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
`
`Page 1
`
`Columbia Ex. 2036
`Illumina, Inc. v. The Trustees
`of Columbia University
`in the City of New York
`IPR2020-01177
`
`

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`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
`
`Page 5
`
`

`

`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
`
`Page 6
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`

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`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
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`Page 7
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`

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`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
`
`Page 8
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`

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`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
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`Page 9
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`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.
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`DNA is a chain, made up of links known as nucleotides. There are four different
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`nucleotides, each defined by one of four different “bases”—adenine (“A”), guanine
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`(“G”), cytosine (“C”), and thymine (“T”). Bases are the part of DNA that stores
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`information and gives DNA the ability to encode a person’s traits. DNA is formed
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`by two strands of nucleotides, where A always pairs with T, and C always pairs
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`with G.
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`SBS recognizes that if one were to take a strand of DNA and expose it to
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`nucleotides in the presence of an enzyme called a polymerase, the nucleotides
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`would pair with their complementary bases to produce a second strand of DNA.
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`The inventions at issue seek to harness this natural process by modifying the
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`nucleotides to add an R (a chemical group of atoms that will “block” other
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`nucleotides from joining the growing strand), a tag (i.e., some form of a label), and
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`a Y, which is the part of the modified nucleotide that links the tag to the base of the
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`modified nucleotide. This allows each tagged nucleotide to be added one at a time,
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`because the R blocking group prevents the addition of additional nucleotides.
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`Once joined, a scientist uses the tag to identify its base, which allows the scientist
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`to also know the base of the target strand it paired with. Once this is complete, the
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`scientist can wash the strand with a chemical that cuts off, or “cleaves,” R and Y,
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`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
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`next modified nucleotide to be joined, and so on and so on.
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`The challenge that the Columbia inventors overcame is to choose the R, Y
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`and tag—and add them to the natural nucleotideIin such a way so that the
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`nucleotide works for its sequencing purpose, but is not so different that it is not
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`recognized as a nucleotide at all.
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`Here, there are five claim terms in dispute, with four pertaining to all 5
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`Patents-in-Suit, and a fifth pertaining only to the method patent.2
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`We start with the four disputed claim terms common to all of the patents.
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`Each of these four terms relate to two fundamental parts of the structure shown
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`aboveIY (the part of the modified nucleotide that links the tag to the base) and R
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`(the protecting group).
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`For constructions related to the symbol Y—there are two terms at issue: “Y”
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`itself, and the part of the patent claim stating that Y must be “chemically
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`cleavable.” For Y itself, Columbia and QIAGEN rely on plain and ordinary
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`meaning and the picture in the claim, that each and together show that “Y” serves
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`as a linker—that part of the nucleotide that links the tag to the nucleotide base.
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`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.
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`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
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`intrinsic evidence or legal canons of claim construction.
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`The patents also require that both R and Y be “chemically cleavable.”
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`Illumina does not dispute the term as it applies to R, but it does as it applies to Y.
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`Again, for Columbia and QIAGEN, plain and ordinary meaning guides:
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`“chemically cleavable” simply means “cleavable by chemical means.” Illumina’s
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`additional limitation that “chemically cleavable” excludes other cleavage means is
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`unduly complicated and not supported by the intrinsic evidence.
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`Regarding R, at issue are claim terms requiring R to be “small,” and “stable
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`during a DNA polymerase reaction.” With regard to the term “small,” the parties
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`agree that the chemical group must be less than 3.7Å. The parties, however,
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`disagree as to which dimension must be less than 3.7Å. Plaintiffs’ “diameter (i.e.,
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`width)” dimension finds literal support in the prosecution history. Defendant’s
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`“longest dimension” contradicts the use of the term “diameter” in the prosecution
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`history, contradicts its own view of “small” in a prior proceeding, and would be
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`inconsistent with the intrinsic evidence as it would exclude the chemical groups
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`specifically designated as “small” in the specification and prosecution history—a
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`legally improper outcome.
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`Regarding the term “R . . . is stable during a DNA polymerase reaction,”
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`plaintiffs’ construction parallels the construction for “Y . . . is stable during a DNA
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`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,
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`however, adds the additional requirement that R has at least the stability of a MOM
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`or allyl group. There is no support for defendant’s construction.
