Enzo Biochem, Inc. et al v. Applera Corp. et al

Filing 573

ORDER: Plaintiffs' Motion 566 for Entry of Judgment on the Current Jury Verdict is DENIED. Defendants' Motion 568 for Summary Judgment is GRANTED. Judgment is entered in Defendants' favor. The Clerk is directed to close this case. Signed by Judge Janet Bond Arterton on 2/22/16. (Harris, J)

UNITED STATES DISTRICT COURT
DISTRICT OF CONNECTICUT
ENZO BIOCHEM, INC., ENZO LIFE SCIENCES,
INC. and YALE UNIVERSITY,
Civil No. 3:04cv929 (JBA)
Plaintiffs,
v.
February 22, 2016
APPLERA CORP. and TROPIX, INC.,
Defendants.
RULING ON PLAINTIFFS’ MOTION FOR ENTRY OF JUDGMENT AND
DEFENDANTS’ MOTION FOR SUMMARY JUDGMENT
This twelve-year old case is before this Court after a second remand from the
Federal Circuit which vacated this Court’s finding of infringement and directed the Court
to “determine, consistent with” the Federal Circuit’s analysis, “whether the accused
product infringes.” Plaintiffs Enzo Biochem, Inc., Enzo Life Sciences, Inc. and Yale
University (“Enzo”) now move [Doc. # 566] for entry of judgment on the current jury
verdict, and Defendants Applera Corp. and Tropix, Inc. (“Applera”) move [Doc. # 568]
for summary judgment. For the following reasons, Plaintiffs’ motion is denied and
Defendants’ motion is granted.
I. Background
The parties’ familiarity with the background of this case is presumed. Briefly,
Plaintiffs initiated this patent infringement suit in 2004, accusing Defendants of
infringement of six patents, including United States Patent Nos. 5,476,928 (“‘928 patent”),
5,449,767 (“‘767 patent”), and 5,328,824 (“‘824 patent”), which cover various techniques
and processes for detecting the presence of a particular strand of nucleic acids (i.e., DNA
or RNA) in a sample. (See Compl. [Doc. # 1].) Relevant here, the ‘824, ‘928, and ‘767

patents disclose the invention of non-radioactive labeling and specify formation of a
complex of hybridized 1 nucleotides and a detectable polypeptide.
Specifically, the ‘767 and ‘824 patents claim in part: “A method of detecting the
presence or absence of a nucleic acid in a sample which comprises the steps of (a)
contacting under hybridizable conditions said sample with at least one compound
comprising the structure [DIAGRAM] wherein A comprises at least three carbon atoms
and represents at least one component of a signaling moiety capable of producing a
detectable signal . . . .” (Claim Construction Ruling [Doc. # 137] at 5 (quoting ‘824 Pat.
30:49–31:29).) The parties disputed whether this language should be read to encompass
both direct and indirect identification systems or only indirect systems. 2 On October 13,
2006, following a Markman hearing, this Court issued its Claim Construction Ruling
[Doc. # 137], finding in Plaintiffs’ favor that the patents cover both direct and indirect
detection.

1

“Hybridization” is “the binding of two separate, complementary strands of
nucleic acids to form nucleic acid hybrids.” (Claim Constr. Ruling at 1 n.1.)
2

As the Federal Circuit explained: “[b]ecause hybridization occurs in a predictable
manner between complementary strands [of nucleic acids], it is possible to detect the
presence of a nucleic acid of interest in a sample. For example, a chemical entity, called a
‘label,’ can be attached to or incorporated into a nucleic acid strand of a known sequence,
called a ‘probe,’ which will hybridize with a complementary sequence of interest, called a
‘target.’ Once the probe is hybridized with the target, a detectable signal is generated
either from the label itself (referred to as ‘direct detection’) or from a secondary chemical
agent that is bound to the label (referred to as ‘indirect detection’). If a signal is detected
from the sample after all unhybridized probes have been removed, detection of the signal
implies the presence of a target in that sample.” Enzo Biochem Inc. v. Applera Corp. (Enzo
I), 780 F.3d 1149, 1151 (Fed. Cir. 2015).
2

