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

Patent Trial and Appeal Board

Oct 28, 2014

12804025 (P.T.A.B. Oct. 28, 2014)

Trials@uspto.gov Paper 73
571-272-7822 Entered: October 28, 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 IPR2013-00266
Patent 8,158,346 B2
___________

Before LORA M. GREEN, SCOTT E. KAMHOLZ, and
CHRISTOPHER L. CRUMBLEY, Administrative Patent Judges.

CRUMBLEY, 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 1, “Pet.”) for inter partes review of claims 1, 2, 4, 11, 12, 17, 18, and
19 of U.S. Patent No. 8,158,346 B2 (Ex. 1001, “the ’346 patent”) pursuant
to 35 U.S.C. §§ 311–319 and 37 C.F.R. §§ 42.1–42.123.
On October 28, 2013, the Board instituted inter partes review of
claims 1, 2, 4, 11, 12, 17, 18, and 19 of the ’346 patent on the following
three grounds of unpatentability:
1. Whether claims 1, 2, 4, 11, 12, 17, 18, and 19 are unpatentable
under 35 U.S.C. § 102(a) or (e) as anticipated by Ju;1
2. Whether claims 1, 2, 4, 11, 12, 17, 18, and 19 are unpatentable
under 35 U.S.C. § 102(b) as anticipated by Tsien;2 and
3. Whether claims 1, 2, 4, 11, and 12 are unpatentable under 35
U.S.C. § 102(b) as anticipated by Stemple.3
Paper 20 (“Dec.”), 13.
Following institution of inter partes review, Patent Owner, Illumina
Cambridge Limited (“Illumina”), filed a Motion to Amend Claims (Paper
31, “Mot.”), but did not file a response under 37 C.F.R. § 42.120 to the
Decision instituting inter partes review. IBS filed an opposition to
Illumina’s Motion to Amend (Paper 37), and both parties filed Motions to
Exclude Evidence (Papers 46, 49).

1 As used in our Decision to Institute, “Ju” collectively referred to both Ju,
U.S. 6,664,079 B2 (Dec. 16, 2003) (Ex. 1002) and Ju, WO 02/29003 A2
(Apr. 11, 2002) (Ex. 1003).
2 Tsien, WO 91/06678 A1 (May 16, 1991) (Ex. 1006).
3 Stemple, WO 00/53805 A1 (Sept. 14, 2000) (Ex. 1007).
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Pursuant to requests by both parties, an oral hearing was held on May
28, 2014, and the transcript of the hearing was entered into the record. Paper
69, “Tr.”
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. For
the reasons that follow, Illumina’s Motion to Amend is granted to the extent
it requests to cancel claims 1, 2, 4, 11, 12, 17, 18, and 19; Illumina’s Motion
to Amend is denied to the extent that it requests entry of substitute claims
20–26.
B. The ’346 Patent
The ’346 patent relates to DNA sequencing using nucleotides that are
labeled and blocked. Ex. 1001, 2:18–22. A detectable label is attached to
the base of a nucleotide by a cleavable linker, and a polymerase-blocking
group is removably attached at the 3ʹ (or 2ʹ) position of the sugar moiety of
the nucleotide. Id. at 2:38–44. A target DNA is sequenced by synthesizing
its complement polynucleotide using the labeled and blocked nucleotides.
Id. at 9:3–7. The blocking group prevents the polymerase from adding more
than one nucleotide at a time. Id. at 8:13–20. The label then is detected,
thereby identifying the newly-added nucleotide. Id. at 3:17–19. The label
and the blocking group then are removed from the added base under
identical conditions. Id. at 8:27–28. The process repeats with the next base.
Id. at 3:20–22. The sequence of the target DNA then may be determined
from the complementary sequence. Id. at 3:21–22.
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C. Related Proceedings
The ’346 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 (D. Del.). Pet. 5.
II. ORIGINAL CLAIMS
As noted above, Illumina did not file a Response following our
Decision instituting inter partes review of claims 1, 2, 4, 11, 12, 17, 18, and
19. Instead, Illumina filed a Motion to Amend pursuant to 35 U.S.C.
§ 316(d)(1) (“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.”). In its Motion, Illumina requested
cancellation of claims 1, 2, 4, 11, 12, 17, 18, and 19 and proposed substitute
claims 20–26 to replace the cancelled claims, and asserted that each of the
grounds upon which the inter partes review was instituted “is rendered moot
in light of Illumina’s proposed substitute claims.” Mot. 1. We shall grant
Illumina’s Motion to Amend to the extent it requests to cancel claims 1, 2, 4,
11, 12, 17, 18, and 19.

