the Scripps Research Institute v. Illumina, Inc.

N OTE: This disposition is nonprecedential.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-JLS-
BGS, Judge Janis L. Sammartino.
______________________
Decided: August 29, 2019
______________________
J USTIN SCOTT C OHEN, Thompson & Knight LLP, Dal-
las, TX, argued for plaintiff-appellant. Also represented by
HERBERT J. HAMMOND, J AMES M ICHAEL H EINLEN; D EREK
T OD G ILLILAND, Nix Patterson & Roach LLP, Daingerfield,
TX.
J UANITA ROSE BROOKS , Fish & Richardson, PC, San Di-
ego, CA, argued for defendant-appellee. Also represented
by MICHAEL ARI AMON, CRAIG E. C OUNTRYMAN.
______________________

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 2
Before WALLACH , CLEVENGER , and T ARANTO, Circuit
Judges.
Opinion for the court filed by Circuit Judge T ARANTO.
Dissenting opinion filed by Circuit Judge C LEVENGER .
T ARANTO, Circuit Judge.
The Scripps Research Institute owns now-expired U.S.
Patent No. 6,060,596, which describes and claims bifunc-
tional molecules having certain properties, along with li-
braries 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 involv-
ing the a terms and the linker molecule phrase. Both par-
ties agree that, if the rulings involving the a terms are
correct, the district court’s judgment should stand. Be-
cause we agree with the district court regarding the a
terms, we affirm the judgment without reaching the dis-
pute over the linker molecule phrase.
I
A
The ’596 patent is titled “Encoded Combinatorial
Chemical Libraries.” Its specification describes bifunc-
tional molecules, represented by the formula A–B–C, gath-
ered 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.

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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 oligonu-
cleotide.” Id., col. 5, lines 56–57. The specification explains
that oligonucleotide C is made up of unit identifiers corre-
sponding 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 iden-
tifier 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 nucleo-
tides, 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 some-
times 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.

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 4
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 synthe-
sis methods,” a bifunctional molecule A–B–C is created ac-
cording 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 cor-
responding 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 poly-
mer A, B is a linker molecule operatively linked to
A and C[,] and identifier oligonucleotide C is repre-
sented by the formula (Zn)a, wherein a unit identi-
fier 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 pol-
ymer 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 oligosaccha-
ride, pol[y]peptide, glycolipid, lipid, proteoglycan, glyco-
peptide or oligonucleotide.” Id., col. 43, lines 18–20.

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 5
Unlike claims 1 and 3, which involve a single bifunc-
tional molecule, claims 10 and 16 claim libraries containing
multiple bifunctional molecules. Claim 10 recites “[a] li-
brary comprising a plurality of species of bifunctional mol-
ecules 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 Bead-
Chip products could not meet the requirements of claim 1
(and hence of claims 3, 10, and 16) under any plausible con-
struction 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 lit-
igation 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 dis-
puted 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

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 6
similarly construed (Zn)a to mean “a representation of iden-
tifier 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 mole-
cule operatively linked to A and C. The Board had already
construed the linker molecule phrase in its decision deny-
ing Illumina’s petition for an inter partes review. Analyz-
ing the prosecution history of earlier patents in the same
family as the ’596 patent, the Board determined that
Scripps had disclaimed some linker molecules. Accord-
ingly, 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 decou-
pling from a solid support without cleaving either the pol-
ypeptide 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 mo-
tion for final judgment, stipulating that, under the district
court’s claim-construction rulings, “Illumina has not in-
fringed, 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 construc-
tions 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 ba-
sis why Illumina has not infringed the Asserted Claims.”
Id. The next day, on May 18, 2018, the district court

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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 oligo-
nucleotide C. Scripps answers each of those questions in
the negative, maintaining that a counts individual nucleo-
tides for oligonucleotide C, that a counts monomers for pol-
ymer 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 re-
lated because (Zn)a and (Xn)a are closely related, so our res-
olutions 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 compo-
nents 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 ex-
traordinary 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;

