The opinion of the court was delivered by: Fogel, U.S. District Judge.
ORDER*fn1 CONSTRUING CLAIMS OF U.S. PATENTS NOS. 5,445,934,
5,744,305, 5,800,992, AND 5,795,716
Both of the cases captioned above are patent infringement suits.
Affymetrix, plaintiff in both cases, asserts four separate patents
against the named defendants. The cases were consolidated for the
purpose, inter alia, of construing disputed patent claim terms. On
November 29 and 30, 2000, the Court conducted a tutorial and hearing to
assist it in construing the claims of United States Patents Nos.
5,445,934 (the '934 patent), 5,744,305 (the '305 patent), 5,800,992 (the
'992 patent), and 5,795,716 (the '716 patent). After considering the
arguments and evidence presented by all parties, the Court will construe
the principal disputed terms as set forth below. Certain of the disputed
terms have not been construed. If necessary, the parties may request the
Court to construe the remaining terms at a later date. The Court will
request supplemental briefing as to the term "substantially
Affymetrix's four patents relate to "DNA chip" or "array" technology.
Two of the patents, the '934 and the '305 patents, claim "arrays" or
"substrates," wherein a high density of different nucleic acids (RNA or
DNA) is placed on a solid support, such that users may perform
experiments on a large number of different nucleic acids at one time, in
a single reaction. The '992 patent claims methods of detecting nucleic
acid sequences in the arrays by using labeled complementary nucleic acids
that hybridize to nucleic acid sequences in the arrays. The fourth
patent, the '716 patent, concerns computer programs which translate the
raw data from the experiments into genetic information about the sample.
In the two cases captioned above, Affymetrix asserts that Defendants
Incyte Pharmaceuticals, Inc. and Synteni (collectively, "Incyte")
infringe the '934, '305, and '992 patents; and that Defendant Hyseq,
Inc. ("Hyseq") infringes the '305, '992, and '716 patents. A brief
discussion of each of the patents in suit follows.
A. The '934 Patent, Entitled "Array of Oligonucleotides on a Solid
The '934 patent claims a "substrate," which has a surface comprising at
least 1,000 groups of oligonucleotides with different, known sequences
covalently attached to the surface in discrete known regions. The 1,000
or more groups of oligonucleotides occupy a total area of less than one
square centimeter. The '934 patent was filed on September 30, 1992 and
issued on August 29, 1995.
Affymetrix accuses Incyte of infringing claims 1, 5, 6, and 7 of the
'934 patent. Claims 1 and 7 are independent claims.
B. The '305 Patent, Entitled "Arrays of Materials Attached To A
The '305 patent, like the '934 patent, claims a chip apparatus. In this
case, the claims recite an "array of oligonucleotides" or an "array of
polynucleotides." The apparatus is comprised of a solid support and
oligonucleotides or polynucleotides attached to the solid support at a
density of greater than 400 different oligonucleotides or polynucleotides
per square centimeter. The oligonucleotides or polynucleotides are
attached to the surface of the solid support in different predefined
regions, and the different oligonucleotides have different determinable
sequences. The '305 patent was filed on June 6, 1995 and issued on April
Affymetrix accuses Hyseq of infringing claims 1, 2, 5, 8, 15, 17, and
20 of the '305 patent, and accuses Incyte of infringing claims 1, 3-13,
and 15-25. Claims 1 and 15 are the only independent claims.
C. The '992 Patent, Entitled "Method of Detecting Nucleic Acids."
The '992 patent claims a method for detecting nucleic acid sequences
that may be used in connection with an array of polynucleotides, where
the polynucleotides are comprised of a determinable nucleic acid. The
method utilizes the well-known ability of nucleic acid sequences to
"hybridize" to complementary sequences.
The '992 patent claims a method of simultaneously detecting the
presence of two sets of specific nucleic acid sequences, where one
collection of nucleic acids is labeled with one label, and another
collection of nucleic acids is labeled with a different label,
distinguishable from the first. The two collections of labeled nucleic
acids are substantially complementary to a nucleic acid of the array. The
collections of labeled nucleic acids are made to contact the arrays so as
to detect hybridization of the labeled nucleic acids to complementary
nucleic acids in the arrays.
