A PRIORITY
`DATE OF AT LEAST AUGUST 26, 2003 .................................................... 9
`A.
`The Legal Standard for Written Description ....................................... 10
`B.
`Claim 1 of the ‘799 Patent Is Entitled to a Priority Date of at
`Least August 26, 2003 ......................................................................... 12
`The First Application Discloses a Representative Number of
`Species Falling Within Claim 1 .......................................................... 13
`1.
`First Working Example: Example 3 in the First
`Application ................................................................................ 14
`Second Working Example: Example 5 in the First
`Application ................................................................................ 14
`Third Working Example: Incorporated by Reference
`from Provisional Example 2 ..................................................... 18
`Fourth Working Example: Incorporated by Reference
`from Provisional Example 3 ..................................................... 19
`
`C.
`
`2.
`
`3.
`
`4.
`
`-i-
`
`
`
`TABLE OF CONTENTS
`(Cont’d)
`
`Page No.
`
`D.
`
`E.
`
`F.
`
`G.
`
`H.
`
`5.
`
`2.
`
`3.
`
`The Four Working Examples Disclosed in the First
`Application Provide a Sufficient Representative
`Number of Species to Meet Written Description ..................... 25
`Two Working Examples Were Also Known to Those of Skill
`in the Art as of August 20, 2002 ......................................................... 26
`The General Teachings in the First Application Further
`Support That the First Application Contains Adequate
`Written Description of the Claims of the ’799 Patent ......................... 29
`The ’799 Patent Discloses Adequate Structure-Function
`Correlation ........................................................................................... 35
`Thermo Argued Extensively That Structure-Function
`Correlation and Numerous Representative Structures Within
`the Claimed Genera Were Known as of August 26, 2002 .................. 38
`1.
`Thermo Contradicts Its Own Lack of Written
`Description Argument by Asserting That Structures of
`the Claimed Components Were Known ................................... 39
`In a Prior Proceeding, Thermo Argued That Achieving
`a Greater Than 4 Fold Increase in Fluorescence Was
`Routine ...................................................................................... 40
`Thermo Contradicted Its Present Assertions Regarding
`Structure-Function Correlation ................................................. 42
`Extensive Case Law with Highly Similar Facts Supports That
`the Claims Satisfy the Written Description Requirement ................... 43
`1.
`Ariad Is Readily Distinguishable from the Present
`Facts .......................................................................................... 44
`The First Application Discloses More Than Cases
`Finding Adequate Written Description ..................................... 46
`
`2.
`
`-ii-
`
`
`
`TABLE OF CONTENTS
`(Cont’d)
`
`Page No.
`
`I.
`
`3.
`
`Presence of an Unbounded Numerical Range Is Not
`Dispositive for Written Description .......................................... 52
`Thermo Makes No Argument Regarding Priority for the
`Additional Limitations in Dependent Claims 3, 4, 6, and 7 ............... 54
`V. BECAUSE THE CLAIMS ARE ENTITLED TO A PRIORITY
`DATE OF AT LEAST AUGUST 26, 2003, THERMO’S SOLE
`GROUND IN ITS PETITION FAILS ........................................................... 54
`VI. WRITTEN DESCRIPTION IS NOT A PROPER GROUND FOR
`INTER PARTES REVIEW ............................................................................. 55
`VII. CONCLUSION ................................................................................................ 58
`
`
`
`
`-iii-
`
`
`
`TABLE OF AUTHORITIES
`
`Page No(s).
