Cornell University et al v. Illumina Inc.
MEMORANDUM OPINION re 449 Report and Recommendation regarding claim construction. Signed by Judge Leonard P. Stark on 1/10/17. (ntl)
IN THE UNITED STATES DISTRICT COURT.
FOR THE DISTRICT OF DELAWARE
CORNELL UNIVERSITY, CORNELL
RESEARCH FOUNDATION, INC., LIFE
TECHNOLOGIES CORPORATION, and
APPLIED BIOSYSTEMS, LLC,
C.A. No. 10-433-LPS-MPT
John W. Shaw, Karen E. Keller, and David M. Fry, SHAW KELLER LLP, Wilmington, DE
Rip Finst and Sean Boyle, THERMO FISHER SCIENTIFIC INC., Carlsbad, CA
Dianne B. Elderkin, Matthew A. Pearson, Angela Verrecchio, and Jason E. Weil, AKIN GUMP
STRAUSS HAUER & FELD LLP, Philadelphia, PA
Rachel J. Elsby, AKIN GUMP STRAUSS HAUER & FELD LLP, Washington, DC
Attorneys for Plaintiffs.
Steven J. Balick, ASHBY & GEDOES, Wilmington, DE
Christopher N. Sipes, Jay I. Alexander, Bradley Ervin, Matthew Kudzin, Jared Frisch, and
Christopher Zirpoli, COVINGTON & BURLING LLP, Washington, DC
Alexa Hansen, COVINGTON & BURLING LLP, San Francisco, CA
Attorneys for Defendant.
January 10, 2017
STARK, U.S. District Judge:
Pending before the Court are issues of claim construction of a number of disputed claims
terms in the asserted patents as well as Defendant's motion for leave to amend its answer and
Cornell University, Cornell Research Foundation, Inc., Life Technologies Corporation,
and Applied Biosystems, LLC (collectively, "Cornell" or "Plaintiffs") filed a patent infringement
suit against Illumina, Inc. ("Illumina" or "Defendant") on May 24, 2010, alleging infringement of
two families of patents: the Array patents and the LDR-PCRpatents. The ,Array patents (U.S.
Patent Nos. 7,083,917; 7,892,746; 7,893,233; 8,288,521; 8,624,016; and 8,703,928) relate to
tools that utilize oligonucleotides with particular sequence properties to detect target molecules
in a sample. 1 The LDR-PCR patents (U.S. Patent Nos. 6,797,470; 7,166,434; 7,312,039;
7,332,285; and 7,429,453) describe the combination ofa ligase detection reaction ("LDR") with
polymerase chain reaction ("PCR") to test for genetic changes with high specificity arid
Chief Magistrate Judge Thynge issued a Report and Recommendation ("R&R") on May
6, 2016, recommending resolution of the claim construction disputes involving the Array patents
and LDR-PCR patents. (D.I. 449) Judge Thynge also issued an R&R on May 27, 2016,
recommending that the Court grant Illumina' s motion for leave to amend its answer and
Because the specifications of the Array patents are identical in substance, the Court's
citations are generally to the '91 7 patent.
Because the specifications of the LDR-PCR patents are identical in substance, the
Court's citations are generally to the '928 patent.
counterclaims to allege inequitable conduct before the Patent and Trademark Office ("PTO")
with respect to the prosecution of the LDR-PCR patents. (D.I. 451)
Cornell's objections to the R&Rs on claim construction and on Illumina's motion for
leave to amend are pending before the Court. The parties completed briefing on July 21, 2016.
(See D.I. 474) The Court held a hearing on November 29, 2016. (See D.I. 517 ("Tr."))
The ultimate question of the proper construction of a patent is a question oflaw. See Teva
Pharm. USA, Inc. v. Sandoz, Inc., 135 S. Ct. 831, 837 (2015) (citing Markman v. Westview
Instruments, Inc., 517 U.S. 370, 388-91 (1996)). "It is a bedrock principle of patent law that the
claims of a patent define the invention·to which the patentee is entitled the right to exclude."
Phillips v. A WH Corp., 415 F.3d 1303, 1312 (Fed. Cir. 2005) (internal quotation marks omitted).
"[T]here is no magic formula or catechism for conducting claim construction." Id. at 1324.
Instead, the court is free to attach the appropriate weight to appropriate sources "in light of the
statutes and. policies that inform patent law." Id.
"[T]he words of a claim are generally given their ordinary and customary meaning ...
[which is] the meaning that the term would have to a person of ordinary skill in the art in
question at the time of the invention, i.e., as of the effective filing date of the patent application."
Id. at 1312-13 (internal citations and quotation marks omitted). "[T]he ordinary meaning of a
claim term is its meaning to the ordinary artisan after reading the entire patent." Id. at 1321
(internal quotation marks omitted). The patent specification "is always highly relevant to the
claim construction analysis. Usually, it is dispositive; it is the single best guide to the meaning of
a disputed term." Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 15.82 (Fed. Cir. 1996).
While "the claims themselves provide substantial guidance as to the meaning of particular
claim terms," the context of the surrounding words of the claim also must be considered.
Phillips, 415 F.3d at 1314. Furthermore, "[o]ther claims of the patent in question, both asserted
and unasserted, can also be valuable sources of enlightenment ... [b]ecause claim terms are
normally used consistently throughout the patent .... " Id. (internal citation omitted).
