Source: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-casd-3_16-cv-00661/USCOURTS-casd-3_16-cv-00661-2/pdf.json

Nature of Suit Code: 830
Nature of Suit: Patent
Cause of Action: 35:0271 Patent Infringement

---

1

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

UNITED STATES DISTRICT COURT

SOUTHERN DISTRICT OF CALIFORNIA

THE SCRIPPS RESEARCH 

INSTITUTE,

Plaintiff,

v.

ILLUMINA, INC.,

Defendant.

Case No.: 16-CV-661 JLS (BGS)

ORDER ON CLAIM 

CONSTRUCTION

(ECF Nos. 54, 55)

In March 2016, Plaintiff The Scripps Research Institute brought suit against 

Defendant Illuminia, Inc. alleging infringement of U.S. Patent No. 6,060,596 (“the ’596 

patent”), entitled “Encoded Combinatorial Chemical Libraries.” Presently before the Court 

is claim construction. The Court held a claim construction hearing on January 30, 2018.

The ’596 patent generally relates to a library of bifunctional molecules, each 

molecule having a chemical polymer and an identifier oligonucleotide sequence that 

defines the structure of the chemical polymer. See U.S. Patent No. 6,060,596 (filed May 

9, 2000).) The libraries are used in the manufacture of DNA microarrays. (ECF No. 55, 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 1 of 18
2

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

at 5.)1 Each DNA bead in a microarray contains many copies of specific DNA sequences 

(known as “probes,” “oligonucleotides,” or “oglios.”) (Id. at 5–6.) These probes “can be 

used to bind to and detect a complementary DNA or RNA sample.” (Id. at 6.) Scripps 

asserts claims 1, 3, 10, and 16, and the Parties dispute six terms within claim 1. Defendant 

filed a claim construction brief, (“Def. CC Brief,” ECF No. 54), as did Plaintiff, (“Pl. CC 

Brief,” ECF No. 55). Both Parties also filed a response, (“Def. Response,” ECF No. 56; 

“Pl. Response,” ECF No. 57).

LEGAL STANDARD

“A determination of infringement involves a two-step analysis. ‘First, the claim 

must be properly construed to determine its scope and meaning. Second, the claim as 

properly construed must be compared to the accused device or process.’” Omega Eng’g, 

Inc. v. Raytek Corp., 334 F.3d 1314, 1320 (Fed. Cir. 2003) (quoting Carroll Touch, Inc. v. 

Electro Mech. Sys., Inc., 15 F.3d 1573, 1576 (Fed. Cir. 1993)).

The first step, commonly known as claim construction, is presently before the Court. 

Claim construction is a matter of law for the Court’s determination. Markman v. Westview 

Instruments, Inc., 517 U.S. 370, 388 (1996) (“[J]udges, not juries, are the better suited to 

find the acquired meaning of patent terms.”). 

Words of a claim are “generally given their ordinary and customary meaning.” 

Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996). “[T]he 

ordinary and customary meaning of a claim term is the meaning that the term would have 

to a person of ordinary skill in the art in question at the time of the invention, i.e., as of the 

effective filing date of the patent application.” Phillips v. AWH Corp., 415 F.3d 1303, 

1313 (Fed. Cir. 2005) (en banc). Because the inquiry into the meaning of claim terms is 

an objective one, “a court looks to those sources available to the public that show what a 

 

1 Pin citations to docketed material refer to the CM/ECF numbers electronically stamped at the top of each 

page.

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 2 of 18
3

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

person of skill in the art would have understood disputed claim language to mean.” 

Innova/Pure Water, Inc. v. Safari Water Filtration Sys., Inc., 381 F.3d 1111, 1116 (Fed. 

Cir. 2004). “Those sources include the words of the claims themselves, the remainder of 

the specification, the prosecution history, and extrinsic evidence concerning relevant 

scientific principles, the meaning of technical terms, and the state of the art.”2 Id. (citing 

Vitronics, 90 F.3d at 1582–83).

Claim construction begins with an analysis of the words of the claims themselves. 