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`Finally, regarding the method patent (’380 Patent), Columbia and QIAGEN
`
`submit that it is proper and necessary to construe its preamble, “a method for
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`sequencing a nucleic acid,” to limit the invention to nucleic acid sequencing
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`methods, because the essence of the invention is to detect the identity and sequence
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`of a strand of nucleotides.
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`Accordingly, the Court should adopt plaintiffs’ constructions.
`
`2.
`
`Technical Background
`
`a.
`
`DNA and Nucleotides
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`A nucleotide consists of a sugar, a base, and one or more phosphate groups
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`as shown below. There are four nucleotide bases—adenine (“A”), guanine (“G”),
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`cytosine (“C”), and thymine (“T”). The sugar in the nucleotide contains five
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`carbon atoms, numbered 1H @7><A67 ’H% /74 ;A294<@834 70? 0 7E3><DE9 ",*# 6><A=
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`0@@02743 0@ @74 &H =<?8@8<; <5 @74 ?A60> "F&H-OH group” (circled below)).
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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
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`After each round of invalidation, however, Columbia has gone back to the
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`Patent Office to contort its claims by adding limitations in the hopes of avoiding the
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`prior art, including, in the newest version, carving out the very protecting group used
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`in all of its research publications. Although the claims at issue in this case represent
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`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.
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`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
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`relevant to construing the claims of the Patents-in-Suit. To try and avoid the prior
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`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
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`declarations during prosecution explicitly defining these terms and then doubled-
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`down on these very definitions during IPR proceedings.
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`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
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`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 22 of 115 PageID #: 2287
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`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
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`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
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`attach a label or tag (such as a fluorescent label or mass tag) to the nucleotide base.
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`(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.
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`Indeed, the specification provides examples of Y being assembled from
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`multiple molecules (each of which could be termed a “linker”). For example,
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`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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`Page 25
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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
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`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. Patent No. 9,718,852
`
`(“the ’852 Patent”)7, Illumina argued that prior art would have taught a POSA to
`
`make Y from two linkers that nonetheless met all of the same limitations that exist
`
`with the Patents-in-Suit. Specifically, in asserting that the related ’852 Patent was
`
`allegedly invalid over the combination of Tsien and Prober, Illumina argued that
`
`7 The Patents-in-Suit and the ’852 Patent are in the same patent family, and share
`the same specification and claim language for Y. (See, e.g., IPR2018-00291, Ex.
`1001 (JA0043–44 at claim 1).) Thus, the prosecution history of the ’852 Patent is
`intrinsic evidence that the Court may consider in construing the term “Y.” See E.I.
`du Pont de Nemours & Co. v. Unifrax I LLC, 921 F.3d 1060, 1070 (Fed. Cir. 2019)
`(noting that “familial patents” with common subject matter “inform the
`construction of a claim term and are appropriately treated as intrinsic evidence”);
`See Galderma Labs., L.P. v. Amneal Pharms. LLC, 2020 U.S. App. LEXIS 9341,
`**6, 7 (Fed. Cir. March 25, 2020), (assessing the patent owner’s and PTAB’s
`statements in affirming claim construction).
`25
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`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 28 of 115 PageID #: 2293
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`construction with a single “Y” chemical linker accords with the claim language,
`
`specification, and prosecution history (including the IPR record) and should be
`
`adopted.
`
`a.
`
`The Claim Language Confirms Illumina’s
`Construction
`
`The claim language requires that “Y” be “a single linker that directly connects
`
`the base to the label.” Claim 1 of the ’458 Patent8 in relevant part states:
`
`’458 Patent (JA0020 at cl. 1 (highlighting added)).
`
`This claim refers to a “deoxyribonucleotide analogue having the structure”
`
`and—to make sure there is no confusion—includes a figure showing a single “Y”
`
`chemical linker bonded to a nucleotide base on one end and a tag on the other end.
`
`8 Four of the Patents-in-Suit—the ’458 Patent, ’459 Patent, ’742 Patent, and ’984
`Patent—contain this same claim language and “modular” chemical structure
`diagram with variations only for the nucleotide analogue. The fifth Patent-in-Suit—
`the ’380 Patent—is directed a method that uses any of these nucleotide analogues
`and contains functionally the same claim language and “modular” chemical
`structure.
