Agilent Technologies, Inc. v. Affymetrix, Inc.

United States Court of Appeals for the Federal Circuit
2008-1466

AGILENT TECHNOLOGIES, INC.,

Plaintiff-Appellant,

v.

AFFYMETRIX, INC.,

Defendant-Appellee.

Thomas H. Jenkins, Finnegan, Henderson, Farabow, Garrett & Dunner, L.L.P.,
of Washington, DC, argued for plaintiff-appellant. With him on the brief was Tina E.
Hulse, of Palo Alto, California.

Stephen C. Holmes, Dewey & LeBoeuf LLP, of East Palo Alto, California, argued
for defendant-appellee. With him on the brief were Barbara A. Caufield, and Michael J.
Malecek.

Appealed from: United States District Court for the Northern District of California

Judge James Ware
United States Court of Appeals for the Federal Circuit

2008-1466

AGILENT TECHNOLOGIES, INC.,

Plaintiff-Appellant

v.

AFFYMETRIX, INC.,

Defendant-Appellee

Appeal from the United States District Court for the Northern District of California in
Case No. 06-CV-05958, Judge James Ware.
___________________________

DECIDED: June 4, 2009
___________________________

Before MAYER, RADER, Circuit Judges, and POSNER, Circuit Judge. *

RADER, Circuit Judge.

The United States District Court for the Northern District of California reviewed an

interference action that Agilent Technologies, Inc. (Agilent) brought under 35 U.S.C.

§ 146 against Affymetrix, Inc. (Affymetrix). The district court sustained the decision of

the Board of Patent Appeals and Interferences (the Board) and awarded priority to

Affymetrix. Agilent Techs. v. Affymetrix, Inc., No. C-06-05958 (N.D. Cal. June 13, 2008)

(SJ Order). Because the district court erred with regard to claim construction,

improperly denied Agilent’s motion for summary judgment with regard to written

*
The Honorable Richard A. Posner, Circuit Judge, United States Court of Appeals
for the Seventh Circuit, sitting by designation.
description under § 112 ¶ 1, and improperly granted Affymetrix’s cross-motion on the

same issue, this court reverses.

I.

This case arises out of an interference proceeding, No. 105,285, between Agilent

and Affymetrix. The claims at issue originated in Agilent’s “Schembri” patent, U.S.

Patent No. 6,513,968, which claims priority to an application filed August 21, 1998.

After Agilent’s Schembri patent issued on February 4, 2003, Affymetrix, believing

it had earlier invented the claimed methods, copied the Schembri claims into its

“Besemer” application, U.S. Patent Application No. 10/619,244, to provoke an

interference. The Besemer application claims priority, through a long string of

continuations, to an application filed June 7, 1995. The Board declared an interference

on February 16, 2006 to determine which party had priority of inventorship. Because

the Besemer application claims the benefit of an earlier filing date, the Board declared

Affymetrix the senior party to the interference under 37 C.F.R. § 2.96. Agilent thus had

the burden to show prior entitlement to its patented technology.

The disputed claims pertain to “microarray hybridization,” a technique for

performing multiple genetic analyses on a small fluid sample. Using this technique, a

testor can perform millions of genetic tests in a single small assay. A microarray is a

solid substrate (e.g., a glass slide) bearing millions of molecular probes. These probes

are generally short DNA sequences that bind (hybridize) to specific targets. To conduct

a microarray test, the testor introduces a fluid sample containing the genetic material of

interest onto the microarray surface. The fluid contacts the probes. The probes then

bind to their fluid targets, revealing the presence of those hybridized targets on the

2008-1466 2
microarray. To achieve proper hybridization results, the testor must make sure that the

fluid contacts the entire microarray surface. The disputed invention focuses primarily

upon the method of mixing the fluid for thorough contact with the microarray surface.

The interfering subject matter in this appeal is claim 20 of the Schembri patent, or

claim 66 of the Besemer application. The invention claims a method for mixing a fluid

sample during hybridization:

A method comprising:

providing a first substrate and a second substrate having inner
surfaces that define a closed chamber therebetween, said chamber
adapted to retain a quantity of fluid so that the fluid is in contact with
both inner surfaces, and wherein at least one of said inner surfaces is
functionalized with polynucleotides, polypeptides, or polysaccharides;

introducing a fluid containing a plurality of components into the closed
chamber so as to provide a quantity of fluid therein in contact with both
inner surfaces;

providing a bubble in the fluid; and

moving a bubble within the fluid to result in mixing.

Schembri Patent col.10 ll.33-45, Besemer Application at 39.

