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’ Construction Is UnsupportedWW4}
`
`I um1na A1n1ts t1at Y May Be Constructe Us1ng More
`WWW-E5
`
`P a1nt1 s’ Opening Pos1tion—
`
`ilu IWE
`
`E m
`
`EL
`
`DNA ano Nuc eot1es
`
`"E
`
`[in L-flm mmmmmmmmmmmiflfl
`
`De en ant’s Answering Pos1tion
`
`I“
`
`H” WM
`
`[fl [ml—fl
`
`AGREED
`
`1101
`
`——El
`
`-—m
`
`nu
`
`EL
`
`De en ant’s Answering Pos1tionWJ’G
`
`e C aim Language Con rms I uinlna’s Constructio
`__,m............................m.........................Pl'fl
`
`a
`
`e Spe01 ication Con rms I urn1na’s Constructlon JD}
`
`he Prosecution History Requires Illumina’s
`
`[a
`
`EL
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 3 of 115 PageID #: 2268
`
`Plaintiffs’ Reply Position.
`
`‘!il
`
`a]:
`
`E:
`
`I llumina Mischaracterizes Plaintiffs’ Position WEE
`
`he Claims and Specification Support Plaintiffs’
`
`‘ E
`
`e Prosecution History Favors P a1nt1 s’ Construction
`WWJM
`
`| umina anu Ot ers Teac T at a “Lin er” Can Be Maue
`
`u Moret an One Lin ermmmmmfllfl
`
`EL “—1st
`
`“Wm
`
`Ho
`
`[:1
`
`33
`
`SE
`
`, Not Longest D1mens1onmmmmmnmmfll
`
`‘Sma ” S iou u Be De 1neu W1t1 Respect To Rat
`Po ymeraseWJ}
`
`[IL
`
`Defendant’s Construction Would Exclude Chemical
`
`roups Designated as Small in the Specification and
`Prosecution H1story
`
`Defendant’s Answering Position
`
`91
`
`o umuia’s De n11t1on O “Sma ” During Prosecution
`Anu IPR
`
`'65
`
`‘Sma ” S ou u Be De neu In Terms O _...W
`
`e Court S ou u Not Construe T e C aims In Terms 0
`
`A “Width”
`
`he Prosecution History Is Clear that Diameter Refers to
`Wiut
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 4 of 115 PageID #: 2269
`
`lllumina’s Limitation Regarding Having to Fit Within the
`Rat DNA Polymerase ls Unnecessary and Unhelpful mail
`
`Defendant’s Sur l' eply PositionWWES
`
`a]:
`
`o umia’s Representations Regar 1ng “Sma ” During
`Prosecution An IPR S ou o [ii-WEE
`
`‘R .
`
`.
`
`. 1s sta e urmg a DNA po ymerase—WEW
`
`ilu
`
`E”
`
`P a1nt1 s’ Opening Pos1tionWHJfl
`
`De en ant’s Answermg Pos1t10nv
`
`" E
`
`Defendant’s Sur I' eply Position
`
`‘A method for sequencing a nucleic acid”
`
`ilu
`
`Plaintiffs’ Opening Position—
`
`Dr. Kur1yan’s “Cons1stency” W1t T 1e Ju Dec aration ls
`WWWMEB
`
`Defendant’s Answering Position
`
`

`

`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
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 10 of 115 PageID #: 2275
`
`Pursuant to the Court’s Scheduling Order (D.I. 17) and the tipulated Order
`
`xtending claim construction deadlines (D.I. 50, as ordered July 15, 2020,
`
`El a1nt1 s T e Trustees 0 Co urnia Un1vers1ty in t e City 0 New Yor<
`
`“Co uin1a”) an QIAGEN Sc1ences, LLC “QIAGEN”)
`
`II: c.
`
`“1 1111111121”, su1n1tt e o 0W1ng J01nt C a1rn Construction Br1e .
`
`[I
`
`N 'IOUC ON I CGOUND
`
`I' laintiffs’ ’0 penlng P0s1t10n
`
`flu
`
`Introduction
`
`he Paterits:l"iil:§lfil"
`
`a11n mo1eo nuc eot1 es, as we as a met 0. o
`
`1sing them to sequence DNA in a process called Sequencing [Emm—
`
`“SBS”, . T e c a1rns 1nc ue .