III. PROPOSED SUBSTITUTE CLAIMS
In the Motion to Amend, Illumina proposed substitute claim 20 to
replace claim 2. The claim, as annotated by Illumina to show the differences
between original claim 2 and proposed substitute claim 20, is reproduced
below:
20. A method according to claim 1 for determining the
sequence of a target single-stranded polynucleotide, comprising
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monitoring the sequential incorporation of complementary
nucleotides, the method further comprising the steps of
(a) providing said nucleotides, wherein the nucleotides
each have a base that is linked to a detectable label via a
cleavable linker, wherein the cleavable linker contains a
disulfide linkage, wherein each of the nucleotides has a ribose
or deoxyribose sugar moiety and the ribose or deoxyribose
sugar moiety comprises a protecting group attached via the 3'
oxygen atom; and wherein said monitoring comprises
(b) incorporating a nucleotide of (a) into the complement
of the target single stranded polynucleotide;
(c) detecting the label linked to the base of the nucleotide
of (b), thereby determining the identity type of the nucleotide
incorporated;
(d) subsequently removing the label and the protecting
group of the nucleotide of (b) under a single set of chemical
cleavage conditions, wherein the chemical cleavage conditions
cleave the disulfide linkage and permit further nucleotide
incorporation into the complement of the target single stranded
polynucleotide to occur; and
(e) optionally repeating steps (b)-(d) one or more times;
thereby determining the sequence of a target single-stranded
polynucleotide.
Mot. 2.
Proposed substitute claim 20 combines the limitations found in
original claims 1 and 2, and also recites a newly added limitation that the
cleavable linker “contains a disulfide linkage,” which was not present in the
original claims.
For illustrative purposes, an annotated generic nucleotide from Figure
1B of Stemple is reproduced below to show the main parts of a nucleotide
used in sequencing-by-synthesis (“SBS”) processes such as the one of
proposed claim 20:
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Proposed substitute dependent claims 21–26 replace claims 4, 11, 12,
and 17–19, respectively. The sole changes to these claims are to change
their dependency from claim 1 or 17 to claims 20 and 24. Mot. 3.
As movant, Illumina 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). In other words, Illumina bears the burden of showing the
patentability of the amended claims. Illumina must, therefore, 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 for the prior art cited in the Petition or the grounds upon which
trial was instituted. See Idle Free Sys., Inc. v. Bergstrom, Inc., Case IPR
2012-00027, slip op. at 7 (PTAB June 11, 2013) (Paper 26).