See Scanner Techs. Corp. v. ICOS Vision Sys. Corp., 365 F.3d 1299, 1303 (Fed. Cir. 2004) 

(holding that claim construction “begins and ends” with a claim’s actual words). “In some 

cases, the ordinary meaning of claim language as understood by a person of skill in the art 

may be readily apparent even to lay judges, and claim construction in such cases involves 

little more than the application of the widely accepted meaning of commonly understood 

words.” Phillips, 415 F.3d at 1314. However, the meaning of a claim term as understood 

by ordinarily skilled artisans often is not immediately apparent. Id. In those situations, the 

court looks to “sources available to the public that show what a person of skill in the art 

would have understood disputed claim language to mean.” Id. Or, when a patentee 

“chooses to be his own lexicographer and use terms in a manner other than their ordinary 

meaning,” the court can use the patentee’s meaning “as long as the special definition of the 

term is clearly stated in the patent specification or file history.” Vitronics, 90 F.3d at 1582.

In examining the claims themselves, “the context in which a term is used can be 

highly instructive.” Phillips, 415 F.3d at 1314. Moreover, “[o]ther claims of the patent in 

question, both asserted and unasserted can . . . be valuable sources of enlightenment as to 

the meaning of a claim term.” Id. (citing Vitronics, 90 F.3d at 1582). “Because claim 

terms are normally used consistently throughout the patent, the usage of a term in one claim 

 

2 The first three sources are considered “intrinsic evidence” of claim meaning. See generally Phillips, 415 

F.3d at 1314–17.

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 3 of 18
4

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

can often illuminate the meaning of the same term in other claims.” Id. Conversely, under 

the doctrine of claim differentiation, “‘different words or phrases used in separate claims 

are presumed to indicate that the claims have different meanings and scope.’” Andersen 

Corp. v. Fiber Composites, LLC, 474 F.3d 1361, 1369 (Fed. Cir. 2007) (quoting Karlin 

Tech., Inc. v. Surgical Dynamics, Inc., 177 F.3d 968, 971–72 (Fed. Cir. 1999)).

“Importantly, the person of ordinary skill in the art is deemed to read the claim term 

not only in the context of the particular claim in which the disputed term appears, but in 

the context of the entire patent, including the specification.” Phillips, 415 F.3d at 1313. 

“The specification acts as a dictionary when it expressly defines terms used in the claims 

or when it defines them by implication.” Vitronics, 90 F.3d at 1582. “In addition to 

providing contemporaneous technological context for defining claim terms, the patent 

applicant may also define a claim term in the specification ‘in a manner inconsistent with 

its ordinary meaning.’” Metabolite Labs., Inc. v. Lab. Corp. of Am., 370 F.3d 1354, 1360 

(Fed. Cir. 2004). “Usually, [the specification] is dispositive; it is the single best guide to 

the meaning of a disputed term.” Vitronics, 90 F.3d at 1582; accord Phillips, 415 F.3d at 

1317 (“It is . . . entirely appropriate for a court, when conducting claim construction, to 

rely heavily on the written description for guidance as to the meaning of the claims.”).

Patent claims should ordinarily be construed to encompass the preferred 

embodiments described in the specification, for “[a] claim construction that excludes a 

preferred embodiment . . . ‘is rarely, if ever, correct.’” SanDisk Corp. v. Memorex Prods., 

Inc., 415 F.3d 1278, 1285 (Fed. Cir. 2005) (quoting Vitronics, 90 F.3d at 1583). However, 

a court should not import limitations from the specification into the claims, Phillips, 415 

F.3d at 1323 (“[A]lthough the specification often describes very specific embodiments of 

the invention, we have repeatedly warned against confining the claims to those 

embodiments.”), absent a specific reference in the claims themselves, Reinshaw PLC v. 

Marposs Societa’ per Azioni, 158 F.3d 1243, 1248 (Fed. Cir. 1998) (“[A] party wishing to 

use statements in the written description to confine or otherwise affect a patent’s scope 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 4 of 18
5

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

must, at the very least, point to a term or terms in the claim with which to draw in those 

statements.”).

The patent’s prosecution history, if in evidence, may also shed light on claim 

construction. Vitronics, 90 F.3d at 1582. “This history contains the complete record of all 

proceedings before the Patent and Trademark Office [(“PTO”)], including any express 

representations made by the applicant regarding scope of the claims.” Id. “Like the 

specification, the prosecution history provides evidence of how the PTO and the inventor 

understood the patent.” Phillips, 415 F.3d at 1317. Although the prosecution history 

“often lacks the clarity of the specification,” it is nevertheless useful to show “how the 

inventor understood the invention and whether the inventor limited the invention in the 

course of prosecution, making the claim scope narrower than it would otherwise be.” Id.