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`Case 1:19-cv-01681-CFC-SRF Document 54 Filed 08/10/20 Page 29 of 115 PageID #: 2294
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`The claim
`
`language “having
`
`the structure” means
`
`that
`
`the claimed
`
`deoxyribonucleotide nucleotide analogue must possess the identified structure and
`
`immediately rules out Plaintiffs’ overbroad claim construction encompassing serial
`
`linkers. See Regents of Univ. of Cal. v. Eli Lilly & Co., 119 F.3d 1559, 1567 (Fed.
`
`Cir. 1997) (holding claim language stating “having the structure” requires that
`
`structure to be present).
`
`The claim depicts a single “Y” chemical linker bonded to the base on one end
`
`and a tag on the other end with a single continuous and unbroken black line.
`
`Plaintiffs’ proposed construction violates this figure—which was included in the
`
`claims to ensure clarity—by effectively redrawing it to encompass two or more
`
`successively-bonded “Y” chemical linkers each bonded to one another on one end
`
`such that they could not be bonded to the base on one end and the tag on the other
`
`end, as the figure in the claim shows.
`
`Had the patentee intended to capture two or more successively-bonded “Y”
`
`chemical linkers (and had support for that in the specification) as Plaintiffs seek to
`
`do now via claim construction, it could have drafted the claim using various
`
`established chemistry patent claim drafting conventions. For instance, Columbia
`
`could have included the structures “-Y-Y-,” “-X-Y-,” or some variation thereof in
`
`its figure. Alternatively, Columbia could have used the chemical structure “–(Y)n–
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`where n is 1 or greater.” Likewise if Columbia wanted to capture serial linkers of
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`different types, it could have used the general chemical structure “–(X)m-(Y)n–
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`where m and n are 1 or greater.” Columbia could have used an open ended term
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`such as “comprises” or “includes” to describe Y – e.g. “Y represents comprises a
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`chemically cleavable, chemical linker.”
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`Columbia could have claimed serial linkers in so many different ways using
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`figures or text. But Columbia did none of these things. “If [the patentee] desired
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`broad patent protection for any [invention] that performed a function similar to its
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`claimed [invention],
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`it could have sought claims with fewer structural
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`encumbrances...[A]s between the patentee who had a clear opportunity to negotiate
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`broader claims but did not do so, and the public at large, it is the patentee who must
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`bear the cost of its failure to seek protection for this foreseeable alteration of its
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`claimed structure.” SciMed Life Sys., Inc. v. Adv. Cardiovascular Sys., Inc., 242
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`F.3d 1337, 1346 (Fed. Cir. 2001) (quoting Sage Prods., Inc. v. Devon Indus., Inc.,
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`126 F.3d 1420, 1425 (Fed. Cir. 1997)).
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`The Markman decision of the district court in Enzo Biochem, Inc. v.
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`Amersham PLC is instructive on whether a patent claim is limited to the chemical
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`structure disclosed and whether intervening structures are permissible. 439 F.
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`Supp.2d 309 (S.D.N.Y. 2006). In Enzo, the patent at-issue, like the Patents-in-Suit,
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`claimed a “modular” chemical formula:
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`1. A detectable molecule of the formula
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`A3-(-X-R1-E-Detb)m
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`See id. at 319 (relevant portion of claim 1 of U.S. Patent No. 4,707,440).
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`The parties disputed the orientation of the chemical group “X” in the above
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`formula. Id. at 320. The Enzo Court resolved this dispute in the defendant’s favor,
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`holding: “Given the plain language of the claim, this Court finds that the chemical
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`groups provided for as ‘X’ must be oriented as pictured in the claim, with the left-
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`most element attached to ‘A3’ and the rightmost element attached to ‘R1.’”9 Id. The
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`Enzo Court further stated there “was also much discussion at the Markman Hearing
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`about whether intervening structures could be placed between the various
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`components.... [F]or the record, the Court finds that the claim does not allow
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`intervening structures since allowing such structures would undermine the claim
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`language and infinitely expand the scope of the claim.” Id. at 320 n.19. As in
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`Enzo, Illumina’s proposed construction adheres to the chemical structure depicted in
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`the claim. Defendants’ proposed construction meanwhile repeats the same positions
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`rejected in Enzo and should be rejected again here.
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`b.
