Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.375 Page 1 of 32
`
`Douglas E. McCann (Pro Hac Vice)
`dmccann@fr.com
`Fish & Richardson P.C.
`222 Delaware Avenue
`17th Floor, P.O. Box 1114
`Wilmington, DE 19801
`Phone: 302-652-5070
`Fax: 302-652-0607
`
`
`
`
`
`
`Juanita R. Brooks, SBN 75934
`
`brooks@fr.com
`
`
`Craig E. Countryman, SBN 244601
`countryman@fr.com
`
`
`Michael A. Amon, SBN 226221
`amon@fr.com
`
`
`
`Robert M. Yeh, SBN 286018
`
`ryeh@fr.com
`
`
`
`Ryan L. Frei, SBN 310722
`rfrei@fr.com
`Fish & Richardson P.C.
`12390 El Camino Real
`San Diego, CA 92130
`Phone: 858-678-5070
`Fax: 858-678-5099
`
`Attorneys for Defendant
`ILLUMINA, INC.
`
`UNITED STATES DISTRICT COURT
`
`SOUTHERN DISTRICT OF CALIFORNIA
`
`THE SCRIPPS RESEARCH INSTITUTE,
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`Case No. 16-cv-661 JLS (BGS)
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`Date:
`Time:
`Judge:
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` January 30, 2018
` 9:00 a.m.
` Hon. Janis L. Sammartino
`
`Courtroom: 4D
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`
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`
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`v.
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`Plaintiff,
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`ILLUMINA, INC.,
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`Defendant.
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`

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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.376 Page 2 of 32
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`TABLE OF CONTENTS
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`Page
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`I.
`
`INTRODUCTION .......................................................................................................... 1
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`II. STATEMENT OF FACTS ............................................................................................. 2
`
`
`A. The ’596 Patent Claims a “Bifunctional Molecule” With a Specific Structure
`Depicted Using Chemical Formulas........................................................................... 2
`
`B. The ’596 Patent Defines Variable “a” in the Claimed Formulas (Xn)a and (Zn)a,
`and Illumina’s Constructions Adopt those Definitions. ......................................... 3
`
`C. Scripps Narrowed Its Definition of the “Linker Molecule” Claim Limitation
`to Avoid Prior Art at the Patent Office. .................................................................... 6
`
`III. LEGAL STANDARDS ................................................................................................... 9
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`IV. ARGUMENT .................................................................................................................. 10
`
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`A. The Patent Defines the Term “(Zn)a” so that Parameter “a” Refers to the
`Number of Chemical Unit Identifiers. ..................................................................... 10
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`B. The Patent Defines the Term “(Xn)a” so that Parameter “a” Refers to the
`Number of Chemical Units X in the Polymer A. .................................................. 13
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`C. Subscript “a” is Properly Defined in the Context of “(Zn)a” and “(Xn)a.” ....... 18
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`D. Scripps’s Disclaimers Limit the Term “B is a Linker Molecule Operatively
`Linked to A and C,” as the PTO Correctly Determined. ..................................... 19
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`E. The Preamble Term “Bifunctional Molecule” Is Not Limiting. ......................... 22
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`F. The Court Should Reject Scripps’s Attempts to Read Limitations Into the
`Term “Identifier Oligonucleotide C” ....................................................................... 24
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`V. CONCLUSION .............................................................................................................. 25
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.377 Page 3 of 32
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`
`
`
`
`
`Cases
`
`TABLE OF AUTHORITIES
`
` Page(s)
`
`Abbott Labs. v. Novopharm Ltd.,
`323 F.3d 1324 (Fed. Cir. 2003) ........................................................................................ 14
`
`AIA Eng’g Ltd. v. Magotteaux Int’l S/A,
`657 F.3d 1264 (Fed. Cir. 2011) .......................................................................................... 9
`
`Alcon Research Ltd. v. Apotex, Inc.,
`687 F.3d 1362 (Fed. Cir. 2012) ........................................................................................ 12