“In most situations, an analysis of the intrinsic evidence alone will resolve any 

ambiguity in a disputed claim term. In such circumstances, it is improper to rely on 

extrinsic evidence.” Vitronics, 90 F.3d at 1583. Thus, expert testimony on the proper 

construction of disputed claim terms “may only be relied upon if the patent documents, 

taken as a whole, are insufficient to enable the court to construe disputed claim terms.” Id.

at 1585.

However, Vitronics does not state a rule of admissibility, nor does it “prohibit courts 

from examining extrinsic evidence, even where the patent document is itself clear.” Pitney 

Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1308 (Fed. Cir. 1999). As the Federal 

Circuit has made clear:

[B]ecause extrinsic evidence can help educate the court regarding the field of 

the invention and can help the court determine what a person of ordinary skill 

in the art would understand claim terms to mean, it is permissible for the 

district court in its sound discretion to admit and use such evidence.

Phillips, 415 F.3d at 1319; accord Key Pharms. v. Hercon Labs. Corp., 161 F.3d 709, 716 

(Fed. Cir. 1998) (“[T]rial courts generally can hear expert testimony for background and 

education on the technology implicated by the presented claim construction issues, and 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 5 of 18
6

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

trial courts have broad discretion in this regard.”). The court is not “barred from 

considering any particular sources or required to analyze sources in any specific sequence, 

as long as those sources are not used to contradict claim meaning that is unambiguous in 

light of the intrinsic evidence.” Phillips, 415 F.3d at 1324; see also Biagro W. Sales, Inc. 

v. Grow More, Inc., 423 F.3d 1296, 1302 (Fed. Cir. 2005) (“Extrinsic evidence, such as 

expert testimony, may be useful in claim construction, but it should be considered in the 

context of the intrinsic evidence.”).

DISCUSSION

The Parties dispute the meaning of six claim terms or phrases in claim 1 of the ’596 

patent. 

I. The ’596 Patent

The ’596 patent is titled “Encoded Combinatorial Chemical Libraries.” Claim 1 of 

the patent is reproduced below:

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. 

’596 patent, at 43:1–14.

The patent is directed to methods for creating encoded combinatorial chemical 

libraries made up of many bifunctional molecules. These molecules are made of both a 

chemical polymer and an identifier oligonucleotide sequence that defines the structure of 

the chemical polymer. ’596 patent, abstract. The chemical polymer can be, for example, 

a series of amino acids, and the identifier oligonucleotide is a series of nucleotides (e.g., 

adenosine (A), guanine (G), cytosine (C), and thymine (T)). Id. at 4:44–55; 6:12–24. The 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 6 of 18
7

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

bifunctional molecules are built by starting with the linker, (“B”) and adding chemical units 

(X) to one end and identifier nucleotide sequences (Z) to the other end. Id. at 10:18–25. 

For example: X1–B–Z1. Id. at 6:1. The series of chemical units (Xs) are called “polymer 

A” and the series of unit identifiers (Zs) are called “identifier oligonucleotide C.” Id. at 

4:31–36; 5:56–61. A and C are joined by “linker molecule B.” Id. at 8:20–24. Thus, the 

formula is depicted as A–B–C. One can determine the structure of the first chemical unit 

(X1) by reading the first unit identifier (Z1). Id. at 2:66–3:1 (“The identity of the active 

molecule is determined by reading the genetic tag, i.e., the identifier oligonucleotide 

sequence.”). “n” is a position identifier for both X and Z. Id. at 43:10–12. “n” has a value 

of 1+i where i is an integer from 0 to 10. Id. In the example above, X1–B–Z1, n = 1, 

meaning X and Z are located “most proximal to the linker [B].” Id. at 43:13. The term 

“a”, the formulas “(Zn)a” and “(Xn)a”, and other terms are construed herein.

II. Disputed Terms

The Parties dispute in which order the Court should review the terms. (See generally 

“Joint Hearing Statement,” ECF No. 50.) Because the dispute regarding the construction 

of “a” is intertwined with the construction of “(Zn)a” and “(Xn)a”, the Court evaluates these 

three terms together, and then proceeds with the remaining terms.

