Intelligent Bio-Systems, Inc.v.Illumina Cambridge Limited

Patent Trial and Appeal Board

Jul 25, 2014

10227131 (P.T.A.B. Jul. 25, 2014)

Trials@uspto.gov Paper 92
571-272-7822 Entered: July 25, 2014
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

INTELLIGENT BIO-SYSTEMS, INC.,
Petitioner,

v.

ILLUMINA CAMBRIDGE LIMITED,
Patent Owner.
___________

Case IPR2013-00128
U.S. Patent 7,057,026 B2
___________

Before LORA M. GREEN, RICHARD M. LEBOVITZ, and
CHRISTOPHER L. CRUMBLEY, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

FINAL WRITTEN DECISION
35 U.S.C. § 318(a) and 37 C.F.R. § 42.73

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I. BACKGROUND
A. Introduction
Petitioner, Intelligent Bio-Systems, Inc. (“IBS”), filed a Petition
(Paper 15, “Pet.”) for inter partes review of claims 1-8 of U.S. Patent No.
7,057,026 B2 (“the ’026 patent”) pursuant to 35 U.S.C. §§ 311-319 and 37
C.F.R. §§ 42.1–42.123.
On July 29, 2013, inter partes review of claims 1-8 was instituted on
five grounds of unpatentability. Decision on Petition (“Dec. Pet.”) (Paper
23). After institution of the inter partes review, Patent Owner, Illumina
Cambridge Limited (“Illumina”), did not file a response under 37 C.F.R.
§ 42.120 to the decision instituting inter partes review.
Illumina filed a Motion to Amend (Paper 61, “Mot. Amend”) and a
Motion to Exclude Evidence (Paper 70). IBS filed an opposition to
Illumina’s Motion to Amend (Paper 53) and its own Motion to Exclude
Evidence (Paper 67). An oral hearing was held on April 23, 2014. Record
of Oral Hearing (Paper 89).
The Board has jurisdiction under 35 U.S.C. § 6(c). This final written
decision is issued pursuant to 35 U.S.C. § 318(a) and 37 C.F.R. § 42.73.
Illumina’s Motion to Amend is GRANTED to the extent it requests to
cancel claims 1-8; Illumina’s Motion to Amend is DENIED to the extent
that it requests entry of substitute claims 9-12.

B. The ’026 Patent
The ’026 patent issued on June 6, 2006. The named inventors are
Colin Barnes, Shankar Balasubramanian, Xiaohai Liu, Harold Swerdlow,
and John Milton. The ’026 patent describes labeled nucleotides and
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nucleosides used in “sequencing reactions, polynucleotide synthesis, nucleic
acid amplification, nucleic acid hybridization assays, single nucleotide
polymorphism studies, and other techniques using enzymes such as
polymerases, reverse transcriptases, terminal transferases, or other DNA
modifying enzymes.” Ex. 1001, col. 2, ll. 10-14. A detectable label (such as
a fluorophore) is attached to the base of the nucleotide via a cleavable linker
group. Id. at col. 2, ll. 6-8. In DNA sequencing by synthesis (“SBS”),
nucleotides are added sequentially to a newly synthesized DNA strand
complementary to the template DNA in the double-stranded DNA. The
detectable label enables the nucleotide to be detected when it is incorporated
into the newly synthesized DNA strand. Id. at col. 2, ll. 56-64. Once the
identity of the nucleotide is determined by detecting the label linked to the
base, the detectable label is cleaved from the nucleotide by the cleavable
linker. Id. at col. 2, ll. 60-64, col. 6, ll. 26-30. The 3ʹ-OH of the sugar
residue of the nucleotide contains a protecting group, which can be removed
to expose the 3ʹ-OH group for further addition of a nucleotide. Id. at col. 2,
ll. 30-32, col. 8, ll. 8-15.

C. Related Proceedings
The ’026 patent is asserted in the following copending district court
case: Trustees of Columbia University in the City of New York v. Illumina,
Inc., 1:12-cv-00376-GMS in the United States District Court for the District
of Delaware. Pet. 1.

D. The Alleged Grounds of Unpatentability
Inter partes review was instituted on the following five grounds of
unpatentability (Dec. Pet. 18):
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1. Claims 1-6 under 35 U.S.C. § 102(b) as anticipated by Tsien.
1

2. Claims 1-6 under 35 U.S.C. §§ 102(a) or 102(e) as anticipated by
Ju.
2

3. Claim 3 under 35 U.S.C. § 103(a) as obvious in view of Tsien and
Prober.
3

4. Claims 7 and 8 under 35 U.S.C. § 103(a) as obvious in view of
Tsien and CEQ.
4

5. Claims 7 and 8 under 35 U.S.C. § 103(a) as obvious in view of Ju
and CEQ.

II. CLAIMS 1-8
Illumina did not file a response to the Decision on Petition instituting
inter partes review of claims 1-8. Instead, Illumina filed a non-contingent
Motion to Amend. Paper 61. “During an inter partes review . . . the patent
owner may file 1 motion to amend the patent in 1 or more of the following
ways: (A) Cancel any challenged patent claim. (B) For each challenged
claim, propose a reasonable number of substitute claims.” 35 U.S.C. §
316(d)(1). In the Motion, Illumina requested cancellation of claims 1-8,
which request was not contingent on the original claims being determined
unpatentable, and proposed substitute claims 9-12 to replace the cancelled
claims. Illumina stated that each of the grounds upon which the inter partes

1
Tsien, WO 91/06678 (published May 16, 1991). Ex. 1012.
2
Ju, U.S. 6,664,079 B2 (published Dec. 16, 2003). Ex. 1008.
3
Prober et al., “A System for Rapid DNA Sequencing with Fluorescent
Chain-Terminating Dideoxynucleotides.” 238 SCIENCE 336
(Oct. 16, 1987). Ex. 1013.
4
CEQ
TM
User’s Guide, Beckman Coulter CEQ
TM
2000 DNA
Analysis System User’s Guide (June 2000). Ex. 1006.
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review was instituted “is rendered moot in light of Illumina’s proposed
substitute claims.” Paper 61, 2. We shall GRANT Illumina’s Motion to
Amend to the extent it requests to cancel claims 1-8.

