REPORT AND RECOMMENDATION

MARY PAT THYNGE, Magistrate Judge.

I. INTRODUCTION

On May 10, 2010, Cornell University, Cornell Research Foundation, Inc. (collectively, "Cornell"), Life Technologies Corporation ("Life Technologies"), and Applied Biosystems, LLC ("Applied Biosystems") (collectively, "plaintiffs") brought this action against Illumina, Inc. ("Illumina" or "defendant"), alleging infringement of several patents.1 The currently asserted patents are in two distinct patent families, the Array Patent family and the LDR-PCR Patent family. The patents in the Array Patent family are U.S. Patent Nos. 7,083,917 ("the `917 patent"), 7,892,746 ("the `746 patent"), 7,893,233 ("the `233 patent), 8,288,521 (`the `521 patent"), 8,624,016 ("the `016 patent"), and 8,703,928 ("the `928 patent").2 The patents in the LDR-PCR Patent family are U.S. Patent Nos. 6,797,470 ("the `470 patent"), 7,166,434 ("the `434 patent"), 7,312,039 ("the `039 patent"), 7,332,285 ("the `285 patent"), and 7,429,453 ("the `453 patent").3 The remaining asserted claims are: claim 4 of the `470 patent; claims 1, 2, and 18 of the `917 patent; claim 5 of the `434 patent; claim 5 of the `039 patent; claim 3 of the `285 patent; claim 10 of the `453 patent; claims 1 and 2 of the `746 patent; claims 1, 2, 4, 5, 7, 8, 13, 15, and 26 of the `233 patent; claims 18 and 19 of the `521 patent; claims 1, 2, 3, 5, 13, and 18 of the `016 patent; and claims 1, 2, and 3 of the `928 patent.4

A Markman hearing was held on February 22, 2016. The court's construction of disputed claim terms is set forth below.

II. CLAIM CONSTRUCTION

The asserted patents cover instruments and methods for determining whether a certain DNA sequence is present in a sample. The Abstract of the Array Patent family recites:

The Abstract of the LDR-PCR Patent family recites:

The parties agree to the construction of the following claim terms.

"Oligonucleotide probe set(s)" means "oligonucleotide sequences that hybridize to a target sequence in a ligase detection reaction."

"Primer-specific portion" means "portion of an oligonucleotide capable of hybridizing to a nucleotide sequence used to initiate PCR amplification."

"Ligation product sequence(s)" and "ligation product(s)" mean "oligonucleotide sequence(s) resulting from a ligase detection reaction."

"Composite oligonucleotides" means "an oligonucleotide having to or more portions."

Based on the parties' agreement as to the meaning of those terms, the court adopts the parties' proposed constructions.

The meanings of the following claim terms are in dispute.

1. "solid support"

Representative claim 1 of the `917 patent recites:

Plaintiffs' proposed construction is: "solid-phase substrate."

Defendant's proposed construction is: "a single unitary substrate."

The parties agree the construction of "solid support" includes "substrate," but disagree whether the substrate comprises one or more components or structures (plaintiffs) or just a "single unitary" structure (defendant).8

Plaintiffs state the specification provides for beads or slides to be used individually or together as supports and describes coupling oligonucleotides to a solid support via another solid support.9 They argue, therefore, that a combination of supports is within the scope of the claims.10 Defendant maintains a person of ordinary skill in the art reading the intrinsic evidence, including the prosecution history, would understand the claims do not cover the use of intermediate supports coupling the oligonucleotide to the solid support.11 The court agrees with defendant that the "solid support" is "a single unitary substrate."

In support of their position, plaintiffs rely on the specification's statement that "[t]he solid support can be made from a wide variety of materials. The substrate may be biological, nonbiological, organic, inorganic, or a combination of any of these, existing as particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, discs, membranes, etc."12 As defendant explained during the Markman hearing, however, the "combined" reference is to composite materials, for instance a slide coated with a polymer, which is nevertheless a unitary structure like a piece of plywood is a unitary structure.13 The specification describes such composite: "[p]olymer-coated slides were tested for their capture capacity of addressable oligonucleotide probes following different procedures for immobilization of capture oligonucleotides."14 Those "polymer-coated slides" are a unitary structure.

Plaintiffs also rely on the specification's statement that:

That passage indicates the "linker" or "support" for coupling an oligonucleotide to the "solid support" are distinct, separate, structures; not that "support" is a species of "linker" as plaintiffs suggest.16 The specification thus contemplates use of a linker or a support to couple an oligonucleotide to the solid support. That use of an intervening support structure, however, was foreclosed during prosecution. The patentees originally attempted to claim either a linker or a support for oligonucleotide coupling. During prosecution, claim 120 of the application leading to the `917 patent claimed "a linker or support for coupling an oligonucleotide to the solid support attached to the solid support at each of the array positions."17 The examiner rejected that claim as indefinite, stating:

In response to that rejection, the patentees amended the claims to remove the words "or support" from the limitation clarifying that the oligonucleotides are coupled to the solid support using only a "linker"19 and stated to the patent office "[t]he rejection of claims 120-125, 128, and 136-137 under 35 U.S.C. § 112 (2nd para.) for indefiniteness is respectfully traversed in view of the above amendments."20 The court agrees with defendant that, in addition to reviewing the specification, the amendment removing "or support" in response to the examiner's question of whether the original language of application claim 120 was meant to indicate an oligonucleotide was coupled to the solid support by using a different support, a person of ordinary skill in the art would understand that a "solid support" means a single unitary object without any intermediate supports.21

The court adopts defendant's proposed construction that "solid support" means "a single unitary substrate."

2. "array of positions"

Representative claim 1 of the `928 patent recites:

Plaintiffs' proposed construction is: "arrangement of positions"

Defendant's proposed construction is: "positions organized in known locations."

