NOTE: This disposition is nonprecedential.

United States Court of Appeals 

for the Federal Circuit ______________________

THE SCRIPPS RESEARCH INSTITUTE,

Plaintiff-Appellant

v.

ILLUMINA, INC.,

Defendant-Appellee

______________________

2018-2089

______________________

Appeal from the United States District Court for the 

Southern District of California in No. 3:16-cv-00661-JLSBGS, Judge Janis L. Sammartino.

______________________

Decided: August 29, 2019

______________________

JUSTIN SCOTT COHEN, Thompson & Knight LLP, Dallas, TX, argued for plaintiff-appellant. Also represented by 

HERBERT J. HAMMOND, JAMES MICHAEL HEINLEN; DEREK 

TOD GILLILAND, Nix Patterson & Roach LLP, Daingerfield, 

TX. 

 JUANITA ROSE BROOKS, Fish & Richardson, PC, San Diego, CA, argued for defendant-appellee. Also represented 

by MICHAEL ARI AMON, CRAIG E. COUNTRYMAN. 

 ______________________
2 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

Before WALLACH, CLEVENGER, and TARANTO, Circuit 

Judges.

Opinion for the court filed by Circuit Judge TARANTO.

Dissenting opinion filed by Circuit Judge CLEVENGER.

TARANTO, Circuit Judge.

The Scripps Research Institute owns now-expired U.S. 

Patent No. 6,060,596, which describes and claims bifunctional molecules having certain properties, along with libraries of such molecules. Scripps sued Illumina, Inc. in 

the Southern District of California, asserting infringement 

of claims 1, 3, 10, and 16 of the ’596 patent. The district 

court issued claim-construction rulings that addressed 

three terms that involve the variable a and a claim phrase 

that refers to a linker molecule. Shortly thereafter, Scripps 

and Illumina filed a joint motion stipulating that, under 

the claim-construction rulings, Illumina has not infringed

the asserted claims. The district court granted the motion 

and entered a final judgment in Illumina’s favor.

Scripps appeals the claim-construction rulings involving the a terms and the linker molecule phrase. Both parties agree that, if the rulings involving the a terms are

correct, the district court’s judgment should stand. Because we agree with the district court regarding the a

terms, we affirm the judgment without reaching the dispute over the linker molecule phrase.

I

A

The ’596 patent is titled “Encoded Combinatorial 

Chemical Libraries.” Its specification describes bifunctional molecules, represented by the formula A–B–C, gathered into a library. At a general level, the A side of each 

bifunctional molecule is the molecule of interest (such as a 

molecule that binds to a particular target, ’596 patent, col. 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 3

2, lines 64–66), the C side is a molecule serving an indexing 

function in the library, and B is a linker between A and C.

The “chemical moiety” A in the A–B–C bifunctional 

molecule is a “polymer.” ’596 patent, col. 4, lines 31, 33. 

The polymer “comprises a linear series of chemical units

represented by the formula (Xn)a, wherein X is a single 

chemical unit in polymer A and n is a position identifier.” 

Id., col. 4, lines 33–36.1 The specification notes that “a is 

an integer,” typically between four and fifty. Id., col. 4, 

lines 41–42.

The C in the A–B–C molecule is the “identifier oligonucleotide.” Id., col. 5, lines 56–57. The specification explains 

that oligonucleotide C is made up of unit identifiers corresponding to the chemical units of polymer A. Id., col. 5, 

lines 58–61. Specifically, oligonucleotide C has “a sequence 

represented by the formula (Zn)a, wherein Z is a unit identifier nucleotide sequence within oligonucleotide C that 

identifies the chemical unit X at position n.” Id. Each unit 

identifier Z typically includes between two and ten nucleotides, preferably chosen from the bases found in DNA: 

adenosine, cytosine, guanosine, and thymidine. Id., col. 6, 

lines 7–19.

The B portion of the bifunctional molecule is the “linker 

molecule” that connects polymer A and oligonucleotide C. 

See id., col. 8, lines 20–24. The specification explains that 

linker molecule B “can be any molecule that performs the 

function of operatively linking the chemical moiety to the 

identifier oligonucleotide.” Id. It further notes that linker 

 

1 The ’596 patent and papers in the record sometimes use italics for numerical variables such as a and n 

and sometimes do not. For clarity and consistency, we use 

italics for such variables throughout this opinion. We do so 

even when quoting language not italicized in the original, 

without flagging each formatting change.
4 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

molecule B preferably “has a means for attaching to a solid 

support” and also “separat[ing] from the solid support.” 

Id., col. 8, lines 25–33.

The specification teaches a “method for producing a 

plurality of bifunctional molecules to form a library of this 

invention.” Id., col. 9, lines 62–63. “In the present synthesis methods,” a bifunctional molecule A–B–C is created according to “an alternating parallel synthesis procedure.” 

Id., col. 9, line 66, through col. 10, line 7. The procedure 

involves “add[ing] chemical unit X and then add[ing] a unit 

identifier nucleotide sequence Z that defines (codes for) 

that corresponding chemical unit.” Id. With a library of 

bifunctional molecules formed in that way, researchers can 

discern the identity of bound polymer A by reading the corresponding genetic tag, i.e., oligonucleotide C. Id., col. 2, 

line 66, through col. 3, line 1.