`
`Allergan, Inc. v. Sandoz, Inc.,
`796 F.3d 1293 (Fed. Cir. 2015) .............................................................. 50, 51, 52
`
`Amgen Inc. v. Hoeschst Marion Roussel, Inc.,
`314 F.3d 1313 (Fed. Cir. 2003) .......................................................................... 25
`
`Anderson Corp. v. Fiber Composites, LLC
`474 F.3d 1361 (Fed. Cir. 2007) .................................................................... 52, 53
`
`Ariad Pharms., Inc. v. Eli Lilly and Co.,
`598 F.3d 1336 (Fed. Cir. 2010) ...................................................................passim
`
`Capon v. Eshhar,
`418 F.3d 1349 (Fed. Cir. 2005) ...................................................................passim
`
`Falko-Gunter Falkner v. Inglis,
`448 F.3d 1357 (Fed. Cir. 2006) .............................................................. 25, 51, 52
`
`Invitrogen Corp. v. Clontech Labs., Inc.,
`429 F.3d 1052 (Fed. Cir. 2005) .............................................................. 25, 49, 50
`
`In re Katz,
`687 F.2d 450 (C.C.P.A. 1982) ............................................................................ 24
`
`Monsanto Co. v. Scruggs,
`459 F.3d 1328 (Fed. Cir. 2006) .......................................................................... 11
`
`Ralston Purina Co. v. Far-Mar-Co, Inc.
`772 F.2d 1570 (Fed. Cir. 1985) .......................................................................... 53
`
`SAP America, Inc. v. Pi-Net Int’l, Inc.,
`IPR2014-00414, Paper 11 (P.T.A.B. Aug. 18, 2014) ................................... 56, 57
`
`
`
`-iv-
`
`
`
`TABLE OF AUTHORITIES
`(Cont’d)
`
`OTHER AUTHORITIES
`
`Page No(s).
`
`35 U.S.C. § 102 ............................................................................................ 24, 55, 57
`
`35 U.S.C. § 112 ...................................................................................... 55, 56, 57, 58
`
`35 U.S.C. § 311 .................................................................................................. 55, 58
`
`
`
`
`
`-v-
`
`
`
`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`For the reasons that follow, Patent Owner The Regents of the University of
`
`California (hereinafter “UC”) submits that the Petition fails to show that there is a
`
`reasonable likelihood that the Petitioner (hereinafter “Thermo”) would prevail with
`
`respect to at least one of the claims of U.S. Patent 9,085,799 (“the ’799 patent”)
`
`challenged in the Petition. Therefore, the Petition should be denied.
`
`I. INTRODUCTION
`
`The ’799 patent is the result of years of work and innovation by scientists at
`
`the University of California at Santa Barbara (“UCSB”) in the field of analyte
`
`detection. This technology was subsequently licensed to Becton, Dickinson and
`
`Company (“BD”), a leading manufacturer of research reagents used in biological
`
`assays. BD has leveraged UCSB’s invention to offer a powerful flow cytometry
`
`platform. BD’s customers range from academic institutions conducting basic
`
`research to biopharma companies engaged in clinical development of new medical
`
`therapies. Unable to develop a viable alternative, Thermo chose to copy UCSB’s
`
`fluorescent dye system for its own flow cytometry platform. Instead of
`
`acknowledging this innovation, Thermo now attempts to avoid liability by alleging
`
`that Claims 1, 3, 4, 6, and 7 of the ’799 patent are unpatentable.
`
`Thermo’s grounds in its Petition are entirely premised on a thinly-veiled
`
`attack on the written description support for the claims. Thermo argues that Claims
`
`1, 3, 4, 6, and 7 of the ’799 patent lack written description support in the priority
`
`- 1 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`applications upon which the ’799 patent is based. However, rather than using this
`
`priority-based attack to rely on third-party intervening prior art, Thermo uses the
`
`publication of one of the ’799 patent’s own priority applications, which contains the
`
`identical specification as the ’799 patent, as the basis for an anticipation ground.
`
`Thus, Thermo’s Petition is indistinguishable from an argument that the claims of the
`
`’799 patent lack written description in the patent’s own specification, which is an
`
`impermissible basis for inter partes review. The Board should reject Thermo’s
`
`invitation to broaden the grounds by which claims can be challenged in an IPR.
`
`Even if Thermo’s written description argument is considered permissible,
`
`Thermo’s argument is wrong. Thermo acknowledges that disclosure of a
`
`representative number of species falling within the claims can meet the written
`
`description requirement. But Thermo argues that the ’799 patent priority
`
`applications fail the written description requirement because they disclose only a
`
`single example. Thermo’s argument deceptively ignores and mischaracterizes clear
`
`disclosures in the priority applications of additional working examples, representing
`
`numerous species within the scope of the claims. Thermo also ignores extensive
`
`structural guidance in the priority applications that further support the claims.