A. “a”, “(Zn)a”, and “(Xn)a”

Plaintiff would construe “a” as: “the length of polymer A or identifier 

oligionucleotide C and is an integer from 4 to 50.” (“Joint CC Worksheet,” ECF No. 50-2, 

at 8–9.) Defendant would construe “a” as: “an integer from 4 to 50 that is further defined 

in the context of the formulas (Zn)a and (Xn)a.” (Id.) These proposed constructions do not 

speak to the crux of the matter. The real dispute is the proper construction of “a” within 

the constructions of “(Zn)a” and “(Xn)a.” Defendant proposes “(Xn)a” be construed as: “A 

representation of polymer A, where ‘a’ is the number of chemical units of X forming the 

polymer A.” (Id. at 3–4 (emphasis added).) Similarly, Defendant proposes “(Zn)a” be 

construed as: “A representation of identifier oligonucleotide C, where ‘a’ is the number of 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 7 of 18
8

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

chemical unit identifiers in the oligonucleotide.” (Id. at 7–8 (emphasis added).)

Generally, Defendant argues “a” is defined as the number of chemical units (X) and 

the number of corresponding unit identifiers (Z). Plaintiff argues “a” is not limited to the 

number of chemical units but refers to the length of polymer A and oligonucleotide C. 

Plaintiff would construe “(Xn)a” as: “the formula that represents polymer A comprising a 

linear series of chemical units, where ‘a’ is the length of polymer A and is an integer from 

4 to 50, ‘X’ and ‘n’ are defined by Claim 1 and require no further construction.” (Id. at 3–

4 (emphasis added).) Plaintiff would construe “(Zn)a” as: “the formula that represents 

identifier oligonucleotide C, where ‘a’ is the length of identifier oligonucleotide C and is 

an integer from 4 to 50, ‘Z’ and ‘n’ are defined by Claim 1 and require no further 

construction.” (Id. at 7–8 (emphasis added).)

To sum up the arguments with an illustration, both Parties interpret Figure 2. 

See ’596 patent, fig. 2 (with additions, in color). Plaintiff argues “a” for oligonucleotide 

C in Figure 2 has a value of 18 which is the “total number of A, T, C, and G bases that 

comprise identifier oligonucleotide C.” (“Metzker Decl.,” ECF No. 55-2, 

¶ 53.) Plaintiff argues “a” for polymer A in Figure 2 has a value of 3, “which is the length 

of the polymer of glycine and methionine residues.” (Id.) Defendant argues “a” for 

oligonucleotide C in Figure 2 has a value of 3 “because there are 3 chemical unit identifiers 

in the oligonucleotide.” (“Chelsky Decl.,” ECF No. 54-18, ¶ 27.) Defendant agrees with 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 8 of 18
9

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

Plaintiff that “a” is 3 for polymer A. (Id. ¶ 37.)3

At the claim construction hearing, Plaintiff requested leave to present supplemental 

briefing and documents. In the supplemental briefs, the Parties again summarize their 

proposed construction: Plaintiff argues “a” is the length of polymer A and identifier 

oligonucleotide C. (“Pl. Supp. Br.,” ECF No. 66, at 3.) Plaintiff argues “polymer A is 

determined by counting the number of monomers” and “the length of an oligonucleotide is 

measured in nucleotide bases.” (Id.) Plaintiff does not propose these units of measurement 

be officially added to the claim construction for “a” but argues a person of ordinary skill 

in the art reading the patent would understand that length is measured in these units. (Id.

at 5.)

Plaintiff submitted 37 C.F.R. § 1.823 as an exhibit to its brief. This regulation 

provides what shall be included in a sequence listing. The sequence listing, which sets 

“forth the nucleotide and/or amino acid sequence and associated information,” shall 

include “length” in “an integer expressing the number of bases or amino acid residues.” 37 

C.F.R. § 1.823(b). Plaintiff argues this regulation, which governs “submission of sequence 

listings of oligonucleotides and polypeptides,” “expressly required that the length be 

measured by the number of nucleotide bases or amino acid residues, respectively.” (Pl. 

