Trials@uspto.gov
`571-272-7822
`
`
`
`
` Paper 73
`
`
` Entered: October 28, 2014
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`____________
`
`INTELLIGENT BIO-SYSTEMS, INC.,
`Petitioner,
`
`v.
`
`ILLUMINA CAMBRIDGE LIMITED,
`Patent Owner.
`___________
`
`Case IPR2013-00266
`Patent 8,158,346 B2
`___________
`
`
`Before LORA M. GREEN, SCOTT E. KAMHOLZ, and
`CHRISTOPHER L. CRUMBLEY, Administrative Patent Judges.
`
`CRUMBLEY, Administrative Patent Judge.
`
`
`
`
`
`FINAL WRITTEN DECISION
`35 U.S.C. § 318(a) and 37 C.F.R. § 42.73
`
`
`Illumina Ex. 1080
`IPR Petition - USP 10,435,742
`
`
`571-272-7822
`
`
`
`
` Paper 73
`
`
` Entered: October 28, 2014
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`____________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`____________
`
`INTELLIGENT BIO-SYSTEMS, INC.,
`Petitioner,
`
`v.
`
`ILLUMINA CAMBRIDGE LIMITED,
`Patent Owner.
`___________
`
`Case IPR2013-00266
`Patent 8,158,346 B2
`___________
`
`
`Before LORA M. GREEN, SCOTT E. KAMHOLZ, and
`CHRISTOPHER L. CRUMBLEY, Administrative Patent Judges.
`
`CRUMBLEY, Administrative Patent Judge.
`
`
`
`
`
`FINAL WRITTEN DECISION
`35 U.S.C. § 318(a) and 37 C.F.R. § 42.73
`
`
`Illumina Ex. 1080
`IPR Petition - USP 10,435,742
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`
`I. BACKGROUND
`
`A.
`
`Introduction
`Petitioner, Intelligent Bio-Systems, Inc. (“IBS”), filed a Petition
`(Paper 1, “Pet.”) for inter partes review of claims 1, 2, 4, 11, 12, 17, 18, and
`19 of U.S. Patent No. 8,158,346 B2 (Ex. 1001, “the ’346 patent”) pursuant
`to 35 U.S.C. §§ 311–319 and 37 C.F.R. §§ 42.1–42.123.
`On October 28, 2013, the Board instituted inter partes review of
`claims 1, 2, 4, 11, 12, 17, 18, and 19 of the ’346 patent on the following
`three grounds of unpatentability:
`1. Whether claims 1, 2, 4, 11, 12, 17, 18, and 19 are unpatentable
`under 35 U.S.C. § 102(a) or (e) as anticipated by Ju;1
`
`2. Whether claims 1, 2, 4, 11, 12, 17, 18, and 19 are unpatentable
`under 35 U.S.C. § 102(b) as anticipated by Tsien;2 and
`3. Whether claims 1, 2, 4, 11, and 12 are unpatentable under 35
`U.S.C. § 102(b) as anticipated by Stemple.3
`Paper 20 (“Dec.”), 13.
`Following institution of inter partes review, Patent Owner, Illumina
`Cambridge Limited (“Illumina”), filed a Motion to Amend Claims (Paper
`31, “Mot.”), but did not file a response under 37 C.F.R. § 42.120 to the
`Decision instituting inter partes review. IBS filed an opposition to
`Illumina’s Motion to Amend (Paper 37), and both parties filed Motions to
`Exclude Evidence (Papers 46, 49).
`
`1 As used in our Decision to Institute, “Ju” collectively referred to both Ju,
`U.S. 6,664,079 B2 (Dec. 16, 2003) (Ex. 1002) and Ju, WO 02/29003 A2
`(Apr. 11, 2002) (Ex. 1003).
`2 Tsien, WO 91/06678 A1 (May 16, 1991) (Ex. 1006).
`3 Stemple, WO 00/53805 A1 (Sept. 14, 2000) (Ex. 1007).
`
`
`
`2
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`
`Pursuant to requests by both parties, an oral hearing was held on May
`28, 2014, and the transcript of the hearing was entered into the record. Paper
`69, “Tr.”
`
`The Board has jurisdiction under 35 U.S.C. § 6(c). This final written
`decision is issued pursuant to 35 U.S.C. § 318(a) and 37 C.F.R. § 42.73. For
`the reasons that follow, Illumina’s Motion to Amend is granted to the extent
`it requests to cancel claims 1, 2, 4, 11, 12, 17, 18, and 19; Illumina’s Motion
`to Amend is denied to the extent that it requests entry of substitute claims
`20–26.