`
`Thermo’s suppression of the specification’s relevant working examples and
`
`structural disclosures from the Board should not be rewarded.
`
`- 2 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`Thermo further acknowledges that written description may be satisfied with a
`
`disclosure in the specification or understanding in the art of a structure-function
`
`correlation, but argues that the priority applications fail to provide this disclosure.
`
`Thermo once again ignores the teachings of the priority applications. The priority
`
`applications provide clear guidance regarding the features that lead to the claimed
`
`result of “greater than 4 fold increase in fluorescence emission.”
`
`Thermo’s arguments also ignore the fact that the written description
`
`requirement is contingent on what was known to a person of ordinary skill in the art.
`
`In fact, Thermo argued extensively in a prior proceeding regarding “the advanced
`
`state of the art” and that the claimed “greater than 4 fold increase in fluorescence
`
`emission” could be achieved by “routine ways.” Thermo asserted that various
`
`structures were known in the art, and Thermo referenced the same structure-function
`
`correlation disclosed in the priority applications as some of the ways in which a
`
`person of ordinary skill in the art could achieve a “greater than 4 fold increase in
`
`fluorescence emission.” Thus, Thermo’s assertions undermine its present
`
`arguments.
`
`Thermo’s written description arguments barely reference the extensive case
`
`law on written description, and a review of this case law demonstrates that the facts
`
`of the present proceeding confirm the priority applications provide written
`
`description support for the claims. In fact, the priority applications in the present
`
`- 3 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`proceeding disclose well more than the cases in several prior Federal Circuit
`
`decisions that found adequate written description of claims containing generic and
`
`functional language. Thermo fails to distinguish these cases, and cites selected
`
`portions of Ariad Pharm., Inc. v. Eli Lilly and Co. that contain highly dissimilar
`
`facts. However, an objective view of the present facts place the ’799 patent squarely
`
`within the cases finding adequate written description.
`
`For all of these reasons, the Petition fails to establish a reasonable likelihood
`
`that the claims lack written description in the priority applications. Accordingly, the
`
`Board should deny institution of Thermo’s Petition.
`
`II. THE PERSON OF ORDINARY SKILL
`
`A person of ordinary skill in the art would possess a Ph.D. in chemistry or
`
`related fields and some experience with fluorescence or, alternatively, a master’s
`
`degree in chemistry or related fields and industry experience in the field of biological
`
`detection systems and/or the use and design of fluorescent dyes.
`
`III. CLAIM CONSTRUCTION
`
`Thermo proposes claim construction of seven terms. For many of these
`
`constructions
`
`(i.e., “multichromophore system,” “sample,” “water-soluble
`
`conjugated polymer,” and “polymer”), Thermo never indicates how they relate to
`
`the ground asserted in the Petition. Thus, Thermo’s proposed constructions of those
`
`terms are simply an invitation to the Board to issue advisory opinions that may help
`
`- 4 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`Thermo in future proceedings. The Board should decline to do so. For the remaining
`
`terms, Thermo purports to rely on the district court claim construction order in the
`
`concurrent litigation of the ’799 patent, but deceptively attempts to alter the district
`
`court’s constructions.
`
`A.
`
`“greater than 4 fold increase in fluorescence emission”
`
`Thermo asserts that the phrase “greater than 4 fold increase in fluorescence
`
`emission” in Claim 1 has “no upper limit” and should be construed to be “an increase
`
`in fluorescence emission that is at least 4 fold and includes at least 10-fold and 100-
`
`fold increases, for example.” Petition at 18 and 20. Thermo cites to the district court
`
`claim construction order in the concurrent litigation, but notably departs from that
`
`order. Petition at 18. Contrary to Thermo’s suggestions, the district court denied
`
`Thermo’s request to include “no upper limit” in the claim construction. Ex-1044 at
`
`19, n.7. Specifically, the court stated, “The Court slightly alters Defendants’
`
`proposed construction to delete the phrase ‘no upper limit.’” Id. (emphasis added).
