UNITED STATES PATENT AND TRADEMARK OFFICE
`___________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`___________________
`
`
`TWINSTRAND BIOSCIENCES, INC.
`Petitioner,
`v.
`GUARDANT HEALTH, INC.
`Patent Owner.
`
`___________________
`
`Case IPR2022- 01115
`U.S. Patent No. 10,801,063
`___________________
`
`PETITION FOR INTER PARTES REVIEW
`OF U.S. PATENT NO. 10,801,063
`
`
`
`
`
`
`
`
`
`
`
`Mail Stop "PATENT BOARD"
`Patent Trial and Appeal Board
`U.S. Patent and Trademark Office
`P.O. Box 1450
`Alexandria, VA 22313-1450
`
`

`

`Case IPR2022-01115
`Patent 10,801,063
`
`
`TABLE OF CONTENTS
`
`I.
`II.
`
`III.
`
`B.
`
`C.
`
`Introduction ..................................................................................................... 1
`Statement of Precise Relief Requested and Reasons Therefor (37 C.F.R.
`§42.22(A)) ...................................................................................................... 2
`State of the art before December 2013 ........................................................... 2
`A. Optimization techniques for DNA library preparation were
`well known. ........................................................................................... 2
`Cell-free DNA isolated from blood was widely used in NGS
`platforms. ............................................................................................... 5
`1.
`The presence of cell-free tumor DNA in human blood
`was well known. ......................................................................... 5
`Isolating cfDNA from blood was routine with off-the-
`shelf kits. .................................................................................... 6
`The prior art taught that Duplex Sequencing dramatically
`lowers NGS error rate. .......................................................................... 7
`The prior art taught applying Duplex Sequencing to cfDNA. ............ 13
`D.
`IV. The ’063 patent and prosecution history ...................................................... 14
`V.
`Person of ordinary skill in art ....................................................................... 18
`VI. Claim construction ........................................................................................ 18
`VII.
`Identification of the challenge (37 C.F.R. §42.104(b)) ................................ 19
`VIII. The facts and law weigh against discretionary denial of institution. ........... 21
`A.
`This Petition satisfies 35 U.S.C. §325(d). ........................................... 21
`B.
`Fintiv does not support discretionary denial. ...................................... 24
`IX. Ground 1: claims 1-7, 9-11, 15-18, and 22-28 would have been obvious over
`Narayan, Schmitt, and Meyer ....................................................................... 26
`A.
`Claim 1 ................................................................................................ 26
`1.
`“A method for classifying consensus sequences
`generated from sequencing reads derived from
`double-stranded
`cell-free deoxyribonucleic
`acid
`(cfDNA) molecules from a sample of a human
`subject…” ................................................................................. 26
`“(a) non-uniquely tagging a population of double-
`stranded cfDNA molecules from the sample with
`more than a 10x molar excess of adapters comprising
`
`2.
`
`2.
`
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`Case IPR2022-01115
`Patent 10,801,063
`
`
`molecular barcodes, relative to the double-stranded
`cfDNA molecules in the population, to generate non-
`uniquely tagged parent polynucleotides...” .............................. 27
`“wherein the double-stranded cfDNA molecules that
`map to a mappable base position of a reference
`sequence are tagged with a number of different
`molecular barcodes ranging from at least 2 to fewer
`than a number of double-stranded cfDNA molecules
`that map to the mappable base position...” .............................. 29
`“wherein at least 20% of the double-stranded cfDNA
`molecules are non-uniquely tagged with the adapters
`comprising the molecular barcodes at both ends of a
`molecule of the double-stranded cfDNA molecules...” ........... 30
`“(b) amplifying a plurality of the non-uniquely tagged
`parent
`polynucleotides
`to
`produce
`progeny
`polynucleotides...”.................................................................... 31
`“(c)
`enriching
`a plurality of
`the progeny
`polynucleotides for target regions of interest to
`generate enriched progeny polynucleotides...” ........................ 31
`“(d) sequencing a plurality of the enriched progeny
`polynucleotides to produce a set of sequencing
`reads…” ................................................................................... 31
`“(e) mapping a plurality of sequencing reads from the
`set of sequencing reads to the reference sequence…” ............. 32
`“(f) grouping a plurality of the mapped sequencing
`reads into families of mapped sequencing reads based
`at
`least on (i) sequence
`information from
`the
`molecular barcodes and (ii) a beginning base position
`and an ending base position of the mapped sequencing
`reads...” .................................................................................... 32
`“(g) generating a consensus sequence for each family
`from among one or more of the families to produce a
`set of consensus sequences…”................................................. 33
`“(h) classifying one or more consensus sequences
`from among the set of consensus sequences as (1)
`paired
`consensus
`sequences
`generated
`from
`sequencing reads representing a Watson strand and a
`Crick strand of a non-uniquely
`tagged parent
`polynucleotide or (2) unpaired consensus sequences
`
`3.
`
`4.
`
`5.
`
`6.
`
`7.
`
`8.
`
`9.
`
`10.
`
`11.
`
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`

