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`
`Derek Gilliland (admitted pro hac) (Texas 24007239)
`Robert Winn Cutler (admitted pro hac) (Texas 24084364)
`Christian Hurt (admitted pro hac) (Texas 24059987)
`NIX PATTERSON & ROACH
`1845 Woodall Rodgers Fwy., Suite 1050
`Dallas, Texas 75201
`Telephone: (972) 831-1188
`
`and
`
`Bruce J. Zabarauskas (State Bar No. 248601)
`Bruce S. Sostek (admitted pro hac) (Texas 18855700)
`Herbert Hammond (admitted pro hac) (Texas 08858500)
`Vishal Patel (admitted pro hac) (Texas 24065885)
`THOMPSON & KNIGHT LLP
`707 Wilshire Blvd., Suite 4100
`Los Angeles, California 90017
`Telephone: (310) 203-6900
`and
`1722 Routh Street, Suite 1500
`Dallas, Texas 75201
`Telephone: (214) 969-1700
`
`Attorneys for Plaintiff
`The Scripps Research Institute
`
`
`UNITED STATES DISTRICT COURT
`FOR THE SOUTHERN DISTRICT OF CALIFORNIA
`
`
`THE SCRIPPS RESEARCH INSTITUTE,
`
`Plaintiff,
`
`
`
`v.
`
`ILLUMINA, INC.,
`
`
`Defendant.
`
`
`
`
`Case No. 3:16-cv-661-JLS-BGS
`
`SCRIPPS’S OPENING CLAIM
`CONSTRUCTION BRIEF
`
`January 30, 2018
`Date:
`9:00 am
`Time:
`Hon. Janis L. Sammartino
`Judge:
`Courtroom: 4D
`
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`TABLE OF CONTENTS
`
`INTRODUCTION .......................................................................................... 1
`
`BACKGROUND ............................................................................................ 1
`
`THE CLAIMS AT ISSUE .............................................................................. 2
`
`
`TABLE OF AUTHORITIES .................................................................................... ii
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`I.
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`II.
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`II.
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`IV. APPLICABLE LAW ...................................................................................... 3
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`V. ARGUMENT .................................................................................................. 4
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`VI. CONCLUSION ............................................................................................ 20
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`A.
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`B.
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`C.
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`D.
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`E.
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`“a” ......................................................................................................... 4
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`“(Xn)a” and “(Zn)a” ................................................................................ 9
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`“B is a linker molecule operatively linked to A and C” ..................... 10
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`“bifunctional molecule” ..................................................................... 14
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`“identifier oligonucleotide C” ............................................................ 15
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`TABLE OF AUTHORITIES
`
`Cases
`
`Aylus Networks, Inc. v. Apple Inc.
`
`856 F.3d 1353 (Fed. Cir. 2017) ...................................................................... 3
`
`Blast Motion, Inc. v. Zepp Labs, Inc.
`
`2017 U.S. Dist. LEXIS 16549 (S.D. Cal. Feb. 6, 2017) ................................. 3
`
`CAE Screenplates, Inc. v. Heinrich Fiedler Gmbh & Co.
`
`224 F.3d 1308 (Fed. Cir. 2000) ...................................................................... 5
`
`Catalina Mktg. Int’l, Inc. v. Coolsavings.com, Inc.
`
`289 F.3d 801 (Fed. Cir. 2002) ...................................................................... 14
`
`Chi. Bd. Options Exh., Inc. v. Int’l Sec. Exh., LLC
`
`677 F.3d 1361 (Fed. Cir. 2012) ...................................................................... 5
`
`Depuy Orthopaedics, Inc. v. Orthopaedic Hosp.
`
`2016 U.S. Dist. LEXIS 2030 (N.D. Ind. Jan. 8, 2016) ................................. 11
`
`GE Lighting Sols., LLC v. AgiLight, Inc.
`
`750 F.3d 1304 (Fed. Cir. 2014) ...................................................................... 6
`
`Hill-Rom Servs., Inc. v. Stryker Corp.
`
`755 F.3d 1367 (Fed. Cir. 2014) ...................................................................... 5
`
`Info-Hold, Inc. v. Applied Media Techs. Corp.