Supp. Br. 4.) Plaintiff argues one can read this federal regulation, which dictates how 

sequences must be described in a patent, to determine how to measure the length of a 

polypeptide of oligonucleotide. (Id. at 5.) Defendant argues this regulation is not relevant 

to interpreting the formula “(Xn)a” because the patent’s sequence listing relates to 

 

3 Defendant previously brought a motion to dismiss, which dealt with the term “a.” As it does in the 

present claim construction, Defendant argued the patent defines “a” to be the number of chemical units in 

polymer A and the number of corresponding unit identifiers in identifier oligonucleotide C. (ECF No. 30-

1, at 15.) The Court denied Defendant’s motion to dismiss, finding it “cannot say at this stage that 

Defendant’s construction is correct as a matter of law.” (ECF No. 34, at 10.) The Court held that passages 

from the patent illustrate “a” can be defined by the number of chemical units, it does not specify it must 

be so defined. (Id.) The Court noted that the Parties would have another opportunity to contest the 

meaning of “a” at the claim construction phrase. (Id. at 13.) 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 9 of 18
10

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

oligonucleotide C, not polymer A. (“Def. Supp. Br.,” ECF No. 67, at 7; see ’596 patent, at 

29.) As to the construction of “(Xn)a”, Defendant does not disagree that the patent describes 

“a” as “the length of the polymer A.” ’596 patent, at 4:39–42 (“[T]he length of the polymer 

can vary, defined by a.”). But Defendant reaffirms its position that “length” is measured 

in chemical units. (Def. Supp. Br. 4 (citing ’569 patent, at 9:9–11 (in 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.”)).)

The Court agrees with Defendant’s construction. Critically, Plaintiff cannot point 

to evidence or to any part of the patent that would allow “a” to be two different integers or 

measured by two different units for polymer A and oligonucleotide C. Instead, “a” is 

specifically defined as “an integer”—indicating it is the same for both “(Xn)a” and “(Zn)a”.

See ’596 patent, at 4:43–44 (for Polymer A, “‘a’ is an integer from 4 to 50”); id. at 5:63–

65 (for oligonucleotide C, “‘a’ is an integer as described previously to connote the number 

of chemical unit identifiers in the oligonucleotide”). As Defendant points out, “when 

Scripps wanted to represent two different things (like chemical units (X) and chemical unit 

identifiers (Z)), it did so by using different variables for each of them in claim 1.” (Def. 

Supp. Br. 10.) Had Plaintiff intended “a” to represent different values with different units 

of measurement for polymer A and for oligonucleotide C, it should have specified this, or 

used two different variables. Plaintiff’s proposed construction leaves open the units of 

measurement, which will result in two different values for “a” due to the two different units 

of measurement indicated by Plaintiff in its briefing (monomers and nucleotide bases). (Pl. 

Supp. Br. 5 (stating “‘a’ need not have the same value in the case of polymer A and 

oligonucleotide C for a given bifunctional molecule.”).) This is not supported by the patent 

language nor by 37 C.F.R. § 1.823(b). Plaintiff has not defined “a” with any form of clarity 

in the sequence listing or in the specification, thus the Court declines to construe “a” based 

on Plaintiff’s proposed lexicography. And, 37 C.F.R. § 1.823(b), even read in connection 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 10 of

 18
11

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

with the patent’s sequence listing, does not provide that an integer can represent two 

different lengths with two different units of measurement.

The Court construes “a” as “an integer from 4 to 50 that is further defined in the 

context of the formulas (Zn)a and (Xn)a.”

4 The Court construes “(Xn)a” as “a representation 

of polymer A, where ‘a’ is the number of chemical units of X forming the polymer A.” 

The Court construes “(Zn)a” as “a representation of identifier oligonucleotide C, where ‘a’

is the number of chemical unit identifiers in the oligonucleotide.”

B. “B is a linker molecule operatively linked to A and C”

Plaintiff would construe this term as “single molecule B that performs the function 

of operatively linking a single polymer A to single identifier oligonucleotide C.” (Joint 

CC Worksheet 4.) Defendant would construe this term as “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 from linker molecule B.” (Id. at 4–5.) Alternatively, if 

the Court does not accept this, Defendant proposes “a molecule B that performs the 

function of operatively linking a chemical moiety A to an identifier oligonucleotide C.” 

(Id. at 5.)

In February 2017, the Patent Trial and Appeal Board (“PTAB”) construed the 

present term. See Illuminia, Inc. v. The Scripps Research Institute, No. IPR2016-01619 

(P.T.A.B. Feb. 13, 2017) (hereinafter “Illuminia”). Defendant proposes the Court construe 

the term exactly as the PTAB construed it.