`
`In addition, the district court’s construction did not include the phrase “and includes
`
`at least 10-fold and 100-fold increases, for example,” which Thermo now adds under
`
`the guise of it being the district court’s construction.
`
`The district court’s actual construction of this phrase was just a reiteration of
`
`the claim language:
`
`- 5 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`The Court construes the term “the polymer can transfer energy from its
`excited state to the signaling chromophore to provide a greater than 4
`fold increase in fluorescence emission from the signaling chromophore
`. . .” as “the polymer can transfer energy from its excited state to the
`signaling chromophore to provide an increase in fluorescence emission
`from the signaling chromophore of more than 4 fold . . . .”
`
`Id. at 19. In consonance with the district court ruling, UC submits that no
`
`construction of this phrase is necessary (it can be given its plain and ordinary
`
`meaning). At a minimum, Thermo’s distorted construction should be disregarded
`
`because it goes beyond the construction applied by the district court, i.e., “an
`
`increase in fluorescence emission from the signaling chromophore of more than 4
`
`fold.” Id.
`
`B.
`
`“in the absence of the polymer”
`
`Thermo asserts that the term “absence of the polymer” in Claim 1 should be
`
`construed to mean that “the polymer is not physically present when measuring direct
`
`emission of the signaling chromophore.” Petition at 17. Thermo again refers to the
`
`district court’s claim construction order, but deceptively departs from the district
`
`court’s construction. Petition at 16. The district court construed this phrase to mean
`
`“without the polymer present.” Ex-1044 at 19 (“The Court construes the term ‘. . .
`
`in the absence of polymer’ as ‘. . . without the polymer present.’”). In fact, the
`
`district court adopted the construction that Thermo proposed in the district court
`
`proceeding. Id. at 16 (“Defendants propose that this claim term be construed as ‘. . .
`
`- 6 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`without the polymer present.’”). The Board should decline to adopt Thermo’s new
`
`inconsistent construction. Specifically, the Board should not now interpret Claim 1
`
`as requiring an affirmative method step of measuring direct emission of the signaling
`
`chromophore without the polymer physically present.
`
`C.
`
`“multichromophore system”
`
`Thermo asserts that the term “multichromophore system” in Claim 1 should
`
`be construed as “a polycationic multichromophore.” Petition at 14. As a first matter,
`
`Thermo’s arguments do not rely on this narrowing construction. Thus, there is no
`
`need for the Board to construe the term “multichromophore system” in reaching its
`
`institution decision.
`
`Furthermore, the proposed narrowing construction is unwarranted. The term
`
`“polycationic” is absent from Claim 1. Ex-1001 at Claim 1. In fact, the term
`
`“polycationic” was explicitly removed from the claims in a broadening amendment
`
`made during prosecution. Ex-1014 at 3 and 39 (the original independent Claim 1
`
`containing a “polycationic multichromophore” was replaced with new Claim 21
`
`containing a “multichromophore system”). The specification of the ’799 patent does
`
`not equate a “multichromophore” with “a polycationic multichromophore.” Indeed,
`
`the specification provides several examples of “multichromophore systems,”
`
`including
`
`- 7 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`conjugated polymers, aggregates of conjugated molecules, luminescent
`dyes attached to saturated polymers, semiconductor quantum dots and
`dendritic structures.
`
`Ex-1001 at 10:56-60. None of these examples are restricted to being polycationic.
`
`With respect to conjugated polymers, the ’799 patent merely states that
`
`[c]onjugated polymers (CPs) are characterized by a delocalized
`electronic structure and can be used as highly responsive optical
`reporters for chemical and biological targets.
`
`Id. at 11:19-22. Thus, the specification does not imply that the claimed
`
`“multichromophore” must be polycationic, and Thermo’s importation of this
`
`limitation from one embodiment of the specification into the claims is
`
`impermissible.
`
`D.
`
`“sample”
`
`Thermo asserts that the term “sample” in Claim 1 should be construed as “a
`
`biological material that is analyzed for a target polynucleotide.” Petition at 14.
