Document ID: s3://data.kl3m.ai/documents/govinfo/USCOURTS/USCOURTS-ca13-22-02172/USCOURTS-ca13-22-02172-0/pdf.json

Parties Involved:
Integrated DNA Technologies, Inc.
Appellant
Pillar Biosciences, Inc.
Appellee

Document Text:

NOTE: This disposition is nonprecedential.

United States Court of Appeals 

for the Federal Circuit

______________________

INTEGRATED DNA TECHNOLOGIES, INC.,

Appellant

v.

PILLAR BIOSCIENCES, INC.,

Appellee

______________________

2022-2172

______________________

Appeal from the United States Patent and Trademark 

Office, Patent Trial and Appeal Board in No. IPR2021-

00401.

______________________

Decided: December 20, 2024

______________________

RONALD E. CAHILL, Barnes & Thornburg LLP, Boston, 

MA, argued for appellant. Also represented by MATTHEW 

S. GIBSON, MARK CHRISTOPHER NELSON, Dallas, TX; 

STEVEN SHIPE, Washington, DC.

 BRIAN ROBERT MATSUI, Morrison & Foerster LLP, 

Washington, DC, argued for appellee. Also represented by 

MATTHEW IAN KREEGER, San Francisco, CA; JIAN XIAO, 

Palo Alto, CA.

 ______________________

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INTEGRATED DNA TECHNOLOGIES, INC. v.

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Before REYNA, MAYER, and CUNNINGHAM, Circuit Judges.

CUNNINGHAM, Circuit Judge. 

Integrated DNA Technologies, Inc. (“IDT”) appeals 

from a final written decision of the Patent Trial and Appeal 

Board in an inter partes review, finding claims 1–6 of U.S. 

Patent No. 10,316,359 unpatentable. Pillar Biosciences, 

Inc. v. Swift Biosciences, Inc., No. IPR2021-00401, 2022 WL 

2308112, at *1 (P.T.A.B. June 27, 2022) (“Decision”).

1 On 

appeal, IDT challenges the Board’s claim construction, 

argues that the Board’s factual findings were not supported 

by substantial evidence, and asserts that the Board erred 

in ruling that IDT had forfeited2 certain arguments. For 

the reasons below, we affirm the Board’s decision.

I. BACKGROUND

The ’359 patent is titled “Methods for Multiplex PCR.” 

It is generally directed to methods for the preparation of 

polymerase chain reaction (“PCR”) mixtures and for 

performing multiplex PCR amplification that limit the 

production of non-target amplicons. ’359 Patent, Abstract. 

Claim 1 is illustrative of the issues on appeal and recites:

1 Swift Biosciences, Inc. was the named patent 

owner when the IPR was filed. J.A. 608. While the IPR 

was pending Swift Biosciences merged with IDT, making

IDT the real party-in-interest. J.A. 609.

2 The parties and the Board use the term “waiver,” 

but for consistency we use “forfeiture” throughout this 

opinion. See In re Google Tech. Holdings LLC, 980 F.3d 

858, 862 (Fed. Cir. 2020) (“By and large, in reviewing this 

court’s precedent, it is evident that the court mainly uses 

the term ‘waiver’ when applying the doctrine of 

‘forfeiture.’”).

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1. A method of multiplex PCR amplification of a 

target nucleic acid substrate comprising the steps 

of:

(i) combining a plurality of target-specific 

primers with the target nucleic acid

substrate to yield a single polymerase 

chain reaction (PCR) reaction mixture,

wherein the plurality of target-specific 

primers comprise a first forward primer, a

second forward primer, a first reverse 

primer and a second reverse primer, 

wherein each of the first and second 

forward and reverse primers comprise a 3′

complementary sequence that is 

complementary to the target nucleic acid 

substrate and a 5′ noncomplementary 

sequence that is not complementary to the 

target nucleic acid substrate, wherein the 

3′ complementary sequence for each of the 

first and second forward and reverse 

primers is different;