`
`Allen Eng’g Corp. v. Bartell Indus., Inc.,
`299 F.3d 1336 (Fed. Cir. 2002) ........................................................................................ 23
`
`Am. Med. Sys. v. Biolitec, Inc.,
`618 F.3d 1354 (Fed. Cir. 2010) ........................................................................................ 23
`
`Apple, Inc. v. Ameranth, Inc.,
`842 F.3d 1229 (Fed. Cir. 2016) ........................................................................................ 16
`
`Bayer CropScience AG v. Dow AgroSciences LLC,
`728 F.3d 1324 (Fed. Cir. 2013) ........................................................................................ 18
`
`Biogen Idec, Inc. v. GlaxoSmithKline LLC,
`713 F.3d 1090 (Fed. Cir. 2013) .......................................................................................... 9
`
`ContentGuard Holdings, Inc. v. Amazon.com, Inc.,
`2015 WL 1289321 (E.D. Tex. Mar. 20, 2015) ............................................................... 22
`
`Dow Chem. Co. v. Nova Chem. Co.,
`803 F.3d 620 (Fed. Cir. 2015) .......................................................................................... 18
`
`Edwards Lifesciences LLC v. Cook Inc.,
`582 F.3d 1322 (Fed. Cir. 2009) .................................................................................. 14, 15
`
`Elkay Mfg. Co. v. Ebco Mfg. Co.,
`192 F.3d 973 (Fed. Cir. 1999) ...................................................................................... 9, 20
`
`Fisher & Paykel Healthcare Ltd. v. Resmed Corp.,
`2016 WL 9488705 (S.D. Cal. Nov. 22, 2016) ................................................................ 22
`
`
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`ii
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.378 Page 4 of 32
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`
`
`
`Geneva Pharms., Inc. v. GlaxoSmithKline, LLC,
`349 F.3d 1373 (Fed. Cir. 2003) ........................................................................................ 17
`
`Indacon, Inc. v. Facebook, Inc.,
`824 F.3d 1352 (Fed. Cir. 2016) ........................................................................................ 17
`
`Irdeto Access, Inc. v. Echostar Satellite Corp.,
`383 F.3d 1295 (Fed. Cir. 2004) ........................................................................................ 17
`
`Kraft Foods, Inc. v. Int’l Trading Co.,
`203 F.3d 1362 (Fed. Cir. 2000) ........................................................................................ 16
`
`Phillips v. AWH Corp.,
`415 F.3d 1303 (Fed. Cir. 2005) (en banc) ............................................................... 9, 10, 22
`
`Plantronics, Inc. v. Aliph, Inc.,
`724 F.3d 1343 (Fed. Cir. 2013) ........................................................................................ 25
`
`SkinMedica, Inc. v. Histogen Inc.,
`2011 WL 206619 (S.D. Cal. May 24, 2011) (Sammartino, J.) ...................................... 16
`
`SkinMedica, Inc. v. Histogen Inc.,
`727 F. 3d 1187 (Fed. Cir. 2013) ....................................................................................... 14
`
`Southwall Techs., Inc. v. Cardinal IG Co.,
`54 F.3d 1570 (Fed. Cir. 1995) .......................................................................................... 16
`
`Summit 6, LLC v. Samsung Elecs. Co., Ltd.,
`802 F.3d 1283 (Fed. Cir. 2015) ........................................................................................ 24
`
`Technological Properties Ltd. LLC v. Huawei Techs. Co., Ltd.,
`849 F.3d 1349 (Fed. Cir. 2017) ........................................................................................ 20
`
`Teva Pharms. USA, Inc. v. Sandoz, Inc.,
`789 F.3d 1335 (Fed. Cir. 2015) ........................................................................................ 18
`
`In re Varma,
`816 F.3d 1352 (Fed. Cir. 2016) ........................................................................................ 16
`
`Weiland Sliding Doors and Windows, Inc. v. Panda Windows and Doors LLC,
`2011 WL 3490481 (S.D. Cal. Aug. 10, 2011) ................................................................. 23
`
`Wi-LAN USA, Inc. v. Apple Inc.,
`830 F.3d 1374 (Fed. Cir. 2016) ........................................................................................ 20
`
`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`iii
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`CASE NO. 16-cv-661 JLS (BGS)
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.379 Page 5 of 32
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`Statutes
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`35 U.S.C. § 112(d) ................................................................................................................... 12
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`iv
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.380 Page 6 of 32
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`I.
