Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 1 of 115 PageID #: 2266
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`THE TRUSTEES OF COLUMBIA
`UNIVERSITY IN THE CITY OF
`NEW YORK and QIAGEN
`SCIENCES, LLC,
`
`Plaintiffs,
`
`v.
`
`ILLUMINA, INC.,
`
`Defendant.
`
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`
`Civil Action No. 19-1681-CFC
`
`JOINT CLAIM CONSTRUCTION BRIEF
`
`Illumina Ex. 1157
`Illumina v. Columbia
`IPR2020-01177
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 2 of 115 PageID #: 2267
`
`ABLE OF CONTENTS
`
`Plaintiffs’ Opening Posi__————
`
`[trOCUCtOfenna)
`iF
`
`
`Ue
`
`echnicalBackground
`
`NAandNucleotidesee1
`
`Plaintiffs’ Construction Is Unsupported1 /|
`
`e Claim Language Confirms I[fumina’s Constructio
`| eee|/
`
`Da
`
`OtCOtS |SUt|)
`
`IDefendant’s Answering Position
`
`T/
`
`Il.
`
`Introduct0)a| /|
`
`Plants’ji,enna 10)
`
`| AGREEDIUPON CONSTRUCTIONS
`
`2K)
`
`TTT DISPUTED CONSTRUCTIONSSin)
`
`a)
`
`le
`
`Plaintiffs’ Opening Position
`
`ae
`
`he Intrinsic Evidence Supports Plaintiffs’ Construction
`
`(tlumina Admits that Y May Be Constructed Using More
`a)
`
`IDefendant’s Answering Position=a1)
`
`Al,
`
`e Specification Confirms [[umina’s Construction Faa30)
`
`he Prosecution History Requires IIlumina’s
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 3 of 115 PageID #: 2268
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`Plaintiffs’ Reply Position |
`
`Ai
`
`lumina Mischaracterizes Plaintiffs’ Position ——
`
`he Claims and Specification Support Plaintiffs’
`
`45
`
`e Prosecution History Favors Plaintiffs’ Construction
`enn|)/
`
`Width, Not Longest Dinens1 ———————nn/|3)
`
`Wlumina and Others Teach That a “Linker” Can Be Made
`of More than One Linkexn i)
`
`AR Defendant’sSurgReply Position=|)
`
`Sa]|nnn |
`
`IF
`
`Plaintiffs’ Opening Position
`
`S
`
`aeTheIntrinsicJEvidence Supports Plaintiffs’ Construction
`b
`
`Defendant’s Construction Would Exclude Chemical
`roups Designated as Small in the Specification and
`Prosecution History
`
`IDefendant’s Answering Position
`
`as
`
`olumbia’s Definition Of “Small” During Prosecution
`And IPR
`
`OD
`
`“Small” Should Be Defined With Respect To Rat
`POLYMCrasCee/|()
`
`‘Small’ Should Be Defined In Terms Off‘Diameter’ #/
`
`e Court Should Not Construe The Claims In Terms O
`A “Width”
`
`he Prosecution History Is Clear that Diameter Refers to
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 4 of 115 PageID #: 2269
`
`llumina’s Limitation Regarding Having to Fit Within the
`Rat DNA Polymerase Is Unnecessary and Unhelpful B&B
`
`Defendant’s SurgReply Position inner)
`
`olumbia’s Representations Regarding “Small” During
`Al.
`Prosecution And IPR Should |GoVcrnnan)
`
`Dr. Kurtyan’s “Consistency” With The Ju Declaration Is
`WC1)noonnnenenS|°
`
`Defendant’s SuriReply Posi)|||
`
`‘R...18 stable during a DNA polymerase[reaction”a/
`
`le
`
`Plaintiffs’ Opening Positionnnn)/
`
`Defendant’s Answering Position}
`
`OD
`
`Defendant's SurgReply Position
`
`‘A method for sequencing a nucleic acid”’
`
`le
`
`Plaintiffs’ Opening Pos!ticres
`
`IDefendant’s Answering Position
`
`Plaintiffs’ ReplyPosito:
`
`W.