(ii) subjecting the PCR reaction mixture to 

a multiplex polymerase chain reaction

thereby generating at least three 

amplicons, wherein the at least three 

amplicons comprise a first amplicon 

produced by the first forward primer and 

the first reverse primer, a second amplicon 

produced by the second forward primer and 

the second reverse primer, and a third 

amplicon produced by the second forward 

primer and the first reverse primer, 

wherein at least a portion of the 5′ 

noncomplementary sequence of the second 

forward primer and the first reverse primer 

is the same such that each strand of the 

third amplicon comprises a 3′ end and a 5′ 

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end that are complementary to each other, 

wherein the third amplicon possesses 

overlapping sequence with the first and 

second amplicons, wherein the first 

amplicon possesses overlapping sequence 

with the second amplicon, wherein when 

the third amplicon is denatured, each 

strand of the third amplicon forms a 

secondary structure as a result of the 3′ end 

being complementary to the 5′ end, and 

wherein the secondary structure is stable 

during a primer annealing step of the 

multiplex polymerase chain reaction.

Id. col. 133 ll. 56–67, col. 134 l. 55 to col. 135 l. 12.

On January 7, 2021, Pillar Biosciences, Inc. (“Pillar”) 

filed the IPR underlying this appeal, challenging claims 1–

6 of the ’359 patent. Decision at *1; see also J.A. 162. 

Among other things, Pillar asserted that the claims of the 

’359 patent were obvious over the combination of prior art 

references Lao3 and Gardner.

4 Decision at *1. The Board

instituted review on July 19, 2021. Id. The Board

subsequently held that Pillar proved by a preponderance of 

the evidence that all challenged claims were unpatentable 

under 35 U.S.C. § 103(a) over Lao and Gardner. Decision

at *13. 

IDT timely appeals. We have jurisdiction under 28 

U.S.C. § 1295(a)(4)(A).

3 U.S. Patent Application 2009/0291475 (filed Apr. 

22, 2009), J.A. 940–87 (“Lao”).

4 Shea N. Gardner et al., Multiplex Degenerate 

Primer Design for Targeted Whole Genome Amplification of 

Many Viral Genomes, Advances in Bioinformatics, Aug. 3,

2014, J.A. 1000–07 (“Gardner”). 

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II. STANDARD OF REVIEW

“We review the Board’s legal conclusions de novo and 

its fact findings for substantial evidence.” Game & Tech.

Co. v. Wargaming Grp. Ltd., 942 F.3d 1343, 1348 (Fed. Cir. 

2019). “Substantial evidence means such relevant 

evidence as a reasonable mind might accept as adequate to 

support a conclusion.” Fanduel, Inc. v. Interactive Games 

LLC, 966 F.3d 1334, 1343 (Fed. Cir. 2020) (internal 

quotation marks and citation omitted).

“Whether a claimed invention is unpatentable as 

obvious is a question of law that is reviewed de novo, based 

on underlying findings of fact reviewed for substantial 

evidence.” Redline Detection, LLC v. Star Envirotech, Inc., 

811 F.3d 435, 449 (Fed. Cir. 2015). “The Court can review 

de novo, however, whether the Board failed to consider the 

appropriate scope of the patent’s claimed invention in 

evaluating the reasonable expectation of success.” 

Intelligent Bio-Sys., Inc. v. Illumina Cambridge Ltd., 821 

F.3d 1359, 1366–67 (Fed. Cir. 2016) (cleaned up).

“Decisions related to compliance with the Board’s 

procedures are reviewed for an abuse of discretion.” Id. at 

1367. “An abuse of discretion is found if the decision: (1) is 

clearly unreasonable, arbitrary, or fanciful; (2) is based on 

an erroneous conclusion of law; (3) rests on clearly 

erroneous fact finding; or (4) involves a record that contains 

no evidence on which the Board could rationally base its 

decision.” Ericsson Inc. v. Intell. Ventures I LLC, 901 F.3d 

1374, 1379 (Fed. Cir. 2018) (quoting Bilstad v. 