III. MOTION TO AMEND THE CLAIMS
In the Motion to Amend, Illumina proposed substitute claim 9 to
replace claim 1. The claim, as annotated by Illumina to show the differences
between original claim 1 and proposed substitute claim 9, is reproduced
below:
9. A nucleotide triphosphate or nucleoside molecule,
having a 7-deazapurine base that is linked to a detectable label
via a cleavable linker, wherein the cleavable linker is attached
to the 7-position of the 7-deazapurine base and wherein the
cleavable linker contains a disulfide linkage, and wherein the
nucleotide triphosphate molecule has a ribose or deoxyribose
sugar moiety comprising a protecting group attached via the 2′
or 3′ oxygen atom, and the disulfide linkage of the cleavable
linker and the protecting group are cleavable under identical
conditions.
Paper 61, 2.
Proposed substitute claim 9 requires a nucleotide having a 1)
triphosphate group; 2) a deazapurine base; 3) a disulfide linkage as a
cleavable linker; and 4) a protecting group on the 3ʹ oxygen. Original claim
3, now canceled, recited that the base of the nucleotide is a deazapurine as
recited in proposed substitute claim 9. This limitation, therefore, had been
considered in the Decision on Petition. None of the original claims,
however, comprised the limitation that the cleavable linker “contains a
disulfide linkage.” The obviousness of using a disulfide linkage is the main
issue to be decided in whether to grant the Motion to Amend.
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Proposed substitute dependent claims 10 and 12 replace claims 5 and
8, respectively. Proposed substitute independent claim 11 replaces claim 7,
and recites a nucleotide with the same features of claim 9.
Patent Owner bears the burden of proof to establish that it is entitled
to the relief requested in the Motion to Amend. 37 C.F.R. § 42.20(c). Patent
Owner, therefore, bears the burden of showing the patentability of the
amended claims.
Patent Owner must show that the conditions for novelty and non-
obviousness are met for the prior art available to one of ordinary skill in the
art at the time the invention was filed, not just the prior art cited in the
Petition. See Idle Free Sys., Inc. v. Bergstrom, Inc., Case IPR 2012-00027,
slip op. at 7 (PTAB June 11, 2013) (Paper 26). Also, a motion to amend
“must include a claim listing, show the changes clearly, and set forth: (1)
The support in the original disclosure of the patent for each claim that is
added or amended.” 37 C.F.R. § 42.121(b)(1).

IV. PATENTABILITY OF CLAIMS 9-12
A. Background
The ’026 patent relates to labeled nucleotides. For illustrative
purposes, an annotated generic nucleotide from Figure 1B of Stemple,
5
one
of the prior art publications cited in this inter partes review, is reproduced
below to show the nucleotide’s main parts.

5
Stemple, WO 00/53805 (published Sep. 14, 2000). Ex. 1002.
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Figure 1B of Stemple shows a generic nucleotide’s main
parts, including a detectable label (“label”), a linker, and a chemical
group attached to the 3ʹ-OH position.
The ’026 patent describes its invention as nucleotide molecule “linked
to a detectable label via a cleavable linker group attached to the base.” Ex.
1001, col. 2, ll. 6-8. The figure reproduced above shows a single ring-like
structure, labeled “linker,” which links a three-ringed structure, labeled
“label,” to the base. The ’026 patent discloses that the sugar “can include a
protecting group attached via the 2' or 3' oxygen atom. The protecting group
can be removed to expose a 3ʹ-OH.” Id. at col. 2, ll. 30-33. The figure
shows a protecting group attached to the 3ʹ-OH of the sugar molecule.
Original claim 1 was drawn to a nucleotide or nucleoside with the
following features:
1. “a base that is linked to a detectable label via a cleavable linker”
(see “label,” “linker,” and “base” in Figure 1B of Stemple reproduced
above);
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2. “a ribose or deoxyribose sugar moiety comprising a protecting
group attached via the 2′ or 3′ oxygen atom” (the figure shown above shows
a protecting group attached to the oxygen of the 3ʹ-OH group); and
3. “the cleavable linker and the protecting group are cleavable under
identical conditions.”
Proposed substitute claim 9 contains these features, but further recites
that the linker comprises a disulfide linkage (two sulfur atoms bonded
together) and that the nucleotide base is a deazapurine.

B. Claim Interpretation
Before a claim can be compared to the prior art, it must be interpreted.
In an inter partes review, claim terms in an unexpired patent are given their
broadest reasonable interpretation consistent with the specification of the
patent in which they appear. 37 C.F.R. § 42.100(b). Under the broadest
reasonable interpretation standard, claim terms are given their ordinary and
customary meaning as they would be understood by one of ordinary skill in
the art at the time of the invention. In re Morris, 127 F.3d 1048, 1054 (Fed.
Cir. 1997).
1. deazapurine
A deazapurine, as recited in proposed substitute claim 9, is interpreted
to mean a nitrogen base in which one of the natural nitrogen atoms in the
base ring is substituted with a carbon atom. Ex. 1008, col. 8, ll. 4-6.
2. the cleavable linker and the protecting group are cleavable under
identical conditions
The proposed claim requires a “cleavable linker,” which is used to
attach the “detectable label” to the 7-position of the deazapurine base. The
reason for having a cleavable linker at this position is explained as follows.
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In sequencing by synthesis reactions (“SBS”), nucleotides are added
sequentially, one at a time. Ex. 1001, col. 2, ll. 56-61. The “identity of each
nucleotide incorporated is determined by detection of the label linked to the
base, and subsequent removal of the label.” Id. at col. 2, ll. 61-64. The base
is removed by cleaving the disulfide linkage of the cleavable linker (“the
disulfide linkage of the cleavable linker [is] . . . cleavable”). Id. at Claim 9.
The claimed “cleavable linker” is, therefore, necessary to carry out SBS
sequencing.
The 3ʹ oxygen, labeled as the “3ʹ OH of the sugar” in the figure
reproduced above, is recited in proposed substitute claim 9 to comprise a
“protecting group.” The “protecting group” is described in the ’026 patent
as “intended to prevent nucleotide incorporation onto a nascent
polynucleotide strand.” Ex. 1001, col. 8, ll. 11-12. It can be removed by
cleavage to allow sequential addition of a nucleotide during SBS
sequencing. Id. at col. 8, ll. 12-14.
The claims do not specify the type of protecting group. The ’026
patent teaches at column 8, lines 28-31, “[s]uitable protecting groups will be
apparent to the skilled person, and can be formed from any suitable
protecting group disclosed in Green and Wuts, supra. Some examples of
such protecting groups are shown in FIG. 3.”
Proposed substitute claim 9 recites that “the cleavable linker and the
protecting group are cleavable under identical conditions.” The ’026 patent
discloses that the “labile linker may consist of functionality cleavable under
identical conditions to the block [the protecting group]. This will make the
deprotection process [of the 3ʹ-OH group] more efficient as only a single
treatment will be required to cleave both the label and the block.” Ex. 1001,
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col. 8, ll. 35-44. Thus, “cleavable under the identical conditions,” under the
broadest reasonable interpretation standard, limits the structure of the
protecting group to one which can be cleaved under the same conditions as a
disulfide linkage, but does not require a specific structure, such as a disulfide
linkage. See Paper 61, 6-7.