The '992 patent further claims a method of detecting differential
expression of each of a plurality of genes in one cell type compared to
expression of the same genes in a second cell type. This method involves
adding a mixture of labeled nucleic acid from the two cell types to an
array of polynucleotides representing genes derived from the two cell
types. The labels are distinct fluorescent labels, which are examined
under fluorescence excitation conditions. The method is practiced under
conditions that allow hybridization to complementary sequence
polynucleotides in the array. The '992 patent was filed on June 25, 1996
and issued on September 1, 1998.
Affymetrix accuses Hyseq of infringing claims 1 and 3 of the '992
patent, and Incyte of infringing claims 1, 3, 4, and 5. Claims 1 and 4 are
Although the specifications of the '934, '305, and '992 patents differ
in many respects, the patents are related in that all three derive from
the originally filed U.S. Patent Application No. 362,901 (the '901
Application). Each of the patents is based on separate
continuation-in-part applications that are based, either directly or
indirectly, on the '901 Application.*fn2
D. '716 Patent, Entitled "Computer-Aided Visualization and Analysis
System for Sequence Evaluation"
Affymetrix accuses Hyseq of infringing claims 3, 4, 7, 8, 9, and 10.
Claims 3, 4, 7, and 8 are independent claims.
Claim construction is purely a matter of law, to be decided exclusively
by the Court. Markman v. Westview Instruments, Inc., 517 U.S. 370, 387,
116 S.Ct. 1384, 134 L.Ed.2d 577 (1996). Claims are construed from the
perspective of a person of ordinary skill in the art at the time of the
invention. Markman v. Westview Instruments, Inc., 52 F.3d 967, 986
(Fed.Cir. 1995). To determine the meaning of the claim terms, the Court
initially must look to intrinsic evidence, that is, the claims, the
specification, and, if in evidence, the prosecution history. Autogiro v.
United States, 181 Ct.Cl. 55, 384 F.2d 391 (1967). The Court must look
first to the words of the claims themselves. See Vitronics Corp. v.
Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed.Cir. 1996). These words are
to be given their ordinary and customary meaning unless it is clear from
the specification and prosecution history that the inventor used the term
with a different meaning. Id. The claims should be interpreted
consistently with the specification. See Renishaw PLC v. Marposs Societa'
per Azioni, 158 F.3d 1243, 1250 (Fed.Cir. 1998). Arguments and amendments
made during prosecution of a patent application limit claim terms so as
to exclude any interpretation that was disclaimed during prosecution.
Southwall Tech., Inc. v. Cardinal IG Co., 54 F.3d 1570, 1576 (Fed.Cir.
Where intrinsic evidence alone resolves any ambiguity in a disputed
claim term, it is improper to rely on extrinsic evidence. Vitronics, 90
F.3d at 1583, 1585. However, extrinsic evidence may be considered in the
rare instances where the intrinsic evidence is insufficient to enable the
court to construe disputed claim terms. Id. at 1585.
As a preliminary matter, the Court addresses a threshold argument that
Incyte repeatedly offers concerning claim construction.*fn3 Incyte
relies on the canon of claim construction which states that, "[w]hen
claims are amenable to more than one construction, they should when
reasonably possible be interpreted so as to preserve their validity."
Modine Mfg. v. U.S. Int'l Trade Comm'n, 75 F.3d 1545, 1557 (Fed.Cir.
1996). Arguing that the '934, '305, and '992 specifications do not enable
Affymetrix's claim constructions under 35 U.S.C. § 112, ¶ 1,
Incyte urges rejection of Affymetrix's proffered constructions.
Specifically, Incyte asserts that Affymetrix's true invention is the
"Very Large Scale Immobilized Polymer Synthesis" or "VLSIPS" technology.
This technology originally involved the use of light sensitive compounds
in the stepwise formation, monomer-by-monomer, of polypeptides, not
polynucleotides, such that the synthesis occurs on the solid support, or
chip apparatus. Incyte argues that even if, arguendo, the specifications
of the '934, '305, and '992 patents enable chips with polynucleotides,
those chips are only enabled for polynucleotides synthesized
monomer-by-monomer directly on the solid support. Accordingly, Incyte
imposes the limitation requiring monomer-by-monomer
synthesis on multiple disputed terms in the claims.
Although the Court acknowledges that it must attempt to interpret
claims in a manner which will sustain their validity, courts do not have
authority to redraft claims for this purpose. Process Control Corp. v.