It is likewise true that"[ d]ifferences among claims can also be a useful guide .... For
example, the presence of a dependent claim that adds a particular limitation gives rise to a
presumption that the limitation in question is not present in the independent claim." Id. at 131415 (internal citation omitted). This "presumption is especially strong when the limitation in
dispute is 'the only meaningful difference between an independent and dependent claim, and one
party is urging that the limitation in the dependent claim should be read into the independent
claim." SunRace Roots Enter. Co., Ltd. v. SRAM Corp., 336 F.3d 1298, 1303 (Fed. Cir. 2003).
It is also possible that "the specification may reveal a special definition given to a claim
term by the patentee that differs from the meaning it would otherwise possess. In such cases,·the
inventor's lexicography governs." Phillips, 415 F.3d at 1316. It bears emphasis that "[e]ven
when the specification describes only a single embodiment, the claims of the patent will not be
read restrictively unless the patentee has demonstrated a clear intention to limit the claim scope
using words or expressions of manifest exclusion or restriction." Hill-Rom Servs., Inc. v. Stryker
Corp., 755 F.3d 1367, 1372 (Fed. Cir. 2014) (quoting Liebel-Flarsheim Co.
Medrad, Inc., 358
F.3d 898, 906 (Fed. Cir. 2004)) (internal quotation marks omitted).
In addition to the specification, a court "should also consider the patent's prosecution
history, if it is in evidence." Markman v. Westview Instruments, Inc., 52 F.3d 967, 980 (Fed. Cir.
1995), aff'd, 517 U.S. 370 (1996). The prosecution history, which is "intrinsic evidence,"
"consists of the complete record of the proceedings before the PTO and includes the prior art
cited during the examination of the patent." Phillips, 415 F.3d at 1317. "[T]he prosecution
history can often inform the meaning of the claim language by demonstrating how the inventor
understood the invention and whether the inventor limited the invention in the course of
prosecution, making the claim scope narrower than it would otherwise be." Id.
In some cases, "the district court will need to look beyond the patent's intrinsic evidence
and to consult extrinsic evidence in order to understand, for example, the background science or·
the meaning of a term in the relevant art during the relevant time period." Teva, 135 S. Ct. at
841. Extrinsic evidence "consists of all evidence external to the patent and prosecution history,
including expert and inventor testimony, dictionaries, and learned treatises." Markman, 52 F.3d
at 980. For instance, technical dictionaries can assist the court in determining the meaning of a
term to those of skill in the relevant art because such dictionaries "endeavor to· collect the
accepted meanings of terms used in various fields of science and technology." Phillips, 415 F.3d
at 1318. In addition, expert testimony can be useful "to ensure that the court's understanding of
the technical aspects of the patent is consistent with that of a person of skill in the art, or to ·
establish that a particular term in the patent or the prior art has a particular meaning in the
pertinent field." Id. Nonetheless, courts must not lose sight of the fact that "expert reports and
. testimony [are] generated at the time of and for the purpose of litigation and thus can suffer from
bias that is not present in intrinsic evidence." Id. Overall, while extrinsic evidence "may be
useful" to the court, it is "less reliable" than intrinsic evidence, and its consideration "is unlikely
to result in a reliable interpretation of patent claim scope unless considered in the context of the
intrinsic evidence." Id. at 1318-19. Where the intrinsic record unambiguously describes the
scope of the patented invention, reliance on any extrinsic evidence is improper. See Pitney
Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1308 (Fed. Cir. 1999) (citing Vitronics, 90
F.3d at 1583).
Finally, "[t]he construction tbat stays true to the claim language and most naturally aligns
with the patent's description of the invention will be, in the end, the correct construction."
Renishaw PLC v. Marposs Societa 'per Azioni, 158 F.3d 1243, 1250 (Fed. Cir. 1998). It follows
that "a claim interpretation that would exclude the inventor's device is rarely the correct
interpretation." Osram GmbH v. Int'! Trade Comm 'n, 505 F.3d 1351, 1358 (Fed. Cir. 2007)
(quoting Modine Mfg. Co. v. U.S. Int'! Trade Comm 'n, 75 F.3d 1545, 1550 (Fed. Cir. 1996)).
Motion for Leave to Amend
At this stage of the proceedings, a party "may amend only with leave of the court or the
written consent of the opposing party." Shane v. Fauver, 213 F.3d 113, 115 (3d Cir. 2000)
(citing Fed. R. Civ. P. 15(a)). The court exercises discretion in deciding whether to grant a ·
motion to amend, see Foman v. Davis, 371 U.S. 178, 182 (1962), and "[t]he court should freely
give leave whenjustice so requires," Fed. R. Civ. P. 15(a)(2). Under the Third Circuit's liberal
. policy favoring the amendment of pleadings, which aims to "ensure that a particular claim will
be decided on the merits rather than on technicalities," Dole v. Arco Chem. Co., 921 F.2d 484,
487 (3d Cir. 1990), an amendment ordinarily is permitted absent a showing of "undue delay, bad
faith or dilatory motive on the part of the movant, repeated failure to cure deficiencies by
amendment previously allowed, undue prejudice to the opposing party by virtue of the allowance
of the amendment, futility of the amendment, etc.," Farnan, 371
u.s.· at 182.