`
`B.
`
`The ’346 Patent
`The ’346 patent relates to DNA sequencing using nucleotides that are
`labeled and blocked. Ex. 1001, 2:18–22. A detectable label is attached to
`the base of a nucleotide by a cleavable linker, and a polymerase-blocking
`group is removably attached at the 3ʹ (or 2ʹ) position of the sugar moiety of
`the nucleotide. Id. at 2:38–44. A target DNA is sequenced by synthesizing
`its complement polynucleotide using the labeled and blocked nucleotides.
`Id. at 9:3–7. The blocking group prevents the polymerase from adding more
`than one nucleotide at a time. Id. at 8:13–20. The label then is detected,
`thereby identifying the newly-added nucleotide. Id. at 3:17–19. The label
`and the blocking group then are removed from the added base under
`identical conditions. Id. at 8:27–28. The process repeats with the next base.
`Id. at 3:20–22. The sequence of the target DNA then may be determined
`from the complementary sequence. Id. at 3:21–22.
`
`
`
`3
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`C.
`
`Related Proceedings
`The ’346 patent is asserted in the following copending district court
`case: Trustees of Columbia University in the City of New York v. Illumina,
`Inc., 1:12-cv-00376-GMS (D. Del.). Pet. 5.
`
`II. ORIGINAL CLAIMS
`As noted above, Illumina did not file a Response following our
`Decision instituting inter partes review of claims 1, 2, 4, 11, 12, 17, 18, and
`19. Instead, Illumina filed a Motion to Amend pursuant to 35 U.S.C.
`§ 316(d)(1) (“During an inter partes review . . ., the patent owner may file 1
`motion to amend the patent in 1 or more of the following ways: (A) Cancel
`any challenged patent claim. (B) For each challenged claim, propose a
`reasonable number of substitute claims.”). In its Motion, Illumina requested
`cancellation of claims 1, 2, 4, 11, 12, 17, 18, and 19 and proposed substitute
`claims 20–26 to replace the cancelled claims, and asserted that each of the
`grounds upon which the inter partes review was instituted “is rendered moot
`in light of Illumina’s proposed substitute claims.” Mot. 1. We shall grant
`Illumina’s Motion to Amend to the extent it requests to cancel claims 1, 2, 4,
`11, 12, 17, 18, and 19.
`
`
`III. PROPOSED SUBSTITUTE CLAIMS
`In the Motion to Amend, Illumina proposed substitute claim 20 to
`
`replace claim 2. The claim, as annotated by Illumina to show the differences
`between original claim 2 and proposed substitute claim 20, is reproduced
`below:
`
`20. A method according to claim 1 for determining the
`sequence of a target single-stranded polynucleotide, comprising
`
`
`
`4
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`
`monitoring the sequential incorporation of complementary
`nucleotides, the method further comprising the steps of
`(a) providing said nucleotides, wherein the nucleotides
`each have a base that is linked to a detectable label via a
`cleavable linker, wherein the cleavable linker contains a
`disulfide linkage, wherein each of the nucleotides has a ribose
`or deoxyribose sugar moiety and the ribose or deoxyribose
`sugar moiety comprises a protecting group attached via the 3'
`oxygen atom; and wherein said monitoring comprises
`(b) incorporating a nucleotide of (a) into the complement
`of the target single stranded polynucleotide;
`(c) detecting the label linked to the base of the nucleotide
`of (b), thereby determining the identity type of the nucleotide
`incorporated;
`(d) subsequently removing the label and the protecting
`group of the nucleotide of (b) under a single set of chemical
`cleavage conditions, wherein the chemical cleavage conditions
`cleave the disulfide linkage and permit further nucleotide
`incorporation into the complement of the target single stranded
`polynucleotide to occur; and
`(e) optionally repeating steps (b)-(d) one or more times;
`thereby determining the sequence of a target single-stranded
`polynucleotide.
`Mot. 2.
`Proposed substitute claim 20 combines the limitations found in
`original claims 1 and 2, and also recites a newly added limitation that the
`cleavable linker “contains a disulfide linkage,” which was not present in the
`original claims.
