UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`)
`THE TRUSTEES OF COLUMBIA
`UNIVERSITY IN THE CITY OF NEW
`)
`)
`YORK and QIAGEN SCIENCES, LLC,
`
`)
`)
`)
`)
`)
`)
`)
`
`
`v.
`
`ILLUMINA, INC.,
`
`
`Plaintiffs,
`
`Defendant.
`
`
`
`
`
`Civil Action No.
`19-1681-CFC
`
`
`
`
`
`
`
`
`
`DEFENDANT ILLUMINA, INC.’S RESPONSE TO
`PLAINTIFFS’ OPENING CLAIM CONSTRUCTION BRIEF
`
`Columbia Ex. 2001
`Illumina, Inc. v. The Trustees
`of Columbia University
`in the City of New York
`IPR2020-01177
`
`

`

`TABLE OF CONTENTS
`
`I.
`
`II.
`
`Page
`INTRODUCTION ...............................................................................................................1
`
`ARGUMENT .......................................................................................................................3
`
`A.
`
`“Y” ...........................................................................................................................3
`
`1.
`
`2.
`
`3.
`
`4.
`
`The Claim Language Confirms Illumina’s Construction .............................4
`
`The Specification Confirms Illumina’s Construction ..................................7
`
`The Prosecution History Requires Illumina’s Construction ........................8
`
`Plaintiffs’ Construction Is Unsupported ....................................................14
`
`B.
`
`“Small” ...................................................................................................................18
`
`1.
`
`2.
`
`3.
`
`5.
`
`Columbia’s Definition Of “Small” During Prosecution And IPR .............18
`
`“Small” Should Be Defined With Respect To Rat Polymerase .................22
`
`“Small” Should Be Defined In Terms Of “Diameter” ...............................24
`
`The Court Should Not Construe The Claims In Terms Of A
`“Width” ......................................................................................................27
`
`C.
`
`D.
`
`“R...is stable during a DNA polymerase reaction” ................................................30
`
`“A method for sequencing a nucleic acid” ............................................................32
`
`CONCLUSION ..................................................................................................................35
`
`III.
`
`
`
`
`
`i
`
`

`

`TABLE OF AUTHORITIES
`
`Page(s)
`
`Cases
`Aspex Eyewear, Inc. v. Marchon Eyewear, Inc.,
`672 F.3d 1335 (Fed. Cir. 2012) ................................................................................................ 32
`
`Aylus Networks, Inc. v. Apple Inc.,
`856 F.3d 1353 (Fed. Cir. 2017) .................................................................................................. 9
`
`Baldwin Graphic Sys., Inc. v. Siebert, Inc.,
`512 F.3d 1338 (Fed. Cir. 2008) ................................................................................................ 14
`
`Becton, Dickinson & Co. v. Tyco Healthcare Grp., LP,
`616 F.3d 1249 (Fed. Cir. 2010) ................................................................................................ 31
`
`Boehringer Ingelheim Vetmedica, Inc. v. Schering-Plough Corp.,
`320 F.3d 1339 (Fed. Cir. 2003) ................................................................................................ 35
`
`Catalina Mktg. Int’l, Inc. v. Coolsavings.com, Inc.,
`289 F.3d 801 (Fed. Cir. 2002) ............................................................................................ 33, 34
`
`Cordis Corp. v. Boston Sci. Corp.,
`658 F.3d 1347 (Fed. Cir. 2011) .......................................................................................... 11, 14
`
`Enzo Biochem, Inc. v. Amersham PLC,
`439 F. Supp.2d 309 (S.D.N.Y. 2006) ......................................................................................... 6
`
`Fenner Investments, Ltd. v. Cellco Partnership,
`778 F.3d 1320 (Fed. Cir. 2015) .......................................................................................... 13, 17
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York, IPR2012-00007 ........... 29
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 1 ................................................................................................... 17
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 13 ................................................................................................. 10
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 30 ................................................................................................... 8
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 48 (Feb. 5, 2019) .................................................................... 11, 17
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 66 ................................................................................................. 11
`ii
`
`

