`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`____________________________________________
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`____________________________________________
`
`FOUNDATION MEDICINE, INC.,
`Petitioner,
`v.
`
`GUARDANT HEALTH, INC.,
`Patent Owner.
`
`_____________________
`
`Case No. IPR2019-00636
`U.S. Patent No. 9,902,992
`_____________________
`
`PETITION FOR INTER PARTES REVIEW
`OF U.S. PATENT NO. 9,902,992
`
` 
`
`
`
`
`

`

` 
`
`
`
`TABLE OF CONTENTS
`
`
`I. 
`INTRODUCTION ............................................................................................... 1 
`II.  OVERVIEW ..................................................................................................... 1 
`III.  TECHNOLOGY BACKGROUND ................................................................. 1 
`A.  DNA and Cell-Free DNA .............................................................................. 2 
`B.  Genetic Mutations ......................................................................................... 3 
`C. 
`Sequencing .................................................................................................... 4 
`D.  Base Calling................................................................................................... 6 
`E.  Alignment/Mapping ...................................................................................... 6 
`F. 
`Error Correction and Molecular Barcodes .................................................... 8 
`G. 
`Identifying Errors ........................................................................................ 11 
`H.  Analysis of Sequence Reads ....................................................................... 13 
`IV.  THE ’992 PATENT AND THE SKILL IN THE ART .................................. 13 
`A.  Brief Description of ’992 Patent ................................................................. 13 
`B. 
`Prosecution History ..................................................................................... 16 
`C. 
`Person of Ordinary Skill in the Art ............................................................. 17 
`V.  CLAIM CONSTRUCTION ........................................................................... 18 
`VI.  PRIOR ART RELIED ON ............................................................................. 20 
`A. 
`Schmitt (EX1011) ........................................................................................ 20 
`B. 
`Fan (EX1048) .............................................................................................. 25 
`C. 
`Forshew (EX1004) ...................................................................................... 26 
`VII. 
`STATEMENT OF THE PRECISE RELIEF REQUESTED FOR EACH
`CLAIM CHALLENGED ......................................................................................... 27 
`VIII.  DETAILED EXPLANATION OF GROUNDS FOR
`UNPATENTABILITY............................................................................................. 27 
`
`i
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`

` 
`
`A.  Ground 1: Claims 1-11, 13, 15-26 Are Unpatentable under 35 U.S.C. § 103
`over Schmitt and Fan or Forshew ......................................................................... 29 
`1.  Motivation to Combine Schmitt with Fan or Forshew ............................... 29 
`2.  Reasonable Expectation of Success ............................................................ 33 
`3.  Claim 1 ........................................................................................................ 36 
`4.  Claim 2: The method of claim 1, comprising providing less than 100
`nanograms (ng) of the cfDNA molecules. ......................................................... 50 
`Claim 3: The method of claim 1, comprising providing less than 10 nanograms
`(ng) of the cfDNA molecules. ........................................................................... 50 
`5.  Claim 4: The method of claim 1, comprising providing between 100 and
`100,000 human haploid genome equivalents of the cfDNA molecules, wherein
`the cfDNA molecules are tagged with between 2 and 1,000,000 unique
`identifiers. .......................................................................................................... 51 
`Claim 5: The method of claim 1, comprising providing between 1,000 and
`50,000 human haploid genome equivalents of the cfDNA molecules, wherein
`the cfDNA molecules are tagged with between 2 and 1,000 unique identifiers.
` ........................................................................................................................... 51 
`6.  Claim 6: The method of claim 1, wherein each of the plurality of different
`barcode sequences is at least 5 nucleotides in length. ....................................... 53 
`7.  Claim 7: The method of claim 1, wherein the attaching comprises non-
`uniquely tagging the cfDNA molecules with at least 10 and at most 1,000
`different barcode sequences. .............................................................................. 53 
`8.  Claim 8: The method of claim 1, wherein the attaching comprises uniquely
`tagging the cfDNA molecules. .......................................................................... 54 
`9.  Claim 9: The method of claim 1, wherein the attaching comprises
`performing blunt-end ligation or sticky end ligation. ........................................ 55 
`10.  Claim 10: The method of claim 1, wherein the attaching comprises non-
`uniquely tagging the cfDNA molecules such that no more than 5% of the
`tagged parent polynucleotides are uniquely tagged........................................... 55 
`11.  Claim 11: The method of claim 1, wherein at least 50% of the cfDNA
`molecules are tagged by the attaching. .............................................................. 56 
`
`ii
`
`

`

` 
`
`12.  Claim 13: The method of claim 1, further comprising selectively
`enriching for polynucleotides mapping to one or more selected reference
`sequences prior to the sequencing, wherein the selectively enriching comprises
`(i) subjecting the cfDNA molecules to selective amplification against the one
`or more selected reference sequences, (ii) subjecting the tagged parent
`polynucleotides to selective amplification against the one or more selected
`reference sequences, (iii) subjecting the amplified progeny polynucleotides to
`selective sequence capture against the one or more selected reference
`sequences, or (iv) subjecting the cfDNA molecules to selective sequence
`capture against the one or more selected reference sequences. ......................... 57 
`13.  Claim 15: The method of claim 1, wherein sequencing comprises
`massively parallel sequencing. .......................................................................... 58 
`14.  Claim 16: The method of claim 1, wherein the amplified tagged progeny
`polynucleotides are sequenced to produce an average of 5 to 10 sequence reads
`for each family. .................................................................................................. 58 
`15.  Claim 17: The method of claim 1, wherein the base call for each family
`possesses an error rate below 0.0001%. ............................................................ 59 
`16.  Claim 18: The method of claim 1, wherein each base of the tagged parent
`polynucleotides has at least 99% chance of being represented by at least one
`sequence read among the sequence reads mapped in e). ................................... 59 
`17.  Claim 19: The method of claim 4, wherein grouping the sequence reads
`mapped in e) is further based on one or more of: sequence information at a
`beginning of the sequence derived from the cfDNA molecule, sequence
`information at an end of the sequence derived from the cfDNA molecule, and
`length of the sequence read. .............................................................................. 61 
`18.  Claim 20: The method of claim 4, wherein grouping the sequence reads
`mapped in e) is further based on a plurality of: sequence information at a
`beginning of the sequence derived from the cfDNA molecule, sequence
`information at an end of the sequence derived from the cfDNA molecule, and
`length of the sequence read. .............................................................................. 62 
`19.  Claim 21: The method of claim 1, wherein at least one single base
`substitution is detected. ...................................................................................... 63 
`
`iii
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`