3. cleavable linker contains a disulfide linkage
The main limitation at issue in Illumina’s Motion to Amend is the
recitation in all the proposed substitute claims that a 7-deazapurine base is
linked to a detectable label through a “cleavable linker [which] contains a
disulfide linkage.” A disulfide linkage is a bond between two sulfur atoms.
Ex. 1001, Fig. 2.

C. Illumina’s Burden to Show Nonobviousness
The issue in this inter partes review is the obviousness of using a
cleavable disulfide linker to attach a label to the nucleotide base, where the
linker and protecting group of the nucleotide are cleaved under identical
conditions.
Because Illumina bears the burden of showing that it is entitled to
have its Motion to Amend granted, it must show that one of ordinary skill in
the art would not have considered the proposed substitute claims obvious in
view of the prior art available before the filing date of the claimed invention.
More specifically, the issue is whether it would have been nonobvious at the
time of the invention to have attached a detectable label to a deazapurine
base using a disulfide linkage, where the base is present in a nucleotide
triphosphate having “a ribose or deoxyribose sugar moiety comprising a
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protecting group attached via the 2′ or 3′ oxygen atom” and where “the
disulfide linkage of the cleavable linker and the protecting group are
cleavable under identical conditions.” Proposed claim 9.
A patent claim is invalid for obviousness if “the differences between
the claimed invention and the prior art are such that the claimed invention as
a whole would have been obvious before the effective filing date of the
claimed invention to a person having ordinary skill in the art to which the
claimed invention pertains.” 35 U.S.C. § 103.
[The] underlying factual considerations in an obviousness
analysis include the scope and content of the prior art, the
differences between the prior art and the claimed invention, the
level of ordinary skill in the art, and any relevant secondary
considerations. Relevant secondary considerations include
commercial success, long-felt but unsolved needs, failure of
others, and unexpected results.
Allergan, Inc. v. Sandoz Inc., 726 F.3d 1286, 1291 (Fed. Cir. 2013).
An important consideration is “whether a person of ordinary skill in
the art would, at the relevant time, have had a ‘reasonable expectation of
success’ in pursuing the possibility that turns out to succeed and is claimed.”
Institute Pasteur & Universite Pierre et Marie Curie v. Focarino, 738 F.3d
1337, 1344 (Fed. Cir. 2013).

D. Prior Art
Before turning to the specific arguments presented by both parties, we
shall summarize some of the prior art of record that was known at the time
the application resulting in the ’026 patent was filed on August 23, 2002.
This discussion is not meant to be exhaustive, but rather provides a brief
description of what was known about modified nucleotides prior to the filing
date of the ’026 patent.
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The claimed nucleotides are used in nucleic acid SBS, a process in
which 3ʹ-OH protected and detectably labeled nucleotides are added
stepwise to a nucleic acid primer during sequencing. In that process, it was
known to use a nucleotide labeled at its base with a detectable label in order
to identify when the nucleotide is incorporated into the newly synthesized
strand. Ex. 1012, p. 27, l. 33-p. 28, l. 2; Ex. 1014,
6
col. 18, l. 64–col. 19, l.
2. It also was known to attach a protecting group to the 3ʹ-OH of the
nucleotide. Ex. 1012, p. 9, l. 32-p. 10, l. 3. During DNA synthesis,
nucleotides are added sequentially to the 3ʹ-OH group of the nucleotide
sugar. The 3ʹ-OH group contains a removable protecting group so the
labeled nucleotides can be added one at a time. After each addition, the
label is detected and the 3ʹ-OH group is deblocked and new nucleotide (with
its own 3ʹ-OH protecting group) is added. Id. at 13. In sum, it was not new
to employ a nucleotide in sequencing which comprised a detectable label on
the nucleotide base and a 3ʹ-OH protecting group.
The prior art also had described attaching a label to the nucleotide
base using a cleavable linker as recited in the proposed claims. Ex.1012, p.
28, ll. 20-23; Ex. 1008, Abstract, col. 2, ll. 50-53. Furthermore, as found in
the Decision on Petition, Tsien described removing the detectable label and
the protecting group simultaneously, as required by the proposed claims.
Ex.1012, p. 28, ll. 5-8; Dec. Pet. 8.
The newly added limitation that the cleavable linker is a disulfide
bond also is described in the prior art. As discussed in more detail below,
Rabani
7
and Church
8
both describe attaching a detectable label to a

6
Dower, W.J. & Fodor, S.P.A. U.S. 5,547,839, issued Aug. 20. 1996.
7
Rabani, E. WO 96/27025 (published Sept. 6, 1996). Ex. 2015.
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nucleotide base via a disulfide linkage, where the nucleotide is used in
nucleic acid sequencing. An example is shown in Figure 5 of Church,
reproduced below, which we have annotated to identify specific structures.