A. Schembri’s Disclosure of Fluid Mixing

Agilent’s Schembri patent discloses a method of conducting a hybridization

reaction in a closed chamber. The method forms a bubble in the fluid, and then moves

the bubble to cause mixing. According to the Schembri specification, conventional

mixing methods (rapidly shaking or rocking fluid in a container) do not adequately mix

(or test) assays with small fluid samples. In these situations, where the fluid forms a

mere film with a thickness of a few microns, the capillary strength of the fluid often

exceeds the forces generated by shaking or rocking. In that case, incomplete mixing

2008-1466 3
compromises the rate, extent, and percentage yield of the hybridization reaction.

Schembri claims a new method of mixing fluid via nucleation of bubbles within the film

of liquid.

Figure 1, above, shows an apparatus with a closed chamber sandwiched

between a first substrate 10 and second substrate 11. As seen in the cross-sectional

view of Figure 4, DNA probes are attached to the inner surface 12 of substrate 10. The

second substrate 11 forms a closed reaction chamber due to the seal 15 between the

surfaces. The testor then introduces a fluid sample with DNA targets into the closed

chamber 16. The invention then forms a bubble that moves in response to heat

resistors 13 inside the chamber. A controller creates this temperature gradient by

systemically switching on and off. These temperature changes cause the bubble to

move and mix the fluid sample in the closed chamber.

B. Besemer’s Disclosure of Fluid Mixing

Affymetrix’s Besemer application, entitled “Bioarray Chip Reaction Apparatus and

its Manufacture,” describes microarray chips and “chip packages” onto which chips are

mounted. The chip package serves as a “sealed thermostatically controlled chamber in

which fluids can easily be introduced, a practical medium for sequencing by

2008-1466 4
hybridization . . . .“ Besemer Application at 2. Figure 3 illustrates a chip packaging

device:

The invention mounts a microarray chip above the cavity 310. Inlets 350 and 360

communicate with cavity 310 such that “fluids are circulated through the cavity via inlets

350 and 360.” Id. at 9.

The Besemer application discloses three embodiments, called “agitation

systems,” for mixing fluid through the cavity during hybridization. Figures 28 and 30

represent particular embodiments that circulate fluid through the chip package. For

purposes of this appeal, these “circulator” embodiments are not materially different.

The embodiment in Figure 28 illustrates this mixing technology:

2008-1466 5
 The hybridization chip and cavity 310 attach to containers 2810 and 2820.

These containers hold fluid targets for hybridization with probes on the chip. Agitator

2801 holds a gas, e.g., nitrogen. Using ports, vents, and valves, the agitator injects gas

into the containers in an alternating manner, thereby forcing fluid into and out of the

cavity 310. As the fluid flows in and out of the cavity 310, the targets and probes mix to

effect hybridization. Notably, in the discussion of this embodiment, Besemer teaches

that “[t]he bubbles formed by the N2 agitate the fluid as it circulates through the system.”

Id. at 28.

The embodiment in Figure 29, the “vortexer” system, accomplishes fluid mixing in

a different manner:

This embodiment mounts a hybridization chip package on vortexer 2910. Container

2930 then fills with fluid containing targets. At that point, various valves open to allow

nitrogen gas from 2901 to enter container 2930, thereby forcing fluid into the cavity 310.

2008-1466 6
The valves then seal fluid in the cavity and the vortexer vibrates the chip package

“similar to a paint mixer” at 3000 cycles per minute. Id. at 29. This motion mixes the

targets in the fluid, completing the hybridization reaction.

II.

Before the Board, Agilent filed a single substantive preliminary motion

challenging the validity of the copied claims on the grounds that the Besemer

application did not describe the invention adequately under § 112 ¶ 1 to show actual

possession of the bubble-mixing invention. After a hearing, the Board ruled that Agilent

did not prove that the Besemer application lacked adequate written description to

support the count (the interfering claims). Schembri v. Besemer, Interference No.

105,285 (B.P.A.I. June 28, 2006) (Board Decision). Because it found that the Besemer

application showed support for the claimed invention, the Board awarded priority to

Affymetrix’s application and cancelled the contested claims of Agilent’s Schembri

patent.

Agilent sought review of this decision by filing a complaint in the Northern District

of California under 35 U.S.C. § 146. The parties submitted new expert reports and

testimony from their respective expert witnesses. In April 2008, the district court held a

claim construction hearing. The court also entertained cross motions for summary

judgment on the written description issue. Soon after, the district court granted

Affymetrix’s motion for summary judgment that the Besemer application satisfies the

written description requirement, thereby affirming the Board. The instant appeal

challenges the trial court’s claim construction and written description decisions. This

court has jurisdiction over Agilent’s appeal under 28 U.S.C. § 1295(a)(1).

2008-1466 7
 III.