Thereafter, on September 6, 2007, the Court entered summary judgment [Doc.
# 261] in favor of Defendants. Plaintiffs appealed, and in a March 26, 2010 decision, the
Federal Circuit reversed this Court’s judgment that the ‘767, ‘824, and ‘928 patents are
invalid for indefiniteness and that the ‘767 and ‘824 patents are invalid as anticipated, and
affirmed the Court’s judgment that the ‘928 patent is invalid as anticipated. Enzo Biochem
Inc. v. Applera Corp. (Enzo II), 599 F.3d 1325 (Fed. Cir. 2010). On remand, this Court
denied [Doc. # 418] Applera’s motion for summary judgment on infringement and
equitable defenses. Plaintiffs waived their claims for infringement of the ‘824 patent and
limited their assertion of the ‘767 patent to claims 1, 3 8, 4 67, 5 68, 6 and 70, 7 and the case
proceeded to trial.
Following seven days of evidence, the jury returned a verdict finding that
Defendants’ accused BigDye and dRhodamine dye-terminator products directly

3

Claim 1 is an independent claim, which reads in relevant part: “An oligo- or
polynucleotide containing a nucleotide having the structure [Diagram] . . . wherein A
comprises at least three carbon atoms and represents at least one compound of a
signaling moiety capable of producing a detectable signal . . . .” (‘767 Pat., Ex. 3 to Stone
Decl. in Supp. Def.’s Mot. Summ. J. [Doc. # 568-2] 30:48–68.)
4

Claim 8 covers: “An oligo- or polynucleotide of claim 1 wherein the linkage
group includes the moiety –CH2–NH–.” (Id. 31:36–37.)
5

Claim 67 states: “An oligo- or polynucleotide of claim 1 . . . wherein A comprises
an indicator model.” (Id. 36:42–44.)
6

Claim 68 reads: “An oligo- or polynucleotide of claim 67 wherein said indicator
model is fluorescent, electron dense, or is an enzyme capable of depositing insoluble
reaction products.” (Id. 36:44–47.)
7

Claim 70 covers: “”An oligo- or polynucleotide of claim 68 wherein the
fluorescent indicator molecule is selected from the group consisting of fluorescein and
rhodamine.” (Id. 36:51–54.)
3

infringed, and induced customers to infringe, claims 1, 8, 67, 68, and 70 by Defendants’
manufacture, use, or sale of their reagent products and sales of DNA sequencing
instruments. (See Jury Verdict [Doc. # 476].) The jury rejected Defendants’ invalidity
defenses of lack of written description, lack of enablement, and anticipation, and issued
two advisory findings that (1) Enzo had not unreasonably delayed in filing suit, and (2)
ABI was not materially prejudiced by the delay in filing this lawsuit. (Id.) The jury
awarded Enzo $48,587,500.00 in reasonable royalty damages. (Id.) Judgment [Doc. # 544]
entered in Plaintiffs’ favor on January 7, 2014. Defendants appealed.
On appeal, Defendants raised three issues: (1) “[w]hether the finding of
infringement should be reversed because, contrary to the district court’s claim
construction, the ‘767 patent does not cover the directly detectable terminator nucleotides
of the accused products”; (2) “[w]hether, assuming the ‘767 patent covers direct
detection, the patent is invalid for lack of written description because nothing in the
specification describes possession of directly detectable nucleotides, and the only
disclosure of such nucleotides is prior art which presented problems overcome by the
described indirectly detected nucleotides”; and (3) “[w]hether, assuming the ‘767 patent
covers directly detectable nucleotides, the patent is invalid for lack of enablement because
nothing in the specification explains how to make or use a directly detectable nucleotide
other than certain prior art detection systems, which presented problems overcome by
the enabled indirect detection methods.” (Defs.’ Opening Br., Ex. 1 to Stone Decl. at 16. 8)

8

All page numbers cited in this Ruling correspond to ECF’s page numbering,
found in the header on each page.
4