`

`Jack Guttman, Inc. v. Kopykake Enterp., Inc.,
`302 F.3d 1352 (Fed. Cir. 2002) ................................................................................................ 10
`
`Pacing Techs., LLC v. Garmin Int'l, Inc.,
`778 F.3d 1021 (Fed. Cir. 2015) ................................................................................................ 16
`
`Personalized Media Commc’ns, LLC v. Apple Inc.,
`952 F.3d 1336 (Fed. Cir. 2020) .................................................................................................. 8
`
`Phillips v. AWH Corp.,
`415 F.3d 1303 (Fed. Cir. 2005) ...................................................................................... 8, 12, 13
`
`PPC Broadband, Inc. v. Corning Optical Commc'ns RF, LLC,
`815 F.3d 734 (Fed. Cir. 2016) .................................................................................................. 12
`
`Princeton Digital Image Corp. v. Konami Digital Entm’t Inc.,
`No. 12-1461-LPS-CJB, 2017 WL 6375173 (D. Del. Dec. 13, 2017) ........................................ 9
`
`Rolls-Royce, PLC v. United Techs. Corp.,
`603 F.3d 1325 (Fed. Cir. 2010) ................................................................................................ 16
`
`Rowe v. Dror,
`112 F. 3d 473 (Fed. Cir. 1997) ................................................................................................. 33
`
`Sage Prods., Inc. v. Devon Indus., Inc.,
`126 F.3d 1420 (Fed. Cir. 1997) .................................................................................................. 6
`
`SciMed Life Sys., Inc. v. Adv. Cardiovascular Sys., Inc.,
`242 F.3d 1337 (Fed. Cir. 2001) .................................................................................................. 6
`
`Symantec Corp. v. Computer Assoc. Int’l, Inc.,
`522 F.3d 1279 (Fed. Cir. 2008) .......................................................................................... 33, 34
`
`Teva Pharms. USA, Inc. v. Sandoz, Inc.,
`789 F.3d 1335 (Fed. Cir. 2015) ................................................................................................ 29
`
`TomTom, Inc. v. Adolph,
`790 F.3d 1315 (Fed. Cir. 2015) ................................................................................................ 33
`
`Statutes and Regulations
`37 C.F.R. §1.132 ........................................................................................................................... 10
`
`
`
`
`
`iii
`
`

`

`
`
`Pursuant to Paragraph 16 of the Court’s Scheduling Order (D.I. 17) and the
`
`Stipulation and Order Extending Claim Construction Deadlines (D.I. 45, as ordered
`
`June 26, 2020), defendant Illumina, Inc. (“Illumina”) submit this answering brief to
`
`plaintiffs The Trustees of Columbia University in the City of New York
`
`(“Columbia”) and Qiagen Sciences, LLC’s (collectively, “Plaintiffs”) opening brief
`
`regarding the construction of disputed claim terms of U.S. Patent Nos. 10,407,458
`
`(the “’458 Patent”); 10,407,459 (the “’459 Patent”); 10,428,380 (the “’380 Patent”);
`
`10,435,742 (the “’742 Patent”); and 10,457,984 (the “’984 Patent”) (collectively, the
`
`“Patents-in-Suit”).
`
`I.
`
`INTRODUCTION
`The instant suit is the latest of three that Plaintiffs have filed against Illumina
`
`in this district since 2012. All three of Plaintiffs’ lawsuits have involved the same
`
`family of Columbia patents, and the prior two lawsuits have followed an identical
`
`pattern. Specifically, after Plaintiffs accused Illumina of infringing, Illumina
`
`successfully invalidated Plaintiffs’ patents in inter partes review (“IPR”). Across
`
`the first two lawsuits, Illumina has invalidated the asserted claims in eight of
`
`Plaintiffs’ patents.1
`
`
`1 The Federal Circuit affirmed the PTAB’s decision on appeal for the patents
`asserted in the first suit; the Federal Circuit appeal of the second suit is pending.
`1
`
`

