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,
`
`)))))))))))))
`
`Civil Action No. 19-1681-CFC
`
`Plaintiffs,
`
`v.
`
`ILLUMINA, INC.,
`
`Defendant.
`
`PLAINTIFFS’ MOTION FOR RECONSIDERATION OF THE COURT’S
`CLAIM CONSTRUCTION ORDER
`
`Pursuant to D. Del. LR 7.1.5(a), plaintiffs, by and through their undersigned
`
`counsel, respectfully request clarification, or, in the alternative, reconsideration of
`
`this Court’s construction of the term “
`
`”. In support of this motion, plaintiffs
`
`state as follows:
`
`1
`
`
`FOR THE DISTRICT OF DELAWARE
`THE TRUSTEES OF COLUMBIA
`UNIVERSITY IN THE CITY OF NEW
`YORK and QIAGEN SCIENCES, LLC,
`
`)))))))))))))
`
`Civil Action No. 19-1681-CFC
`
`Plaintiffs,
`
`v.
`
`ILLUMINA, INC.,
`
`Defendant.
`
`PLAINTIFFS’ MOTION FOR RECONSIDERATION OF THE COURT’S
`CLAIM CONSTRUCTION ORDER
`
`Pursuant to D. Del. LR 7.1.5(a), plaintiffs, by and through their undersigned
`
`counsel, respectfully request clarification, or, in the alternative, reconsideration of
`
`this Court’s construction of the term “
`
`”. In support of this motion, plaintiffs
`
`state as follows:
`
`1
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 2 of 17 PageID #: 2809
`
`single linker even if it was originally synthesized from multiple smaller chemical
`
`groups.1
`
`If the Court agrees that its construction does not exclude such a single linker
`
`just because the single linker was itself made from multiple chemical groups,
`
`plaintiffs seek no further relief from the Court. However, if the Court disagrees,
`
`plaintiffs respectfully ask for reconsideration because such a construction:
`
`a.
`
`permits Illumina to simultaneously obtain diametrically opposite
`
`claim constructions under the same Phillips standard for non-
`
`infringement and invalidity;
`
`b.
`
`is mistakenly premised on the belief that plaintiffs sought a
`
`construction of “
`
`” to mean both the one structure connecting the
`
`base to the tag, and subgroups (see Ex. 1 at 55:12-23), and this would
`
`improperly read out all of the embodiments in the patents-in-suit;
`
`c.
`
`improperly denies plaintiffs the benefit of the canon of construction
`
`that “a singular noun encompasses the plural for claim construction
`
`purposes”;
`
`1 A POSA understands that a “single linker” connecting the base to the tag is
`typically made from smaller chemical groups that can also be referred to as linkers.
`(Ex. 4, ¶ 72.)
`
`2
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 3 of 17 PageID #: 2810
`
`d.
`
`does not appear to have considered the evidence that “everybody
`
`knows linker can include multiple linkers” (Ex. 1 at 50:9-11); and
`
`e.
`
`improperly considers statements by Columbia in a prior IPR as
`
`“disclaimers” even though the PTAB rejected the statement and
`
`invalidated the patent.
`
`ARGUMENT
`
`The Federal Circuit recognizes that “district courts may engage in rolling
`
`claim construction, in which the court revisits and alters its interpretation of the
`
`claim terms” as new evidence becomes available. Pfizer, Inc. v. Teva Pharms.,
`
`USA, Inc., 429 F.3d 1364, 1377 (Fed. Cir. 2005); ViiV Healthcare v. Gilead Scis.,
`
`437 F. Supp. 3d 395, 402 (D. Del. 2020). Reconsideration is appropriate when
`
`needed to prevent manifest injustice or clear errors of law, and when new evidence
`
`is available. Lazaridis v. Wehmer, 591 F.3d 666, 669 (3d Cir. 2010). Motions for
`
`reconsideration also are appropriate when the court has misunderstood a party or
`
`made an error not of reasoning but of apprehension. Pacific Biosciences v. Oxford
`
`Nanopore Techs., No. 17-275, 2019 U.S. Dist. LEXIS 98526, at *4 (D. Del. Jun.
`
`12, 2019).
`
`The Current Construction Would Result in Manifest Injustice
`
`The current claim construction would result in manifest injustice. If the
`
`Court’s construction precludes “single linker” from encompassing linkers made
`
`3
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 4 of 17 PageID #: 2811
`
`from multiple chemical groups, it would unfairly permit Illumina to achieve
`
`different claim constructions under the same Phillips standard for purposes of
`
`infringement and invalidity. See Amgen Inc. v. Hoechst Marion Roussel, Inc., 314
`
`F.3d 1313, 1330 (Fed. Cir. 2003) (“It is axiomatic that claims are construed the
`
`same way for both invalidity and infringement.”)