The Federal Circuit began by reciting the language of claim 1, which it stated was
“representative.” Enzo II, 599 F.3d at1152. The entirety of the court’s discussion then
focused on construing the language of claim 1, at the end of which the court concluded
that “as claim 1 is limited to indirect detection by its own plain meaning, it would be
inappropriate to use the doctrine of claim differentiation to broaden claim 1 to include a
limitation imported from a dependent claim, such as direct detection.” Id. at 1157. The
court therefore held that this Court “erred in construing the disputed claims of the
patent-in-suit to cover both direct and indirect detection,” and reversed this Court’s
“claim construction, vacate[d]” the Court’s “finding of infringement,” and “remand[ed]”
to the Court “with instruction to determine, consistent with the analysis in this opinion,
whether the accused product infringes.” Id.
II. Discussion
The parties’ motions raise several distinct issues pertaining to claims 67, 68, and
70 on the one hand, and claims 1 and 8 on the other. These arguments are discussed in
turn below.
A. Claims 67, 68, and 70
With respect to claims 67, 68, and 70, the parties’ briefs attempt to reason through
the Federal Circuit’s somewhat cryptic mandate and its effect on claims 67, 68, and 70.
The confusion arises because while Defendants raised the issue on appeal of whether any
of the claims of the ‘767 patent cover direct detection (in Defendants’ words, whether the
“‘767 patent . . . cover[s] the directly detectable terminator nucleotides of the accused
products” (Defs.’ Opening Br. at 16)), the Federal Circuit’s opinion analyzes only the
language of claim 1, before concluding that “[t]he district court erred in construing the
5

disputed claims of the patent-in-suit to cover both direct and indirect detection,” Enzo II,
599 F.3d at 1157 (emphasis added).
Plaintiffs contend that the Court should enter judgment in its favor on claims 67,
68, and 70 because the jury already found that the accused products infringed those
claims, and that finding is not affected by the Federal Circuit’s decision. (See Pls.’ Mem.
Supp. Mot. for Entry of J. [Doc. # 567] at 13.) According to Plaintiffs, the Federal Circuit
construed only claim 1, leaving the scope of claims 67, 68, and 70 unchanged. (See id.)
Although Plaintiffs acknowledge that under this theory, claims 67, 68, and 70 are broader
than claim 1, 9 from which they depend, in violation of 32 U.S.C. § 112 ¶ 4, 10 they argue
that Defendants have waived this defense by not raising it earlier, and that if the Federal
Circuit thought otherwise, it would have remanded for a determination of invalidity
rather than of infringement. (See id. at 14–16.) Indeed, Plaintiffs assert, in light of the
Federal Circuit’s mandate to determine “whether the accused product infringes,” Enzo II,
599 F.3d at 1157, this Court does not have the discretion to take up invalidity (Pls.’ Mem.
Supp. at 23–27).
As further support for their reading of the Federal Circuit’s decision, Plaintiffs
note that while the Federal Circuit took issue with this Court’s finding “that dependent
claims 67, 68, and 70 . . . involved direct detection and therefore independent claim 1

9

The Federal Circuit construed claim 1 to cover indirect detection while under
Plaintiffs’ construction, claims 67, 68, and 70 cover direct detection.
10

Under § 112 ¶ 4, “a claim in dependent form shall contain a reference to a claim
previously set forth and then specify a further limitation of the subject matter claimed. A
claim in dependent form shall be construed to incorporate by reference all the limitations
of the claim to which it refers.”
6

must not be limited to indirect detection,” Enzo II, 599 F.3d at 1156, on the grounds that
“dependent claims cannot broaden an independent claim from which they depend,” id.,
under Defendants’ interpretation, the Federal Circuit will have “‘construe[d] away’ that
very limitation from the dependent claims it cited as having it” (Pls.’ Reply [Doc. # 571] at
2–3).
Plaintiffs argue that their reading best comports with Federal Circuit precedent,
citing Pfizer, Inc. v. Ranbaxy Labs. Ltd., in which the Federal Circuit held that where a
dependent claim and the claim upon which it depends “deal with non-overlapping
subject matter,” the dependent claim should be held invalid, rather than be construed to
cover the same subject matter as the claim upon which it depends. 457 F.3d 1284, 1291–
92 (Fed. Cir. 2006). As Plaintiffs put it, “[i]nstead of holding that a circle is a square, the
Court accepted that a circle is indeed a circle and held the claim invalid for improper
dependency.” (Pls.’ Reply at 5.)
Defendants, for their part, urge the Court to “enter judgment of noninfringement” in their favor because “[t]he Federal Circuit held that none of ‘the claims at
issue’ in this case covers direct detection” and there is no dispute that the accused
products do not infringe a claim limited to indirect detection. (Defs.’ Mem. Supp. Mot.
Summ. J. [Doc. # 568-1] at 7.) In support of their reading of the Federal Circuit’s
decision, Defendants note that “[f]rom the first page of the Federal Circuit’s decision to
the last, the court treated the asserted claims collectively” (id. at 15), and discussed the
language of claim 1 only after “explaining that ‘[c]laim 1 is representative’ of the asserted
claims’” (id. at 12 (quoting Enzo II, 599 F.3d at 1152); see Defs.’ Opp’n Mot. for Entry J.
[Doc. # 570] at 8–9). Moreover, in its conclusion, the court specifically held that “‘[t]he
7