Independent claim 1 recites the following:

1. A bifunctional molecule according to the formula 

A–B–C, wherein A is a polymer comprising a linear 

series of chemical units represented by the formula 

(Xn)a, wherein X is a single chemical unit in polymer A, B is a linker molecule operatively linked to 

A and C[,] and identifier oligonucleotide C is represented by the formula (Zn)a, wherein a unit identifier nucleotide sequence Z within oligonucleotide C 

identifies the chemical unit X at position n; and 

wherein n is a position identifier for both X in polymer A and Z in oligonucleotide C having the value 

of 1+i where i is an integer from 0 to 10, such that 

when n is 1, X or Z is located most proximal to the 

linker, and a is an integer from 4 to 50.

Id., col. 43, lines 2–14. Claim 3 depends on claim 1 and 

additionally requires that “said polymer is an oligosaccharide, pol[y]peptide, glycolipid, lipid, proteoglycan, glycopeptide or oligonucleotide.” Id., col. 43, lines 18–20.
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 5

Unlike claims 1 and 3, which involve a single bifunctional molecule, claims 10 and 16 claim libraries containing 

multiple bifunctional molecules. Claim 10 recites “[a] library comprising a plurality of species of bifunctional molecules according to claim 1.” Id., col. 44, lines 4–5. Claim 

16 depends on claim 10 and further requires that “each of 

said species of bifunctional molecules in said plurality is 

present in molar equivalents of from 0.2 to 10.0.” Id., col. 

44, lines 29–31.

B

In December 2016, Scripps sued Illumina, asserting 

that Illumina’s making, using, selling, and offering to sell 

its BeadChip products infringed claims 1, 3, 10, and 16 of 

the ’596 patent. After the Patent Trial and Appeal Board 

denied Illumina’s petition for an inter partes review of all 

claims of the ’596 patent except claims 7–9, Illumina moved 

to dismiss the district-court case, arguing that its BeadChip products could not meet the requirements of claim 1 

(and hence of claims 3, 10, and 16) under any plausible construction of the a terms. The court, concluding that it could 

not at that stage reject Scripps’s proposed constructions of

the a terms, denied Illumina’s motion to dismiss.

The parties then engaged in full claim-construction litigation over the terms a, (Zn)a, and (Xn)a (the a terms), and 

the claim phrase B is a linker molecule operatively linked 

to A and C, and a couple of other terms not involved in this 

appeal. After accepting briefs from both sides, the district 

court heard testimony and argument at a hearing. On 

April 10, 2018, the court issued an order construing all disputed terms. Scripps Research Inst. v. Illumina, Inc., No. 

16-CV-661, 2018 WL 1726597 (S.D. Cal. Apr. 10, 2018).

First, the court construed a to mean “an integer from 4 

to 50 that is further defined in the context of the formulas 

(Zn)a and (Xn)a.” Id. at *6. Next, it construed (Xn)a to mean 

“a representation of polymer A, where ‘a’ is the number of 

chemical units of X forming the polymer A.” Id. It 
6 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

similarly construed (Zn)a to mean “a representation of identifier oligonucleotide C, where ‘a’ is the number of chemical 

unit identifiers in the oligonucleotide.” Id. Relatedly, the 

court determined that the value of a must be the same for

both (Xn)a and (Zn)a. Id. at *5.

The court then turned to the phrase B is a linker molecule operatively linked to A and C. The Board had already 

construed the linker molecule phrase in its decision denying Illumina’s petition for an inter partes review. Analyzing the prosecution history of earlier patents in the same 

family as the ’596 patent, the Board determined that 

Scripps had disclaimed some linker molecules. Accordingly, the Board construed the linker molecule phrase to 

mean that “linker molecule B (1) links to A and to C, (2) 

allows for alternat[ing] addition of nucleotides and amino 

acids to itself, and (3) is capable of coupling to and decoupling from a solid support without cleaving either the polypeptide or oligonucleotide from linker molecule B.” J.A. 

977. The district court adopted the Board’s construction, 

deeming it “reasoned” and “persuasive.” Scripps, 2018 WL 

1726597, at *6–7.

On May 17, 2018, Scripps and Illumina filed a joint motion for final judgment, stipulating that, under the district 

court’s claim-construction rulings, “Illumina has not infringed, did not infringe, and cannot infringe” the asserted

claims. J.A. 7. Both parties agreed that, under the court’s 

construction of a, the value of a for Illumina’s BeadChip

products is one, which falls outside the claimed range of 

four to fifty. They also agreed that Illumina’s BeadChip 

products do not contain linker molecules under the court’s 

construction of the linker molecule phrase. The parties 

acknowledged that “[e]ach of these rulings”—the constructions of the a terms; the determination that a must have 

the same value in (Xn)a and (Zn)a; and the construction of 

the linker molecule phrase—“provides an independent basis why Illumina has not infringed the Asserted Claims.” 

Id. The next day, on May 18, 2018, the district court 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 7

granted the joint motion and entered judgment against 

Scripps.

Scripps timely appealed on June 15, 2018. We have 

jurisdiction under 28 U.S.C. § 1295(a)(1).

II

We see the dispute over the a terms as raising three 

separate but related questions: (1) whether a in (Zn)a

counts the number of chemical unit identifiers, (2) whether 

a in (Xn)a counts the number of chemical units, and (3) 

whether a must be the same for both polymer A and oligonucleotide C. Scripps answers each of those questions in 

the negative, maintaining that a counts individual nucleotides for oligonucleotide C, that a counts monomers for polymer A, and that a need not be the same for (Zn)a and (Xn)a. 

We address each issue in turn, though the issues are related because (Zn)a and (Xn)a are closely related, so our resolutions of the issues are mutually reinforcing.