This court must first decide as a legal matter which specification to consult when

construing a claim whose written description is challenged in an interference. The

district court construed the disputed claims in light of the host application whose written

description (possession of the invention at the time of invention) was challenged – in

this case, the Besemer specification. SJ Order, slip op. at 7. Agilent counters that the

proper reference point for claim construction was the Schembri specification, the

disclosure from which the claims originated. Because this question presents a matter of

law, this court reviews the district court’s decision without deference. Gould v. Quigg,

822 F.2d 1074, 1077 (Fed. Cir. 1987).

To decide which specification informs the interpretation of the contested claims,

this court must examine two of its prior decisions, In re Spina, 975 F.2d 854 (Fed. Cir.

1992), and Rowe v. Dror, 112 F.3d 473 (Fed. Cir. 1997). In Spina, the applicant copied

a claim from the “Barron” patent to provoke an interference. The Board, in considering

whether Spina’s specification contained an adequate written description of the claim

clause at issue, viewed the claim in light of the Barron disclosure, from which the claim

had been copied. This court agreed with that approach: “When interpretation is

required of a claim that is copied for interference purposes, the copied claim is viewed

in the context of the patent from which it was copied.” Spina, 975 F.2d at 856.

In Rowe v. Dror, Rowe copied several claims from the Dror patent to provoke an

interference. During the motions period before the Board, Dror filed a motion seeking

judgment against Rowe on the ground that a third party patent anticipated some of

Rowe’s claims corresponding to the interference count. On appeal from a holding of

2008-1466 8
invalidity, this court discussed which specification – Rowe’s or Dror’s – should be used

to interpret Rowe’s claims:

[37 C.F.R.] section 1.633(a) allows the PTO to consider the novelty or
non-obviousness of each application's claims as if the application stood
alone. In this posture, the PTO properly interprets the claim in light of its
host disclosure, just as it would during ex parte prosecution. Thus, this
court looks to the Rowe application to determine the meaning of the
phrase at issue.

Rowe, 112 F.3d at 479. Recognizing that this result was at odds with Spina, this court

expressly distinguished the two cases:

In Spina, this court considered whether an applicant was eligible to copy a
patentee’s claim and thereby challenge priority of invention, a question
that turned on whether the copying party’s specification adequately
supported the subject matter claimed by the other party. This court held,
in that context, that a copied claim is interpreted in light of its originating
disclosure. This Spina rule sought to ensure that the PTO would only
declare an interference if both parties had a right to claim the same
subject matter. However, that rule does not apply in cases, such as this
one, where the issue is whether the claim is patentable to one or the other
party in light of prior art. In this posture, the PTO and this court must
interpret the claim in light of the specification in which it appears.
Id.

This case calls for application of the Spina rule, because the question is “whether

the copying party’s specification [Besemer] adequately supported the subject matter

claimed by the other party [Schembri].” Id. Stated more directly, does Besemer have

adequate basis to copy Schembri’s claim and thereby challenge Schembri’s priority of

invention? This case does not present the Rowe situation, “where the issue is whether

the claim is patentable to one or the other party in light of prior art.” Id.

Affymetrix places great emphasis on the language of 37 C.F.R. § 41.200(b)

(2004), which provides: “A claim shall be given its broadest reasonable construction in

light of the specification of the application or patent in which it appears.” This regulation

2008-1466 9
was not in effect at the time of the Spina decision, and thus, per Affymetrix, Spina

cannot stand in the way of following the plain language of Rule 200 today.

To the contrary, Rowe explicitly recognized that administrative regulations cannot

trump judicial directives. In considering the effect of Rule 200’s substantially similar

predecessor (37 C.F.R. § 1.633(a) (1996)) on the rule from Spina, this court stated:

“This court does not accept the PTO’s statement that it can ‘administratively set aside

the judicially created rule of In re Spina.’ Judicial precedent is as binding on

administrative agencies as are statutes.” Id. at 479 n.2 (internal citations omitted).

Indeed, Rowe’s differentiating characteristic was that it involved a situation,

unlike Spina, where the issue was whether the claim was “patentable to one or the other

party in light of prior art.” Id. at 479. In such situations, where the PTO assesses the

viability of an applicant’s claims in the face of § 102 or § 103 challenges, the proper

reference point for determining claim meaning is the host disclosure, just as in ex parte

prosecution. By contrast, as in the instant case, where the PTO must assess whether

both parties have a right to claim the same subject matter, the claim construction

analysis properly occurs in the context of the specification from which the claims were

copied.