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`INTRODUCTION
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`This case presents five claim construction issues for the Court, three of which
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`are potentially case-dispositive and two of which are relatively minor. Scripps’s patent
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`covers a “bifunctional molecule” that has three parts: A—B—C. A is a polymer. C is
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`an oligonucleotide (short strand of DNA). B is a “linker molecule” that operatively
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`links A and C. The claims require that oligonucleotide C has a structure represented by
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`the formula (Zn)a and that polymer A has a structure represented by the formula (Xn)a.
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`Two of the parties’ case-dispositive disputes are over what the variable “a”
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`means in the formulas (Zn)a and (Xn)a. Illumina’s proposed constructions adopt the
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`patent’s express definition of variable “a” in each formula. Illumina’s constructions are
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`also the only constructions consistent with the dependent claims and with how skilled
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`artisans would interpret a subscript like variable “a” using well-known conventions for
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`chemical formulas. The Court’s initial observations on these terms at the motion to
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`dismiss stage, (Doc. No. 34 at 10–13), have aided Illumina in presenting its
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`constructions, and we address those observations below.
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`The parties’ other case-dispositive dispute involves the construction of the
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`“linker molecule” limitation. A panel of three specialized judges on the Patent Trial
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`and Appeal Board previously construed this same term and adopted the same
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`construction Illumina now proposes. The Board reached its construction by a finding
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`that Scripps made a “clear and unequivocal disavowal” of claim scope when initially
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`prosecuting its family of patents. The Board’s finding is well-supported and persuasive
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`given its detailed analysis applying the same legal standard applicable here. Scripps
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`should not be permitted to obtain a broader construction in litigation, as its claims
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`could not have survived an inter partes review without the Board’s narrow construction.
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`Finally, Scripps seeks construction of two terms—“bifunctional molecule” and
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`“identifier oligonucleotide C”—to try to impose limitations to distinguish the prior art.
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`But the first term is in the claim’s preamble, making it non-limiting, while the meaning
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`of the latter is already recited in the claim and needs no further elaboration.
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.381 Page 7 of 32
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`II.
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`STATEMENT OF FACTS
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`A. The ’596 Patent Claims a “Bifunctional Molecule” With a Specific
`Structure Depicted Using Chemical Formulas.
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`Scripps’s ’596 patent proposes a technique it hoped would allow scientists to
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`simultaneously test libraries of compounds for biological activity. (Ex. A at 1:16–3:18.)
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`Scientists can test for activity by assessing if a compound binds to a known biological
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`receptor of interest. But, when a scientist tests many compounds simultaneously, it can
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`be hard to determine which compound, if any, actually binds. (Id.) To address this
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`issue, the ’596 patent proposes “tagging” each compound with a piece of DNA that has
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`a unique “sequence” (i.e., arrangement of the nucleotide bases adenosine, thymine,
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`guanine, and cytosine). (Id.) A scientist can then identify any compound that binds by
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`reading the sequence of DNA. The patent refers to the resulting combination as a
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`“bifunctional molecule,” with the structure A—B—C. (Id.) “A” is the compound the
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`scientist is testing for biological activity, “C” is an oligonucleotide tag (short piece of
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`DNA) that identifies the compound’s structure, and “B” is a linker molecule. (Id.)
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`The ’596 patent gives further detail about the structure of each part of the
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`bifunctional molecule. The patent explains that “A” is a polymer made of a series of
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`chemical units that are labeled X1, X2, and so on. (Ex. A at 4:31–38.) Identifier
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`oligonucleotide C is a series of unit identifier nucleotide sequences that are labelled Z1,
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`Z2, and so on. (Id. at 5:55–65.) The subscript for each chemical unit Xn and unit
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`identifier Zn is a “position identifier n” that indicates where that building block is
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`located relative the linker molecule B. (Id. at 4:31–38, 5:55–65.) For example, the
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`patent shows the following bifunctional molecule with 4 chemical units Xn and 4
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`chemical unit identifier sequences Zn, where “n” ranges from 1 to 4:
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`(Id. at 5:66-6:6, 10:18-11:25.) In this example, polymer A is X4X3X2X1, and identifier
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`oligonucleotide C is Z1Z2Z3Z4. When speaking more generally, the ’596 patent uses the
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`formulas (Xn)a and (Zn)a to represent, respectively, polymer A and oligonucleotide C.