A

We agree with the district court that a in (Zn)a counts 

chemical unit identifiers, not individual nucleotides. In its 

introductory paragraph explaining C and its Zn components and their correspondence to the already described A 

and its Xn components, the specification states that, in 

(Zn)a, a is “an integer as described previously to connote the 

number of chemical unit identifiers in the oligonucleotide.” 

’596 patent, col. 5, lines 63–65 (emphasis added). This is a 

definition, and at least where (as here) there is nothing extraordinary to the contrary, “the inventor’s lexicography 

governs.” See Phillips v. AWH Corp., 415 F.3d 1303, 1316 

(Fed. Cir. 2005) (en banc). 

At the same time, the specification nowhere says that 

a in the formulas refers to the number of nucleotides in the 

overall oligonucleotide C, i.e., (Zn)a. It does use nucleotides 

to measure the length of the individual “unit identifier[s],”

i.e., each Zn, see, e.g., ’596 patent, col. 6, lines 7–14, 61–63; 
8 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

and it also notes both a preferable number of nucleotides 

in an overall identifier oligonucleotide “for effective hybridization” and the considerations that “contribute to length 

of the identifier oligonucleotide,” id. col. 6, line 64–col. 7, 

line 3. See also id., col. 18, lines 14–34 (discussing polymerase chain reaction, involving hybridization to which 

sheer number of nucleotides relevant). But the specification does not use nucleotides as the unit for a, or even label 

a the “length” of C, having defined that variable in terms 

of “the number of chemical unit identifiers.” Id., col. 5, 

lines 63–65. Moreover, the specification makes plain that 

each individual “unit identifier nucleotide sequence” (each 

Zn, corresponding to a chemical unit Xn) typically has multiple nucleotides, id., col. 6, lines 61–63 (emphasis added) 

(six is “typical and exemplary”), so in the complete “identifier oligonucleotide” C consisting of multiple “unit identifier” sequences (Z1, Z2, Z3, . . .), the nucleotide count would 

not equal the “chemical unit identifier” count.

We see no sound basis for understanding the word “connote” in this setting to mean anything but “is.” In its opening brief in this court, Scripps made no argument about the 

significance of the word “connote” in the specification. In 

its reply brief, Scripps asserted that “connote the number 

of chemical unit identifiers” means stating one number 

(nucleotides) that by calculation with another number (the 

number of nucleotides per chemical unit identifier, if it is 

uniform) can lead to identification of the number of chemical unit identifiers. Aside from its lateness, this assertion

is unduly strained. Scripps points to no such use of “connote” in scientific contexts like this one. And it would be 

especially odd to find such an unusual (or entirely novel) 

use given where “connote” appears in this patent—namely, 

in the opening, concept-introducing paragraph of the section that defines and explains the identifier oligonucleotide 

C and its makeup—without any language that points to a 

need for calculation or the assumptions and method of such 

a calculation. The only reasonable understanding of 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 9

“connote” in this setting, we think, is the straightforward 

one that a is “the number of chemical unit identifiers”

(which correspond to the “chemical units” in (Xn)a on a oneto-one basis).

Notably, this understanding reflects ordinary chemical 

nomenclature—which Illumina’s expert confirmed in testimony that we do not see meaningfully contradicted. J.A. 

1015–16. For example, the formula CH3(CH2)8CH3 represents the straight-chain hydrocarbon decane. The subscript outside the parentheses indicates how many times 

the group inside the parentheses repeats, i.e., that there 

are eight saturated carbons singly bonded to one another 

in between two methyl groups. Under the specification’s 

definition, Scripps used the subscript a in the same way. 

Although the chemical unit identifiers at different positions of n will differ depending on their corresponding 

chemical units, a identifies how many chemical unit identifiers are linked together.

B

For similar reasons, we agree with the district court 

that a in (Xn)a counts chemical units. In the context of 

chemical libraries, the specification explains, “‘a’ . . . represents the number of chemical units of X forming the polymer A, i.e., the length of polymer A.” ʼ596 patent, col. 9, 

lines 9–11 (emphasis added); see also id., col. 44, lines 9–11

(similar language in claim 11). We have no reason to believe that a in (Xn)a means something different elsewhere 

in the same patent. See In re Varma, 816 F.3d 1352, 1363 

(Fed. Cir. 2016) (“[T]he principle that the same phrase in 

different claims of the same patent should have the same 

meaning is a strong one, overcome only if ‘it is clear’ that 

the same phrase has different meanings in different 

claims.” (quoting Fin Control Systems Pty., Ltd. v. OAM, 

Inc., 265 F.3d 1311, 1318 (Fed. Cir. 2001))). We so conclude 

following ordinary principles of internal-document coherence—part of the legal task of interpreting intrinsic 
10 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

evidence. See Teva Pharm. USA, Inc. v. Sandoz, Inc., 135 

S. Ct. 831, 841 (2015); Teva Pharm. USA, Inc. v. Sandoz, 

Inc., 789 F.3d 1335, 1342 (Fed. Cir. 2015).

C

We also agree with the district court that the value of 

a must be the same for both (Xn)a and (Zn)a. The claim language itself states, after introducing both (Xn)a and (Zn)a, 

that “a is an integer.” ’596 patent, col. 43, lines 13–14 (emphasis added). That definitional assertion about the previously used a logically refers without differentiation to both 

(Xn)a and (Zn)a and means that it is the same integer for 

both (Xn)a and (Zn)a. And the two claim constructions we 

have already discussed effectively compel this conclusion, 

as those constructions reflect the definitional correspondence between C with its Zn components and A with its Xn

components.