`

`Case IPR2022-01115
`Patent 10,801,063
`
`
`B.
`
`2.
`
`3.
`
`4.
`
`generated from sequencing reads representing only
`one of either a Watson strand or a Crick strand of a
`non-uniquely tagged parent polynucleotide.” .......................... 34
`12. A POSA would have had a reason to combine
`Narayan, Schmitt, and Meyer .................................................. 35
`13. A POSA would have had a reasonable expectation of
`success. ..................................................................................... 41
`Claim 15 .............................................................................................. 44
`1.
`“A method for classifying unique sequencing reads
`generated from sequencing reads derived from
`double-stranded
`cell-free deoxyribonucleic
`acid
`(cfDNA) molecules from a bodily fluid sample of a
`human subject…” ..................................................................... 44
`“(a) tagging a population of double-stranded cfDNA
`molecules from the bodily fluid sample with more
`than a 10x molar excess of adapters comprising
`molecular barcodes, relative to the double-stranded
`cfDNA molecules in the population, to generate
`tagged parent polynucleotides, wherein at least 20%
`of the cfDNA molecules are ligated with the adapters
`comprising the molecular barcodes at both ends of a
`molecule of the double-stranded cfDNA molecules…” .......... 45
`“(b) amplifying a plurality of the tagged parent
`polynucleotides
`to
`produce
`progeny
`polynucleotides…”................................................................... 45
`“(c)
`sequencing a plurality of
`the progeny
`polynucleotides to produce a set of sequencing
`reads…” ................................................................................... 46
`“(d) mapping a plurality of sequencing reads from the
`set of sequencing reads to a reference sequence...” ................. 46
`“(e) determining unique sequencing reads from the set
`of mapped sequencing reads based at least on the
`molecular barcode sequences, wherein a unique
`sequencing read from among the unique sequencing
`reads
`is
`representative of
`a
`tagged parent
`polynucleotide
`from among
`the
`tagged parent
`polynucleotides...”.................................................................... 46
`“(f) classifying one or more of the unique sequencing
`reads as either (1) paired sequences generated from
`
`5.
`
`6.
`
`7.
`
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`