Figure 5 of Church is annotated to identify the specific
structures of the nucleotide, including a detectable label, a
triphosphate, and a disulfide bond. Ex. 1031, p. 17, ll. 10-11
(“Figure 5 is a schematic drawing of a disulfide-bonded cleavable
nucleotide fluorophore complex.”). The nucleotide, however, lacks
the claimed protecting group on the 3ʹ-OH.
In addition to Church, six additional publications
9
are cited in this
inter partes review for their description of nucleotides comprising cleavable

8
Church, G.M. WO 00/53812 (published Sept. 14, 2000). Ex. 1031.
9
(1) Herman, US Patent No. 4,772, 691, issued Sep. 20, 1988. Ex. 2017.
(2) S.W. Ruby, et al., Affinity Chromatography with Biotinylated RNAs, Vol.
181, Methods in Enzymology, 97-121 (1990). Ex. 2016.
(3) Short, WO 99/49082 (published Sep. 30, 1999). Ex. 2018.
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linkers with disulfide bonds. One of these publications, Herman, shows a
nucleotide with disulfide bond attaching a biotin to a nucleotide base.
Exhibit 2017. The orientation of the nucleotide reproduced below is flipped
180 degrees from Church’s nucleotide, reproduced above.

Herman’s Figure (col. 5) shows a nucleotide with a cleavable linker
comprising a disulfide bond joining a biotin (“detectable label”) to a
nucleotide base. Ex. 2017, col. 7, ll. 24-27. The nucleotide lacks the
protecting group on the 3ʹ-OH as required in proposed claim 9.

(4) Barbara A. Dawson, et al., Affinity Isolation of Transcriptionally Active
Murine Erythroleukemia Cell DNA Using a Cleavable Biotinylated
Nucleotide Analog, Vol. 264, No. 22, The Journal of Biological Chemistry,
12830-37 (1989). Ex. 1030.
(5) Barbara A. Dawson, et al., Affinity Isolation of Active Murine
Erythroleukemia Cell Chromatin: Uniform Distribution of Ubiquitinated
Histone H2A Between Active and Inactive Fractions, Vol. 46, Journal of
Cellular Biochemistry, 166-173 (1991). Ex. 2039.
(6) Basil Rigas, et al., Rapid plasmid library screening using RecA-coated
biotinylated probes, Vol. 83, Proc. Natl. Acad. Sci. USA, 9591-9595 (1986).
Ex. 2040.

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E. Reason to Use a Disulfide Bond on Nucleotides
In the Decision on Petition, inter partes review was authorized for
claim 3 (reciting that the nucleotide base is a deazapurine) as anticipated
under 35 U.S.C. § 102 in view of Tsien (Ground I) and Ju (Ground II); and
as obvious under 35 U.S.C. § 103 in view of Tsien and Prober (Ground IV).
Those publications, however, do not describe using a cleavable disulfide
linker for attaching the detectable label to a base or the specific deazapurine
base recited in the proposed substitute claims. A disulfide bond as a linker is
described in the prior art (see pages 12-13 above), along with a reason to
have used one.

Rabani
Rabani, in the section titled “Cleavable linkers,” teaches that
“[l]abeling moieties are favorably in communication with or coupled to
nucleotides via a linker of sufficient length to ensure that the presence of
said labeling moieties on said nucleotides will not interfere with the action
of a polymerase enzyme on said nucleotides.” Ex. 2015, p. 32, ll. 10-13.
Rabani specifically mentions disulfide linkages as useful when a cleavable
linker is desired:
Linkages comprising disulfide bonds within their length have
been developed to provide for cleavability
24
; reagents
comprising such linkages are commercially available
25
and
have been used to modify nucleotides
26
in a manner which may
be conveniently reversed by treatment with mild reducing
agents such as dithiothreitol.
Id. at p. 32, ll. 29-33. Footnotes 24 and 26 of the above quoted passage cite
to Ruby, S.W. et al. (1990), Methods in Enzymology, 181:97, which is
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Exhibit 2016. Id. at 49. Footnote 25 references “for example, from Pierce
Chemical Co., [ ] of Rockford, IL., U.S.A.” Id.
Rabani, therefore, would have given a skilled worker reason to have
used a cleavable linker with a disulfide bond to ensure that the labeling
moieties on the nucleotides will not interfere with the action of a polymerase
enzyme during the synthesis reaction.

Church
IBS cited Church as evidence of the obviousness of using a disulfide
linker in a sequencing reaction. Paper 53, 2. Church provides another
example of the use of a disulfide linker to attach a label to base of a
nucleotide, further establishing its conventionality at the time of the
invention. Ex. 1031, 17:10-18, 68:12-21. Church describes a working
example in which a label was attached to a nucleotide base using a disulfide
linker and then cleaving it off with DTT. Id. at 86:6-30.
Dr. Bruce P. Branchaud,
10
a declarant for IBS, testified:
Church teaches a SBS [sequencing by synthesis] method
termed fluorescent in situ sequencing extension quantification
(FISSEQ). In one embodiment, Church teaches the sequential
addition of fluorescently labeled nucleotides in which the label

10
To support its obviousness challenge, IBS provided two Declarations by
Bruce P. Branchaud, Ph.D., Ex. 1015 and Ex. 1035, respectively.
Dr. Branchaud is Professor Emeritus in the Department of Chemistry at the
University of Oregon. Ex. 1015 ¶ 5. He has a Ph.D. in Organic Chemistry
from Harvard University, and has held positions in industry, including as an
internal consultant and advisor for DNA sequencing projects. Ex. 1015 ¶¶ 5,
7, 12-15. Dr. Branchaud has the requisite familiarity with DNA sequencing
to qualify as one of ordinary skill in the art at the time of the invention.
Consequently, we conclude that Dr. Branchaud is qualified to testify on the
matters addressed in his Declaration.
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is attached to the base via a “cleavable linkage”. Church at p.
67, l. 30 to p. 68, l. 11.
Ex. 1035 ¶ 13.