The Court agrees with the PTAB’s construction. The decision is reasoned, 

 

4 The Court notes that Plaintiff’s proposed construction of “a” specifically (not in the context of the two 

formulas) is not technically incorrect. Plaintiff proposes “a” be construed as “the length of polymer A or 

identifier oligionucleotide C and is an integer from 4 to 50.” (Joint CC Worksheet 8–9.) Defendant would 

construe “a” as: “an integer from 4 to 50 that is further defined in the context of the formulas (Zn)a and 

(Xn)a.” (Id.) Both Parties agree “a” is “the length” of polymer A and oligonucleotide C, thus, both

proposed constructions are correct. But, Defendant’s construction for “a” as consistent with the 

constructions of (Zn)a and (Xn)a.

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 11 of

 18
12

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

persuasive, and provides the Court with guidance on the construction of the term. (See id.

at 9–17.) Further, the PTAB noted, because the ’596 patent expired in 2012, its review of 

the patent “is similar to that of a district court’s review.” Id. at 9; see In re Rambus, 

Inc., 694 F.3d 42, 46 (Fed. Cir. 2012) (“[T]he Board’s review of the claims of 

an expired patent is similar to that of a district court’s review.” (citations omitted)). The 

PTAB applied the principles set forth in Phillips, 415 F.3d at 1312–13. Illuminia, at 10. 

The PTAB concluded the term “B is a linker molecule operatively linked to A and C” to 

mean “that 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 from linker 

molecule B.” Illuminia, at 17. In sum, the PTAB looked at the language of the claim 

language, the “disclosure in the specification” and the “narrowing statements” made by 

Plaintiff during prosecution. Id.; see also id. (“[T]he arguments made to distinguish the 

prior art constitute a clear and unequivocal disavowal of linker molecules that fail to allow 

for alternative addition (or synthesis) of an oligonucleotide and amino acid onto the linker 

molecule, while separately allowing for coupling and decoupling of the linker molecule 

from a solid support.”).

The Court agrees and adopts the PTAB’s construction as to this term. See 

Evolutionary Intelligence, LLC v. Spring Nextel Corp., No. C-13-04513, 2014 WL 

4802426, at *4 (N.D. Cal. Sept. 26, 2014) (stating PTAB decisions are not binding on the 

court but they may “inform” the court’s ultimate reasoning). The term is construed as 

“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 from linker molecule 

B.”

C. “bifunctional molecule”

Plaintiff would construe this term as “a single molecule of the formula A–B–C, 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 12 of

 18
13

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

whereby one molecule of chemical moiety A and one molecule of identifier 

oligonucleotide C are operatively linked by one molecule of linker B.” (Pl. CC Brief 18.) 

Defendant argues this preamble term is not limiting and “is merely a descriptive name to 

the set of limitations in the body of the claim.” (Def. CC Brief 28.) If the Court determines 

the term is limiting, Defendant would construe the term as “a molecule that can be

represented by the formula A–B–C, where A is a chemical moiety, B is a linker molecule 

operatively linked to A and C, and C is an identifier oligonucleotide comprising a sequence 

of nucleotides that identifies the structure of chemical moiety A.” (Id.)

A preamble is an introductory phrase that may summarize the invention, its relation 

to the prior art, or its intended use or properties. E. I. du Pont de Nemours & Co. v. 

Monsanto Co., 903 F. Supp. 680, 693 (D. Del. 1995) (quoting 8 Donald S. Chisum, Chisum 

on Patents § 8.06 (Matthew Bender ed. 3d ed.)), aff’d, 92 F.3d 1208 (Fed. Cir. 

1996) (unpublished). A recurrent problem in construing patent claims is whether language 

in a claim is a limitation of the claim’s scope or merely a non-limiting statement of intended 

use or effect. Chisum, § 8.06. “If the preamble adds no limitations to those in the body of 

the claim, the preamble is not itself a claim limitation and is irrelevant to proper 

construction of the claim.” IMS Tech., Inc. v. Haas Automation, Inc., 206 F.3d 1422, 1434 

(Fed. Cir. 2000) (citing Pitney Bowes, 182 F.3d at 1305).