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 8
and it also notes both a preferable number of nucleotides
in an overall identifier oligonucleotide “for effective hybrid-
ization” 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 poly-
merase chain reaction, involving hybridization to which
sheer number of nucleotides relevant). But the specifica-
tion 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 mul-
tiple nucleotides, id., col. 6, lines 61–63 (emphasis added)
(six is “typical and exemplary”), so in the complete “identi-
fier oligonucleotide” C consisting of multiple “unit identi-
fier” sequences (Z1, Z2, Z3, . . .), the nucleotide count would
not equal the “chemical unit identifier” count.
We see no sound basis for understanding the word “con-
note” in this setting to mean anything but “is.” In its open-
ing 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 chemi-
cal unit identifiers. Aside from its lateness, this assertion
is unduly strained. Scripps points to no such use of “con-
note” 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 sec-
tion 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

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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 one-
to-one basis).
Notably, this understanding reflects ordinary chemical
nomenclature—which Illumina’s expert confirmed in testi-
mony that we do not see meaningfully contradicted. J.A.
1015–16. For example, the formula CH3(CH2)8CH3 repre-
sents the straight-chain hydrocarbon decane. The sub-
script 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 posi-
tions of n will differ depending on their corresponding
chemical units, a identifies how many chemical unit iden-
tifiers 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’ . . . repre-
sents the number of chemical units of X forming the poly-
mer 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 be-
lieve 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 coher-
ence—part of the legal task of interpreting intrinsic

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 10
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 lan-
guage itself states, after introducing both (Xn)a and (Zn)a,
that “a is an integer.” ’596 patent, col. 43, lines 13–14 (em-
phasis added). That definitional assertion about the previ-
ously 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 correspond-
ence 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 com-
parable.
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 oligo-
nucleotide. E.g., ’596 patent, col. 6, line 1 (a = 4); id., Fig.

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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 se-
quence is always added to oligonucleotide C for every cor-
responding chemical unit added to polymer A, the synthetic
procedure taught in the patent will always result in a uni-
form 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 chem-
ical 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 iden-
tifiers 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 in-
consistency 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

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 12
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 in-
dependent 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 ex-
ceeding 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 oth-
erwise clear claim language and explicit interacting defini-
tions 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 agree-
ment 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 con-
struction of the linker molecule phrase.
The parties shall bear their own costs.
AFFIRMED

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N OTE: 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-JLS-
BGS, 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 effective-
ness 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

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 2
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 func-
tional groups using a linker molecule B, thereby construct-
ing the inventive bifunctional molecule. Id. col. 4 ll. 26–30.
Thus, A—B—C is a formula that represents the bifunc-
tional molecule. Id.
The ’596 patent provides “[p]olymer A can be any mon-
omeric chemical unit that can be coupled and extended in
polymeric form.” Id. col. 4 ll. 46–47. The specification fur-
ther 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 se-
quence 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 de-
scribed 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 pa-
tent, 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 repeat-
ing the sub-formulas and definitions provided in the speci-
fication, 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.

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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 an-
swered that question, our analysis would be complete. Un-
fortunately, and not uncommonly, neither the claims
themselves nor the specification expressly supply an an-
swer.
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 chemi-
cal 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 bifunc-
tional 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.

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 4
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 meas-
urement for length “a” across all formulas in the ’596 pa-
tent 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 con-
tends 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 pa-
tent’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 construc-
tion, “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 max-
imum 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 to-
ward giving effect to all terms in the claim’” and avoiding
“a claim construction which would render a claim limita-
tion 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 “con-
trary 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) (re-
fusing to adopt a claim construction that would read an ex-
press limitation out of the claims “because ‘[c]ourts can