To be clear, as this court explained in Rowe, when a party challenges written

description support for an interference count or the copied claim in an interference, the

originating disclosure provides the meaning of the pertinent claim language. When a

party challenges a claim’s validity under § 102 or § 103, however, this court and the

Board must interpret the claim in light of the specification in which it appears. Thus, the

2008-1466 10
district court erred in construing claim language in light of the host Besemer application,

rather than the originating Schembri disclosure.

IV.

The district court construed the term “a closed chamber . . . adapted to retain a

quantity of fluid” to mean “an enclosed cavity, or some other enclosure or system of

enclosures, which is capable of being sealed or set apart from its surroundings to retain

a quantity of fluid.” SJ Order, slip op. at 12. The district court arrived at this

construction by referring to Figure 28 of the Besemer application. The district court

created the following markup of Figure 28 to demonstrate its understanding of the

“closed chamber”:

Id. at 20. As the above figure shows, the district court concluded that the claimed

closed chamber includes not only the cavity 310, but also “containers 2810 and 2820,

and associated tubes.” Id. at 18. Agilent challenges two aspects of the district court’s

construction.

A.

First, Agilent argues that the district court erroneously interpreted “a closed

chamber” to mean a “system of enclosures.” According to Agilent, the term is defined

by the language of the claim itself, and should mean “the space between the inner

2008-1466 11
surfaces of the first and second substrate, wherein at least one of the inner surfaces is

functionalized.” Appellant’s Br. 43.

This court reviews a district court’s claim construction without deference. Cybor

Corp. v. FAS Techs., Inc., 138 F.3d 1448, 1451 (Fed. Cir. 1998) (en banc). This court

generally assigns claim terms their ordinary and customary meanings, according to the

customary understanding of a person of ordinary skill in the art who reads them in the

context of the intrinsic record. See Phillips v. AWH Corp., 415 F.3d 1303, 1312-13

(Fed. Cir. 2005) (en banc). “[T]he claims themselves provide substantial guidance as to

the meaning of particular claim terms.” Id. at 1314.

The claim language in this case makes the district court’s definition dubious. The

district court’s definition includes a “system of enclosures.” The claim itself recites a

closed chamber “define[d]” by “a first substrate and a second substrate having inner

surfaces.” Thus, the claim requires that the chamber be bounded by two discrete

substrates. The chamber is not a nebulous space that could ambiguously span a

“system of enclosures.” Instead, it is an enclosure explicitly defined by two surfaces.

The specification further impeaches the trial court’s definition. As discussed

above, the district court erred by looking to the Besemer specification to derive this

claim term’s meaning. Because the specification “is the single best guide to the

meaning of a disputed term,” Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582

(Fed. Cir. 1996), this was an error of no small consequence. The “closed chamber . . . ”

term should have been construed in light of Schembri’s specification, which consistently

uses this term to refer simply to the space between a first and second substrate. As the

Summary of Invention section states:

2008-1466 12
 The invention, in one embodiment, is an apparatus for mixing a film of
fluid, particularly a chemical, biochemical, or biological fluid which typically
comprises a reaction mixture, the apparatus comprising a first substrate
having an inner surface and a substantially parallel second substrate
having an inner surface that defines a closed chamber therebetween. The
closed chamber is adapted to retain a quantity of fluid so that the fluid is in
contact with both inner surfaces.

Schembri Patent col.2 ll.44-52 (emphasis added). Indeed, the closed chamber is

“define[d]” by two substantially parallel substrates with inner surfaces. Id. The

Schembri specification provides no indication that a closed chamber is a “system of

enclosures.” Rather, it is an enclosure.

Consistent with the disclosure’s focus on a method of mixing precise quantities of

fluid, Schembri indicates at many points that the closed chamber is an interstitial space

defined by two surfaces in which nucleated bubbles move in response to a temperature

gradient to achieve mixing. See, e.g., id. col.6 ll. 36-38 (“a second substrate 11 . . . is

placed on top of the seal where the substantially parallel substrates define a closed

chamber”); id. col.6 ll.38-41 (“The closed chamber may be a micron to several

millimeters in thickness, preferably from about 5 microns to about 100 microns in

thickness.”); id. col.7 ll.9-15 (“The apparatus having closed edges, shown in FIG. 3, may

additionally include a seal 15 between the two opposing inner surfaces . . . The

apparatus preferably includes an opening in one of the substrates or in the seal for

introducing fluid into the closed chamber.”).

Moreover, the district court’s interpretation ignores, or at the least frustrates, the

explicit requirement that “at least one of said inner surfaces is functionalized with [probe

materials].” This language requires that probes attach to at least one (possibly both) of

the chamber’s two substrate surfaces for hybridization. Under the district court’s

2008-1466 13
“system” definition, however, it makes little sense to speak of a hybridization chamber

with only two microarray chamber substrates, let alone functionalizing “at least one” of

these two substrates. In this context, if a chamber really means several chambers, the

Schembri specification provides no guidance as to where, amongst the several

chambers, the first and second substrates are located. Indeed, the Schembri patent

uniformly teaches that a closed chamber is simply an enclosure formed by two

substrates, at least one of which is functionalized. Thus, for various reasons, this court

rejects the district court’s expansive interpretation of “closed chamber.” Instead the

language of the claim and specification defines the chamber.