`For illustrative purposes, an annotated generic nucleotide from Figure
`1B of Stemple is reproduced below to show the main parts of a nucleotide
`used in sequencing-by-synthesis (“SBS”) processes such as the one of
`proposed claim 20:
`
`
`
`5
`
`
`
`
`
`IPR22013-002666
`
`
`Patennt 8,158,3446 B2
`
`
`d a chemiccal
`
`
`
`process ussing a nuclleotide
`
`
`
`(Ex. 1001, 2:188–20) (illuustrated as ““label,” “liinker,” andd “base” inn Figure 1BB
`
`ugar moietty . . . commpris[ing] aa protectingg
`
`
`
`mple showsFigure 1B of Stem
`
`
`nucleotidee’s main
`a generic
`
`“label”), a
`
`
`
`able label (g a detectapartss, including
`a linker, an
`
`
`
`
`grouup attachedd to the 3ʹ-OOH positioon.
`
`
`
`
`Originall claim 1 wwas drawn tto an SBS
`
`
`
`
`withh, inter aliaa, the followwing featuures:
`
`
`
`
`inked to a detectablee label via aa cleavablee linker”
`
`1. “a baase that is l
`
`
`
`
`
`
`
`
`
`
`
`of Sttemple repproduced abbove);
`xyribose s
`
`2. “a ribose or deo
`
`
`
`
`
`
`grouup attachedd via the 2′ or 3′ oxyggen atom” ((Id. at 2:433–45) (illu
`
`
`
`
`strated in
`
`
`
`
`
`
`
`the ffigure abovve as a prottecting grooup attacheed to the oxxygen of thhe 3ʹ-OH
`
`grouup); and
`3. “rem
`
`
`condditions.”
`
`
`
`oval of thee label and the proteccting groupp under a s
`
`
`
`
`
`ingle set o
`
`f
`
`Propose
`
`
`
`
`
`d substitutte claim 200 contains tthese featuures, but fuurther
`
`recittes that the
`
`
`
`linker conntains a dissulfide linkkage. The
`
`
`
`
`a dissulfide linkkage is the
`
`
`
`
`main issuee to be deccided in whhether to grrant the
`
`
`Motiion to Ameend.
`
`obviousneess of usingg
`
`
`
`6
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`Proposed substitute dependent claims 21–26 replace claims 4, 11, 12,
`
`and 17–19, respectively. The sole changes to these claims are to change
`their dependency from claim 1 or 17 to claims 20 and 24. Mot. 3.
`
`As movant, Illumina bears the burden of proof to establish that it is
`entitled to the relief requested in the Motion to Amend. 37 C.F.R.
`§ 42.20(c). In other words, Illumina bears the burden of showing the
`patentability of the amended claims. Illumina must, therefore, show that the
`conditions for novelty and non-obviousness are met for the prior art
`available to one of ordinary skill in the art at the time the invention was
`filed, not just for the prior art cited in the Petition or the grounds upon which
`trial was instituted. See Idle Free Sys., Inc. v. Bergstrom, Inc., Case IPR
`2012-00027, slip op. at 7 (PTAB June 11, 2013) (Paper 26).
`
`
`IV. PATENTABILITY OF CLAIMS 20–26
`
`Claim Interpretation
`A.
`In an inter partes review, “[a] claim in an unexpired patent shall be
`
`given its broadest reasonable construction in light of the specification of the
`patent in which it appears.” 37 C.F.R. § 42.100(b). Under this standard, we
`construe claim terms using “the broadest reasonable meaning of the words in
`their ordinary usage as they would be understood by one of ordinary skill in
`the art, taking into account whatever enlightenment by way of definitions or
`otherwise that may be afforded by the written description contained in the
`applicant’s specification.” In re Morris, 127 F.3d 1048, 1054 (Fed. Cir.
`1997). We presume that claim terms have their ordinary and customary
`meaning. See In re Translogic Tech., Inc., 504 F.3d 1249, 1257 (Fed. Cir.
`2007) (“The ordinary and customary meaning is the meaning that the term
`
`
`
`7
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`would have to a person of ordinary skill in the art in question.”) (internal
`quotation marks and citations omitted). A patentee may rebut this
`presumption, however, by acting as his own lexicographer, providing a
`definition of the term in the specification with “reasonable clarity,
`deliberateness, and precision.” In re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir.
`1994).