We do not see how the relevant public could be expected 

to understand that a could differ for (Xn)a and (Zn)a without 

some linguistic clue. There is none. If Scripps wanted to 

indicate that the lengths of polymer A and oligonucleotide 

C might differ, it could have done so in at least three ways. 

It could have used another variable, such as c, to represent 

the length of the oligonucleotide, which would generate the 

formula (Xn)a–B–(Zn)c. Alternatively, Scripps could have 

used prime notation to differentiate between the different 

values of a, which would produce the formula (Xn)a–B–

(Zn)aʹ. Similarly, Scripps could have used sub-subscripts on 

a (e.g., a1 and a2) to indicate that a might take on different 

values. Scripps did none of these things or anything comparable.

The specification confirms that a has the same value in 

both (Xn)a and (Zn)a—and not just through the interacting 

meanings of the effectively definitional provisions we have 

discussed. Every embodiment in the specification has the 

same value of a for both the chemical moiety and the oligonucleotide. E.g., ’596 patent, col. 6, line 1 (a = 4); id., Fig. 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 11

2 (a = 3). And that symmetry necessarily flows from the 

specification’s teaching of how to make the bifunctional 

molecules—building them according to “an alternating 

parallel synthesis procedure.” Id., col. 9, line 66, through 

col. 10, line 7. Because a unit identifier nucleotide sequence is always added to oligonucleotide C for every corresponding chemical unit added to polymer A, the synthetic 

procedure taught in the patent will always result in a uniform value of a.

D

Scripps points to only one fact about the patent that 

legitimately weighs against the above conclusions. It notes 

that defining a as the number of chemical units and chemical unit identifiers (i.e., the maximum value of n) limits 

the length of polymer A to no more than eleven chemical 

units because claim 1 limits the values of n to between one 

and eleven. See id., col. 4, lines 36–38 (n = 1 + i, where 0 ≤ 

i ≤ 10). And yet claim 1, following the specification, states 

that the value of a ranges from four to fifty. Id., col. 4, lines 

41–42. In Scripps’s view, this result means that a is not 

properly measured in chemical units or chemical unit identifiers and must have a smaller unit of measure.

We do not think that this consequence should be given 

enough weight to override the compelling support for the 

district court’s conclusions about the a terms—including 

the notation used in the claim language, the intertwined 

definitions of the specification, and the embodiments and 

synthesis method taught in the specification. We note that 

the district court’s conclusions do not produce an actual inconsistency within the claim language. They mean only 

that the limited range of n effectively further narrows the 

requirement that a be an integer from four to fifty. That is 

odd, suggesting some lack of care in drafting, but it is not 

an internal contradiction. Moreover, there is already odd, 

careless drafting in claim 1. Scripps agrees that there is 

no explanation for the claim’s saying that n is i + 1, with i 
12 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

ranging from zero to ten, rather than simply saying that n 

ranges from one to eleven. See Oral Arg. at 30:58–31:11.

In addition, a somewhat similar oddity arises for claim 

2 under Scripps’s nucleotide-counting construction of the a 

term on the C side. Claim 2 recites that each chemical unit 

identifier may be up to eight nucleotides long. ’596 patent, 

col. 43, lines 15–17. Applying Scripps’s construction of a, 

claim 2 would contemplate an oligonucleotide in which a is 

eighty-eight, which far exceeds the limit of fifty set by independent claim 1. Of course, the necessarily present limit 

of claim 1 would restrict claim 2, but that would still be an 

odd bit of drafting, leaving a suggestion of permissibly exceeding fifty further limited by a requirement not to do so.

In these circumstances, Scripps’s point about limiting 

the possible values of a is not enough to overcome the otherwise clear claim language and explicit interacting definitions in the specification, along with the embodiments and 

synthesis method taught in the specification. Accordingly, 

we agree with the district court’s rulings on the a terms.

III

We have considered Scripps’s other arguments but do 

not find them persuasive. It is undisputed that our agreement with the district court regarding the a terms suffices 

for us to affirm the district court’s judgment. We therefore 

affirm that judgment, without considering the court’s construction of the linker molecule phrase.

The parties shall bear their own costs.

AFFIRMED
NOTE: This disposition is nonprecedential.

United States Court of Appeals 

for the Federal Circuit ______________________

THE SCRIPPS RESEARCH INSTITUTE,

Plaintiff-Appellant

v.

ILLUMINA, INC.,

Defendant-Appellee

______________________

2018-2089

______________________

Appeal from the United States District Court for the 

Southern District of California in No. 3:16-cv-00661-JLSBGS, Judge Janis L. Sammartino.

______________________

CLEVENGER, Circuit Judge, dissenting.

I

The Scripps Research Institute owns U.S. Patent No. 

6,060,596 (“the ’596 patent”), which recites an inventive 

molecule intended to improve the efficiency and effectiveness of the drug discovery process—the search “for novel 

bioactive chemicals.” ’596 patent col. 1 ll. 15–34; id. col. 2 

ll. 48–54. The purpose of the invention is the construction 

of so-called “bifunctional molecules” that have two main 

chemical components that serve two distinct functions. Id.

col. 2 ll. 48–67; id. col. 3 ll. 1–17. The first component is a 

chemical moiety that serves as a novel bioactive chemical 
2 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

candidate. Id. col. 3 ll. 12–23. The second is a genetic tag 

that uniquely identifies the specific chemical moiety. Id. 