`

`Case IPR2022-01115
`Patent 10,801,063
`
`
`sequencing reads representing a Watson strand and a
`Crick strand of a tagged parent polynucleotide or (2)
`unpaired sequences generated from sequencing reads
`representing only one of either a Watson strand or a
`Crick strand of a tagged parent polynucleotide.” .................... 47
`Claim 2 ................................................................................................ 48
`C.
`Claim 3 ................................................................................................ 49
`D.
`Claim 4 ................................................................................................ 49
`E.
`Claims 5 and 24 ................................................................................... 50
`F.
`Claims 6 and 25 ................................................................................... 52
`G.
`Claims 7 and 22 ................................................................................... 53
`H.
`Claim 9 ................................................................................................ 53
`I.
`Claim 10 .............................................................................................. 54
`J.
`Claims 11 and 18 ................................................................................. 56
`K.
`Claim 28 .............................................................................................. 58
`L.
`M. Claim 16 .............................................................................................. 60
`N.
`Claim 17 .............................................................................................. 60
`O.
`Claim 23 .............................................................................................. 62
`P.
`Claim 26 .............................................................................................. 62
`Q.
`Claim 27 .............................................................................................. 63
`X. Ground 2: claim 8 would have been obvious over Narayan, Schmitt, Meyer,
`and Craig ....................................................................................................... 64
`XI. Ground 3: claims 12-14 and 19-21 would have been obvious over Narayan,
`Schmitt, Meyer, and Kivioja ......................................................................... 67
`A.
`Claims 12-13 and 19-20 ...................................................................... 67
`B.
`Claims 14 and 21 ................................................................................. 71
`XII. Objective indicia do not support patentability. ............................................. 72
`XIII. Certification of standing and Patent IPR eligibility (37 C.F.R. §42.104(a)) 72
`XIV. Mandatory Notices (37 C.F.R. §42.8(a)(1)) ................................................. 72
`XV. Conclusion. ................................................................................................... 74
`
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`

`

`TABLE OF AUTHORITIES
`
`Case IPR2022-01115
`Patent 10,801,063
`
`
` Page(s)
`
`Cases
`Abbott Labs. v. Sandoz, Inc.,
`544 F.3d 1341 (Fed. Cir. 2008) .................................................................... 43, 51
`
`Advanced Bionics, LLC v. MED-EL Elektromedizinische Geräte
`GmbH,
`IPR2019-01469 (P.T.A.B., Feb, 13, 2020) ................................................... 20, 21
`Apple Inc. v. Fintiv, Inc.,
`IPR2020-0019 (P.T.A.B., March 20, 2020) .................................... 24, 25, 27, 28
`Bayer Healthcare Pharms., Inc. v. Watson Pharms., Inc.,
`713 F.3d 1369 (Fed. Cir. 2013) .................................................................... 70, 71
`Bristol-Myers Squibb Co. v. Teva Pharms. USA, Inc.,
`752 F.3d 967 (Fed. Cir. 2014) ............................................................................ 23
`Dynamic Drinkware, LLC v. Nat’l Graphics, Inc.,
`800 F.3d 1375 (Fed. Cir. 2015) ...................................................................... 4, 20
`Guardant Health, Inc. v. Foundation Medicine, Inc.,
`1-20-cv-01580 (D. Del.) ..................................................................................... 73
`Medtronic, Inc. v. Niazi Licensing Corp.,
`IPR2018-00609 (P.T.A.B. Aug. 20, 2018) ......................................................... 20
`Ormco Corp. v. Align Technology, Inc.,
`463 F. 3d 1299 (Fed. Cir. 2006) ..................................................................passim
`In re Peterson,
`315 F.3d 1325 (Fed. Cir. 2003) .................................................................... 43, 51
`TwinStrand Biosciences, Inc. et al v. Guardant Health, Inc.,
`1-21-cv-01126 (D. Del.) ..................................................................................... 73
`
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`

`Case IPR2022-01115
`Patent 10,801,063
`
`
`Statutes
`35 U.S.C. §102(a)(1) ................................................................................................ 20
`35 U.S.C. §102(a)(2) ............................................................................................ 3, 20
`35 U.S.C. §314(a) .................................................................................................... 24
`35 U.S.C. §325(d) .............................................................................................. 20, 24
`Other Authorities
`37 C.F.R. §42.8(A)(1) .............................................................................................. 72
`37 C.F.R. §42.8(b)(1) ............................................................................................... 72
`37 C.F.R. §42.8(b)(2) ............................................................................................... 73
`37 C.F.R. §42.8(b)(3) ............................................................................................... 73
`37 C.F.R. §42.10(b) ................................................................................................. 74
`37 C.F.R. §42.63(e) .................................................................................................. 74
`37 C.F.R. §42.100(b) ............................................................................................... 18
`37 C.F.R. §42.104(A) .............................................................................................. 72
`37 C.F.R. §42.104(B) ............................................................................................... 19
`37 C.F.R. §42.106(a) ................................................................................................ 74
`
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`