`
`1. the cleavable linker and the protecting group are cleavable under
`identical conditions
`Proposed substitute claim 20 recites, inter alia, “a base that is linked
`
`to a detectable label via a cleavable linker,” a “protecting group attached via
`the 3' oxygen atom” of the nucleotide, and a step of “removing the label and
`the protecting group of the nucleotide . . . under a single set of chemical
`cleavage conditions.” Mot. 2 (emphasis added). These limitations are
`similar to those present in original claim 1, which we construed in our
`Decision on Institution. Specifically, we construed removal of the label and
`the protecting group under a single set of conditions “to mean what its plain
`language indicates: removal of the label and the protecting group under a
`single set of conditions.” Dec. 6. Neither of the parties contested this
`construction subsequent to institution, and we discern no reason to modify
`our initial construction for the purposes of this decision.
`
`Proposed claim 20 also requires that the cleavable linker comprise a
`disulfide linkage, but does not specify the protecting group. Thus, “a single
`set of chemical cleavage conditions,” under the broadest reasonable
`interpretation standard, limits the structure of the protecting group to one
`which can be cleaved under the same conditions as a disulfide linkage, but
`does not require a specific structure, such as a disulfide linkage.
`
`
`
`8
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`
`2. cleavable linker contains a disulfide linkage
`All proposed substitute claims contain a new limitation, not present in
`
`the original claims, that the cleavable linker contains a disulfide linkage.
`Neither party proposes a specific construction for this new claim element.
`We note that a disulfide linkage contains a bond between two sulfur atoms.
`Ex. 1001, Fig. 2.
`
`B.
`
`Illumina’s Burden to Show Nonobviousness
`As noted above, the primary remaining issue in this inter partes
`review is the obviousness of using a cleavable disulfide linker to attach a
`label to the nucleotide base, where the linker and protecting group of the
`nucleotide are cleaved under identical conditions.
`Because Illumina bears the burden of showing that it is entitled to
`entry of its proposed substitute claims, it must show that one of ordinary
`skill in the art would not have considered the proposed substitute claims
`obvious in view of the prior art available before the filing date of the
`claimed invention. More specifically, the issue is whether it would have
`been nonobvious at the time of the invention to have attached a detectable
`label to a base using a disulfide linkage, where the base is present in a
`nucleotide having “ribose or deoxyribose sugar moiety compris[ing] a
`protecting group attached via the 3' oxygen atom” and where the disulfide
`linkage and the protecting group are removed “under a single set of chemical
`cleavage conditions.”
`A patent claim is invalid for obviousness “if the differences between
`the claimed invention and the prior art are such that the claimed invention as
`a whole would have been obvious before the effective filing date of the
`
`
`
`9
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`claimed invention to a person having ordinary skill in the art to which the
`claimed invention pertains.” 35 U.S.C. § 103.
`The underlying factual considerations in an obviousness
`analysis include the scope and content of the prior art, the
`differences between the prior art and the claimed invention, the
`level of ordinary skill in the art, and any relevant secondary
`considerations. Relevant secondary considerations include
`commercial success, long-felt but unsolved needs, failure of
`others, and unexpected results.
`Allergan, Inc. v. Sandoz Inc., 726 F.3d 1286, 1291 (Fed. Cir. 2013) (internal
`citations omitted).
`An important consideration is “whether a person of ordinary skill in
`the art would, at the relevant time, have had a ‘reasonable expectation of
`success’ in pursuing the possibility that turns out to succeed and is claimed.”
`Institute Pasteur & Universite Pierre et Marie Curie v. Focarino, 738 F.3d
`1337, 1344 (Fed. Cir. 2013) (citations omitted).
`
`Prior Art
`C.
`Before turning to the specific arguments presented by both parties, we
`
`summarize some of the prior art of record that was known at the time of the
`invention claimed in the ’346 patent. This discussion is not meant to be
`exhaustive, but rather to provide a brief description of what was known
`about modified nucleotides prior to the priority date of the ’346 patent.
`
`The claimed method is nucleic acid sequencing-by-synthesis (“SBS”),
`a process in which 3ʹ-OH protected and detectably labeled nucleotides are
`added stepwise to a nucleic acid primer during sequencing. In that process,
`it was known to use a nucleotide labeled at its base with a detectable label in
`order to identify when the nucleotide is incorporated into the newly
`
`
`
`10
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`synthesized strand. Ex. 1006, 27:33–28:2; Ex. 1010,4 18:64–19:2. It also
`was known to attach a protecting group to the 3ʹ-OH of the nucleotide. Ex.