`
`Recently, Illumina averred in five IPR Petitions against the patents-in-suit
`
`(all subject to the Phillips standard of claim construction) that Columbia’s claimed
`
`“
`
`”-based “linker” reads on prior art where the linker includes multiple
`
`chemical linkers; and, critically, that “no [Illumina] proposed litigation
`
`construction affects the merits of this petition.” (See, e.g., Ex. 2 [IPR2020-00988,
`
`Paper 1 (Petition)] at 12.) Notably, the “linker” construction that Illumina seeks in
`
`those recent IPRs matches (a) Columbia’s construction (Ex. 3 [IPR2020-00988,
`
`Paper 11 (Patent Owner’s Preliminary Resp.)] at 6-8; Ex. 4 [IPR2020-00988, Ex.
`
`2020 (Declaration of Kenneth Johnson)] at ¶ 71), (b) the PTAB’s construction in
`
`the prior IPRs (JA0040-41, n.33),2 and (c) Illumina’s position in its invalidity
`
`contentions in this case (see Ex. 5 [Illumina’s Initial Invalidity Contentions, App’x
`
`B] at 35 [8].).
`
`2 “JA” is the Joint Appendix [D.I. 55].
`
`4
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 5 of 17 PageID #: 2812
`
`In particular, in the pending IPRs and its current invalidity disclosures in this
`
`case, Illumina argues that “the linker” disclosed in Prober’s Figure 2A (along with
`
`Dower) discloses Columbia’s “linker.” (See e.g., Ex. 2 at 53.) It is undisputed that
`
`Prober’s singular “linker” in Figure 2A contains multiple chemical groups:
`
`(See Ex. 4 at ¶ 75 (annotating Ex. 6 [Prober] at Fig. 2A, to show multiple chemical
`
`groups); Ex. 7 [IPR2018-00291, Ex. 1139 (Illumina’s Demonstratives)], Slide 49.)
`
`Thus, Illumina uses a construction of Y/linker that includes linkers made of
`
`multiple chemical groups.
`
`Finally, Illumina filed the ongoing IPRs in 2020, after Columbia’s alleged
`
`disclaimer in 2019, confirming that Illumina understood that Columbia’s alleged
`
`disclaimer did not exclude a linker made of multiple chemical groups. In these
`
`IPRs, while stating that its proposed construction did not conflict with any claim
`
`construction in this litigation, Illumina used a construction of “linker” that would
`
`encompass a linker made of multiple chemical groups. Given these facts, it would
`
`be manifestly unjust to reward Illumina’s actions and permit the claim construction
`
`5
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 6 of 17 PageID #: 2813
`
`here to directly contradict it and Columbia’s common position in the prosecution
`
`history of the patents-in-suit.
`
`Plaintiffs Did Not Seek Two Constructions of “Linker,” and the
`Construction Incorrectly Excludes All Embodiments
`
`Plaintiffs believe the Court misunderstood their position with respect to
`
`“linker.” During the hearing, the Court stated that the patent owner had not made
`
`it clear whether “linker” was “the overall structure that lies between and connects
`
`the tag to the base, or . . . a subgroup within that overall structure.” (Ex. 1 at
`
`53:22-54:5.) But plaintiffs did not seek to construe “linker” or “subgroups.”
`
`Misunderstanding on this point between the Court and the parties justifies
`
`reconsideration. Pacific Biosciences, 2019 U.S. Dist. LEXIS 98526, at *4
`
`(granting motion for reconsideration, noting that the Court “misapprehended
`
`certain factual arguments”).
`
`Plaintiffs have consistently stated in their briefs and at the hearing that both
`
`“
`
`” and “linker” refer to the entire structure that connects the base to the tag.
`
`(Joint Claim Construction Br. (“Joint Br.”) [D.I. 54] at 10, 11, 23, 24, 41, 43, 44,
`
`46, 47; Ex. 1 at 6:2-4, 6:11-12, 9:7-9, 10:20-21, 11:24-12:1, 12:15-20, 27:10-12,
`
`30:21-22, 34:8-9.) Plaintiffs sought to avoid a construction that could exclude a
`
`single linker made of smaller linkers, because there was nothing in the claims or
`
`written description supporting such a limiting construction. See e.g., Renishaw
`
`PLC v. Marposs Societa’ Per Azioni, 158 F.3d 1243, 1250 (Fed. Cir. 1998) (“if an
`6
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 7 of 17 PageID #: 2814
`
`apparatus claim recites a general structure (e.g., a noun) without limiting that
`
`structure to a specific subset of structures (e.g., with an adjective), we will
`
`generally construe the claim to cover all known types of that structure that are
`
`supported by the patent disclosure.”)