B.

Agilent further argues that the district court erred by construing a “closed

chamber . . . adapted to retain a quantity of fluid” to mean a chamber that is “capable of

being sealed or set apart from its surroundings to retain a quantity of fluid.” As per

Agilent, a “closed chamber” is a “chamber from which there is no egress of fluid.”

Appellants’ Br. at 47.

Again, this court finds error in the district court’s construction. A “closed chamber

. . . adapted to retain a quantity of fluid” must mean something different than just a

“chamber . . . adapted to retain a quantity of fluid.” Otherwise, the word “closed”

becomes superfluous. See Merck & Co. v. Teva Pharms. USA, Inc., 395 F.3d 1364,

1372 (Fed. Cir. 2005) (“A claim construction that gives meaning to all the terms of the

claim is preferred over one that does not do so.”); Mangosoft, Inc. v. Oracle Corp., 525

F.3d 1327, 1330-31 (Fed. Cir. 2008) (rejecting claim construction that “ascribes no

meaning to the term . . . not already implicit in the rest of the claim.”). At best, the

2008-1466 14
district court’s construction equates the term “closed” with “closable,” contrary to the

plain language of the claim.

Notably, the district court explicitly recognized that the ordinary meaning of

“closed” in the context of a fluid retention chamber is simply “not open” or “sealed.” SJ

Order, slip op. at 11. A sealed chamber does not allow fluid to escape. However, the

district court compromised this ordinary meaning out of a need to harmonize its own

assumptions that a) the claims should be construed in light of the Besemer application,

and b) a “closed chamber” can be a “system of enclosures.” No doubt, the various

enclosures (containers, valves, channels, etc.) of Besemer’s agitation systems are not

always closed or sealed. But, as discussed above, Schembri, not Besemer, is the

proper reference point for claim construction, and a “closed chamber” is not a system of

enclosures.

In Schembri’s disclosure, the closed chamber is not merely capable of being set

apart from its surroundings – it is in fact set apart. Indeed, the hybridization chamber,

once closed or sealed, allows no fluid to escape. At column 6, Schembri teaches that

“a seal 15 can be attached to the outer periphery of the substrate, thus creating a

chamber for the fluid with a defined thickness.” Schembri Patent col.6 ll.28-30. At this

point in the explanation, the patent describes only a “chamber” that is capable of

retaining a film of fluid. Next, however, “a second substrate 11, or a simple glass cover

slip is placed on top of the seal where the substantially parallel substrates define a

closed chamber 16.” Id. col.6 ll.36-38 (emphasis added). Thus, whereas a

hybridization “chamber” is formed by attaching a seal to the substrate, that chamber

becomes “closed” once another substrate is placed over the seal. This teaching of

2008-1466 15
closing a chamber is repeatedly discussed in each example provided in Schembri. See

id. col.7 ll.49-53; col.8 ll.20-25; col.8 ll.53-55.

Thus, this court reverses the district court’s construction, which was not

grounded in the right disclosure and did not honor the customary meaning of the claim

language to one of skill in the art. The proper meaning of a “closed chamber . . .

adapted to retain a quantity of fluid” is “an enclosed cavity defined by the inner surfaces

of the first and second substrates, from which there is no egress of fluid.”

V.

The next issue is whether the district court properly granted Affymetrix’s motion

for summary judgment that the Besemer application shows adequate possession of the

claimed invention at the time of invention, the written description requirement of § 112

¶ 1. This court reviews a district court’s grant of summary judgment without deference.

Monsanto Co. v. Scruggs, 459 F.3d 1328, 1344 (Fed. Cir. 2006). Summary judgment is

appropriate “if the pleadings, depositions, answers to interrogatories, and admissions on

file, together with affidavits, if any, show that there is no genuine issue as to any

material fact and that the moving party is entitled to a judgment as a matter of law.”

Fed. R. Civ. P. 56(c). On appeal from a grant of summary judgment, this court

construes the facts in the light most favorable to the non-movant, here Agilent. Bose

Corp. v. JBL, Inc., 274 F.3d 1354, 1358 (Fed. Cir. 2001).