`1006, 9:32–10:3. During DNA synthesis, nucleotides are added sequentially
`to the 3ʹ-OH group of the nucleotide sugar. The 3ʹ-OH group contains a
`removable protecting group so the labeled nucleotides can be added one at a
`time. After each addition, the label is detected and the 3ʹ-OH group is
`deblocked and new nucleotide (with its own 3ʹ-OH protecting group) is
`added. Id. at 13:14–35. In sum, it was not new to employ a nucleotide in
`sequencing which comprised a detectable label on the nucleotide base and a
`3ʹ-OH protecting group.
`The prior art also described attaching a label to the nucleotide base
`using a cleavable linker as recited in the proposed claims. Id. at 28:20–23;
`Ex. 1002, Abstract, 2:50–53. Furthermore, as we discussed in the Decision
`on Institution, Tsien described removing the detectable label and the
`protecting group simultaneously. Ex. 1006, 28:5–8; Dec. 9.
`The newly added limitation that the cleavable linker is a disulfide
`bond also is described in the prior art. As discussed in more detail below,
`Rabani5 and Church6 both describe attaching a detectable label to a
`nucleotide base via a disulfide linkage, where the nucleotide is used in
`nucleic acid sequencing. An example is shown in Figure 5 of Church,
`reproduced below, which we have annotated to identify specific structures.
`
`
`4 Dower, W.J. & Fodor, S.P.A. U.S. 5,547,839 (Aug. 20. 1996).
`5 Rabani, E. WO 96/27025 A1 (Sept. 6, 1996) (Ex. 2017).
`6 Church, G.M. WO 00/53812 A2 (Sept. 14, 2000) (Ex. 1019).
`
`
`
`11
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`
`
`
`Figure 5 of Church is annotated to identify the structures of
`the nucleotide, including a detectable label, a triphosphate, and a
`disulfide bond. Ex. 1019, 17:10–11 (“Figure 5 is a schematic
`drawing of a disulfide-bonded cleavable nucleotide fluorophore
`complex.”). The nucleotide, however, lacks the claimed protecting
`group on the 3ʹ-OH.
`In addition to Church, six additional publications7 are cited in this
`
`inter partes review for their description of nucleotides comprising cleavable
`
`
`7 (1) Herman, U.S. Patent No. 4,772,691 (Sept. 20, 1988) (Ex. 2019).
`(2) S.W. Ruby, et al., Affinity Chromatography with Biotinylated RNAs,
`METHODS IN ENZYMOLOGY, vol. 181, 97–121 (1990) (Ex. 2016).
`(3) Short, WO 99/49082 A2 (Sept. 30, 1999) (Ex. 2020).
`(4) Barbara A. Dawson, et al., Affinity Isolation of Transcriptionally Active
`Murine Erythroleukemia Cell DNA Using a Cleavable Biotinylated
`
`
`
`12
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`linkers with disulfide bonds. One of these, Herman, shows a nucleotide with
`disulfide bond attaching a biotin to a nucleotide base. Ex. 2019. In the
`figure from Herman, reproduced below, orientation of the nucleotide is
`flipped 180 degrees from Church’s nucleotide, reproduced above.
`
`Herman’s Figure (col. 5) shows a nucleotide with a cleavable linker
`comprising a disulfide bond joining a biotin (“detectable label”) to a
`nucleotide base. Ex. 2019, 7:24–27. The nucleotide lacks the protecting
`group on the 3ʹ-OH as required in proposed claim 20.
`
`
`
`
`
`Nucleotide Analog, THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 264, no.
`22, 12830–37 (1989) (Ex. 1027).
`(5) Barbara A. Dawson, et al., Affinity Isolation of Active Murine
`Erythroleukemia Cell Chromatin: Uniform Distribution of Ubiquitinated
`Histone H2A Between Active and Inactive Fractions, JOURNAL OF CELLULAR
`BIOCHEMISTRY, vol. 46, 166–173 (1991) (Ex. 2038).
`(6) Basil Rigas, et al., Rapid plasmid library screening using RecA-coated
`biotinylated probes, PROC. NATL. ACAD. SCI. USA, vol. 83, 9591–9595
`(1986) (Ex. 2039).
`
`
`
`
`13
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`D.
`
`Reason to Use a Disulfide Bond on Nucleotides
`In the Decision on Institution, we instituted inter partes review on
`three grounds based on Ju, Tsien, and Stemple. Those publications,
`however, do not describe using a cleavable disulfide linker for attaching the
`detectable label to a base. A disulfide bond as a linker is described in the
`prior art (see discussion, supra), however, along with a reason to have used
`one.
