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`EXHIBIT 2002
`
`EXHIBIT 2002
`
`
`
`Trials@uspto.gov
`572-272-7822
`
`
`
`
`
`
`Paper 43
` Mailed: May 10, 2013
`
`
`
`
`
`
`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 IPR2012-00006
`U.S. Patent 7,713,698
`___________
`
`
`
`Before SALLY G. LANE, RICHARD M. LEBOVITZ, and DEBORAH
`KATZ, Administrative Patent Judges.
`
`LEBOVITZ, Administrative Patent Judge.
`
`
`
`DECISION ON REQUEST FOR REHEARING UNDER 37 C.F.R.
`§ 41.71(c) OF DECISION TO INSTITUTE INTER PARTES REVIEW
`& SCHEDULING ORDER
`
`
`
`
`
`
`
`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`
`I. REHEARING REQUEST
`
`
`
`Illumina requests rehearing of the decision under 35 U.S.C.
`
`§ 311 (“the ‘698 Decision”) (Paper 28) denying inter partes review of claims
`
`15 and 16 of US 7,713,698 (“the ‘698 patent”) based on Tsien and Dower as
`
`anticipatory publications (Illumina Request for Reconsideration under 37
`
`C.F.R. 42.71(c), dated March 26, 2013 (“Illumina Req. Reh’g.”; Paper 30))
`
`Under 37 C.F.R. § 42.71(c), “[w]hen rehearing a decision on petition,
`
`a panel will review the decision for an abuse of discretion.” An abuse of
`
`discretion occurs when a “decision was based on an erroneous conclusion of
`
`law or clearly erroneous factual findings, or . . . a clear error of judgment.”
`
`PPG Indus. Inc. v. Celanese Polymer Specialties Co. Inc., 840 F.2d 1565,
`
`1567 (Fed. Cir. 1988). See also 37 C.F.R. § 42.71(d) (“The request must
`
`specifically identify all matters the party believes the Board misapprehended
`
`or overlooked”).
`
`
`
`I.A. THE BOARD ERRED IN NOT AUTHORIZING INTER PARTES
`
`REVIEW OF CLAIMS 1 AND 11 BASED ON TSIEN & DOWER
`
`(ILLUMINA REQ. REH’G 3)
`
`
`
`Nucleotides comprise a sugar, phosphate, and nitrogen base (‘698
`
`patent, Fig. 7). Claim 1 is drawn to nucleic acid sequencing method
`
`comprising employing at least one nucleotide which comprises a
`
`deazapurine as the nitrogen base. Claim 11 is drawn to a primer hybridized
`
`to a nucleic acid template, where at least one of the nucleotides in the primer
`
`comprises a deazapurine as a base. Neither Tsien nor Dower is said by
`
`Illumina to expressly describe a deazapurine base in their written
`
`disclosures. Rather, Illumina contends the nucleotides are present by virtue
`
`
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`2
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`of the incorporation by reference to the Prober I publication by Tsien and
`
`Dower. Dower is said to disclose nucleotides with deazapurine bases
`
`(Petition 26 & 39-40). The issue addressed in the ‘698 Decision with
`
`respect to these rejections was whether Illumina met its burden in
`
`establishing whether Prober I is incorporated into the host document in a
`
`manner that complies with the requirement of 35 U.S.C. § 102 (‘698
`
`Decision 10-11).
`
`
`
`“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. Illumina
`
`contends that we erred by not using “the person of reasonable skill in the
`
`art” standard to evaluate whether Tsien (Exhibit 1002) and Dower (Exhibit
`
`1005) incorporated Prober I’s (Exhibit 1003) disclosure of a 7-deazapurine
`
`base (Illumina Req. Reh’g 4). Specifically, Illumina contends that we “used
`
`a heightened standard that would require recitation of the exact word
`
`‘deazapurine’ (or at least ‘deaza-substituted’) as used in claims 1 and 11”
`
`(id.). To support their argument, Illumina points to declarations by Dr.
`
`Weinstock and Dr. Blanchaud (id. at 5).
`
`
`
`I.A.1. Dower and Prober I
`
`We agree with Illumina that we erred in not instituting inter partes
`
`review of claims 1 and 11 based on Dower as an anticipatory publication.