`
`Critically, clarification is needed so that the Court’s construction does not
`
`improperly read out all of the embodiments. Nellcor Puritan Bennett v. Masimo
`
`Corp., 402 F.3d 1364, 1368-69 (Fed. Cir. 2005) (noting that a construction that
`
`“plac[es] all the embodiments of the invention outside the scope of the claims is
`
`powerful evidence that the court's construction is incorrect” and declining to adopt
`
`such a construction). Illumina stated at the hearing that Figure 21 was consistent
`
`with its “single linker” construction, without any evidence. (Ex. 1 at 50:23-24).
`
`However, after the Markman hearing, in a current IPR representing the still-
`
`developing intrinsic record of the patents-in-suit, Columbia’s expert stated that the
`
`structure shown in Figure 21 contains “a ‘linker’” “consisting of more than one
`
`chemical group”:
`
`7
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 8 of 17 PageID #: 2815
`
`(Ex. 4, ¶ 74 (annotating Fig. 19 (which has the same linker as Figure 21) to show
`
`multiple chemical groups). Clarification is needed to ensure that there is not a
`
`construction that could exclude all embodiments.
`
`As a Matter of Law, a Linker Means One or More Linkers
`
`The Federal Circuit has stated that in claim construction, the “use of the
`
`singular form of a word does not preclude a meaning which includes the plural.”
`
`Embrex, Inc. v. Sev. Eng’g Corp., 216 F.3d 1343, 1348 (Fed. Cir. 2000); see also
`
`Bushnell Hawthorne, LLC v. Cisco Sys., No. 19-2191, 2020 U.S. App. LEXIS
`
`15486, at **10-11 (Fed. Cir. May 14, 2020) (“It is true that, as a general rule, a
`
`singular noun encompasses the plural for claim construction purposes.”);
`
`Renishaw, 158 F.3d at 1250; Mylan Pharma v. Kremers Urban Dev., No. 02-1628,
`
`2004 U.S. Dist. LEXIS 391, at *9 (D. Del. Jan. 13, 2004) (“If the specification
`
`discloses a singular embodiment it ‘does not disclaim a plural embodiment.’”).
`
`Here, the Court erred by finding this rule “inapposite,” simply because the
`
`parties were construing “
`
`” not “a linker.” 3 In construing “
`
`”, the Court and
`
`each party agreed that “
`
`” was “a linker.” (See Ex. 1 at 55:12-15 (Court noting,
`
`3 Moreover, although application of the “singular includes the plural” rule is often
`expressed in terms of singular terms modified by “an” or “a,” Illumina did not raise
`this issue and plaintiffs have found no case finding the rule is unavailable as a
`matter of law when the disputed term is in the singular but there is no article. See
`supra at 8-9.
`
`8
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 9 of 17 PageID #: 2816
`
`“the disputed term is defined in the claim itself as representing a … linker”); 44:2
`
`(defendant agreeing “Y is a linker”); 30:14 (plaintiffs agreeing to same).)
`
`Nonetheless, the Court found that the use of “linker” in the claims and written
`
`description in the “singular” tense served to confine “linker” only to a single linker
`
`itself made of one linker, because linker was preceded by the article “a.” However,
`
`since “linker” is preceded by the article “a,” the Court erred in not construing “
`
`” as not including a single linker itself made of one or more linkers.
`
`The Evidence Shows that a POSA Understands the Term
`“Linker” to Include a Linker Made of Multiple Chemical Groups
`or Linkers
`
`The Court had it right when it suspected “everybody knows linker can
`
`include multiple linkers.” (Ex. 1 at 50:9-11.) Plaintiffs provided evidence that a
`
`POSA used the term “linker” even if made of multiple chemical groups. Illumina
`
`provided zero evidence to the contrary. Thus, the Court erred in finding that a
`
`POSA would not understand linker as one that could be made of multiple chemical
`
`groups or linkers.
`
`Plaintiffs provided both intrinsic and extrinsic evidence that when a POSA
`
`refers to “a linker” the linker may be made from multiple linkers or chemical
`
`groups. For example, the patents refer to the nucleotide analogues in Figures 7 and
`
`8, including 3’-OR-G-Tam, as “labeled with a unique fluorescent dye through a
`
`photocleavable linker” (JA0019 at 23:50-59) (emphasis added), even though it is
`
`9
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 10 of 17 PageID #: 2817
`
`clear that the inventors assembled the linker by attaching two shorter linkers
`
`together.