If a party moves for leave to amend the pleadings after a deadline imposed by a
scheduling order, Rule 16 must also be satisfied. See E. Minerals & Chems. Co. v. Mahan, 225
F.3d 330, 340 (3d Cir. 2000). Under Rule 16(b), "a schedule may be modified only for good
cause and with the judge's consent." "Good cause" exists when the schedule "cannot reasonably
be met despite the diligence of the party seeking the extension." Fed. R. Civ. P. 16(b)(4)
Advisory Committee's Notes (1983 amendments). "In contrast to Rule 15(a), the good, cause
standard under Rule 16(b) hinges on diligence of the movant, and not on prejudice to the
non-moving party." Roquette Freres v. SP! Pharma, Inc., 2009 WL 1444835, at *4 (D. Del. May
The Court may deny leave to amend on the basis that an amendment would be futile. "An
amendment is deemed futile if it could not withstand a motion to dismiss." Enzo Life Scis., Inc.
v. Digene Corp., 270 F. Supp. 2d 484, 489 (D. Del. 2003). "[I]n assessing futility of a proposed
amendment, the same standard of legal sufficiency as under Rule 12(b)(6) is applied." Roquette
Freres, 2009 WL 1444835, at *3. The Court may grant a motion to dismiss only if, after .
"accepting all well-pleaded allegations in the complaint as true, and viewing them in the light
most favorable to plaintiff, plaintiff is not entitled to relief." Maio v. Aetna, Inc., 221 F.3d 472,
481-82 (3d Cir. 2000) (internal quotation marks omitted). "To survive a motion to dismiss, a
civil plaintiff must allege facts that 'raise a right to rel_ief above the speculative level on the
assumption that the allegations in the complaint are true (even if doubtful in fact)."' Victaulic
Co. v. Tieman, 499 F.3d 227, 234 (3d Cir. 2007) (quoting Bell Atlantic Corp. v. Twombly, 550
U.S. 544, 555 (2007)). The complaint must allege "enough facts to state a claim to relief that is
plausible on its face." Twombly, 550 U.S. at 570. A claim is facially plausible "when the
plaintiff pleads factual content that allows the court to draw the reasonable inference that the
defendant is liable for the misconduct alleged." Ashcroft v. Iqbal, 556 U.S. 662, 678 (2009).
Inequitable conduct before the PTO must be pleaded with particularity in accordance with
Rule 9(b ). See Ferguson Beauregard/Logic Controls, Div. ofDover Res., Inc. v. Mega Sys.,
LLC, 350 F.3d 1327, 1344 (Fed. Cir. 2003). In relevant part, Rule 9(b) provides that "[i]n
alleging fraud .. ·. a party must state with particularity the circumstances constituting fraud ....
Malice, intent, knowledge, and other conditions of a person's mind may be alleged generally."
"[T]o plead the 'circumstances' of inequitable conduct with the requisite 'particularity' under
Rule 9(b ), the pleading must identify the specific who, what, when, where, and how of the
material misrepresentation or omission committed before the PTO." Exergen Corp. v. Wal-Mart
Stores, Inc., 575 F.3d 1312, 1328 (Fed. Cir. 2009). Although a party may plead facts upon
"information and belief," it must also set forth the "specific facts upon which the belief is
reasonably based." Id. at 1330. "Moreover, although 'knowledge' and 'intent' may be averred
generally, a pleading of inequitable conduct under Rule 9(b) must include sufficient allegations
of underlying facts from which a court may reasonably infer that a specific individual (1) knew of
the withheld material information or of the falsity of the material misrepresentation, and (2)
withheld or misrepresented this information with a specific intent to deceive the PTO." Id. at
The Claim Construction R&R recommends adoption of Illumina' s proposed construction,
that "solid support" means "a single unitary substrate," which is partly based on prosecution
history estoppel. (D.I. 449 at 4-7) Having reviewed the objections de novo, the Court
SUSTAINS Cornell's objections, REJECTS the R&R with respect to this claim term, and adopts
Cornell's proposed construction of "solid support."
The Court agrees with Cornell that the term "solid support" should not be limited to "a
single unitary substrate." The specification suggests that the support "can be made from a wide
variety of materials" and take any number of forms. '917 patent col. 2211. 1-6; col. 43 11. 49-55.
There is nothing ~n the specification that supports Illumina's argument that the support must be a
single unitary substrate. See Hill-Rom Servs., Inc. v. Stryker Corp., 755 F.3d 1367, 1372 (Fed.
Cir. 2014) ("There are no words of manifest exclusion or restriction."). Illumina contends that in
every embodiment disclosed in the specification, the solid support is a unitary substrate, but that
is not a sufficient basis here to limit the scope of the claims. See Williamson v. Citrix Online,
LLC, 792 F.3d 1339, 1346-47 (Fed. Cir. 2015) (holding that claims are not generally not limited
to disclosed embodiments even when specification discloses only single embodiment); Teleflex,
Pursuant to 28 U.S.C. § 636(b)(l)(B) and Fed. R. Civ. P. 72(b)(3), the Court may accept,
reject, or modify the recommendations of the Magistrate Judge. The Court may also receive
further evidence or return the matter to the Magistrate Judge with instructions for further
proceedings. Objections to the Magistrate Judge's conclusions with regard to the legal issue of
claim construction are reviewed de nova. 28 U.S.C. § 636(b)(l)(C); see also Hand Held Prods.,
Inc. v. Amazon.com, Inc., 2016 WL 1275589, at *1 (D. Del. .Mar. 31, 2016).
Inc. v. Ficosa N. Am. Corp., 299 F.3d 1313, 1328 (Fed. Cir. 2002).