The written description doctrine prohibits new matter from entering into claim

amendments, particularly during the continuation process. As this court stated in In re

Wright:

When the scope of a claim has been changed by amendment in such a
way as to justify an assertion that it is directed to a different invention than

2008-1466 16
 was the original claim, it is proper to inquire whether the newly claimed
subject matter was described in the patent application when filed as the
invention of the applicant. That is the essence of the so-called
“description requirement” of § 112, first paragraph.

866 F.2d 422, 424 (Fed. Cir. 1989) (emphasis in original). Adequate written description

means that the applicant, in the specification, must “convey with reasonable clarity to

those skilled in the art that, as of the filing date sought, he or she was in possession of

the [claimed] invention.” Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64 (Fed. Cir.

1991). Satisfaction of the written description requirement is a question of fact.

Conservolite, Inc. v. Widmayer, 21 F.3d 1098, 1100 (Fed. Cir. 1994).

Patent applications do not enjoy the statutory presumption of validity found in 35

U.S.C. § 282. Thus, Agilent’s burden of proving a lack of written description in

Affymetrix’s Besemer application is a simple preponderance of the evidence. Eli Lilly &

Co. v. Aradigm Corp., 376 F.3d 1352, 1365 (Fed. Cir. 2004).

A.

Before addressing the substantive merits of the district court’s decision, this court

will first address Agilent’s contention that the district court erred by adopting the

incorrect standard of review for considering certain new evidence that had not been

before the Board.

Under 35 U.S.C. § 141, a party to an interference dissatisfied with the Board’s

decision may appeal directly to this court. If a dissatisfied party wishes to supplement

the record, however, 35 U.S.C. § 146 allows that party to initiate a civil action in a

United States District Court to bring forth “further testimony.” “Section 146 actions have

been described as a hybrid of an appeal and a trial de novo.” Estee Lauder v. L'Oreal,

S.A., 129 F.3d 588, 592 (Fed. Cir. 1997). In Section 146 actions, if the parties present

2008-1466 17
new evidence to the district court that conflicts with the record before the Board, the

district court must make de novo factual findings regarding this new evidence. See

Mazzari v. Rogan, 323 F.3d 1000, 1005 (Fed. Cir. 2003).

The Board found that Schembri had not advanced any “meaningful evidence” to

show that one of ordinary skill in the art would not have understood Besemer’s

specification to inherently disclose using bubbles to mix fluid in a closed chamber, as

required by Besemer’s claim 66. Board Decision, slip op. at 28. The Board specifically

told Agilent what kind of additional evidence might have been useful:

Meaningful evidence in this case might, for example, have included an
expert declaration stating that one of ordinary skill in the art would not
have had the requisite knowledge or skills to conclude from the Besemer
’224 specification that the inventor was in possession of the invention as
claimed.

Id.

Before the district court, Agilent attempted to remedy this evidentiary deficiency

by submitting new expert testimony regarding the Besemer application’s disclosure.

Specifically, Agilent submitted deposition testimony from Affymetrix’s own expert

explaining that bubbles are not inherently present in the “vortexer” embodiment of

Figure 29 (discussed below). Agilent further offered admissions from Affymetrix’s

expert that Besemer’s “cavity 310” (under Agilent’s claim construction, the claimed

“closed chamber”), in the embodiments of Figure 28 and 30, is not closed during

hybridization. This evidence was highly probative of the parties’ dispute regarding the

alleged deficiency in the Besemer specification. Moreover, these admissions, viewed in

the light most favorable to Agilent, conflict with Affymetrix’s arguments that the Besemer

application supports the claims at issue.

2008-1466 18
 The district court, however, discarded this evidence, concluding that “Agilent

does not present any new evidence concerning this issue, [so] the Court reviews [the

Board’s decision on written description] for substantial evidence.” SJ Order, slip op. at

20.

The district court’s decision to deferentially review the Board’s written description

holding in the face of newly submitted conflicting evidence constituted legal error.

Section 146 affords a litigant the option of shoring up evidentiary gaps that may have

been evident by the end of the inter partes interference procedure. In this case, the

Board explicitly notified Agilent of such gaps, and Agilent endeavored to fill them. Thus,

Section 146 permits such new evidence and authorizes the trial court to review the

Board’s treatment of the written description issue. This court will examine Agilent’s

newly proffered testimony without deference to the Board’s finding.

B.

Agilent’s argument for finding no written description support in the Besemer

application for the claims at issue can be summarized as follows: the “circulator”

embodiments (illustrated in Figures 28 and 30) do not describe a method that takes

place in a “closed chamber,” whereas the “vortexer” embodiment (Figure 29) does not

describe bubble mixing at all. Thus, as per Agilent, Besemer cannot show possession

of the claimed invention because no embodiments describe a method of both

introducing fluid into a closed chamber and using bubbles to mix the fluid.