district court erred in construing the disputed claims of the patent-in-suit to cover both
direct and indirect detection,’” again using the plural. (Defs.’ Mem. Supp. at 15 (quoting
Enzo II, 599 F.3d at 1157) (emphasis in Defs.’ Mem. Supp. but not in original).)
Like Plaintiffs, Defendants call the Court’s attention to the Federal Circuit’s
decision in Pfizer, but in support of the opposite conclusion. (Id. at 19.) Defendants
maintain that if anything, Pfizer “demonstrate[s] the rigidity of the rule” that “‘a
dependent claim cannot be broader than the claim from which it depends’” (id. (quoting
Alcon Research Ltd. v. Apotex, Inc., 687 F.3d 1362, 1367 (Fed. Cir. 2012)), even if “the
dependent claim covers ‘what might otherwise have been patentable subject matter” (id.
(quoting Pfizer, 457 F.3d at 1292)). For this reason, Defendants argue, the Federal Circuit
would not have interpreted the dependent claims in a way that made them broader than
the claim upon which they depend. (Id. at 18; see Defs.’ Opp’n at 9.)
Finally, Defendants argue that the Federal Circuit never addressed their
alternative argument that if the ‘767 patent covers direct detection, it is invalid for lack of
written description or for lack of enablement, indicating to them that the court was not
holding that the patent covers direct detection. (Defs.’ Mem. Supp. at 16; Defs.’ Opp’n at
9–10.)
Although neither party’s arguments successfully eliminate all ambiguity from the
Federal Circuit’s ruling, the Court finds Defendants’ interpretation to be the more
plausible of the two. It would be odd indeed for the Federal Circuit to continuously use
the plural “claims” if it intended to refer only to claim 1. Further, although the conclusion
Defendants urge does seem to be in tension with Pfizer’s warning that courts “should not
rewrite claims to preserve validity,” 457 F.3d at 1292 (internal quotation marks omitted),
8

the Court can conceive of no reason why the Federal Circuit would not have addressed
Defendants’ alternative arguments if its holding was not that all of the claims cover solely
indirect detection. The Court therefore adopts Defendants’ interpretation of the Federal
Circuit’s opinion, holding that the Federal Circuit intended its ruling to construe all of
the claims at issue to cover only indirect detection. Because there is no dispute that the
accused products utilize direct detection, and Plaintiffs do not claim infringement under
a doctrine of equivalents theory with respect to claims 67, 68, and 70, judgment is entered
in Defendants’ favor on those claims. 11
B. Claims 1 and 8
Turning to claims 1 and 8, both parties agree that “there is no literal infringement
under the Federal Circuit’s construction.” (Pls.’ Opp’n Defs.’ Mot. Summ. J. [Doc. # 569]
at 5.) Nonetheless, “Plaintiffs submit . . . that those claims are—even under that
construction—infringed under the doctrine of equivalents.” (Id.)
As a preliminary matter, the parties dispute whether Plaintiffs waived this
argument by “drop[ping] [their] infringement theory that the accused products could be
covered by claims limited to indirect detection” after the Court issued the Claim
Construction Ruling. (Defs.’ Mem. Supp. at 8.) Defendants contend that “[i]f Enzo
believed . . . that direct detection was an equivalent of indirect detection, it could have
disclosed its view, compiled any evidence in support, offered expert testimony, and
sought to moot the claim-construction issue that it knew was heading for post-trial
appellate review.” (Id.) However, as Plaintiffs argue in response, and as Defendants
11

