Illumina, Inc.v.the Trustees of Columbia University in the City of New York

Patent Trial and Appeal Board

Mar 6, 2014

12804284 (P.T.A.B. Mar. 6, 2014)

Trials@uspto.gov Paper 130
572-272-7822 Mailed: March 6, 2014

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________
ILLUMINA, INC.
Petitioner

v.

THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF
NEW YORK
Patent Owner

___________

Case IPR2013-00011
Patent 8,088,575 B2
___________

Before SALLY G. LANE, RICHARD M. LEBOVITZ, and DEBORAH
KATZ, 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, Illumina, Inc. (“Illumina”), filed a petition on October 3,
2012, for inter partes review of claims 1-3 and 6 of U.S. Patent 8,088,575
B2 (“the ’575 Patent”) pursuant to 35 U.S.C. §§ 311-319 and 37 C.F.R. §§
42.1 - 42.123. On March 12, 2013, the Board instituted inter partes review
of claims 1-3 and 6 on four grounds of unpatentability (Paper 26, Decision
on Petition (“Dec. Pet.”)). Illumina requested rehearing on two of the
grounds of unpatentability (Paper 29), which had been denied in the
Decision on Petition. Upon reconsideration, the Board instituted inter partes
review of one of these grounds of unpatentability as to claim 6 (Paper 44,
Decision on Rehearing (“Dec. Reh’g”)). This corresponded to one of the
same grounds of unpatentability authorized for claims 1-3.
After institution of the inter partes review, Patent Owner, The
Trustees of Columbia University in the City of New York (“Columbia”),
filed a response under 37 C.F.R. § 42.120 to the decision instituting inter
partes review (Paper 70, “PO Resp.”). Columbia also filed a Motion to
Amend Claims (Paper 56) and a Motion to Exclude Evidence (Paper 93).
Illumina filed a reply to Columbia’s response under 37 C.F.R. § 42.120
(Paper 76, “Pet’r” Reply) and a Motion to Exclude Evidence (Paper 90). An
oral hearing was held on December 17, 2013 with both parties in attendance.
(Record of Oral Hearing, Paper 126.)
Among the evidence cited in this proceeding are declarations by
George L. Trainor, Ph.D. (Ex. 2033, Trainor Decl.) on behalf of Columbia,
and by George Weinstock, Ph.D. (Ex. 1021, Weinstock Decl.) on behalf of
Illumina. Dr. Trainor has a Ph.D in Organic Chemistry and experience in
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DNA sequencing (Exhibit 2033, Trainor Decl. ¶¶ 3 and 6-8), qualifying him
to testify on the prior art issues discussed in his declaration. Dr. Weinstock
has a Ph.D. in Microbiology and experience in DNA sequencing, including
as a director of large-scale genome centers (Ex. 1021, Weinstock Decl. ¶¶ 4,
6, 8, and 9), qualifying him to testify on the prior art issues discussed in his
declaration.
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 has shown by a preponderance of the evidence that claims 1-3 and
6 are unpatentable.

B. The ‘575 Patent
The ‘575 Patent issued January 3, 2012. The named inventors are
Jingyue Ju, Zengmin Li, John Robert Edwards, and Yasuhiro Itagaki. The
invention of the ‘575 Patent involves sequencing DNA by incorporating a
base-labeled nucleotide analogue into primer DNA strand, and then
determining the identity of the incorporated analogue by detecting a label
attached to the base of the nucleotide. A polymerase is used to incorporate
the nucleotide analogue into the strand of DNA (‘575 Patent, col. 3, ll. 2-3).
The method is generally referred to as “sequencing DNA by synthesis” or
“SBS” because the sequence of the DNA is determined by identifying the
successive additions of labeled nucleotides to a strand of DNA as it is
synthesized using a complimentary DNA strand as a template (id. at col. 2,
ll. 9-13).
Columbia does not argue the novelty of the steps utilized in the
claimed method of “determining the identity of a nucleotide analogue
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incorporated into a nucleic acid primer extension strand,” but rather focuses
its arguments on the novelty and unobviousness of the nucleotide utilized in
the sequencing method. Nucleotides, which are the building blocks of DNA,
comprise a sugar (ribose or deoxyribose), phosphates attached to the
5’-position of the sugar, and a nitrogen base on the 1’-position of the sugar.
During DNA synthesis, the 5’-position in the sugar of a new incoming
nucleotide is linked by DNA polymerase to the 3’-OH group in the sugar of
a preexisting nucleotide in the strand under synthesis. In order to identify
the newly incorporated nucleotide, one approach described in the prior art is
to attach a detectable label to the nucleotide at its 3’-OH group (‘575 Patent,
col. 2, ll. 35-39). For reference, the 3’-OH corresponds to 3’-position of the
deoxyribose sugar of the nucleotide and serves as the site where a new
nucleotide is added during DNA synthesis.
The approach described in the ‘575 Patent is to make nucleotide
analogues by linking a unique label, such as fluorescent dye, through a
cleavable linker to the nucleotide base or to an analogue of the nucleotide
base and to use a small removable chemical moiety to cap the 3’-OH group
of the deoxyribose to make it reversibly nonreactive (id. at col. 2, ll. 59-65).
The reason the 3’-OH group is made reversibly nonreactive is to allow the
sequencing reaction to be terminated after each nucleotide is added in order
to determine its identity (id. at col. 3, ll. 1-4). According to the ‘575 Patent,
the prior art teaches attaching the label to the 3’-OH group. The ‘575 Patent,
in contrast, puts the label on the nucleotide base and the removable chemical
moiety on the 3’-OH group. These latter features are at the center of the
patentability challenges.
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Claims 1-3 in this inter partes review involve a nucleotide analogue
that comprises: 1) a base labeled with a unique label; and 2) a removable
chemical moiety capping the 3’-OH group. Claim 6 further requires a base
that is deaza-substituted. A deaza-substituted nucleotide is a nucleotide
analogue that includes a deazabase as the nitrogen base (id. at col. 7, ll. 46-
65). A deazabase is a nitrogen base in which one of the natural nitrogen
atoms in the base ring is substituted with a carbon atom (id.). For example,
in a 7-deazapurine, the natural 7-position nitrogen in the base ring is
replaced with a carbon atom (id.).
In summarizing the state of the art in Columbia’s Patent Owner
Response, Columbia states that, “[d]uring the 1990s, despite some interest in
base-labeled nucleotide analogues, efforts focused on including a label on
the 3’OH group on the sugar in a nucleotide analogue and on the design and
synthesis of new nucleotide analogues that could be incorporated by a
polymerase into a primer extension strand.” (Paper 70, PO Resp. 8).
Columbia cites paragraphs 30-35 of Dr. Trainor’s Declaration as evidence
that “[r]esults were mixed and it was recognized that new nucleotide
analogues were needed [for use in] BASS [sequencing by synthesis; also
known as SBS] sequencing.” (Id.)
As discussed in more detail below, Columbia’s characterization of the
prior art as having “some interest in base-labeled nucleotide analogues”
understates the interest level shown in the prior art. Tsien1 and Dower,2

1 Roger Tsien et al., WO 91/06678 (May 16, 1991), Exhibit 1002 (“Tsien”).
2 William Dower et al., US 5,547,839 (August 20, 1996), Exhibit 1005
(“Dower”).
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cited in this inter partes review, and Stemple III,3 which is cited in related
proceedings, describe SBS methods that use base-label nucleotides and
nucleotides containing a removable chemical moiety at the 3’-OH position
(Ex. 2033, Trainor Decl. ¶¶ 26-29). Columbia acknowledges that base-
labeled nucleotides were described in the prior art (id. at ¶ 28). We
understand it to be Columbia’s position that because there is no single
example in the cited prior art of a nucleotide with the base-label and
removable 3’-OH blocking group being used in a DNA sequencing reaction,
the disclosure of such a nucleotide is somehow diminished and amounts only
to “some interest.” Columbia, however, has not identified where in the prior
art a nucleotide with a label on the base and removable 3’-OH chemical
moiety was so disparaged that a person of ordinary skill in the art would
have been dissuaded from using it in SBS methods. To the contrary, the
disclosure in several publications of nucleotides with a label on the
nucleotide base and a removable 3’-OH group (e.g., Tsien, Dower, and
Stemple III) shows a recognition within the prior art that such nucleotide
analogues were useful and effective in SBS methods.