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.382 Page 8 of 32
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`Each unit identifier Zn “identifies” the chemical unit Xn at the same position
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`“n.” (Ex. A at 5:55–6:6, 43:8–10.) This means that the sequence of unit identifier Z1
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`allows a scientist to determine the structure of chemical unit X1, unit identifier Z2
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`allows a scientist to identify chemical unit X2, and so on. (Id.) The scientist can
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`determine the complete structure of polymer A (the compound of interest) by reading
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`the sequence of oligonucleotide C, because each chemical unit Xn forming polymer A
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`has a corresponding unit identifier Zn within oligonucleotide C. (Id.)
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`Claim 1 of the ’596 patent covers a “bifunctional molecule” with such an A—
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`B—C structure. The parties dispute the construction of the five emphasized terms:
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`1. A bifunctional molecule according to the formula A—B—C, wherein
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` A
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` 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,
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` B is a lin
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`ker molecule operatively linked to A and C, and
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`identifier oligonucleotide C is represented by the formula (Zn)a,
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`wherein a unit identifier nucleotide sequence Z within oligonucleotide C
`identifies the chemical unit X at position n; and
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`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,
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`and a is an integer from 4 to 50.
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`(Ex. A at 43:2-14 (emphases added).) The parties’ key disputes concern what variable
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`“a” means in the formulas “(Zn)a” and “(Xn)a” and whether this Court should adopt the
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`Board’s construction of the “linker molecule” limitation given Scripps’s disclaimers.
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`B. The ’596 Patent Defines Variable “a” in the Claimed Formulas (Xn)a
`and (Zn)a, and Illumina’s Constructions Adopt those Definitions.
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`The ’596 patent defines the variable “a” separately for the formulas (Xn)a and
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`(Zn)a, so we will discuss each separately, followed by an overview of the ’596 patent’s
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`remaining disclosure on how to build a bifunctional molecule covered by the claims.
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`The patent’s definition of variable “a” in the formula (Xn)a is found in two
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`sections. The parties agree that, in the general section discussing polymer A and the
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.383 Page 9 of 32
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`formula (Xn)a, the patent introduces the variable “a” when discussing “library size
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`limitations” and explains that variable “a” is “defined” by “the length” of polymer A:
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`Although the length of the polymer can vary, defined by a, practical library
`size limitations arise if there is a large alphabet size as discussed further herein.
`Typically, a is an integer from 4 to 50.
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`(Ex. A at 4:39–42.) Scripps’s construction stops there and requires that “a” be the
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`“length of the polymer,” without specifying how “length” is measured. But “length”
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`must be measured in terms of a specific unit (e.g., inches, feet, miles), otherwise it has
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`no meaning. The ’596 patent prescribes what that unit of measure must be when it
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`resumes its discussion of “library size limitations.” It explains that variable “a” is “the
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`number of chemical units of X forming the polymer A, i.e., the length of polymer A”:
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`The number of different species in a library represents the complexity of a
`library and is defined by the polymer length of the chemical moiety, and by the
`size of the chemical unit alphabet that can be used to build the chemical unit
`polymer. The number of different species referred to by the phrase “plurality of
`species” in a library can be defined by the formula Va, i.e., V to power of a
`(exponent a). V represents the alphabet size, i.e., the number of different
`chemical units X available for use in the chemical moiety. “a” is an exponent
`to V and represents the number of chemical units of X forming the
`polymer A, i.e., the length of polymer A.
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`(Id. at 9:1-11.) Illumina’s construction adopts this complete definition, requiring that
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`“a” and the “length of the polymer” are the number of chemical units X in polymer A.