`
`(JA0005, Fig. 8 (annotated to show multiple linkers below); see also ’458 Patent,
`
`JA0006, at Fig. 16.) Similarly, the Zhu reference (cited in the ’458 patent (JA0010
`
`at 2:63) and thus intrinsic evidence)4 uses the term “linker” to refer to the structure
`
`used to link the base to the tag, despite attaching multiple successive linkers to
`
`make that “linker.” (JA0128-131; Ex. 4, ¶¶ 77-78.) Plaintiffs also pointed to
`
`Illumina’s own patent that refers to the chemical structure between the nucleotide
`
`base and the label as a “linker” (singular) even though Illumina teaches that such
`
`4 Although plaintiffs identified Zhu as extrinsic evidence during the hearing (Ex. 1
`at 51:24-52:5), it is intrinsic evidence. V-Formation, Inc. v. Benetton Grp. SpA,
`401 F.3d 1307, 1311 (Fed. Cir. 2005) (“This court has established that ‘prior art
`cited in a patent . . . constitutes intrinsic evidence.’”); Waters Techs. Corp. v.
`Applera Corp., No. 02-1285, 2004 U.S. Dist. LEXIS 390, at *4 (D. Del. Jan. 13,
`2004) (considering counsel’s misstatement when addressing a motion for
`reconsideration).
`
`10
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 11 of 17 PageID #: 2818
`
`linkers may be composed of more than one shorter linker. (JA0119-121 at Figs. 1-
`
`3; JA0122-125 at 2:19-24, 2:33-37, 4:13-19, 4:37-40, 6:4-5, 6:39-67, 7:1-43.)
`
`A few days after the claim construction hearing, Columbia filed a Patent
`
`Owner Preliminary Response (“POPR”) and supporting expert declaration in the
`
`IPR proceeding involving the ’458 patent. Thus, the POPR and expert declaration
`
`are part of the intrinsic record that the Court may consider in construing the claims.
`
`Power Integrations v. Fairchild Semiconductor Int’l, No. 08-309, U.S. Dist.
`
`LEXIS 118320, at *47 (D. Del. Dec. 18. 2009) (considering statements made
`
`during reexamination as “new intrinsic” evidence for the purposes of claim
`
`construction); Cross Atl. Capital Partners v. Facebook, No. 07-2768, 2011 U.S.
`
`Dist. LEXIS 27505, at *3 n.5 (E.D. Pa. Mar. 17, 2011) (considering “supplemental
`
`intrinsic” evidence in amending claim construction).
`
`In the ’458 patent IPR, Columbia’s expert testified that “[a] POSA would
`
`understand that the term ‘chemical linker’ refers to the entire chemical structure
`
`linking the base to the tag, regardless of whether the structure consists of one or
`
`more chemical groups.” (Ex. 4 at ¶ 71.) He further testified that a POSA would
`
`refer to a structure as a singular “linker” even if made of smaller chemical groups,
`
`which “on their own can be referred to as linkers.” (Id. at ¶ 72.) Finally, as
`
`discussed above, he testified that the “linker” shown in Figure 2A of Prober, which
`
`is cited in the patents (JA0019 at 23:66-24:2) and thus part of the intrinsic record,
`
`11
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 12 of 17 PageID #: 2819
`
`is made of “multiple chemical groups.” (Ex. 4 at ¶ 75.)5 Thus, the record is clear
`
`that a POSA understands “a linker” to include one made from smaller chemical
`
`groups.
`
`As a Matter of Law, Columbia’s Statements in the Prior IPR
`Proceeding Are Not a Disclaimer
`
`In construing “
`
`,” the Court found “at least two explicit disclaimers in the
`
`intrinsic evidence.” (Ex. 1 at 56:6-11.) To the extent the Court relied on
`
`Columbia’s statements as prosecution disclaimer, it erred as a matter of law.
`
`Statements made before the PTAB do not control claim scope where, as
`
`here, the PTAB rejects them and invalidates, rather than upholds, the claims.
`
`Galderma Labs, L.P. v. Amneal Pharms., 806 F. App’x 1007, 1011 (Fed. Cir.
`
`2020). Here, the PTAB expressly rejected the argument that “the claim requires
`
`one linker, not two linkers,” finding instead that a linker “carr[ies] the meaning of
`
`‘one or more’” and found the challenged claims unpatentable. (Joint Br. at 49;
`
`JA0036.)