`
`783 F.3d 1262 (Fed. Cir. 2015) ...................................................................... 3
`
`Phillips v. AWH Corp.
`
`415 F.3d 1303 (Fed. Cir. 2005) ...................................................................... 3
`
`Pitney Bowes, Inc. v. Hewlett-Packard Co.
`
`182 F.3d 1298 (Fed. Cir. 1999) .................................................................... 14
`
`Power Integrations, Inc. v. Fairchild Semiconductor Int’l, Inc.
`
`711 F.3d 1348 (Fed. Cir. 2013) .................................................................... 17
`
`Pragmatus AV, LLC v. Yahoo! Inc.
`
`2014 U.S. Dist. LEXIS 65813 (N.D. Cal. May 13, 2014) ........................ 3, 11
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`Regents of the Univ. of Minn. v. AGA Med. Corp.
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`717 F.3d 929 (Fed. Cir. 2013) ...................................................................... 11
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`Rowe v. Dror
`
`112 F.3d 473 (Fed. Cir. 1997) ...................................................................... 14
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`Teva Pharms. USA, Inc. v. Sandoz, Inc.
`
`135 S. Ct. 831 (2015) ...................................................................................... 3
`
`TomTom, Inc. v. Adolph
`
`790 F.3d 1315 (Fed. Cir. 2015) ...................................................................... 4
`
`
`Vitronics Corp. v. Conceptronic, Inc.
`
`90 F.3d 1576 (Fed. Cir. 1996) ........................................................................ 3
`
`Warner-Lambert Co. v. Apotex Corp.
`
`316 F.3d 1348 (Fed. Cir. 2003) ...................................................................... 9
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`I.
`
`INTRODUCTION
`The Patent-in-Suit involves complicated technical subject matter—encoded
`combinatorial chemical libraries. Technology aside, the Court can reject Illumina’s
`constructions because they violate basic claim-construction principles. As the Court
`determined in its denial of Illumina’s Motion to Dismiss (Dkt. No. 34), Illumina improperly
`tries to limit the “a”-related terms to an exemplary disclosure in an embodiment and does
`so even though the doctrine of claim differentiation and the plain claim language support
`a broader construction. Illumina likewise attempts to shoehorn into the “linker molecule”
`limitations based on a misreading of the prosecution history of other patents relating to
`different claim limitations—language not found in the Patent-in-Suit. Illumina also seeks
`to read out the word “identifier” from the term “identifier oligonucleotide C.” Federal
`Circuit precedent rejects those approaches to claim construction, and Scripps respectfully
`requests that this Court do so as well.
`II. BACKGROUND
`The Scripps Research Institute (“Scripps”) developed the inventions described and
`claimed in the Patent-in-Suit, U.S. Patent No. 6,060,596 (the “’596 Patent”). The ’596
`Patent, entitled “Encoded Combinatorial Chemical Libraries,” claims priority to an
`application filed in March, 1992. The three inventors of the ’596 Patent each hold doctoral
`degrees, and one inventor is a Nobel Laureate. Because the Court is already familiar with
`the technology in the context of Illumina’s Motion to Dismiss (Dkt. No. 34), Scripps will
`provide only a brief technical background here.1
`In general, the ’596 Patent relates to encoding a library of chemical polymers with
`genetic information to track the structure of each chemical polymer. Metzker Decl., at ¶
`39. These libraries are used in the manufacture of DNA microarrays. Each DNA substrate
`or bead in a microarray product contains hundreds of thousands of copies of specific DNA
`
`1 Scripps’s technical expert has provided in his declaration a more extensive background
`of DNA, biological systems, chemical synthesis, and the ’596 Patent. See Declaration of
`Dr. Michael L. Metzker, at ¶¶ 22–38 (attached as Exh. 1).
`
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`sequences, known variously as “probes,” “oligonucleotides,” or “oligos” for short. These
`probes can be a short section of a gene or other DNA element, and they can be used to bind
`to and detect a complementary DNA or RNA sample. Associated with each probe is a
`genetic tag, or address, that identifies the specific sequence of the probe. The address and
`the probe are linked by a “linker molecule” to make up a bifunctional molecule.
