Document ID: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-cand-3_03-cv-03779/USCOURTS-cand-3_03-cv-03779-4/pdf.json

Parties Involved:
Affymetrix, Inc.
Counter-defendant
Multilyte Ltd.
Counter-claimant

Document Text:

United States District Court

For the Northern District of California

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IN THE UNITED STATES DISTRICT COURT

FOR THE NORTHERN DISTRICT OF CALIFORNIA

AFFYMETRIX, INC., a Delaware corporation,

Plaintiff and Counterdefendant,

 v.

MULTILYTE LTD., a British corporation,

Defendant and Counterclaimant. /

No. C 03-03779 WHA

ORDER GRANTING 

SUMMARY JUDGMENT OF

NON-INFRINGEMENT UNDER

DOCTRINE OF EQUIVALENTS

INTRODUCTION

Pursuant to the order of May 17, 2005, plaintiff Affymetrix, Inc. now moves for

summary judgment of non-infringement under the doctrine of equivalents based on the claim

terms “binding agent” and “binding site.” This motion is GRANTED.

STATEMENT

Defendant Multilyte Ltd. is the assignee of the three patents-in-suit: United States

Patent Nos. 5,599,720 (“the ’720 patent”), 5,432,099 (“the ’099 patent”) and 5,807,755, (“the

’755 patent”). Affymetrix manufactures and sells DNA microarray systems which utilize

oligonucleotide probes to detect the presence of complementary target strands via hybridization. 

There is no dispute that the accused products, whether used for RNA analysis or DNA analysis,

only involve interactions between nucleic acids.

On February 22, 2005, the claim term “binding agent” was construed to mean “a

molecule used in an immunoassay that is capable of binding to an analyte and has an affinity

constant (measured at equilibrium) of 1013 liters/mole or less.” Because there was insufficient

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information in the record at that time, that order declined to rule whether nucleic acids and

oligonucleotides were “binding agents.”

At a status conference later held on March 3, 2005, however, Multilyte insisted that

explicitly including (or excluding) oligonucleotides from the definition of binding agent would

be “case dispositive.” Mr. Lex Brainerd, speaking on behalf of Multilyte, persuaded the Court

that a second round of claim construction would be worthwhile (March 3, 2005 Hearing Tr. at

3:13–23; 4:10–17; 7:14–18):

As we set forth in our portion of the status conference statement, the

whole issue of “binding agent” and its ultimate claim construction, which I

know you have left open for the reasons stated in your order, is really the

issue that is going to drive this case.

“Binding agent” appears in every claim of all three patents. A

resolution of the remaining claim construction issue, which you left open,

which is whether or not “binding agent” would capture or include nucleic

acids, in our opinion, it’s a, for want of a better word, kind of a

case-dispositive issue.

* * *

Very frankly, if we win, we are happy to go to trial November 7th. If

we lose, then I think the most efficient thing is for us to find some way to

enter into a stipulated judgment and take this matter to the Federal Circuit. 

Our goal here is to move forward as efficiently as possible. If we can take the

matter to trial, fine, so be it. If we have to seek relief elsewhere, then we

ought to know that as quickly as possible and we can efficiently go in that

direction. 

* * *

The most efficient way to move is to do that [further claim

construction on the term “binding agent”]. And then if we lose then, very

frankly, then we would, as indicated in our response to your request, the status

conference statement, we would probably find a way to enter some kind of a

stipulated judgment or some kind of a judgment and move on.

Based thereon, Multilyte was granted leave to file a motion for further claim

construction of “binding agent.” Meanwhile, Affymetrix was granted leave to file two motions

for summary judgment of non-infringement: (1) based on the phrases “determining the ambient

concentrations” and “loading a plurality of different binding agents . . . onto a support means”

and (2) based on the term “binding agent.” These motions were briefed simultaneously.

Another hearing was held on all three motions, at which the parties focused primarily on

the further claim construction of “binding agent.” As previously noted in another order, the

parties were expected to argue whether “binding agent,” as already defined, would include or

exclude oligonucleotides or other molecules comprised of nucleic acids. Instead, Multilyte took

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*

 The first claim-construction order had relied upon a representation by Multilyte’s counsel at oral

argument that the other types of binding agents referenced in the ’720 patent (i.e., binding proteins and receptor

preparations) were also molecules used in immunoassays (Feb. 16, 2005 Hearing Tr. at 32:18–25). In the

opening brief on Multilyte’s motion for further claim construction, however, counsel confessed that this was

scientifically inaccurate.

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advantage of the opportunity for further claim construction to move for reconsideration,

arguing that the “immunoassay” limitation had improperly restricted the invention to the

preferred embodiment, namely antibodies.*

On April 28, 2005, the Court re-construed the term “binding agent” to mean “a molecule

conventionally having one or at most two binding sites and an affinity constant (measured at

equilibrium) of 1013 liters/mole or less.” That order also construed the term “binding site,” as it

would be understood by a person of ordinary skill in the relevant art, to mean a structurally and

functionally distinct region of a protein. Contrary to Multilyte’s contentions, a non-scientific

definition of “binding site” — i.e., any site where binding occurs, such as the region within a

nucleic acid sequence recognized by a protein or protein complex — was explicitly rejected. 