C. Related Proceedings
The ’575 Patent is the subject of the litigation, The Trustees of
Columbia University in the City of New York v. Illumina, Inc., 1:12-cv-
00376-UNA, currently pending in the United States District Court for the
District of Delaware (Petition 3-4). According to Illumina, Columbia

3 Derek L. Stemple et al., U.S. Pat. No. 7,270,951 B1 (September 18, 2007),
Exhibit 1008 (“Stemple III”).
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alleges in that proceedings that Illumina has infringed, and continues to
infringe, the ’575 Patent (id.).
There are two pending inter partes trials which are related to this trial:
A petition for inter partes review was filed on September 16, 2012 for
U.S. Pat. No. 7,713,698 B2 (“the ’698 patent”).4 The ’698 patent is assigned
to Columbia, has claims directed to related subject matter, and has a similar
lineage as the ’575 Patent. We instituted inter partes review on March 12,
2013.
A petition for inter partes review was filed on September 16, 2012 for
U.S. Pat. No. 7,790,869 B2 (“the ‘869 patent”).5 The ’869 patent is assigned
to Columbia and has claims directed to related subject matter. The ’575
Patent is a continuation of the ‘869 Patent. We instituted inter partes review
on March 12, 2013.

D. The Alleged Grounds of Unpatentability
We instituted inter partes review on the following four grounds of
unpatentability:
I. Claims 1-3, and 6 under 35 U.S.C. § 102(b) as anticipated by
Dower;
II. Claims 1-3, under 35 U.S.C. § 102(b) as anticipated by Tsien;
III. Claim 6 under 35 U.S.C. § 103(a) as obvious in view of Tsien and
Prober I;6 and

4 IPR2012-00006.
5 IPR2012-00007.
6 James M. Prober et al., A System for Rapid DNA Sequencing with
Flourescent Chain-Terminating Dideoxynucleotides, 238 SCI. 336 (1987),
Exhibit 1003 (“Prober I”).
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IV. Claim 6 under 35 U.S.C. § 103(a) as obvious in view of Tsien
and Seela I.7

E. The Claims
The ’575 Patent was granted with claims 1-6. Illumina challenges the
patentability of independent claim 1 and claims 2, 3, and 6, which depend
from claim 1. Claims 1 and 6 read as follows (bracketed numerals added to
emphasize certain claim limitations):
1. A method of determining the identity of a nucleotide
analogue incorporated into a nucleic acid primer extension
strand, comprising: a) contacting a nucleic acid template
attached to a solid surface with a nucleic acid primer which
hybridizes to the template; b) simultaneously contacting the
product of step a) with a polymerase and four nucleotide
analogues which are either (i) aA, aC, aG, and aT, or (ii) aA,
aC, aG, and aU, so as to incorporate one of the nucleotide
analogues onto the nucleic acid primer and form a nucleic acid
primer extension strand, wherein each nucleotide analogue
within (i) or (ii) comprises [1] a base labeled with a unique
label and contains [2] a small removable chemical moiety
capping the 3’-OH group of the sugar of the nucleotide
analogue, wherein said small cleavable chemical group does not
interfere with the recognition of the nucleotide analogue by
polymerase as a substrate; and c) detecting the unique label of
the incorporated nucleotide analogue, so as to thereby
determine the identity of the nucleotide analogue incorporated
into the nucleic acid primer extension strand.

6. The method of claim 1, wherein said base of at least one of
said nucleotide analogues is a deazapurine.

7 Frank Seela, US 4,804,748 (February 14, 1989), Exhibit 1014 (“Seela I”.
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PATENTABILITY CHALLENGES
II. CLAIM INTERPRETATION
Claim 6 recites that the base of at least one of the nucleotide
analogues is a “deazapurine.” One of ordinary skill in the art would
understand that a “deazapurine” is a nitrogen base in which one of the
natural nitrogen atoms in the base ring is substituted with a carbon atom.
(’575 Patent, col. 7, ll. 39-65.) For example, in a 7-deazapurine, the natural
7-position nitrogen in the base ring is replaced with a carbon atom. Id.

ANTICIPATION
Independent claim 1 is directed to a method of “determining the
identity of a nucleotide analogue incorporated into a nucleic acid primer
extension strand,” comprising three recited steps using a nucleotide analogue
with “a base labeled with a unique label” and “small removable chemical
moiety capping the 3’-OH group of the sugar of the nucleotide analogue.”
Claim 6 further recites that the base is a deazapurine. Columbia does not
dispute that the claimed methods steps were known in the art, but rather
argues that the claimed nucleotide analogue was not.

III. DOWER
Claims 1-3
We instituted inter partes review of claims 1-3 based on Dower as an
anticipatory publication. Dower describes methods for sequencing DNA
(Dower, col. 6, ll. 19-20). In one embodiment, a primer is elongated, one
nucleotide at a time, using labeled nucleotide analogues in a polymerase-
catalyzed enzymatic reaction (id. at col. 14, ll. 37-59; col. 15, l. 56 to col. 16,
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l. 21). As explained in more detail below, Dower describes nucleotides with
a label attached to the base and a small removable chemical moiety capping
the 3’-OH group of the sugar of the nucleotide analogue, the two structural
features of the nucleotide utilized in the claimed method of “determining the
identity of a nucleotide analogue incorporated into a nucleic acid primer
extension strand” (’575 Patent, claim 1). We address each of these features
below.

A. “a base labeled with a unique label”
The phrase “unique label” is not defined in the ’575 patent. We adopt
the ordinary meaning of “unique” as “being the only one of its kind.”8
Therefore, the phrase “unique label” would be understood to mean that each
of the recited four nucleotides has a different label (see ’575 patent, col. 21,
ll. 31-35). Dower has express disclosure of each nucleotide bearing its own
distinct label (Dower, col. 23, ll. 22-24 (“This is done in a one-step process
where each of the four dNTP analogs is identified by a distinct dye, such as
described in Prober et al. Science 238:336-341 . . .”)).
Illumina also points to disclosure in Dower, which is said to describe
a label attached to a base of a nucleotide (Petition 20).
FIG. 9 schematically illustrates the synthesis of a generic
protected nucleotide. A suitable nucleotide is labeled with the
FMOC fluorescently detectable label by reaction under the
conditions described, e.g., in Ser. No. 624,114 filed Dec 6,
1990, FMOC-Cl, and H2O. A protection moiety will be added
using conditions also described there.
(Dower, col. 18, l. 64-col. 19, l. 2.)
Figure 9 is reproduced below:

8 http://www.thefreedictionary.com/unique. Accessed February 9, 2013.
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nitroindolinyl, o-hydroxy-2-methyl cinnamoyl, 2-oxymethylene
anthraquinone, and t-butyl oxycarbonyl (TBOC).
(Id. at col. 18, ll. 52-77.)

C. Discussion
In its preliminary comments, Columbia argued, unsuccessfully, that
Dower is not anticipatory because there is no single example of a nucleotide
with both structural features [1] and [2]. However, a single example is not
required to establish anticipation. In re Petering, 301 F.2d 676, 681 (CCPA
1962); WM. Wrigley Jr. Co. v. Cadbury Adams USA LLC, 683 F.3d 1356,
1361-62 (Fed. Cir. 2012). For a prior art reference to anticipate a claim, it
must disclose all of the limitations of the claim, “arranged or combined in
the same way as in the claim.” Net MoneyIN, Inc. v. VeriSign, Inc., 545 F.3d
1359, 1370 (Fed. Cir. 2008).
With respect to limitation [2], Dower expressly describes blocking the
3’-OH group of the sugar molecule in order to halt polymerase catalyzed
elongation of the primer strand (Dower, col. 15, ll. 35-37 (reproduced
above)). The blocking group is, thus, necessary for Dower’s one-step
process (id. at Fig. 8; col. 23, ll. 26-30). The nucleotide must also be
detectably labeled in order to determine whether it was added to the primer
end. Thus, the reversibly blocked nucleotide must be labeled as recited in
limitation [1] of claim 1. Dower expressly teaches a nucleotide detectably
labeled on a base, for example, as shown in Figure 9 (id. at col. 5, ll. 35-37;
col. 18, l. 64-col. 19, l. 2; Figure 9). While Figure 9 does not depict the
nucleotide with a blocked 3’-OH group, the skilled worker would have
understood that a blocked nucleotide is needed to carry out Dower’s process
(see infra).
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Columbia did not respond substantively to the patentability challenge
of claims 1-3 based on Dower under 35 U.S.C. § 102 in their subsequent
response under 37 C.F.R. § 42.120. The evidence as outlined above
persuades us that Illumina has met its burden of proof by a preponderance of
the evidence in showing that claims 1-3 of the ’575 Patent are anticipated by
Dower under 35 U.S.C. § 102.