`Prior to the invention of the claimed bifunctional molecule, it was difficult, if not
`impossible, to reliably determine the chemical structure of a probe within a library of
`probes via conventional analytical methods. ’596 Patent, col. 2 ll. 35-45; Metzker Decl.,
`at ¶ 39. To overcome this challenge, the ’596 Patent created a bifunctional molecule by
`appending genetic tags (e.g., an address) to the chemical polymers (e.g., a probe). ’596
`Patent, col. 2 ll. 35–45, col. 17 l. 28–col. 21 l. 40; Metzker Decl., at ¶ 39. The tags are
`genetic sequences that can be easily amplified, if needed, and can be easily determined by
`a number of molecular biology methods involving nucleic acid sequence analysis. Id.
`III. THE CLAIMS AT ISSUE
`In this case, Scripps asserts claims 1, 3, 10, and 16. All of the disputed terms are
`contained in claim 1 below:
`
`1. A bifunctional molecule according to the formula A—B—C, wherein
`
` A
`
` is a polymer comprising a linear series of chemical units represented by the
`formula (Xn)a, wherein X is a single chemical unit in polymer A,
`
` B
`
` is a linker molecule operatively linked to A and C. and
`
`
`identifier oligonucleotide C is represented by the formula (Zn)a,
`
`wherein a unit identifier nucleotide sequence Z within oligonucleotide C identifies
`the chemical unit X at position n; and
`
`wherein n is a position identifier for both X in polymer A and Z in oligonucleotide
`C having the value of 1+i where i is an integer from 0 to 10, such that when n is 1,
`X or Z is located most proximal to the linker, and a is an integer from 4 to 50.
`
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`’596 Patent, claim 1 (emphases supplied).2
`IV. APPLICABLE LAW
`The construction of a patent’s claims is a mixed question for the Court to resolve.
`The “ultimate interpretation” of a claim term and interpretations of intrinsic evidence (the
`claims, written description, and prosecution history) are legal conclusions, and subsidiary
`determinations based on extrinsic evidence are findings of fact. Teva Pharms. USA, Inc. v.
`Sandoz, Inc., 135 S. Ct. 831, 841 (2015); Info-Hold, Inc. v. Applied Media Techs. Corp.,
`783 F.3d 1262, 1265 (Fed. Cir. 2015).
`
`The purpose of claim construction is “to give claim terms the meaning understood
`by a person of ordinary skill in the art at the time of invention.” Aylus Networks, Inc. v.
`Apple Inc., 856 F.3d 1353, 1358 (Fed. Cir. 2017) (citing Phillips v. AWH Corp., 415 F.3d
`1303, 1312–14 (Fed. Cir. 2005) (en banc)). Absent a disavowal or definition clearly set
`forth in the intrinsic record, words of a claim are “generally given their ordinary and
`customary meaning.” Order (Dkt. No. 34), at 9, available at Scripps Research Inst. v.
`Illumina, Inc., No. 16-CV-661 JLS (BGS), 2017 U.S. Dist. LEXIS 57740, at *12–13 (S.D.
`Cal. Apr. 14, 2017) (quoting Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582
`(Fed. Cir. 1996)). In construing the claims, the Court considers the plain language of the
`claims themselves, the specification, the prosecution history, and any relevant extrinsic
`evidence. See id. at 9–11; Blast Motion, Inc. v. Zepp Labs, Inc., No. 15-CV-700 JLS
`(NLS), 2017 U.S. Dist. LEXIS 16549, at *2–7, *23–28 (S.D. Cal. Feb. 6, 2017). In
`construing the claims, the Court is not bound by the initial determinations of the Patent
`Trial and Appeal Board (“Board”). Pragmatus AV, LLC v. Yahoo! Inc., No. C-13-1176-
`EMC, 2014 U.S. Dist. LEXIS 65813, at *13 (N.D. Cal. May 13, 2014) (“[T]his Court owes
`no deference to the PTAB’s claim construction done as part of an inter partes review.”)
`(collecting cases).
`
`
`
`2 All emphases are supplied unless otherwise noted.
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`V. ARGUMENT
`A.