The prosecution-history does not persuade the Court otherwise. Illumina argues that the
patentee disclaimed during prosecution any use of intermediate supports that may have been
contemplated by the specification. (D.I. 449 at 6) During prosecution of the '917 patent,
pending claim 120 recited "a linker or support suitable for coupling an oligonucleotide to the
solid support." (D.I. 421 at A1548) The examiner rejected the claim for indefiniteness, stating
"it is not clear what does applicants mean by support suitable for coupling to the solid support.
Does applicants mean the oligonucleotide is coupled to the solid support by using a different
support." (Id. at Al399-1400) In response, the patentees deleted "or support" from the claim
and traversed the indefiniteness rejection in view of the amendment. (Id. at A1416, A1424)
"When the prosecution history is used solely to support a conclusion of patentee
disclaimer, the standard for justifying the conclusion is a high one. For prosecution disclaimer to
attach, [Federal Circuit] precedent requires that the alleged disavowing actions or statements
made during prosecution be both clear and unmistakable." Avid Tech., Inc. v. Harmonic, Inc.,
812 F.3d 1040, 1045 (Fed. Cir. 2016) (internal quotation marks and alterations omitted). The
claim amendment here is not sufficiently clear to allow the Court to conclude that the patentees
disclaimed non-unitary solid supports. While one reading of the prosecution history is consistent
with Illumina' s view, another plausible reading is that the patentees merely simplified the
language without changing claim scope. (See D.I. 454 at 6-7) There is no argument or
discussion accompanying the amendment that provides additional insight. In sum, where, as
here, "the alleged disavowal is ambiguous, or even 'amenable to multiple reasonable
interpretations,' [courts] have declined to find prosecution disclaimer." Avid Tech, 812 ~.3d at
1045 (internal citation omitted).
Accordingly, the Court will adopt Cornell's proposal and construe "solid support" as
Claim Terms Related to the Connection
of Oligonucleotides to the Solid Support
The Claim Construction R&R recommends adopting Illumina' s proposals, with some
modifications·, for the claim terms "linker," "immobilized," "attached," "suitable for attachment,"
and "coupled to." (D.I. 449 at 9-13) This recommendation is based on the R&R's agreement
with Illumina that "solid support" means "a single unitary substrate." Having rejected that
construction and having reviewed Cornell's objections to the construction of these related terms
de novo, the Court SUSTAINS Cornell's objections, REJECTS the R&.R with respect to these
claim terms, and adopts Cornell's proposed constructions of them.
The parties agree that the proper constructions of the "solid support" and "linker" terms
tum on the same issue, which is the claim amendment made during prosecution of the '91 7
patent. (Tr. at 4, 13-14) As discussed above, the Court finds that this prosecution history is not
clear and unmistakable. Therefore, the Court disagrees with the R&R's conclusion that "the
claims do not cover intervening structures, like an additional support, for connecting
oligonucleotides to solid supports.". (D.I. 449 at 11)
Accordingly, the Court will adopt Cornell's proposed constructions of the terms "linker,"
"immobilized," "attached," "suitable for attachment," and "coupled to.'' 4
The adopted constructions are as follows:
"linker" means "feature that connects an oligonucleotide to
a solid support"
Claim Terms Related to Capture Oligonucleotides
The Claim Construction R&R recommends adoption of Ilhimina' s proposals for the claim
terms "capture oligonucleotide probes," "capture oligonucleotide(s)," and "capturing said one or
more amplification products to a solid support." (D.I. 449 at 13-26) Having reviewed the
objections de novo, the Court OVERRULES Cornell's objections and ADOPTS the R&R with
respect to these claim terms.
The R&R recommends construing "capture oligonucleotide probes" and "capture
oligonucleotide(s)" to mean "oligonucleotide [probe] which has no homology to a target
sequence and is complementary to the addressable array specific portion of an oligonucleotide
containing an addressable array specific portion and a target specific portion." (Id. at 23)
Cornell argues that homology and complementarity are not required for every capture
oligonucleotide, pointing to certain claims that explicitly recite those features. (D.I. 454 at 1213) These claim differentiation arguments are not compelling here. See Atlas IP, LLC v.
Medtronic, Inc., 809 F.3d 599, 607 (Fed. Cir. 2015). Cornell's claim differentiation arguments
relate to independent claims of different patents, and Cornell does not argue thatits construction
is "needed to maintain different claim scope." World Class Tech. Corp. v. Ormco Corp., 769
F.3d 1120, 1126 (Fed. Cir. 2014) ..
Cornell also asserts that the capture oligonucleotide need only be capable of hybridizing
to a complementary nucleic acid. But Cornell's proposed construction fails to give any meaning
"immobilized" means "restricted in mobility"
"attached" means "connected"
"suitable for attachment" means "capable of being
"coupled to" means "connected to"
to the word "capture," as every oligonucleotide is capable of hybridizing to a complementary
. nucleic acid. (D.I. 469 at 12 n.2) The specification makes clear that a "capture" oligonucleotide
is a type of oligonucleotide that has specific properties. First,"[ a] capture oligonucleotide probe
sequence does not have any homology to either the target sequence or to other sequences on
genomes which may be present in the sample." '917 patent col. 20 L 65 - col. 211. 1. Second,
"[t]he capture oligonucleotides are complementary to the addressable array-specific portions."