`
`‘p1cture” 0 tie overa structure 0 tie 1no11e:
`
`nuc eot1 es, as o ows:
`
`“’984 Patent”) and 10,428,380 (“’380 Patent”).
`
`_flmfl uit” are collectively US. Patent Nos. 10,407,458 (“’458
`Patent”), 10,407,459 (“’459 Patent’”), 10,435,742 (“’742 Patent”), 10,457,984
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 11 of 115 PageID #: 2276
`
`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
`
`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
`
`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
`
`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 Fl eu 08 10 20
`
`Phosphate{s}
`
`I}
`1
`
`H
`['
`
`H
`
`H
`
`w1t T anu C a ways palrs w1t G.
`
`’uetween comp ementary uase palrs o u t e stranus toget er, W ere A a ways palrs
`
`IJ'
`
`3’— OH Group
`
`’uetween a p osp ate group 0 one nuc eot1ue anu a ELOH group 0 anot er
`
`nuc eot1 e, as s own ue ow.
`
`In nature, two stranus o nuc eot1ues orm a uuou e
`
`6 1X structure. Bonus
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 16 of 115 PageID #: 2281
`
`o duplicate, or “synthesize,” DNA, the two strands of the double helix are
`
`separated. Each strand of nucleotides then serves as the template to synthesize its
`
`An enzyme ca ec a_grows t e primer a ong t e temp ate cy ac c1ng
`
`orrespon 1ng nuc eot1ces att e ceg1nn1ng o t e -cstran, as s own .6 ow.
`
`ecnt1ty o eac 1 nuc eot1ce as it 1s ac cec 1nto a growmg tranc 0 DNA, anc
`
`TEMPLATE
`
`As s own acove, t1€ po ymerase a01 1tates-con1ngcetween a p osp late
`
`_roup 0 tie 1ncom1ng nuc eot1ce anc t e 3’ ‘OH group 0 tie ast 1ncorporatec
`
`nucleotide, thus adding the incoming nucleotide to the growing strand.
`
`LIL WHEE-
`
`he PatentSI-r
`
`'.
`
`.
`
`V
`
`nuc eot1ces)
`
`1sec or DNA sequencmg met o's (e.g. SBS). SBS wor {s
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 17 of 115 PageID #: 2282
`
`requires the use of modified nucleotides. The claimed modified nucleotides
`
`(i) a removable capping group (also called a “protecting” or “blocking” group)
`
`[J
`
`II.
`
`WmM_ pos1tion, ano (11) a tag (suc as a ooetecta e uorescent
`
`modified nucleotides needed for successful SBS. For example, the Patentsflm-
`
`1.1—} —I..|—}-—1'-—}-'—
`I!
`li. ]'
`
`II '
`
`Dur1ng SBS, tie po ymerase “1ncorporates” a comp ementary moo11eo
`
`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
`
`“MEI—I143- an A, C T, 01‘ G- A ter
`
`'etectlon, t e capping group ano
`
`. ow1ng t e po ymerase to ao o anot er moo11eo nuc eot1oe to t e growmg strano.
`
`he PatentsSuit 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
`
`an work for SBS. Flased on their analysis of a crystal structure of a polymerase,
`
`t e inventors001scovere t at SBS requires t e use 0 part1cu ar y sma capping
`
`1.e.
`
`less than 3.71 in diameter, such that the capping group could fit within
`
`t e act1ve Site 0 a DNA po ymerase.
`
`( ee, 6.g. 458 Patent JA0020
`
`requ1r1ng “sma ” capping group), JA0010 [IJm- A000 .t F1g. l); ’485
`
`Patent PH, 5 9 l9 upplemental Communication at 4 (JA003 1).)
`
`apping group has to not only meet the patents’ various structural limitations, but
`
`lso important functional ones. For example, whichever capping group is selected
`
`must .6 sta e enoug to stay onto t e nuc eot1e ur1ng t e po ymerization
`
`process. S1m1 ar y, t e tag 1s to -e connecte to t e
`
`y a c eava e 1 {er (“Y”
`
`1nt e gure aove).