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`The patent defines “a” in the formula (Zn)a in a section generally describing the
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`structure of oligonucleotide C. Illumina’s construction reflects that definition, which is
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`that “a” is “the number of chemical unit identifiers in the oligonucleotide”:
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`An identifier oligonucleotide in a bifunctional molecule of this invention is
`represented by C in the above formula A--B--C and is an oligonucleotide having
`a sequence represented by the formula (Zn)a, wherein Z is a unit identifier
`nucleotide sequence within oligonucleotide C that identifies the chemical unit X
`at position n. n has the value of 1+i where i is an integer from 0 to 10, such that
`when n is 1, Z is located most proximal to the linker (B). a is an integer as
`described previously to connote the number of chemical unit identifiers in
`the oligonucleotide.
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`(Ex. A at 5:55–65.) Scripps ignores this definition and interprets “a” as the “length of
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`identifier oligonucleotide C,” even though the ’596 patent never ties variable “a” in the
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`formula (Zn)a to “length,” much less to the length of “identifier oligonucleotide C.”
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`4
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.384 Page 10 of 32
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`Having defined the nomenclature used to describe a bifunctional molecule’s
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`structure, the ’596 patent then explains how to make a library of such molecules. The
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`patent’s discussion here uses variable “a” consistently with Illumina’s constructions
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`(and the patent’s definitions). The scientist starts with the linker molecule (B) and then
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`uses “an alternating parallel synthesis procedure to add chemical unit X and then add a
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`unit identifier nucleotide sequence Z that defines (codes for) that corresponding
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`chemical unit.” (Ex. A at 10:1–4.) The scientist can repeat this process for each
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`additional chemical unit X and unit identifier Z that she wants to add. The patent
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`shows the resulting bifunctional molecules after 1, 2, and 3 synthesis cycles, where A'
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`and C' are ends that are ready for the addition of another unit, if desired:
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`(Id. at 10:35–11:15.) The patent explains that “adding a next set of building blocks X
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`and Z can be repeated at positions n = 4, 5, 6 . . . and so on depending on the length of
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`polymers desired.” (Id. at 11:21–23.) “For each cycle, the polymer length a increases
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`by one and the library complexity therefore increases exponentially according to the
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`formula Va.” (Id.; see also 11:55–58.) Each cycle adds one chemical unit X, showing
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`that “polymer length a” and the number of chemical units X forming polymer A are
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`the same. The patent’s reference to the formula Va underscores this point, because that
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`formula uses “a” to refer to “the number of chemical units of X forming the polymer
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`A, i.e., the length of polymer A.” (Id. at 9:10–11.) Each cycle also adds one new unit
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`identifier Z, so the value of “a” in (Zn)a increases by one as well.
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`The ’596 specification concludes with a section titled “Examples,” which
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`recommends specific materials for building a bifunctional molecule where polymer A is
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`a peptide. (Ex. A at 23:47–29:6.) Figure 2 shows making a small library where each
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`chemical unit X is one of two amino acids (glycine or methionine) and each amino acid
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`is identified by a unique, 6-nucleotide unit identifier nucleotide sequence Z (CACATG
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`and ACGGTA, respectively). (Id. at 27:59–28:20.) This example follows the synthesis
`5
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`procedure discussed earlier: the scientist starts with linker molecule B, and then adds
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`each chemical unit X and unit identifier nucleotide sequence Z in alternating fashion:
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`The result is a library of 8 bifunctional molecules, as dictated by the formula Va.
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`There are 2 possible chemical units X at each step (glycine or methionine) and 3
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`chemical units in polymer A, so Va = 23 = 8. Variable “a” is 3 in both the formulas
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`(Xn)a and (Zn)a, because each bifunctional molecule has 3 chemical units X and 3 unit
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`identifier nucleotide sequences Z. (Chelsky Decl., at ¶¶ 27, 37.) The value of “n” in
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`the formula ranges from 1–3, depending on which position is being referenced. (Id.)
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`C.
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`Scripps Narrowed Its Definition of the “Linker Molecule” Claim
`Limitation to Avoid Prior Art at the Patent Office.