`

`After each round of invalidation, however, Columbia has gone back to the
`
`Patent Office to contort its claims by adding limitations in the hopes of avoiding the
`
`prior art, including, in the newest version, carving out the very protecting group used
`
`in all of its research publications. Although the claims at issue in this case represent
`
`the narrowest versions of Columbia’s claims to date, they are still unlikely to survive
`
`Illumina’s IPR requests, which have already been filed. Simply put, there is
`
`nothing novel or nonobvious in Columbia’s patents.
`
`Nevertheless, Columbia’s repeated rounds of prosecution and failed efforts to
`
`fend off Illumina’s IPRs have created a rich history of representations directly
`
`relevant to construing the claims of the Patents-in-Suit. To try and avoid the prior
`
`art, Columbia has repeatedly offered narrow definitions of claim terms and/or made
`
`clear and unmistakable disavowals of claim scope. This is most apparent with
`
`respect to the claim terms “Y” and “small,” for which Columbia submitted inventor
`
`declarations during prosecution explicitly defining these terms and then doubled-
`
`down on these very definitions during IPR proceedings.
`
`Columbia’s claim constructions in this case reflect an attempt to undo these
`
`representations and recapture territory it has surrendered. Under black letter
`
`Federal Circuit law, this is impermissible and should be rejected. For these reasons
`
`and others, this Court should adopt Illumina’s proposed claim constructions across
`
`the board.
`
`2
`
`

`

`II. ARGUMENT
`“Y”
`A.
`Patent(s):
`Claim(s)
`’458 Patent:
`Claim 1, 2
`’459 Patent:
`Claim 1, 2
`’742 Patent:
`Claim 1, 2
`’984 Patent:
`Claim 1, 2
`’380 Patent:
`Claim 1, 3
`
`Plaintiffs’ Proposed
`Construction
`“Represents a part of the
`nucleotide analogue, attaching the
`base of the nucleotide analogue to
`a tag, as depicted in the
`illustration of the nucleotide
`analogue in the claim”
`
`Illumina’s Proposed
`Construction
`“A single linker that
`directly connects the
`base to the label”
`
`The parties’ dispute whether the claims are limited to only one “Y” chemical
`
`linker (Illumina’s position) or whether there can be two or more successively-
`
`bonded “Y” chemical linkers (Plaintiffs’ position).
`
`
`
`Illumina’s proposed
`
`construction with a single “Y” chemical linker accords with the claim language,
`
`specification, and prosecution history (including the IPR record) and should be
`
`adopted.
`
`
`
`
`
`3
`
`

`

`The Claim Language Confirms Illumina’s Construction
`1.
`The claim language requires that “Y” be “a single linker that directly connects
`
`the base to the label.” Claim 1 of the ’458 Patent2 in relevant part states:
`
`1. A guanine deoi,;yribonucleotide analogue having the
`structure:
`
`
`
`’458 Patent, cl. 1 (highlighting added).
`This claim refers to a “deoxyribonucleotide analogue having the structure”
`
`and—to make sure there is no confusion—includes a figure showing a single “Y”
`
`chemical linker bonded to a nucleotide base on one end and a tag on the other end.
`
`The claim
`
`language “having
`
`the
`
`structure” means
`
`that
`
`the claimed
`
`deoxyribonucleotide nucleotide analogue must possess the identified structure and
`
`immediately rules out Plaintiffs’ overbroad claim construction encompassing serial
`
`linkers. See Regents of Univ. of Cal. v. Eli Lilly & Co., 119 F.3d 1559, 1567 (Fed.
`
`
`2 Four of the Patents-in-Suit—the ’458 Patent, ’459 Patent, ’742 Patent, and ’984
`Patent—contain this same claim language and “modular” chemical structure
`diagram with variations only for the nucleotide analogue. The fifth Patent-in-
`Suit—the ’380 Patent—is directed a method that uses any of these nucleotide
`analogues and contains functionally the same claim language and “modular”
`chemical structure.
`
`4
`
`

