Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-cand-3_07-cv-02845/USCOURTS-cand-3_07-cv-02845-15/pdf.json

Nature of Suit Code: 830
Nature of Suit: Patent
Cause of Action: 28:1338 Patent Infringement

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United States District Court

For the Northern District of California

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IN THE UNITED STATES DISTRICT COURT

FOR THE NORTHERN DISTRICT OF CALIFORNIA

APPLERA CORPORATION – APPLIED

BIOSYSTEMS GROUP, a Delaware

corporation,

Plaintiff,

 v.

ILLUMINA, INC., a Delaware corporation,

SOLEXA, INC., a Delaware corporation, and

STEPHEN C. MACEVICZ, an individual,

Defendants. /

No. C 07-02845 WHA

CLAIM CONSTRUCTION

ORDER

INTRODUCTION

This is a claim construction order for United States Patent Nos. 5,750,341 and 6,306,597. 

This order addresses the six phrases selected for construction by the parties. A technology

tutorial, as well as a full round of briefing and a hearing, preceded this order. 

STATEMENT

Defendant Solexa, Inc., is the assignee of the ’341 patent, ’119 patent, and the

’597 patent. The patents are directed towards methods of learning unknown sequences in DNA. 

DNA consists of a long polymer of simple units called nucleotides. Each nucleotide in human

DNA consists of a deoxyribose sugar linked to both a phosphate group and one of four

characteristic nitrogen “bases”: adenine (A), cystosine (C), guanine (G), or thymine (T). 

The deoxyribose sugar has five carbons, numbered 1’ to 5’, respectively. It is the sequence of

these bases that encodes information about the functioning of living organisms. The bases bond

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with one another, or “hybridize,” to create a structure known as a double helix consisting of

two intertwined strands of DNA. These two strands are perfectly complementary to one another,

such that A bonds with its complement T and C bonds with its complement G. 

When a single strand of DNA exists in isolation, its sequence is unknown, i.e., the exact

lineup of the A, C, G, and T’s is unknown. The patents teach a method whereby a target single

strand of DNA may be sequenced, i.e., the lineup of A, C, G, and T’s may be exactly discovered. 

A method used in the prior art for DNA sequencing was known as “Sanger sequencing.” 

In a single DNA strand, adjacent nucleotides are chemically bonded. A dideoxynucleotide, or a

ddNTP, is a type of nucleotide that lacks the hydroxyl group of a standard deoxynucleotide, or a

dNTP. The lack of this hydroxyl group means that when a ddNTP is added to a sequence of

DNA on a strand no further nucleotides, a ddNTP or a dNTP, may be added. The Sanger

sequencing method made use of this chemical property. In Sanger sequencing, each base

(e.g., A, C, G, and T) was assigned a fluorescent color and the target DNA to be sequenced was

bonded with a known DNA sequence. The known DNA sequence was then hybridized by an

initializing primer, which added stability to the entire structure. Several strands of the target

DNA were then brought into contact with single probe ddNTPs and dNTPs. The result was that

several strands of the target DNA would hybridize to the different probes at various points on the

DNA strand. Because ddNTPs halt further hybridization on any given single strand of the target

DNA, many strands would have varying lengths depending on where the ddNTP hybridized. 

Some strands that hybridized with the target would be longer (i.e., a ddNTP hybridized at a

much later point in the sequence) and some would be shorter (i.e., a ddNTP hybridized at a

much earlier point in the sequence). These several strands that hybridized to the target DNA

were then collected and placed in a capillary tube to form a group of strands of varying lengths. 

A magnetic field was then placed on the capillary tube causing the various strands to line up in

order of length (e.g., shortest to longest). Each individual strand would then be taken out of the

tube and put through a light source which allowed the user to identify the fluorescent light

associated with the ddNTP of that sequence. Because the varying strands were lined up

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1

 Unless otherwise stated, all citations to column and lines numbers in this order refer to the

’341 patent. 

2

 Unless otherwise stated, all figures in this order were submitted by the parties as part of the claim

construction briefing. The online version of this order is in color.