The parties disagree whether the positions of the array can be either random or pre-defined (plaintiffs) or must be pre-defined (defendant).23

Plaintiffs contend defendant's proposed construction improperly imposes a temporal requirement on the "array of positions," i.e. that the positions of each oligonucleotide be known before they are attached to the solid support.24 They maintain nothing in the patent requires the oligonucleotides to be placed at a pre-determined location rather than at a location determined after the solid support is manufactured.25

In briefing, plaintiffs also maintained that "Illumina correctly states that, by having discrete locations for attachment on the array, a spacial relationship can be observed between the oligonucleotides attached to the solid support," but reiterated "the specific identity and position of the oligonucleotides at each discrete spot can be determined before or after the oligonucleotides are attached to the array."26 At the Markman hearing they stated there was no dispute that when an array is used one must know which oligonucleotide is where on the array.27

At the hearing, defendant explained its proposed construction did not require the positions be pre-determined, just that those positions are known.28 It also stated its construction was not about how the arrays are manufactured.29

Because the parties agree that when the arrays are used the positions of the oligonucleotides must be known, and with defendant's representation that its construction does not set a temporal limit (does not require pre-determination of oligonucleotide positions) or relate to how the solid supports are manufactured, the court adopts defendant's proposed construction of "array of positions" to mean "positions organized in known locations."

3. Claim Terms Related to the Connection of Oligonucleotides to the Solid Support

This group of terms relate to oligonucleotides being connected to a solid support.30

a. "linker"

Representative claim 1 of the `917 patent recites:

Representative claim 15 of the `233 patent recites:

Plaintiffs' proposed construction is: "feature that connects an oligonucleotide to a solid support."

Defendant's proposed construction is: "a molecule that covalently binds an oligonucleotide to the solid support without an intervening support."

Defendant states the critical difference in the parties' proposed constructions is whether a "linker" is a chemical molecule (defendant) or a "feature" which would allow a linker to be something else, such as an intervening solid structure, like a bead, between the oligonucleotide and the solid support (plaintiffs).33

Defendant's proposed construction defines a linker as "a molecule that covalently binds an oligonucleotide to the solid support without an intervening support."34 Plaintiffs note the specification discloses linkers that result in both covalent and non-covalent interactions. The specification describes covalent linkages when stating "linker molecules can be attached to the substrate via carbon-carbon bonds . . . or, preferably, by siloxane bonds" or as parts of a polymer on the substrate.35 It also discloses non-covalent linkages in "alternative embodiments" where "the linker molecules are absorbed to the surface of the substrate."36 Plaintiffs argue their construction provides for linkers that result in both covalent and non-covalent interactions.37 They state that construction also embraces intervening structures for connecting oligonucleotides to solid supports.38

The court has determined in its construction of the term "solid support," above, that the claims do not cover intervening structures, like an additional support, for connecting oligonucleotides to solid supports. As plaintiffs' proposed constructions for "linker" and the other terms in this group would cover intervening structures, the court rejects those proposed constructions. The court now addresses plaintiffs' additional criticisms of defendant's proposed constructions.

In addition to the purportedly improper exclusion of non-covalent connections, the disclosed absorption of the linker molecules to the surface of the substrate, plaintiffs argue defendant improperly limits the claimed linkers to "linker molecules." That criticism is based on plaintiffs' contention that in addition to linker molecules which can only be attached to a solid support through "chemical" linkers, plaintiffs assert attachment may be made through an "intervening solid structure." The court has rejected that argument.39 Because there is no other description in the patent of linkers other than linker molecules attached to the support through chemical bonds, the court adopts defendant's proposed constructions for linker and the other terms in this group. The court modifies defendant's proposed constructions for "linker" and "attached" to reflect the possibility of absorption in light of the specification's recitation that "[i]n alternative embodiments, the linker molecules are absorbed to the surface of the substrate."40

The court adopts defendant's proposed construction of "linker," as modified, to mean "a molecule that covalently binds an oligonucleotide to the solid support, or is absorbed thereto, without an intervening structure."

b. "immobilized"

Plaintiffs' proposed construction is: "restricted in mobility."

Defendant's proposed construction is: "covalently bound or bound via hybridization."

Plaintiffs' proposed construction is: "capable of being connected."

Defendant's proposed construction is: "functionalized to permit covalent bonding."

Plaintiffs' proposed construction is: "connected to."

Defendant's proposed construction is: "covalently bound or bound via hybridization."

Representative claim 1 of the `917 patent recites:

Representative claim 1 of the `746 patent recites:

Plaintiffs' proposed construction is: "oligonucleotide capable of hybridizing to a complementary nucleic acid."

Defendant's proposed construction is: "oligonucleotide [probe] which has no homology to a target sequence and is complementary to the addressable array specific portion of an oligonucleotide containing an addressable array specific portion and a target specific portion."

The parties disagree whether the capture oligonucleotide (probe) can be any sequence capable of hybridizing to a complementary nucleic acid (plaintiff) or must be a sequence that lacks homology43 to a target sequence and only hybridizes to a specific portion of an oligonucleotide of the array (defendant).44

The Federal Circuit recently reiterated "[t]he only meaning that matters in claim construction is the meaning in the context of the patent."45 "`[W]hen the scope of the invention is clearly stated in the specification, and is described as the advantage and distinction of the invention it is not necessary to disavow explicitly a different scope.'"46

Plaintiffs argue the claim language supports their construction because the term "homology" is never used in any of the claims and not all of the asserted claims include the requirement that the capture oligonucleotide hybridizes to the addressable array-specific portion of the target oligonucleotide.