For this reason, the Court does not reach Defendants’ contention that the claims
are invalid, nor Plaintiffs’ assertion that Defendants have waived this defense.
9

appear to acknowledge in their Reply, 12 when the Federal Circuit addressed this very issue
in Exxon Chemical Patents, Inc. v. Lubrizol Corp., 137 F.3d 1475 (Fed. Cir. 1998), it held
that in circumstances similar to these, the plaintiff was not barred from raising a doctrine
of equivalents argument, writing:
Contrary to Lubrizol’s suggestion, Exxon cannot be charged with having
abandoned its doctrine-of-equivalents theory of liability by not submitting
it to the jury or raising it on the previous appeal. Once the district judge
construed the claim language in Exxon’s favor, the doctrine-of-equivalents
issue in the case became moot. Exxon could not realistically be expected to
request alternative jury instructions asking for an advisory verdict on
whether the patent would be infringed under the doctrine of equivalents
on Lubrizol’s proposed claim construction. Nor could Exxon, as appellee,
have been expected to defend the judgment in its favor on the basis of a
theory of liability that was never given to the jury. The question whether
there could be doctrine-of-equivalents infringement under the claim
construction adopted by this court became a critical issue in the case only
after this court's decision on appeal. For that reason, this court did not
address the merits of Exxon’s claim that it is entitled to a new trial on
infringement under the doctrine of equivalents, and the district court
therefore erred in concluding that it was barred by this court's mandate
from considering Exxon’s new trial motion.
Id. at 1478–79 (internal citations omitted). For substantially the same reasons as recited
by the Federal Circuit in Exxon, this Court finds that Plaintiffs are not barred from
asserting a doctrine of equivalents theory.

12

In their Reply, rather than continuing to pursue the theory that Plaintiffs waived
the doctrine of equivalents argument by failing to raise it earlier, Defendants contend that
“[t]he Court should bar Enzo from asserting the doctrine of equivalents because Enzo
waived that argument by not asserting it in its own motion.” (See Defs.’ Reply [Doc.
# 572] at 9.) This argument, however, for which Defendants cite no authority, does not
appear to have any basis in law. The Court is aware of no rule of law prohibiting a party
from arguing that summary judgment should not be entered in its opponent’s favor on a
particular issue while not seeking judgment in its own favor on that issue.
10

To infringe by equivalence, an accused product or process must “contain elements
identical or equivalent to each claimed element of the patented invention.” WarnerJenkinson Co. v. Hilton Davis Chem. Co., 520 U.S. 17, 40 (1997). “A finding of
infringement under the doctrine of equivalents requires a showing that the difference
between the claimed invention and the accused product or method was insubstantial or
that the accused product or method performs the substantially same function in
substantially the same way with substantially the same result as each claim limitation of
the patented product or method.” AquaTex Indus., Inc. v. Techniche Sols., 479 F.3d 1320,
1326 (Fed. Cir. 2007). The “function, way, result inquiry focuses on an examination of the
claim and the explanation of it found in the written description of the patent.” Id.
(internal quotation marks omitted).
Plaintiffs contend that summary judgment should not be granted in Defendants’
favor as to claims 1 and 8 because there is a genuine dispute of material fact as to whether
indirect and direct detection are insubstantially different such that the accused products
infringe the ‘767 patent by equivalence. (See Pls.’ Opp’n at 5, 11–12.) Relying on the
declaration of their expert, Dr. Richard Sinden, Plaintiffs argue that:
among the problems addressed in the ‘767 patent are those directed to
signal strength and amplification. To detect labeled nucleotides, the
“signal” from the label must be strong enough to come within the
detection threshold of whatever method is applied to detect it. In order to
do that, these signals are typically “amplified” by a variety of techniques,
several of which are disclosed in the patent. One of these techniques is
indirect detection, i.e., reacting the “A” of claim one with something that
yields a stronger signal. Examples of that “something” include antibodies
and avidin, the latter of which was known to form strong complexes with
biotin, a preferred example of indirectly detection “A.” . . .