Hydreclaim Corp., 190 F.3d 1350, 1356-57 (Fed.Cir. 1999) (refusing to
adopt a construction that would avoid invalidity where there was only one
reasonable interpretation of the claim term). Moreover, while the Court
may use the specification to interpret words in the claim, it is improper
to import extraneous limitations from the specification into the claim
terms. E.I du Pont de Nemours & Co. v. Phillips Petro., 849 F.2d 1430,
1433 (Fed.Cir. 1988) (refusing to read limitations into a claim to avoid
invalidity due to prior art). The du Pont court declined "extraneous
limitation" as any limitation read into a claim from the specification
wholly apart from any need to interpret what the patentee meant by
particular words or phrases in the claim. Id.
In light of these various doctrines of claim construction, the Court
rejects Incyte's arguments to the extent that they purport to limit the
claims to only what Incyte asserts is enabled by the specification.
Incyte has provided no authority to support its effort to transform claim
construction analysis into a full non-enablement and written description
analysis. While Incyte cites several cases which demonstrate the Federal
Circuit's strict application of the enablement requirement to
biotechnology inventions — see Enzo Biochem v. Calgene, 188 F.3d 1362
(Fed. Cir. 1999); Regents of the Univ. of California v. Eli Lilly,
119 F.3d 1559 (Fed.Cir. 1997); Amgen, Inc. v. Chugai Pharm. Co.,
927 F.2d 1200 (Fed.Cir. 1991) — none of these cases dictate that
the enablement analysis must be incorporated into claim construction.
None of the other cases relied upon by Incyte require limiting the
meaning of claim terms solely on the basis of an invalidity analysis.
Contrary to Incyte's interpretation, the Federal Circuit in Schering
Corp. v. Amgen Inc., 222 F.3d 1347 (Fed. Cir. 2000), limited the meaning
of the term "Interferon alpha" because the patentee had explicitly
limited that definition during prosecution. Id. at 1352-53. The Federal
Circuit expressly disagreed with the district court's rationale that the
term should be limited because a broader interpretation would render the
claim invalid for improper introduction of new matter. Id. at 1352-54.
Instead, the court based its claim construction on the established
doctrine requiring a court to adopt a patentee's explicit definition of a
term. Id. Likewise, in Cultor Corp. v. A.E. Staley Mfg. Co., 224 F.3d 1328
(Fed.Cir. 2000), the court construed "water-soluble polydextrose" to be
restricted to that prepared with a citric acid catalyst, because the
specification explicitly had limited the term to polydextrose produced
using a citric acid catalyst.*fn4 Id. at 1331.
Collectively, this Court interprets the cases cited above to instruct
that the asserted non-enablement of a proffered claim construction alone
is not a proper basis for rejecting that construction. Instead, the Court
must conduct the traditional claim construction analysis, looking first
to the claim language itself, then to the specification and prosecution
history. If the Court concludes from this analysis that a claim term is
susceptible to two or more meanings, the Court then must, where
possible, adopt a meaning which renders the claim valid. Adopting this
approach, the Court now proceeds to construe the disputed terms.
Claim I of the '934 patent reads:
A substrate with a surface comprising or more groups
of oligonucleotides with different, known sequences
covalently attached to the surface in discrete known
regions, said 103 or more groups of oligonucleotides
occupying a total area of less than 1 cm2 on said
substrate, said groups of oligonucleotides having
different nucleotide sequences.
Claim 7 of the '934 patent reads:
An array of more than 1,000 different groups of
oligonucleotide molecules with known sequences
covalently coupled to a surface of a substrate, said
groups of oligonucleotide molecules each in discrete
known regions and differing from other groups of
oligonucleotide molecules in monomer sequence, each of
said discrete known regions being an area of less than
about 0.01 cm2 and each discrete known region
comprising oligonucleotides of known sequence, said
different groups occupying a total area of less than 1
1. oligonucleotides is construed to mean polymers of nucleotides
ranging in length from 2 to about 100 nucleotides.