Claim 6
Claim 6 depends from claim 1, and further recites that the sequencing
method employs a nucleotide which comprises a deazapurine as a base.
Dower is not said by Illumina to expressly describe a deazapurine base in its
written disclosures. Rather, Illumina contends a nucleotide with a
deazapurine is present by virtue of the incorporation by reference to the
Prober I publication by Dower. “To incorporate material by reference, the
host document must identify with detailed particularity what specific
material it incorporates and clearly indicate where that material is found in
the various documents.” Advanced Display Sys., Inc. v. Kent State Univ.,
212 F.3d 1272, 1282 (Fed. Cir. 2000). When making such determination,
the standard “of one reasonably skilled in the art should be” applied. Id. at
1283.
The following passages were cited in the Decision on Rehearing to
establish that Dower incorporated Prober I for its teaching a deazapurine
base.
DNA polymerase, or a similar polymerase, is used to extend the
chains by one base by incubation in the presence of dNTP
analogs which function as both chain terminators and
fluorescent labels. This is done in a one-step process where
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each of the four dNTP analogs is identified by a distinct dye,
such as described in Prober et al. Science 238:336-341.
(Dower, col. 23, ll. 18-24.)
Fluorescent chain terminators (analogs of dATP, dCTP, dGTP,
and TP, each labeled with fluorophore preferably emitting at a
distinguishable wavelength) are added to the reaction at a
sufficient concentration and under suitable reaction conditions
(time, temperature, pH, ionic species, etc., See Sambrook et al.
(1989) Molecular Cloning, vols. 1-3, and Prober et al.).
(Id. at col. 25, ll. 4-10.)
(c) An alternative polymer stepwise synthetic strategy
can be employed. In this embodiment, the fluorophores need
not be removable and may be attached to irreversible chain
terminators. Examples of such compounds for use in
sequencing DNA include, but are not limited to,
dideoxynucleotide triphosphate analogs as described by Prober
et al. (1987) Science 238:336-341.
(Id. at col. 25, ll. 41-47.)
Upon reconsideration, we agreed with Columbia that Prober I is not
incorporated by reference into Dower for a teaching a deazapurine base in a
nucleotide with a reversible 3’-OH cap (Paper 44, Dec. Reh’g 6-9.) The
primary flaw is that Prober I’s nucleotides with the deazapurine substituent
have an irreversible 3’-OH blocking group (chain terminating dideoxy
ddNTPs) because they were employed in chain terminating sequencing.
Illumina did not identify a teaching in Dower where Dower describes using
Prober I to modify Dower’s nucleotides with a reversible 3’-OH capping
group.
With respect to col 23, ll. 18-24 of Dower, Dr. Trainor testified:
[T]he material being referenced in Dower in the phrase “where
each of four dNTP analogues is identified by a distinct dye” is
only the description of the four distinct dyes used to label four
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ddNTPs. The only dNTPs described in Prober I are unlabeled
nucleotides which are used with four labeled ddNTPs in a
Sanger dideoxy sequencing experiment. Since there is no
disclosure in Prober I of labeled dNTP analogues, one of
ordinary skill would not have understood the referenced
material to be dNTP analogues identified by distinct dyes, but
only the four dyes used to label the ddNTPs.
(Ex. 2033, Trainor Decl. ¶ 52.)
We agree with Dr. Trainor’s analysis and conclusion.
Similarly, we agree with Dr. Trainor that Dower’s disclosure at
col. 25, ll. 4-10, is not adequate because it appears to be only a description of
the conditions that one of ordinary skill in the art would use to accomplish
the polymerase reaction, and not of using the analogues themselves (Ex.
2033, Trainor ¶ 54). In addition, the passage cited at column 24, lines 41-
47, is also inadequate because it only concerns the four fluorescently
labeled, dideoxy ddNTP chain terminators described in Prober I (id. at ¶ 56).
At col. 25, ll. 41-64, Dower describes an alternative (c). This
embodiment refers to nucleotides that have irreversible blocking groups on
the 3’-OH position of the sugar, and thus, do not teach using Prober I’s
deazapurine in nucleotide with a reversible 3’-OH group as claimed (Ex.
2033, Trainor ¶ 57).
Illumina cites to column 15, lines 37-40 of Dower, which states: “In
contrast to a dideoxy nucleotide, typically the blocking agent will be a
reversible blocking agent thereby allowing for deblocking and subsequent
elongation.” Illumina states this disclosure supports the position that Dower
discloses dNTPs for sequencing synthesis methods (Paper 76, p. 12.) We
agree with this statement, but the issue is whether the disclosure of SBS
nucleotides with reversible 3’-OH caps coupled to the reference to Prober’s
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dideoxy irreversibly capped ddNTPs having a deazapurine base is a
description of the claimed nucleotide analogue having a deazapurine base
with a reversible 3’-OH cap. Illumina has not pointed to anything
convincing in Dower that teaches replacing Dower’s dideoxy terminated
nucleotide with a removable 3’-OH cap or vice-versa.
Accordingly, we find that Illumina has not established by a
preponderance of the evidence that Dower anticipates claim 6.

IV. TSIEN
We instituted inter partes review of claims 1-3 based on Tsien as an
anticipatory publication. Tsien describes a method of sequencing DNA
(Tsien, p. 6, ll. 28-30). The method involves the sequential addition to a
primer of labeled nucleotides (dNTP), each with a different detectable label
attached to it (id. at p. 7, ll. 3-14; p. 10, ll. 7-10; p. 14, ll. 12-26). Tsien
describes the claimed [1] detectable label attached to a base (id. at p. 10,
ll. 10-15; Tsien, p. 27, l. 33 to p. 28, l. 2; p. 28, ll. 5-6), in addition to other
locations on the nucleotide analogue (p. 26, ll. 2-5; p. 26, ll. 17-19). Tsien
also describes “[2] a small removable chemical moiety capping the 3’-OH
group of the sugar of the nucleotide analogue” to prevent inadvertent
multiple additions during the sequencing method (id. at p. 12, ll. 27-29).
Columbia had argued in the Preliminary Response that “the large
number of alternative approaches and features disclosed by Tsien form a
‘genus’ of many possible methods, from which the specific method of claim
1 cannot be immediately envisaged.” (Paper 22, Preliminary Response 16.)
We agreed that there were choices to be made, but find that each selection is
made from a defined set of possible choices. Citing Wrigley, 683 F.3d at
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1361-62, in which anticipation was found where each of the specific
ingredients in the claimed formula was recited in a longer list of alternative
agents, we determined that there was a factual and legal basis on which
Illumina would prevail in establishing anticipation by Tsien of claims 1-3,
despite the need for choosing (Paper 26, Dec. Pet. 16).
Columbia did not respond substantively to the patentability challenge
of claims 1-3 based on Tsien under 35 U.S.C. § 102 in their subsequent
Patent Owner Response. The evidence as outlined above persuades us that
Illumina has met its burden of proof by a preponderance of the evidence in
showing that claims 1-3 of the ’575 Patent are anticipated under 35 U.S.C.
§ 102 by Tsien.

V. TSIEN AND PROBER
We instituted inter partes review of claim 6 on the grounds that the
Columbia claims would have been obvious under 35 U.S.C. § 103 in view of
Tsien and Prober I. We first turn to the description in Tsien and Prober I of
key elements of the claims, and then to the reason for combining Tsien and
Prober I to have arrived at the claimed invention.

A. Claim 6
Claim 6 is drawn to the nucleic acid sequencing method of claim 1,
and further recites that at least one of the labeled bases is a “deazapurine.”
We instituted inter partes review of claim 6 under 35 U.S.C. § 103 as
obvious in view of Tsien and Prober I.
A nucleotide analogue of claim 6 has the following structures or
features: 1) a unique label attached to a base; 2) a removable chemical
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moiety capping the 3’-OH group of the nucleotide sugar; and 3) a deaza-
substituted base. Features 1) and 2) are said to be described by Tsien.
Prober I describes deazapurines. The issue to be decided is whether it would
have been obvious to one of ordinary skill in the art to have used Prober I’s
deazapurines in Tsien’s sequencing method.

B. Tsien and Prober I disclosures
Tsien describes a DNA sequencing by synthesis method (Tsien, p. 6-
7). The method uses nucleotides labeled with reporter groups to identify
when they are incorporated into the newly synthesized strand (id. at p. 7,
ll. 3-14).
The following evidence from Tsien supports Illumina’s contention
that structures 1) and 2) are described in Tsien (see also Pet. 31-38 (where
Illumina cited disclosure from Tsien to meet the claim limitations).