F. 90% Cleavage Efficiency of the Detectable Label Is Not Required
Illumina contends sequencing by synthesis processes require that the
disulfide linker joined to the detectable label be cleaved with 90%
efficiency, because of the iterative nature of the process. Paper 61, 11-12.
This reasoning is based on Rabani. Id. Given Rabani’s disclosure, as
discussed below, Illumina argues that a person of ordinary skill in the art
would not have used a disulfide bond because greater than 90% efficiency in
the cleavage reaction could not be achieved.
Rabani disclosed published results “suggest[ing] that the rate of
chemical removal of 3'-hydroxy protecting groups (less than 90% removal
after 10 minutes of treatment with 0.1M NaOH) will be unacceptably low
for such an inherently serial sequencing scheme.” Ex. 2015, 3:5-8
(emphasis added). Illumina contends that since Rabani teaches that less than
90% removal of the protecting group from the 3ʹ-OH “will be unacceptably
low for . . . [a] serial sequencing scheme,” and since “the disulfide linkage of
the cleavable linker and the protecting group are cleavable under identical
conditions,” the disulfide linker joining the detectable label to the nucleotide
base must also achieve 90% or more cleavage. Paper 61, 13; Ex. 2015, 3:5-
8. Illumina provided evidence that the prior art teaches less than 90%
efficiency in cleaving a disulfide linkage at 3ʹ-OH protecting group, leading
Illumina to reason “the expectation of unacceptably low 3ʹ-OH protecting
group cleavage efficiency when using ‘identical conditions’ would not lead a
skilled artisan to believe that one successfully could use 3ʹ-OH protecting
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groups that could be cleaved under identical conditions as a disulfide linkage
during SBS [sequencing by synthesis].” Paper 61, 13.
In other words, Illumina’s argument is that since 90% efficiency in
cleaving the disulfide linkage at the 3ʹ-OH group could not be achieved,
there would not have been a reason to use a disulfide linkage to attach the
detectable label to the base, because the detectable label must cleaved under
identical conditions to the 3ʹ-OH protecting group. Cleavage of the disulfide
linkage at the 3ʹ-OH group requires 90% efficiency Illumina argues 90%
cleavage efficiency must be achieved at the disulfide bond of the detectable
label, as well.
Illumina’s argument is flawed. Rabani’s disclosure is directed to
cleavage of the protecting groups, not the detectable label as claimed.
Illumina’s arguments are based on the logic that if no better than 90%
cleavage of the disulfide bond on the protecting group can be achieved, the
skilled worker would not have used it as a cleavable linker for attaching a
detectable label to a nucleotide in DNA sequencing, because the proposed
substitute claims require it be cleaved under identical conditions to the 3ʹ-
OH group, which requires 90% efficiency.
The proposed substitute claims do not require the linkage between the
3ʹ-OH and protecting group to comprise a disulfide bond. We, therefore,
discern no reason to apply Rabani’s protecting group cleavage efficiency
requirement to the disulfide linkage of the proposed substitute claims.
Significantly, Dr. Floyd Romesberg,
11
a declarant for Illumina,
conceded that he did not choose a 90% efficiency requirement because of

11
A declaration by Floyd Romesberg, Ph.D. was submitted by Illumina in
support of its Motion to Amend. Ex. 2009. Dr. Romesberg is a professor in
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Rabani, but rather because “it was a round number slightly above the values
reported by Ruby and Herman.” Ex. 1033, 198, ll.11-18.
Illumina has not met its burden to show that cleavage of the disulfide
bond, attaching the detectable label to the base, with less than 90%
efficiency would be unacceptable for sequencing.

G. Cleavage Efficiency of the Disulfide Bond
Even were we persuaded by Illumina’s argument that 90% cleavage of
the 3ʹ-OH protecting group is necessary for sequencing, Illumina did not
provide adequate evidence that the skilled worker would have been unable to
choose conditions and linkages that would achieve 90% cleavage of the 3ʹ-
OH group under the same conditions required for cleavage of the label, e.g.,
using a reducing agent (Ex. 1001, col. 6, ll. 31-35).
The ’026 patent suggests that choosing cleavage conditions for the 3ʹ-
OH group were conventional to one of ordinary skill in the art:
Suitable protecting groups will be apparent to the skilled
person, and can be formed from any suitable protecting group
disclosed in Green and Wuts, supra. Some examples of such
protecting groups are shown in FIG. 3. The protecting group
should be removable (or modifiable) to produce a 3' OH group.
The process used to obtain the 3' OH group can be any suitable
chemical or enzymic reaction.
Ex. 1001, col. 8, ll. 28-34.
Dr. Branchaud testified that “even if one of ordinary skill in the art
considered the cleavage efficiency of Ruby . . . in deciding whether to use

the Department of Chemistry at The Scripps Research Institute, where he
has been a faculty member since 1998. Ex. 2009 ¶ 2. Dr. Romesberg
testified that he is an “expert in the field of nucleotide analogue molecules.”
Id. at ¶ 16. Dr. Romesberg’s deposition is Exhibit 1033.

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such a linker for SBS, one of ordinary skill in the art would know that such
cleavage efficiency could be improved by routine experimentation and thus
would not be dissuaded from using such a linker.” Ex. 1035 ¶ 37. As
discussed below, this conclusion is supported by the prior art of record.