That none of the asserted claims recite the term "homology" is not determinative as the claims "must be read in view of the specification, of which they are a part."47 "[T]he specification is always highly relevant to the claim construction analysis. Usually it is dispositive; it is the single best guide to the meaning of a disputed term."48

Plaintiffs also state Illumina's proposed construction requiring the "oligonucleotide [probe] . . . [to be] complementary to the addressable array specific portion of an oligonucleotide containing an addressable array specific portion and a target specific portion" might be appropriate if all the asserted claims included such limitations, as does representative claim 1 of the `746 patent.49 All asserted claims, however, do not recite those limitations. For instance, representative claim 1 of the `917 patent does not require the oligonucleotide probe to have those limitations and asserted claim 18 of `917 patent, depending from claim 1, merely requires the "capture oligonucleotide probes" need only "hybridize" to other oligonucleotides.50 Similarly, claim 1 of the `233 patent recites the "capture oligonucleotide" hybridizes to any "nucleic acid molecule" that has "a complementary nucleotide sequence."51 The differences in the recited limitations of the claims plaintiffs cite are also not determinative. To the extent plaintiffs basing their argument on the doctrine of claim differentiation, that doctrine is not a "hard and fast rule of construction" and "cannot broaden claims beyond their correct scope, determined in light of the specification and the prosecution history and any relevant extrinsic evidence."52 Whether or not plaintiffs are basing their argument on that doctrine:

The intrinsic record demonstrates the claimed invention was an addressable, or universal, array and was meant to improve on prior detection techniques using hybridization arrays where false positive and false negative results could occur due to cross-hybridization. The `917 patent is titled "Detection of Nucleic Acid Sequence Differences Using the Ligase Detection Reaction with Addressable Arrays," and the specification states "[t]he array of the present invention will be universal, making it useful for detection of cancer mutations, inherited (germline) mutations, and infectious diseases."54 During prosecution, the applicants touted the advantage of the claimed invention over prior art hybridization arrays. "In a direct hybridization array, the capture probes, which are covalently linked to the array surface, are complementary to sequences within the gene or target nucleotides to be interrogated."55

The applicants repeatedly distinguished their addressable arrays from prior art hybridization arrays that they viewed as unsatisfactory.

The applicants again touted the superiority of the claimed invention over hybridization arrays.

Plaintiffs' proposed construction of the "capture oligonucleotides" terms is "oligonucleotide capable of hybridizing to a complementary nucleic acid." They characterize that construction as meaning "the capture oligonucleotide (probe) can be any sequence capable of hybridizing to a complementary nucleic acid."61 That construction would cover hybridization arrays that were repeatedly distinguished during prosecution as not being what was described and claimed in the Array Patent family. Consequently, plaintiffs' proposed construction is rejected. The court will next determine whether defendant's construction requiring no homology and complementarity is supported by the intrinsic evidence.

The intrinsic evidence, and extrinsic evidence in the form of deposition testimony of named inventor Dr. George Barany, support defendant's argument that the capture oligonucleotides have no homology to a target sequence. The `917 patent specification states:

That there be no homology was made clear during the prosecution of the `917 patent family. Dr. Barany stated "array hybridization is carried out using divergent capture probe sequences that are not homologous to the target sequence being detected or any other known genomic sequence."63 Dr. Gerry also noted "[a]n addressable array uses capture probes that are de novo sequences separate and distinct from the nucleic acid sequences of interest."64

Finally, Dr. Barany testified it was the inventors' goal to design around the problems associated with hybridization arrays.

The court determines, therefore, that the scope of the invention is limited to capture oligonucleotides having no homology to a target sequence.

The court also determines the intrinsic record supports defendant's construction requiring the capture oligonucleotide to the be "complementary to the addressable array specific portion of an oligonucleotide." In the Summary of the Invention, the `917 patent specification states:

The prosecution history also supports defendant's proposed construction. During prosecution of the `917 patent family, Dr. Barany represented to the PTO that "[t]hese claims further require that the capture probes have nucleotide sequence complementary to the addressable array specific portions of the oligonucleotide probes."68 Dr. Gerry likewise explained "[t]he addressable array-specific portion of a ligation product is complementary to a capture oligonucleotide immobilized on a solid support."69

The court concludes that the "capture oligonucleotides" are limited to those "complementary to the addressable array specific portion of an oligonucleotide containing an addressable array specific portion and a target specific portion." The court determines, therefore, that defendant's proposed constructions are consistent with the terms' "meaning in the context of the patent" and supported by the prosecution history and the specification's description of the "advantage and distinction of the invention" over the prior art. Defendant's proposed construction thus reflects "what the inventors actually invented."70 The court adopts defendant's proposed construction that "capture oligonucleotide probes" and "capture oligonucleotide" mean "oligonucleotide [probe] which has no homology to a target sequence and is complementary to the addressable array specific portion of an oligonucleotide containing an addressable array specific portion and a target specific portion."

Representative claim 10 of the `453 patent recites:

Plaintiffs' proposed construction is: "hybridizing the one or more amplification products to an oligonucleotide immobilized on a solid support."

Defendant's proposed construction is: "hybridizing the amplification products to capture oligonucleotides attached on the solid support."

The parties agree that "capture" means the amplification product hybridizes to an oligonucleotide on a solid support.72 According to defendant, the parties' disagreement over this term is whether the amplification products may hybridize to any oligonucleotide on the solid support, as plaintiffs contend, or whether those products must be hybridized to capture oligonucleotides.73 The court agrees with defendant.

The specification of the `917 patent is incorporated by reference in the `453 specification: "use of a solid support with an array of capture oligonucleotides is fully disclosed in the pending provisional U.S. Patent Application Ser. No. 60/011,359 [resulting in the `917 patent], which is hereby incorporated by reference."74 Therefore, the "capturing" of claim 10 of the `453 patent is accomplished according to the understanding of the meaning of "capture" as it modifies "oligonucleotide" in the `917 patent. The court determined that "capture oligonucleotides" have specific characteristics because the applicants argued those characteristics distinguished their universal array from hybridization arrays. The `453 patent incorporated those characteristics. The court adopts defendant's proposed construction of "capturing said one or more amplification products to a solid support" to mean "hybridizing the amplification products to capture oligonucleotides attached on the solid support."