Thus, the term “binding agent” was expressly defined to include certain molecules, but

exclude others:

To avoid any possible confusion, this order clarifies that this definition of

“binding agent” includes (but is not limited to) antibodies, binding proteins

and receptor preparations. On the other hand, this definition does not

encompass DNA, RNA, oligonucleotides or any other molecules comprised

solely of nucleic acids.

(Order Granting Multilyte’s Motion for Further Claim Construction and Re-Construing

“Binding Agent,” April 28, 2005, at 5:3–6). In a separate order, summary judgment of

non-infringement was also granted based on the phrases (1) “binding agent” and (2) “loading a

plurality of different binding agents . . . onto a support means,” the latter of which was

unopposed. Judgment was entered accordingly.

Contrary to its prior representation that a further round of claim construction would be

“case dispositive,” Multilyte then reversed field and sought yet more proceedings. Multilyte

moved to alter or amend the judgment, on the basis that even if the accused products did not

literally infringe, the Court “failed to consider” the question of infringement under the doctrine

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of equivalents. The doctrine of equivalents had never been raised by Multilyte in the

summary-judgment briefs or at the hearing. 

Nonetheless, Multilyte’s motion was granted. In an order dated May 17, 2005, the

Court expressly declined to engage in a third round of claim construction, but the case file was

re-opened and the parties were given the opportunity to brief the issue of infringement under the

doctrine of equivalents in light of the revised definition of “binding agent.”

ANALYSIS

Because reexamination proceedings for all three patents are still ongoing, any finding of

infringement would be premature because it is not yet known which claims, if any, will emerge

from the reexamination process. Summary judgment of non-infringement, in contrast, would be

appropriate if the Court finds that the accused products would not infringe no matter what

claims are issued. Here, the parties agree that the term “binding agent” will appear in any claim

that ultimately issues. As previously ruled, the accused products do not literally infringe the

“binding agent” limitation of the asserted claims. The question now is whether Affymetrix is

also entitled to a declaratory judgment that its products are non-infringing under the doctrine of

equivalents. This order finds in the affirmative.

An accused product that does not literally infringe upon the express terms of a patent

may nonetheless infringe under the doctrine of equivalents. See generally Warner-Jenkinson

Co., Inc. v. Hilton Davis Chem. Co., 520 U.S. 17 (1997). Regardless of whether the tripartite

“function-way-result” test or an “insubstantial differences” approach is used, the central inquiry

remains whether the accused product embodies each and every element of the claimed

invention, either literally or by an equivalent. Id. at 39–40. 

Yet, there are various legal limitations on the application of this doctrine. For example,

“if prosecution history estoppel would apply or if a theory of equivalence would entirely vitiate

a particular claim element, partial or complete judgment should be rendered by the court, as

there would be no further material issue for the jury to resolve.” Id. at 39 n.8 (emphasis in

original). Likewise, “the concept of equivalency cannot embrace a structure that is specifically

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excluded from the scope of the claims.” Dolly, Inc. v. Spaulding & Evenflo Cos., Inc., 16 F3d

394, 400 (Fed. Cir. 1994). 

The specific exclusion principle applies regardless of whether the exclusion is express or

implied. See SciMed Life Sys., Inc. v. Advanced Cardiovascular Sys., Inc., 242 F.3d 1337,

1345–47 (Fed. Cir. 2001)(discussing various decisions on this principle, and its corollary, the

“all limitations” rule). A particular structure may be specifically excluded from the scope of the

patented invention by the claims either as they are written or as they are construed by the Court. 

The simplest application of the specific exclusion principle arises where the claim

language itself excludes certain structures. See, e.g., Asyst Techs., Inc. v. Emtrak, Inc., 402 F.3d

1188, 1195 (Fed. Cir. 2005)(holding that use of the term “mounted” in the claim language

specifically excluded structures that were unmounted). Yet the Federal Circuit has also found

that the doctrine of equivalents cannot be used to expand the scope of a claim where certain

structures have been excluded during claim construction. See, e.g., Athletic Alternatives v.

Prince Mfg., Inc., 73 F.3d 1573, 1582 (Fed. Cir. 1996)(construing “varies between” to require at

least three different splay-creating offset distances and finding that a two-distance splayed

string system was specifically excluded from the scope of the claims).

In one particularly instructive example, the district court judge granted summary

judgment of non-infringement because allowing the patentee to assert that hydrosols which

form in the stomachs of patients infringe under the doctrine of equivalents would “eviscerate a

claim limitation.” The term “hydrosol” had previously been construed (in relevant part) to

mean “a synthetic pharmaceutical preparation, i.e., it does not encompass a dispersion of solid

particles of cyclosporin which only forms in the stomach of a patient.” Novartis Pharms. Corp.

v. Eon Labs Mfg., Inc., 234 F.Supp.2d 464, 468–69 (D. Del. 2002), affirmed, 363 F.3d 1306,

1312 (Fed. Cir. 2004).