`
`Oe
`
`4h
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 5 of 115 PageID #: 2270
`
`TABLE OF AUTHORITIES
`
` Page(s)
`
`Cases
`
`01 Communique Lab., Inc. v. LogMeIn, Inc.,
`687 F.3d 1292 (Fed. Cir. 2012) .............................................................. 23, 25, 43
`
`3M Innovative Props. Co. v. Tredegar Corp.,
`725 F.3d 1315 (Fed. Cir. 2013) .......................................................................... 48
`
`American Piledriving Equip, Inc. v. Geoquip, Inc.,
`637 F.3d 1324 (Fed. Cir. 2011) .............................................................. 49, 55, 56
`
`Applied Materials, Inc. v. Advanced Semiconductor Materials Am., Inc.
`98 F.3d 1563 (Fed. Cir. 1996) .......................................................................... 105
`
`Aspex Eyewear, Inc. v. Marchon Eyewear, Inc.,
`672 F.3d 1335 (Fed. Cir. 2012) ..........................................................................107
`
`Aylus Networks, Inc. v. Apple Inc.,
`856 F.3d 1353 (Fed. Cir. 2017) ............................................................................32
`
`Baldwin Graphic Sys., Inc. v. Siebert, Inc.,
`512 F.3d 1338 (Fed. Cir. 2008) .................................................................... 23, 38
`
`Becton, Dickinson & Co. v. Tyco Healthcare Grp., LP,
`616 F.3d 1249 (Fed. Cir. 2010) ........................................................... 99, 100, 102
`
`Boehringer Ingelheim Vetmedica, Inc. v. Schering-Plough Corp.,
`320 F.3d 1339 (Fed. Cir. 2003) ............................................... 105, 106, 110, 111
`
`Broadridge Fin. Sols., Inc. v. Inveshare, Inc.,
`2012 U.S. Dist. LEXIS 51246 (D. Del. April 11, 2012) .................................... 82
`
`Catalina Mktg. Int’l, Inc. v. Coolsavings.com, Inc.,
`289 F.3d 801 (Fed. Cir. 2002) ........................................................... 108, 109, 111
`
`Cordis Corp. v. Boston Sci. Corp.,
`658 F.3d 1347 (Fed. Cir. 2011) ..................................................................... 35, 37
`
`iv
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 6 of 115 PageID #: 2271
`
`Cordis Corp. v. Medtronic Ave,
`339 F.3d 1352 (Fed. Cir. 2003) cert. denied, 540 U.S. 1213 (2004) ................. 45
`
`E.I. du Pont de Nemours & Co. v. Unifrax I LLC,
`921 F.3d 1060 (Fed. Cir. 2019) .......................................................................... 25
`
`Elkay Mfg. Co. v. Ebco Mfg. Co.,
`192 F.3d 973 (Fed. Cir. 1999) ............................................................................ 57
`
`Enzo Biochem, Inc. v. Amersham PLC,
`439 F. Supp.2d 309 (S.D.N.Y. 2006) ............................................... 29, 30, 45, 46
`
`EPOS Techs. Ltd. v. Pegasus Techs. Ltd.,
`766 F.3d 1338 (Fed. Cir. 2014) .......................................................................... 80
`
`Fenner Investments, Ltd. v. Cellco Partnership,
`778 F.3d 1320 (Fed. Cir. 2015) .................................................................... 37, 41
`
`Fitness Quest, Inc. v. Monti,
`330 F. App’x 904 (Fed. Cir. 2009) ..................................................................... 63
`
`Galderma Labs., L.P. v. Amneal Pharms. LLC,
`806 F. App’x 1007 (Fed. Cir. 2020) ................................................25, 49, 50, 56,
`
`Hyperphrase Techs., LLC v. Google, Inc.,
`260 F. App’x 274 (Fed. Cir. 2007) ..................................................................... 45
`
`Idenix Pharm. LLC v. Gilead Scis., Inc.,
`No. 13-1987-LPS, 2016 U.S. Dist. LEXIS 158513 (D. Del. Nov.