5. Claim Terms Related to Hybridization of Oligonucleotides to Their Complementary Sequences

These terms are considered together because they all relate to the hybridization of oligonucleotides-or portions of oligonucleotides — with each other.75

a. "each [type of] capture oligonucleotide hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence"/"the capture oligonucleotides hybridize to complementary portions of the target nucleic acid molecules"

Representative claim 1 of the `233 patent recites:

Representative claim 7 of the `233 patent recites:

Plaintiffs' proposed construction is: "each capture oligonucleotide hybridizes to an oligonucleotide containing a complementary nucleotide sequence."

Defendant's proposed construction is: "each capture oligonucleotide hybridizes to an oligonucleotide containing a complement to the entire capture oligonucleotide sequence."

The parties dispute whether the terms allow an oligonucleotide and its complementary sequence to be partially hybridized with or without complete complementarity (plaintiffs) or, instead, require that the oligonucleotide be hybridized to the entire capture sequence (defendant).78

Plaintiffs base their arguments with respect to this term (and the others in this group of terms) on the doctrine of claim differentiation. 35 U.S.C. § 112, ¶ 4 states "a claim in dependent form shall contain a reference" to the claim from which it depends "and then specify a further limitation of the subject matter claimed."79 Under the doctrine of claim differentiation, a dependent claim that adds a limitation gives rise to the presumption that the claim from which it depends is not so restricted.80 As noted above, "[w]hile the doctrine of claim differentiation is not a hard and fast rule of construction, it does create a presumption that each claim in the patent has a different scope."81 "This presumption is especially strong where `there is a dispute over whether a limitation found in a dependent claim should be read into an independent claim, and that limitation is the only meaningful difference between the two claims.'"82

Claim 1 of the `746 patent, one of the selected claims, sets forth a method that includes the step of contacting a sample with:

Dependent claim 4 of the `746 patent requires capture oligonucleotides with complete complementarity to a portion of the target oligonucleotides:

The method according to claim 1, wherein the addressable array-specific portions of the target oligonucleotides hybridize to their complementary capture nucleotides with complete complementarity.84

Similarly, claim 5 of the `746 patent includes a step of contacting a sample with:

Thus, claims 1 and 5 require target oligonucleotides to "hybridize the addressable array-specific portion of each target oligonucleotide to its complementary capture oligonucleotide." Claims 4 and 8 add that the hybridization be "with complete complementarity." That additional requirement is the only meaningful difference added by dependent claims 4 and 8. To include the "complete complementarity" requirement to claims not reciting that requirement would render those dependent claims superfluous. The court therefore rejects defendant's proposed constructions for each of the terms in this group and adopts plaintiffs' proposed constructions for those terms.87 The court defines "each [type of] capture oligonucleotide hybridizes to a nucleic acid molecule comprising a complementary nucleotide sequence"/"the capture oligonucleotides hybridize to complementary portions of the target nucleic acid molecules" to mean "each capture oligonucleotide hybridizes to an oligonucleotide containing a complementary nucleotide sequence."

b. "one or more target nucleic acid molecules hybridized [to complementary portions of the capture oligonucleotides on the solid support]"

Plaintiffs' proposed construction is: "one or more nucleic acid molecules are hybridized to one or more complementary nucleic acid molecules on a solid support."

Defendant's proposed construction is: "one or more nucleic acid molecules are hybridized [to complementary portions of the capture oligonucleotides on the solid support]."

Court's construction: "one or more nucleic acid molecules are hybridized to one or more complementary nucleic acid molecules on a solid support."

c. "each type of capture oligonucleotide . . . hybridizes to its complement"

Plaintiffs' proposed construction is: "at least a portion of each capture oligonucleotide hybridizes to its complement."

Defendant's proposed construction is: "each type of capture oligonucleotide hybridizes to an oligonucleotide containing a complement to the entire capture oligonucleotide sequence."

Court's construction: "at least a portion of each capture oligonucleotide hybridizes to its complement."

d. "wherein the zip code portion of each of the composite oligonucleotides . . . hybridizes to its complement"

Plaintiffs' proposed construction is: "wherein an address portion of each of the composite oligonucleotides, or a portion thereof, hybridizes to its complement."

Defendant's proposed construction is: "wherein the zip code portion of each of the composite oligonucleotides hybridizes to an oligonucleotide containing a complement to the entire zip code portion."

Court's construction: "wherein an address portion of each of the composite oligonucleotides, or a portion thereof, hybridizes to its complement."

e. "the capture oligonucleotides hybridize to the complementary portions of the nucleic acid molecules"

Plaintiffs' proposed construction is: "at least a portion of each capture oligonucleotide hybridizes to a complementary portion of a nucleic acid molecule."

Defendant's proposed construction is: "each capture oligonucleotide hybridizes to one or more oligonucleotides containing a complement to the entire capture oligonucleotide sequence."

Court's construction: "at least a portion of each capture oligonucleotide hybridizes to a complementary portion of a nucleic acid molecule."

6. Claim Terms that Relate to Differences between Oligonucleotide Sequences

The following terms are considered together because they relate to differences in sequence between oligonucleotides or portions of oligonucleotides. The parties disagree whether the each limitation is satisfied when one oligonucleotide differs in sequence from "its adjacent" sequence, "another" sequence, "another type of" sequence, or "other types of sequences" by at least 25% (plaintiff) or whether all of these limitations mean the same thing by requiring an oligonucleotide sequence to be at least 25% different from "every" other oligonucleotide sequence (defendant).88

The court agrees with defendant that the intrinsic record supports its proposed constructions. For instance, each claim of the `233 patents requires "each type of capture oligonucleotide . . . differs from the nucleotide sequence of other types of oligonucleotides" by at least 25%.89 Claim 1 of the `746 patent requires that "each type of capture oligonucleotide . . . differs in nucleotide sequence when aligned to another type of capture oligonucleotide, by at least 25%."90 This language leads to the conclusion that each capture oligonucleotide differs from every other type of capture oligonucleotide, not just one other type as plaintiffs' construction allows. Claim 1 of the `917 patent requires that "each capture oligonucleotide probe of the array differs in sequence from its adjacent capture oligonucleotide, when aligned to each other by at least 25% of the nucleotides."91 Plaintiffs argue that because the `917 patent uses the singular form, the limitation is satisfied when the capture oligonucleotide differs in sequence from "just one other oligonucleotide sequence."92 As a general rule of construction, however, use of the singular form includes the plural form.93 Therefore, that singular form does not require the interpretation put forth by plaintiffs.