`
`
`
`3
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`
`
`On page 12 of the ‘698 Decision, we reproduced the following
`
`passage of Dower which referred to Prober I:
`
`(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.
`
`Dower, col. 25, ll. 41-47.
`
`
`
`On pages 33 and 34-35 of the Petition, Illumina referred to the
`
`following additional disclosure:
`
`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
`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.).
`
`Dower, col. 25, ll. 4-10.
`
`
`
`It is evident from the above quoted disclosure from Dower that Dower
`
`is referencing Prober I for all its dNTP analogues, at least one of which is a
`
`deazapurine. For example, Dower, at column 23, lines 18-24 and column
`
`25, lines 41-47, refers to Prober I’s disclosure of nucleotide analogs (dNTP
`
`and dideoxynucleotide triphosphate) in DNA sequencing.
`
`
`
`4
`
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`
`To support the position that such disclosure is an adequate
`
`incorporation by reference for the purpose of anticipation, Illumina cites
`
`Callaway Golf Co. v. Acushnet Co., 576 F.3d 1331 (Fed. Cir. 2009)
`
`(Illumina Req. Reh’g 8-9, 10, and 12). Illumina contends that Callaway
`
`holds that “reference to a general class of compositions discussed in prior
`
`art is sufficient to incorporate a specific composition by reference.
`
`Callaway, 576 F.3d at 1346-47 (holding reference to a ‘foamable polymeric
`
`composition’ sufficient to specifically incorporate polyurethane as the
`
`foamable composition)” (id. at 10-11). We agree that the holding in
`
`Callaway is relevant in the circumstances before us.
`
`
`
`In Calloway, the Federal Circuit wrote:
`
`Nesbitt [the cited anticipatory publication] states broadly that
`the layers of the golf ball disclosed therein may be made from a
`“natural or synthetic polymeric material.” [U.S. Patent No.
`4,431,193 ] col. 3 ll. 53-54. Nesbitt goes on to directly indicate
`that such materials include all of the foamable polymeric
`materials described in Molitor [U.S. Patent No. 4,274,637]:
`“Reference is made to [Molitor ″637] which describes a number
`of foamable compositions of a character which may be
`employed for one or both layers … for the golf ball of this
`invention.” Id. col.3 ll. 56–61 (emphasis added). Polyurethane
`is a foamable composition. Nesbitt incorporates the entire list
`of foamable compounds (“a number of foamable
`compositions”) disclosed by Molitor ″637 as appropriate
`materials for use in golf ball cover layers, including
`polyurethane and mixtures of ionomer resins.
`
`Callaway, 576 F.3d at 1347-48.
`
`
`
`Dower incorporates all the nucleotide analogues from Prober I, which
`
`includes an analogue comprising a deazapurine base. Consistent with
`
`Callaway, the incorporation by reference to Prober I in Dower is therefore
`
`sufficient to establish that Dower describes within its four corners a method
`
`
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`5
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`Case IPR2012-00006
`U.S. Patent 7,713,698
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`of using a nucleotide comprising a deazapurine base as required by claims 1
`
`and 11.
`
`
`
`Columbia in their opposition to Illumina’s Rehearing Request argues
`
`that Dower refers to Prober I six times, “but not once uses the words
`
`‘incorporated herein by reference’ whereas Dower refers to other specific
`
`references seventeen times using the words ‘incorporated herein by
`
`reference.” (Columbia’s Opposition 2, dated April 26, 2013; Paper 37.)
`
`Columbia has not cited any legal authority that the words “incorporated
`
`herein by reference” are necessary to incorporate Prober I’s disclosure into
`
`Dower. Rather, we find that Dower’s reference to Prober I for dNTP
`
`analogs in DNA sequencing is sufficient for a person of reasonable skill in
`
`the art to have recognized that Prober I is incorporated for this teaching.