`
`Moreover, the purpose of a prosecution disclaimer is “to provide ‘public
`
`notice’” about the limited scope of allowed claims. Power Integrations, Inc. v. On
`
`Semiconductor Corp., 396 F. Supp. 3d 851, 864 (N.D. Cal. 2019) (relying on
`
`5 Illumina admits that Prober’s “linker” is made of multiple linkers. (Ex. 7 at Slide
`49 (describing Prober’s Figure 2A as having a “propargyl amine linker and second
`linker”).)
`
`12
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 13 of 17 PageID #: 2820
`
`Schriber-Schroth Co. v. Cleveland Trust, 311 U.S. 211, 220-21 (1940)). This public
`
`notice rationale does not exist when the PTAB disallows the claim. Id. at 866.
`
`CONCLUSION
`
`For the reasons stated above, Plaintiffs respectfully request that the Court
`
`clarify its construction as requested.
`
`Dated: September 16, 2020
`
`MORRIS, NICHOLS, ARSHT &
`TUNNELL LLP
`
`
`/s/ Jack B. Blumenfeld
`Jack B. Blumenfeld (#1014)
`Derek J. Fahnestock (#4705)
`1201 North Market Street
`P.O. Box 1347
`Wilmington, DE 19899-1347
`(302) 658-9200
`jblumenfeld@mnat.com
`dfahnestock@mnat.com
`
`OF COUNSEL:
`
`John D. Murnane
`Robert S. Schwartz
`Justin J. Oliver
`Zachary L. Garrett
`VENABLE LLP
`1290 Avenue of the Americas
`New York, NY 10104-3800
`(212) 218-2100
`
`Attorneys for Plaintiff The Trustees of
`Columbia University in the City of New York
`
`13
`
`BALLARD SPAHR LLP
`
`/s/ Beth Moskow-Schnoll
`Beth Moskow-Schnoll (#2900)
`Brittany M. Giusini (#6034)
`919 N. Market Street, 11th Floor
`Wilmington, DE 19801-3034
`(302) 252-4465
`moskowb@ballardspahr.com
`giusinib@ballardspahr.com
`
`OF COUNSEL:
`
`Robert R. Baron, Jr.
`Marc S. Segal
`BALLARD SPAHR LLP
`1735 Market Street, 51st Floor
`Philadelphia, PA 19103-7599
`(215) 665-8500
`
`Chittam U. Thakore
`BALLARD SPAHR LLP
`999 Peachtree Street, NE., Suite 1600
`Atlanta, GA 30309
`(404) 420-9484
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 14 of 17 PageID #: 2821
`
`Attorneys for Plaintiff QIAGEN
`Sciences, LLC
`
`14
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 15 of 17 PageID #: 2822
`
`RULE 7.1.1 STATEMENT
`
`Pursuant to D. Del. LR 7.1.1, the parties conferred regarding Plaintiffs’
`
`Motion for Reconsideration but did not reach agreement.
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 16 of 17 PageID #: 2823
`
`CERTIFICATE OF COMPLIANCE
`
`The undersigned counsel for The Trustees of Columbia University in the City
`
`of New York and for QIAGEN Sciences, LLC certify that the foregoing MOTION
`
`FOR RECONSIDERATION OF THE COURT’S CLAIM CONSTRUCTION
`
`ORDER complies with the type, font, and word limitations in the Court’s November
`
`6, 2019 STANDING ORDER REGARDING BRIEFING IN ALL CASES. The
`
`foregoing Motion contains 2497 words (excluding the case caption, and the signature
`
`block) and was prepared using the Times New Roman typeface in 14-point font.
`
`MORRIS, NICHOLS, ARSHT &
`TUNNELL LLP
`
`
`/s/ Jack B. Blumenfeld
`Jack B. Blumenfeld (#1014)
`Derek J. Fahnestock (#4705)
`1201 North Market Street
`P.O. Box 1347
`Wilmington, DE 19899-1347
`(302) 658-9200
`jblumenfeld@mnat.com
`dfahnestock@mnat.com
`
`OF COUNSEL:
`
`John D. Murnane
`Robert S. Schwartz
`Justin J. Oliver
`Zachary L. Garrett
`VENABLE LLP
`1290 Avenue of the Americas
`New York, NY 10104-3800
`(212) 218-2100
`
`BALLARD SPAHR LLP
`
`/s/ Beth Moskow-Schnoll
`Beth Moskow-Schnoll (#2900)
`Brittany M. Giusini (#6034)
`919 N. Market Street, 11th Floor
`Wilmington, DE 19801-3034
`(302) 252-4465
`moskowb@ballardspahr.com
`giusinib@ballardspahr.com
`
`OF COUNSEL:
`
`Robert R. Baron, Jr.