Whether to treat a preamble as a limitation is a determination “resolved only on 

review of the entirety of the patent to gain an understanding of what the inventors actually 

invented and intended to encompass by the claim.” Corning Glass Works v. Sumitomo 

Electric U.S.A., Inc., 868 F.2d 1251, 1257 (Fed. Cir. 1989); see also Applied Materials, 

Inc. v. Advanced Semiconductor Materials Am., Inc., 98 F.3d 1563, 1572–73 (Fed. Cir.

1996) (“Whether a preamble stating the purpose and context of the invention constitutes a 

limitation of the claimed process is determined on the facts of each case in light of the 

overall form of the claim, and the invention as described in the specification and 

illuminated in the prosecution history.”).

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 13 of

 18
14

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

In general, a preamble limits the invention if it recites essential structure or steps, or 

if it is “necessary to give life, meaning, and vitality” to the claim. Pitney Bowes, 182 F.3d

at 1305. Conversely, a preamble is not limiting “where a patentee defines a structurally 

complete invention in the claim body and uses the preamble only to state a purpose or 

intended use for the invention.” Rowe v. Dror, 112 F.3d 473, 478 (Fed. Cir. 1997). “[A] 

preamble generally is not limiting when the claim body describes a structurally complete 

invention such that deletion of the preamble phrase does not affect the structure or steps of 

the claimed invention.” IMS Tech., 206 F.3d at 1434 (holding preamble phrase “control 

apparatus” does not limit claim scope where it merely gives a name to the structurally 

complete invention).

The Court finds the phrase “a bifunctional molecule” is not limiting. The remainder 

of the claim body (the description after “bifunctional molecule”) describes a complete 

claim, beginning with the formula A–B–C and proceeding on to define each piece of the 

formula. The Court finds IMS Technology instructive; similarly, here, the phrase “does not 

limit claim scope” but only gives a name to a “structurally complete invention.” 206 F.3d 

at 1434; see also Weiland Sliding Doors & Windows, Inc. v. Panda Windows & Doors, No. 

10-CV-677-JLS (MDD), 2011 WL 3490481, at *3 (S.D. Cal. Aug. 10, 2011) (finding the 

preamble “names what is being claimed . . . but does little else. And simply naming the 

structure being claimed in the body is insufficient to render the preamble limiting”). Here, 

the phrase only “names what is being claimed” and is not necessary to give life, meaning, 

and validity to the claims. 5 Thus, the Court declines to construct this preamble phrase.

D. “identifier oligonucleotide C”

Plaintiff would construe this term as “a unique nucleotide sequence that is an 

unrelated combination by chance or otherwise during the manipulation of the bifunctional 

 

5 This finding is bolstered by the fact that Plaintiff’s proposed construction of this phrase merely recites 

the remainder of the claim, thus it is unclear how the phrase could be limiting, as Plaintiff suggests.

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 14 of

 18
15

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

molecule.” (Joint CC Worksheet 5.) Defendant argues the term does not require 

construction because claim 1 already defines it, but if the Court chooses to construe the 

term, it should be construed as: “an oligonucleotide having a sequence represented by the 

formula (Zn)a.” (Id. at 5–6.)

Plaintiff argues the dispute pertains to the word “identifier” in this phrase. (Pl. CC 

Brief 20.) Plaintiff argues for the oligonucleotide to be an “identifier,” it must contain a 

unique sequence that is an unrelated combination by chance or otherwise. (Id.; see ’596 

patent, at 6:25–30 (“For the design of the code in the identifier oligonucleotide, it is 

essential to chose [sic] a coding representation such that no significant part of the 

oligonucleotide sequence can occur in another unrelated combination by chance or 

otherwise during the manipulations of a bifunctional molecule in the library.”).) Plaintiff 

argues Defendant’s definition attempts to erase the word “identifier.”

Plaintiff argues the patent is directed to chemical libraries of bifunctional molecules 

that contain millions of unique samples, and each molecule contains a “genetic tag” that 

identifies the sample. To determine the identity of the molecule, one reads the genetic tag. 