The specification also supports defendant's position. As discussed above, the patentees sought to avoid the problem of cross-hybridization experienced in prior art arrays. To accomplish this, "[e]ach of the capture oligonucleotides have substantial sequence differences to minimize any chances of cross-reactivity."94 The specification also explains that:

During prosecution, the applicants told the PTO the capture oligonucleotides were substantially different from each other.

In explaining the claimed invention, Dr. Gerry told the PTO:

Finally, named inventor Dr. Robert Hammer testified that the capture oligonucleotides all needed to be different.

Because the intrinsic records supports defendant's proposed constructions, the court adopts those construction for the terms in this group.

a. "each capture oligonucleotide probe of the array differs in sequence from its adjacent capture oligonucleotide probe, when aligned to each other by at least 25%"

Plaintiffs' proposed construction is: "each capture oligonucleotide probe of the array differs in sequence from an adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

Defendant's proposed construction is: "each capture oligonucleotide probe [of the array] differs in sequence from every adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

Court's construction: "each capture oligonucleotide probe [of the array] differs in sequence from every adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

b. "each type of capture oligonucleotide . . . differs in nucleotide sequence, when aligned to another type of capture oligonucleotide that is located on an adjacent position of said solid support, by at least 25%"

Plaintiffs' proposed construction is: "each capture oligonucleotide probe of the array differs in sequence from an adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

Defendant's proposed construction is: "each capture oligonucleotide probe [of the array] differs in sequence from every adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

Court's construction: "each capture oligonucleotide probe [of the array] differs in sequence from every adjacent capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

c. "each type of capture oligonucleotide . . . differs in nucleotide sequence, when aligned to another type of capture oligonucleotide, by at least 25%"/"each type of capture oligonucleotide . . . differs by at least 25% in nucleotide sequence, when aligned to another type of capture oligonucleotide"

Plaintiffs' proposed construction is: "each type of capture oligonucleotide probe of the array differs in sequence from another type of capture oligonucleotide probe, when aligned, by at least 25% in nucleotide sequence."

Defendant's proposed construction is: "each type of capture oligonucleotide differs by at least 25% in nucleotide sequence, when aligned, to every other type of capture oligonucleotide."

Court's construction: "each type of capture oligonucleotide differs by at least 25% in nucleotide sequence, when aligned, to every other type of capture oligonucleotide."

d. "each type of capture oligonucleotide . . . comprises a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides in the collection by at least 25% when aligned"/"each type of capture oligonucleotide . . . comprising nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotide of the collection by at least 25% when aligned"/"each type of capture nucleotide . . . with a nucleotide sequence that differs from the nucleotide sequence of other types of capture oligonucleotides on the solid support by at least 25% when aligned"

Plaintiffs' proposed construction is: "each type of capture oligonucleotide probe differs in sequence from other types of capture oligonucleotide probes, when aligned, by at least 25% in nucleotide sequence."

Defendant's proposed construction is: "each type of capture oligonucleotide . . . differs by at least 25% in nucleotide sequence, when aligned, to every other type of capture oligonucleotide."

Court's construction: "each type of capture oligonucleotide . . . differs by at least 25% in nucleotide sequence, when aligned, to every other type of capture oligonucleotide."

7. "uniform hybridization conditions"

Representative claim 1 of the `917 patent recites:

Plaintiffs' proposed construction is: "common conditions at which different oligonucleotides are capable of hybridizing to complementary nucleic acids."

Defendant contends this term is indefinite.

"Because a patent is presumed to be valid, the evidentiary burden to show facts supporting a conclusion of invalidity is one of clear and convincing evidence."101

Section 112 ¶ 2 provides: "[t]he specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention."102 "[A] patent is invalid for indefiniteness if its claims, read in light of the specification delineating the patent, and the prosecution history, fail to inform, with reasonable certainty, those skilled in the art about the scope of the invention."103 "[A] claim must be `sufficiently definite to inform the public of the bounds of the protected invention, i.e., what subject matter is covered by the exclusive rights of the patent.'"104 The parties disagree as to whether the specification meets these requirements.

The specification states that prior art arrays required hybridization conditions optimized for each nucleotide sequence of interest: "existing methods in the prior art relying on allele-specific PCR, differential hybridization, or sequencing-by-hybridization methods must have hybridization conditions optimized for each new sequence being analyzed. When attempting to detect multiple mutations simultaneously, it becomes difficult or impossible to optimize hybridization conditions."105

The claimed universal array addressed that difficulty by selecting array sequences that enabled hybridization of a plurality of oligonucleotides to occur under common conditions: "the present invention is a general method for high specificity detection of correct signal, independent of the target sequence, and under uniform conditions."106

Plaintiffs state the specification discloses exemplary common hybridization conditions in which oligonucleotides of the array hybridize to complementary sequences in solution.107 For instance, in Example 3, capture oligonucleotides were hybridized with their complements under identical conditions.108 Plaintiffs maintain from those and other disclosures, a person of ordinary skill in the art would understand that "uniform hybridization conditions" means "common conditions at which different oligonucleotides are capable of hybridizing to complementary nucleic acids" and fully appreciate the "scope of the invention with reasonable certainty."109