`16, 2016) ........................................................................................................... 106
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York, IPR2012-
`00007 ....................................................................................................................77
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 1 ................................................................................40
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 13 ..............................................................................34
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 30 ..............................................................................31
`
`v
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 7 of 115 PageID #: 2272
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 48 (Feb. 5, 2019) ............................................... 40, 41
`
`Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
`IPR2018-00385, Paper No. 66 ..............................................................................34
`
`Illumina, Inc. v. Trustees of Columbia Univ. In The City of New York,
`IPR2018-00385 ........................................................................................................ 54
`
`In re ’318 Patent Infringement Litig.,
`578 F. Supp. 2d 711 (D. Del. 2008).................................................................. 107
`
`In re Cruciferous Sprout Litig.,
`301 F.3d 1343 (Fed. Cir. 2002) ........................................................................ 107
`
`In re CSB-System Int’l, Inc.,
`832 F.3d 1335 (Fed. Cir. 2016) .......................................................................... 50
`
`Jack Guttman, Inc. v. Kopykake Enterp., Inc.,
`302 F.3d 1352 (Fed. Cir. 2002) ............................................................................33
`
`Kaneka Corp. v. Zhejiang Med. Co.,
`No. CV 11-02389 SJO, 2018 U.S. Dist. LEXIS 82023 (C.D. Cal.
`Apr. 5, 2018) ....................................................................................................... 63
`
`Liebel-Flarsheim Co. v. Medrad, Inc.,
`358 F.3d 898 (Fed. Cir. 2004) .................................................................... 98, 103
`
`Lifestream Diagnostics, Inc. v. Polymer Tech. Sys., Inc.,
`109 F. App’x 411 (Fed. Cir. 2004) .......................................................................... 55
`
`Microsoft Corp. v. Multi-Tech Sys.,
`357 F.3d 1340 (Fed. Cir. 2004) .......................................................................... 55
`
`Mondis Tech., Ltd. v. Chimei Innolux Corp.,
`822 F. Supp. 2d 639 (E.D. Tex. 2011) ................................................................ 63
`
`Multiform Desiccants, Inc. v. Medzam, Ltd.,
`133 F.3d 1473 (Fed. Cir. 1988) ................................................................................ 97
`
`Oatey Co. v. IPS Corp.,
`514 F.3d 1271 (Fed. Cir. 2008) .................................................................... 44, 45
`
`vi
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 8 of 115 PageID #: 2273
`
`On-Line Techs., Inc. v. Bodenseewerk Perkin-Elmer GmbH,
`386 F.3d 1133 (Fed. Cir. 2004) .................................................................... 61, 62
`
`Pacing Techs., LLC v. Garmin Int'l, Inc.,
`778 F.3d 1021 (Fed. Cir. 2015) ............................................................................39
`
`Personalized Media Commc’ns, LLC v. Apple Inc.,
`952 F.3d 1336 (Fed. Cir. 2020) ............................................................................32
`
`Phillips v. AWH Corp.,
`415 F.3d 1303 (Fed. Cir. 2005) ............................................................... 31, 32, 36
`
`Phonometrics, Inc. v. N. Telecom Inc.,
`133 F.3d 1459 (Fed. Cir. 1998) ............................................................ 97, 98, 102
`
`Power Integrations, Inc. v. On Semiconductor Corp.,
`396 F. Supp. 3d 851 (N.D. Cal. 2019) ..................................................................49
`
`PPC Broadband, Inc. v. Corning Optical Commc'ns RF, LLC,
`815 F.3d 734 (Fed. Cir. 2016) ....................................................................... 35, 36
`
`Princeton Digital Image Corp. v. Konami Digital Entm’t Inc.,
`No. 12-1461-LPS-CJB, 2017 WL 6375173 (D. Del. Dec. 13, 2017) ..................32
`
`Rolls-Royce, PLC v. United Techs. Corp.,
`603 F.3d 1325 (Fed. Cir. 2010) ..................................................................... 39, 40
`
`Rowe v. Dror,
`112 F. 3d 473 (Fed. Cir. 1997) ......................................................................... 108
`
`Sage Prods., Inc. v. Devon Indus., Inc.,