`
`El
`
`I'ID
`
`Introductlon
`
`teach and claim chemical and structural constraints that limit which capping groups
`
`E ‘JAnnnn” refers to the Joint Claim Construction Appendix filed herewith.
`
`e 1nstant su1t 1s tie atest o tiree tiat P a1nt1 s ave
`
`ea against 1 um1na
`
`1nt 1s 01str1ct Since 2012. A t ree o P a1nt1 s’ awsu1ts
`
`ave 1nvo ve t e same
`
`Co um1a patents, an.
`
`Specifically, after Plaintiffs accused Illumina of infringing, Illumina
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 19 of 115 PageID #: 2284
`
`successfully invalidated Plaintiffs’ patents in inter partes review (“IPR”). Across
`
`the first two lawsuits, Illumina has invalidated the asserted claims in eight of
`
`Plaintiffs’ patents.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
`
`Illumina’s IPR requests, which have already been filed. Simply put, there is nothing
`
`novel or nonobvious in Columbia’s patents.
`
`Nevertheless, Columbia’s repeated rounds of prosecution and failed efforts to
`
`fend off Illumina’s IPRs have created a rich history of representations directly
`
`relevant to construing the claims of the Patents-in-Suit. To try and avoid the prior
`
`art, Columbia has repeatedly offered narrow definitions of claim terms and/or made
`
`clear and unmistakable disavowals of claim scope. This is most apparent with
`
`respect to the claim terms “Y” and “small,” for which Columbia submitted inventor
`
`declarations during prosecution explicitly defining these terms and then doubled-
`
`down on these very definitions during IPR proceedings.
`
`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
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 20 of 115 PageID #: 2285
`
`olumbia’s claim constructions in this case reflect an attempt to undo these
`
`'- entations and recapture territory it has surrendered. Under black letter Federal
`
`1rcu1t aw, t 1s 1s 1mperm1ss1c
`
`J
`
`. For t ese reasons anc
`
`ct ers, t 1s Court 5 cu c c opt I um1na’s propose c a1m constructlons across t e
`
`m
`
`[E
`
`glalntl
`
`s Reply
`
`I llumina asserts that Columbia has made “clear and unmistakable disavowals
`
`c c a1m scope”t at compe I um1na’s constructions o
`
`ontrary, p a1nt1 s’ constructions are cons1stentw1t
`
`t e prosecutlon 1story,
`
`n 1 e I um1na’s constructlons. Regar 1ng “Y,” I um1na see (s to 11n1t c a1m
`
`scope based on an ambiguous statement by Columbia that the PTAB expressly
`
`laims even though the preamble recites the “essence of the invention.”
`
`rejected. The law is clear that such statements do not limit claim scope. Regarding
`
`‘sma ,” I um1na see (s to ac c 1m1tat10ns, suc as “ ongest c11nens1on,”t at
`
`ontra1ctt1e 1ntr1ns1c recorc, w 1ereas p a1nt1 s’ constructlon 1s cons1stent W1t1
`
`I um1na’s ot1er constructlons s1m1 ar y V10 ate t e cas1c cannons o c aim
`
`onstructlon. W1t1 respect to t e term ‘R .
`
`.
`
`. ls stac e cur1ng a DNA po ymerase
`
`mm Illumina improperly seeks to limit the construction to the examples in
`
`the specification. Finally, Illumina 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
`
`he Court should adopt plaintiffs’ constructions.
`
`e construction 0 terms on W 10 1t1€ parties agree is s own ue ow
`
`(Patelnetfgzms)
`
`Joint Proposed Construction
`
`|' roposed onstruction:
`
`458 Patent: C aim 1, 2
`459 Patent: Claim 1, 2
`
`742 Patent: C aim l, 2
`
`984 Patent: C aim l, 2
`
`380 Patent: C aim l, 3
`
`“oes not inter ere Wit
`
`'ropose ’ onstructlon:
`
`necognition 0 tie ana ogue
`as a sustrate 0y a DNA
`.0 ymerase”
`
`6
`
`.
`Does not 1nte1 ere Witi tie use 0 t e ana ogue
`,.