`

`Cir. 1997) (holding claim language stating “having the structure” requires that
`
`structure to be present).
`
`The claim depicts a single “Y” chemical linker bonded to the base on one end
`
`and a tag on the other end with a single continuous and unbroken black line.
`
`Plaintiffs’ proposed construction violates this figure—which was included in the
`
`claims to ensure clarity—by effectively redrawing it to encompass two or more
`
`successively-bonded “Y” chemical linkers each bonded to one another on one end
`
`such that they could not be bonded to the base on one end and the tag on the other
`
`end, as the figure in the claim shows.
`
`Had the patentee intended to capture two or more successively-bonded “Y”
`
`chemical linkers (and had support for that in the specification) as Plaintiffs seek to
`
`do now via claim construction, it could have drafted the claim using various
`
`established chemistry patent claim drafting conventions. For instance, Columbia
`
`could have included the structures “-Y-Y-,” “-X-Y-,” or some variation thereof in
`
`its figure. Alternatively, Columbia could have used the chemical structure “–(Y)n–
`
`where n is 1 or greater.” Likewise if Columbia wanted to capture serial linkers of
`
`different types, it could have used the general chemical structure “–(X)m-(Y)n–
`
`where m and n are 1 or greater.” Columbia could have used an open ended term
`
`such as “comprises” or “includes” to describe Y – e.g. “Y represents comprises a
`
`chemically cleavable, chemical linker.”
`
`5
`
`

`

`Columbia could have claimed serial linkers in so many different ways using
`
`figures or text. But Columbia did none of these things. “If [the patentee] desired
`
`broad patent protection for any [invention] that performed a function similar to its
`
`claimed [invention],
`
`it could have sought claims with fewer structural
`
`encumbrances...[A]s between the patentee who had a clear opportunity to negotiate
`
`broader claims but did not do so, and the public at large, it is the patentee who must
`
`bear the cost of its failure to seek protection for this foreseeable alteration of its
`
`claimed structure.” SciMed Life Sys., Inc. v. Adv. Cardiovascular Sys., Inc., 242
`
`F.3d 1337, 1346 (Fed. Cir. 2001) (quoting Sage Prods., Inc. v. Devon Indus., Inc.,
`
`126 F.3d 1420, 1425 (Fed. Cir. 1997)).
`
`The Markman decision of the district court in Enzo Biochem, Inc. v.
`
`Amersham PLCis instructive on whether a patent claim is limited to the chemical
`
`structure disclosed and whether intervening structures are permissible. 439 F.
`
`Supp.2d 309 (S.D.N.Y. 2006). In Enzo, the patent at-issue, like the Patents-in-Suit,
`
`claimed a “modular” chemical formula:
`
`1. A detectable molecule of the formula
`
`
`
`
`
`A3-(-X-R1-E-Detb)m
`
`See id. at 319 (relevant portion of claim 1 of U.S. Patent No. 4,707,440).
`The parties disputed the orientation of the chemical group “X” in the above
`
`formula. Id. at 320. The Enzo Court resolved this dispute in the defendant’s
`
`6
`
`

`

`favor, holding: “Given the plain language of the claim, this Court finds that the
`
`chemical groups provided for as ‘X’ must be oriented as pictured in the claim, with
`
`the left-most element attached to ‘A3’ and the rightmost element attached to ‘R1.’”3
`
`Id. The Enzo Court further stated there “was also much discussion at the Markman
`
`Hearing about whether intervening structures could be placed between the various
`
`components…. [F]or the record, the Court finds that the claim does not allow
`
`intervening structures since allowing such structures would undermine the claim
`
`language and infinitely expand the scope of the claim.” Id. at 320 n.19. As in
`
`Enzo, Illumina’s proposed construction adheres to the chemical structure depicted in
`
`the claim. Defendants’ proposed construction meanwhile repeats the same
`
`positions rejected in Enzo and should be rejected again here.
`
`The Specification Confirms Illumina’s Construction
`2.
`The written description for the ’458 Patent states in “one embodiment, the
`
`unique label is attached through a cleavable linker to a 5-position of cytosine or
`
`thymine or to a 7-position of deza-adenine or deazaguanine.” ’458 Patent at 10:64-
`
`66; id. at 14:8-10. Columbia has previously confirmed that this description
`
`“requires” that “Y” “means a chemical moiety attached by covalent bonds at one
`
`end to a specified position on the base of a nucleotide and at the other end to a tag.”
`
`
`3 Emphasis supplied unless otherwise noted.
`7
`
`