1) Unique label attached to a base
Tsien has the following teachings:
When they [deoxynucleotide triphosphates or dNTPs] are each
tagged or labeled with different reporter groups, such as
different fluorescent groups, they are represented as dA’TP,
dC’’TP, dG’’’TP and dT’’’’TP. As will be explained in more
detail below, the fact that the indication of labeling appears
associated with the “nucleoside base part” of these
abbreviations does not imply that this is the sole place where
labeling can occur. Labeling could occur as well in other parts
of the molecule.
(Tsien, p. 10, ll. 7-15 and Fig. 2.)
While the above-described approaches to labeling focus
on incorporating the label into the 3’-hydroxyl blocking group,
there are a number of alternatives - particularly the formation of
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a 3’-blocked dNTP analogue containing a label such as a
fluorescent group coupled to a remote position such as the base.
(Id. at p. 27, l. 33 to p. 28, l. 2.)
One method involves the use of a fluorescent tag attached
to the base moiety . . . This method is included because a
number of base moiety derivatized dNTP analogues have been
reported to exhibit enzymatic competence.
(Id. at p. 28, ll. 5-6.)
2) Removable 3’-OH chemical moiety (capping group)
During DNA synthesis, nucleotides are sequentially added to the 3’-
OH group of the nucleotide sugar. The 3’-OH group contains a removable
blocking group in Tsien’s sequencing method so the labeled nucleotides can
be added one at a time. After each addition, the label is detected and the 3’-
OH group is deblocked and new nucleotide is added (Tsien, p. 13).
Specifically, Tsien teaches:
A deblocking solution is added via line 28 [Fig. 2] to remove
the 3’ hydroxyl labeled blocking group. This then generates an
active 3’ hydroxyl position on the first nucleotide present in the
complementary chain and makes it available for coupling to the
5’ position of the second nucleotide.
(Id. at p. 13, ll. 17-19.)
The coupling reaction generally employs 3’ hydroxyl
blocked dNTPs to prevent inadvertent extra additions [of
nucleotides to the 3’-OH end].
(Id. at p. 20, ll. 25-26.)
Structures 1) and 2) combined
Figure 2 of Tsien, reproduced below, shows nucleotides used in a
sequencing reaction, each with a unique label and a blocked 3’-OH group
(18a, 18b, 18c, and 18d) (id. at p. 12, ll. 14-18; p. 9, l. 35 to p. 10, 15):

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A portion of Tsien’s Figure 2, reproduced above, shows nucleotides
each with a unique label attached to the nucleotide and a blocked 3’-OH
group. The figure indicates that the labeling is on the base, but “these
abbreviations [do] not imply that this is the sole place where labeling can
occur.” (Tsien, p. 10, ll. 7-15 and Fig. 2.)

3) A deaza-substituted base
Tsien does not disclose a deaza-substituted base, but references
Prober I, which does:
One method involves the use of a fluorescent tag attached
to the base moiety. . . . This method is included because a
number of base moiety derivatized dNTP analogues have been
reported to exhibit enzymatic competence. [citing Sarfati et al.
(1987)] . . . [Prober I] show enzymatic incorporation of
fluorescent ddNTPs by reverse transcriptase and Sequenase™.
(Tsien, p. 28, ll. 5-18.)
Prober I discloses the “set of four fluorescence tagged chain-
terminating reagents we have designed and synthesized is shown in Fig. 2A.
These are ddNTP's to which succinylfluorescein has been attached via a
linker to the heterocyclic base . . . The linker is attached . . . to the 7 position
in the 7-deazapurines.” (Prober I, p. 337.) In sum, Prober I describes a
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nucleotide comprising a deazapurine base to which a label has been
attached.

C. Reason to combine
In making an obviousness determination, “it can be important to
identify a reason that would have prompted a person of ordinary skill in the
relevant field to combine the elements in the way the claimed new invention
does.” KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398, 418 (2007). Illumina
contends that Tsien’s reference to Prober I’s fluorescent nucleotides would
have provided one of ordinary skill in the art with a reason to have used
Prober I’s labeling technique in Tsien’s method (Ex. 1021, Weinstock Decl.
¶ 83).
Even absent disclosure of Prober I in Tsien, Dr. Weinstock testified
that it would have been obvious to have used Prober I’s teachings in Tsien.
because the nucleotide analogues disclosed in Prober I, wherein
“a linker is attached to the 5 position in the pyrimidines and to
the 7 position in the 7-deazapurines,” is shown to be an
effective way to attach a fluorescent label to a nucleic acid base
while maintaining the ability of the Sequenase™ polymerase
used by Tsien to incorporate the associated dNTP into the
primer extension strand. See Tsien, page 28, lines 5-18. The
combination of Tsien and Prober I would additionally offer the
benefit of the “stable linker arm attachment” taught by Prober I.
Prober I, p. 337, col. 1.
(Ex. 1021, Weinstock Decl. ¶ 85)

D. Discussion
Columbia contends that the patentability challenge based on Tsien and
Prober I is insufficient because “no starting point is identified and no
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rationale for the obviousness of the novel nucleotide analogue is provided.”
(Paper 70, PO Resp. 15-16).
Columbia’s argument is not persuasive. Illumina, in the Petition,
cited Tsien’s reference to Prober I for teaching labeled nucleotides and
expressly stated that “Tsien thus provides an express teaching, suggestion,
and motivation to combine Tsien with the disclosures of Prober I with
respect to ‘base moiety derivatized’ nucleotide analogues.” (Petition 37.)
Furthermore, Illumina stated that Tsien teaches that “the synthesis scheme
for ddNTPs used in Prober I should be used in Tsien to produce ‘fluorescent
dNTPs.’ Tsien, p. 29, ll. 10-19.” (Id.) Columbia’s “starting point”
argument is therefore unsubstantiated. A rationale to combine the
publications was described above.
Columbia identified five differences between the nucleotide described
in Tsien and the nucleotide recited in claim 6 (Ex. 2033, Trainor Decl. ¶ 79),
The differences, as stated in Dr. Trainor’s Declaration, are as follows:
1. remove the labels from the 3’-OH capping group of the
sugars and place them on the bases;
2. include removable chemical capping groups that did not
include labels on the 3’-OH of the sugar;
3. attach four unique labels to the bases;
4. change at least one purine base to a deazabase; and
5. retain the property of being incorporated onto a primer
extension strand.
(Ex. 2033, Trainor Decl. ¶ 79.)
We address these differences below:
Deaza-substituted nucleotide (No. 4 in Ex. 2033, Trainor Decl. ¶ 79)
Citing the Trainor Declaration, Columbia argues “there was no reason
to use a deaza-purine labeled at the 7-position given Tsien’s specific
guidance to the contrary that a label on the 8-position of a non-deaza purine
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was ‘ideal’ (Exhibit 2033, Trainor Decl., ¶88-96.)” (Paper 70, PO Resp.
20). Columbia further argues that there would have been no reason “to
change the uncleavable linkers on the 8-position of the purine labeled
nucleotide analogues of Tsien to a cleavable linker, particularly since the
linker in Prober I is uncleavable (Exhibit 2033, Trainor Decl., ¶98)” (id.).
Dr. Trainor cites Tsien’s statement that the “C-8 position of the purine
structure presents an ideal position for attachment of a label.” (Tsien, p. 29,
ll. 3-4.) Dr. Trainor acknowledges that Tsien cites Prober I in the same
paragraph in which purine labeling is described and that Prober I describes
producing labeled deazapurines (Ex. 2033, Trainor Decl. ¶ 91). However,
Dr. Trainor states that Tsien ignored Prober I’s teaching because Tsien
“refers to Prober I for teaching an approach to producing fluorescently
labeled derivatives of pyrimidines.” (Id.) The mentioned teaching in Prober
I is reproduced below:
A number of approaches are possible to produce fluorescent
derivatives of thymidine and deoxycytidine. One quite versatile
scheme is based on an approach used by Prober et al. (1987) to
prepare ddNTPs with fluorescent tags.
(Tsien, p. 29, ll. 10-14.)
Columbia’s argument is not persuasive or consistent with the full
labeling disclosure in Tsien. Beginning at page 26, Tsien describes reporter
groups on dNTPs and how they can be incorporated into a dNTP. Tsien
states that one “approach employs fluorescent labels. These can be attached
to the dNTP’s via the 3’OH- blocking groups or attached in other positions.”
(Id. at p. 26, ll. 17-19). After describing approaches to label the 3’-OH
blocking group, Tsien goes on to write that “there are a number of
alternatives - particularly the formation of a 3’-blocked dNTP analogue
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containing a label such as a fluorescent group coupled to a remote position
such as the base. This dNTP can be incorporated and the fluorescence
measured and removed according to the methods described below.” (Id. at
p. 27, l. 33 to p. 28, l. 4). In the following paragraph, Tsien describes
attaching a fluorescent label to the base, and states:
This method is included because a number of base moiety
derivatized dNTP analogues have been reported to exhibit
enzymatic competence. Sarfati et al, (1987) demonstrates the
incorporation of biotinylated dATP in nick translations, and
other biotinylated derivatives such as 5-biotin (19)-dUTP
(Calbiochem) are incorporated by polymerases and reverse
transcriptase. Prober et al. (1987) [Prober I] show enzymatic
incorporation of fluorescent ddNTPs by reverse transcriptase
and Sequenase™.
(Id. at p. 28, ll. 10-18.)
This passage, expressly mentions Prober I’s method in its discussion
of base labeling, reasonably suggesting that Tsien considered it suitable for
Tsien’s sequencing method. While subsequently Tsien discloses C-8
position of the nucleotide base as “ideal” for labeling a purine, that
disclosure would not have dissuaded one of ordinary in the art from labeling
at other positions in the base. “[J]ust because better alternatives exist in the
prior art does not mean that an inferior combination is inapt for obviousness
purposes.” In re Mouttet, 686 F3d 1322, 1334 (Fed. Cir. 2012). “A
reference may be said to teach away when a person of ordinary skill, upon
reading the reference, would be discouraged from following the path set out
in the reference, or would be led in a direction divergent from the path that
was taken by the applicant.” In re Gurley, 27 F.3d 551, 553 (Fed. Cir.
1994). For a reference to “teach away” from using a particular approach, it
must be shown that “the line of development flowing from the reference’s
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disclosure is unlikely to be productive of the result sought by the applicant.”
Id. Dr. Trainor, himself, admitted that fluorescently labeled deazapurines
had been used in the prior art (Ex. 2033, Trainor Decl. ¶ 20-21).
In this case, as mentioned above, there is generic disclosure in Tsien
of labeling the base moiety, including a specific reference to Prober I, the
latter describing C-7 deaza-labeled purine bases. Thus, even if labeling at
the C-8 position is superior, Prober I’s method is still reasonably suggested
by Tsien, which characterizes Prober I as showing “enzymatic incorporation
of fluorescent ddNTPs by reverse transcriptase and Sequenase™” (Tsien, p.
2, ll. 6-9; p. 19, ll. 9-18). Thus, those of skill in the art would have found the
use of Prober I’s analogues to be useful, even if nucleotide analogues with a
label on the 8-position of a non-deaza purine might have been better.