`

`EXHIBIT LIST
`
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`Case IPR2022-01115
`Patent 10,801,063
`
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`Case IPR2022-01115
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`
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`with Suppl. Material (2015)
`Complaint, Illumina, Inc. v. Guardant Health, Inc.; Helmy Eltoukhy;
`And Amirali Talasaz, 22-cv-00334 (D.Del.) (March 17, 2022)
`Krimmel, J.D., et al., “Ultra-deep sequencing detects ovarian cancer
`cells in peritoneal fluid and reveals somatic TP53 mutations
`in noncancerous tissues,” PNAS 113(21): 6005-6010 (2016)
`Billet, H., “151 Hemoglobin and Hematocrit,” Clinical Methods The
`History, Physical and Laboratory Examinations, pp. 718-719, Third
`Edition, Butterworths United States (1990)
`Brown, T.A., Ed., “Chapter 4: Studying DNA,” Genomes, pp. 96-
`124, Second Edition, John Wiley & Sons, Inc., United States (2002)
`Stasinopoulos, D.M., et al., “Generalized Additive Models for
`Location Scale and Shape (GAMLSS) in R,” Journal of Statistical
`Software 23(7): 1-46 (2007)
`Final Written Decision, Foundation Medicine, Inc. v. Guardant
`Health, Inc., IPR2019-00652, Paper 47 (August 18, 2020)
`Dr. Spellman’s Calculations for prior art disclosures of molar ratios
`of adapters relative to DNA fragments
`Kitzman, J.O., et al., “Non-invasive whole genome sequencing of a
`human fetus,” Sci Transl Med. 4(137): 137ra76 (2012)
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`Case IPR2022-01115
`Patent 10,801,063
`
`
`Exhibit #
`
`Description
`
`1077
`
`1078
`
`1079
`
`1080
`
`1081
`
`1082
`
`1083
`
`
`
`ThruPLEX™ DNA-seq Kit Instruction Manual, Rubicon Genomics
`Complaint, Twinstrand Biosciences, Inc. & The University of
`Washington v. Guardant Health, Inc., 1-21-cv-01126 (D. Del.)
`(August 3, 2021)
` Decision Denying Institution for Inter Partes Review, Foundation
`Medicine, Inc. v. Guardant Health, Inc., IPR2019-00636 and
`IPR2019-00637 (August 20, 2019)
`Pray, L.A., “Eukaryotic Genome Complexity,” Nature Education
`1(1):96 (2008)
`Semsarian, C. and Seidman, C.E., “Molecular medicine in the 21st
`century,” Internal Medicine Journal 31: 53–59 (2001)
`Narayan et al., “Ultrasensitive Measurement of Hotspot Mutations
`in Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep
`Sequencing,” Cancer Research, 72(14):3492-3498 (2012)
`U.S. Provisional Application No. 61/625,623, filed on April 17, 2012
`
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`INTRODUCTION
`Guardant’s claimed methods were already known in the prior art. As
`
`Case IPR2022-01115
`Patent 10,801,063
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`I.
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`detailed below, Guardant’s claimed steps of tagging, amplifying, enriching,
`
`sequencing, mapping, grouping, generating a consensus sequence, and classifying
`
`consensus sequences as paired or unpaired, are all straight from Schmitt’s Duplex
`
`Sequencing, with only trivial additions.
`
`Further, Guardant misled the Office during prosecution in two significant
`
`ways. First, Guardant misrepresented the quantity of cell-free DNA (cfDNA) in a
`
`human blood sample, arguing that a skilled artisan would not have expected
`
`Schmitt’s methods to be applicable to cfDNA because human blood (according to
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`Guardant) contained insufficient quantities of cfDNA. Tellingly, Guardant never
`
`provided the Examiner with any prior art evidence to support its argument. It’s no
`
`wonder. The prior art flatly contradicts Guardant’s argument, showing that ample
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`quantities of cfDNA are present in human blood. In fact, the prior art expressly
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`suggested benefits of using Duplex Sequencing with cfDNA. EX1008, 7.
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`Second¸ Guardant misled the Examiner by relying on a statement from a
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`2017 publication—not prior art—as alleged evidence that a person of skill in the
`
`art in 2013 would not have expected Schmitt’s methods to work with cfDNA. But,
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`as explained above, Guardant’s position is contradicted by contemporaneous
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`evidence—including Schmitt itself—that taught applying Duplex Sequencing