`

`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York, IPR2018-
`
`00385, Paper No. 30 (“Patent Owner Columbia’s Response”) (U.S. Patent No.
`
`9,725,480 (the “’480 Patent”)) 4 , 5 at 10. Just like the figure in the claim,
`
`Columbia’s description in the specification describes the chemical moiety at one end
`
`of the linker and the nucleotide is at the other end of the linker. There is thus only
`
`one linker. The claim should be construed as it is depicted in the claim, which
`
`matches the description in the specification.
`
`The Prosecution History Requires Illumina’s Construction
`3.
`A patent’s prosecution history can “inform the meaning of the claim language
`
`by demonstrating how the inventor understood the invention and whether the
`
`inventor limited the invention in the course of prosecution, making the claim scope
`
`narrower than it would otherwise be.” Phillips v. AWH Corp., 415 F.3d 1303, 1317
`
`(Fed. Cir. 2005); see also Personalized Media Commc’ns, LLC v. Apple Inc., 952
`
`F.3d 1336, 1345 (Fed. Cir. 2020) (finding that an “applicant’s repeated and
`
`consistent remarks during prosecution can define a claim term” and “the prosecution
`
`history provides persuasive evidence that informs the meaning of the disputed claim
`
`
`4 The ’480 Patent and ’458 Patent have the same relevant claim language and
`identical specifications.
`5 Further proving the relevance of the ’480 Patent to the ’458 Patent at-issue in this
`litigation, Columbia filed a terminal disclaimer during prosecution of the ’458 Patent
`admitting that the ’458 Patent is non-obvious over the ’480 Patent
`8
`
`

`

`phrase.”). Statements made by a patent owner during an IPR proceeding (including
`
`patent owner preliminary responses) can support a finding of prosecution history
`
`disclaimer. Aylus Networks, Inc. v. Apple Inc., 856 F.3d 1353, 1361-62 (Fed. Cir.
`
`2017); Princeton Digital Image Corp. v. Konami Digital Entm’t Inc., No. 12-1461-
`
`LPS-CJB, 2017 WL 6375173, at *5 (D. Del. Dec. 13, 2017). Here, the prosecution
`
`history establishes that Illumina’s construction must be adopted.
`
`During prosecution, the patent examiner raised doubts as to whether the
`
`functional limitations for “Y” “set forth well-defined boundaries of the invention
`
`because they only state a problem solved or a result achieved.” Applicant
`
`Columbia’s Arguments/Remarks Made In An Amendment (U.S. Pat. App. No.
`
`16/149,098, the application that lead to the ’458 Patent) (dated Feb. 12, 2019)
`
`(“Applicant Columbia’s Remarks”) at 6. Columbia responded that “the structures
`
`in the claims show the structural features of covalent bonds joining Y to a specific
`
`position on the base at one end and to the fluorescent tag at the other end.” Id.
`
`at 7.
`
`Dr. Jingyue Ju, the lead inventor of the ’458 Patent and the other Patents-in-
`
`Suit, submitted a declaration similarly stating: “Y is defined as a chemically
`
`cleavable, chemical linker and as shown in the pending claim, Y is attached by
`
`covalent bonds at one end to the base of a nucleotide analogue at a specific
`
`position and at the other end to a detectable fluorescent moiety.” Declaration
`
`9
`
`