The ’596 patent refers to the chemical moiety as a polymer 

A and to the genetic tag as an oligonucleotide C. Id.; id.

col. 4 ll. 43–54. The invention connects those two functional groups using a linker molecule B, thereby constructing the inventive bifunctional molecule. Id. col. 4 ll. 26–30. 

Thus, A—B—C is a formula that represents the bifunctional molecule. Id.

The ’596 patent provides “[p]olymer A can be any monomeric chemical unit that can be coupled and extended in 

polymeric form.” Id. col. 4 ll. 46–47. The specification further states the linear series of chemical units making up 

polymer A is represented by the formula (Xn)a, wherein “X” 

is a single chemical unit, “n” is an integer between 1 and 

11 that identifies the position of a given chemical unit X 

within polymer A, and “a” is an integer from 4 to 50 that 

defines the length of polymer A. Id. col. 4 ll. 31–42. The 

’596 patent provides oligonucleotide C is represented by the 

formula (Zn)a, wherein “Z” is a unit identifier nucleotide sequence that identifies the chemical unit X at position n, “n” 

is an integer between 1 and 11 that identifies the position 

of Z within oligonucleotide C, and “a is an integer as described previously to connote the number of chemical unit 

identifiers in the oligonucleotide.” Id. col. 5 ll. 56–65. The 

length of a unit identifier nucleotide sequence Z “can be 

from about 2 to about 10 nucleotide[]” bases. Id. col. 6 ll. 

12–14.

Claim 1 is the only independent claim in the ’596 patent, and it is representative of the claims at issue in this 

appeal. It recites “[a] bifunctional molecule according to 

the formula A—B—C,” with additional limitations repeating the sub-formulas and definitions provided in the specification, including (Xn)a represents polymer A, (Zn)a

represents oligonucleotide C, and “a” is an integer from 4 

to 50. Id. col. 43 ll. 1–14.
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 3

II

A

To apply the invention as claimed, we must determine 

how to measure the length “a”. Specifically, our task is to 

determine the units of measurement for the length “a”. Do 

we measure A and C by the number of chemical units1 X 

and Z? Or do we measure by the number of monomers in 

each X and Z? If the claim language or the specification 

clearly identified the units of measurement, and thus answered that question, our analysis would be complete. Unfortunately, and not uncommonly, neither the claims 

themselves nor the specification expressly supply an answer.

B

The district court and the majority conclude that we 

must measure polymer A and oligonucleotide C by the 

number of chemical units X and Z, respectively. Simply 

put, “a” is an integer that represents the number of chemical units. The majority provides four justifications for its 

construction. First, it cites a statement in the specification 

that, with respect to oligonucleotide C and the formula 

(Zn)a, “a is an integer as described previously to connote the 

number of chemical unit identifiers in the oligonucleotide.” 

Maj. Op. at 7–8. The majority reads that sentence to mean 

“a” is the number of chemical units Z in the oligonucleotide 

chain, as a matter of inventor lexicography. Second, it cites 

a statement in the specification that the library of bifunctional molecules is represented by the formula Va, wherein 

“‘a’ . . . represents the number of chemical units of X 

 

1 Throughout the remainder of this opinion, I use 

“chemical unit” to refer to both a single chemical unit of X 

and a unit identifier nucleotide sequence Z. And I use 

“monomer” to refer to both the individual monomers that 

comprise X and the nucleotide bases that comprise Z.
4 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

forming the polymer A, i.e., the length of polymer A.” Id.

at 9–10. The majority reads that part of the specification 

to be a definitive answer to the appropriate units of measurement for length “a” across all formulas in the ’596 patent that rely on length “a” as a variable. Third, the 

majority points to the claim language itself, which provides 

“a is an integer.” Id. at 10. It uses that language as proof 

that “a” must be a single integer that is the same across all 

formulas disclosed in the patent. Last, the majority contends its construction is consistent with “ordinary chemical 

nomenclature.” Id. at 9.

However, the majority readily admits, as it must, that 

its construction reads out a substantial part of the ’596 patent’s claims. Id. at 11–12. In fact, the construction it 

adopts reads out 83% of the claimed range of “a”. Although 

the patent claims are clear that “a” can be any integer from 

4 to 50, under the district court’s and majority’s construction, “a” can only be an integer from 4 to 11. By measuring 

“a” by chemical units of X and Z, “a” can be no greater than 

the maximum number of chemical units, which is the maximum value of n, which everyone agrees is 11. Contrary to 

the express claim language, “a” can never be greater than 

11; it can never be an integer from 12 to 50.

According to this court’s almost cardinal rule of claim 

construction, “[c]laims must be ‘interpreted with an eye toward giving effect to all terms in the claim’” and avoiding

“a claim construction which would render a claim limitation meaningless.” Becton, Dickinson & Co. v. Tyco 

Healthcare Grp., LP, 616 F.3d 1249, 1257 (Fed. Cir. 2010) 

(citations omitted); see also Bicon, Inc. v. Straumann Co., 

441 F.3d 945, 951 (Fed. Cir. 2006) (holding a patent claim 

construction that reads limitations out of a claim is “contrary to the principle that claim language should not [be] 

treated as meaningless”); Tex. Instruments Inc. v. U.S. Int’l 

Trade Comm’n, 988 F.2d 1165, 1171 (Fed. Cir. 1993) (refusing to adopt a claim construction that would read an express limitation out of the claims “because ‘[c]ourts can 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 5

neither broaden nor narrow claims to give the patentee 

something different than what he has set forth’” (citation 

omitted)). So this case boils down to whether the support 

the majority cites for its claim construction is enough to 

justify eviscerating most of a claim limitation—83% of the 

claimed range of possible “a” values. It is not.