`126 F.3d 1420 (Fed. Cir. 1997) ............................................................................29
`
`Sanofi-Aventis United States LLC v. Sandoz, Inc.,
`345 F. App’x 594 (Fed. Cir. 2009) ..................................................................... 45
`
`Seachange Int'l, Inc. v. C-COR Inc.,
`413 F.3d 1361 (Fed. Cir. 2005) ................................................................................55
`
`SciMed Life Sys., Inc. v. Adv. Cardiovascular Sys., Inc.,
`242 F.3d 1337 (Fed. Cir. 2001) ............................................................................29
`
`vii
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 9 of 115 PageID #: 2274
`
`Symantec Corp. v. Computer Assoc. Int’l, Inc.,
`522 F.3d 1279 (Fed. Cir. 2008) ............................................................... 108, 109
`
`Teva Pharms. USA, Inc. v. Sandoz, Inc.,
`789 F.3d 1335 (Fed. Cir. 2015) ..................................................................... 76, 93
`
`TiVo, Inc. v. Echostar Communs. Corp.,
`516 F.3d 1290 (Fed. Cir. 2008)................................................................................ 43
`
`TomTom, Inc. v. Adolph,
`790 F.3d 1315 (Fed. Cir. 2015)...................................................................... 108, 109
`
`Verizon Servs. Corp. v. Vonage Holdings Corp.,
`503 F.3d 1295 (Fed. Cir. 2007) .......................................................................... 25
`
`Yodlee, Inc. v. Plaid Techs., Inc.,
`No. 14-1445-LPS, 2016 U.S. Dist. LEXIS 5603 (D. Del. Jan. 15,
`2016) ................................................................................................................... 63
`
`X One, Inc. v. Uber Techs., Inc.,
`440 F. Supp.3d 1019 (N.D. Cal. 2020) .................................................................... 56
`
`Statutes and Regulations
`
`37 C.F.R. §1.132 ...................................................................................................... 33
`
`viii
`
`

`

`“Columbia”) and QIAGENSciences, LLC (“QIAGEN”)
`
`inc. “Tllumina’’) submit the following Joint Claim Construction Brief.
`
`T
`
`NIERODUCTION AND BACKGROUND
`
`Plaintiffs’ (Opening Position
`
`iF
`
`Introduction
`
`be PatentsauMaSuity
`
`ising them to sequence DNA in a processcalled Sequencing{bYgSynthesis
`
`“SBS”). The claimsfincludela “picture” of
`
`the overall
`
`structure of
`
`the modified
`
`Pursuant to the Court’s Scheduling Order((D.I. 17) and thef[Stipulated Order
`
`extending claim construction deadlines (D.I. 50, as ordered July 15, 2020)
`
`plaintiffs The Trustees of Columbia University in the City of New York
`
`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 10 of 115 PageID #: 2275
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`Nucleotides, as Iollows:
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 11 of 115 PageID #: 2276
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`This invention takes advantage of natural DNA processes to sequence DNA.
`
`DNA is a chain, made up of links known as nucleotides. There are four different
`
`nucleotides, each defined by one of four different “bases”—adenine (“A”), guanine
`
`(“G”), cytosine (“C”), and thymine (“T”). Bases are the part of DNA that stores
`
`information and gives DNA the ability to encode a person’s traits. DNA is formed
`
`by two strands of nucleotides, where A always pairs with T, and C always pairs
`
`with G.
`
`SBS recognizes that if one were to take a strand of DNA and expose it to
`
`nucleotides in the presence of an enzyme called a polymerase, the nucleotides
`
`would pair with their complementary bases to produce a second strand of DNA.
`
`The inventions at issue seek to harness this natural process by modifying the
`
`nucleotides to add an R (a chemical group of atoms that will “block” other
`
`nucleotides from joining the growing strand), a tag (i.e., some form of a label), and
`
`a Y, which is the part of the modified nucleotide that links the tag to the base of the
`
`modified nucleotide. This allows each tagged nucleotide to be added one at a time,
`
`because the R blocking group prevents the addition of additional nucleotides.
`
`Once joined, a scientist uses the tag to identify its base, which allows the scientist
`
`to also know the base of the target strand it paired with. Once this is complete, the
`
`scientist can wash the strand with a chemical that cuts off, or “cleaves,” R and Y,
`
`10
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 12 of 115 PageID #: 2277
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`thereby removing the nucleotide’s blocking group (R) and tag, allowing for the
`
`next modified nucleotide to be joined, and so on and so on.