3

according to their length, the user would go through strand by strand to decode each color,

and hence base, associated with each nucleotide of the sequence in the correct order, thereby

allowing the perfect complement to the target DNA sequence to be determined. In sum, the

Sanger sequencing method allowed a target DNA strand to be sequenced by associating

fluorescent labels with specific nucleotides that had hybridized with the target DNA sequence. 

Once the identities of the nucleotides that hybridized were determined, it was simply a matter of

taking their complements to determine the sequence of the target DNA strand.

The patent specification teaches a method of DNA sequencing known as “sequencing

by ligation” that builds upon the fluorescent-color identification scheme of Sanger sequencing. 

It begins by attaching the unknown target DNA sequence (along either the 5’ to 3’ carbon bonds

or the 3’ to 5’ carbon bonds) to a binding region, whose sequence is known, that has already

been hybridized by an “initializing oligonucleotide” (col. 2:66–3:3)1

. This collective structure is

then attached to a solid support structure called a “bead.” The unknown DNA sequence is then

brought into a contact with a set of “oligonucleotide probes” that cover “all possible sequences

of a predetermined length” (col. 6:34–36). For example, if it is determined that the

oligonucleotide probes should be eight bases long, then the set of oligonucleotide probes that are

brought into contact with the first eight nucleotides of the target DNA sequence will contain all

65,536 (i.e., 4 ^ 8) possible sequences. Out of these 65,536 possibilities, one will be the perfect

complement for the first eight nucleotides of the target DNA sequence. In addition, each

oligonucleotide probe in the set of probes is assigned a label corresponding to the identity of one

of the bases located in the same position as the other probes (col. 3:7–9). To illustrate with the

same example, every probe in the set of 65,536 whose fifth nucleotide has a base of A may be

assigned a fluorescent color (e.g., yellow) as shown in the figure below.2

 

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After the set of oligonucleotide probes are brought into contact with the DNA target sequence

only the perfectly complementary oligonucleotide probe will hybridize with the DNA target

sequence (col. 11:49). The oligonucleotide probe which hybridizes with the target DNA

sequence is then “ligated” (i.e., glued) using an adhesive, ligase, to the adjacent probe (e.g., the

initializing oligonucleotide probe in the first iteration) forming a single longer probe that is

more stably hybridized to the unknown DNA target sequence (col. 3:3–7). Once the specific

oligonucleotide probe has hybridized, the remaining uncomplementary probes can be washed

away and the hybridized oligonucleotide probe may be cut at the nucleotide whose base has

been designated with a color. The specific oligonucleotide probe that hybridized may then

be identified by recording the label that had previously been assigned to it (e.g., yellow)

(col. 5:10–12). Once the color for the probe is determined, the user then knows the specific

identity of a nucleotide in the probe (e.g., the fifth nucleotide is an A).

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Repeating this process by ligating further oligonucleotide probes to the previously ligated probe

allows additional nucleotide bases in the DNA target sequence to be identified. For instance, if

every fifth nucleotide is assigned a color and the process is repeated, then the identity of every

fifth nucleotide (i.e., 5, 10, 15, 20, etc.) in the target DNA sequence could be determined. 

The oligonucleotide probes can then be shifted one position over from the original starting point

to interrogate different nucleotides in the target DNA sequence (e.g., every fourth nucleotide). 

For example, if the first oligonucleotide probe began hybridizing at position N in the sequence,

the next cycle may begin by hybridizing at position N - 1. Repeating this process would then

allow for identification of every fourth nucleotide (i.e., 4, 9, 14, 19, etc.) in the target DNA

sequence to be determined and then every third position for N - 2 (i.e., 3, 8, 13, 18, etc.). 

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Continuing this process ultimately allows for identification of every nucleotide in the target

DNA sequence. This method allows a target DNA to be sequenced in much shorter time and

with greater accuracy than the prior art.

* * *

This action was filed on May 31, 2007 by Applied Biosystems, alleging that the inventor

of the patents had wrongfully assigned them to defendant Solexa who was later acquired by

defendant Illumina. Illumina counterclaimed alleging plaintiff infringed the ’341 patent,

’119 patent, and the ’597 patent. The ’341 patent was the first out of the group to be filed and

issued. The ’119 patent was filed as a divisional application to the ’341 patent. The ’597 patent

is a continuation of the ’119 patent. Only terms from the ’341 patent and ’597 patent are

presented for construction. A technology tutorial was held on January 30, 2008, and a hearing

was held on February 13, 2008. Trial is set for September 29, 2008. 