` “a”
`
`
`
`Illumina’s Construction
`“a” is an integer from 4 to 50 that is further
`defined in the context of the formulas (Zn)a
`and (Xn)a
`
`Scripps’s Construction
`“a” is the length of polymer A or
`identifier oligonucleotide C and is an
`integer from 4 to 50
`
`The parties’ dispute as to the meaning of parameter “a” was previously the subject
`of Illumina’s Motion to Dismiss, in which the Court rejected Illumina’s position that the
`term “a” is restricted to “the number of chemical units” of X and Z.
`The term “a” refers to the length of polymer A or identifier oligonucleotide C. ’596
`Patent, col. 4 ll. 39–42, col. 5 ll. 63–65; see also Metzker Decl., at ¶¶ 49–55. Those skilled
`in the art would have understood that “a” could be expressed in terms of the building blocks
`that make up a sequence (e.g., a sequence with 10 nucleotides or 5 nucleotides). E.g.,
`Metzker Decl., at ¶¶ 50–54, 56, 62. Those skilled in the art would have also understood
`that “a” could take on different values for polymer A and identifier oligonucleotide C. Id.
`The Court has already rejected Illumina’s narrow construction and should do so
`again as Illumina has already fully briefed this issue in its Motion to Dismiss and has
`“thoroughly addressed the intrinsic evidence already.” Reply (Dkt. No. 33), at 7. Further,
`Illumina has argued that the Court could resolve this issue based solely on the intrinsic
`record that was before the Court. E.g., id. at 3. The Court considered the intrinsic record
`and rejected Illumina’s proposed construction. Order (Dkt. No. 34), at 10–12.
`“The starting point for any claim construction must be the claims themselves,”
`TomTom, Inc. v. Adolph, 790 F.3d 1315, 1328 (Fed. Cir. 2015) (citation omitted). A careful
`review of all claims in the Patent shows that “a” is not limited to the number of chemical
`units for two reasons: First, Illumina’s proposed construction violates the principle of
`claim differentiation, as the Court found when it denied Illumina’s Motion to Dismiss.
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`Second, Illumina’s proposed construction would erase the distinction between parameters
`“a” and “n,” resulting in a construction that is presumptively incorrect.
`The presence of a dependent claim “that adds a particular limitation raises a
`presumption that the limitation in question is not found in the independent claim.” Hill-
`Rom Servs., Inc. v. Stryker Corp., 755 F.3d 1367, 1374 (Fed. Cir. 2014) (citation omitted).
`That presumption is especially strong when “the limitation in dispute is the only
`meaningful difference between an independent and dependent claim.” Id.
`As the Court concluded, that presumption applies here and strongly counsels against
`Illumina’s construction where it seeks to import language from a dependent claim to
`support its narrow construction. Order (Dkt. No. 34), at 11. Independent claim 1 recites a
`bifunctional molecule represented by formulas in which “a is an integer from 4 to 50,” and
`dependent claim 10 covers “[a] library comprising a plurality of species of bifunctional
`molecules according to claim 1.” ’596 Patent, claims 1, 10. Neither of those claims recite
`that “a” represents the number of chemical units, the limitation that Illumina seeks to read
`into all claims.
`Dependent claim 11, however, provides that the species of bifunctional molecules is
`“defined by the formula Va, where V represents the number of different chemical units
`forming an alphabet of possible chemical units of X, and a is an exponent to V and
`represents the number of chemical units of X forming polymer A.” Id. at claim 11.
`Because “parameter ‘a’ in claim 11, the dependent claim, represents ‘the number of
`chemical units of X forming polymer A,’ whereas parameter ‘a’ in claim 1, the independent
`claim, only requires ‘an integer from 4 to 50,’” Order (Dkt. No. 34), at 11, the claims
`themselves provide that “a” is not limited to the number of chemical units.
`In addition, Illumina’s attempt to improperly equate two claim terms—“a” and
`“n”— which in turn narrows the full scope of the claims, violates the “general presumption
`that different terms have different meanings.” Chi. Bd. Options Exh., Inc. v. Int’l Sec. Exh.,
`LLC, 677 F.3d 1361, 1369 (Fed. Cir. 2012); CAE Screenplates, Inc. v. Heinrich Fiedler
`
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`Gmbh & Co., 224 F.3d 1308, 1317 (Fed. Cir. 2000) (“In the absence of any evidence to the
`contrary, we must presume that the use of these different terms in the claims connotes
`different meanings.”).