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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 measure-
ment for “a” as used in either (Xn)a or (Zn)a. Although the
specification instructs “a is an integer as described previ-
ously 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, indi-
cate, or involve as an attribute: bear as connotation – con-
trasted 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 quan-
tity, 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 oligo-
nucleotide 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 pa-
tentee intended those two words to carry different mean-
ings. Moreover, ascertaining the length “a” based on
monomers “connotes” the number of chemical unit identifi-
ers 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

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 6
Z and the total number of monomers “a”. As a result, the
majority’s suggestion that Scripps’s construction of “con-
note,” 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 form-
ing 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 differ-
ent possible polymer As, which is based on the total num-
ber of unique combinations of the available chemical unit
Xs. V is the size of the alphabet, which simply is the num-
ber 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 2 3, or 8 bifunctional molecules.
There are eight unique ways to arrange the two available
chemical unit Xs to construct a three-chemical-unit poly-
mer 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 con-
sistent with the specification. The specification in several

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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 poly-
meric form,” “[a] typical length [for unit identifier nucleo-
tide sequence Z] can be from about 2 to about 10
nucleotides,” “[a] typical and exemplary unit identifier nu-
cleotide sequence [Z] is based on the commaless code hav-
ing 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 oligonucle-
otide” 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 mon-
omeric composition of the chemical units, intended to cap-
ture 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 ol-
igonucleotide C is relevant. The majority’s construction
treats the information as irrelevant.
The majority is not troubled by the fact that its con-
struction 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

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 8
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 nu-
cleotide 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]ref-
erably, an identifier oligonucleotide has at least 15 nucleo-
tides 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 dis-
cusses building both polymer A and identifier oligonucleo-
tide 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 addi-
tion of nucleotides and amino acids. The following alter-
nating cycles are repeated until the conjugate has desired
length amino acid polymer [i.e., A] and oligonucleotide pol-
ymer [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 poly-
mers 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 pol-
ymer 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

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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 inte-
ger that must be the same number across all formulas re-
cited 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 deter-
mine 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 com-
pounds 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 rea-
son to believe that may be true. Although both the formu-
las (Xn)a and (Zn)a use the same “a”, they do not necessarily

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 10
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 nam-
ing 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 mean-
ings among the formulas if giving “a” the same meaning
across all formulas reads out 83% of an express claim limi-
tation.
The majority argues that we should ignore the re-
striction 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

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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. Fortu-
nately, the claims do not require that “a” and “n” be able to
simultaneously achieve their maximum values. What mat-
ters 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 mole-
cule. The argument Illumina makes, and the majority
adopts, simply demonstrates that the claims of the ’596 pa-
tent have boundaries, as all claims must. Illumina’s con-
struction 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 con-
struction of the claim phrase “B is a linker molecule opera-
tively 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 construc-
tion 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”) is-
sued a decision denying Illumina’s petition for inter partes
review of the ’596 patent. In that decision, the PTO con-
strued the “linker molecule” phrase to mean “linker mole-
cule 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

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THE SCRIPPS RESEARCH INSTITUTE v. ILLUMINA, INC. 12
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 dur-
ing prosecution of grandparent patent application
07/860,445 (“the ’445 application”) and parent application
08/665,511 (“the ’511 application”) by using those limita-
tions as bases to distinguish the invention over the prior
art. The district court adopted wholesale the PTO’s con-
struction of the “linker molecule” phrase and the PTO’s as-
sociated 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 ei-
ther A or C from the linker molecule. But there is no justi-
fication 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 sub-
sequent patent if that patent contains the same claim lim-
itation as its predecessor.” Regents of Univ. of Minn. v.
AGA Med. Corp., 717 F.3d 929, 943 (Fed. Cir. 2013). Un-
like the claims at issue in the grandparent ’445 application
and the parent ’511 application, which restrict A to poly-
peptides, 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 an-
cestral patent applications, Scripps did not disavow claim
scope with respect to linker molecule B. Therefore, the dis-
trict court’s construction of the “linker molecule” phrase is

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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 engage-
ment 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 (in-
cluding 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 in-
ventors could have used more precise claim language.
With respect, I dissent.

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