ANALYSIS

1. LEGAL STANDARD.

Claim construction is a matter of law to be decided by a judge, not a jury. Markman v.

Westview Instruments, Inc., 517 U.S. 370, 388 (1996). Courts must give words in the claims

their ordinary and customary meaning, which “is the meaning that the term would have to a

person of ordinary skill in the art in question at the time of the invention.” Phillips v. AWH

Corp., 415 F.3d 1303, 1312–13 (Fed. Cir. 2005) (en banc). 

Where this ordinary and customary meaning is not immediately clear, courts must

primarily look to intrinsic evidence (i.e., the claims, the specification, and the prosecution

history) to determine the meaning. Id. at 1314. With respect to the specification, although a

difficult task, a court must distinguish “between using the specification to interpret the meaning

of a claim and importing limitations from the specification into the claim.” Id. at 1323. 

The latter is not permissible. 

Although courts have the discretion to consider extrinsic evidence, including expert and

inventor testimony, dictionaries and scientific treatises, such evidence is “less significant than

the intrinsic record in determining the legally operative meaning of claim language.” Id. at 1317

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(citation omitted). “The construction that stays true to the claim language and most naturally

aligns with the patent’s description of the invention will be, in the end, the correct construction.” 

Id. at 1315. “Nonetheless, any articulated definition of a claim term ultimately must relate to the

infringement questions it was intended to answer.” E-Pass Tech., Inc. v. 3Com Corp., 473 F.3d

1213, 1219 (Fed. Cir. 2007) (citing Wilson Sporting Goods Co. v. Hillerich & Bradsby Co.,

442 F.3d 1322, 1326 (Fed. Cir. 2006)). 

2. DISPUTED CLAIM TERMS AND PHRASES.

AB and Solexa do not stipulate to any definitions prior to the hearing. The parties jointly

selected six phrases for construction at this time. Those six phrases are: (1) “initializing

oligonucleotide probe;” (2) “ligating an extension oligonucleotide probe to said extendable probe

terminus;” (3) “extended oligonucleotide probe;” (4) “identifying;” (5) “just-ligated extension

probe;” and (6) “repeating steps (b), (c) and (d) until a sequence of nucleotides in the target

polynucleotide is determined.” 

All of the disputed terms and phrases appear in claim 1 of the ’341 patent. It recites

(col. 21:36–65):

1. A method for determining a sequence of nucleotides in a

target polynucleotide, the method comprising the steps of:

(a) providing a probe-target duplex comprising an

initializing oligonucleotide probe hybridized to a

target polynucleotide, said probe having an

extendable probe terminus;

(b) ligating an extension oligonucleotide probe to

said extendable probe terminus, to form an extended

duplex containing an extended oligonucleotide

probe;

(c) identifying, in the extended duplex, at least one

nucleotide in the target polynucleotide that is either

(1) complementary to the just-ligated extension

probe or (2) the nucleotide residue in the target

polynucleotide which is immediately downstream of

the extended oligonucleotide probe;

(d) generating an extendable probe terminus on the

extended probe, if an extendable probe terminus is

not already present, such that the terminus generated

is different from the terminus to which the last

extension probe was ligated; and

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(e) repeating steps (b), (c) and (d) until a sequence

of nucleotides in the target polynucleotide is

determined.

A. “Initializing Oligonucleotide Probe.”

Solexa proposes that “initializing oligonucleotide probe” should mean “the

oligonucleotide probe that hybridizes to a known sequence in a polynucleotide and establishes

registration for extension.” AB proposes that the term should mean “the oligonucleotide to

which the first extension oligonucleotide probe will be ligated.” The problem with Solexa’s

construction is that it is expressly proscribed by the language of the claim. To be sure, the

specification teaches a different method than what is claimed, but the law is full of patents that

claim less than taught in the specification (and, sadly, vice versa). The specification teaches

(col. 5:13–27):

Binding region (40) has a known sequence, but can vary greatly in

length and composition. It must be sufficiently long to

accommodate the hybridization of an initializing

oligonucleotide . . . . Preferably, the binding region should be long

enough to accommodate a set of different initializing

oligonucleotides, each hybridizing to the template to produce a

different starting point for subsequent ligation.