IV. PATENTABILITY OF CLAIMS 20–26
A. Claim Interpretation
In an inter partes review, “[a] claim in an unexpired patent shall be
given its broadest reasonable construction in light of the specification of the
patent in which it appears.” 37 C.F.R. § 42.100(b). Under this standard, we
construe claim terms using “the broadest reasonable meaning of the words in
their ordinary usage as they would be understood by one of ordinary skill in
the art, taking into account whatever enlightenment by way of definitions or
otherwise that may be afforded by the written description contained in the
applicant’s specification.” In re Morris, 127 F.3d 1048, 1054 (Fed. Cir.
1997). We presume that claim terms have their ordinary and customary
meaning. See In re Translogic Tech., Inc., 504 F.3d 1249, 1257 (Fed. Cir.
2007) (“The ordinary and customary meaning is the meaning that the term
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would have to a person of ordinary skill in the art in question.”) (internal
quotation marks and citations omitted). A patentee may rebut this
presumption, however, by acting as his own lexicographer, providing a
definition of the term in the specification with “reasonable clarity,
deliberateness, and precision.” In re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir.
1994).
1. the cleavable linker and the protecting group are cleavable under
identical conditions
Proposed substitute claim 20 recites, inter alia, “a base that is linked
to a detectable label via a cleavable linker,” a “protecting group attached via
the 3' oxygen atom” of the nucleotide, and a step of “removing the label and
the protecting group of the nucleotide . . . under a single set of chemical
cleavage conditions.” Mot. 2 (emphasis added). These limitations are
similar to those present in original claim 1, which we construed in our
Decision on Institution. Specifically, we construed removal of the label and
the protecting group under a single set of conditions “to mean what its plain
language indicates: removal of the label and the protecting group under a
single set of conditions.” Dec. 6. Neither of the parties contested this
construction subsequent to institution, and we discern no reason to modify
our initial construction for the purposes of this decision.
Proposed claim 20 also requires that the cleavable linker comprise a
disulfide linkage, but does not specify the protecting group. Thus, “a single
set of chemical cleavage 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.
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2. cleavable linker contains a disulfide linkage
All proposed substitute claims contain a new limitation, not present in
the original claims, that the cleavable linker contains a disulfide linkage.
Neither party proposes a specific construction for this new claim element.
We note that a disulfide linkage contains a bond between two sulfur atoms.
Ex. 1001, Fig. 2.
B. Illumina’s Burden to Show Nonobviousness
As noted above, the primary remaining 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
entry of its proposed substitute claims, 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 base using a disulfide linkage, where the base is present in a
nucleotide having “ribose or deoxyribose sugar moiety compris[ing] a
protecting group attached via the 3' oxygen atom” and where the disulfide
linkage and the protecting group are removed “under a single set of chemical
cleavage conditions.”
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
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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) (internal
citations omitted).
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) (citations omitted).
C. Prior Art
Before turning to the specific arguments presented by both parties, we
summarize some of the prior art of record that was known at the time of the
invention claimed in the ’346 patent. This discussion is not meant to be
exhaustive, but rather to provide a brief description of what was known
about modified nucleotides prior to the priority date of the ’346 patent.
The claimed method is nucleic acid sequencing-by-synthesis (“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
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synthesized strand. Ex. 1006, 27:33–28:2; Ex. 1010,4 18:64–19:2. It also
was known to attach a protecting group to the 3ʹ-OH of the nucleotide. Ex.
1006, 9:32–10:3. 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 13:14–35. 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 described attaching a label to the nucleotide base
using a cleavable linker as recited in the proposed claims. Id. at 28:20–23;
Ex. 1002, Abstract, 2:50–53. Furthermore, as we discussed in the Decision
on Institution, Tsien described removing the detectable label and the
protecting group simultaneously. Ex. 1006, 28:5–8; Dec. 9.
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,
Rabani5 and Church6 both describe attaching a detectable label to a
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.

4 Dower, W.J. & Fodor, S.P.A. U.S. 5,547,839 (Aug. 20. 1996).
5 Rabani, E. WO 96/27025 A1 (Sept. 6, 1996) (Ex. 2017).
6 Church, G.M. WO 00/53812 A2 (Sept. 14, 2000) (Ex. 1019).
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Figure 5 of Church is annotated to identify the structures of
the nucleotide, including a detectable label, a triphosphate, and a
disulfide bond. Ex. 1019, 17:10–11 (“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 publications7 are cited in this
inter partes review for their description of nucleotides comprising cleavable

7 (1) Herman, U.S. Patent No. 4,772,691 (Sept. 20, 1988) (Ex. 2019).
(2) S.W. Ruby, et al., Affinity Chromatography with Biotinylated RNAs,
METHODS IN ENZYMOLOGY, vol. 181, 97–121 (1990) (Ex. 2016).
(3) Short, WO 99/49082 A2 (Sept. 30, 1999) (Ex. 2020).
(4) Barbara A. Dawson, et al., Affinity Isolation of Transcriptionally Active
Murine Erythroleukemia Cell DNA Using a Cleavable Biotinylated
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linkers with disulfide bonds. One of these, Herman, shows a nucleotide with
disulfide bond attaching a biotin to a nucleotide base. Ex. 2019. In the
figure from Herman, reproduced below, orientation of the nucleotide 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. 2019, 7:24–27. The nucleotide lacks the protecting
group on the 3ʹ-OH as required in proposed claim 20.