`3’
`- s a DNA po ymerase sustiate
`
`‘A chemical group used to cap the 3’ OH group,
`. s depicted in the illustration of the nucleotide
`nalogue in the claim”
`
`742 Patent: C aim l, 2
`
`*****
`
`458 Patent: C aim l, 2
`
`459 Patent: C aim l, 2
`
`742 Patent: C aim l, 2
`
`984 Patent: C aim l, 2
`
`380 Patent: C aim l, 3
`
`. 1s sta e uring a
`.
`‘Y .
`II NA po ymerase reactlon”
`
`'roposed onstructlon:
`6
`
`Y rema1ns noncec to ase an: tag uring a DNA
`
`po ymerase reaction
`
`458 Patent: C aim l, 2
`
`459 Patent: C aim l, 2
`
`

`

`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
`
`[III DISPUTED CONSTRUCTIONS
`
`Claims
`
`Plaintiffs’ Proposed
`Construction
`
`Defendant’s Proposed
`Construction
`
`458 Patent: C aims
`
`‘Represents a part 0 tie
`
`'1rect y connects t e ase
`
`459 Patent: C 31111
`
`matent: C aims
`
`984 Patent: C alm
`
`380 Patent: Claim
`
`.ttac mg tie ase 0 tie
`uc eot1e ana o ue to a
`g
`ag, as depicted in the
`'llustration of the nucleotide
`.nalogue in the claim”
`
`a efendant’s prior positions.
`
`5 P a1nt1 s1eo a searc an e .p copy 0 eac o t e PatentszflLLSuit with the Joint
`laim Construction Chart. (D.l. 36 l to 36 5.) For the Court’s convenience, and in
`.cccorance Wit paragrap s 14 an: 16 o t e Sc eu mg Orer(D.I. 17 ,t e Jomt
`Appen 1x inc c es on yt ose pages 0 tie Patents Hm uits re erence mt 1s Jomt
`aim Construction Brie .
`
`IPR proceeding involving the exact same claim term, the PTAB rejected such a
`
`__ We“ ‘
`
`, Paper .7 at 5
`
`JA0040 ‘lilmfilfiil
`
`E ‘ tt 1s stage, oe en ant as not yet exp aine W at it means uy a “s1ng e 1 <er.”
`As a 1scusse ne ow, researc ers o ten construct
`in ers rom sma er groups.
`0
`the extent that defendant is asserting that the claims would not cover such linkers,
`o efendant’s position is contrary to the specification, prosecution history, an
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 24 of 115 PageID #: 2289
`
`neither the claim language, _nnjj prosecution history supports
`
`a efendant’s “single linker” position.
`
`P11.
`
`he Intr1ns1c EVldence upports Plalntl
`
`s
`
`As s own int c 1 ustration ne ow, Y in st 6 ase o t e nuc eot1ce
`
`.na ogue (t e ouou e I mg structure 1nt 1s examp e) to t e {la};
`
`intent 0 limit ‘a’ or ‘an’ to ‘one. Ba. win Grap ZiC Sys., Inc. v. Sieert, Inc. ,, 5
`
`-settled that use of the singular in a patent claim fig ot limited 0 the singular
`
`(’458 Patent,
`
`:JA0020).)
`
`he claim language states that “Y represents a
`
`(SIR
`
`m eava e, c emica 1n era-I'D] I ere,ne1t er ec aimsm
`
`nyt 1ng 1n tie spem 1cat10n or 1ntr1ns1c recor state t at Y (I
`
`a c emica y
`
`eava e, c emica 1n er
`
`s “one” or a “s1ng e” in er. Moreover, t c act tiat
`
`the claim itself refers to a “linker” In the singular tense is of no moment, as it is
`
`[am
`
`mm“ II Con/umtnz'que Lab, Inc. v.
`
`LogMeIn, Inc. 687 F.3 1292, l29_7 Fed. Cir. 2012) emphasis added)
`
`mT e except1ons to t11s ru e are extreme y imite: a patentee must eV1nce a c ear
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 25 of 115 PageID #: 2290
`
`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
`
`

`

`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 26 of 115 PageID #: 2291
`
`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 Be Constructed Using
`More Than a Single Linker
`
`In Illumina’s IPR of a related Columbia patent, U.S.