Ruby
Ruby is cited expressly by Rabani for its teaching of a disulfide bond
that is cleavable with a reducing agent, such as dithiothreitol (“DTT”), and
describes attaching a biotin molecule attached to a nucleotide base of a RNA
“via a linker containing a disulfide bond.” Ex. 2016, 98. The RNA is bound
to a column containing avidin, based on the affinity of the biotin for the
avidin. Id. at 98-99 (Fig. 1). The RNA is “eluted [from the column] by
adding dithiothreitol (DTT) to reduce the disulfide bonds linking biotin to
the anchor RNA.” Id. at 98; Ex. 1035 ¶ 31. Relying on testimony by
Dr. Romesberg, Illumina states that “Ruby reports that disulfide linkages are
cleaved with only ~86% efficiency after more than 100 minutes, which is
significantly less than 90% efficient.” Paper 61, 12 (citing Ex. 2016, 117-
18; Ex. 2009 ¶ 54). The “~86% efficiency” comes from Figure 4 of Ruby, a
graph of % RNA eluted using DTT under different conditions. Ex. 2016,
117. Dr. Branchaud did not dispute that Ruby recovered “about 86% of the
RNA.” Ex. 1035, ¶ 31.
Dr. Romesberg testified that, “[s]ince Ruby’s cleavage efficiency
under disulfide cleavage conditions is less than 90%, Ruby does not provide
an expectation that disulfide cleavage conditions would cleave a 3ʹ-OH
protecting group with greater than 90% efficiency.” Ex. 2008 ¶ 55.
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In response, Dr. Branchaud testified that “even if one of ordinary skill
in the art considered the cleavage efficiency of Ruby . . . in deciding whether
to use such a linker for SBS, one of ordinary skill in the art would know that
such cleavage efficiency could be improved by routine experimentation and
thus, would not be dissuaded from using such a linker.” Ex. 1035 ¶ 37.
Dr. Branchaud’s testimony is supported factually. Ruby teaches
“[e]lution by reduction of the disulfide bonds on the biotinylated anchor
RNA depends on the pH of the buffer, the DTT concentration, and the time
of incubation in DTT (Fig. 4) in addition to the type of avidin binding.”
Ex. 2016, 117-118. Ruby describes manipulating the conditions to alter the
elution profile: “By increasing the pH and DTT concentration of the elution
buffer slightly, one can effectively elute the RNA during longer incubation
times.” Id. at 118. Thus, Ruby expressly teaches conditions that modify
cleavage of the disulfide bond, and that cleavage of the bond can be
manipulated by adjusting these conditions. In view of this teaching, one of
ordinary skill in the art reasonably would have believed that disulfide bond
cleavage could be modified to achieve the desired amount of cleavage.
Dr. Romesberg testified that the 86% value of Ruby could not be
exceeded, but did not provide sufficient factual evidence to support this
testimony. It is true that Ruby describes an experiment in which, apparently,
a maximum of 86% cleavage was obtained, but Ruby did not characterize it
as a limit. As Dr. Branchaud testified, it was not critical for Ruby to achieve
higher efficiency, so it was not evident why Ruby would have done
experimentation to achieve even higher cleavage of the 86% value shown in
Figure 4. Ex. 1035 ¶ 37.

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Herman
Illumina also cited Herman as evidence that 90% cleavage of a
disulfide linkage could not be achieved. Paper 63, 12-13. Herman describes
a similar system to Ruby, where RNA is immobilized to a column using a
biotin-avidin interaction. Ex. 2017, Abstract, col. 3, ll. 20-25. Herman
describes using a biotin attached to a nucleotide base through linker
comprising a disulfide bond, as required by the proposed substitute claims.
Id. at col. 7, ll. 24-34. The disulfide S-S bond is cleaved with a reducing
agent, such as DTT or 2-mercaptoethanol. Id. at col. 7, l. 47-48; col. 10, ll.
3-19. Herman describes the results of one experiment:
Bio-SS-DNA with buffer containing 50 mM dithiothreitol
resulted in the recovery of a total of 87% of the DNA from the
affinity column. Only 7.3% of the 32
P
-labeled Bio-SS-DNA
remained bound to the resin.
Id. at col. 11, ll. 14-17.
Dr. Romesberg makes the same conclusions for Herman that he did
for Ruby. That is, since Herman’s cleavage was less than 90%, “Herman
does not provide an expectation that disulfide cleavage conditions would
cleave a 3ʹ-OH protecting group with greater than 90% efficiency.”
Ex. 2009 ¶ 58. IBS challenged the conclusion that one of ordinary skill in
the art reading Herman would have determined the cleavage efficiency to be
87%, providing testimony by Dr. Branchaud that the real efficiency value
was above 90% when calculated properly. Ex. 1035 ¶ 36. Dr. Romesberg
acknowledged that Herman’s values did not “add up,” but he testified that
there were several possible explanations, of which Dr. Branchaud’s was only
one. Ex. 2012 (Romesberg Tr.), 193:19–194:13. We are not persuaded,
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therefore, that one of ordinary skill in the art would have understood Herman
to describe disulfide bond cleavage efficiency above 90%.
The parties cited two additional publications, both co-authored with
the same Timothy M. Herman who is listed as inventor of Herman, U.S.
Patent No. 4,772, 691: Dawson (1989) (Ex. 1030) (see supra fn. 9), cited by
IBS, and Dawson (1991) (Ex. 2039) (see supra fn. 9), cited by Illumina.
Dawson (1989) was cited by IBS for its statement in the abstract that
“[c]leavage of the disulfide bond in the linker arm of the biotinylated
nucleotide resulted in elution of virtually all of the affinity isolated
sequences.” Ex. 1035 ¶ 37. Dawson (1991) was identified by Illumina for
its disclosure that “[r]eduction of the disulfide bond in the biotinylated
nucleotide eluted approximately one-half of the affinity isolated chromatin.”
Ex. 2039, 166.
In other words, the “Herman” publications report varying degrees of
cleavage: from “virtually all” in Dawson (1989) (Ex. 1030), to 87% in
Herman (Ex. 2017), to approximately 50% in Dawson (1991) (Ex. 2039). It
is evident, consistent with Ruby, that the conditions can be routinely varied
to achieve a desired level of disulfide bond cleavage.
Moreover, as stated by Dr. Branchaud:
While it is desirable to achieve a high elution percentage by
achieving a high cleavage efficiency of the disulfide linker,
unlike SBS, it is not crucial that such elution percentage be
greater than 90%. One of ordinary skill in the art would be
aware that Ruby and Herman were not necessarily motivated to
achieve a high elution percentage and thus a high cleavage
efficiency (e.g., greater than 90%). Thus, one of ordinary skill
in the art would not be dissuaded from using a disulfide linkage
in a modified nucleotide by the cleavage efficiencies shown in
Ruby and Herman.
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Id. ¶ 35.
In an attempt to rebut this testimony, Illumina cites a 1986 publication
by a different group which stated: “Release of the nick-translated probe-
plasmid complex from avidin by reduction of the disulfide bond of Bio-19-
SS-dUTP gave variable results and was not pursued rigorously.” Ex. 2040,
9594. In the ensuing years, however, the Herman group (Exs. 1030, 2017, &
2039) did pursue it and showed that higher cleavage rates could be achieved.
Exhibits 1030 & 2017.