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`The Specification Confirms Illumina’s Construction
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`The written description for the ’458 Patent states in “one embodiment, the
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`unique label is attached through a cleavable linker to a 5-position of cytosine or
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`9 Emphasis supplied unless otherwise noted.
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`thymine or to a 7-position of deza-adenine or deazaguanine.” ’458 Patent (JA0014
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`at 10:64-66); id. (JA0016 at 14:8-10). Columbia has previously confirmed that this
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`description “requires” that “Y” “means a chemical moiety attached by covalent
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`bonds at one end to a specified position on the base of a nucleotide and at the other
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`end to a tag.” Illumina, Inc. v. Trustees Of Columbia Univ. In The City Of New York,
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`IPR2018-00385, Paper No. 30 (“Patent Owner Columbia’s Response”) (U.S. Patent
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`No. 9,725,480 (the “’480 Patent”))10,11 at 10 (JA0054). Just like the figure in the
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`claim, Columbia’s description in the specification describes the chemical moiety at
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`one end of the linker and the nucleotide is at the other end of the linker. There is
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`thus only one linker. The claim should be construed as it is depicted in the claim,
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`which matches the description in the specification.
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`c.
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`The Prosecution History Requires Illumina’s
`Construction
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`A patent’s prosecution history can “inform the meaning of the claim language
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`by demonstrating how the inventor understood the invention and whether the
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`inventor limited the invention in the course of prosecution, making the claim scope
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`narrower than it would otherwise be.” Phillips v. AWH Corp., 415 F.3d 1303, 1317
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`10 The ’480 Patent and ’458 Patent have the same relevant claim language and
`identical specifications.
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`11 Further proving the relevance of the ’480 Patent to the ’458 Patent at-issue in this
`litigation, Columbia filed a terminal disclaimer during prosecution of the ’458 Patent
`admitting that the ’458 Patent is non-obvious over the ’480 Patent
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`(Fed. Cir. 2005); see also Personalized Media Commc’ns, LLC v. Apple Inc., 952
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`F.3d 1336, 1345 (Fed. Cir. 2020) (finding that an “applicant’s repeated and
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`consistent remarks during prosecution can define a claim term” and “the prosecution
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`history provides persuasive evidence that informs the meaning of the disputed claim
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`phrase.”). Statements made by a patent owner during an IPR proceeding (including
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`patent owner preliminary responses) can support a finding of prosecution history
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`disclaimer. Aylus Networks, Inc. v. Apple Inc., 856 F.3d 1353, 1361-62 (Fed. Cir.
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`2017); Princeton Digital Image Corp. v. Konami Digital Entm’t Inc., No. 12-1461-
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`LPS-CJB, 2017 WL 6375173, at *5 (D. Del. Dec. 13, 2017). Here, the prosecution
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`history establishes that Illumina’s construction must be adopted.
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`During prosecution, the patent examiner raised doubts as to whether the
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`functional limitations for “Y” “set forth well-defined boundaries of the invention
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`because they only state a problem solved or a result achieved.” Applicant
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`Columbia’s Arguments/Remarks Made In An Amendment (U.S. Pat. App. No.
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`16/149,098, the application that lead to the ’458 Patent) (dated Feb. 12, 2019)
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`(“Applicant Columbia’s Remarks”) at 6 (JA0033). Columbia responded that “the
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`structures in the claims show the structural features of covalent bonds joining Y to
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`a specific position on the base at one end and to the fluorescent tag at the other
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`end.” Id. at 7 (JA0034).
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`Dr. Jingyue Ju, the lead inventor of the ’458 Patent and the other Patents-in-
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`Suit, submitted a declaration similarly stating: “Y is defined as a chemically
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`cleavable, chemical linker and as shown in the pending claim, Y is attached by
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`covalent bonds at one end to the base of a nucleotide analogue at a specific
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`position and at the other end to a detectable fluorescent moiety.” Declaration
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`Under 37 C.F.R. §1.132 (dated May 26, 2017) (“Ju Declaration”) at 5 (JA0065).
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`Notably, Dr. Ju “defined” “Y” to have this particular structure. See Jack Guttman,
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`Inc. v. Kopykake Enterp., Inc., 302 F.3d 1352, 1358-59 (Fed. Cir. 2002) (holding as
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`proper a district court’s adoption of a claim construction that the patentee explicitly
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`defined in the prosecution history). The examiner allowed the ’458 Patent aft