Col. 6 11. 5-7; col. 911. 44-46. Further, in describing the array invention, the specification states
that "the present invention allows for the design of arrays of capture oligonucleotides with
sequences which are very different from each other. Each LDR product will have a unique
addressable array-specific portion, which is
selectively by a capture oligonucleotide at a
specific address on the solid support." Col. 4211. 31-37. The specification makes clear that it is
these features that make the claimed arrays universal and addressable. (D .I. 449 at 17-19)
Cornell also argues that the "capturing said one or more amplification products to a solid
support" step of claim 10 of the '453 patent does not require the amplification products to
hybridize to "capture oligonucleotides." This argument is unavailing. Each amplification
product of claim 10 includes an addressable array-specific portion. See '453 patent col. 83 11. 5256. As the specification of the '453 patent describes, "the addressable array-specific portions ..
hybridize to the capture oligonucleotides during a capture phase." Col. 35 11. 60-63. Therefore,
"capturing said one or more amplification products to a solid support" necessarily involves
hybridization of the addressable array-specific portions of amplification products to capture
oligonucleotides. Thus, Illumina' s proposed construction - which is "hybridizing the
amplification products to capture oligonucleotides attached on the solid support" - is supported
by the specification.
Accordingly, the Court will adopt the R&R' s constructions of "capture oligonucleotide
probes," "capture oligonucleotide(s)," and "capturing said one or more amplification products to
a solid support."
Claim Terms Related to Differences
between Oligonucleotide Sequences
The Claim Construction R&R recommends adopting Illumina' s proposals for these claim
terms. (D.I. 449 at 31-36). Having reviewed the objections de novo, the Court OVERRULES
Cornell's objections and ADOPTS the R&R with respect to these claim terms.
The parties dispute whether these claim terms require each capture oligonucleotide to
differ by 25% from every other capture oligonucleotide. The R&R construed the terms to
include such a requirement.
The claim language does not provide a clear answer. For example, claim 1 of the '928
patent recites "a solid support comprising at least 25 types c;>f capture oligonucleotides
immobilized on the solid support at an array of positions, wherein each type of capture
oligonucleotide ... differs in nucleotide sequence, when aligned to another type of capture
oligonucleotide that is located on an adjacent position of said solid support, by at least 25%."
'928 patent col. 61 11. 61-67. This language could mean, as Cornell suggests, that each type of
capture oligonucleotide need only be compared one other type located on an adjacent position.
Alternatively, this language could instead mean that any time one type of capture oligonucleotide
is compared to another type of capture oligonucleotide adjacently located, they must differ by at
least 25%. 5
Because the claim language leaves ambiguity, the Court turns to the specification. The
specification is clear that capture oligonucleotides must be sufficiently different from one another
to reduce cross-hybridization and allow for "high specificity detection of correct signal." '917
patent col. 42 1. 66 -·col. 43 1. 1. For example, the specification states that "the present invention
allows for the design of arrays of capture oligonucleotides with sequences which are ve1y
different from each other. Each LDR product will have a unique addressable array-specific
portion, which is captured selectively by a capture oligonucleotide at a specific address on the
solid support." Col. 4211. 31-37 (emphasis added); see also col. 361. 55 - col. 371. 3. The
patent repeatedly stresses the importance of designing capture oligonucleotides to have
substantial sequence differences from all other capture oligonucleotides, in order to reduce crossreactivity. (See D.I. 449 at 33) Cornell's proposed constructions are inconsistent with these
teachings, as they would not require capture oligonucleotides to be sufficiently different from one ·
another. Accordingly, the Court will adopt the R&R's recommended construction ofthese ·
Illumina argues that "an" in "another type" or "its" in "its adjacent" is conclusive. But
here the general rule that "the words 'a' or 'an' in a patent claim carry the meaning of 'one or
more,"' TiVo, Inc. v. EchoStar Commc 'ns Corp., 516 F.3d 1290, 1303 (Fed. Cir. 2008), does not
compel Illumina's proposed constructions. Illumina's proposed construction is not stated in
terms of "one or more than" but, rather, in terms of"all."
For example, the term "each capture oligonucleotide probe of the array differs in
sequence from its adjacent capture oligonucleotide probe, when aligned to each other by at least
25%" is construed to mean "each capture oligonucleotide probe [of the array] differs in sequence
from every adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide
Claim Terms Related to Addressable Array-Specific Portions .
The Claim Construction R&R recommends adopting Illumina' s proposals for the claim
terms "addressable array-specific portion," "address specific portion," and "zip code portion."
(D.I. 449 at 40-44) Having reviewed the objections de novo, the Court OVERRULES Cornell's
objections and ADOPTS the R&R with respect to these claim terms.
The R&R construed these terms to mean "portion of an oligonucleotide that selectively
hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to
naturally occurring nucleic acids or to other oligonucleotides located on an array." (D.I. 449 at
43-44) Cornell objects to the requirement that the address array-specific portion binds to its
complementary oligonucleotide on the array and to nothing else. But the claims themselves
make clear that the addressable portion of a target oligonucleotide hybridizes to its
complementary capture oligonucleotide. See, e.g., '746 patent col. 61 11. 62-67 (claim 1 reciting
"contacting the sample ... with the array ... to hybridize the addressable array-specific portion
of each target oligonucleotide to its complementary capture oligonucleotide."). The specification
reinforces that the addressable portion is complementary to its capture oligonucleotide in order to
enable hybridization. See, e.g, '917 patent col. 42 11. 34-37.