`The terms “n” and “a” are presumed to have different meanings. The term “n” refers
`to a position identifier for the Xs within polymer A or the Zs within oligonucleotide C
`relative to the linker molecule B. ’596 Patent, claim 1. For example, in a bifunctional
`molecule containing three Xs within polymer A and three Zs within identifier
`oligonucleotide C, “n” is three in each of the formulas (Xn)a and (Zn)a. In the claims, “n”
`has a range of 1 to 11. Id. Conversely, the term “a” references a different variable—the
`length—and contains a different range—“an integer from 4 to 50.” Id.
`The use of different variables and ranges makes clear that “a” is not limited to the
`number of chemical units within a structure. If it were, there would be no reason to
`separately claim “n” and “a” and recite different ranges for each variable. That is because
`“a” would always equal “n” in the (Zn)a and (Xn)a formulas and both variables would cover
`the same numerical range.
`Illumina’s proposed construction, however, would improperly force that reading
`onto the claims. Illumina limits “n” and “a” to the ranges in which they overlap—between
`4 and 11. It thus excludes from the claims the significant bulk of the range expressly
`covered by the plain claim language: bifunctional molecules in which “n” is between 1 and
`3 or “a” is between 12 and 50. See Metzker Decl., at ¶¶ 60–62 (discussing an example
`bifunctional molecule in which “a” for polymer A is 10 nucleotides and “a” for identifier
`oligonucleotide C is 5 nucleotides and “n” is 1 for both structures).
`A narrowing of the claimed ranges of “n” and “a” and an erasure of the differences
`between dependent claim 11 and independent claim 1 can only be proper in the context of
`a clear disclaimer in the intrinsic record, an exacting standard. Order (Dkt. No. 34), at 9,
`12 (citing GE Lighting Sols., LLC v. AgiLight, Inc., 750 F.3d 1304, 1309 (Fed. Cir. 2014)).
`
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`The Court has already considered the intrinsic evidence and found that it failed to clear that
`hurdle. Id. at 10–12.
`Scripps requests that the Court reaffirm its earlier findings. The Court has previsouly
`rejected Illumina’s central argument. Illumina contended that “a” must be the number of
`chemical units X in polymer A because an embodiment disclosed that “‘a’ is an exponent
`to V” in a formula Va and “represents the number of chemical units of X forming the
`polymer A, i.e., the length of polymer A.” Order (Dkt. No. 34) (quoting ’596 Patent, col. 9
`ll. 7–11) (emphasis in Court Order). The Court correctly concluded that the specification
`did not limit “a” to number of chemical units:
`
`
`While this passage illustrates that parameter “a” can be defined
`by the number of chemical units, it does not specify that it must
`be so defined. Specifically the phrasing of the passage suggests
`that “a” is defined as the number of chemical units which in this
`formula—not categorically—connotes the length of polymer A.
`
`Order (Dkt. No. 34), at 10–11 (emphasis in original; citations omitted); see also Metzker
`Decl., at ¶¶ 58–62 (explaining that “a” in the Va formula can also represent the length
`expressed as the number of DNA nucleotide bases in polymer A or identifier
`oligonucleotide C).
`The Court also addressed the balance of the intrinsic evidence, such as Figure 2,
`rightly concluding that the evidence did not limit parameter “a” in the way Illumina
`proposes: “Defendant’s other citations to the specification also illustrate that parameter ‘a’
`can be defined by chemical unit length, not that it must be.” Order (Dkt. No. 34), at 11;
`id. at 12 (concluding, with regard to “a” in connection with identifier oligonucleotide C,
`that Illumina’s evidence “fare[d] no better” because the specification illustrated that “the
`length of parameter ‘a’ can be, not that it must be, measured by the number of chemical
`units”).