`Marc S. Segal
`BALLARD SPAHR LLP
`1735 Market Street, 51st Floor
`Philadelphia, PA 19103-7599
`(215) 665-8500
`
`Chittam U. Thakore
`BALLARD SPAHR LLP
`999 Peachtree Street, NE., Suite 1600
`
`16
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63 Filed 09/16/20 Page 17 of 17 PageID #: 2824
`
`Attorneys for Plaintiff The Trustees of
`Columbia University in the City of New
`York
`
`Atlanta, GA 30309
`(404) 420-9484
`
`Attorneys for Plaintiff QIAGEN
`Sciences, LLC
`
`17
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-1 Filed 09/16/20 Page 1 of 2 PageID #: 2825
`
`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,
`
`
`v.
`
`
`ILLUMINA, INC.,
`
`
`Defendant.
`
`
`
`
`
`Civil Action No. 19-1681-CFC
`
`
`
`
`)))))))))))
`
`
`
`
`
`
`
`
`
`
`
`Plaintiffs,
`
`
`[PROPOSED] ORDER ON PLAINTIFFS’ MOTION FOR
`RECONSIDERATION OF THE CLAIM CONSTRUCTION ORDER
`
`Having considered Plaintiffs’ Motion for Reconsideration (D.I.63),
`
`IT IS ORDERED that the Motion is granted. A claim construction chart with
`
`an updated construction for “
`
`” is below:
`
`Disputed Term
`
` ”
`
` “
`
`(’458 Patent, ’459 Patent, ’742 Patent,
`and ’984 Patent (Claims 1 and 2), and
`’380 Patent (Claims 1 and 3))
`
`Adopted Construction
`A single linker, made of one or more
`chemical groups, that directly connects
`the base to the label
`
`“small”
`
`
`(’458 Patent, ’459 Patent, ’742 Patent,
`and ’984 Patent (Claims 1 and 2), and
`’380 Patent (Claims 1 and 3))
`
`A chemical group that is less than 3.7Å
`in diameter and that fits into the active
`site of the polymerase shown in Figure
`1 of the patent when three-
`dimensionally modeled on chemical
`software
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-1 Filed 09/16/20 Page 2 of 2 PageID #: 2826
`
`Plain and ordinary meaning
`
`Plain and ordinary meaning; preamble
`is limiting
`
`“R . . . is stable during a DNA
`polymerase reaction”
`
`(’458 Patent, ’459 Patent, ’742 Patent,
`and ’984 Patent (Claims 1 and 2), and
`’380 Patent (Claims 1 and 3))
`
`“A method for sequencing a nucleic
`acid”
`
`(’380 Patent (Claims 1 and 3))
`
`
`
`
`
`
`
`
`
`
`__________________________________
`The Honorable Colm F. Connolly
`United States District Judge
`
`
`2
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 1 of 22 PageID #: 2827
`Case 1:19-cv-01681—CFC-SRF Document 63-2 Filed 09/16/20 Page 1 of 22 PageID #: 2827
`
`
`
`
`EXHIBIT 1
`
`EXHIBIT 1
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 2 of 22 PageID #: 2828
`1
`
`IN THE UNITED STATES DISTRICT COURT
`IN AND FOR THE DISTRICT OF DELAWARE
`- - -
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`CIVIL ACTION
`
`NO. 19-1681-CFC
`
`::::::::::::
`
`THE TRUSTEES OF COLUMBIA
`UNIVERSITY IN THE CITY OF
`NEW YORK AND QIAGEN
`SCIENCES, LLC,
`
`Plaintiffs,
`
`vs.
`ILLUMINA, INC.,
`
`Defendant.
`
`
` - - -
`Wilmington, Delaware
`Wednesday, September 2, 2020
`9:00 o'clock, a.m.
` ***Telephone conference
`
` - - -
`BEFORE: HONORABLE COLM F. CONNOLLY, U.S.D.C.J.
` - - -
`
`
`
`APPEARANCES:
`
`MORRIS, NICHOLS, ARSHT & TUNNELL LLP
`BY: JACK B. BLUMENFELD, ESQ.
`
`-and-
`
`Valerie J. Gunning
`Official Court Reporter
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 3 of 22 PageID #: 2829
`2
`
`
`APPEARANCES (Continued):
`
`VENABLE LLP
`BY: JOHN D. MURNANE, ESQ.,
` ROBERT S. SCHWARTZ, ESQ.,
` JUSTIN J. OLIVER, ESQ. and
` ZACHARY L. GARRETT, ESQ.