`
`Thermo’s arguments do not rely on this narrowing construction. Thus, there is no
`
`need for the Board to construe the term “sample” in reaching its institution decision.
`
`In addition, the proposed construction is unwarranted. Claim 1 does not recite
`
`a polynucleotide. Ex-1001 at Claim 1. During prosecution, the claims were
`
`amended to explicitly remove “polynucleotide” from the recitation of “sample” in
`
`the claims. Ex-1014 at 3 and 39 (the original independent Claim 1, reciting “a
`
`- 8 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
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`sample that is suspected of containing a target polynucleotide,” was replaced with
`
`new Claim 21, reciting “a sample”). The Board should decline Thermo’s invitation
`
`to construe this claim term in a way that adds back limitations removed during
`
`prosecution.
`
`E.
`
`“water soluble conjugated polymer” and “polymer”
`
`Thermo also proffers constructions for the terms “water soluble conjugated
`
`polymer” and “polymer.” Petition at 14-15. Thermo’s arguments do not rely on
`
`these constructions. Thus, there is no need for the Board to construe these limitations
`
`in reaching its institution decision, and it should decline to do so.
`
`IV. CLAIMS 1, 3, 4, 6, AND 7 ARE ENTITLED TO A PRIORITY
`DATE OF AT LEAST AUGUST 26, 2003
`
`Thermo’s sole ground in the Petition relies entirely on the allegation that
`
`Claims 1, 3, 4, 6, and 7 of the ’799 Patent are not entitled to a priority date prior to
`
`September 12, 2007. Petition at 21. Thermo asserts that the claims lack written
`
`description support in either U.S. Provisional Application No. 60/406,266, filed
`
`August 26, 2002 (the “Provisional Application”), or U.S. Application No.
`
`10/648,945, filed August 26, 2003 (the “First Application”). Petition at 23-25.
`
`However, Thermo asserts
`
`this position by completely
`
`ignoring and
`
`mischaracterizing significant portions of the First Application and the Provisional
`
`Application, ignoring its own prior admissions that undermine its present assertions,
`
`and ignoring written description case law. As demonstrated below, the claims of the
`
`- 9 -
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`
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`’799 Patent are fully supported by the First Application and are thus entitled to a
`
`priority date of at least August 26, 2003.1 Since the Petition’s sole ground relies on
`
`this priority claim attack, the Petition fails to present a ground in which Petitioner
`
`would prevail in demonstrating unpatentability.
`
`A. The Legal Standard for Written Description
`
`The Written description requirement is met when the description “‘clearly
`
`allow[s] persons of ordinary skill in the art to recognize that [the inventor] invented
`
`what is claimed.’” Ariad Pharms., Inc. v. Eli Lilly and Co., 598 F.3d 1336, 1351
`
`(Fed. Cir. 2010) (quoting Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563 (Fed. Cir.
`
`1991)). The written description analysis requires “an objective inquiry into the four
`
`corners of the specification from the perspective of a person of ordinary skill in the
`
`art.” Id. Thus, “the level of detail required to satisfy the written description
`
`requirement varies depending on the nature and scope of the claims and on the
`
`complexity and predictability of the relevant technology.” Id. For example, the
`
`
`
`1 Demonstrating entitlement to priority as of the First Application is sufficient
`
`to defeat the ground asserted in Thermo’s petition. By focusing on written
`
`description support in the First Application, UC does not concede that Claims 1, 3,
`
`4, 6, and 7 of the ‘799 patent are not entitled to priority to the Provisional
`
`Application.
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
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`analysis must consider “‘the existing knowledge in the particular field, the extent
`
`and content of the prior art, the maturity of the science or technology, [and] the
`
`predictability of the aspect at issue.’” Id. (quoting Capon v. Eshhar, 418 F.3d 1349,
`
`1359 (Fed. Cir. 2005)). To that end, a specification need not set forth what is already
`
`known. Capon, 418 F.3d at 1357 (written description does not “require a re-
`
`description of what was already known.”); Monsanto Co. v. Scruggs, 459 F.3d 1328,
`
`1337 (Fed. Cir. 2006) (holding that it was unnecessary for a specification to include
`
`specific gene sequences to meet the written description requirement “[g]iven the
`
`knowledge in the art.”).