Wakalopulos, 386 F.3d 1116, 1121 (Fed. Cir. 2004)).

III. DISCUSSION

IDT presents several arguments on appeal. IDT 

argues that the Board erred in construing “each strand of 

the third amplicon forms a secondary structure . . . and 

wherein the secondary structure is stable during a primer

annealing step.” Appellant’s Br. 31–35; Appellant’s Reply 

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Br. 17–18. IDT also argues that the Board’s finding of a 

motivation to combine the prior art contained factual and

legal errors. See Appellant’s Br. 46–55. IDT further 

contends that the Board’s finding of a reasonable 

expectation of success was based on hindsight. See id. at 

35–46. Lastly, IDT argues that the Board erred in ruling 

that IDT had forfeited arguments based on an additional 

reference, Schenk.5 Id. at 55–57. We address each 

argument in turn.

A.

IDT argues that the Board erred in its claim 

construction of “each strand of the third amplicon forms a 

secondary structure . . . and wherein the secondary 

structure is stable during a primer annealing step” by 

concluding that “the claims did not require complete 

elimination of short amplicons.” Appellant’s Br. 31

(internal quotation marks omitted). At oral argument, IDT 

presented a different construction, arguing that the 

quantity of short amplicons “needs to be reduced to a level 

[at which] it doesn’t dominate.” Oral Arg. 12:50–13:02, 

https://oralarguments.cafc.uscourts.gov/default.aspx?fl=22

-2172_02092024.mp3.

Regardless of which claim construction position IDT 

presents, we need not reach the merits of IDT’s claim 

construction arguments because it has forfeited them. See

In re Google Tech. Holdings LLC, 980 F.3d 858, 862 (Fed. 

Cir. 2020) (explaining that Google forfeited the claim 

construction arguments that it failed to present to the 

Board). IDT concedes in its briefing that neither party 

5 Desiree Schenk et al., Amplification of Overlapping 

DNA Amplicons in a Single-Tube Multiplex PCR for 

Targeted Next-Generation Sequencing of BRCA1 and 

BRCA2, PLoS ONE, July 12, 2017, J.A. 1700–15

(“Schenk”). 

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proposed a construction for the term at issue, and neither 

party briefed a construction for this term before the 

Board. Appellant’s Br. 33; Oral Arg. 12:34–

13:23. Generally, absent exceptional circumstances, we 

will not consider on appeal claim construction arguments 

that were not first presented to the Board. 

IDT argues that it has not forfeited its claim 

construction arguments because the Board construed the 

“each strand” limitation in its final written decision

inconsistently with the plain and ordinary meaning of the 

term after both parties had relied on the plain and ordinary 

meaning throughout the proceedings below. Appellant’s 

Reply Br. 16–18. However, the Board was only applying 

the plain and ordinary meaning of the challenged claims, 

which nowhere reference “complete elimination of short 

amplicons.” See, e.g., Decision at *9. To the extent that 

IDT thinks that complete elimination of short amplicons is 

required, or that the short amplicons had to be reduced to 

a level that does not dominate the PCR amplification 

process, IDT was required to raise those arguments to the 

Board to preserve them on appeal.

B.

IDT further argues that the Board’s finding of a

motivation to combine Gardner and Lao was not supported 

by substantial evidence because there was allegedly no 

dispute that the combination “does not work for its 

intended purpose[;] Gardner teaches away from the 

combination[;] and the combination would result in the loss 

of key functionality in Gardner.” Appellant’s Br. 46. IDT

additionally faults the Board for purportedly shortcircuiting the proper analysis without considering whether 

the proposed combination would provide the advantages 

that Gardner specifically sought. Id.; see also id. at 48–49. 

IDT’s arguments are unpersuasive.