` (New York, New York)
`
` Counsel for Plaintiff
` The Trustees of Columbia University in the.
` City of New York
`
`
`BALLARD SPAHR LLP
`BY: BETH MOSKOW-SCHNOLL, ESQ.
`
` -and-
`
`BALLARD SPAHR LLP
`BY: ROBERT R. BARON, JR., ESQ.,
` SCOTT MARTY, ESQ. and.
` MARC S. SEGAL, ESQ.
` (Philadelphia, Pennsylvania)
`
` Counsel for Plaintiff
` Qiagen Sciences, LLC
`
`ASHBY & GEDDES
`BY: STEVEN J. BALICK, ESQ.
`
`-and-
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 4 of 22 PageID #: 2830
`3
`
`
`APPEARANCES (Continued):
`
`WEIL, GOTSHAL & MANGES LLP
`BY: EDWARD R. REINES, ESQ. and
`DEREK C. WALTER, ESQ.
`(Redwood Shores, California)
`
`Counsel for Defendant
`
`- - -
`
`
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 5 of 22 PageID #: 2831
`6
`
`certain features, but we call these picture claims for a
`reason. The picture is I think important, and what it
`shows is that Y is a structure that links the base to the
`tag.
`
`So these are modified nucleotides. Natural
`nucleotides don't have a tag. You have to link a tag so
`that we know what the identity of this nucleotide is in the
`sequencing process, and linkers are a very well-known
`chemical structure that does that, that links two things
`together.
`
`And we agree, the parties agree that the linker,
`that Y connects the base to the tag. Our issue is there's
`nothing in the claim or in the patent or in the
`specification that limits it to being a structure that is
`made by one linker.
`So I think that as you'll see in the
`specification, and we cite this in our briefs, in both the
`specification in our patent, which refers to a single linker
`and that has examples that have been made or synthesized by
`having putting multiple linkers together as well as
`Illumina's, their patent, the same technology where they say
`linker, and then they use --
`THE COURT: All right. Hold up. Let's not get
`
`there yet.
`
`MR. BARON: Okay.
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 6 of 22 PageID #: 2832
`9
`
`substantively what you are trying to accomplish.
`MR. BARON: Your Honor, you're right, and we
`would not have -- we obviously want to get it right and
`clear for the jury, so I don't have a problem with moving
`there like that, and I think that you've put your finger
`exactly on it, that the issue, inelegant words that we may
`have proffered aside, is we think that a linker was clearly
`offered in the patent, known in the field to be the
`structure that connects the base of the tag, and that
`there's nothing in the patent, there's nothing in the
`specification, there's nothing that says that it must be
`made only by one linker, that you can't make -- it can't
`be made up or synthesized by putting various linkers
`together.
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`And that's --
`THE COURT: Frankly, then, I get that. That's a
`summary of, you know, as I say, the bulk of your argument.
`So what term do you want me -- like, how would
`you want the jury to be instructed?
`MR. BARON: So I think that if you would like me
`to shift it from Y to linker --
`THE COURT: First of all, don't get me wrong.
`It's not what I want or what I like.
`MR. BARON: What makes sense.
`THE COURT: I'm just trying to make sense. This
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 7 of 22 PageID #: 2833
`10
`
`is not the first case I've had with patent lawyers where
`they say, well, here's the term and then, you know, for
`instance, I often -- it's amazing how often I get a disputed
`term where the term is indisputably a verb and yet the
`proposed construction is for a noun. It happens all the
`time, and a jury would be completely flummoxed by that. And
`that's what I felt like here. You are asking me to
`substitute this language where Y is and it just makes no
`sense if I do it.
`So --
`MR. BARON: Why don't we try linker wherein Y
`represents the chemically cleavable linker being a chemical
`structure made of one or more linkers that attaches the base
`to the tag?
`THE COURT: So what is the term now you think I
`should be construing?
`MR. BARON: We're still comfortable with Y, and
`I think that because -- I mean, part of the challenge, Your
`Honor, is that this is a very unusual claim because it is an
`illustration, and we think that Y is the chemical structure
`that links the base of the tag and that could be made up of
`one or more linkers.
`THE COURT: Okay.
`MR. BARON: I think --
`THE COURT: So maybe then this. So do you want
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`1 2 3 4 5 6 7 8 9
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 8 of 22 PageID #: 2834
`11
`
`to say the disputed term that we're going to say to the jury
`is, and we'll show it pictorially to them, we'll put Y in
`the rectangle and we're going to define Y in the rectangle
`to mean something. Do you want to do it this way as opposed
`to --
`
`MR. BARON: Yes.