`
`Written description of a genus may be met by simply showing “a
`
`representative number of species falling within the scope of the genus.” Ariad, 598
`
`F.3d at 1350. However, there are no “bright-line rules governing, for example, the
`
`number of species that must be disclosed to describe a genus claim, as this number
`
`necessarily changes with each invention, and it changes with progress in a field.”
`
`Id. at 1351. Additionally, “functional claim language can meet the written
`
`description requirement when the art has established a correlation between structure
`
`and function.” Id. at 1350 (citing Enzo Biochem, Inc. v. Gen-Probe Inc., 323 F.3d
`
`956, 964 (Fed. Cir. 2002)).
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`- 11 -
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`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`B. Claim 1 of the ‘799 Patent Is Entitled to a Priority Date of at Least
`August 26, 2003
`
`Thermo asserts that the First Application does not demonstrate that the
`
`inventors possessed the Claim 1 limitation—“polymer can transfer energy from its
`
`excited state to the signaling chromophore to provide a greater than 4 fold increase
`
`in fluorescence emission from the signaling chromophore than can be achieved by
`
`direct excitation of the signaling chromophore in the absence of the polymer”—at
`
`the time of its filing on August 26, 2003. Petition at 24-25. However, proper
`
`application of the facts to the law confirms that the First Application’s disclosure is
`
`more than sufficient to demonstrate possession.
`
`As explained below, the First Application discloses four working examples,
`
`providing a representative number of species within the scope of Claim 1. Infra at
`
`IV(C). The First Application also provides general teachings that further support
`
`the breadth of Claim 1. Infra at IV(E). In addition to these examples and teachings,
`
`the First Application also provides structure-function guidance to a POSA to achieve
`
`the claimed “greater than 4 fold increase.” Infra at IV(F).
`
`On top of these various teachings in the priority applications, Thermo
`
`concedes that the level of detail required to satisfy written description varies
`
`depending on the complexity and predictability of the technology. Petition at 22.
`
`Yet, Thermo fails to consider this principle in its arguments. As set forth below,
`
`Thermo stipulated in a prior proceeding that the level of knowledge in the art was
`
`- 12 -
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`
`
`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`“advanced” and that achieving a greater than 4 fold increase in fluorescence was
`
`“routine.” Infra at IV(G). Thermo further argued that a POSA would have
`
`recognized the same structure-function correlation taught by the First Application.
`
`Infra at IV(G)(3). Thermo also argued that polymers, such as claimed in Claim 1,
`
`were “known as of August 2002.” Infra at IV(G)(1). Thus Thermo’s own statements
`
`contradict Thermo’s assertions of a lack of written description and at best belie
`
`Thermo’s failure to properly apply the facts of this proceeding to the guidelines
`
`provided in the case law.
`
`When applying these facts to the law, it is clear that the present case matches
`
`closely to the Federal Circuit cases that have found written description. The First
`
`Application discloses more than several cases finding adequate written description.
`
`Infra at IV(H)(2). Accordingly, as explained more fully below, the Board should
`
`find that Claim 1 has adequate written description support in the First Application.
`
`C. The First Application Discloses a Representative Number of Species
`Falling Within Claim 1
`
`Thermo argues that the First Application does not disclose sufficient species
`
`that are representative of the full scope of the limitation “greater than 4 fold
`
`increase.” Petition at 26. In making this assertion, Thermo alleges that only a single
`
`example is presented in the Provisional and First Applications. Petition at 31-32.
`
`However, Thermo arrives at this conclusion by completely ignoring an example
`
`within the Provisional and First Applications and attempting to exclude others by
`
`- 13 -
`
`
`
`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`drawing conclusions that are plainly contradicted by the priority applications
`
`themselves. In fact, the First Application discloses at least four working examples
`
`that are representative of a wide range of increase of fluorescence emission from the
`
`signaling chromophore.