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`Scripps filed its initial patent application in March 1992 and would eventually
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`obtain three patents—two early patents (Nos. 5,573,905 and 5,723,598) that are not in
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`this case, and the ’596 patent-in-suit. The common specification of all 3 patents
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`includes broad language about linker molecule B within the bifunctional molecule. (Ex.
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`A at 8:19–27.) But Scripps made several disclaimers to the Patent Office during the
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`prosecution histories of its earlier ’905 and ’598 patents restricting the scope of that
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`term, disclaimers that apply equally to the ’596 patent-in-suit.
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.386 Page 12 of 32
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`Most of Scripps’s disclaimers occurred during the prosecution of the ’905
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`patent. Scripps initially sought broad claims to a bifunctional molecule with an A—
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`B—C structure, like the one ultimately claimed in the ’596 patent, where “B is a linker
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`molecule operatively linked to A and C.” (Ex. B at 92.) The examiner rejected those
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`claims as obvious based on the Lam and Scott references. (Ex. C at 108–09; Exs. D &
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`E.) The examiner cited Scott’s description of peptides (which qualify as polymer A)
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`linked to DNA (which qualifies as oligonucleotide C) that identifies their structure.
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`(Ex. C at 108–09; Ex. E at 116–17.) Scripps distinguished Scott by arguing its
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`oligonucleotide C was “not ‘operatively linked’ to a chemical moiety [polymer A] in the
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`library by a linker molecule.” (Ex. F at 139.) The examiner responded with an
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`obviousness rejection that added the Warren and Dattagupta patents, which show
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`specific linkers connecting oligonucleotides to peptides. (Ex. G at 148–50; Ex. P at
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`2:1-4; Ex. H at 2:4-22, 3:13-30.)
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`Scripps responded with disclaimers that narrow the claim term “B is a linker
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`molecule operatively linked to A and C.” Scripps distinguished its pending claims by
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`arguing that the prior art didn’t disclose a linker molecule B that (1) is capable of
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`coupling and decoupling from a solid support (like a bead) and (2) can accommodate
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`alternating addition of nucleotides and amino acids. (Ex. I at 167–73.) Scripps’s
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`statements regarding Lam and Scott include both of these disclaimers:
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`Neither Lam nor Scott discloses a DNA/peptide linkage unit and the
`coupling and decoupling of such linkage unit with respect to a bead. In
`contrast, the present application 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 an alternating fashion, i.e., each addition of an amino
`acid to the peptide is followed by the addition of a corresponding set of
`nucleotides to the identifier oligonucleotide for encoding such amino acid. The
`process may then be-repeated as desired, beginning with the addition of another
`amino acid to the peptide etc. This method of alternating synthesis for
`peptide/nucleotide conjugates appears to be novel and patentably unobvious.
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`(Id. at 169.) Scripps distinguished Warren and Dattagupta, which the examiner had
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`specifically selected to show a similar linker molecule B, by repeating the same two
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`arguments:
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.387 Page 13 of 32
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`• “Warren does not disclose whether his linkage unit is capable of
`coupling and decoupling to a bead. However, his DNA/enzyme
`conjugate would be inoperable as a hybridization probe if the linkage
`unit were coupled to a bead. Additionally, Warren discloses only a
`DNA/enzyme conjugation reaction and does not teach a bead based
`method of alternating chemistries for synthesizing libraries of
`encoded peptides.” (Id.)
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`• “Dattagupta does not disclose whether his linkage unit is capable
`of coupling and decoupling to a bead. However, his DNA/protein
`conjugate would be inoperable as a[n] immunoassay signal amplifier if
`the linkage unit were coupled to a bead. Additionally, Dattagupta
`discloses only the conjugation of DNA with protein and does not teach a
`bead based method of alternating chemistries for synthesizing libraries of
`encoded peptides.... Dattagupta does not disclose the alternating
`chemistries which enable the synthesis of a bifunctional molecule.”
`(Id. at 170.)