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`methods to cfDNA.
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`Case IPR2022-01115
`Patent 10,801,063
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`The Board should institute trial and cancel the claims of the ’063 patent.
`
`II.
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`STATEMENT OF PRECISE RELIEF REQUESTED AND REASONS
`THEREFOR (37 C.F.R. §42.22(A))
`TwinStrand Biosciences, Inc. (“TwinStrand”) petitions for IPR, requesting
`
`cancellation of claims 1-28 of U.S. Patent No 10,801,063 (“the ’063 patent”;
`
`EX1001), assigned to Guardant Health, Inc. This Petition is supported by the
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`declaration of Paul Spellman, Ph.D. (EX1002), Professor of Molecular and
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`Medical Genetics and an expert in genetics and genomics approaches to detecting
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`and monitoring human diseases. This Petition demonstrates that claims 1-28 are
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`unpatentable as obvious.
`
`III. STATE OF THE ART BEFORE DECEMBER 2013
`Before the ’063 patent’s earliest possible priority date (December 28,
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`2013)1, next-generation sequencing (“NGS”) methods were well known. EX1011,
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`32-41; EX1002, ¶¶30-62.
`
`A. Optimization techniques for DNA library preparation were well
`known.
`Before December 2013, most NGS methods began with the preparation of a
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`library of template DNA fragments. This was accomplished by fragmenting DNA
`
`1 TwinStrand does not concede the ’063 patent is entitled to this priority
`
`date.
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`or by using previously fragmented DNA, such as cfDNA (discussed below).
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`Case IPR2022-01115
`Patent 10,801,063
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`EX1012, 291; EX1011, 32. Library preparation commonly involved “tagging” the
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`DNA with “adapters,” which were added to the DNA fragment ends. Id. Adapters
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`often contained “molecular barcodes” or “identifiers,” which are nucleotide
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`sequences that help to further identify and distinguish the sequenced DNA
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`fragments from one another. EX1083, ¶¶[0005], [0008]-[0009], [0030]; EX1005,
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`Fig. 1; EX1002, ¶40. A common technique for tagging was ligation. EX1083,
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`¶[0020]; EX1005, Fig. 1; EX1015, 4-5; EX1031, 11-12, Fig. 4; EX1002, ¶38.
`
`Guardant’s claims recite open-ended ranges of “more than a 10×” and “more
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`than a 90×” molar excesses of adapters relative to cfDNA molecules, and ligation
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`efficiencies of “at least 20%” and “at least 40%.” But long before December 2013,
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`artisans already knew to use significant molar excesses of adapters to achieve high
`
`efficiency ligations. EX1020, 18.4.15; EX1031, 2. EX1083, ¶[0005]; EX1002,
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`¶¶43-55; EX1021, 5, Fig. 2; EX10262, ¶¶[0130], [0143], [0159]; EX1025,
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`
`2 EX1026 (“Diehn ’807”) is the publication of U.S. 14/209,807 (filed March
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`13, 2014), which claims priority to U.S. 61/798,925 (filed March 15, 2013)
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`(EX1025, “Diehn ’925”). The Diehn ’925 provisional specification is substantially
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`the same as Diehn ’807’s specification, including identical claim sets. EX1025;
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`EX1026. Thus, Diehn ’807 is prior art to the ’063 patent under 35 U.S.C.
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`¶¶[0106], [0119], [0135].
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`For example, So 2004 taught th