Nucleotide Analog, THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 264, no.
22, 12830–37 (1989) (Ex. 1027).
(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, JOURNAL OF CELLULAR
BIOCHEMISTRY, vol. 46, 166–173 (1991) (Ex. 2038).
(6) Basil Rigas, et al., Rapid plasmid library screening using RecA-coated
biotinylated probes, PROC. NATL. ACAD. SCI. USA, vol. 83, 9591–9595
(1986) (Ex. 2039).

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D. Reason to Use a Disulfide Bond on Nucleotides
In the Decision on Institution, we instituted inter partes review on
three grounds based on Ju, Tsien, and Stemple. Those publications,
however, do not describe using a cleavable disulfide linker for attaching the
detectable label to a base. A disulfide bond as a linker is described in the
prior art (see discussion, supra), however, along with a reason to have used
one.
1. 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. 2017, 32:10–13. 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 cleavability24; reagents
comprising such linkages are commercially available25 and
have been used to modify nucleotides26 in a manner which may
be conveniently reversed by treatment with mild reducing
agents such as dithiothreitol.
Id. at 32:29–33. Footnotes 24 and 26 of the above quoted passage cite to
Ruby.8 Id. at 49. Footnote 25 references “for example, from Pierce
Chemical Co., [ ] of Rockford, IL., U.S.A.” Id.

8 Ruby, S.W. et al., Affinity Chromatography with Biotinylated RNAs,
METHODS IN ENZYMOLOGY, 181:97 (1990) (Ex. 2016).
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Given these disclosures, we find that Rabani 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.
2. Church
IBS cites Church as evidence of the obviousness of using a disulfide
linker in a sequencing reaction. Paper 55, 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. 1019, 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,9 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
is attached to the base via a “cleavable linkage.”
Ex. 1021 ¶ 12 (citing Ex. 1019 at 67:30–68:11).

9 To support its obviousness challenge, IBS provided two Declarations by
Bruce P. Branchaud, Ph.D. Exs. 1011 & 1021. Dr. Branchaud is Professor
Emeritus in the Department of Chemistry at the University of Oregon. Ex.
1011 ¶ 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. 1011 ¶¶ 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 Declarations.
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E. 90% Cleavage Efficiency of the Detectable Label Is Not Required
As discussed in the preceding sections, it was known as of the filing
date of the ’346 patent to use disulfide linkers, and there was a reason to use
such linkers in SBS reactions. Illumina argues, however, that a person of
ordinary skill in the art would not have used a disulfide bond. At oral
hearing, counsel for Illumina conceded that the claimed method does not
recite a particular cleavage efficiency. Tr. 20. Citing Rabani, however,
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. Mot. 10–12.
According to Illumina, greater than 90% efficiency in the cleavage reaction
could not be achieved at the time of the invention if a disulfide linkage were
used. Id.
Rabani teaches 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. 2017, 3:5–8
(emphasis added). Illumina reasons 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,” (Ex. 2017, 3:5–8) and since the
claims require that the disulfide linkage of the cleavable linker and the
protecting group are cleavable under a single set of chemical conditions, the
disulfide linker joining the detectable label to the nucleotide base must also
achieve 90% or more cleavage. Mot. 10–12. Illumina provides evidence
that the prior art teaches less than 90% efficiency in cleaving the 3ʹ-OH
protecting group, leading Illumina to reason “the expectation of
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unacceptably low 3ʹ-OH protecting group cleavage efficiency when using ‘a
single set of chemical conditions’ would not lead a skilled artisan to believe
that one could efficiently cleave 3ʹ-OH protecting groups under the same
single set of chemical conditions with a disulfide linkage during SBS.” Mot.
12.
In other words, Illumina argues that because 90% efficiency in
cleaving 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 3ʹ-OH group requires 90%
efficiency, Illumina argues, thus 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 claimed detectable label.
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, nor does Illumina
argue that the “single set of chemical cleavage conditions” requires that the
protecting group and detectable label be attached to the nucleotide using the
same linker. We, therefore, discern no reason to apply Rabani’s protecting
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group cleavage efficiency requirement to the disulfide linkage of the
proposed substitute claims.
Significantly, Dr. Floyd Romesberg,10 Illumina’s declarant, conceded
that he chose a 90% efficiency requirement not because of Rabani, but rather
because “it was a round number slightly above the values reported by Ruby
and Herman.” Ex. 1022, 198:16–18. Furthermore, we note that Dr.
Romesberg’s rationale that high cleavage efficiency is necessary in SBS
processes uses examples involving 8 or 16 iterations of the process. Ex.
2004 ¶ 63. Yet, as counsel for Illumina conceded at oral hearing, the
claimed process requires far fewer iterations: at most, two and a half cycles.
Tr. 7.
Illumina has not persuaded us that cleavage of the disulfide bond that
attaches the detectable label to the base with less than 90% efficiency would
be unacceptable for SBS processes, such that a person of ordinary skill in the
art would not investigate linkers with less efficient cleavage.
F. 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