Church
Church does not disclose the cleavage efficiency, but shows the
results of the experiment in Figure 6. Illumina and IBS dispute the amount
of cleavage shown in Figure 6. Because the quality of Figure 6 is so poor,
however, the extent of cleavage cannot be determined reliably. A later-filed
version of Figure 6 was provided by Illumina to support their claim that
cleavage was incomplete, but this Figure was not available until after the
August 23, 2002 filing date of the ’026 patent. Ex. 2035 (showing that the
Figure was not available until October 31, 2002). The later-filed Figure,
therefore, does not establish how one of ordinary skill in the art would have
interpreted the results of Church at the time the ’026 patent was filed. We,
therefore, give original filed Figure 6 no weight. Nonetheless, Church
suggested disulfide linkers in a sequencing reaction, and carried out an
example to show their utility (Ex. 1031, 85-87), providing a reason to have
used them in sequencing and a reasonable expectation of success.

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Summary
The record contains numerous publications that utilize a disulfide
bond linker to join a label to a nucleotide base. Rabani and Church used the
linker in the context of DNA sequencing, the primary use for the claimed
nucleotides described by Illumina. Ruby, Herman, Dawson (1989), Dawson
(1991), Short (referenced in footnote 9), and Rigas, each had used disulfide
linkers to attach a label to a base, but not for sequencing purposes. While
the prior art reported variability in the disulfide cleavage rates, Illumina has
not established by a preponderance of the evidence that efficiency yields
above 90% could not be achieved. In particular, Ruby and other
publications had no reason to go above whatever cleavage rate was
achieved, because it was not critical to their experiments. Herman, in at
least one case, described “virtually all” the bond was cleaved. Ex. 1030.
Thus, even if 90% efficiency were necessary for a reasonable expectation of
success, the ordinary artisan would have expected that such cleavage
efficiency of the disulfide bond could be achieved.
Finally, Illumina has not met its burden to show that identical
conditions could not be selected in which the disulfide linkage of the
cleavable linker is cleavable with less than 90% efficiency and the protecting
group is cleavable with greater than 90% efficiency as required by the
proposed substitute claims.

H. Objective Evidence of Nonobviousness
Factual considerations that underlie the obviousness inquiry include
the scope and content of the prior art, the differences between the prior art
and the claimed invention, the level of ordinary skill in the art, and any
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relevant secondary considerations. Graham v. John Deere Co., 383 U.S. 1,
17-18 (1966). Relevant secondary considerations include commercial
success, long-felt but unsolved needs, failure of others, and unexpected
results. KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 406 (2007); In re Soni,
54 F.3d 746 (Fed. Cir. 1995). Secondary considerations are “not just a
cumulative or confirmatory part of the obviousness calculus but constitute
independent evidence of nonobviousness . . . [and] enable [] the court to
avert the trap of hindsight.” Leo Pharm. Prods., Ltd. v. Rea, 726 F.3d 1346,
1358 (Fed. Cir. 2013) (internal quotation marks and citations omitted).
“This objective evidence must be ‘considered as part of all the evidence, not
just when the decisionmaker remains in doubt after reviewing the art.’”
Transocean Offshore Deepwater Drilling, Inc. v. Maersk Drilling USA, Inc.,
699 F.3d 1340, 1349 (Fed. Cir. 2012) (internal citations omitted).
In the Motion to Amend, as objective evidence of nonobviousness,
Illumina provided a Declaration by Mr. Eric Vermaas, Illumina’s Director of
Consumables Product Development, describing sequencing experiments
utilizing a nucleotide within the scope of proposed substitute claim 9. Ex.
2028 ¶ 4. The sequencing experiments were performed under Mr.
Vermaas’s supervision while employed by Illumina. Id. at ¶ 5. The
sequencing experiments used the four nucleotides dATP, dTTP, dGTP, and
dCTP, only one of which – dATP – contained a disulfide base linking a
fluorophore to the nucleotide base. Id. ¶ 6; Ex. 2009 ¶ 61. Each of these
nucleotides also contained an azidomethyl group protecting the 3 ʹ -OH. Ex.
2009 ¶ 61.
Mr. Vermaas describes sequential sequencing reactions on PhiX
Control DNA for over 150 cycles in which nucleotides were added one at a
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time. Ex. 2028 ¶¶ 13-17; Ex. 2009 ¶ 63. After each scan for the fluorophore
incorporated, a solution comprising 2 mM tris(hydroxymethyl)-phosphine
was added. Ex. 2009 ¶ 64. “The 2 mM tris(hydroxymethyl)phosphine
reacts with and cleaves the disulfide linkage of the A [adenine of the dATP]
nucleobase,” but does not cleave the detectable groups on the other
nucleotides. Id. According to Dr. Romesberg, “[b]ased on the results
presented in the Vermaas declaration, a person of skill in the art would
recognize that the yield for cleavage of the disulfide linkage was essentially
100%.” Id. ¶ 74. Dr. Romesberg concluded:
Therefore, the disulfide cleavage yield achieved by Illumina
was essentially 100%. This is a significant and unexpected
improvement over the disulfide cleavages of Ruby (~86%) and
Herman (87%). Accordingly, Illumina’s proposed claims are
nonobvious over the prior art for at least this reason.
Id.
To establish unexpected results, the claimed subject matter must be
compared with the closest prior art. In re Baxter Travenol Labs., 952 F.2d
388, 392 (Fed. Cir. 1991). Illumina does not state what references are the
closest prior art to the claims. Dr. Romesberg, however, in his declaration,
compared the cleavage efficiency reported by Mr. Vermaas with Ruby and
Herman. Ex. 2009 ¶ 74.
There are at least two differences between the experiments described
in Ruby and Herman, and the experiment described by Mr. Vermaas.
First, while both Ruby and Herman used a nucleotide with a cleavable
disulfide bond as did Mr. Vermaas, the references do not use the nucleotide
in a sequencing reaction as it has been used in the experiment described by
Mr. Vermaas. Ruby involved RNA binding to a column and using the
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disulfide linkage to release the bound RNA. Ex. 2016, 98-99. Herman used
a system similar to Ruby. Ex. 2017, Abstract, col. 3.
Secondly, the cleavage agents are different. The cleavage agent used
in Ruby is DTT (Ex. 2016, 10, “Elution buffer” A and B) and in Herman, the
cleavage agent is described as “a reducing agent such as DTT” (Ex. 2017,
col. 7, ll. 47-48) with DTT being used in its example (id. at col. 10, ll. 47-54,
col. 11, ll. 11-22; col. 12, ll. 3-8). Mr. Vermaas describes an experiment that
utilized another cleavage agent, 2 mM tris- (hydroxymethyl)phosphine. Ex.
2028 ¶ 10. Illumina did not offer an explanation as to why the phosphine
compound was used instead of DTT as used by both Ruby and Herman.
Indeed, Church used DTT in a DNA sequencing reaction, similar to the
sequencing carried out in the Vermaas experiments, providing an additional
reason to have used DTT in Dr. Varmaas’s comparison to the prior art. Ex.
1031, Fig. 5; 68, ll. 12-13; 86, ll. 20-23.
There is no testimony that the stated results were due to the claimed
nucleotide rather than the reducing agent. Dr. Romesberg testified:
“Therefore, the disulfide cleavage yield achieved by Illumina was essentially
100%. This is a significant and unexpected improvement over the disulfide
cleavages of Ruby (~86%) and Herman (87%).” Ex. 2009 ¶ 74.
Dr. Romesberg refers to the “disulfide cleavage yield” as being
unexpected, but he did not testify that this yield was attributable to the
claimed nucleotide configuration, rather than the reducing agent which
performs the disulfide bond cleavage.
Illumina has not distinguished the Vermaas results from the prior art
by showing that the nucleotide is responsible for the disulfide yield, rather
than it being a property of the disulfide bond and the yield being “the mere
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recognition” of the bond’s “latent properties,” which “does not render
nonobvious an otherwise known invention.” Baxter, 952 F.2d at 392; In re
Geisler, 116 F.3d 1465, 1468 (Fed. Cir. 1997). Absent such evidence,
Illumina has not shown that the claimed subject matter possesses
“unexpected results relative to the prior art.” Galderma Labs., LP v. Tolmar,
Inc., 737 F3d 731, 738 (Fed. Cir, 2013).