`
`1. Rabani
`Rabani, in the section titled “Cleavable linkers,” teaches that
`“[l]abeling moieties are favorably in communication with or coupled to
`nucleotides via a linker of sufficient length to ensure that the presence of
`said labeling moieties on said nucleotides will not interfere with the action
`of a polymerase enzyme on said nucleotides.” Ex. 2017, 32:10–13. Rabani
`specifically mentions disulfide linkages as useful when a cleavable linker is
`desired:
`Linkages comprising disulfide bonds within their length have
`been developed to provide for cleavability24; reagents
`comprising such linkages are commercially available25 and
`have been used to modify nucleotides26 in a manner which may
`be conveniently reversed by treatment with mild reducing
`agents such as dithiothreitol.
`Id. at 32:29–33. Footnotes 24 and 26 of the above quoted passage cite to
`Ruby.8 Id. at 49. Footnote 25 references “for example, from Pierce
`Chemical Co., [ ] of Rockford, IL., U.S.A.” Id.
`
`
`8 Ruby, S.W. et al., Affinity Chromatography with Biotinylated RNAs,
`METHODS IN ENZYMOLOGY, 181:97 (1990) (Ex. 2016).
`
`
`
`14
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`Given these disclosures, we find that Rabani would have given a
`
`skilled worker reason to have used a cleavable linker with a disulfide bond
`to ensure that the labeling moieties on the nucleotides will not interfere with
`the action of a polymerase enzyme during the synthesis reaction.
`
`2. Church
`IBS cites Church as evidence of the obviousness of using a disulfide
`linker in a sequencing reaction. Paper 55, 2. Church provides another
`example of the use of a disulfide linker to attach a label to base of a
`nucleotide, further establishing its conventionality at the time of the
`invention. Ex. 1019, 17:10–18, 68:12–21. Church describes a working
`example in which a label was attached to a nucleotide base using a disulfide
`linker and then cleaving it off with DTT. Id. at 86:6–30.
`Dr. Bruce P. Branchaud,9 a declarant for IBS, testified:
`Church teaches a SBS [sequencing by synthesis] method
`termed fluorescent in situ sequencing extension quantification
`(FISSEQ). In one embodiment, Church teaches the sequential
`addition of fluorescently labeled nucleotides in which the label
`is attached to the base via a “cleavable linkage.”
`Ex. 1021 ¶ 12 (citing Ex. 1019 at 67:30–68:11).
`
`
`9 To support its obviousness challenge, IBS provided two Declarations by
`Bruce P. Branchaud, Ph.D. Exs. 1011 & 1021. Dr. Branchaud is Professor
`Emeritus in the Department of Chemistry at the University of Oregon. Ex.
`1011 ¶ 5. He has a Ph.D. in Organic Chemistry from Harvard University,
`and has held positions in industry, including as an internal consultant and
`advisor for DNA sequencing projects. Ex. 1011 ¶¶ 5, 7, 12–15. Dr.
`Branchaud has the requisite familiarity with DNA sequencing to qualify as
`one of ordinary skill in the art at the time of the invention. Consequently,
`we conclude that Dr. Branchaud is qualified to testify on the matters
`addressed in his Declarations.
`
`
`
`15
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`90% Cleavage Efficiency of the Detectable Label Is Not Required
`E.
`As discussed in the preceding sections, it was known as of the filing
`
`date of the ’346 patent to use disulfide linkers, and there was a reason to use
`such linkers in SBS reactions. Illumina argues, however, that a person of
`ordinary skill in the art would not have used a disulfide bond. At oral
`hearing, counsel for Illumina conceded that the claimed method does not
`recite a particular cleavage efficiency. Tr. 20. Citing Rabani, however,
`Illumina contends sequencing by synthesis processes require that the
`disulfide linker joined to the detectable label be cleaved with 90%
`efficiency, because of the iterative nature of the process. Mot. 10–12.
`According to Illumina, greater than 90% efficiency in the cleavage reaction
`could not be achieved at the time of the invention if a disulfide linkage were
`used. Id.