`
`The challenge that the Columbia inventors overcame is to choose the R, Y
`
`and tag—and add them to the natural nucleotideIin such a way so that the
`
`nucleotide works for its sequencing purpose, but is not so different that it is not
`
`recognized as a nucleotide at all.
`
`Here, there are five claim terms in dispute, with four pertaining to all 5
`
`Patents-in-Suit, and a fifth pertaining only to the method patent.2
`
`We start with the four disputed claim terms common to all of the patents.
`
`Each of these four terms relate to two fundamental parts of the structure shown
`
`aboveIY (the part of the modified nucleotide that links the tag to the base) and R
`
`(the protecting group).
`
`For constructions related to the symbol Y—there are two terms at issue: “Y”
`
`itself, and the part of the patent claim stating that Y must be “chemically
`
`cleavable.” For Y itself, Columbia and QIAGEN rely on plain and ordinary
`
`meaning and the picture in the claim, that each and together show that “Y” serves
`
`as a linker—that part of the nucleotide that links the tag to the nucleotide base.
`
`2 After plaintiffs served their Opening Claim Construction Brief, Illumina agreed to
`Plaintiffs’ proposed plain and ordinary meaning for the term “chemically
`cleavable,” which appears in all of the Patents-in-Suit. Accordingly, only 4 terms
`now remain in dispute.
`
`11
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 13 of 115 PageID #: 2278
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`Illumina’s construction, that Y must be a “single linker,” is not supported by the
`
`intrinsic evidence or legal canons of claim construction.
`
`The patents also require that both R and Y be “chemically cleavable.”
`
`Illumina does not dispute the term as it applies to R, but it does as it applies to Y.
`
`Again, for Columbia and QIAGEN, plain and ordinary meaning guides:
`
`“chemically cleavable” simply means “cleavable by chemical means.” Illumina’s
`
`additional limitation that “chemically cleavable” excludes other cleavage means is
`
`unduly complicated and not supported by the intrinsic evidence.
`
`Regarding R, at issue are claim terms requiring R to be “small,” and “stable
`
`during a DNA polymerase reaction.” With regard to the term “small,” the parties
`
`agree that the chemical group must be less than 3.7Å. The parties, however,
`
`disagree as to which dimension must be less than 3.7Å. Plaintiffs’ “diameter (i.e.,
`
`width)” dimension finds literal support in the prosecution history. Defendant’s
`
`“longest dimension” contradicts the use of the term “diameter” in the prosecution
`
`history, contradicts its own view of “small” in a prior proceeding, and would be
`
`inconsistent with the intrinsic evidence as it would exclude the chemical groups
`
`specifically designated as “small” in the specification and prosecution history—a
`
`legally improper outcome.
`
`Regarding the term “R . . . is stable during a DNA polymerase reaction,”
`
`plaintiffs’ construction parallels the construction for “Y . . . is stable during a DNA
`
`12
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 14 of 115 PageID #: 2279
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`polymerase reaction” that Illumina did not dispute. Illumina’s construction,
`
`however, adds the additional requirement that R has at least the stability of a MOM
`
`or allyl group. There is no support for defendant’s construction.
`
`Finally, regarding the method patent (’380 Patent), Columbia and QIAGEN
`
`submit that it is proper and necessary to construe its preamble, “a method for
`
`sequencing a nucleic acid,” to limit the invention to nucleic acid sequencing
`
`methods, because the essence of the invention is to detect the identity and sequence
`
`of a strand of nucleotides.
`
`Accordingly, the Court should adopt plaintiffs’ constructions.
`
`2.
`
`Technical Background
`
`a.
`
`DNA and Nucleotides
`
`A nucleotide consists of a sugar, a base, and one or more phosphate groups
`
`as shown below. There are four nucleotide bases—adenine (“A”), guanine (“G”),
`
`cytosine (“C”), and thymine (“T”). The sugar in the nucleotide contains five
`
`carbon atoms, numbered 1H @7><A67 ’H% /74 ;A294<@834 70? 0 7E3><DE9 ",*# 6><A=
`
`0@@02743 0@ @74 &H =<?8@8<; <5 @74 ?A60> "F&H-OH group” (circled below)).