11

Much like the patent’s proposed addition of avidin to amplify the signal of
a biotinated nucleotide, the accused products also employ materials
extraneous to the labeled nucleotides to amplify their signal yield. All of
the accused BigDye and dRhodamine kits include polymerase chain
reaction (PCR) enzymes. These enzymes amplify the fluorescent signal
from DNA sequences labeled with the dye terminators by increasing the
concentration of those sequences. The differences between this
amplification and the avidin/biotin amplification of the patent’s preferred
example is that it works by increasing the concentration of molecules
producing the signal rather than the signal strength for an individual
molecule. . . . As to the indirectly-detectable “A” of claim one, the use of
PCR to amplify the signal of DNA sequences labeled by the fluorescent dye
terminators in the accused products serves the same function (to make the
signal detectable by the methodology employed), in ways that differ
insubstantially (increasing concentration vs. increasing strength), to yield
the identical result (a detectable signal).
(Id. at 11–12 (internal citations omitted).)
Defendants respond that no reasonable jury could find that indirect detection is
insubstantially different from direct detection, and summary judgment should therefore
be granted in their favor. Specifically, they argue that: (1) Dr. Sinden’s theory is “scientific
gibberish,” as the biotin in the invention “gives off no signal;” rather, “[i]t is the avidin
that is detected, after complexing with biotin,” and therefore, contrary to Dr. Sinden’s
declaration, avidin does not “amplify a detectable signal from biotin” (Defs.’ Reply at 9–
10); (2) the ‘767 patent does not claim and did not invent signal-amplification techniques
(id.); and (3) there are fundamental differences between direct and indirect detection (id.
at 11).
The Court finds Defendants’ arguments persuasive. Consistent with the Federal
Circuit’s understanding of the patent as describing “how ‘A,’ a biotin, iminobiotin, or
lipoic acid, forms a detectable unit, i.e., a signaling moiety, upon interaction with avidin
12

or antibodies,” Enzo II, 599 F.3d at 1155, Dr. Sinden himself testified that “[b]iotin in
itself doesn’t generate a signal that’s detectable” (Sinden Dep., Ex. 1 to Defs.’ Reply at 7).
Because that is so, it would not be accurate to describe indirect detection as a method of
signal amplification.
Nor does the patent describe it this way. Rather, the patent describes its method of
indirect detection as a superior means of detection as compared to direct detection, with
“‘detection capacities equal to or greater than products which utilize’” direct detection.
Enzo II, 599 F.3d at 1155 (quoting ‘767 Pat. 3:5–13). Although the specification does
mention signal amplification in a few places (see, e.g., ‘767 Pat. 22:23–54), as Dr. Sinden
acknowledged in his deposition, the patent does not disclose techniques for signal
amplification, but rather “utilize[s] technologies that have been around that do amplify
signal” (Sinden Dep. at 9). In Dr. Sinden’s words, the claimed invention is not directed so
much at improving the “strength of the signal” as improving methods of “signal
generation and detection.” (Id.)
As Defendants aptly note, “[a]n alternative to the claimed invention specifically
criticized in the specification for problems that the invention purports to overcome
cannot be an ‘equivalent’ to the invention itself.” (Defs.’ Mem. Supp. at 28.) Indeed, the
Federal Circuit has left no doubt that methods or structures “[s]pecifically identified,
criticized, and disclaimed” in a specification cannot later be relied upon as equivalents.
Gaus v. Conair Corp., 363 F.3d 1284, 1291 (Fed. Cir. 2004) (internal quotations marks
omitted). Because “the specification’s only discussion of direct detection, here radioactive
labeling, was exclusively in the context of discussing how indirect detection is a superior
method,” and “[t]he specification not only discusses the limitations and drawbacks of
13

using radioactive labeling, but states that the claimed compounds can be used ‘as an
alternative to radioisotopes for detection and localization,’” Enzo II, 599 F.3d at 1155
(quoting ‘767 Pat. 3:5–13), Plaintiffs cannot now claim that indirect and direct detection
are insubstantially different, and no jury could so find. 13 Summary judgment is therefore
granted in Defendants’ favor on claims 1 and 8.
III. Conclusion
For the foregoing reasons, Plaintiffs’ Motion [Doc. # 566] for Entry of Judgment
on the Current Jury Verdict is DENIED, and Defendants’ Motion [Doc. # 568] for
Summary Judgment is GRANTED. Judgment is entered in Defendants’ favor. The Clerk
is directed to close this case.

IT IS SO ORDERED.
/s/
Janet Bond Arterton, U.S.D.J.
Dated at New Haven, Connecticut this 22nd day of February 2016.

13

Because the Court grants Defendants summary judgment on claims 1 and 8, it
does not reach Defendants’ contention that claim 1 does not cover mononucelotides. (See
Defs.’ Mem. Supp. at 27–30.)
14