Defendant argues the scope of the invention in not reasonably certain. It contends the specification provides no guidance as to when hybridization conditions must be uniform, i.e. can the hybridization conditions vary over time?110 Likewise, the specification does not describe which hybridization conditions must be uniform.111 According to defendant, without knowing those parameters, it is impossible to understand the bounds of the claims in order to avoid infringement.112

In light of the purpose of the claimed invention, the court agrees with plaintiffs that defendant's argument is mis-focused. The purpose of the invention was to overcome the difficulty in the prior art of detecting multiple sequences simultaneously. The prior art required optimization of conditions for each different oligonucleotide sequence being analyzed. Because of that requirement, "attempting to detect multiple mutations simultaneously, . . . becomes difficult or impossible to optimize hybridization conditions."113 The claimed invention sought to detect multiple, sometimes thousands, of sequences on the same array and, using zip codes, accomplished that goal whereby all of the oligonucleotides are exposed to the same conditions, i.e., different conditions did not have to be optimized for each sequence. Put another way, the multiple oligonucleotides are detected in a hybridization solution having uniform, or common, conditions.114 If some of those conditions, e.g. temperature, vary during the reaction, each different oligonucleotide is still exposed to the same common condition.

The court, therefore, determines defendant has not shown by clear and convincing evidence that this term is indefinite and adopts plaintiffs' construction of "uniform hybridization conditions" as meaning "common conditions at which different oligonucleotides are capable of hybridizing to complementary nucleic acids."

8. "addressable array-specific portion"/"address-specific portion"/"zip code portion"

Representative claim 1 of the `746 patent recites:

Representative claim 18 of the `521 patent recites:

Representative claim 1 of the `016 patent recites:

The following terms relate to portions of the oligonucleotide sequences in the Array Patents. The parties agree these terms are directed to the portion of the composite oligonucleotide that hybridizes to the complementary capture oligonucleotide on the array.118 Parties disagree as to whether the terms should be construed to prohibit the recited "portions" of oligonucleotides from hybridizing to naturally occurring nucleic acids and other oligonucleotides of the array (defendant) or not (plaintiff).119 Plaintiffs contend nothing in the claims or specification supports defendant's proposed prohibition.120 Defendant argues this prohibition follows from the fundamental objective stated in the specification: to prevent cross-hybridization.121 The parties each reference their arguments concerning the "capture oligonucleotide probe"/"capture oligonucleotide(s)" terms as being applicable here.122 Plaintiffs also state defendant's proposed constructions are also based on its purportedly incorrect arguments with respect to the "25% difference" terms.123

According to the specification, "[t]he capture oligonucleotides are complementary to the addressable array-specific portions"124 and "[t]his oligonucleotide probe is then captured by its addressable array-specific portion, a sequence complementary to the capture oligonucleotide on the addressable solid support array."125 The addressable array-specific portion is complementary to the capture oligonucleotide. Because the parties each rely on their arguments concerning the "capture oligonucleotide" terms and the "25% difference" terms with respect to these terms, and the court adopted defendant's proposed construction of those groups of terms, the court adopts defendant's construction of these terms for the reasons explained in those sections.

a. "addressable array-specific portion"

Plaintiffs' proposed construction is: "a portion of oligonucleotide that hybridizes to a complementary oligonucleotide, or portion thereof, at a particular location on an array."

Defendant's proposed construction is: "portion of an oligonucleotide that selectively hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to naturally occurring nucleic acids or to other oligonucleotides located on the array."

Court's construction: "portion of an oligonucleotide that selectively hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to naturally occurring nucleic acids or to other oligonucleotides located on the array."

b. "address-specific portion"

Plaintiffs' proposed construction is: "a portion of oligonucleotide that hybridizes to a complementary oligonucleotide, or portion thereof, at a particular location on an array."

Defendant's proposed construction is: "portion of an oligonucleotide that selectively hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to naturally occurring nucleic acids or to other oligonucleotides located on an array."

Court's construction: "portion of an oligonucleotide that selectively hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to naturally occurring nucleic acids or to other oligonucleotides located on an array."

c. "zip code portion"

Plaintiffs' proposed construction is: "a portion of oligonucleotide that hybridizes on an array to a complementary oligonucleotide."

Defendant's proposed construction is: "portion of an oligonucleotide that selectively hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to naturally occurring nucleic acids or to other oligonucleotides located on an array."

Court's construction: "portion of an oligonucleotide that selectively hybridizes to a complementary oligonucleotide located on an array, and does not hybridize to naturally occurring nucleic acids or to other oligonucleotides located on an array."

9. "unique nucleotide sequence"/"unique nucleotide sequence portions"

Representative claim 4 of the `470 patent recites:

Plaintiffs' proposed construction is: "a sequence that is different for each locus."

Defendant's proposed construction is: "portion(s) of a ligation product that hybridizes to a complementary address sequence on an addressable array that does not exist in ligation products resulting from any other target sequence."

The parties dispute whether every ligation product has to have a portion that hybridizes to the array and is different from every other ligation product (defendant) or whether such a portion need only be different for each locus analyzed (plaintiffs).127

The parties competing constructions differ based upon whether the claims cover the embodiments illustrated in Figures 13B and 13C of the `917 patent, as plaintiffs contend, or are limited to covering only the Figure 13B embodiment, as defendant contends.

With respect to Figure 13B, on which defendant relies, the specification recites:

With respect to Figure 13C, which plaintiffs rely on, the specification recites:

Defendant acknowledges that Figure 13C is described as allowing a capture probe to have more than one corresponding type of assay product. It maintains that while the independent claims of the asserted `470 patent family cover both embodiments, the asserted dependent claims, through their use of the term "unique," cover only the embodiment depicted in Figure 13B.130 The court disagrees with defendant. Each embodiment describes a "unique" address or portion. The court declines to exclude the Figure 13C embodiment from the construction of these terms and adopts plaintiffs proposed construction of "unique nucleotide sequence" and "unique nucleotide sequence portions" to mean "a sequence that is different for each locus."