Because the addressable array-specific portion must hybridize to its complementary
capture oligonucleotide and, as discussed above, the capture oligonucleotides must differ from
each other by 25%, the addressable array-specific portion will not hybridize to other
oligonucleotides located on an array. (See D.I. 469 at 21) It is this selective hybridization that
allows "addressable array-specific portions [to] guide each LDR product to a designated address
on the solid support." Col. 42 11. 25-26.
Accordingly, the Court will adopt the R&R's construction of the terms "addressable
array-specific portion," "address specific portion," and "zip code portion."
Claim Terms Related to Ligase Detection Reaction
The R&R recommends adoption of Illumina's proposals for the claim terms "ligase
detection reaction," "ligase detection reaction cycles," and "suitable for ligation together." (D.I.
449 at 46-56) Having reviewed the objections de novo, the Court OVERRULES Cornell's
objections and ADOPTS the R&R with respect to these claim terms.
The R&R construed "ligase detection reaction" to mean "reaction which detects the
presence of target nucleotide sequences in a sample by using a ligase and one or more sets of two
oligonucleotide probes in which the ligase joins the two oligonucleotide probes only if they are
hybridized at adjacent positions on a target nucleotide sequence." (Id. at 54) Cornell objects to
the requirement of adjacently hybridizing probes, arguing that claim differentiation compels the
conclusion that adjacently hybridizing probes are not mandatory in a ligase detection reaction.
"[T]he doctrine of claim differentiation is not a hard and fast rule .... " Comark Commc 'ns, Inc.
v. Harris Corp., 156 F.3d 1182, 1187 (Fed. Cir. 1998). For example, "any presumption created
by the doctrine of claim differentiation 'will be overcome by a contrary construction dictated by
the written description or prosecution history."' Retractable Techs., Inc. v. Becton, Dickinson &
Co., 653 F.3d 1296, 1305 (Fed. Cir. 2011) (quoting Seachange Int'/, Inc. v. C-COR, Inc., 413
F.3d 1361, 1369 (Fed. Cir. 2005)).
Here, the claim-differentiation presumption is overcome by the patent's definition of
"ligase detection reaction." The '4 70 patent explicitly incorporates by reference patent
application WO 91/17239 to Barany, which in tum provides express definitions for a number of
terms, including ligase detection reaction. (D.I. 422 at A2191 11. 7-11) In defining ligase
detection reaction, the Barany application states: "'Ligase detection reaction (LDR)' refers to the
use of two adjacent oligonucleotides for the detection of specific sequences with the aid of a
thermophilic ligase with linear product amplification." (Id. at A2196 ll. 1-4 (emphasis added))
"When a document is 'incorporated by reference' into a host document, such as a patent, the
referenced document becomes effectively part of the host.document as if it were explicitly
contained therein." Telemac Cellular Corp. v. Topp Telecom, Inc., 247 F.3d 1316, 1329 (Fed.
Cir. 2001). When a patent's specification demonstrates that the patentee gave a "special
definition  to a claim term ... that differs from the meaning it would otherwise possess ... the
inventor's lexicography governs." Phillips, 415 F.3d at 1316. Therefore, the definition ofligase
detection reaction supplied by the Barany application, subsequently incorporated by reference
into the '4 70 patent, controls.
Accordingly, the Court will adopt the R&R's constructions of "ligase detection reaction,"
"ligase detection reaction cycles," and "suitable for ligation together." 7
Illumina's Motion for Leave to Amend
The R&R recommends that the Court grant Illumina' s motion for leave to amend its
answer and counterclaims to allege inequitable conduct before the Patent and Trademark Office
with respect to the prosecution of the LDR-PCR patents. (D.I. 451)
The parties disagree on the standard of review to be applied. The Court reviews
The latter two terms, "ligase detection re~ction cycles" and "suitable for ligation
together" will be construed as: "cycles comprising at least the following steps: denaturation,
hybridization, and ligation, with the denaturation step occurring at the beginning or the end" and
"able to be ligated together only when hybridized adjacent to one another on the target nucleotide
dispositive motions de novo, see 28 U.S.C. § 636(b)(l)(C); Fed. R. Civ. P. 72(b)(3), while nondispositive motions are modified or set aside only when clearly erroneous or contrary to law, see
28 U.S.C. § 636(b)(l)(A); Fed. R. Civ. P. 72(a). "Under ordinary circumstances a motion to
amend a complaint is 'a pretrial matter not dispositive of a claim or defense of a party' within the
purview of Fed. R. Civ. P. 72(a)." Pagano v. Frank, 983 F.2d 343, 346 (1st Cir. 1993); see also
Cont'lCas. Co. v. DominickD'Andrea,1nc., 150F.3d245,251 (3dCir.1998) (citingPagano
approvingly); Smith v. State ofDelaware, 2009 WL 2175635, at *1 n.1 (D. Del. July 21, 2009)
("Motions for leave to amend pleadings are typically treated as 'non-dispositive' applications
within the pretrial powers of a magistrate judge on referral."). Therefore, the Court will review
any factual findings for clear .error. See 28 U.S.C. § 636(b)(l)(A); Fed. R. Civ. P. 72(a). Legal
conclusions, however, will be.reviewed de novo. See Haines v. Liggett Grp., Inc., 975 F.2d 81,
91 (3d Cir. 1992) ("[T]he phrase 'contrary to law' indicates plenary review as to matters of
law."); Eisai Co. v. Teva Pharm. USA, Inc., 629 F. Supp. 2d 416, 424 (D.N.J. 2009) ("[A]
magistrate judge's legal conclusions on a non-dispositive motion will be reviewed de novo.");
Doe v. Hartford Life &Accident Ins. Co., 237 F.R.D. 545, 548 (D.N.J. 2006); Lo Bosco v. Kure
Eng'g Ltd., 891 F. Supp. 1035, 1037 (D.N.J. 1995).