`
`1.
`
`First Working Example: Example 3 in the First Application
`
`The first working example is presented in the First Application as Example 3.
`
`Ex-1004 at 32. This example describes a method using polymer 1 with a
`
`polynucleotide sequence having an appended fluorescein signaling chromophore.
`
`Id. The “[i]ntegrated fluorescence emission . . . was ~4 fold greater than that of
`
`directly excited (480 nm) probe in the absence of polymer 1.” Id. Thermo readily
`
`admits that this example falls within the scope of Claim 1. Petition at 31-32 (“there
`
`is only one disclosed species within the scope of the claimed ‘greater than 4 fold . . .
`
`in the absence of a polymer’ and that is the species resulting [in] an ‘~4 fold’
`
`emission increase.”); see also Ex-2008 at ¶27.
`
`2.
`
`Second Working Example: Example 5 in the First Application
`
`The second working example falling within Claim 1 is presented in the First
`
`Application as Example 5. Ex-1004 at 33. Thermo admits that this example is a
`
`“disclosure of an emission increase in the First Application,” and recognizes that the
`
`example discloses “an ‘~8 fold’ increase in emission from the chromophore,” but
`
`attempts to explain away this clear disclosure by asserting that only a two-fold
`
`- 14 -
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`
`
`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`increase occurs. Petition at 27-28. Thermo argues that the conjugated polymer in
`
`Example 5 is responsible for a two-fold increase in emission, which is increased in
`
`turn by four-fold due to “other causes.” Id. at 27. But Thermo ignores that Claim 1
`
`is not limited to any particular mechanism for transfer of energy from the polymer
`
`excited state to the signaling chromophore, and ignores the plain teachings in the
`
`First Application that the mechanism used in Example 5 was contemplated to be
`
`within the scope of the invention.
`
`Example 5 in the First Application describes a method using polymer 1 with
`
`a polynucleotide sequence having an appended fluorescein dye and a polynucleotide
`
`specific dye, ethidium bromide (EB). Ex-1004 at 33, Ex-2008 at ¶28. As
`
`acknowledged by Thermo, and plainly disclosed in the First Application, this
`
`arrangement “resulted in emission intensities of EB that were ~8 fold greater than
`
`that of the directly excited (500 nm) EB . . . .”. Ex-1004 at 33. The disclosure could
`
`not be any clearer.
`
`Excitation of [polymer] 1 in a solution of [polymer] 1, sensor
`polynucleotide and polynucleotide specific dye (Ethidium Bromide,
`EB) resulted in emission intensities of EB that were ~ 8 fold greater
`than that of directly excited (500 nm) EB contained in the same double
`stranded DNA sequence which lacked the signaling chromophore on
`the sensor polynucleotide.
`
`- 15 -
`
`
`
`Thermo Fisher v. UC Regents
`Patent 9,085,799 - IPR2018-01347
`
`Id. In other words, polymer 1 was placed into “its excited state,” resulting in transfer
`
`of that energy to the ethidium bromide, which then emitted light (i.e., it is a
`
`“signaling chromophore”). Ex-1001 at Claim 1. This disclosure clearly falls within
`
`the Claim 1 limitation that “the polymer can transfer energy from its excited state to
`
`the signaling chromophore to provide a greater than 4 fold increase in fluorescence
`
`emission.” Ex-1001 at Claim 1; Ex-2008 at ¶30.
`
`The fact that the fluorescein dye may have facilitated the energy transfer does
`
`not remove Example 5 from the scope of Claim 1. Indeed, the First Application
`
`describes this very mechanism as an embodiment of the invention. Ex-1004 at 26-
`
`27. The First Application states
`
`In one variation, a second signaling chromophore, which may be
`directly or indirectly attached to another of the assay components
`and/or to a substrate, is used to receive energy from the initial signaling
`chromophore.
`
`* * *
`
`the excited cationic
`from
`transferred
`then be
`Energy can
`multichromophore
`to the initial signaling chromophore, which
`subsequently transfers energy to the second signaling chromophore.
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