10 Declarations by Floyd Romesberg, Ph.D. were submitted by Illumina in
support of its Motion to Amend. Exs. 2004 & 2037. Dr. Romesberg is a
professor in the Department of Chemistry at The Scripps Research Institute,
where he has been a faculty member since 1998. Ex. 2004 ¶ 2. Dr.
Romesberg testified that he is “qualified to render an opinion in the field of
nucleotide analogue molecules based on [his] experience in this field.” Id. ¶
17. Dr. Romesberg was deposed twice; the transcripts of his depositions are
Exhibits 1022 & 1042.

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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, 6:32–43).
The ’346 patent suggests that choosing cleavage conditions for the
3ʹ-OH group was 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 3ʹ OH group.
The process used to obtain the 3ʹ OH group can be any suitable
chemical or enzymic reaction.
Id. at 8:21–26.
Dr. Branchaud testified that:
even if one of ordinary skill in the art considered the elution
percentages of Ruby . . . in deciding whether to use such a
linker for SBS, one of ordinary skill in the art would know that
such elution percentages could be improved by routine
experimentation to improve the cleavage efficiency of the
disulfide linkers and thus would not be dissuaded from using
such a linker.

Ex. 1021 ¶ 40. As discussed below, this conclusion is supported by the prior
art of record.
1. 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
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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. 1021 ¶ 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.” Mot. 11 (citing Ex. 2016, 117–18; Ex.
2004 ¶ 60). 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 “approximately 86% of the
RNA.” Ex. 1021 ¶ 31.
Dr. Romesberg testified that, because “[t]here is no indication in Ruby
that a 3ʹ-OH protecting group that is cleavable under a single set of
conditions with a disulfide linkage would be cleaved with any greater
efficiency than the approximately 86% cleavage efficiency reported by Ruby
for a disulfide linkage,” a person of ordinary skill “would have had no
reason to expect cleavage efficiency to be greater than 86%.” Ex. 2004 ¶ 61.
In response, Dr. Branchaud testified that:
even if one of ordinary skill in the art considered the elution
percentages of Ruby . . . in deciding whether to use such a
linker for SBS, one of ordinary skill in the art would know that
such elution percentages could be improved by routine
experimentation to improve the cleavage efficiency of the
disulfide linkers and thus, would not be dissuaded from using
such a linker.