Cornell does not challenge any of the factual findings made by Judge Thynge in
recommending that Illumina's motion to amend be granted. (See D.I. 462) For example, Cornell
does not dispute any of the timing facts on which Judge Thynge relied in finding that Illumina
acted diligently and therefore satisfied-Rule 16(b). (See D.I. 451 at 9-12) Nor does Cornell
challenge the findings that support the conclusion that Rule l 5(a) is met, such as that Illumina
did not unduly delay and that Cornell will not face undue prejudice. (See id. at 12-13)
Cornell objects solely tq Judge Thynge's futility analysis. (See D.I. 462) Determining
whether a motion to amend would be futile requires the Court to apply "the same standard of
legal° sufficiency as under Rule 12(b)(6)." Roquette Freres, 2009 WL 1444835, at
determination, whether a claim survives a l 2(b)( 6) motion, is a "purely legal question." Barefoot
Architect, Inc. v. Bunge, 632 F.3d 822, 835 (3d Cir. 2011); see also SB Charles Alan Wright &
Arthur R. Miller, Federal Practice and Procedure § 1357 (3d ed. 2004 & Supp. 2016) ("[T]he
motion to dismiss under [Rule 12(b)] subdivision (6) raises only an issue of law"). Therefore,
the Court will review de nova the determination that Illumina's motion would withstand a
motion to dismiss and, therefore, is not futile. See Maiden Creek Assocs. v. U.S. Dep 't of
Transp., 823 F.3d 184, 189 (3d Cir. 2016) ("[A]lthough we review a denial ofleave to amend for
abuse of discretion, we review the District Court's determination that the amendment would be
futile de nova.").
Having reviewed Cornell's objections de nova, the Court SUSTAINS Cornell's
objections and REJECTS the R&R. Illumina's motion for leave to amend (D.I. 405) is DENIED.
"[A] pleading of inequitable conduct under Rule 9(b) must include sufficient allegations
of underlying facts from which a court may reasonably infer that a specific individual (1) knew of
the withheld material information or of the falsity of the material misrepresentation, and
(2) withheld or misrepresented this information with a specific intent to deceive the PTO."
Exergen, 575 F.3d at 1328-29. "A reasonable inference is one that is plausible and that flows
logically from the facts alleged, including any objective indications of candor and good faith."
Id. at 1329 n.5. Cornell argues that, considering the objective indications of candor and good
faith in this case, it is not reasonable to infer that the applicants and their counsel intended to
deceive the PTO. Cornell also argues that the statement on which Illumina's claim relies could
not be found to have been material to the PTO' s issuance of the patent.
Illumina' s inequitable conduct claim is based on a single inartful sentence in the
prosecution history of the '470 patent. (Tr. at 74, 85) The PTO initially rejected claims in the
'156 application - which later became the '4 70 patent - in light of three references. (D .I. 406 Ex.
A at if 19) The applicants submitted a declaration to swear behind those references, stating:
"Prior to June 22; 1994, we conceived and diligently reduced to practice, in the United States,
the invention claimed in the above-identified patent application." (Id. at if 21 (e) (emphasis
Cornell concedes that reduction to practice did not take place before June 22, 1994; only
conception did. (Tr. at 72-73) Consequently, in Illumina's view, because "the applicants were
aware that reduction to practice did not take place prior to June 22, 1994 and that the applicants'
declaration did not include actual dates of acts of diligence, ... the applicants affirmatively
misrepresented the inventors' reduction to practice and diligence with a false or misleading
declaration." (D .I. 406 Ex. A at if 21 (I)) Cornell counters that what the sentence in the
declaration was intended to convey was that the applicants conceived before June 22, 1994,. and
thereafter subsequently diligently reduced to practice. Thus, any misrepresentation was, at
worst, an inadvertent result of an inartfully-drafted sentence, not the result of intentional
The Court concludes that it is not reasonable to infer from the applicants' statement that
the applicants intended to mislead or deceive the PTO into believing that the applicants had both
conceived and reduced to practice before the critical date. Instead, the more plausible reading is
that the applicants intended to convey to the PTO that they had conceived the invention prior to
June 22, 1994, and had thereafter diligently reduced it to practice. This latter representation (if
true) would be sufficient to enable applicants to swear behind the prior art references the
Examiner had cited in rejecting the claims. See Perfect Surgical Techniques, Inc. v. Olympus
Am., Inc., 841F.3d1004, 1007 (Fed. Cir. 2016). In the Court's view, at worst what occurred is
that the drafter of the declaration inadvertently omitted a word such as "thereafter" or
"subsequently" or "later"before the phrase "reduced to practice."
Objective indications support Cornell's reading of the declaration statement. Had the
applicants been intentionally trying to deceive the PTO into believing that reduction to practice
had taken place before the critical date, the applicants could have said simply that, \\'ithout
making any reference to conception or diligence. Reduction to practice before the critical date,
alone, is sufficient to antedate references. See Loral Fairchild Corp. v. Matsushita Elec., 266
F.3d 1358, 1361 (Fed. Cir. 2001); see also D.I. 406 Ex. A at ifil 21(b), (c)) The concepts of
conception and diligence are relevant only when reduction to practice takes place after the
critical date. (D.I. 406 Ex. A at ii 21(b)) Hence, the declaration's use of the terms conception
and diligence, in addition to reduction to practice, strongly suggests that the applicants were not
attempting to antedate references on the basis of reduction to practice before the critical date but,
instead, were stating that they had conceived before the critical date and subsequently diligently
reduced to practice.