`

`Under 37 C.F.R. §1.132 (dated May 26, 2017) (“Ju Declaration”) at 5. Notably,
`
`Dr. Ju “defined” “Y” to have this particular structure. See Jack Guttman, Inc. v.
`
`Kopykake Enterp., Inc., 302 F.3d 1352, 1358-59 (Fed. Cir. 2002) (holding as proper
`
`a district court’s adoption of a claim construction that the patentee explicitly defined
`
`in the prosecution history). The examiner allowed the ’458 Patent after submission
`
`of the patentee’s representations. Issue Notification For U.S. Appl. No. 16/149,098
`
`(dated Aug. 21, 2019).
`
`In a prior IPR for the ’480 Patent, a Columbia patent that has the same relevant
`
`claim language as the ’458 Patent, Columbia repeatedly affirmed that “Y” is a single
`
`chemical linker bonded to the nucleotide on one end and a tag on the other end:
`
`• “In the context of claimed feature Y, ‘chemical linker’ means a chemical
`moiety attached by covalent bonds at one end to a specified position on
`the base of a nucleotide and at the other end to a tag (detectable
`fluorescent moiety)….The specification of the patent-at-issue requires
`this construction…which was expressly addressed during prosecution of
`the challenged claim.” Patent Owner Columbia’s Response at 10-11.
`
`• “The Columbia inventors conceived nucleotide analogues comprising,
`inter alia…on the 7-position of a deaza-adenine base, a chemically
`cleavable, chemical linker attached to a detectable fluorescent moiety.”
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 13 (Patent Owner Columbia’s Preliminary
`Response) at 1.
`
`• “Illumina has not established that Dower discloses the claimed feature Y,
`a ‘chemically cleavable, chemical linker’ attaching the label to the
`base.” Id. at 51.
`
`10
`
`

`

`Based on these representations and other similar ones throughout Columbia’s
`
`briefing, the Board found in IPR proceedings that “Patent Owner argues that
`
`‘chemical linker’ means a chemical moiety attached by covalent bonds at one end to
`
`a specified position on the base of a nucleotide and at the other end to a tag
`
`(detectable fluorescent moiety).’” Illumina, Inc. v. Trustees Of Columbia Univ. In
`
`The City Of New York, IPR2018-00385, Paper No. 66 (“Final Written Decision”) at
`
`17.
`
`Moreover, Columbia, in an attempt to overcome prior art during this IPR,
`
`stated that “Illumina’s double-linker is excluded from the claim, which requires one
`
`linker (Y), not two linkers (Y Y).” Illumina, Inc. v. Trustees Of Columbia Univ. In
`
`The City Of New York, IPR2018-00385, Paper No. 48 (Feb. 5, 2019) (“Patent Owner
`
`Columbia’s Sur-Reply”) at 24. This explicit embrace of one chemical linker (Y)
`
`and simultaneous disavowal of two chemical linkers (Y Y) is fatal to Plaintiffs’
`
`construction. See Cordis Corp. v. Boston Sci. Corp., 658 F.3d 1347, 1356-57 (Fed.
`
`Cir. 2011) (relying on distinction over prior art in parent application to support claim
`
`construction that required multiple waves and excluded a single wave from meeting
`
`the claim).
`
`Columbia attempts to back away from its prior representation that the “Y Y”
`
`structure is “excluded from the claim” by pointing to a footnote in the PTAB’s Final
`
`Written Decision declining to adopt Columbia’s narrowed construction. See Op.
`
`11
`
`

`

`Br. at 10.6 Yet, Columbia fails to mention that the PTAB was construing the claims
`
`under the broadest reasonable interpretation (“BRI”) claim construction standard,
`
`not the Phillips standard that applies here. IPR2018-00797, paper 65, at 14.
`
`While the claim construction standard for IPRs was recently changed to match the
`
`standard used by district courts, at the time Illumina’s IPR was decided there were
`
`two different standards. Id. n.9.
`
`These standards have different purposes and can lead to different results.
`
`Under the BRI standard, claim language is given its broadest reasonable
`
`interpretation, so that “the patent examiner is able to ‘reduce the possibility that,
`
`after the patent is granted, the claims may be interpreted as giving broader coverage
`
`than is justified.’” PPC Broadband, Inc. v. Corning Optical Commc'ns RF, LLC,
`
`815 F.3d 734, 740 (Fed. Cir. 2016). Under the Phillips standard, by contrast,
`
`district courts “do not assign terms their broadest reasonable interpretation.” Id.
`
`“Instead, district courts seek out the correct construction—the construction that most
`
`accurately delineates the scope of the claimed invention—under the framework laid
`
`out in” Phillips. Id.
`
`Thus, in applying the BRI standard, the PTAB did not carry out an exhaustive
`
`analysis to identify the “correct construction.” In its footnote, the PTAB did not,
`
`
`6 “Op. Br.” refers to Plaintiffs’ Opening Claim Construction Brief (served June 1,
`2020).
`
`12
`
`