Affymetrix correctly argues that the specific exclusion principle would preclude a jury’s

finding of infringement under the doctrine of equivalents as a matter of law. Because the

Court’s definition of “binding agent” and “binding site” specifically excludes certain types of

molecules containing zero binding sites, Multilyte may not assert that assays using these

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molecules infringe under the doctrine of equivalents. Put simply, if a “binding agent” must be a

protein or protein fragment, a non-protein molecule cannot be an equivalent without vitiating

this claim element. See SciMed, 242 F.3d at 1347 (“[I]f a patent states that the claimed device

must be ‘non-metallic,’ the patentee cannot assert the patent against a metallic device on the

ground that a metallic device is equivalent to a non-metallic device.”).

Multilyte contends that whether oligonucleotides perform substantially the same

function, in substantially the same way, to achieve substantially the same result as proteins is a

question of fact for the jury. Not so. Even if this case proceeded to trial on the present record,

Multilyte would not be permitted to invoke the doctrine of equivalents to encompass the

accused oligonucleotide assays because of the specific exclusion principle. Regardless of any

jury verdict rendered, Affymetrix would be entitled to judgment as a matter of law on the issue

of infringement. Compare Novartis Pharms. Corp. v. Abbott Labs., 375 F.3d 1328, 1337–39

(Fed. Cir. 2004)(reversing claim construction, but affirming the district court’s application of

the specific exclusion principle to grant judgment as a matter of law after the jury found

infringement).

It is true, as Multilyte argues, that “[l]iteral failure to meet a claim limitation does not

necessarily amount to ‘specific exclusion.’” Ethicon Endo-Surgery, Inc. v. United States

Surgical Corp., 149 F.3d 1309, 1317 (Fed. Cir. 1998). Of course, the question of infringement

under the doctrine of equivalents always focuses on subject matter that does not literally fall

within the scope of the asserted claim. But even Ethicon recognizes that such subject matter

would not be covered under the doctrine of equivalents if, as here, “its inclusion is somehow

inconsistent with the language of the claim.” Ibid. 

Moreover, its reliance on Aclara is unconvincing. There, Judge Charles Breyer

reasoned that summary judgment was inappropriate because a jury could find a covered

structure equivalent even where the term “trench” had been construed to mean “an uncovered

structure such as a ditch.” In reaching his decision, he noted that it was “extraordinarily

difficult to resolve this dispute” and that “Federal Circuit cases do not provide much guidance.” 

Aclara Biosciences, Inc. v. Caliper Techs. Corp., 2000 WL 1639507, at *9–14 (N.D. Cal.

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2000). Since Judge Breyer wrote Aclara, however, the Federal Circuit has revisited this issue,

such that the undersigned now has the benefit of the more recent decisions cited above.

This order must note that after the first round of claim construction, it was Multilyte that

pressed the Court to engage in further claim construction and provide a definition that

categorically included or excluded oligonucleotides (see March 3, 2005 Hearing Tr. at

3:19–23). Yet, now that “binding agent” has been construed to exclude oligonucleotides, it

attempts to argue that the “specific-exclusion” principle does not apply; in short, it characterizes

these clarifications as “findings of no literal infringement, not further claim construction” (Opp.

5). Ironically, although Multilyte itself proffered numerous items of extrinsic evidence to

demonstrate what “binding agent” and “binding site” meant to a person of ordinary skill in the

relevant art, it now asserts that any reference to such materials would be improper (id. at 5–6).

Multilyte is being too nimble. It cannot change its mind simply because the process of

further claim construction it requested did not produce a result in its favor. Indeed, had

“binding agent” been re-construed to categorically include oligonucleotides or all biological

molecules, Multilyte itself would have characterized this as further claim construction, rather

than infringement analysis. In response to the Court’s concern that Multilyte was seeking a

definition that would necessarily compel a finding of infringement, counsel admitted that

infringement would still need to be proven, even “with ‘binding agent’ construed, for the

purposes of this discussion, in our favor” (March 3, 2005 Hearing Tr. at 6:16–18)(emphasis

added).

In summary, the order re-construing “binding agent” could not have been more clear

that the explicit exclusion of DNA, RNA, oligonucleotides or any other molecules comprised

solely of nucleic acids was part of the definition. In fact, the finding of no literal infringement

was reached in a completely separate order.

As described above, the Court has already engaged in two rounds of claim construction. 

At this point, any argument that “binding agent,” “binding site” or other claim terms were

improperly construed should be presented to the Federal Circuit, as claim construction is

reviewed de novo upon appeal.

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CONCLUSION

For the foregoing reasons, plaintiff’s motion for summary judgment of non-infringement

under the doctrine of equivalents is GRANTED. As counsel raised no objections during the

hearing, the claims of patent invalidity and unenforceability are hereby DISMISSED, without

prejudice to Affymetrix re-asserting them in the event of a remand. At this time, final judgment

will be entered, so this action may proceed to the Federal Circuit for appellate review.

IT IS SO ORDERED.

Dated: June 23, 2005 

WILLIAM ALSUP

UNITED STATES DISTRICT JUDGE

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