C

The ’596 patent does not specify the units of measurement for “a” as used in either (Xn)a or (Zn)a. Although the 

specification instructs “a is an integer as described previously to connote the number of chemical unit identifiers in 

the oligonucleotide,” ’596 patent col. 5 ll. 63–65, that does 

not necessarily mean “a” is the number of chemical unit 

identifiers in the oligonucleotide, or that the patentee so 

defined the term. The word “connote” means “to signify in 

addition to its exact explicit meaning” or “to imply, indicate, or involve as an attribute: bear as connotation – contrasted with denote.” Connote, Webster’s Third New 

International Dictionary (Unabridged ed. 1993). It does 

not mean “is.” In fact, when the patentee wanted to give 

notice that some variable in a formula “is” a certain quantity, the patentee knew how to say so. The specification 

tells us in no uncertain terms that “A is a chemical moiety,”

“B is a linker molecule,” “C is an identifier oligonucleotide,”

“X is a single chemical unit in polymer A,” “n is a position 

identifier for X in polymer A,” “a is an integer from 4 to 50,”

and “Z is a unit identifier nucleotide sequence within oligonucleotide C.” ’596 patent col. 4 ll. 26–29, 35–36, 41–42

(emphasis added); id. col. 4 ll. 59–60 (emphasis added). 

Under those circumstances, the patentee’s choice of the 

word “connote” rather than the word “is” implies the patentee intended those two words to carry different meanings. Moreover, ascertaining the length “a” based on 

monomers “connotes” the number of chemical unit identifiers Z in oligonucleotide C just as well as measuring the 

length “a” by chemical units. One necessarily knows the 

number of Zs if she knows the number of monomers in each 
6 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

Z and the total number of monomers “a”. As a result, the 

majority’s suggestion that Scripps’s construction of “connote,” which is consistent with the dictionary definition, is 

somehow in tension with its regular use in the scientific 

context is unpersuasive.

Nor does the discussion in the ’596 patent of “a” as used 

in the library formula Va resolve the proper construction of 

“a” as used in (Xn)a or (Zn)a. The specification tells us that, 

with respect to the library formula Va, “‘a’ is an exponent 

to V and represents the number of chemical units of X forming the polymer A, i.e., the length of polymer A.” Id. col. 9 

ll. 7–11. But that does not mean “a” has those same units 

in the formulas (Xn)a and (Zn)a. In fact, there is reason to 

believe “a” is not measured in chemical units as used in 

(Xn)a and (Zn)a, despite being so measured as used in Va.

The size of the library is based on the number of different possible polymer As, which is based on the total number of unique combinations of the available chemical unit 

Xs. V is the size of the alphabet, which simply is the number of available chemical unit Xs used to construct polymer 

A. And “a” is the number of chemical unit Xs in polymer A. 

For example, if there are two chemical units available for 

use and each polymer contains three chemical unit Xs, the 

size of the library Va is 23, or 8 bifunctional molecules. 

There are eight unique ways to arrange the two available 

chemical unit Xs to construct a three-chemical-unit polymer A in that example. What do we notice? The library is 

built based on chemical units, not monomers. Indeed, the 

number of monomers in each chemical unit X is irrelevant. 

The size of the library depends on only the arrangement of 

chemical unit Xs, irrespective of what is inside each X.

The same is not true of polymer A, represented by (Xn)a, 

or oligonucleotide C, represented by (Zn)a. Counting length 

“a” in monomers for purposes of (Xn)a and (Zn)a is more consistent with the specification. The specification in several 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 7

instances discusses with seeming importance the number 

of monomers in polymer A and in oligonucleotide C. The 

’596 patent states “[p]olymer A can be any monomeric

chemical unit that can be coupled and extended in polymeric form,” “[a] typical length [for unit identifier nucleotide sequence Z] can be from about 2 to about 10 

nucleotides,” “[a] typical and exemplary unit identifier nucleotide sequence [Z] is based on the commaless code having a length of six nucleotides (hexanucleotide) per 

chemical unit,” “an identifier oligonucleotide [preferably] 

has at least 15 nucleotides in the tag (coding) region for 

effective hybridization,” “length of the identifier oligonucleotide” is based on “considerations of the complexity of the 

library, the size of the alphabet of chemical units, and the 

length of the polymer length [sic] of the chemical moiety,” 

“the unit identifier nucleotide sequence is 6 nucleotides” 

and the sequence characteristics of the oligonucleotide Z 

such as length are described by the number of monomeric 

nucleotide bases. Id. col. 4 ll. 46–47 (emphasis added); id.

col. 6 ll. 12–13, 61–63, 64–67; id. col. 7 ll. 1–3, id. col. 28 ll. 

4–5; id. col. 29–42. Are we to believe the patentee, despite 

discussing over and over again the importance of the monomeric composition of the chemical units, intended to capture nowhere in the formulas (Xn)a or (Zn)a the number of 

monomers in polymer A and oligonucleotide C? Unlike the 

library size, the number of monomers in polymer A and oligonucleotide C is relevant. The majority’s construction 

treats the information as irrelevant.