`
`
`
`Columbia also notes that the Board relied upon the disclosure at
`
`column 25, lines 41-47 of Dower in the ‘698 Decision, but that this passage
`
`was not cited by Illumina in their petition (Columbia Opposition 3). We
`
`acknowledge this fact to be true, but the disclosure appears on the same
`
`column 25 (at lines 4-10 and lines 35-37) cited by Illumina in their petition
`
`(Petition 35, 37, 39, and 41), and thus our attention was clearly drawn to
`
`column 25 for its pertinence. In addition, the passage at column 25, lines 4-
`
`10 expressly cited by Illumina refers to “[f]luorescent chain terminators”
`
`and the passage at column 25, lines 41-47 appears in the section titled
`
`“There are several suitable labeled, terminator structures as follows.”
`
`Thus it was reasonable to consider the disclosure at column 25, lines 41-47
`
`based on the passage expressly cited by Illumina in their petition.
`
`
`
`Columbia further argues that even if Dower had incorporated by
`
`reference the deazapurines disclosed in Prober I, the ‘698 Decision “that
`
`
`
`6
`
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`Case IPR2012-00006
`U.S. Patent 7,713,698
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`Dower did not anticipate the claims at issue would still be correct. The
`
`deaza-substituted dideoxynucleotides of Prober I do not contain a removable
`
`chemical moiety capping the 3’-OH group of the sugar as required by the
`
`claims.” (Columbia Opposition 5, n.4).
`
`
`
`Illumina in their petition points to specific passages of Dower which
`
`describe modified analogs which “should” be blocked at the 3’-end of
`
`elongation (Petition 35). Columbia has not identified a defect in this specific
`
`disclosure which teaches utilizing 3’-blocked analogs in DNA sequencing,
`
`and we find none.
`
`For the foregoing reasons, we authorize an inter partes review of
`
`claims 1 and 11 instituted with respect to Illumina’s patentability challenge
`
`based on Dower.
`
`
`
`Claims 2-7, 11, 12, 14, 15, and 17
`
`With respect to dependent claim 2-7, 11, 12, 14, 15, and 17, Illumina
`
`identified specific disclosure in Dower where each limitation is found
`
`(Petition 35-39). We find Illumina’s factual assertions to be supported, and
`
`authorize an inter partes review of claims 2-7, 11, 12, 14, 15, and 17 to be
`
`instituted with respect to Illumina’s patentability challenge based on Dower
`
`as an anticipatory publication.
`
`
`
`
`
`I.A.2. Tsien & Prober I
`
`Contrary to Illumina’s contention, the ‘698 Decision did not ignore
`
`how a person of reasonable skill in the art would have viewed Tsien’s
`
`incorporation by reference to Prober I. The only evidence of how such a
`
`
`
`7
`
`
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`person would have understood the reference to Prober I in Tsien was the
`
`declaration of Dr. George Weinstock.
`
`Dr. Weinstock stated in his declaration (Exhibit 1021):
`
`In discussing sequencing by synthesis methods utilizing a
`dNTP in which the fluorescent label group is coupled to the
`base of the dNTP, Tsien references the disclosure of Prober I,
`Science 238, 336-341 (1987) for its teaching of preparing
`nucleotides with fluorescent tags that can be successfully
`incorporated by Tsien’s preferred polymerase. See Tsien et al.,
`page 5, lines 22- 23, page 19, lines 4-18; and page 28, lines 5-
`18. Tsien also states that Prober I, and the other references
`discuss in Tsien, are referenced “for their teaching of synthetic
`methods, coupling and detection methodologies, and the like.”
`Tsien, p. 3, ll. 11-16 and p. 5, ll. 22-23.
`
`(Weinstock Decl. ¶ 63.)
`
`Based on the cited disclosure in Tsien, Dr. Weinstock concluded that
`
`he understood “Tsien to incorporate the teachings of Prober I for its
`
`teachings regarding of fluorescent label attachment, and in particular,
`
`regarding its teaching regarding attachment of a linker to the 7 position in
`
`the 7-deazapurine” (id. at ¶ 63).
`
`The ‘698 Decision did not find Dr. Weinstock’s testimony persuasive
`
`because “Dr. Weinstock did not provide a factual basis for his testimony as
`
`to why this teaching would have been recognized by one of ordinary skill in
`
`the art.” (‘698 Decision 13.) In particular, it was noted in the Decision that
`
`“Illumina provided testimony by Dr. George Weinstock that Prober I is
`
`incorporated by Tsien for ‘its teaching regarding attachment of a linker to
`
`the 7 position in the 7-deazapurine,’ but these words do not appear in Tsien.