IDT’s main argument for why the Board lacked 

substantial evidence for its determination that a skilled 

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artisan would have had a motivation to combine Gardner 

and Lao concerns the size of the overlapping amplicons in 

each of the references. See Appellant’s Br. 46–55. 

According to IDT, there is no motivation to combine the 

prior art references because 30 of the 36 overlapping

amplicons in Gardner exceeded 100 base pairs and Lao 

does not suppress amplicons of that size. Id. at 38, 49. The 

Board addressed this argument in the final written

decision, finding that “even under the most restrictive 

reading of Lao,” “six of the amplicons listed in Gardner’s 

example are shorter than 100 nucleotides and therefore 

would have been removed.” Id. at *10. There is no dispute 

about the relevant teachings of Gardner and Lao. Oral 

Arg. 4:24–4:30 (IDT agreeing “that Gardner discloses at 

least some amplicons that are within Lao’s size 

limitations”). For example, Gardner expressly teaches “a 

step to remove short amplicons before sequencing,” J.A. 

1003, and Lao discloses the ability of “shorter insert 

sections to self-hybridize, and thus take themselves out of 

a reaction.”

6 J.A. 972 ¶ 116. In summary, we conclude that 

there is substantial evidence support for the Board’s 

conclusion that a skilled artisan would have had a 

motivation to combine Gardner with Lao, see Decision at 

*7–9, and thus we conclude that the Board did not err in

its motivation-to-combine determination. 

C.

Substantial evidence also supports the Board’s factual 

finding that a skilled artisan would have a reasonable 

6 Lao defines insert sections as the portion of the 

amplicon between the complementary ends of the linear 

primers used to form the amplicon. J.A. 965 ¶ 0064. The 

size comparisons in this case were done on an apples-toapples basis, and “amplicons,” “insert sections,” and “insert 

regions” are terms all used by the parties. J.A. 1800–01; 

see Appellant’s Br. 42 n. 5. 

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expectation of success in combining Lao and Gardner to 

achieve the claimed invention. IDT argues that the Board’s 

conclusion was unsupported by substantial evidence 

because there is “undisputed evidence that the 

combination of Gardner with Lao will fail abjectly . . . for 

the purpose of claim 1 of the ’359 patent, . . . for the 

purpose of Gardner, and . . . for the stated motivation for 

making the combination.” Appellant’s Br. 30. “The 

reasonable-expectation-of-success analysis must be tied to 

the scope of the claimed invention.” Teva Pharms. USA, 

Inc. v. Corcept Therapeutics, Inc., 18 F.4th 1377, 1381 (Fed. 

Cir. 2021). IDT does not demonstrate any flaw with the 

evidence the Board did rely on in reaching its conclusion

regarding reasonable expectation of success. Decision at 

*10 (citing evidence from Lao, Gardner and the testimony 

of Pillar’s expert in support of a reasonable expectation of 

success); Appellant’s Br. 35–43. The Board did not err in 

finding that a skilled artisan would have a reasonable 

expectation of success in combining Gardner with Lao to 

achieve the claimed invention. 

IDT argues that the evidence the Board relied on was 

merely conclusory and that its finding was based on 

hindsight. See Appellant’s Br. 42–43. We disagree. IDT’s 

argument is premised on its claim construction arguments, 

which IDT forfeited. See id. at 42 (“This finding can only 

be justified by applying the Board’s faulty claim 

construction where it found that removal of some 

amplicons met the claim.”). Regardless, the Board found 

that Lao discloses “self-hybridizing,” a process where

amplicons take themselves out of the reaction. Decision at 

*4, 9. Contrary to IDT’s assertions, that finding was not 

hindsight; it was based on the express disclosure of Lao. 

J.A. 972 ¶ 116. (“[T]he double extended linear primers 

having shorter insert sections to self-hybridize, and thus 

take themselves out of a reaction . . . .”). Indeed, several 

parts of Lao support the Board’s determination. See, e.g.,

J.A. 950 (Fig. 8), 961 ¶ 0034, 964 ¶ 0053. The expert 

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testimony the Board relied on provides additional support

for this finding. Decision at *10.