Ex. 1021 ¶ 40.
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
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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. 1021 ¶¶ 39–40.
2. Herman
Illumina also cites Herman as evidence that 90% cleavage could not
be achieved with a disulfide linkage attaching a detectable label to the base
of a nucleotide. Mot. 11–12. Herman describes a similar system to Ruby,
where RNA is immobilized to a column using a biotin-avidin interaction.
Ex. 2019, Abstract, 3:20–25. 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 7:24–34. The disulfide S-S bond is
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cleaved with a reducing agent, such as DTT or 2-mercaptoethanol. Id. at
7:47–48, 10:3–19. 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 32P-labeled Bio-SS-DNA
remained bound to the resin.
Id. at 11:14–17.
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. 2004 ¶ 67. 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. 1021 ¶ 38. 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. 1022 (Romesberg Tr.), 193:6–194:13. We are not persuaded,
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. 1027) (see supra n.7), cited by
IBS, and Dawson (1991) (Ex. 2038) (see supra n.7), cited by Illumina. IBS
cites Dawson (1989) 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. 1021 ¶ 40.
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Illumina identifies Dawson (1991) for its disclosure that “[r]eduction of the
disulfide bond in the biotinylated nucleotide eluted approximately one-half
of the affinity isolated chromatin.” Ex. 2038, 166.
In other words, the “Herman” publications report varying degrees of
cleavage: from “virtually all” in Dawson (1989) (Ex. 1027), to 87% in
Herman (Ex. 2019), to approximately 50% in Dawson (1991) (Ex. 2038). 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, in the experiments described in
Ruby and Herman:
[I]t 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 higher cleavage efficiency. Thus,
one of ordinary skill in the art would not be dissuaded from
using a disulfide linkage in a modified nucleotide by the elution
percentages shown in Ruby and Herman.
Ex. 1021 ¶ 39.
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. 2039,
9594. In the ensuing years, however, the Herman group (Exs. 1027, 2019,
2038) did pursue disulfide linkers and showed that higher cleavage rates
could be achieved. Exs. 1027, 2019.
3. Church
Church does not numerically disclose cleavage efficiency, but shows
the results of an experiment in Figure 6. Illumina and IBS dispute the
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degree of cleavage shown in Figure 6. Because the quality of Figure 6 is so
poor, however, the extent of cleavage cannot be determined reliably. We,
therefore, give originally filed Figure 6 no weight.
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 ’346 patent. Ex. 2033
(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 ’346
patent was filed. Nonetheless, Church suggested disulfide linkers in a
sequencing reaction, and carried out an example to show their utility (Ex.
1019, 85–87), providing a reason to have used them in sequencing and a
reasonable expectation of success.
4. 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 7), and Rigas, each 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, even if there were a 90% efficiency
threshold required for SBS.
In particular, Ruby and other publications had no reason to go above
whatever cleavage rate was achieved, because it was not critical to their
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experiments. Herman, in at least one case, described “virtually all” the bond
was cleaved. Ex. 1027. Thus, even if 90% efficiency were required for a
reasonable expectation of success of using the claimed compounds in an
SBS reaction, the ordinary artisan reasonably would have expected that such
cleavage efficiency could be achieved.
In sum, the art (e.g., Ju and Tsien) teaches SBS processes using a
3ʹ-OH protecting group and a single set of chemical cleavage conditions; the
proposed substitute claim substitutes a known cleavable linker for the linkers
used in the prior processes, for the art-recognized purpose of linking the
detectable label to the nucleotide (e.g., Rabani and Church). In other words,
the improvement claimed is no more than “the predictable use of prior art
elements according to their established functions.” KSR Int'l Co. v. Teleflex
Inc., 550 U.S. 398, 417 (2007).
G. 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
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, 550 U.S. at 406; 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
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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
performed under Mr. Vermaas’s supervision while employed by Illumina.
Ex. 2023 ¶¶ 4–5. The sequencing experiments used the four nucleotides
dATP, dTTP, dGTP, and dCTP, only one of which—dATP—contained a