Unique labels (No. 3 in Ex. 2033, Trainor Decl. ¶ 79)
In his Declaration, Dr. Trainer testifies that to have arrived at the
claimed nucleotide analogues from Tsien, a person of ordinary skill would
have had to change the identical labels on the pyrimidines to unique labels.
Tsien has express disclosure on using different reporter groups on each
dNTP.
The detected florescence is then correlated to the fluorescence
properties of the four different labels present on the four
different deoxynucleotide triphosphates to identify exactly
which one of the four materials was incorporated at the first
position of the complementary chain. This identity is then
noted.
(Tsien, p. 13, ll. 8-12.)
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Thus, Tsien gives an express reason for using a unique label on
each of the four different dNTPs: to identify what nucleotide is
incorporated into the newly synthesized DNA molecule.

Removable chemical moiety capping the 3'-OH group of the sugar
(No. 2 in Ex. 2033, Trainor Decl. ¶ 79)
In paragraph 87 of his declaration, Dr. Trainor mentions one
difference between Tsien and the claimed nucleotide analogues as having to
“include removable 3’-OH capping groups on the uncapped 3’-OH groups of
the nucleotide analogues.”
Dr. Trainor did not identify where uncapped 3’-OH groups were
found in Tsien. The claims require a removable 3’-OH capping group.
Tsien, as discussed above, also describes capped 3’-OH groups, a fact
acknowledged by Dr. Trainer (Ex. 2033, Trainor Decl. ¶ 28). A blocking
group on the 3’-OH is required to prevent inadvertent multiple additions
(Tsien, p. 12, ll. 27-29).
The nucleotide analogues of Prober I are chain terminating and do not
have an -OH group on the 3’ carbon of the sugar (Prober I, Fig. 2).
However, Tsien was relied upon for the 3’-OH capping group, not Prober I.
Consequently, we find Dr. Trainor’s argument unavailing. Tsien teaches the
nucleotides are added to the 3’-OH of the primer, extending it (Tsien, p. 11,
1-13; No. 5 in Ex. 2033, Trainor Decl. ¶ 79).

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Was there a reason to move the label from the 3’-OH group to the
base? (No. 1 in Ex. 2033, Trainor Decl. ¶ 79)
Columbia contends that there would have been no reason
. . . to change the preferred reversibly terminating 3’OH labeled
nucleotide analogues of Tsien to move the label from the 3’OH
group to the base since introducing modifications at two
positions in a nucleotide analogue would have been understood
by a person of ordinary skill to be more likely to result in a
nucleotide analogue that a polymerase would not incorporate
into a primer extension strand.
(Paper 70, PO Resp. 17). Dr. Trainor testifies that having the label on the
3’-OH group “was to accomplish both labeling and removable capping at a
single position on the nucleotide in a single series of chemical reactions.”
(Trainer Decl. ¶ 70). Dr. Trainor states that there were no reports of
incorporating a nucleotide analogue into a primer, where the analogue had a
removable cap on the 3’-OH group and a label on a base (id.).
As already discussed, Tsien expressly teaches placing the label on the
base, rather than the 3’-OH group. Columbia’s arguments to the contrary
ignore the explicit disclosure by Tsien of base-labeled nucleotides.
Moreover, Columbia’s argument that a nucleotide with a label on the 3’-OH
group is the appropriate starting point is factually incorrect because Tsien
teaches nucleotides with the label on the base and the capping group on the
3’-OH position. Even were there a preference for 3’-OH labeled
nucleotides, this would not detract from the explicit disclosure of base-
labeled nucleotides. Columbia’s argument to the contrary is contradicted, as
shown by the passages from Tsien reproduced below:
As will be explained in more detail below, the fact that the
indication of labeling appears associated with the “nucleoside
base part” of these abbreviations does not imply that this is the
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sole place where labeling can occur. Labeling could occur as
well in other parts of the molecule.
(Tsien, p. 10, ll. 10-15 (emphasis added).)
One simple labeling approach is to incorporate a
radioactive species within the blocking group or in some other
location of the dNTP units.
(Id. at p. 26, ll. 13-14 (emphasis added).)
Another labeling approach employs fluorescent labels.
These can be attached to the dNTP’s via the 3’OH-blocking
groups or attached in other positions.
(Id. at p. 26, ll. 17-19 (emphasis added).)
While the above-described approaches to labeling focus
on incorporating the label into the 3’-hydroxyl blocking group,
there are a number of alternatives - particularly the formation of
a 3’-blocked dNTP analogue containing a label such as a
fluorescent group coupled to a remote position such as the base.
(Id. at p. 27, l. 33 to p. 28, l. 2 (emphasis added).)
One method involves the use of a fluorescent tag attached to the
base moiety.
(Id. at p. 28, ll. 5-6 (emphasis added).)
Columbia attempts to distinguish Prober I because Prober I teaches
chain terminating nucleotides that lack a removable group. But Prober I was
relied upon only for its teaching of how to label a purine base with a
detectable label. Tsien was relied upon for its teaching DNA sequencing
using nucleotides with removable 3’-OH groups.
Dr. Trainor cited several publications for describing on-going efforts
to create modified nucleotides with labels on the 3’-OH (Ex. 2033, Trainor
¶¶ 26-28), said to teach against labeling the nucleotide base. Columbia’s
argument ignores explicit disclosure in Tsien of a base-labeled nucleotide.
The fact that more than one type of nucleotide was being pursued for
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sequencing is not evidence that one approach would have been discouraged
or abandoned over the other. We have not been directed to evidence that
base-labeled nucleotides would have been ignored or seen as an unworkable
alternative for use in sequencing by synthesis methods.
In addition to requiring a reason to have combined the prior art, the
skilled worker must also have had a reasonable expectation of success of
doing so. Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1361 (Fed. Cir. 2007).
Columbia raises the issue of whether there would have been a reasonable
expectation of success that a nucleotide analogue with a label on the base
and a capping group on the 3’-OH would be incorporated into a DNA. A
preponderance of the evidence supports an affirmative answer.
Prober I teaches that base labeled nucleotides can be incorporated into
a newly synthesized DNA strand by appropriate enzymes (Prober I, p. 337,
col. 2; p. 340, col. 1, second paragraph). Dr. Trainor admitted that 3-OH
removably capped nucleotides had been used in DNA sequencing methods
(Ex. 2033, Trainor Decl. ¶¶ 26-28). Dr. Trainor cites several publications in
support of unpredictability, but did not sufficiently explain the pertinence of
these publications.
Dr. Trainor cites page 4263 of Metzker9 (Ex. 2033, Trainor Decl.
¶ 106). On page 4263, Metzker describes testing 3’-OH modified
terminators for their ability to be substrates for polymerases. As shown in
Table 2 of Metzker, terminators had different activities when tested against
various polymerases. However, the publication shows the routineness of