`
`13
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 15 of 115 PageID #: 2280
`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 15 of 115 PagelD #: 2280
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`Phosphate(s)
`
`
`
`3’— OH Group
`
`IDNAconsists of a strand or chain of nucleotides,
`
`between a phosphate group of one nucleotide and aBMBOH group of another
`
`nucleotide, as shown below,
`
`with T and C alwayspairs with G.
`
`éay Adenine
`Tt
`o—l—oue-oO
`Sox Thymine
`
`i
`
`|—=Pp—
`
`Ak
`
`In nature, two strands of nucleotides form a double helix structure. Bonds
`
`between complementary base pairs
`
`hold the strands together, where A always pairs
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 16 of 115 PageID #: 2281
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`o duplicate, or “synthesize,” DNA,the two strands of the double helix are
`
`Separated. Each strand of nucleotides then serves as the template to synthesizeits
`
`omplementary strand. Synthesis typically uses a short strand
`
`is designed to complement, and
`
`template strand, as shown below.
`
`Anenzymecalledalpolymerase|growsthe primer along the template by adding
`
`template. For example, if the next nucleotide base in the template 1s G, the
`
`polymerase incorporates its complement C into to thelgrowingcopy™
`
`
`
`usedforDNAsequencingmethods (e.g. SBS). SBS works by detecting the
`
`TEMPLATE
`
`As shownabove,the polymerase facilitates bonding between a phosphate
`
`group of
`
`the incoming nucleotide and the 3’fOH groupof the last incorporated
`
`nucleotide, thus adding the incoming nucleotide to the growing strand.
`
`
`
`DE atentstingsuit|
`
`ThePatentsaingouitic
`
`

`

`requires the use of modified nucleotides. The claimed modified nucleotides
`
`(1) a removable capping group(also called a “protecting” or “blocking” group)
`
`attachedtosthe3'Boxyeenjposition, and (11) a tag (such as a detectable fluorescent
`
`During SBS, the polymerase “incorporates” a complementary modified
`
`modified nucleotide has a capping group bound to the 3’ oxygen, the polymerase
`
`annot incorporate any further nucleotides beyond the modified nucleotide.
`
`During this pause in synthesis, the signal from the label attached to the nucleotide
`
`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 17 of 115 PageID #: 2282
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`modified nucleotides needed tor successful SBS. Hor example, the PatentsiiagSuit|
`
`identifies which nucleotide has been incorporated, |Le,, an A, C, T, or G. After
`
`detection, the capping group and the label are chemically removed, thereby
`
`allowing the polymerase to add another modified nucleotide to the growing strand.
`
`he PatentssingSuit teach and claim the precise characteristics of the
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 18 of 115 PageID #: 2283
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`teach and claim chemicaland structural constraints that limit which capping groups
`
`
`
`
`
`Biasedontheiranalysisofacrystalstructureofapolymerase,
`
`the inventors discovered that SBS requires the use of particularly small capping
`
`Lc.,
`
`less than 3.7A in diameter, such that the capping group could fit within
`
`
`
`
`
`the active site of a DNA polymerase. (See, e.g.458Patent(JA0020,
`
`we JAnnnn”refers to the Jomt Claim Construction Appendix filed herewith.
`
`
`
`
`
`
`
`(requiring“small”cappinggroup),PAQOTOM) Tat 2/6353:3, A005
`
`Iso important functional ones. For example, whichever capping group 1s selected
`
`process. Similarly, the tag is to be connected to the
`
`by a
`
`B.
`
`le
`
`Introduction
`
`e instant suit is the latest of
`
`three that Plaintiffs
`
`have
`
`filed against [lumina
`
`in this district since 2012. All
`
`three of Plaintiffs’
`
`lawsuits
`
`have involved the same
`
`Specifically, after Plaintiffs accused Illumina of infringing, Illumina
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`

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`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 19 of 115 PageID #: 2284
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`successfully invalidated Plaintiffs’ patents in inter partes review (“IPR”). Across
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`the first two lawsuits, Illumina has invalidated the asserted claims in eight of
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`Plaintiffs’ patents.4
`
`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
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`Illumina’s IPR requests, which have already been filed. Simply put, there is nothing
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`novel or nonobvious in Columbia’s patents.