`
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`Indeed, those skilled in the art would have interpreted Figure 2 as also supporting
`Scripps’s construction. Metzker Decl., at ¶¶ 51–54. Illumina previously annotated Figure
`2 to show three Zs for oligonucleotide C and three Xs for polymer A, arguing that “a” was
`three for both polymer A and oligonucleotide C:
`
`
`’596 Patent, Fig. 2 (annoted by Illumina in its Motion to Dismiss)
`
`Those of skill in the art, however, would have understood this Figure to disclose that
`“a” is 18 for oligonucleotide C. Metzker Decl., at ¶ 53. The length of the oligonucleotide
`is 18, the length of the oligonucleotide in terms of A,T,C and G bases. Id. Those skilled
`artisans would also have concluded that “a” is three for polymer A, which contains three
`amino acids, with each being glycine or methionine. Id. In the parlance of the ’596 Patent,
`Figure 2 depicts polymer A represented by the formula (X3)3 and oligonucleotide C
`represented by the formula (Z3)18. Id. at ¶ 54. The Patent thus supports Scripps’s
`construction because it shows that “a” encompasses a length measured in nucleotides and
`that “a” may be a different value in the formula (Xn)a than it is in the formula (Zn)a.
`The plain language of the claims raises a strong presumption that “a” is not limited
`to the number of chemical units, i.e., the number of Xs and Zs. As the Court previously
`concluded, the intrinsic evidence does not rebut that presumption. The evidence instead
`shows that “a” is not limited to number of chemical units. For these reasons, Scripps
`
`SCRIPPS’S OPENING CLAIM CONSTRUCTION BRIEF
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`respectfully requests that the Court define “a” as “the length of polymer A or identifier
`oligonucleotide C and is an integer from 4 to 50,” as provided by the language of the claim.
`B.
` “(Xn)a” and “(Zn)a”
`
`
`
`Illumina’s Construction
`“(Xn)a” is a representation of polymer A,
`where “a” is the number of chemical units
`of X forming the polymer A
`
`“(Zn)a” is a representation of identifier
`oligonucleotide C, where “a” is the number
`of chemical unit
`identifiers
`in
`the
`oligonucleotide
`
`
`Scripps’s Construction
`“(Xn)a” is the formula that represents
`polymer A comprising a linear series of
`chemical units, where “a” is the length
`of polymer A and is an integer from 4
`to 50, “X” and “n” are defined by
`Claim 1 and
`require no
`further
`construction.
`“(Zn)a” is the formula that represents
`identifier oligonucleotide C, where “a”
`is
`the
`length
`of
`identifier
`oligonucleotide C and is an integer
`from 4 to 50, “Z” and “n” are defined
`by Claim 1 and require no further
`construction.
`
`The parties’ dispute as to the meaning of the terms (Xn)a and (Zn)a boils down to the
`same dispute as the parameter “a” term. As explained, Illumina attemps to incorrectly limit
`“a” to “the number of chemical units” of X and Z. The term “a,” however, refers to the
`length of polymer A or the length of oligonucleotide C.
`In addition, Illumina seeks to define (Xn)a and (Zn)a as “a representation of” polymer
`A and oligonucleotide C. The claims, however, do not recite the indefinite article “a.” The
`claims recite the definite article “the”—(Xn)a and (Zn)a are “the formula[s]” that represent
`polymer A and oligonucleotide C, respectively. ’596 Patent, claim 1; Metzker Decl., at ¶¶
`66, 91. The recitation provided in the claims should be reflected in the construction of this
`term. See generally Warner-Lambert Co. v. Apotex Corp., 316 F.3d 1348, 1356 (Fed. Cir.
`2003) (“It is a rule of law well established that the definite article ‘the’ particularizes the
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`subject which it precedes. It is a word of limitation as opposed to the indefinite or
`generalizing force of ‘a’ or ‘an.’” (internal quotation omitted)).
`C.