9 Michael L. Metzker et al., Termination of DNA synthesis by novel 3’-
modified-deoxyribonucleoside 5’-triphoshpates, 22 NUCLEIC ACIDS RES.
4259-4267 (1994), Exhibit 2015.
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testing for activity. Dr. Trainor did not explain how these results with
different nucleotides than those which are claimed make it unpredictable that
two structures (3-OH cap and base-label) which are known to work with
polymerase would not work when combined in the same nucleotide
molecule. In fact, the publication shows the routineness of testing for the
ability of an analogue to be incorporated into DNA by a polymerase.
Dr. Trainor also cites page 3 of Canard and Sarfati (1994),10 but
without explaining its significance (Ex. 2033, Trainor Decl. ¶ 106). The
abstract of the paper describes synthesizing nucleotide analogs which “acted
as substrates with several DNA polymerases leading to chain termination.”
Page 3 appears to describe some differences in the effectiveness of the
synthesized nucleotides with the different polymerases, but Dr. Trainor did
not point to any specific instance or what relevance it had to unpredictability
in view of the success pointed out in the abstract.
Finally, Dr. Trainor contrasts these publications with page 200 of
Welch and Burgess (1999) (Ex. 2033, Trainor Decl. ¶ 106). According to
Dr. Trainor, Welsh showed that preliminary tests of compounds 1a and 1b as
polymerase substrates did not show evidence of incorporation (id. at ¶ 31).
However, Dr. Trainor did not explain the pertinence of these compounds and
their underlying chemistry to a nucleotide having a labeled deaza-purine and
a removable 3’-OH group.
In sum, the preponderance of the evidence establishes that there was a
reasonable expectation of success and Columbia has not directed us to

10 Bruno Canard et al., DNA polymerase fluorescent substrates with
reversible 3’-tags, 148 GENE 1-6 (1994), Exhibit 2030.
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sufficient evidence to establish that it was unpredictable to have used the
claimed nucleotide analogue as a polymerase substrate for DNA sequencing.

Was there a basis for reasonably expecting that a nucleotide with a
removable 3’-OH group and a label attached to the base could be
made?
Columbia contends that neither Tsien nor Prober I disclose any
chemistry relevant to making a nucleotide analogue with the claimed
features, requiring a person of ordinary skill “to design new chemical
procedures to attempt to address the differences between the nucleotide
analogues described by Tsien and the nucleotide analogue recited in the
claim.” (Paper 70, PO Resp. 18-19), Furthermore, Dr. Trainor testifies that
Prober I’s nucleotides cannot be modified to include a removable 3’-OH
group (Ex. 2033, Trainor Decl. ¶¶ 98-99). Dr. Trainor concludes that new
chemical procedures would have been needed, the development of which
were complex and fraught with difficulties (id. at ¶ 101).
This argument is not persuasive. First, the patentability challenge is
not based on converting Prober I’s nucleotide into the claimed nucleotide
analogue. Rather, the analysis begins with Tsien, who describes nucleotides
with a base-label and 3’-OH removable blocking group. Secondly, a
preponderance of evidence establishes a reasonable expectation of success as
addressed above.
VI. TSIEN AND SEELA I
We instituted inter partes review of claim 6 on the grounds that the
Columbia claims would have been obvious under 35 U.S.C. § 103 in view of
Tsien and Seela I. Columbia in their response under § 41.120 states the
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claim is patentable for the same reasons discussed in the section on Tsien
and Prober I (Paper 70, p. 22).

VII. SECONDARY CONSIDERATIONS
The question of obviousness is resolved on the basis of underlying
factual determinations including: (1) the scope and content of the prior art;
(2) the level of ordinary skill in the art; (3) the differences between the
claimed invention and the prior art; and (4) secondary considerations of
nonobviousness, if any. Graham v. John Deere Co. of Kansas City, 383
U.S. 1, 17 (1966). Secondary considerations are “not just a cumulative or
confirmatory part of the obviousness calculus but constitute[] independent
evidence of nonobviousness . . . [and] enables the court to avert the trap of
hindsight.” Leo Pharm. Prods., Ltd. v. Rea, 726 F.3d 1346 (Fed. Cir. 2013)
(internal quotations and citation omitted). “[E]vidence of secondary
considerations may often be the most probative and cogent evidence in the
record. It may often establish that an invention appearing to have been
obvious in light of the prior art was not.” Stratoflex, Inc. v. Aeroquip Corp.,
713 F.2d 1530, 1538 (Fed. Cir. 1983). “This objective evidence must be
‘considered as part of all the evidence, not just when the decisionmaker
remains in doubt after reviewing the art.’ Id. at 1538-39.” Transocean
Offshore Deepwater Drilling, Inc. v. Maersk Drilling USA, Inc., 699 F.3d
1340, 1349 (Fed. Cir. 2012) (citing Stratoflex, 713 F.2d 1538-39).
Columbia contends that Illumina’s obviousness challenges fail
because objective evidence shows: 1) the claimed invention has yielded
unexpectedly improved properties and results not present in the prior art;
(2) the claimed invention has received praise and awards; (3) the claimed
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invention is responsible for Illumina’s commercial success; (4) Illumina
copied the claimed nucleotide analogues; (5) others in the art were skeptical
that the claimed nucleotide analogues and methods would be successful; and
(6) Illumina attempted to license the challenged patents (Paper 70, p. 24).
We have considered this evidence, but do not find it persuasive.

A. “unexpectedly improved properties”
Relying on data in Ju’s 2006 publication11 in which sequencing of a
20 nucleotide template was accomplished using “four nucleotide analogues,
each having both a unique detectable label attached through a chemically
cleavable linker to the base (two pyrimidines and two deazapurines), and a
chemically cleavable chemical group capping the 3’-OH group of the sugar,”
Dr. Trainor testified that the properties of the claimed nucleotide analogues
“have revolutionized the DNA sequencing industry.” (Ex. 2033, Trainor
Decl. ¶¶ 191-92). Specifically, Dr. Trainor testified that Ju’s results show
that the sequencing with the claimed nucleotide analogues are unexpectedly
better than pyrosequencing by facilitating clear identification of all 20
nucleotides in the DNA template while pyrosequencing did not (id. ¶¶ 193-
196). Dr. Trainor testified that this “accurate identification was made
possible by the fact that Dr. Ju’s nucleotide analogues separated the
cleavable chemical group at the 3’-OH position of the sugar from the
detectable label, which was placed instead on the base” (id. ¶ 195). Dr.

11 Jingyue Ju et al., Four-color DNA sequencing by synthesis using cleavable
fluorescent nucleotide reversible terminators, 103 PROC. NAT’L ACAD. SCI.
19635-19640 (2006), Exhibit 2034. The Ju publication is said to correspond
to the claimed invention with respect to the nucleotides and methods.