`THE COURT: -- as opposed to when we get to the
`Y, the capital Y in the language of the claim at line 56 of
`column 33?
`
`So are you proposing then what we do is we tell
`the jury when they look at the picture in the third, what
`would be the third line of claim 1, we tell them Y in the
`rectangle means, and then you tell me what do we tell the
`jury it means? What does Y in the rectangle mean?
`MR. BARON: Chemical structure made of one or
`more linkers.
`THE COURT: Okay. Hold on. Chemical structure.
`All right. A chemical structure made of what? One or more
`linkers?
`
`MR. BARON: That attaches the base to the tag.
`But to your point, Your Honor.
`THE COURT: Hold on. Let me write it down.
`That attaches the base to the tag. Okay. Go ahead.
`MR. BARON: And on the point that Y is a
`chemical structure that attaches the base to the tag, the
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 9 of 22 PageID #: 2835
`12
`
`parties don't disagree about that. They are trying to make
`this --
`
`THE COURT: Right.
`MR. BARON: You said Y. That means one linker.
`THE COURT: Yes. Actually, I'm really familiar
`with that argument.
`MR. BARON: Okay.
`THE COURT: Honest to God, you must have
`repeated your briefing, you know. I think you repeated
`yourself like five times at least in the briefing on that.
`It was tortious to get through the repetition. I get that
`argument. I'm just trying to get clarity on what we are
`going to actually construe for the jury.
`So it sounds to me where you are right now is,
`the disputed term is really Y in the box. We would show
`that to the jury and we would instruct them if you had your
`way, that that box with the Y in it is a chemical structure
`made of one or more linkers that attaches the base to the
`tag, unquote. Is that right?
`MR. BARON: Yes.
`THE COURT: All right. Let me hear from the
`defense. What do you think we should be construing for the
`jury here?
`
`MR. REINES: Thank you, Your Honor. This is Ed
`
`Reines.
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 10 of 22 PageID #: 2836
`27
`
`
`sufficient.
`The also directed us to other art that also was
`used by Illumina in the IPRs that also used two linkers.
`That's not in the joint appendix, but it's in there.
`And so I think that people understood, and I
`think this also gets to the nub of the kind of semantic
`issue here. A linker -- I'm trying to think of a metaphor,
`Your Honor. The only thing I can come up with is a garden
`hose.
`
`Sometimes, you know, a linker is the structure
`that connects the base to the tag, but it's made up
`sometimes of linkers. Just like if you have ever watered a
`flower bed 50 feet away and you don't have a 50-foot hose,
`you sometimes tie two or three hoses together to get to it
`and it's still a hose and it's the same thing.
`The bottom line is there's nothing in this
`patent that would achieve the relatively extraordinary
`situation where how someone makes this Y structure is
`limited to only using one linker. You can't put any more
`than one linker, you can't use any more than one linker.
`THE COURT: All right.
`MR. BARON: It's precluding someone from
`synthesizing with more than one.
`THE COURT: All right.
`MR. BARON: I do want -- sorry, Your Honor.
`
`1 2 3 4 5 6 7 8 9
`
`10
`11
`12
`13
`14
`15
`16
`17
`18
`19
`20
`21
`22
`23
`24
`25
`
`
`
`
`
`
`Case 1:19-cv-01681-CFC-SRF Document 63-2 Filed 09/16/20 Page 11 of 22 PageID #: 2837
`30
`
`I can't find it anywhere in the patent, so can
`you point me anywhere in the patent where there's an article
`that precedes Y?
`MR. BARON: I know they're there for linker.
`
Accessing this document will incur an additional charge of $.
After purchase, you can access this document again without charge.
Accept $ Charge
Still Working On It
This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.
Give it another minute or two to complete, and then try the refresh button.
A few More Minutes ... Still Working
It can take up to 5 minutes for us to download a document if the court servers are running slowly.
Thank you for your continued patience.
This document could not be displayed.
We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.
Your account does not support viewing this document.
You need a Paid Account to view this document. Click here to change your account type.
Your account does not support viewing this document.
Set your membership
status to view this document.
With a Docket Alarm membership, you'll
get a whole lot more, including:
- Up-to-date information for this case.
- Email alerts whenever there is an update.
- Full text search for other cases.
- Get email alerts whenever a new case matches your search.
One Moment Please
The filing “” is large (MB) and is being downloaded.
Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.
Your document is on its way!
If you do not receive the document in five minutes, contact support at support@docketalarm.com.
Sealed Document
We are unable to display this document, it may be under a court ordered seal.
If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.
Access Government Site