Affymetrix contends that "oligonucleotides" means polymers, or small
polymeric stretches, of nucleotides, ranging in length from 2 to about 100
Incyte contends that "oligonucleotides" means single-stranded polymers
of nucleotides synthesized monomer by monomer and less than about 20
nucleotides in length.*fn5
The Court looks to the plain meaning of the term, which suggests small
polymers of nucleotides. At the time of the hearing, the parties agreed
that oligonucleotides range from 2 to 100 nucleotides in length. The
Court rejects Affymetrix's assertion that the term also encompasses small
polymeric stretches, given that such a definition would effectively expand
"oligonucleotides" to include polynucleotides of unlimited length. A
patentee may be his own lexicographer, provided the definition is clearly
set forth in the specification. Beachcombers v. WildeWood Creative
Prods., Inc., 31 F.3d 1154, 1158 (Fed.Cir. 1994). However, Affymetrix
fails to cite any intrinsic evidence to support its unconventional
The Court rejects Incyte's argument that the term, "oligonucleotides,"
must be limited to single stranded synthetic nucleotides made monomer by
monomer. Incyte has failed to cite any portion of the specification or
prosecution history indicating that patentee intended the specific term,
"oligonucleotide," to be limited in this manner.*fn6 Instead, Incyte
relies exclusively on the argument that, without this limitation, the
claim would be invalid for non-enablement. The Court rejects this
argument for the reasons discussed above. Further, the Court finds that
in this case, "oligonucleotide" is not reasonably amenable to a
definition restricting it to single stranded synthetic nucleotides
made monomer by monomer. In such a case, the Court cannot rewrite the
claims, even if necessary to avoid a finding of invalidity. Process
Control, 190 F.3d at 1357.
2. known sequences is construed to mean sequences of monomers
identified prior to attachment to the surface.
Affymetrix contends that "known sequences" means sequences of
identified or identifiable monomers.
Incyte contends that "known sequences" means a polymer synthesized
monomer by monomer, and whose sequence is determined by the monomer by
monomer synthesis process used to generate it.
The Court adopts the plain and ordinary meaning of the words, "known
sequences," as there are no statements in the specification or
prosecution history which indicate that the inventors intended the words
to have a meaning inconsistent with the ordinary meaning. Accordingly,
the Court finds that Affymetrix's assertion that unknown but
identifiable sequences are encompassed by the ordinary meaning of "known
sequences" is untenable, as this definition contradicts the ordinary
meaning of "known."
Furthermore, for the reasons previously discussed, the Court finds that
"known sequences" cannot be restricted only to those sequences which
Incyte asserts are enabled by the specifications. "Known sequences" is
not reasonably amenable to a definition restricting it to polymers
synthesized monomer by monomer, whose sequence is determined by a monomer
by monomer synthesis process, and the Court will not import this
extraneous limitation into the claim.
3. covalently attached is construed to mean directly secured or joined
to the solid surface such that every chemical bond between the
oligonucleotide and the surface is a covalent bond. Affymetrix contends
that "covalently attached" means secured to the solid surface through a
covalent bond, either directly or indirectly. Affymetrix's definition
requires that only the bond at the point of attachment to the surface,
whether to the oligonucleotide or to the linker, be a covalent bond.
(Markman hearing transcript at 413:9-415:26).
Incyte contends that "covalently attached" means the oligonucleotide is
covalently bonded to the surface by the 3' end of the oligonucleotide.
Incyte's definition requires that, if a linker molecule is used to
covalently attach the oligonucleotide to the surface, every bond between
the surface and the oligonucleotide must be a covalent bond. (Id. at
The Court adopts the plain and ordinary meaning of the words,
"covalently attached" to determine that the oligonucleotide is secured or
joined to the solid surface by covalent bonding. The Court rejects
Affymetrix's suggestion that the oligonucleotide may be "indirectly"
covalently attached to the surface via a noncovalent bond between the
oligonucleotide and a linker molecule, as long as a covalent bond exists
between the linker and the surface. Such an interpretation contradicts
the plain language of the claim, which requires covalent attachment
between the oligonucleotide and the surface, not merely between a linker
and the surface. Affymetrix has failed to point to any intrinsic evidence
to suggest that it intended "covalent attachment" to have any meaning
other than this conventional meaning.
4. discrete known regions are construed to mean identified localized
areas on a surface which are, were, or are intended to be activated for
formation of a polymer, where the activation is accomplished through
exposure of the localized area to an energy source adapted to render a
group active for synthesis of the polymer on the surface or for
immobilization of a pre-existing polymer on a surface.
Incyte contends that a "discrete known region" is a localized area on a
surface which is, was, or is intended to be activated for synthesis of a
polymer, and which is also spatially addressable for activation of monomer
by monomer synthesis.
Both parties accept the definition of "regions" that the patentee
explicitly offers in the specification. In defining "predefined ...