`
`Nevertheless, Columbia’s repeated rounds of prosecution and failed efforts to
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`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
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`clear and unmistakable disavowals of claim scope. This is most apparent with
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`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.
`
`4 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.
`18
`
`

`

`olumbia’s claim constructions in this case reflect an attempt to undo these
`
`others, this Court should adopt II[tumina’s proposed claim constructions across the
`
`board.
`
`C Beeblaintifis’ Reply
`
`lumina asserts that Columbia has made “‘clear and unmistakable disavowals
`
`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 20 of 115 PageID #: 2285
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`laims even thoughthe preamble recites the “essence of the invention.”
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`ontrary, plaintiffs’ constructions are consistent with
`
`the prosecution history,
`
`nlike Iumina’s constructions. Regarding “Y,” Illumina seeksto limit claim|
`
`Scope based on an ambiguous statement by Columbia that the PTAB expressly
`
`rejected. The law is clear that such statements do not limit claim scope. Regarding
`
`“small,” I[tumina seeks to add limitations, such
`
`as “longest dimension,” that
`
`ontradict the intrinsic record, whereas plaintiffs’ construction 1s consistent with
`
`the intrinsic record and prior Columbia statements|
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`(tumina’s other constructions similarly violate the basic cannonsof claim|
`
`onstruction. With respect to the term
`
`reactionMal lumina improperly seeks to limit the construction to the examples in
`
`the specification. Finally, [lumina seeks to ignore the preamble of the method
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 21 of 115 PageID #: 2286
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`he Court should adoptplaintiffs’ constructions.
`
`e construction of
`
`terms on which the parties agreefis shown below
`
`Terms
`(Patent/Claims)
`
`Joint Proposed Construction
`
`742 Patent: Claim 1, 2
`
`does not interfere wit
`Proposed jC onstruction:
`
`doesnotinterferewith|
`the analogueC
`recognition of
`KZ © oOZ>|
`ray
`Ss a Substrate
`is ° Ns5OQ43aoO
`
`458 Patent: Claim 1,
`459 Patent: Claim 1,
`742 Patent: Claim 1,
`984 Patent: Claim 1,
`380 Patent: Claim 1,
`
`\Oa—~aRS
`
`458 Patent: Claim 1,
`59 Patent: Claim 1,
`42 Patent: Claim 1,
`84 Patent: Claim 1,
`380 Patent: Claim 1,
`
`QoNOBDBNBN
`
`“Y ...18 stable during a
`IDNA polymerase reaction”
`
`458 Patent: Claim 1,
`459 Patent: Claim 1,
`
`Proposed Construction:
`
`‘A chemical group used to cap the 3° OH group,
`as depicted in the illustration of the nucleotide
`analogue in the claim”
`
`‘Does not interfere with the use of
`as a DNA polymerase substrate”
`
`the analogue
`
`Proposed Construction
`cs
`
`‘Y remains bonded to base and tag during a DNA
`polymerase reaction’
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 22 of 115 PageID #: 2287
`
`Terms
`(Patent/Claims)
`
`’984 Patent: Claim 1, 2
`’380 Patent: Claim 1, 3
`
`Joint Proposed Construction
`
`“chemically cleavable”
`
`Proposed Construction:
`
`Plain and ordinary meaning, namely “cleavable
`by chemical means”
`
`*****
`
`’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
`
`21
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 23 of 115 PageID #: 2288
`
`TL eDISPUTEDICONSTRUCTIONS:
`
`defendant’s prior positions.
`
`the PatentsmineSuit with the Joint
`of
`each
`maPlaintifts filed a searchable .pdf copy of
`laim Construction Chart. (D.I. 36@1_ to 3695.) For the Court’s convenience, and in
`accordance with paragraphs 14 and 16 of
`the Scheduling Order (D.I. 17), the Joint
`[Appendix includes only those pages of
`the PatentsfnmiSuits referenced in this Joint
`aim Construction Brief.