`Rabani teaches published results “suggest[ing] that the rate of
`chemical removal of 3'-hydroxy protecting groups (less than 90% removal
`after 10 minutes of treatment with 0.1M NaOH) will be unacceptably low
`for such an inherently serial sequencing scheme.” Ex. 2017, 3:5–8
`(emphasis added). Illumina reasons that since Rabani teaches that less than
`90% removal of the protecting group from the 3ʹ-OH “will be unacceptably
`low for . . . [a] serial sequencing scheme,” (Ex. 2017, 3:5–8) and since the
`claims require that the disulfide linkage of the cleavable linker and the
`protecting group are cleavable under a single set of chemical conditions, the
`disulfide linker joining the detectable label to the nucleotide base must also
`achieve 90% or more cleavage. Mot. 10–12. Illumina provides evidence
`that the prior art teaches less than 90% efficiency in cleaving the 3ʹ-OH
`protecting group, leading Illumina to reason “the expectation of
`
`
`
`16
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`unacceptably low 3ʹ-OH protecting group cleavage efficiency when using ‘a
`single set of chemical conditions’ would not lead a skilled artisan to believe
`that one could efficiently cleave 3ʹ-OH protecting groups under the same
`single set of chemical conditions with a disulfide linkage during SBS.” Mot.
`12.
`
`In other words, Illumina argues that because 90% efficiency in
`cleaving the 3ʹ-OH group could not be achieved, there would not have been
`a reason to use a disulfide linkage to attach the detectable label to the base,
`because the detectable label must cleaved under identical conditions to the
`3ʹ-OH protecting group. Cleavage of the 3ʹ-OH group requires 90%
`efficiency, Illumina argues, thus 90% cleavage efficiency must be achieved
`at the disulfide bond of the detectable label, as well.
`Illumina’s argument is flawed. Rabani’s disclosure is directed to
`cleavage of the protecting groups, not the claimed detectable label.
`Illumina’s arguments are based on the logic that if no better than 90%
`cleavage of the disulfide bond on the protecting group can be achieved, the
`skilled worker would not have used it as a cleavable linker for attaching a
`detectable label to a nucleotide in DNA sequencing, because the proposed
`substitute claims require it be cleaved under identical conditions to the
`3ʹ-OH group, which requires 90% efficiency.
`The proposed substitute claims do not require the linkage between the
`3ʹ-OH and protecting group to comprise a disulfide bond, nor does Illumina
`argue that the “single set of chemical cleavage conditions” requires that the
`protecting group and detectable label be attached to the nucleotide using the
`same linker. We, therefore, discern no reason to apply Rabani’s protecting
`
`
`
`17
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`group cleavage efficiency requirement to the disulfide linkage of the
`proposed substitute claims.
`Significantly, Dr. Floyd Romesberg,10 Illumina’s declarant, conceded
`that he chose a 90% efficiency requirement not because of Rabani, but rather
`because “it was a round number slightly above the values reported by Ruby
`and Herman.” Ex. 1022, 198:16–18. Furthermore, we note that Dr.
`Romesberg’s rationale that high cleavage efficiency is necessary in SBS
`processes uses examples involving 8 or 16 iterations of the process. Ex.
`2004 ¶ 63. Yet, as counsel for Illumina conceded at oral hearing, the
`claimed process requires far fewer iterations: at most, two and a half cycles.
`Tr. 7.
`
`Illumina has not persuaded us that cleavage of the disulfide bond that
`attaches the detectable label to the base with less than 90% efficiency would
`be unacceptable for SBS processes, such that a person of ordinary skill in the
`art would not investigate linkers with less efficient cleavage.
`
`F. Cleavage Efficiency of the Disulfide Bond
`Even were we persuaded by Illumina’s argument that 90% cleavage of
`the 3ʹ-OH protecting group is necessary for sequencing, Illumina did not
`provide adequate evidence that the skilled worker would have been unable to
`
`10 Declarations by Floyd Romesberg, Ph.D. were submitted by Illumina in
`support of its Motion to Amend. Exs. 2004 & 2037. Dr. Romesberg is a
`professor in the Department of Chemistry at The Scripps Research Institute,
`where he has been a faculty member since 1998. Ex. 2004 ¶ 2. Dr.
`Romesberg testified that he is “qualified to render an opinion in the field of
`nucleotide analogue molecules based on [his] experience in this field.” Id. ¶
`17. Dr. Romesberg was deposed twice; the transcripts of his depositions are
`Exhibits 1022 & 1042.
`
`
`
`
`18
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`choose conditions and linkages that would achieve 90% cleavage of the
`3ʹ-OH group under the same conditions required for cleavage of the label,
`e.g., using a reducing agent (Ex. 1001, 6:32–43).