10. "ligase detection reaction"/"ligase detection reaction cycles"/"suitable for ligation together"

Representative claim 1 of the `285 patent recites:

Representative claim 1 of the `470 patent recites:

a. "ligase detection reaction"

Plaintiffs' proposed construction is: "reaction capable of forming a ligation product that can be detected."

Defendant's proposed construction is: "reaction which detects the presence of target nucleotide sequence in a sample by using a ligase and one or more sets of two oligonucleotide probes in which the ligase joins the two oligonucleotide probes only if they are hybridized at adjacent positions on a target nucleotide sequence."

b. "suitable for ligation together"

Plaintiffs' proposed construction is: "capable of forming a ligation product."

Defendant's proposed construction is: "able to be ligated together only when hybridized adjacent to one another on the target nucleotide sequence."

c. "ligase detection cycles"

Plaintiffs' proposed construction is: "cycles comprising at least the following steps: denaturation, hybridization, and ligation, with the denaturation step occurring at the beginning or the end."

Defendant's proposed construction is: "ligase detection reaction comprising: (1) denaturation; (2) hybridization of the oligonucleotide probe set; and (3) ligation of adjacently hybridized oligonucleotide probe sets."

The Parties have two disputes about these terms. First, is whether a ligation detection reaction requires that the oligonucleotides must hybridize adjacent or abutting each other (defendant) or do not have to (plaintiff).133 The second dispute relates to whether a "ligase detection cycle" requires a denaturation step to be at the beginning of the cycle (defendant) or whether it can be at the end, after the oligonucleotide probes are hybridized and (some) are ligated (plaintiff).134

Beginning with the first dispute, plaintiffs primarily rely a claim differentiation argument.

Claim 1 of the `039 patent recites:

Claim 2 of the `039 patent depends from claim 1 and recites:

Because claim 2 adds the "adjacently hybridizing" requirement, plaintiffs maintain it would be improper to impose that requirement on claims not explicitly requiring adjacency.137 However, "[i]t is axiomatic that the claim construction process entails more than viewing the claim language in isolation. Claim language must always be read in view of the written description and any presumption created by the doctrine of claim differentiation will be overcome by a contrary construction dictated by the written description or prosecution history."138

The court determines that in this case the presumption is overcome. The `470 specification incorporates by reference the definition of "ligase detection reaction" in the disclosure of Barany's prior art patent application WO 91/17239. The specification states "[t]he ligase detection reaction is described generally in WO 9[1]/17239 to Barany et al. . . ., the disclosures of which are hereby incorporated by reference."139 That application recites:

When the specification "reveal[s] a special definition given to a claim term by the patentee . . . the inventor's lexicography governs."141 This includes definitions included in documents incorporated by reference.142

The specification consistently and exclusively describes the ligase detection reaction of the invention as requiring adjacent hybridization:

Figure 16 of the `470 patent illustrates successful ligation where the oligonucleotide probes are adjacently hybridized and unsuccessful ligation where there is a gap between the hybridized probes.144 Describing Figure 16, the specification states "LDR products are only formed on the correct length target sequence, and thus the presence of that target is distinguished (step 4)."145 Named inventor Dr. Matthew Lubin confirmed in deposition that Figure 16 illustrates unsuccessful ligation where there is a gap between the hybridized oligonucleotide probes:

The specification distinguishes prior art gap ligase chain reaction methods.

During prosecution, Dr. Barany also distinguished the gap ligase chain reaction disclosed in prior art by Zaun:

Based on the foregoing evidence, the court concludes the claims require the two oligonucleotide probe to hybridize at adjacent positions. Therefore, the court construes "ligase detection reaction" to mean "reaction which detects the presence of target nucleotide sequence in a sample by using a ligase and one or more sets of two oligonucleotide probes in which the ligase joins the two oligonucleotide probes only if they are hybridized at adjacent positions on a target nucleotide sequence" and "suitable for ligation together" to mean "able to be ligated together only when hybridized adjacent to one another on the target nucleotide sequence."

The parties' second dispute with whether a ligase detection reaction cycle requires a denaturation step at the beginning of the cycle or whether it can be at the end, after oligonucleotide probes are hybridized and (some) are ligated.

"[A] claim requires an ordering of steps when the claim language, as a matter of logic or grammar, requires that the steps be performed in the order written, or the specification directly or implicitly requires an order of steps."150

Defendant does not disagree that an additional denaturation step may be included in a ligase detection reaction cycle but insists an initial denaturation step is required for separation of double stranded DNA to create a single stranded target.151 It points to the figures in the patent and the related descriptions of those figures for its position. For example defendant notes Figure 10 illustrates the cycle, and is described in the specification, in a manner consistent with its proposed order of steps.

That and the other figures defendant cites in its brief do require denaturation of double stranded DNA at the beginning of the cycle. Those figures, and related descriptions, are specific embodiments. Plaintiffs, however, note that if the reaction starts with a single-stranded target, such as a strand of RNA, there is nothing to denature as a first step.153 The court agrees with plaintiffs that in that case, an initial denaturation step is not required as defendant's proposed construction does. Consequently the court adopts plaintiffs' proposed construction of "ligase detection reaction cycle" to mean "cycles comprising at least the following steps: denaturation, hybridization, and ligation, with the denaturation step occurring at the beginning or the end."

11. "ligase detection reaction mixture"/"ligation detection reaction mixture"/"reaction mixture"/"polymerase chain reaction (PCR) mixture"

Representative claim 1 of the `470 patent recites:

a. "ligase detection reaction mixture"/"ligation detection reaction mixture"/"reaction mixture"

Plaintiffs' proposed construction is: "mixture containing the components or products of a ligase detection reaction."

Defendant's proposed construction is: "mixture that contains all of the components used to perform a ligase detection reaction, including a sample, a ligase and one or more oligonucleotide probe sets, in either ligated or unligated form."

b. "polymerase chain reaction (PRC) mixture"

Plaintiffs' proposed construction is: "mixture containing the components or products of a polymerase chain reaction."