The majority is not troubled by the fact that its construction ignores that meaningful monomer information 

because, in its view, “the specification nowhere says that a

in the formulas refers to the number of nucleotides in the

overall oligonucleotide C, i.e., (Zn)a.” Maj. Op. at 8. The 

majority mistakenly contends, while the specification 

“use[s] nucleotides to measure the length of the individual 

‘unit identifier[s],’ i.e., each Zn,” it “does not use nucleotides 

as the unit for a, or even label a the ‘length’ of C, having 
8 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

defined that variable in terms of ‘the number of chemical 

unit identifiers.’” Id. The ’596 patent defines C as the 

“identifier oligonucleotide” and Z as the “unit identifier nucleotide sequence.” ’596 patent col. 5 ll. 56–60. Although 

the specification makes reference to the length of the unit 

identifier oligonucleotide Z in terms of nucleotides, it also 

refers to the length of the identifier oligonucleotide C in 

terms of nucleotides. See, e.g., id. col. 6 ll. 64–66 (“[P]referably, an identifier oligonucleotide has at least 15 nucleotides in the tag (coding) region for effective hybridization. 

In addition, considerations of the complexity of the library, 

the size of the alphabet of chemical units, and the length of 

the polymer length of the chemical moiety all contribute to 

length of the identifier oligonucleotide as discussed in more 

detail herein.” (emphasis added)). In fact, the patent discusses building both polymer A and identifier oligonucleotide C based on their monomeric composition, not based on 

their chemical units X and Z. See id. col. 26 ll. 17–21 (“The 

conjugate can be lengthened by alternating cycles of addition of nucleotides and amino acids. The following alternating cycles are repeated until the conjugate has desired 

length amino acid polymer [i.e., A] and oligonucleotide polymer [i.e., C].” (emphasis added)); id. col. 26 ll. 34–36 (“The 

cycle of [the steps] above adding alternate nucleotides and 

amino acids can be repeated until the conjugate has polymers of the desired length and structure.” (emphasis 

added)).

Furthermore, the majority overlooks critical facts 

when it contends that “a” is nowhere tied to the length of 

oligonucleotide C, which is instead defined in terms of its 

unit identifier Zs. Polymer A, represented by the formula

(Xn)a, is defined the same way as oligonucleotide C: in 

terms of its chemical unit Xs. And yet the specification tells 

us in a separate place that variable “a” is the length of polymer A. The same is true of oligonucleotide C, which the 

specification describes as being represented by the formula 

(Zn)a, where “a is an integer as described previously,” and 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 9

“a” was previously described as the length of the polymer. 

Compare ’596 patent col. 4 ll. 31–42, with id. col. 5 ll. 56–

65. There is no reasonable basis for treating the length of 

polymer oligonucleotide C any differently than the length 

of polymer A.

The fact that the claims recite “a is an integer” does not

resolve the proper construction of “a” either. The majority 

adopts Illumina’s argument in its brief that, because the 

claims say “a is an integer,” that proves “a” is a single integer that must be the same number across all formulas recited in the ’596 patent. Maj. Op. at 10; Appellee’s Br. at 

19–20. But the fact that “a” is an integer simply means it 

is a whole number, not a fraction. And that is all we can 

take it to mean. That must be true in light of the claim 

language, which also says “n” is defined by the formula 

“1+i, where i is an integer from 0 to 10.” ’596 patent col. 43 

ll. 10–12. We know that “i,” and thus “n” by association, is 

not always the same number; it necessarily changes with 

every chemical unit X and Z that is added to the polymer 

chain A and oligonucleotide chain C. How can we reach a 

contrary conclusion for the same language with respect to 

“a”?

Nor do general chemical naming conventions determine the proper construction of “a”. The majority treats as 

a decided issue that the proper construction of the variable 

“a” and the formulas “(Xn)a” and “(Zn)a” should comport with 

“ordinary chemical nomenclature.” Maj. Op. at 9. Not so. 

While no one disputes the ordinary rules for naming compounds in the chemical arts, which Illumina made record 

evidence through its expert, Scripps’s expert testified that 

variable “a”, formula “(Xn)a”, and formula “(Zn)a”, do not 

have a conventional meaning in the art. J.A. 1280–81. The 

testimony from Scripps’s expert suggests, regardless of the 

ordinary chemical nomenclature, the formulas in the ’596 

patent do not necessarily follow it. And there is good reason to believe that may be true. Although both the formulas (Xn)a and (Zn)a use the same “a”, they do not necessarily 
10 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

represent the same value because we do not know the units 

of measurement. Therefore, on this record, it is disputed 

whether “a” as used in the formulas “(Xn)a” and “(Zn)a” 

should be construed consistent with general chemical naming conventions. And the district court did not resolve that 

dispute of fact in the record. This court should not decide

that factual dispute now on appeal. For those reasons, the 

majority’s reliance on “ordinary chemical nomenclature” is 

most seriously misplaced. Maj. Op. at 9.

Finally, and most importantly, measuring length “a” by 

monomers rather than chemical units neither broadens nor 

limits the claim language. It operationalizes all aspects of 

the claim, and thus indisputably is more consistent with 

the claimed invention. To the extent the majority relies on 

the rule that the same claim term in different parts of a 

claim are generally given the same meaning, Maj. Op. at 

9–10, that principle is overcome “if it is clear that the same 

phrase has different meanings in different claims [or claim 

limitations],” In re Varma, 816 F.3d 1352, 1363–64 (Fed 

Cir. 2016) (internal quotation marks and citation omitted).

The patentee clearly intended “a” to have different meanings among the formulas if giving “a” the same meaning 

across all formulas reads out 83% of an express claim limitation.