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Trainor further cited additional publications said to have reported similar
successes (id. ¶¶ 198-199).
Ju 2006 reported DNA sequencing in which “four nucleotides (A, C,
G, T) are modified as reversible terminators by attaching a cleavable
fluorophore to the base and capping the 3’-OH group with a small
chemically reversible moiety so that they are still recognized by DNA
polymerase as substrates.” (Ju, p. 19635 (Exhibit 2034).) Dr. Trainor
attributes Ju’s success to this configuration, i.e., the label on the base and the
3-OH removable cap, but not to the deaza substitution. (Trainor Decl. ¶¶
192 and 195). Claims 1 and 6 of the ’575 Patent are drawn to methods
which have a nucleotide with the removable capping group and the
fluorophore label on the base, but do not require that the label be cleavable.
Thus, the evidence is not commensurate with the full scope of the claims.
While there is no working example in Tsien of a nucleotide with the
claimed features, as explained above, Tsien suggests attaching a label to the
base moiety and utilizing a cleavable tether to release the label before the
next successive nucleotide is added (Tsien, p. 28, ll. 5-25). Tsien’s method
also requires removable 3’-OH groups in its sequencing (id. at p. 21, ll. 9-12;
p. 23, ll. 28-32). In considering the weight of the evidence militating in
favor of the “unexpectedly improved properties” over pyrosequencing, we
must take into account that a single reference describes both features, i.e.,
attachment of a label to the base and a cleavable linker as the attachment
means. This implicates the legal principles enunciated in In re Baxter
Travenol Labs., 952 F.2d 388, 392 (Fed. Cir. 1991).
In Baxter, the applicant had argued that the claimed plasticized blood
donor bag comprised of DEHP had unexpected properties in suppressing
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hemolysis of red blood cells stored inside it. Id. at 389. The court found
that such evidence did not rebut prima facie obviousness because the prior
art disclosed a DEHP-plasticized donor bag, and therefore, Baxter’s blood
bag had the same hemolytic-suppressing function as the prior art – albeit
unappreciated at the time of the invention. Id. at 391. The court concluded
that “[m]ere recognition of latent properties in the prior art does not render
nonobvious an otherwise known invention.” Id. at 392. Likewise, Tsien has
a written description of a nucleotide with the features relied upon by
Columbia as possessing unexpected properties. Thus, it could be said that
the finding that a nucleotide analogue with the 3’-OH and label on the base
is better than pyrosequencing, is merely recognizing an advantage of a
nucleotide described by Tsien. The description is not anticipatory to claim 6
because the claim further requires a deazapurine base. However, the
deazapurine is not said by Columbia to be responsible for the unexpected
result.
Dr. Trainor also testified that an “unexpected benefit” associated with
the claimed nucleotide analogues was identified by Illumina’s expert
Dr. Weinstock (Ex. 2033, Trainor Decl. ¶ 201). According to Dr. Trainor,
Dr. Weinstock stated during his deposition that “nucleotide analogues
having a label on the base have the beneficial property of being useable in
sequencing methods that require repetitive incorporation of nucleotide
analogues, in particularly dGTPs, to sequence DNA having G:C rich
regions.” (Id.) Dr. Trainor stated that he “was surprised to learn that
nucleotide analogues having a label on the base have solved the problem of
sequencing G:C rich regions.” (Id. at ¶ 202.) This testimony is not
persuasive.
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Dr. Weinstock, in his deposition, specifically stated that Prober I had
used “2’-deoxy-7-deazaguanosine triphosphates . . . in place of dGT to
minimize” the effects of secondary structure when sequencing GC-rich
regions. (Weinstock Tr. 141:5-18; 145:10-22.) Dr. Weinstock also testified
that GC-rich regions “had a tendency to form secondary structures that were
difficult for a DNA polymerase to get through during a DNA synthesis
reaction and that the addition of deazabases to the end of the primer may
have some benefit” in sequencing (id. at 147:8-13; see also 148:24 to 150:5).
Based on this deposition testimony, it is evident that Dr. Weinstock believed
that the problem of sequencing in GC-rich areas had already been addressed
by Prober I in their use of the deazaguanosine, inconsistent with Dr.
Trainor’s testimony that the problem was solved using analogues with a
label on the base. Indeed, Dr. Weinstock’s testimony is supported by Prober
I, which taught that 2’-deoxy-7-guanosine triphosphates had been used to
minimize secondary structure in sequencing (Prober I, p. 341, ll. 14-20).
In response to questioning about the effect of a labeled deazabase, Dr.
Weinstock added that “if a small change of substituting a carbon for a
nitrogen has a benefit on reducing secondary structure in GC-rich regions,
sticking anything larger than that at that position is likely to have an even
bigger benefit.” (Weinstock Tr. 151:13-21.) We understand Dr. Weinstock
to be saying that further attaching a label to the deazapurine base would have
been expected (“is likely”) to have “an even bigger benefit” than the
deazapurine alone, which is inconsistent with Dr. Trainor’s statement of
unexpected benefit of the deazapurine labeled base.
A showing of “new and unexpected results” must be “relative to the
prior art.” Iron Grip Barbell Co., Inc. v. USA Sports, Inc., 392 F.3d 1317,
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1322 (Fed. Cir. 2004). To establish unexpected results, the claimed subject
matter must be compared with the closest prior art. Baxter, 952 F.2d at 392.
In this case, Patent Owner’s comparison was performed with
pyrosequencing, but pyrosequencing is not the closest prior art. Rather,
closer prior art is described in Tsien of a nucleotide with a label and
removable group on the 3’-OH group. Patent Owner thus did not perform a
comparison with the closest prior art.

B. Commercial success
Illumina sells products used in sequencing by synthesis (SBS), the
same type of sequencing described in the Tsien and Dower publications.
Columbia introduced evidence that Illumina’s SBS products included
nucleotide analogues with a removable chemical moiety capping 3’-OH
group and a label on the base and that these features were “crucial to the
commercial success” of Illumina’s SBS products (Ex. 2033, Trainor Decl. ¶¶
213-214). A nucleotide analogue with the latter two features is embodied by
claim 6 of the ’575 patent. These Illumina products are also the subject of a
patent infringement action by Columbia against Illumina (Paper 70, PO
Resp. 34).
Commercial success involves establishing success in the marketplace
of a product encompassed by the claims and a nexus between the
commercial product and the claimed invention. “Evidence of commercial
success, or other secondary considerations, is only significant if there is a
nexus between the claimed invention and the commercial success.” Ormco
Corp. v. Align Tech. Inc., 463 F3d 1299, 1311-12 (Fed. Cir. 2006). “For
objective evidence to be accorded substantial weight, its proponent must
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establish a nexus between the evidence and the merits of the claimed
invention.” In re GPAC Inc., 57 F.3d 1573, 1580 (Fed. Cir. 1995). “While
objective evidence of nonobviousness lacks a nexus if it exclusively relates
to a feature that was ‘known in the prior art,’ Ormco Corp. v. Align Tech.,
Inc., 463 F.3d 1299, 1312 (Fed. Cir. 2006), the obviousness inquiry centers
on whether ‘the claimed invention, as a whole,’ would have been obvious,
35 U.S.C. § 103.” Rambus Inc. v. Rea, 731 F.3d. 1248, 1257-58 (Fed. Cir.
2013).
With regard to whether a nexus has been established between
the products upon which commercial success has been based and the
claimed invention, Dr. Trainor testified that he reviewed Illumina’s
technical documents and that each of the nucleotide analogues “has a
cleavably-linked label on the nucleotide base, namely a fluorescent
dye molecule.” (Ex. 2033, Trainer Decl., ¶ 219-222.) Dr. Trainor
also testified these commercial nucleotide analogs have a removable
chemical moiety capping the 3’-OH group of the nucleotide sugar (id.
at ¶ 223-227). Dr. Trainor reproduced a nucleotide which appears to
be a C-substituted guanine at position 7 as it would be for
deazapurine, although Dr. Trainer did not provide specific testimony
in support (id. at ¶ 224). To the extent the nucleotides used by
Illumina are not deazapurines, a nexus is not established because
claim 6 requires a deazapurine base.
As evidence that these features are responsible for the success of the
commercial products, Dr. Trainor cited a February 17, 2006 email from Dr.
Colin Barnes – a scientist at the predecessor company to Illumina – written
to two other scientists at the same company. In the email, Dr. Barnes stated:
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“Our original concept of having a very small 3’-block and leaving the fluor
on the base is the reason our SBS works so well.” (Ex. 2033, Trainor Decl.
¶ 231). Dr. Barnes’s email was written in 2006 at the time Mr. Sims12 stated
Illumina entered the SBS sequencing market with its nucleotide analogues
having removable 3’OH groups and cleavable labels on the nucleotide base
(Ex. 2091, Sims Decl. ¶ 14). Dr. Trainor also cited a Deposition from Dr.
Xiaohai Liu, Illumina’s Director of SBS Sequencing Chemistry Research,
who testified that he agrees with Dr. Barnes assessment, stating it “is part of
a jigsaw.” (Ex. 2033, Trainor Decl. ¶ 232-233; Ex. 2049, Liu Tr. 202:17-
21.).
As held in J.T. Eaton & Co., Inc. v. Atlantic Paste & Glue Co., 106
F.3d 1563, 1571 (Fed. Cir. 1997), “the asserted commercial success of the
product must be due to the merits of the claimed invention beyond what was
readily available in the prior art.”
In this case, Dr. Trainor testified that “a nucleotide analogue
combining all the features arranged as in Columbia patent claims – [1] a
cleavable chemical group capping the 3’-OH position of the sugar and [2] a
label attached to the nucleotide base via a cleavable linker” were responsible
for the nucleotides success. (Ex. 2033, Trainor Decl. ¶¶ 190, 214, and 217).
Dr. Barnes also attributed the success to these features. Illumina marketed
its SBS products as having the cleavable label and removable 3’-OH group
(“using a proprietary reversible terminator-based method that enables

12 Exhibit 2091 is the declaration of Raymond Sims which was provided by
Columbia to establish commercial success of Illumina’s products said to
embody the claimed subject matter. Based on Mr. Sims’s education and
experience, we find him qualified to give opinions on financial data, the
topic of his declaration.