`The ’346 patent suggests that choosing cleavage conditions for the
`3ʹ-OH group was conventional to one of ordinary skill in the art:
`Suitable protecting groups will be apparent to the skilled
`person, and can be formed from any suitable protecting group
`disclosed in Green and Wuts, supra. [Some examples of such
`protecting groups are shown in FIG. 3.] The protecting group
`should be removable (or modifiable) to produce a 3ʹ OH group.
`The process used to obtain the 3ʹ OH group can be any suitable
`chemical or enzymic reaction.
`Id. at 8:21–26.
`Dr. Branchaud testified that:
`even if one of ordinary skill in the art considered the elution
`percentages of Ruby . . . in deciding whether to use such a
`linker for SBS, one of ordinary skill in the art would know that
`such elution percentages could be improved by routine
`experimentation to improve the cleavage efficiency of the
`disulfide linkers and thus would not be dissuaded from using
`such a linker.
`
`Ex. 1021 ¶ 40. As discussed below, this conclusion is supported by the prior
`art of record.
`
`1. Ruby
`Ruby is cited expressly by Rabani for its teaching of a disulfide bond
`that is cleavable with a reducing agent, such as dithiothreitol (“DTT”), and
`describes attaching a biotin molecule attached to a nucleotide base of a RNA
`“via a linker containing a disulfide bond.” Ex. 2016, 98. The RNA is bound
`to a column containing avidin, based on the affinity of the biotin for the
`
`
`
`19
`
`
`
`IPR2013-00266
`Patent 8,158,346 B2
`
`avidin. Id. at 98–99 (Fig. 1). The RNA is “eluted [from the column] by
`adding dithiothreitol (DTT) to reduce the disulfide bonds linking biotin to
`the anchor RNA.” Id. at 98; Ex. 1021 ¶ 31. Relying on testimony by
`Dr. Romesberg, Illumina states that “Ruby reports that disulfide linkages are
`cleaved with only ~86% efficiency after more than 100 minutes, which is
`significantly less than 90% efficient.” Mot. 11 (citing Ex. 2016, 117–18; Ex.
`2004 ¶ 60). The “~86% efficiency” comes from Figure 4 of Ruby, a graph
`of % RNA eluted using DTT under different conditions. Ex. 2016, 117. Dr.
`Branchaud did not dispute that Ruby recovered “approximately 86% of the
`RNA.” Ex. 1021 ¶ 31.
`Dr. Romesberg testified that, because “[t]here is no indication in Ruby
`that a 3ʹ-OH protecting group that is cleavable under a single set of
`conditions with a disulfide linkage would be cleaved with any greater
`efficiency than the approximately 86% cleavage efficiency reported by Ruby
`for a disulfide linkage,” a person of ordinary skill “would have had no
`reason to expect cleavage efficiency to be greater than 86%.” Ex. 2004 ¶ 61.
`In response, Dr. Branchaud testified that:
`even if one of ordinary skill in the art considered the elution
`percentages of Ruby . . . in deciding whether to use such a
`linker for SBS, one of ordinary skill in the art would know that
`such elution percentages could be improved by routine
`experimentation to improve the cleavage efficiency of the
`disulfide linkers and thus, would not be dissuaded from using
`such a linker.
`
`Ex. 1021 ¶ 40.
`Dr. Branchaud’s testimony is supported factually. Ruby teaches
`“[e]lution by reduction of the disulfide bonds on the biotinylated anchor
`RNA depends on the pH of the buffer, the DTT concentration, and the time
`
`
`
`20
`
`
Accessing this document will incur an additional charge of $.
After purchase, you can access this document again without charge.
Accept $ Charge
Still Working On It
This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.
Give it another minute or two to complete, and then try the refresh button.
A few More Minutes ... Still Working
It can take up to 5 minutes for us to download a document if the court servers are running slowly.
Thank you for your continued patience.
This document could not be displayed.
We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.
Your account does not support viewing this document.
You need a Paid Account to view this document. Click here to change your account type.
Your account does not support viewing this document.
Set your membership
status to view this document.
With a Docket Alarm membership, you'll
get a whole lot more, including:
- Up-to-date information for this case.
- Email alerts whenever there is an update.
- Full text search for other cases.
- Get email alerts whenever a new case matches your search.
One Moment Please
The filing “” is large (MB) and is being downloaded.
Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.
Your document is on its way!
If you do not receive the document in five minutes, contact support at support@docketalarm.com.
Sealed Document
We are unable to display this document, it may be under a court ordered seal.
If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.
Access Government Site