As discussed above, the proper construction of “closed chamber . . . adapted to

retain a quantity of fluid” is “an enclosed cavity defined by the inner surfaces of the first

2008-1466 19
and second substrates, from which there is no egress of fluid.” First, this court will look

to the Besemer specification to identify a disclosure of such an enclosed cavity.

Throughout the Besemer specification, the enclosed space between a

hybridization chip and its associated chip package is interchangeably called a “cavity” or

a “reaction chamber.” See, e.g., Besemer Application at 3 (“A chip is then mated to a

package having a reaction chamber with fluid inlets. When mated, the probe array is in

fluid communication with the reaction chamber.”); id. at 9 (“Package 300 contains a

cavity 310 on which a chip is mounted. The package includes inlets 350 and 360 which

communicate with cavity 310. Fluids are circulated through the cavity via inlets 350 and

360.”). Figure 6 shows a cross-sectional view of the cavity, which is situated between

the chip 120 and the chip casing 410:

The Besemer application explains that this reaction chamber or cavity can be “sealed”

to prevent egress of fluid. Id. (“A septum, plug, or other seal may be employed to seal

the fluids in the cavity.”). Thus, the relevant “chamber” in the Besemer application is the

reaction chamber or cavity 310.

Notably, in the “circulator” agitation embodiments of Figures 28 and 30, the

reaction chamber or cavity 310 is not sealed to prevent the escape of fluid. Quite to the

contrary, these embodiments actually require circulation of fluid in and out of the cavity

to facilitate mixing. As Agilent’s expert Dr. Arthur Schleifer explained in his report

2008-1466 20
submitted to the district court, “[d]uring the hybridization and mixing process using the

apparatuses depicted in Figure 28 and Figure 30 of the Besemer specification, fluid

moves in and out of the chamber for the mixing process.” Expert Report at 11. Indeed,

Affymetrix’s expert, Dr. Dorian Liepmann, also testified to his view that the hybridization

reaction cavity 310 is not closed in either the Figure 28 or Figure 30 embodiment.

Liepmann Dep. 110:22-111:6, Jan. 9, 2008. The district court’s finding that these

circulator embodiments disclose “introducing a fluid . . . into the closed chamber” was

thus necessarily predicated upon an erroneous and expansive interpretation of a closed

chamber that spans an entire system of containers, channels, and cavities. In light of

the proper claim construction and the undisputed facts, the circulator embodiments

simply provide no disclosure of the claimed method of introducing fluid into a closed

chamber.

The record shows, and the parties appear to agree, that Figures 28-30 are the

only bubble mixing embodiments disclosed in the Besemer application. Thus, having

eliminated Figures 28 and 30 as the source of written description support for the

claimed method, this court turns to the Figure 29 embodiment.

This “vortexer” embodiment teaches introducing fluid into a closed reaction

chamber from which fluid does not egress. Specifically, nitrogen gas forces fluid into

the reaction cavity, and “[w]hen the cavity is filled, valves 2935, 2936, and 2955 are

closed to seal the fluid in the cavity.” Besemer Application at 29. Thus, the next

question is whether this vortexer embodiment further describes “providing a bubble in

the fluid” and “moving a bubble within the fluid to result in mixing,” as required by the

claims in question.

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 Affymetrix relies on two mentions of bubbles in the Besemer application as

providing support for bubble mixing in the vortexer embodiment. In the first such

mention, the application teaches that bubbles are formed when fluid circulates in and

out of the cavity 310:

Cavity 310 may include inlets 350 and 360. Selected fluids are introduced
into and out of the cavity via the inlets. In some embodiments, the inlets
are located at opposite ends of the cavity. This configuration improves
fluid circulation and regulation of bubble formation in the cavity. The
bubbles agitate the fluid, increasing the hybridization rate between the
targets and complementary probe sequences.

Id. at 10 (emphases added). This reference to bubble formation and agitation cannot

satisfy the written description requirement for the claim at issue, however, because this

excerpt pertains to the “circulator” embodiments of Figures 28 and 30, not the vortexer

embodiment of Figure 29. This discussion of bubble formation is explicitly directed at

embodiments where fluid is “introduced into and out of the cavity via the inlets” to

“improve[] fluid circulation.” However, as discussed above, the Besemer embodiments

where fluid circulates in and out of the reaction chamber are incompatible with the

claimed requirement that fluid is introduced into a “closed chamber . . . adapted to retain

a quantity of fluid.” Indeed, a method of creating bubbles by flushing fluid in and out of

a cavity is at odds with a method of using bubbles to mix fluid within a sealed cavity.