`
`Weinstock Decl. ¶ 63.” (Id. at 13.) Dr. Weinstock’s testimony was
`
`determined to be inadequate to make up for this deficiency.
`
`
`
`8
`
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`
`Tsien does not indicate that Prober I is being referenced for its
`
`teaching of a deazapurine nucleotide. Tsien refers to Prober I for its
`
`teaching that fluorescent ddNTPs can be incorporated by two different
`
`enzymes, but did not identify the fluorescent ddNTPs as comprising a
`
`deazapurine base as recited in claims 1 and 11 (‘698 Decision 11-12). Dr.
`
`Weinstock’s testimony did not bridge the gap. Thus, while the Decision
`
`addressed Tsien’s failure to specifically identify the deazapurines in Prober
`
`I, the Decision found the incorporation defective for the purpose of
`
`establishing anticipation because Dr. Weinstock’s testimony did not
`
`sufficiently explain why the reasonably skilled person would have
`
`understood the reference to Prober I to be a reference to deazapurines.
`
`
`
`In the Request for Rehearing, Illumina attempts to remedy this
`
`deficiency, stating “[s]ignificantly, the only analogs of dATP and dGTP
`
`present in the Prober I reference are 7-deazapurines” and explains why this
`
`is the case (Illumina Req. Reh’g 6). However, as pointedly stated by
`
`Illumina, the determination of “incorporation by reference” for the purpose
`
`of establishing anticipation is from the viewpoint of one reasonably skilled
`
`in the art. The identification of where Prober I described deazapurines, and
`
`the explanation of why Tsien’s disclosure “fluorescent ddNTPs” would be
`
`understood to be these deazapurines was not discussed in Dr. Weinstock’s
`
`declaration, but rather is only described in this Request for Rehearing signed
`
`by Illumina’s attorney. The argument of counsel cannot take the place of
`
`evidence lacking in the record. Estee Lauder Inc. v. L'Oreal, S.A., 129 F.3d
`
`588, 595 (Fed. Cir. 1997).
`
`Moreover, 37 C.F.R. § 41.71(d) states a Request for Rehearing “must
`
`specifically identify . . . the place where each matter was previously
`
`
`
`9
`
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`addressed in a motion, an opposition, or a reply.” Illumina has not cited
`
`where in the ‘698 Petition it was argued that the only analogs of dATP and
`
`dGTP described in Prober I are 7-deazapurines.
`
`
`
`Blanchaud Declaration
`
`
`
`Illumina also states that “Blanchaud understood certain features to be
`
`included in the incorporation of Prober based on the general description of
`
`the incorporated matter in Tsien and Dower, respectively.” (Illumina Req.
`
`Reh’g 5.) In fact, Blanchaud only appears in the list of references cited on
`
`pages v-vi of the Petition, but was not mentioned in any other place in the
`
`Petition. Accordingly, we did not address Blanchaud in the Decision. It is
`
`therefore not a matter misapprehended or overlooked by the Board as
`
`required by 37 C.F.R. § 42.71(d).
`
`
`
`Calloway
`
`Unlike in Calloway (reproduced above), Tsien did not disclose that all
`
`the materials in Prober I are to be included in their sequencing methods.
`
`For example, Tsien does not refer to Prober I for disclosing fluorescent
`
`nucleotides that could be used in its method, but rather referred to Prober I
`
`for “show[ing] enzymatic incorporation of fluorescent ddNTPs” using two
`
`different enzymes (‘698 Decision 25). Illumina did not direct us to adequate
`
`factual evidence or testimony by one reasonably skilled in the art that such
`
`sentence serves to incorporate the specific ddNTPs described in Prober I.