I. Summary
After considering all the evidence as a whole, we conclude that
Illumina has not met its burden in showing that the proposed substitute
claims are patentable over the prior art considered in this Decision. The
Motion to Amend is DENIED to the extent that it requests entry of substitute
claims 9-12.

V. MOTIONS TO EXCLUDE EVIDENCE
Both Illumina (Paper 70) and IBS (Paper 67) filed Motions to Exclude
Evidence. Illumina’s motion is dismissed as moot. IBS’s motion is denied
in part and dismissed in part as moot.

Illumina’s Motion
Illumina requests that Figure 6 from Ex. 1031 (Church), all
characterizations of Figure 6 from Ex. 1031, and all arguments based on it
be excluded as evidence from this inter partes review. Illumina argues that
the Figure should be excluded “because it includes poor quality black and
white reproductions of images that do not accurately reflect the original
underlying data.” Paper 70, 1. We agreed with Illumina that the figure of
Church is of poor quality and gave it no weight. We, therefore, did not rely
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on Figure 6 of Church in reaching our decision. Accordingly, Illumina’s
motion is dismissed as moot.

IBS’s Motion
IBS requests that Illumina’s Exhibits 2029, 2030, 2032, 2033, 2035,
2036, and 2039-2042 be excluded as evidence from this inter partes review.
As we did not rely on Exhibits 2029, 2030, 2032, 2033, and 2042, we
dismiss this part of the motion as moot.
Exhibits 2035 and 2036 relate to Figure 6 of Church (Ex. 1031). We
did not rely on Figure 6 of Church because it is of such poor quality that the
amount disulfide cleavage cannot be determined reliably. To remedy this
deficiency, Illumina sought to introduce a substitute Figure 6 from another
patent publication by Church. Ex. 2035, 2036. Illumina did not establish
that this substitute figure was available prior to the filing date of the ’026
patent, however. We, therefore, did not consider it. Consequently, we
dismiss this part of the motion as moot.
Exhibits 2039 and 2040 were provided by Illumina as further evidence
of the efficacy of disulfide bond cleavage. Paper 64, 3. IBS argues that
these Exhibits are not relevant and “without foundation . . . and misleading,”
because they discuss elution percentages, not cleavage efficiency. Paper 67,
8. We disagree. The Exhibits describe cleavage of a disulfide bond in a
nucleotide, the same chemical reaction that is at issue in this inter partes
review, making them reasonably relevant to the obviousness determination.
Nor has IBS explained sufficiently why the documents lack foundation. As
to the statement that the Exhibits are “misleading,” this argument appears to
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go to the weight of the Exhibits, rather than their admissibility.
Consequently, we deny IBS’s Motion to Exclude Exhibits 2039 and 2040.

VI. ORDER
In consideration of the foregoing, it is
ORDERED that Illumina’s Motion to Amend is denied in part, to the
extent it seeks to add substitute claims 9-12, and granted in part, to the
extent it seeks to cancel claims 1-8;
FURTHER ORDERED that Illumina’s motion to exclude evidence is
dismissed as moot; and
FURTHER ORDERED that IBS’s motion to exclude evidence is
denied in part with respect to Exhibits 2039 and 2040 and dismissed in part
as moot with respect to Exhibits 2029, 2030, 2032, 2033, 2035, 2036, and
2042.

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Petitioner:

Scott Marty
Marc Segal
martys@ballardspahr.com
segalm@ballardspahr.com

Patent Owner:
James Morrow
James Borchardt
ipadmin@reinhartlaw.com
illuminaiprs@reinhartlaw.com
jborchardt@reinhartlaw.com