`

`for instance, consider Dr. Ju’s definition of “Y” during prosecution or any of
`
`Columbia’s other representations confirming that the linker is connected at one end
`
`to the nucleotide and the dye on the other end. That the PTAB applied a different
`
`claim construction standard than the one applicable to this court is evident from the
`
`footnote itself, where the PTAB expressly stated that it gave no weight to the Patent
`
`Owner’s statements about what the claim meant. See Final Written Decision at 53-
`
`54, n.33 (declining to give weight to Columbia’s “bare argument”). In this light,
`
`Columbia’s attempt to have the Court disregard its representations regarding claim
`
`scope on the basis of the Board’s dicta about claim construction under the BRI
`
`standard, specifically failing to take into account the prosecution history as is
`
`required for an analysis under Phillips, is without merit.
`
`Ultimately, Columbia’s assertion in the IPR about the meaning of “Y” are part
`
`of the intrinsic record of the patent that must be considered under Phillips, and are
`
`highly relevant whether relied on by the Patent Office or not. See Fenner
`
`Investments, Ltd. v. Cellco Partnership, 778 F.3d 1320, 1325-26 (Fed. Cir. 2015)
`
`(“The fact that an examiner placed no reliance on an applicant’s statement
`
`distinguishing prior art does not mean that the statement is inconsequential for
`
`purposes of claim construction.”).
`
`13
`
`