The specification further states, “[p]referably, a target polynucleotide is conjugated to a

binding region to form a template, and the template is attached to a solid phase support . . .”

(col. 8:8–10). The language makes clear that a binding region and the target polynucleotide are

connected, and together form the template. 

As Described in the ’341 Specification

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The binding region, target polynucleotide, and template are each distinct items. The initializing

oligonucleotide then hybridizes with the binding region, a known sequence, and subsequent

ligations are done.

Claim 1, however, states (col. 21:38–41):

(a) providing a probe-target duplex comprising an initializing

oligonucleotide probe hybridized to a target polynucleotide, said

probe having an extendable probe terminus;

The claim language expressly provides that the initializing oligonucleotide probe hybridizes to a

target polynucleotide, which is clearly not always a fully-known sequence. 

As Described in Claim 1 of the ’341 Patent

After much study of the specification, the undersigned judge is of the view that the inventor,

patent counsel, and the examiner all made a drafting error. While it is tempting to just fix it up

in the claim construction process, that temptation would be dangerous course, for it should be up

to the PTO in the first instance to amend claims. As the Federal Circuit has held, “courts may

not redraft claims, whether to make them operable or to sustain their validity.” Chef America v.

Lamb-Weston, Inc., 358 F.3d 1371, 1374 (Fed. Cir. 2004). Even “a nonsensical result does not

require the court to redraft the claims.” Process Control Corp. v. Hydreclaim Corp., 190 F.3d

1350, 1357 (Fed. Cir. 1999). It may be that, once redrafted, the examiner might recognize prior

art problems that escaped attention before. The express language of the claim must govern. 

Solexa’s construction must be rejected.

AB’s construction also slightly misses the mark because it fails to take into account that

the first extension oligonucleotide probe is ligated to the initializing probe and the second

extension probe. As the specification teaches, “such extension starts from duplex formed

between an initializing oligonucleotide and the template” (col. 3:1–3). From there, subsequent

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ligations are made. The meaning for the term should thus take into account that the initializing

oligonucleotide probe is the starting point for subsequent ligations.

Accordingly, the term “initializing oligonucleotide probe” is held to mean “the

oligonucleotide to which the first extension oligonucleotide probe is first ligated.” 

B. “Ligating An Extension Oligonucleotide Probe 

To Said Extendable Probe Terminus.” 

The next battle is over the word “said,” more particularly the phrase “said extendable

probe terminus” in subparagraph (b). The issue comes down to whether the view of “said” is

taken literally to refer only to the preceding subparagraph (a) or whether we take into account

the iterative process called out by the claim whereby paragraphs (b) through (d) are repeated and

the referent for “said” is viewed as in paragraph (d). The latter is correct and this time Solexa

has the better argument.

Solexa proposes the term “ligating an extension oligonucleotide probe to said extendable

probe terminus” should mean “forming a covalent bond between an extension oligonucleotide

probe and the extendable probe terminus of either an initializing oligonucleotide or an extended

oligonucleotide probe while hybridized to a target polynucleotide.” 

AB contends that Solexa’s proposed construction is once again contradicted by the

express language of the claim. Specifically, the term refers to “said extendable probe terminus”

(col. 21:42–43) The only other preceding use of the term “extendable probe terminus” is in step

(a) of the claim 1, which states, “providing a probe-target duplex comprising an initializing

oligonucleotide probe hybridized to a target polynucleotide, said probe having an extendable

probe terminus” (col. 21:37–40). AB argues that Solexa’s construction rewrites the claim term

from “said extendable probe terminus” to “an extendable probe terminus” because step (a) of

claim 1 expressly requires that the extendable probe terminus must be that of the initializing

oligonucleotide probe. Accordingly, AB proposes that the term should mean “forming a

covalent bond between a short oligonucleotide probe and the extendable probe terminus of the

initializing oligonucleotide of step 1 (a).”