` “B is a linker molecule operatively linked to A and C”
`
`
`
`Scripps’s Construction
`single molecule B that performs the
`function of operatively linking a single
`polymer A
`to
`single
`identifier
`oligonucleotide C
`
`Illumina’s Construction
`linker molecule B (1) links to A and to C,
`(2) allows for alternative addition of
`nucleotides and amino acids to itself, and
`(3) is capable of coupling to and decoupling
`from a solid support without cleaving either
`the polypeptide or oligonucleotide from
`linker molecule B
`
`Alternatively, if the Court does not adopt
`the PTAB’s construction, then: a molecule
`B that performs the function of operatively
`linking a chemical moiety A to an identifier
`oligonucleotide C
`
`
`The ’596 Patent specification defines the term “linker molecule” in the way proposed
`by Scripps: “A linker molecule in a bifunctional molecule of this invention is represented
`by B in the above formula A—B—C and can be any molecule that performs the function
`of operatively linking the chemical moiety to the identifier oligonucleotide.” ’596 Patent,
`col. 8 ll. 20–24; Metzker Decl., at ¶¶ 68–72. The Patent goes on to state that the linker
`molecule provides “at least two features: (1) operative linkage to chemical moiety A, and
`(2) operative linkage to identifier oligonucleotide C.” ’596 Patent, col. 8 ll. 34–37.
`Illumina now seeks to rely on extrinsic evidence in the form of a Board decision
`denying Illumina’s petition for Inter Partes Review of the ‘596 Patent. In that decision,
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`the Board declined to apply Illumina’s proposed construction of “linker molecule”3 and
`found that the term “linker molecule” is a molecule that “(1) links to A and to C, (2) allows
`for alternative addition of nucleotides and amino acids to itself, and (3) is capable of
`coupling to and decoupling from a solid support without cleaving either the polypeptide or
`oligonucleotide from linker molecule B.” Decision Denying Institution, at 17.
`The Court, however, is not bound by the Board’s findings, which are considered
`extrinsic evidence. Depuy Orthopaedics, Inc. v. Orthopaedic Hosp., No. 3:12-CV-299,
`2016 U.S. Dist. LEXIS 2030, at *15 (N.D. Ind. Jan. 8, 2016) (“Extrinsic evidence may
`include a PTAB decision regarding IPR, but the court ‘owes no deference to the PTAB's
`claim construction done as part of an inter partes review.’”) (quoting Pragmatus, 2014 U.S.
`Dist. LEXIS 65813, at *13). Moreover, the Board entered its prosecution history findings
`at the stage denying institution and reached that conclusion on its own. Neither side argued
`that the prosecution history limited the “linker molecule” term or disclaimed the claim
`scope. See Decision Denying Institution, at 11–13.
`And, indeed, there was no prosecution history disclaimer. Each of the statements
`the Board relied upon are from the prosecution histories of the parent and grandparent
`applications of the ’596 Patent—not the ’596 Patent. And each of the statements
`specifically relate to amino acid and polypeptide-focused claim limitations that were in
`those prior applications—but are not in the ’596 Patent. See Metzker Decl., at ¶ 72. Unlike
`those applications,
`the ’596 Patent covers non-polypeptide polymers, such as
`oligonucleotides. E.g., ’596 Patent, claim 3; Metzker Decl., at ¶¶ 71–72. As a result, any
`prosecution history disclaimer based on statements made during the prosecution of the
`parent and grandparent applications do not attach to the ’596 Patent claims due to the
`different claim limitations. Regents of the Univ. of Minn. v. AGA Med. Corp., 717 F.3d
`
`
`3 In its Petition for Inter Partes Review of the ‘596 Patent, Illumina proposed a different
`construction of the term “linker molecule”—“any group of atoms that operatively links
`polymer A and oligonucleotide C,” which it now abandons. Decision Denying Institution,
`at 11 (attached as Ex. 2).
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`929, 943 (Fed. Cir. 2013) (explaining that Federal Circuit case law “establish[es] that the
`two patents must have the same or closely related claim limitation language” for
`prosecution history disclaimer to attach).
`Specifically, the Board relied on two office action responses to find a disclaimer—
`one from the grandparent application of the ’596 Patent (the ’445 Application) and one
`from the parent application of the ’596 Patent (the ’511 Application). Those statements do
`not evidence a disclaimer of the “linker molecule” in the ’596 Patent.
`Regarding the ’445 Application, the Board seized on two statements: (1) that “the
`present application [’445] discloses the coupling and decoupling of a linkage unit identified
`as 5' Branched-Modifier C3 or 5'BMC3 to a bead and the use of this linkage unit for
`sequentially synthesizing peptides and identifier oligonucleotides in