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detection of single bases as they are incorporated into growing DNA strands.
A fluorescently-labeled terminator is imaged as each dNTP is added and
then cleaved to allow incorporation of the next base”), the same features
embodied in claim 6. Both these features, however, are described in Tsien,
making them known and “readily available in the prior art.” The record
indicates, therefore, that the success did not stem from the merits of the
claimed invention. Neither Columbia in their response under § 42.120
(Paper 70, PO Resp.) or in Trainor’s Declaration described any other feature
of the invention as a whole that should be considered when evaluating
commercial success. Rambus, 731 F.3d at 1257-1258.
In addition to this, Columbia argues that the success is due to a label
attached to the base by a cleavable linker. However, the claim 6 does not
require a cleavable linker in this position. Commercial success cannot be
established by relying on an unclaimed feature. Ormco Corp., 463 F.3d at
1312.
As discussed above, Tsien’s nucleotides have a cleavable chemical
group capping the 3’-OH position of the sugar in order to prevent
inadvertent additions during the sequencing by synthesis method. A
detectable label is described by Tsien on either the 3’-OH position or on the
nucleotide base, and thus a nucleotide with label on the nucleotide base is
one of two choices. The features said by Dr. Barnes, Dr. Liu, and Illumina
to have been responsible for the commercial success of Illumina’s product
are thus described and “readily available” in Tsien. Indeed, Tsien’s Figure 2
shows four unique labeled nucleotides, each with a removable 3’-OH
blocking group and label depicted on the nucleotide base (“As will be
explained in more detail below, the fact that the indication of labeling
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appears associated with the “nucleoside base part” of these abbreviations
does not imply that this is the sole place where labeling can occur.” (Tsien,
p. 10, ll. 10-14.)

C. Evidence of attempted licensing
Licensing of a patented technology can be evidence of
nonobviousness because it can indicate the licensor recognizes the merits of
the invention by licensing it. Stratoflex, 713 F.2d at 1539.
In this case, Columbia provided evidence that Illumina sought to
license the technology developed by Dr. Ju (Paper 70, PO Resp. 34-38).
Columbia states that it elected to license the technology to another company,
not Illumina (id. at p. 37). Subsequently, Columbia states that Illumina had
discussions about acquiring the company which gained a license to Ju’s
technology (id.). Columbia states that Illumina tried to acquire the licensed
technology just prior to Columbia suing Illumina for patent infringement
(id). Illumina did not challenge Columbia’s description of its attempt to
license the technology in their response to Columbia’s § 41.120 filing. The
only response was in their motion to exclude the evidence of attempted
licensing as either hearsay or on relevance.
Columbia has direct knowledge of Illumina’s licensing attempts
(Paper 70, PO Resp. 34-38). While Illumina never licensed the technology,
Columbia argued that this was because Columbia had licensed to another
company. Nonetheless, based on statements by Illumina’s witness Dr.
Barnes and their own marketing literature, the invention recognized by
Illumina as having merit is one which is described in Tsien with the
removable 3-‘OH capping group and base label. There is insufficient
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evidence that Illumina’s licensing strategy was driven by recognition of the
merits of the claimed invention, rather than knowledge of a patent
potentially covering their own product.

D. Praise and skepticism
We have considered Columbia’s evidence of praise and skepticism,
but find it of insufficient weight and relevance to deem it persuasive as to
the merits of the claimed invention particularly when we consider it within
the totality of the evidence before us.

E. Summary
After considering the evidence of record, including the secondary
considerations, we are persuaded that a preponderance of the evidence
supports Illumina’s contention that claim 6 is unpatentable over the
combination of I) Tsien and Prober I; and II) Tsien and Seela I.

MOTIONS
VIII. COLUMBIA’S MOTION TO AMEND
A motion to amend the claims under 37 CF.R. § 42.121 was filed by
Columbia on June 25, 2013 (Paper 56). In the motion, Columbia proposed
cancelling claims 1-6 and replacing them with claims 7-11 (id. at 4).
Proposed claim 7 is identical to original claim 6, rewritten in independent
form and reciting all of the features of original claim 1. Proposed claims 8-
11 are identical to original claims 2-5, respectively, except that they depend
directly or indirectly from proposed claim 7 and therefore also incorporate
the feature of original claim 6.
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Claim 7 is drawn to the identical subject matter as claim 6. Since
claim 6 is already under inter partes review, it is unclear why claim 7 is
necessary or how it is a response to a ground of unpatentability under
37 C.F.R. § 42.121(a)(2)(i). It is merely duplicative to a claim already under
inter partes review.
In any event, all the claims proposed in the Columbia amendment are
of the same scope as claims already before us in this review and which have
been determined to be unpatentable. In the opposition to the motion,
Illumina contends that Columbia’s motion is defective (Paper 74, p. 1). We
need not and do not reach Illumina’s contention however since the claims,
even as Columbia proposes to amend them, are unpatentable.

IX. COLUMBIA’S MOTION TO EXCLUDE
A motion to exclude evidence under 37 C.F.R. § 42.64 was filed by
Columbia on November 12, 2013 (Paper 93).
A. Columbia seeks to exclude Exhibits 1029-1033 which were said to
have been introduced for the first time at the deposition of Illumina’s expert,
Dr. Weinstock, during redirect examination by Illumina’s counsel (Paper 93,
p. 1). As we do not rely on this portion of Dr. Weinstock’s testimony or the
exhibits cited in it, we dismiss this part of the motion as moot.
B. Columbia seeks to exclude Exhibits 1041-1049 which were
introduced at Dr. Trainor’s deposition (Paper 93, p. 4).
Exhibits 1041-1048 were introduced by Illumina for the purpose of
impeaching Dr. Trainor’s opinions in his Declaration regarding the non-
obviousness of the claimed subject matter (Ex. 2094, Trainor Tr. 277: 21 to
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278: 6). Columbia contends that these references were belatedly introduced
so that they could be cited in Illumina’s Reply and in Exhibit 1053
(Declaration of Kevin Burgess, Ph.D. in order to make out Illumina’s prima
facie case, in violation of the Trial Practice Guide. (77 Fed. Reg. at 48,767.)”
(Paper 93, p. 6). Exhibit 1049 is a declaration from an IPR to which
Columbia is not a party, previously introduced as Ex. 1024, which was
previously expunged by the Board as improperly filed (Paper No. 46.)
We have determined there was a reason to have made the claimed
nucleotide analogues based on the combination of Tsien and Prober I
without relying on Exhibits 1041-1049. Thus, we dismiss this part of the
motion as moot.
C. Columbia seeks to exclude Exhibits 1050-1054 (Paper 93, p. 7).
Exhibits 1050, 1051, 1052, and 1054 are said by Columbia to belatedly
raised new issues and evidence to make out its prima facie case (id.).
Exhibit 1053 is a Declaration of Kevin Burgess filed by Illumina and cited
for the first time in their reply (Paper 76, p. 2) to Columbia’s response under
§ 42.120 (Paper 70).
We determine that the Columbia claims are unpatentable without
relying on Exhibits 1050-1054 and thus we dismiss this portion the motion
as moot as well.

X. ILLUMINA’S MOTION TO EXCLUDE
A motion to exclude evidence was filed by Illumina on November 12,
2013 (Paper 90). This evidence goes to the secondary considerations that
were argued by Columbia in their response to the petition under § 42.120.
As we conclude that the Columbia claims are unpatentable even if we
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consider this evidence, we need not and do not decide this motion and
dismiss it as moot.

XI. ORDER
In consideration of the foregoing, it is
ORDERED that claims 1-3 and 6 of U.S. Patent 8,088,575 B2 are
cancelled;
FURTHER ORDERED that Columbia’s motion to amend claims is
dismissed as moot;
FURTHER ORDERED that Columbia’s motion to exclude evidence
is dismissed as moot; and
FURTHER ORDERED that Illumina’s motion to exclude evidence is
dismissed as moot.

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Petitioner:

James Borchardt
and
James Morrow
Reinhart Boerner Van Deuren s.c.
ipadmin@reinhartlaw.com

Patent Owner:

John P. White
Cooper & Dunham LLP
jwhite@cooperdunham.com

and

Anthony M. Zupcic
Fitzpatrick, Cella, Harper & Scinto
ColumbiaIPR@fchs.com