IDT attempts to incorporate one reference’s 

embodiments into the other reference. See, e.g., 

Appellant’s Br. 38, 40 (focusing its analysis on the 

interaction between a limitation present “in some 

embodiments” of Lao, J.A. 966 ¶ 73, and a subset of 

overlapping amplicons in an example in Gardner). Here 

too, we disagree with IDT’s approach. “[A] determination 

of obviousness based on teachings from multiple references 

does not require an actual, physical substitution of 

elements.” In re Mouttet, 686 F.3d 1322, 1332 (Fed. Cir. 

2012). The correct inquiry is instead whether a skilled 

artisan would reasonably expect success in combining the 

prior art’s teachings to achieve the claimed invention. 

Intelligent Bio-Sys., 821 F.3d at 1367–68; see also In re 

Applied Materials, Inc., 692 F.3d 1289, 1298 (Fed. Cir. 

2012) (“A reference must be considered for everything that 

it teaches, not simply the described invention or a preferred 

embodiment.”). We agree with Pillar that because 

“Gardner . . . teaches a multiplex PCR reaction with 

primers that produce overlapping amplicons” and “never 

suggests that its overlapping amplicons in multiplex PCR 

reactions must exceed Lao’s supposed size limitation,” the 

Board did not err in holding that a skilled artisan would 

reasonably expect to succeed in combining the prior art 

references to achieve the subject matter claimed by the ’359 

patent. Appellee’s Br. 37–38; Decision at *12.

IDT argues that the Board erred by failing to consider 

all of IDT's arguments against finding a reasonable 

expectation of success. Appellant’s Br. 43 (quoting Decision

at *9). But the Board is “not required to address every 

argument raised by a party or explain every possible 

reason supporting its conclusion.” Yeda Rsch. v. Mylan 

Pharms. Inc., 906 F.3d 1031, 1046 (Fed. Cir. 2018) (cleaned 

up). The Board committed no reversible error here, and it 

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supported its factual determination with substantial 

evidence.

D.

IDT’s contention that the Board erred by finding IDT’s 

arguments based on Schenk forfeited under 37 C.F.R. 

§ 42.23(b) is similarly unavailing. See Appellant’s Br. 56–

57. IDT argues that it maintained its reliance on the 

Schenk reference throughout the proceedings, id., but

IDT’s characterization of the procedural history does not 

align with the record, and its argument therefore fails.

During the IPR, the Board cautioned IDT “that any 

arguments not raised in the response may be deemed 

[forfeited].” J.A. 315. Although IDT had extensively 

discussed Schenk in its preliminary response, J.A. 272–76, 

IDT’s citations to Schenk in the Patent Owner’s Response 

were minimal and without much elaboration. See, e.g., J.A. 

350, 353–55, 392. The Board did not abuse its discretion 

in finding that IDT had therefore forfeited the argument. 

See Decision at *11; In re NuVasive, Inc., 842 F.3d 1376, 

1380 (Fed. Cir. 2016) (finding the patent owner “[forfeited]

its public accessibility arguments” where it challenged 

public accessibility “during the preliminary proceedings of 

the inter partes review but failed to challenge public 

accessibility during the trial phase” (citations omitted)); 

Broadcom Corp. v. ITC, 28 F.4th 240, 252 (Fed. Cir. 2022) 

(declining to address argument not raised with the Board 

and explaining that “[t]he Board’s scheduling order 

specifically informed [patent owner] that ‘any arguments 

not raised in the response may be deemed [forfeited]’”). 

The Board acted within its discretion when it found that 

IDT had forfeited the argument and that it would not 

consider the parties’ arguments with respect to Schenk.

IV. CONCLUSION

We have considered IDT’s remaining arguments and 

find them unpersuasive. For the above reasons, we affirm.

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AFFIRMED

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