`
`
`
`
`
`10
`
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`Case IPR2012-00006
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`
`
`I.B. DUPLICATIVE REJECTIONS
`
`
`
`Citing 37 C.F.R. § 42.108, we denied certain unpatentability
`
`challenges to the claims. Illumina contends that “the Board abused its
`
`discretion by considering an improper factor when deciding whether to
`
`authorize inter partes review.” (Req. Reh’g 13.) Illumina contends that the
`
`Board’s “discretion is limited to determining whether, in fact, the references
`
`render the challenged patent unpatentable. The Patent Rules do not
`
`authorize the Board to exercise discretion based on whether or not certain
`
`references are cumulative or duplicative of each other.” (Id.at 14.)
`
`Under 37 C.F.R. § 42.108(a), the Board has discretion to “authorize
`
`the review to proceed on all or some of the challenged claims and on all or
`
`some of the grounds of unpatentability asserted for each claim.” The Board
`
`also “may deny some or all grounds for unpatentability for some or all of the
`
`challenged claims.” 37 C.F.R. § 42.108(b). As stated in the ‘698 Decision,
`
`in making such determinations, the Board must also take into account 37
`
`C.F.R § 42.1(b) which requires “the just, speedy, and inexpensive resolution
`
`of every proceeding.”
`
`In this case, the decision not to authorize inter partes review on certain
`
`unpatentability challenges was based on the finding that the challenges
`
`appeared to rely on the same prior art facts as other challenges for which
`
`inter partes review had been authorized. The determination not to proceed
`
`on all of the proposed unpatentability challenges by Illumina was therefore
`
`grounded on the determination that the same facts were being applied to the
`
`claims, albeit using different publications to establish that a fact was prior art
`
`to the claims. The concern was that the redundant unpatentability challenges
`
`would impede “the just, speedy, and inexpensive resolution of every
`
`
`
`11
`
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`Case IPR2012-00006
`U.S. Patent 7,713,698
`
`proceeding” as required under 37 C.F.R § 42.1(b). In other words,
`
`considering multiple rejections for the same unpatentability issue would
`
`unnecessarily consume the time and resources of all parties involved. As
`
`Illumina did not provide a meaningful distinction between the different,
`
`redundant rejections, we perceived no unfairness by not authorizing what
`
`appeared to be redundant challenges because an inter partes review had been
`
`instituted on the same factual basis.
`
`
`
`Illumina contends:
`
`[A]lthough the references are used to support invalidity
`contentions regarding the same claims, the references
`themselves are not identical. Thus, the Patent Owner may assert
`that a claim element is not present, or would not be obvious to
`combine with another reference, when that same element is
`more clearly set forth in a different reference.
`
`(Req. Reh’g 14.)
`
`
`
`While it is true that the cited references are not identical, the cited
`
`references appear to have been cited for the same facts. Illumina speculates
`
`that in certain publications an element may be more clearly set forth in one
`
`publication rather than another, but has not provided a persuasive example
`
`of such a case.
`
`
`
`Dower
`
`
`
`Illumina contends that Dower is not duplicative to Tsien, and cites one
`
`such difference (Req. Reh’g 14-15). However, Illumina did not provide an
`
`adequate explanation as to how this difference would impact the
`
`unpatentability challenge.
`
`
`
`
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`12
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`
`
`II. SCHEDULING ORDER
`
`
`
`In the conference call on April 16, 2013 between Illumina, Columbia,
`
`and the PTAB panel, Columbia requested a change in the Scheduling Order
`
`(Paper 29) to provide more time, depending on the outcome of the decision
`
`on Illumina’s Request for Rehearing. While the ‘698 Decision on Petition
`
`has been modified, the modification is not deemed sufficient to warrant a
`
`time extension on any of the dates in the Scheduling Order. Columbia’s
`
`request is therefore DENIED.
`
`
`
`III. SUMMARY
`
`The ‘698 Decision is modified as follows:
`
`Pursuant to 35 U.S.C. § 314, in addition to challenges I-III identified
`
`in the ‘698 Decision, we authorize inter partes review to be instituted as
`
`follows:
`
`
`
`IV. Claim 1-7, 11, 12, 14, 15, and 17 under 35 U.S.C. § 102(b) as
`
`anticipated by Dower.
`
`
`
`
`
`GRANTED-IN-PART
`
`
`
`
`
`
`
`
`
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`
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`13
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`
`Petitioner:
`
`Robert Lawler
`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
`
`
`
`
`14
`
`
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