The problem with AB’s argument and construction is that they are inconsistent with the

remaining steps of the claim and take steps (a) and (b) of claim 1 in isolation. “While certain

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terms may be at the center of the claim construction debate, the context of the surrounding words

of the claim also must be considered in determining the ordinary and customary meaning of

those terms.” ACTV, Inc. v. Walt Disney Co., 346 F.3d 1082, 1088 (Fed. Cir. 2003); see also

Hockerson-Halberstadt, Inc. v. Converse Inc., 183 F.3d 1369, 1374 (Fed. Cir. 1999)

(“Proper claim construction, however, demands interpretation of the entire claim in context,

not a single element in isolation”). Claim 1 goes on to state, “(e) repeating steps (b), (c) and

(d) until a sequence of nucleotides in the target polynucleotide is determined” (col. 21:55–56). 

AB’s construction would require that all extension probes be ligated only to the initializing

oligonucleotide. But because ligations to the initializing oligonucleotide probe occur during the

first iteration of steps (b)-(d), it would be impossible to repeat the process as directed by step (e),

making step (e) entirely superfluous and the claim internally inconsistent at all times. It is

significant that step (a) of claim 1 is only performed once, i.e., step (e) of claim 1 does not refer

to step (a).

Step (d) of claim 1 makes clear that the identity of the oligonucleotide with an extendable

probe terminus to which extension oligonucleotide probes attach changes depending on which

iteration is currently being processed. After identifying the probe that hyrbridized to the target

sequence the claim proceeds to the next step of (col. 21:50–54):

(d) generating an extendable probe terminus on the extended

probe, if an extendable probe terminus is not already present, such

that the terminus generated is different from the terminus to which

the last extension probe was ligated;

A new extendable probe terminus is thus generated on each cycle as required by step (e),

meaning the “said extendable probe terminus” of step (b) refers to whatever extendable probe

terminus was generated on the previous cycle in step (d). Because step (e) does not require

step (a) to be repeated, the“said” refers to the “extendable probe terminus” created in (d). 

The specification further provides, “[g]enerally, the oligonucleotide probes should be capable of

being ligated to an initializing oligonucleotide or extended duplex to generate the extended

duplex of the next extension cycle . . . ” (col. 5:17–6:2). Solexa’s proposed construction

sufficiently captures this procedure.

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This order holds “ligating an extension oligonucleotide probe to said extendable probe

terminus” means “forming a covalent bond between an extension oligonucleotide probe and the

extendable probe terminus of either an initializing oligonucleotide or an extended

oligonucleotide probe while hybridized to a target polynucleotide.” 

C. “Extended Oligonucleotide Probe” 

And “Just-Ligated Extension Probe.”

The parties’ disagreement over the terms “extended oligonucleotide probe” and

“just-ligated extension” centers around the same argument regarding the meaning of the term

“ligating an extension oligonucleotide probe to said extendable probe terminus.” The term

“extended oligonucleotide probe” appeared in step (b) of claim 1. It recites, “ligating an

extension oligonucleotide probe to said extendable probe terminus, to form an extended duplex

containing an extended oligonucleotide probe” (col. 21:42–44). AB argues under the same

reasoning employed for its proposed construction for “ligating an extension oligonucleotide

probe to said extendable probe terminus” that the “extended oligonucleotide probe” must always

be the product of the extension oligonucleotide probe of step (b) ligating to the initializing

oligonucleotide probe of step (a). Similarly, AB contends that the “just-ligated extension probe”

means “the extension oligonucleotide probe of step (b) that was ligated within that cycle to the

initializing oligonucleotide of step (a).” The parties essentially agree that the “just-ligated

extension probe” is the oligonucleotide probe that was just ligated within the current iteration,

but they part company as to what it is ligated to. AB urges that because step (b) refers to “said

extendable probe terminus” the “just-ligated extension” must be ligated to the initializing

oligonucleotide probe. Solexa argues that the “just-ligated extension” may be ligated to either

the initializing oligonucleotide probe or other extension probes that were ligated on previous

cycles.

For the same reasons analyzed above, AB’s construction must be rejected. Step (d) of

claim 1 requires that the previous steps be repeated such that further extension probes are ligated

to the current extended duplex to form the next extended duplex. The specification states, “the

oligonucleotide probe probes should be capable of being ligated to an initializing

oligonucleotide or extended duplex to generate the extended duplex of the next extension

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cycle . . .” (col. 5:66–6:2). Requiring all extension oligonucleotide probes to be ligated to the

initializing probe would be inconsistent with this process.