The only other mention of bubbles is also inextricably wedded to the circulator

embodiments and therefore inconsistent with bubble mixing in a closed chamber:

Fig. 28 illustrates an agitation system in detail. . . . In operation, a fluid is
placed into container 2810. The fluid, for example, may contain targets
that are to be hybridized with probes on the chip. Container 2810 is
sealed by closing port 2811 while container 2820 is vented by opening
port 2821. Next, N2 is injected into container 2810, forcing the fluid
through tube 2850, cavity 310, and finally into container 2820. The
bubbles formed by the N2 agitate the fluid as it circulates through the

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 system. When the amount of fluid in container 2810 nears empty, the
system reverses the flow of the fluid by closing valve 2840 and port 2821
and opening valve 2841 and port 2811. This cycle is repeated until the
reaction between the probes and targets is completed .

Id. at 27-28 (emphases added). Here, bubbles are formed by repeatedly forcing fluid in

and out of the cavity 310, using containers 2810 and 2820 as fluid repositories. The

stated purpose of this embodiment is to cause repeated ingress and egress of fluid out

of the cavity to facilitate the hybridization reaction between targets and probes. Thus, in

no sense can this mention of bubbles constitute a disclosure of bubble mixing in a

“closed chamber.”

Affymetrix, recognizing that the Besemer application makes no explicit mention of

bubbles or bubble mixing in the context of the vortexer embodiment, argues that

bubbles are inherently produced in the vibrating chip package because “[a] person

skilled in the art would have known in 1994 that to achieve mixing, there must be a void

in the chamber – that is, it is not completely filled with fluid. As a result, a bubble is

provided in the fluid, and when the chip package is vibrated, the bubble is moved within

the fluid to result in mixing.” Appellee’s Br. 17 (emphasis in original). This assertion,

however, is belied by a critical admission from Affymetrix’s expert that bubbles are not

necessarily formed by nitrogen gas in the vortexer reaction chamber:

Q. Now, does this system as depicted in Figure 29 and described in the
Besemer application necessarily generate bubbles in the fluid that is
flowing from container 2930 into container 310?
A. No, it does not necessarily have to do that.

Liepmann Dep. 22:22-111:6 (emphasis added).

The very essence of inherency is that one of ordinary skill in the art would

recognize that a reference unavoidably teaches the property in question. See In re

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Oelrich, 666 F.2d 578, 581 (CCPA 1981) (“Inherency, however, may not be established

by probabilities or possibilities. The mere fact that a certain thing may result from a

given set of circumstances is not sufficient.”); Hitzeman v. Rutter, 243 F.3d 1345, 1355

(Fed. Cir. 2001) (“an inherent property must necessarily be present in the invention . . .

and it must be so recognized by persons of ordinary skill in the art”). Especially in light

of this admission, Affymetrix’s argument that the vortexer chamber might include an

unmentioned void, and in turn, that that void might result in bubble generation, is

insufficient under this court’s precedent to establish inherency.

In sum, the formation of bubbles in the Besemer disclosure is part and parcel of a

process of moving fluid in and out of the hybridization reaction chamber. Besemer

simply does not disclose a method of bubble mixing in a closed hybridization chamber,

as required by the claims. Viewing the record in the light most favorable to Agilent, the

district court erred by granting summary judgment in Affymetrix’s favor.

Moreover, in light of the new evidence submitted to the district court, which this

court reviews without deference to the Board’s earlier finding, this court finds no dispute

of material fact that the Besemer application does not teach the claimed method. This

court is mindful that continuing applications, such as Affymetrix’s application here, can

only receive the benefit of an earlier-filed parent application if that parent fully supports

the claims. If not supported in the parent application, fundamental fairness requires that

claims to new matter receive, at best, the filing date of the continuing application. In this

case, the record shows by a preponderance of the evidence that Affymetrix copied

Agilent’s claims into its continuation application despite not having disclosed the method

in question. As this court stated in Amgen Inc. v. Hoechst Marion Roussel Inc., “[t]he

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purpose of the written description requirement is to prevent an applicant from later

asserting that he invented that which he did not; the applicant for a patent is therefore

required to recount his invention in such detail that his future claims can be determined

to be encompassed within his original creation.” 314 F.3d 1313, 1330 (Fed. Cir. 2003)

(citation omitted). Affymetrix’s current claims are not encompassed by Besemer’s

original creation. Thus, this court reverses the district court’s denial of Agilent’s cross

motion for summary judgment.

CONCLUSION

As discussed above, the district court’s claim construction was erroneous.

Further, the district court erroneously granted Affymetrix’s motion for summary judgment

regarding written description. Because there is no dispute of material fact that the

Besemer application does not satisfy the written description requirement for the claims

at issue, this court reverses the judgment of the district court.

REVERSED

COSTS

Each party shall bear its own costs.

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