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`Having considered those arguments, the examiner maintained the rejections,
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`noting that Scripps was “arguing limitations not recited in the claims.” (See Ex. J at 184;
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`see also id. at 181.) But Scripps was undeterred. It did not rescind or clarify those
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`arguments. Instead, it appealed to the Board of Patent Appeals and Interferences
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`within the Patent Office and repeated the exact same arguments. Scripps’s appeal brief
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`again distinguished Lam, Scott, Warren, and Dattagupta by arguing that (1) they do
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`“not disclose whether his linkage unit is capable of coupling and decoupling to a bead,”
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`and (2) they do “not teach a bead based method of alternating chemistries for
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`synthesizing libraries of encoded peptides.” (Ex. K at 202–06.)
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`Scripps made similar statements while prosecuting its ’598 patent. The examiner
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`rejected claims that required a linker molecule B as lacking enablement, because the
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`specification includes only “a single working example” of a linker. (Ex. L at 220–21).
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`Scripps responded by arguing that the claims covered “a specific linker molecule,” and
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`that the patent’s example (5’BMC3) is “representative of all linkers which are adapted
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`for amino acid and nucleotide precursors.” (Ex. M at 235.) The implication was that
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`the claims were limited to linker molecules with the properties of 5’BMC3, which the
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`specification shows is capable of (1) coupling and decoupling to a solid support and (2)
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`permitting the alternate addition of amino acids and nucleotides. (Ex. A at 8:46–50,
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`25:4–7; Ex. O at 253–54.)
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.388 Page 14 of 32
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`III. LEGAL STANDARDS
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`Claim construction begins with the claim language, which can “provide
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`substantial guidance as to the meaning of particular claim terms.” Phillips v. AWH
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`Corp., 415 F.3d 1303, 1314 (Fed. Cir. 2005) (en banc). “[T]he context in which a term is
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`used in the asserted claim can be highly instructive.” Id. In addition, “[b]ecause claim
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`terms are normally used consistently throughout the patent, the usage of a term in one
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`claim can often illuminate the meaning of the same term in other claims.” Id.
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`The specification “is always highly relevant to the claim construction analysis.
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`Usually, it is dispositive; it is the single best guide to the meaning of a disputed term.”
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`Phillips, 415 F.3d at 1315. “Consistent with that general principle, our cases recognize
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`that the specification may reveal a special definition given to a claim term by the
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`patentee that differs from the meaning it would otherwise possess. In such cases, the
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`inventor’s lexicography governs.” Id. at 1316. “Moreover, the specification need not
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`reveal such a definition explicitly, but may do so by implication.” AIA Eng’g Ltd. v.
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`Magotteaux Int'l S/A, 657 F.3d 1264, 1276 (Fed. Cir. 2011). Absent lexicography or
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`disavowal, courts must not import limitations into the claims. Phillips, 415 F.3d at 1323.
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`The prosecution history is also an important tool in claim construction. See, e.g.,
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`Phillips, 415 F.3d at 1317. “[W]hen the patentee unequivocally and unambiguously
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`disavows a certain meaning to obtain a patent, the doctrine of prosecution history
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`disclaimer narrows the meaning of the claim consistent with the scope of the claim
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`surrendered.” Biogen Idec, Inc. v. GlaxoSmithKline LLC, 713 F.3d 1090, 1095 (Fed. Cir.
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`2013). “When multiple patents derive from the same initial application, the
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`prosecution history regarding a claim limitation in any patent that has issued applies
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`with equal force to subsequently issued patents that contain the same claim limitation.”
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`Elkay Mfg. Co. v. Ebco Mfg. Co., 192 F.3d 973, 980 (Fed. Cir. 1999).
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` Extrinsic evidence is generally “less reliable than the patent and its prosecution
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`history” and is “less significant than the intrinsic record in determining the legally
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`operative meaning of claim language.” Phillips, 415 F.3d at 1317–18.
`9
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`ILLUMINA’S OPENING CLAIM
`CONSTRUCTION BRIEF
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`Case 3:16-cv-00661-JLS-BGS Document 54 Filed 11/28/17 PageID.389 Page 15 of 32
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`IV. ARGUMENT
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`A. The Patent Defines the Term “(Zn)a” so that Parameter “a” Refers
`to the Number of Chemical Unit Identifiers.
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`Illumina begins with th