`

`Columbia’s consistent and repeated representations regarding the scope of
`
`“Y” throughout the prosecution history (including the IPR record) are persuasive
`
`evidence favoring Illumina’s construction and precluding Plaintiffs’ construction.
`
`Plaintiffs’ Construction Is Unsupported
`4.
`Plaintiffs’ responses to Illumina’s construction all lack merit.
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`As to the claim language, Plaintiffs assert that nothing in the claim language
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`states that “Y” is “one” or a “single” linker. As noted above, however, the claim
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`definitively shows only one linker and uses closed language. See, supra, Sec. A.1.
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`Plaintiffs’ position cannot be reconciled with Columbia’s prior admission that
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`“Illumina’s double-linker is excluded from the claim, which requires one linker (Y),
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`not two linkers (Y Y).” Patent Owner Columbia’s Sur-Reply at 24. This
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`admission prevents Columbia from broadening the scope of the claims. See
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`Cordis, 658 F.3d at 1356-57. Moreover, the overwhelming intrinsic evidence—
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`which was not before the Board—“evince[s] a clear intent to limit ‘a’ or ‘an’ to
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`‘one.’” See Baldwin Graphic Sys., Inc. v. Siebert, Inc., 512 F.3d 1338, 1342 (Fed.
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`Cir. 2008) (internal quotation marks and citation omitted).
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`Further, even if “a” in the phrase “a chemically-cleavable, chemical linker”
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`could be read to mean “one or more,” as Columbia asserts, this still does not support
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`Columbia’s proposed construction. Following Columbia’s logic, each of the
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`“more than one” linkers must still be chemically cleavable. For example, replacing
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`“a” with “two” in this claim phrase would then read “two chemically-cleavable,
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`chemical linkers;” “Y” would still not cover a second, uncleavable linker.
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`Columbia’s construction, however, fails to capture this point, and thus cannot be
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`correct, even if one were to follow Columbia’s own flawed logic on claim
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`construction for this phrase.
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`Regarding the specification, Columbia retreads the same ground that nothing
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`in the specification states that “Y” is “one” or a “single” linker. Columbia,
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`however, previously admitted that the description and embodiments in the
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`specification “requires” the claim language to mean “a chemical moiety attached by
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`covalent bonds at one end to a specified position on the base of a nucleotide and at
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`the other end to a tag.” Patent Owner Columbia’s Response at 10.
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`Columbia further argues that Illumina’s construction would exclude the
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`embodiments in Figures 8 and 16 which supposedly disclose serial linkers. Even
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`if it is true that Figures 8 and 16 disclose serial linkers, however, these embodiments
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`are not within the scope of the claims anyhow because they use photocleavable
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`linkers, not “chemically cleavable” linkers, as the claims require. See ’458 Patent
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`at Fig. 8 (referring to “Photocleavable Linker”); id. at 6:64-65 (“FIG. 16: The
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`synthesis of a photocleavable energy transfer dye - labeled nucleotide.”). Thus,
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`Illumina’s construction of linker “Y” can, at best, only be said to exclude certain
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`embodiments that are already excluded by the claims; a distinction without a
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`difference for purposes of claim construction. Further, to the extent Columbia
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`believes it is appropriate to rely on embodiments that are not chemically cleavable,
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`the specification discloses structures that undisputedly use a single linker. See id.
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`at Figs. 19-21.
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`Even if Columbia believed that the remainder of the claim had not already
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`excluded Figs. 8 and 16, there is no reason to conclude that the photocleavable
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`linkers in Figures 8 and 16 are necessarily within the scope of the claims. See, e.g.,
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`Pacing Techs., LLC v. Garmin Int'l, Inc., 778 F.3d 1021, 1026 (Fed. Cir. 2015)
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`(Where “the patent describes multiple embodiments, every claim does not need to
`
`cover every embodiment. This is particularly true where the plain language of a
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`limitation of the claim does not appear to cover that embodiment.”); Rolls-Royce,
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`PLC v. United Techs. Corp., 603 F.3d 1325, 1334-35 (Fed. Cir. 2010) (“Although
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`reluctant to exclude an embodiment, this court must not allow the disclosed
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`embodiment to ‘outweigh the language of the claim, especially when the court’s
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`construction is supported by the intrinsic evidence.’”).
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`Plaintiffs’ final argument—that Illumina admitted in IPR that “Y” can be
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`constructed using more than a single chemical linker—is also without merit.
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`Plaintiffs point to a figure submitted by Illumina in the IPR that supposedly includes
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`serial linkers. See Op. Br. at 13. The issue in the IPR, however, was simply
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`whether the claims would have been obvious in view of the prior art under the
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`broadest reasonable interpretation standard. Illumina’s arguments focused on this
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`specific issue, not the topic of serial versus single linkers. Illumina’s description
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`of the figure relied upon by Plaintiffs—which Plaintiffs exclude from their opening
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`brief—confirms this: “[f]ollowing Tsien’s direction to use an allyl linker, a POSA
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`would have arrived at a deaza-adenine deoxyribonucleotide analogue having a
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`fluorescent group attached through a cleavable allyl linker to the 7-position of the
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`base and a 3′-O-allyl capping group.” Illumina, Inc. v. Trustees Of Columbia
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`Univ. In The City Of New York, IPR2018-00385, Paper No. 1 (Illumina’s Petition
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`For Inter Partes Review) at 49.
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`Afterwards, it was Columbia that raised the issue of serial linkers, attempting
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`to distinguish the art on this basis: “Illumina’s double-linker is excluded from the
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`claim, which requires one linker (Y), not two linkers (Y Y).” Illumina, Inc. v.
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`Trustees Of Columbia Univ. In The City Of New York, IPR2018-00385, Paper No.
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`48 (Feb. 5, 2019) (“Patent Owner Columbia’s Sur-Reply”) at 24. The law is clear
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`that the public is entitled to rely upon Columbia’s rep