Accordingly, this order holds that “extended oligonucleotide probe” means “an

initializing oligonucleotide probe effectively extended by one or more nucleotides” and

“just-ligated extension probe” means “the extension oligonucleotide probe ligated to either the

initializing oligonucleotide probe or an extended oligonucleotide probe in the present cycle of

the method.”

D. “Identifying.”

The parties spill much ink over how the term “identifying” should be construed. 

The term appears in claim 1 of the ’341 patent and claim 1 of the ’597 patent in the same

context. Step (c) of claim 1 recites:

identifying, in the extended duplex, at least one nucleotide in the

target polynucleotide that is either (1) complementary to the

just-ligated extension probe or (2) the nucleotide residue in the

target polynucleotide which is immediately downstream of the

extended oligonucleotide probe;

The parties dispute is generally over how specific of an identification the claim requires. 

Solexa urges that “identifying” should mean “obtaining information sufficient to distinguish.” 

AB proposes that “identifying” should mean “within each cycle determining the identity of a

base, as either A, T, G, or C, in the target polynucleotide.” AB’s candidate, this order holds, is

closer to the true mark.

For Solexa the word “identifying” can include merely gathering information that could

eventually be used to distinguish between nucleotides even if insufficient to make a precise

determination in the (b) to (e) cycle. Such a broad construction is not supported by the

specification. The specification teaches (col. 3:7–10):

During each cycle, the identity of one or more nucleotides in the

template is determined by a label on, or associated with, a

successfully ligated oligonucleotide probe.

The specification further explains (col. 6:14–33 (emphasis added)):

Generally, the oligonucleotide probe need not form a perfectly

matched duplex with the template, although such binding is

preferred. In preferred embodiments in which a single nucleotide

in the template is identified in each extension cycle, perfect base

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pairing is only required for identifying that particular

nucleotide. . . . Likewise, in embodiments that rely on polymerase

extension for base identification, the probe primarily serves as a

spacer, so specific hybridization to the template is not critical,

although it is desirable.

In his first office action with the USPTO, Inventor Stephen Macevicz overcame a prior art

reference, Brennan, by arguing (Pai. Decl. Exh. D at 11):

Brennan et al. also teaches preparing long chains of labeled

oligonucleotides which are digested by exonuclease to derive

sequence information. Nowhere does this reference suggest

iterative cycles of single-probe ligation and target nucleotide

identification in a probe-target duplex, in accordance with the

present invention.

Collectively, this language indicates that the very purpose of the identification process is to

determine the base of specific nucleotides in the target polynucleotide during each iterative

cycle. This process is then repeated as required by claim 1 until “the sequence of the target

polynucleotide is determined” (col. 18:16–17). 

Solexa cites nothing in the specification that indicates identity should mean anything

other than determining the base for a specific nucleotide. At the claim construction hearing,

Solexa highlighted that the examples given in the specification employ the patented invention to

sequence target DNA strands whose sequences are fully known. For instance, the specification

shows how the patented method may be used to sequence pUC19, whose sequence was well

known in the prior art (col. 14:43). Solexa argues that these examples show that identifying does

not mean base identification because the examples involve sequences whose bases are known. 

The examples, however, are shown in the specification to show how the patented invention

works and to confirm its operation with a known DNA sequence. Logically, why would a user

want to use the claimed method, whose express purpose is “determining the nucleotide sequence

of a polynucleotide” (col. 1:5–6), to sequence a target DNA strand that is already full known in

the prior art? Solexa’s argument is a far stretch.

Solexa next wrongly relies on the following excerpt from the specification (col.

3:53–60):

As used herein ‘sequence determination,’ ‘determining a

nucleotide sequence,’ ‘sequencing,’ and like terms, in reference to

polynucleotides includes determination of partial as well as full

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sequence information of the polynucleotide. That is, the term

includes sequence comparisons, fingerprinting, and like levels of

information about a target polynucleotide, as well as the express

identification and ordering of each nucleoside of the test

polynucleotide.