disulfide linker attaching a fluorophore to the nucleotide base. Id. ¶ 6; Ex.
2004 ¶ 71. Each of these nucleotides also contained an azidomethyl group
protecting the 3ʹ-OH. Ex. 2004 ¶ 71.
Mr. Vermaas describes sequential sequencing reactions on PhiX
Control DNA for over 150 cycles in which nucleotides were added one at a
time. Ex. 2023 ¶¶ 13–17; Ex. 2004 ¶ 73. After each scan for the
fluorophore incorporated, a solution comprising 2 mM tris(hydroxymethyl)-
phosphine was added. Ex. 2004 ¶ 74. “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 ordinary skill in the art
would recognize that the yield for cleavage of the disulfide linkage was
essentially 100%.” Id. ¶ 84. 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
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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. 2004 ¶ 84.
There are at least two differences between the experiments described
in Ruby and Herman, and the experiment described by Mr. Vermaas. First,
while Ruby, Herman, and Vermaas each used a nucleotide with a cleavable
disulfide bond, the Ruby and Herman 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 disulfide
linkage to release the bound RNA. Ex. 2016, 98–99. Herman used a system
similar to Ruby. Ex. 2019, Abstract, col. 3.
Secondly, the cleavage agents are different. The cleavage agent used
in Ruby is DTT (Ex. 2016, 103, “Elution buffer” A and B) and in Herman,
the cleavage agent is described as “a reducing agent such as DTT” (Ex.
2019, 7:47–48) with DTT being used in its example (id. at 10:47–54, 11:11–
22; 12:3–8). Mr. Vermaas describes an experiment that utilized another
cleavage agent, 2 mM tris(hydroxymethyl)phosphine. Ex. 2023 ¶ 12.
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
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have used DTT in Dr. Vermaas’s comparison to the prior art. Ex. 1019, Fig.
5, 68:12–13, 86:20–23.
Dr. Romesberg testifies that “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. 2004 ¶ 84. There is no testimony, however, that the stated
results were due to the claimed nucleotide rather than the reducing agent.
While Dr. Romesberg refers to the “disulfide cleavage yield” as being
unexpected, he does 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
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). “The combination of familiar
elements according to known methods is likely to be obvious when it does
no more than yield predictable results.” KSR, 550 U.S. at 416.
H. 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
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Motion to Amend is DENIED to the extent that it requests entry of substitute
claims 20–26.
V. MOTIONS TO EXCLUDE EVIDENCE
Both IBS (Paper 46) and Illumina (Paper 49) filed Motions to Exclude
Evidence. Both motions are dismissed as moot.
A. Illumina’s Motion
Illumina requests that Figure 6 from Ex. 1019 (Church), all
characterizations of Figure 6 from Ex. 1019, and all arguments based on it
be excluded as evidence from this inter partes review. Paper 49, 1. Illumina
argues that the Figure should be excluded because the Exhibit “is not the
best evidence of the data contained in Fig. 6. It is a poor quality copy that
has drawn objections from IBS’ own counsel, and it cannot be used to draw
conclusions regarding cleavage efficiency.” Id. at 1. As discussed above,
we agree with Illumina that the figure of Church is of poor quality and gave
it no weight. We, therefore, did not rely on Figure 6 of Church in reaching
our decision, and for this reason Illumina’s motion is moot.
B. IBS’s Motion
IBS requests that Illumina’s Exhibits 2033, 2034, 2035, 2041, and
2042, as well as a portion of IBS’s Exhibits 1030 and 1031 relied upon by
Illumina, be excluded from evidence. Paper 46, 1. As we did not rely on
Exhibits 2034, 2035, 2041, 2042, or 1031, we dismiss this part of the motion
as moot.
Exhibits 2033 and 1030 relate to Figure 6 of Church (Ex. 1019). 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
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deficiency, Illumina sought to introduce a substitute Figure 6 from another
patent publication by Church. Exs. 2033, 1030. Illumina did not establish
that this substitute figure was available prior to the filing date of the ’346
patent. We, therefore, did not consider it. Consequently, we dismiss this
part of the motion as moot.
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 20–26, and granted in part, to the
extent it seeks to cancel claims 1, 2, 4, 11, 12, 17, 18, and 19;
FURTHER ORDERED that Illumina’s motion to exclude evidence is
dismissed as moot; and
FURTHER ORDERED that IBS’s motion to exclude evidence is
dismissed as moot.

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For PETITIONER:

Scott Marty
Marc Segal
Robert Baron
BALLARD SPAHR LLP
martys@ballardspahr.com
segalm@ballardspahr.com
baron@ballardspahr.com

For PATENT OWNER:

James Morrow
James Borchardt
REINHART BOERNER VAN DEUREN s.c.
ipadmin@reinhartlaw.com
jborchardt@reinhartlaw.com