Defendant's proposed construction is: "mixture that contains all of the components used to perform a polymerase chain reaction, including a polymerase, a template sequence, and unextended and/or extended primer sequences containing sequences that are the same as, and sequences that are complementary to, the template sequence."

These terms relate to mixtures of components at stages of the claimed methods.

The parties' dispute is whether the components used in a reaction must still be present after the reaction has been performed.155

Plaintiffs contend each of these mixtures refer to two mixtures that necessarily contain different components.156 According to plaintiffs, the first ligase reaction mixture contains the components that are input into the ligase detection reaction and the second ligase detection reaction mixture contains the output of the ligase detection mixture than is, in turn, input into the PCR reaction.157 They make the same argument regarding the polymerase chain reaction mixture. These arguments are contrary to the claim language and the specification.

Claim 1 of the `470 patent introduces "a ligase detection reaction mixture" and then twice refers back to "the ligase reaction mixture." The meaning of "a ligase detection reaction mixture" does not change in the claim to include a product of the reaction. Also, the claims recites "subjecting the ligase detection reaction mixture to one or more ligase detection reaction cycles to form a ligation product sequence," making clear the "ligase detection reaction mixture" is distinct from "a ligation product." Furthermore, the ligase detection mixture is subjected to "one or more ligase detection reaction cycles." For there to be more than one cycle, at least some of each of the original components necessarily must be present.

The same analysis applies to polymerase chain reaction mixture. The claim introduces "a polymerase chain reaction mixture" and refers back to "the polymerase chain reaction mixture." And again, the polymerase chain reaction mixture is subject to "one or more polymerase chain reaction cycles to form extension products." As with the ligase detection reaction mixture, the polymerase chain reaction mixture is different than the product of the polymerase chain reaction. Because the mixture is subjected to "one or more" cycles, at least some of each of the original components necessarily must be present.

Moreover, the specification describes both mixtures consistent with the above understanding: "[t]he sample, the plurality of oligonucleotide probe sets, and a ligase are blended together to form a ligase detection reaction mixture"158 and "[t]he ligase detection reaction mixture is blended with the one or a plurality of oligonucleotide primer sets and the polymerase to form a polymerase chain reaction mixture."159 Neither description includes the products of LCR/PCR reactions as part of the reaction mixtures.

Because defendant's proposed constructions are consistent with the claim language and the specification, the court construes "ligase detection reaction mixture"/"ligation detection reaction mixture"/"reaction mixture" to mean "mixture that contains all of the components used to perform a ligase detection reaction, including a sample, a ligase and one or more oligonucleotide probe sets, in either ligated or unligated form" and "polymerase chain reaction (PRC) mixture" to mean "mixture that contains all of the components used to perform a polymerase chain reaction, including a polymerase, a template sequence, and unextended and/or extended primer sequences containing sequences that are the same as, and sequences that are complementary to, the template sequence."

12. "target-specific portion(s)"

Representative claim 18 of the `521 patent recites:

Plaintiffs' proposed construction is: "portion of oligonucleotide capable of hybridizing to a target nucleic acid."

Defendant's proposed construction is: "portion of an oligonucleotide capable of hybridizing to a target nucleic acid sequence of interest from naturally occurring nucleic acids."

The parties' dispute is whether the "target nucleic acid" that hybridizes to a "portion of an oligonucleotide" is restricted to "naturally occurring nucleic acids" (defendant) or not (plaintiffs). In support of such restriction, defendant notes the specification repeatedly describes target nucleic acids as naturally occurring and contains no description of target-specific portions hybridizing to artificial target nucleic acids.161 It also points to the specification's description of the invention as being used to detect cancer and other human diseases where the target nucleic acids in the sample are naturally occurring: "[t]he array of the present invention will be universal, making it useful for detection of cancer mutations, inherited (germline) mutations, and infectious diseases."162 Defendant also cites statements made during prosecution and in depositions relating to use of the invention in disease detection. During prosecution, Dr. Barany submitted a declaration describing how the claimed invention "provides a rapid and reliable method for the detection of genomic mutations (e.g., genetic disease mutations and cancer related mutations), promoter methylation, and infectious diseases (e.g., bacterial, fungal and viral infections."163 At deposition, Dr. Barany testified that "detection of cancer mutations, inherited (germline) mutations, and infectious diseases" was "a very important part of the invention."164

Although disease detection, using naturally occurring nucleic acids, is an important focus of the invention, the evidence defendant relies on does not convince the court there was a clear and unambiguous disavowal of detection of non-naturally occurring nucleic acids.165 Therefore, the court adopts plaintiffs' proposed construction of "target-specific portion(s)" as meaning "portion of oligonucleotide capable of hybridizing to a target nucleic acid."

Order: The Court's Claim Construction

At Wilmington, this 6th day of May, 2016, having heard oral argument, having reviewed the papers submitted with the parties' proposed claim constructions, and having considered all of the parties' arguments (whether or not explicitly discussed herein);

IT IS ORDERED that the disputed claim language in asserted claims of the patent-in-suit, as identified by the parties, shall be construed below consistent with the tenets of claim construction set forth by the United States Court of Appeals for the Federal Circuit in Phillips v. AWH Corp.,166 as follows:

Pursuant to 28 U.S.C. § 636(b)(1)(B), FED. R. CIV. P. 72 (b)(1), and D. DEL. LR 72.1, any objections to the Report and Recommendation shall be filed within fourteen (14) days limited to twenty-five (25) pages after being served with the same. Any response shall be limited to twenty-five (25) pages.

The parties are directed to the Court's Standing Order in Non-Pro Se Matters for Objections Filed under FED. R. CIV. P. 72 dated November 16, 2009, a copy of which is found on the Court's website (www.ded.uscourts.gov.)