`
`Claims
`
`Plaintiffs’ Proposed
`Construction
`
`Defendant’s Proposed
`Construction
`
`458 Patent: Claims
`
`‘Represents a part of
`
`the
`
`4) Patent Claim
`
`MiaPatent: Claim.
`:
`
`O84 Patent: Claim
`
`380 Patent: Claim
`
`the
`attaching the base of
`ucieotide analogue to a
`ag, as depicted in the
`illustration of the nucleotide
`analogue in the claim”
`
`directly connects the base
`
`Plaintiffs’ Opening |Position|
`
`As shown above,the parties agree that Y 1s the part of
`
`the nucleotide
`
`analogue that attaches (or connects) the base to the tag (or
`
`label)
`
`nnecessarilyfadds the limitation that Y must be fia single linker ain an
`
`IPR proceeding involving the exact same claim term, the PT'AB rejected such a
`
`constructionmE IPR2018800291, Paper 67 at 53KJA0040-S400 1.33)
`
`has not yet explained what it means by a “single linker.”
`ma At this stage, defendant
`As discussed below, researchers often construct
`linkers from smaller groups.
`To
`the extent that defendant1s asserting that the claims would not cover such linkers,
`defendant’s position 1s contrary to the specification, prosecution history, and
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 24 of 115 PageID #: 2289
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`ncither the claim language, specification,Norprosecution history supports
`
`defendant’s “single linker” position.
`
`al
`
`he Intrinsic Evidence Supports Plaintiffs
`
`[As shown 1nthe illustration below, Y links the base of
`
`the nucleotide
`
`analogue (the double{ring structure in this example) to the[tag™|
`
`(458 Patent,
`
`JA0020).)—The claim language states that “Y represents a
`
`chemically cleavable, chemical
`
`linker!” C/g:)™Here, neither
`
`the claimsinon
`
`anything in the specification orintrinsic record statefthat Y (Le} a chemically
`
`toflimit ‘a’ or ‘an’ to ‘onc Mm Baldwin Graphic Sys., Inc. v. Siebert, Inc., 5
`
`ts
`
`but,Ormoremm™ 1 Communique Lab., Inc. v.
`
`
`
`LogMeln,Inc.,687F.3d1292,1296,129]
`
`alhe exceptionsto this rule are extremely limited: a patentee must evince a clear
`
`intent
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 25 of 115 PageID #: 2290
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`Here, the specification consistently describes using a cleavable linker to
`
`attach a label or tag (such as a fluorescent label or mass tag) to the nucleotide base.
`
`(See, e.g.,’458 Patent (JA0011 at 3:4-7, 4:61–62; JA0014 at 10:31–66).) Nowhere
`
`in the specification does it state that the base and tag must be attached by “one” or
`
`a “single” linker.
`
`Indeed, the specification provides examples of Y being assembled from
`
`multiple molecules (each of which could be termed a “linker”). For example,
`
`Figure 8 shows a “representative scheme for the synthesis of the nucleotide
`
`analogue &H-RO-G-Tam.” (Id. (JA0012 at 6:24–25).) Specifically, the bottom of
`
`Figure 8 shows Y as comprised of two linkers, one made of a chemical group
`
`known as alkynylamino that attaches the nucleotide base to a photocleavable
`
`linker, which is itself attached to the molecule Tam (a fluorescent tag).
`
`(Id., (JA0019 at 23:67–24:2; JA0005, FIG. 8 (annotations added)); see also id.,
`
`(JA0006 at FIG. 16 (showing the use of multiple interlinked groups to assemble
`24
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`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 26 of 115 PageID #: 2291
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`the final linker)).) As shown above, the structure that equates to Y in the claimed
`
`structures shown in Figures 8 and 16 are not limited to a “single linker.”
`
`Accordingly, Illumina’s construction is not just contrary to the canons of
`
`construction taught by 01 Communique Lab and Baldwin, but also should be
`
`rejected on the ground that it would exclude embodiments shown in Figures 8 and
`
`16 of the specification. See, e.g., Verizon Servs. Corp. v. Vonage Holdings Corp.,
`
`503 F.3d 1295, 1305 (Fed. Cir. 2007) (“We normally do not interpret claim terms
`
`in a way that excludes disclosed examples in the specification.”).
`
`b.
`
`Illumina Admits that Y May B