Significantly, this express definition does not define the word “identifying.” Solexa contends

that this language shows that the term “identity,” includes both “partial as well as full sequence

information of the polynucleotide,” thereby supporting their proposed construction because the

terms “determining” and “identity” are used interchangeably in the patent. Solexa’s argument is

unsupported by the express language of the definition. The definition indicates that

“identification” was meant to be a more narrow term than the terms defined because it is

included as a smaller subset to those terms. While the definition does include both partial and

full sequence information, it only applies to the broader terms defined. In addition, even if the

term “identifying” encompassed both partial and full sequence information, Solexa’s

construction would still be unsupported. Obtaining partial sequencing information does not

mean “obtaining information sufficient to distinguish” as Solexa would have it. It simply means

that only part of the sequence that is targeted for sequencing is identified, i.e., only a portion of

nucleotides in the sequence are identified by base. If identification beyond the bases of a

nucleotide was meant to be claimed, the prosecutor could have readily claimed it by stating

“sequencing” instead of “identifying” or by expressly saying information beyond base

identification in the claim.

AB’s proposed construction for “identifying,” “within each cycle determining the

identity of a base, as either A, T, G, or C, in the target polynucleotide,” while generally in line

with the specification, has a few minor problems. For clarity sake, the definition should make

certain that more than one nucleotide may be identified during each cycle. This is expressly

written in the claim, which states: “identifying . . . at least one nucleotide in target

polynucleotide . . .” (col. 21:45–46). AB’s construction states “the identity of a base,” which

may be interpreted as only a single base being identified each cycle. In addition, as AB

concedes, the definition should not be limited to the four bases of DNA because the specification

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also teaches that the invention may be used to sequence RNA, which has uracil as one its bases

instead of thymine.

Accordingly, the term “identifying” is held to mean “within each cycle determining the

identity of a base in the target polynucleotide.”

E. “Repeating Steps (b), (c) And (d) Until A Sequence 

Of Nucleotides In The Target Polynucleotide Is Determined.”

AB proposes that the term “repeating steps (b), (c) and (d) until a sequence of nucleotides

in the target polynucleotide is determined” should mean “completing, and then performing again,

exactly what is described in steps (b), (c), and (d) until two or more nucleotides in the unknown

sequence that is targeted for analysis are identified.” Implicitly within this definition AB has

defined “target polynucleotide” as necessarily containing a fully-unknown sequence. Such a

limitation, however, cannot be read into the claim. AB primarily relies on one embodiment of

the invention taught in the specification. The specification states, “[p]referably, a target

polynucleotide is conjugated to a binding region to form a template . . .” (col. 8:8–10).

Fig. 1

In explaining Figure 1 above, the specification further teaches: “[t]emplate (20) comprising a

polynucleotide of unknown sequence and binding region (40) is attached to solid support (10)”

(col. 4:46–48). AB urges that this description shows that the target polynucleotide must

necessarily be a fully-unknown sequence. As the specification made clear, however, “the

invention is not meant to be limited by the particular features of this embodiment” (col.

4:45–46). Nowhere in the specification does it state that the target polynucleotide must always

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be a fully-unknown sequence. At times, the sequence may very well be a partially-known

sequence that the user desires to be further sequenced. AB’s construction does not comport with

this possibility.

Solexa proposes the term should mean “repeating steps (b), (c), and (d) until partial or

complete sequence information of the target polynucleotide is obtained, including, for example,

sequence comparisons, fingerprinting, and like levels of information, as well as the express

identification and ordering of nucleotides.” Solexa’s proposed construction is hopelessly long

and complicated given the clear-cut language of the term being construed. This order finds that

the term “repeating steps (b), (c) and (d) until a sequence of nucleotides in the target

polynucleotide is determined” requires no construction and may be sufficiently understood by a

layperson without any guidance from this Court.

As such, the term “repeating steps (b), (c) and (d) until a sequence of nucleotides in the

target polynucleotide is determined” shall have its ordinary and plain meaning.

CONCLUSION

This claim construction order will govern for the remainder of this action. 

IT IS SO ORDERED.

Dated: February 21, 2008. 

WILLIAM ALSUP

UNITED STATES DISTRICT JUDGE

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