The majority argues that we should ignore the restriction in the scope of claim 1 effected by the construction 

it adopts because claim 2 suffers from “a somewhat similar 

oddity.” Maj. Op. at 12. That argument has no force. 

Claim 2 recites “[t]he bifunctional molecule of claim 1 

wherein said unit identifier nucleotide sequence Z has a 

length of from 2 to 8 nucleotides.” ’596 patent col. 43 ll. 15–

17. The majority latches onto an argument Illumina made 

in its appellate brief that applying Scripps’s construction of 

“a” might cause the oligonucleotide recited in claim 2 to 

reach a length of eighty-eight, which exceeds the length 

limit of fifty established by independent claim 1. Maj. Op. 

at 12; Appellee’s Br. at 23. In doing so, the majority is led 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 11

astray by a red herring. It is of course true that “a” and “n” 

cannot simultaneously have their maximum values for a 

given bifunctional molecule. If that were not the case, “a” 

would readily exceed fifty as the majority suggests. Fortunately, the claims do not require that “a” and “n” be able to 

simultaneously achieve their maximum values. What matters to make use of the entire scope of claims 1 and 2 is that 

“a” and “n” can have their minimum and maximum values 

individually for any given hypothetical bifunctional molecule. The argument Illumina makes, and the majority 

adopts, simply demonstrates that the claims of the ’596 patent have boundaries, as all claims must. Illumina’s construction makes 83% of the claimed range of “a” 

inaccessible in all cases. Meanwhile, Scripps’s construction

makes accessible the entire claimed range of “a” and “n” 

values. Unlike the construction adopted by the majority, 

Scripps’s construction breathes life into all aspects of all 

the claims of the ’596 patent.

III

The majority does not address the district court’s construction of the claim phrase “B is a linker molecule operatively linked to A and C” because both parties agreed that 

the appeal would be resolved if we affirmed either of the 

district court’s constructions. Maj. Op. at 6–7, 12. Because 

I disagree with the district court’s and majority’s construction of “a”, I also address the district court’s construction of 

the “linker molecule” phrase.

Before the district court issued its claim construction 

order, the U.S. Patent and Trademark Office (“PTO”) issued a decision denying Illumina’s petition for inter partes

review of the ’596 patent. In that decision, the PTO construed the “linker molecule” phrase to mean “linker molecule B (1) links to A and to C, (2) allows for alternative 

addition of nucleotides and amino acids to itself, and (3) is 

capable of coupling to and decoupling from a solid support 

without cleaving either the polypeptide or oligonucleotide 
12 THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC.

from linker molecule B.” J.A. 977. The PTO recognized 

that the ability of linker molecule B to alternatively add 

nucleotides and amino acids, as well as its ability to couple

to and decouple from a solid support, were not limitations 

recited in the claims. But it reasoned those limitations 

were expressly recited in the specification, and Scripps 

made them necessary attributes of the linker molecule during prosecution of grandparent patent application 

07/860,445 (“the ’445 application”) and parent application 

08/665,511 (“the ’511 application”) by using those limitations as bases to distinguish the invention over the prior 

art. The district court adopted wholesale the PTO’s construction of the “linker molecule” phrase and the PTO’s associated analysis. In doing so, the district court erred.

I do not find fault with most of the district court’s

“linker molecule” construction. Linker molecule B must 

link to A and to C, it must allow for alternative addition of 

chemical species to itself, and it must be capable of coupling 

to and decoupling from a solid support without cleaving either A or C from the linker molecule. But there is no justification for limiting polymer A as recited in the claims of 

the ’596 patent to polypeptides composed of amino acids. 

“In general, prosecution disclaimer will only apply to a subsequent patent if that patent contains the same claim limitation as its predecessor.” Regents of Univ. of Minn. v. 

AGA Med. Corp., 717 F.3d 929, 943 (Fed. Cir. 2013). Unlike the claims at issue in the grandparent ’445 application

and the parent ’511 application, which restrict A to polypeptides, the claims of the ’596 patent are broader because 

they allow A to be any polymer. Claim 3 of the ’596 patent 

makes clear that polymer A is not limited to polypeptides 

made up of amino acid monomers. ’596 patent col. 43 ll. 

18–20. And during prosecution of the application that led 

to the ’596 patent, unlike the prosecutions of the earlier ancestral patent applications, Scripps did not disavow claim 

scope with respect to linker molecule B. Therefore, the district court’s construction of the “linker molecule” phrase is 
THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 13

incorrect to the extent it limits linker molecule B to those 

chemical species that connect with polypeptides composed 

of amino acids.

IV

The majority disregards significant rules of engagement by failing to apply the claim construction principles

oft-repeated in our precedent. See, e.g., Merck & Co. v. 

Teva Pharm. USA, Inc., 395 F.3d 1364, 1372 (Fed. Cir. 

2005) (“A claim construction that gives meaning to all the 

terms of the claim is preferred over one that does not do 

so.”). As a result, it repeats the same mistake made by the 

district court, upholds a construction that unduly lops off 

83% of a claim limitation without adequate justification, 

and dismisses a competing construction that everyone (including the district court) agrees is technically correct. By 

actually applying our claim construction principles, I 

would reach the correct constructions, vacate the district 

court’s erroneous interpretations of “a” and “B is a linker 

molecule operatively linked to A and C”, and remand for 

further proceedings. 

As a parting aside, looking back over almost thirty 

years of deciding patent appeals, I hate to think of how 

many patents should have been neutered because their inventors could have used more precise claim language. 

With respect, I dissent.