This tag must contain a unique nucleotide sequence so that it may identify the single 

molecule. (Pl. CC Brief 20.) Otherwise, one decoding the tag would not know “which 

active chemical molecule was on the other end of the bifunctional molecule and the 

identifier oligonucleotide would not serve its purpose.” (Id.) Plaintiff argues this 

description is “essential to the invention.” (Id. at 21.) On the other hand, Plaintiff argues 

Defendant’s proposed construction could cover any oligonucleotide sequence represented 

by (Zn)a. (Id. at 22.) This cannot be the case because “identifier oligonucleotide C must 

be unique to its polymer A because reading the identifier alone determines the identify of 

polymer A.” (Id.)

Defendant argues claim 1 already specifies this term—as “represented by the 

formula (Zn)a.” (Def. CC Brief 29.) Defendant does not disagree the oligonucleotide must 

be “unique,” but finds no need to incorporate that limitation via claim construction. (Def. 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 15 of

 18
16

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

Response 13.) Defendant also argues Plaintiff did not include the language “no specific 

part” in its proposed construction, thus changing the meaning of the sentence. (Def. CC 

Brief 29.)

“The appropriate starting point [in claim construction] is always with the language 

of the asserted claim itself.” Comark Commc’ns, 156 F.3d at 1186. Claim terms are 

generally given their ordinary and customary meaning as understood by a person of 

ordinary skill in the art when read in the context of the specification and prosecution 

history. Thorner v. Sony Computer Entm’t Am. LLC, 669 F.3d 1362, 1365 (Fed. Cir. 2012). 

“The specification acts as a dictionary when it expressly defines terms used in the claims 

or when it defines them by implication.” Vitronics, 90 F.3d at 1582. “[A]ny special 

definition given to a word must be clearly defined in the specification.” Markman, 517 

U.S. at 989–90. An inventor may choose to be his own lexicographer if he defines the 

specific terms used to describe the invention “with reasonable clarity, deliberateness, and 

precision.” In re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir. 1994). “However, claims are not 

to be interpreted by adding limitations appearing only in the specification.” Id. “Thus, 

although the specifications may well indicate that certain embodiments are preferred, 

particular embodiments appearing in a specification will not be read into the claims when 

the claim language is broader than such embodiments.” Id.

The Court finds it would be inappropriate to read the specification into this element, 

as Plaintiff proposes. The claim language is broader than the language in the specification, 

and the Court finds no clear intent by Plaintiff to limit the claim term to “a unique 

nucleotide sequence that is an unrelated combination by chance or otherwise during the 

manipulation of the bifunctional molecule.” The claim specification provides “identifiers 

oligonucleotide C is represented by the formula (Zn)a.” The claim itself therefore shows the 

ordinary meaning of the term. Further, the Court finds that the specification does not 

“expressly” nor “clearly” define the term and it would be incorrect to read limitations from 

the specification into the claims. See Teleflex, Inc. v. Ficosa N. Am. Corp., 299 F.3d 1313, 

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 16 of

 18
17

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

1325 (Fed. Cir. 2002) (“The patentee may demonstrate an intent to deviate from the 

ordinary and accustomed meaning of a claim term by including in the specification 

expressions of manifest exclusion or restriction, representing a clear disavowal of claim 

scope.”); Raytheon Co. v. Roper Corp., 724 F.2d 951, 957 (Fed. Cir. 1983) (“That claims 

are interpreted in light of the specification does not mean that everything expressed in the 

specification must be read into all the claims.”). Further, the Court finds the claim itself 

contains the proper construction. Thus, the Court construes the term as “an oligonucleotide 

having a sequence represented by the formula (Zn)a.”

CONCLUSION

The terms in dispute are construed as follows:

Term Construction

“a” an integer from 4 to 50 that is further 

defined in the context of the formulas (Zn)a

and (Xn)a

“(Xn)a” a representation of polymer A, where “a” is 

the number of chemical units of X forming 

the polymer A

“(Zn)a” a representation of identifier 

oligonucleotide C, where “a” is the number 

of chemical unit identifiers in the

oligonucleotide

“B is a linker molecule operatively linked 

to A and C”

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 from 

linker molecule B

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 17 of

 18
18

16-CV-661 JLS (BGS)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

“bifunctional molecule” The Court declines to construct this 

preamble phrase.

“identifier oligonucleotide C” an oligonucleotide having a sequence 

represented by the formula (Zn)a

IT IS SO ORDERED.

Dated: April 10, 2018

Case 3:16-cv-00661-JLS-BGS Document 77 Filed 04/10/18 PageID.<pageID> Page 18 of

 18