This reading of the declaration is further supported by the amendment which was
accompanied by the declaration. The amendment states: "In particular, prior to June 22, 1994,
applicants conceived, in the United States, the invention claimed in the above-identified patent
application, and diligently reduced it to practice (Barany et al. Declaration~ 2)." (O.I. 429 Ex. C
at 1258) ·Stated this way, applicants made even clearer that they were asserting that they had
conceived before June 22, 1994, and then diligently reduced to practice. The amendment goes on
to state that "[e]vidence of this conception prior to June 22, 1994, is provided," again reinforcing
that applicants' intent was to state that they conceived before the critical date and thereafter
diligently reduced to practice. (Id.; Ex. D at 1261)
Illumina notes that the declaration supplies no dates to prove diligence (D .I. 406 Ex. A at
~ 2l(f)), arguing that the lack of dates supports inferring deceptive intent. 8 The lack of dates,
however, does not detract from the fact that the declaration and accompanying amendment are
replete with references to conception and diligence - references that would have been wholly
unnecessary were applicants relying on reduction to practice. Moreover, the lack of an express
showing of diligence only reaffirms that the declaration is not drafted in an ideal manner;
applicants would need to provide additional information to prove their assertion of diligence.
Still, however, the declaration does not provide a sufficient factual basis to support an inference
of intent to deceive. ·
Illumina points to the depositions of inventors Francis Barany and Matthew Lubin and of
attorney Michael Goldman as further support for an inference of deceptive intent. Illumina
claims, based on these depositions, that "Applicants Francis Barany and Matthew Lubin now
admit that they knew, at the time that the applicants signed the § 1.131 declaration that was
subsequently filed, that the claimed LDRIPCR methods had not been reduced to practice '[p]rior
As n'?ted in the R&R, the Manual of Patent Examinillg Procedure requires that when
relying on conception and diligent reduction to practice "the actual dates of acts relied on to
establish diligence must be provided." (D .I. 451 at 18)
to June 22, 1994,' and that the laboratory work relating to the claimed LDR/PCR methods· did
not begin until July 11, 1994," and further that "Michael Goldman now admits that he knew, at
the time of filing the Amendment and the accompanying § 1.131 declaration, that the claimed
LDR/PCR methods had not been reduced to practice '[p]rior to June 22, 1994."' (Id. at ifif 20(e),
(f)) These statements, taken as true, do not strengthen Illumina's position. The most reasonable
inference to be drawn from the inventors' and prosecuting attorney's statements that there was no
reduction to practice before June 22, 1994 is that the declaration sentence was inartfully drafted,
in that it could be misunderstood to contradict the fact that reduction to practice took place after a
(legally sufficient) pre-critical date conception.
Further, in other portions of the depositions, Drs. Barany and Lubin testified that they
believed the declaration was true at the time they filed it (see DJ. 429 Ex. Hat 27-28, 58; Ex. F
at 412), and Mr. Goldman testified that he took steps to ensure that the inventors understood the
declaration before they signed it (see id. Ex.Eat 103-104). As Illumina relies on the depositions
in the proposed amended counterclaim asserting inequitable conduct, the Court may consider
these statements. See Brody v~ Hankin, 145 F. App'x 768, 772 (3d Cir. 2005) (stating that when
plaintiff mentions information from document in complaint, district court may consider that
document, including deposition transcript, in evaluating Rule 12(b)(6) motion) (citing Pension
Benefit Guar. Corp. v. White, 998 F.2d 1192, 1196 (3d Cir. 1993)). The inventors' belief that the
. declaration was true when submitted to the PTO further negates any inference of an intent to
deceive the PTO. See Vita-Mix Corp. v. Basic Holding, Inc., 581F.3d1317, 1332 (Fed. Cir.
2009) (affirming finding of no deceptive intent where inventor "believed the statement to be true
at the time that he made it"); Juicy Whip, Inc. v. Orange Bang, Inc., 292 F.3d 728, 745 (Fed. Cir.
The Court also agrees with Cornell that Illumina' s contentions regarding materiality are
futile. Illumina insists that "'a false ... declaration is per se material.'~' (D .I. 4 74 at 6 n.2
(quoting Outside the Box Innovations, LLC v. Travel Caddy, Inc., 695 F.3d 1285, 1294 (Fed.
Cir. 2012)) But here Illumina's allegation that the declaration was false is not based on a
reasonable inference. Additionally, Illumina does not suggest that the applicants were not
diligent or that they "could not have provided the dates of their diligent reduction to practice if
the examiner had asked for them" (D.I. 462 at 10 n.5), detracting from any inference that the
applicant's declaration was but-for material. See generally Network Signatures, Inc. v. State
Farm Mut. Auto. Ins. Co., 731 F.3d 1239, 1242 (Fed. Cir. 2013).
Accordingly, Illumina's inequitable conduct claims would not survive a motion to dismiss
and are, therefore, futile. Therefore, the Court will deny Illumina' s motion to amend.
The Court construes the disputed terms as explained above and will deny Illumina's
motion to amend its answer and counterclaims. An Order consistent with this Memorandum
Opinion follows . .
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