` 
`
`Claim 22: The method of claim 1, wherein the two or more members comprise
`a copy number variation (CNV). ....................................................................... 63 
`20.  Claim 23: The method of claim 1, wherein at least one indel is detected.
`
`63 
`Claim 24: The method of claim 1, wherein at least one gene fusion is detected.
` ........................................................................................................................... 63 
`21.  Claim 25: The method of claim 1, wherein at least one single base
`substitution and at least one copy number variation is detected. ...................... 65 
`22.  Claim 26: The method of claim 1, further comprising detecting, at one or
`more genetic loci, one or more genetic aberrations selected from: a
`transversion, a translocation, an inversion, a deletion, aneuploidy, partial
`aneuploidy, polyploidy, chromosomal instability, chromosomal structure
`alterations, chromosome fusions, a gene truncation, a gene amplification, a
`gene duplication, a chromosomal lesion, a DNA lesion, abnormal changes in
`nucleic acid chemical modifications, abnormal changes in epigenetic patterns
`and abnormal changes in nucleic acid methylation. .......................................... 66 
`B.  No Objective Indicia of Nonobviousness.................................................... 66 
`IX.  THE BOARD SHOULD NOT DENY INSTITUTION UNDER § 325(d) ... 67 
`X.  CONCLUSION .............................................................................................. 70 
`XI.  MANDATORY NOTICES ............................................................................ 70 
`A.  Real Party-in-Interest (37 C.F.R § 42.8(b)(1)) ............................................ 70 
`B.  Related Matters (37 C.F.R. § 42.8(b)(2)) .................................................... 70 
`C.  Counsel (37 C.F.R. §§ 42.8(b)(3) and 42.10(a)) ......................................... 72 
`D. 
`Service Information (37 C.F.R. § 42.8(b)(4)) ............................................. 72 
`E. 
`Standing (37 C.F.R. § 42.104(a)) ................................................................ 73 
`
`
`
`
`
`
`
`iv
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`

` 
`
`TABLE OF AUTHORITIES
`
`Page(s)
`
`Federal Cases
`
`Dynamic Drinkware, LLC v. Nat’l Graphics, Inc., 800 F.3d 1375
`(Fed. Cir. 2015)…………………………………………………………………...21
`
`In re Huai-Hung Kao, 639 F.3d 1057, 1068 (Fed. Cir. 2011……………………..67
`
`Leapfrog Enters., Inc. v. Fisher-Price Inc., 485 F.3d 1157 (Fed. Cir. 2007)……..67
`
`MCM Portfolio LLC v. Hewlett-Packard Co., 812 F.3d 1284 (Fed. Cir. 2015)…..69
`
`Phillips v. AWH Corp., 415 F.3d 1303 (Fed. Cir. 2005)………………………….18
`
`Patent Trial and Appeal Board Cases
`
`Donghee America, Inc. v. Plastic Omnium Advanced Innovation and Research,
`IPR2017-01654, Slip. Op (PTAB Jan. 19, 2018)…………………………………68
`
`Eli Lilly & Co. v. Trustees of U. Penn., IPR2016-00458, Slip. Op (PTAB July 14,
`2016)………………………………………………………………………………67
`
`Medtronic, Inc. v. Niazi Licensing Corp., IPR2018-00609, Slip. Op (PTAB Aug.
`20, 2018)…………………………………………………………………………..20
`
`Umicore AG & Co. KG v. BASF Corp., IPR2015-01124, Slip. Op (PTAB Nov. 2,
`2015)………………………………………………………………………………67
`
`Statutes
`
`35 U.S.C. § 102(a)(1)…………………………………………………………25, 26
`
`35 U.S.C. § 102(a)(2) …………………………………………………………….21
`
`v
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`

` 
`
`35 U.S.C. § 103………………………………………………………………27, 29
`35 U.S.C. § 103 ........................................................................ 27, 29
`
`35 U.S.C. § 119 …………………………………………………………………..20
`35 U.S.C. § 119 ............................................................................. 20
`
`35 U.S.C. 282(b) …………………………………………………………………18
`35 U.S.C. 282(b) ........................................................................... 18
`
`35 U.S.C. § 311………………………………………………………………...1, 27
`35 U.S.C. § 311 ........................................................................... 1, 27
`
`35 U.S.C. § 325(d) ………………………………………………………………..68
`35 U.S.C. § 325(d) .......................................................................... 68
`
`Regulations
`Regulations
`
`37 C.F.R § 42.8……………………………………………………………70, 71, 72
`37 CPR § 42.8 ..................................................................... 70, 71, 72
`
`37 C.F.R. § 42.6(e) ……………………………………………………………….75
`37 C.F.R. § 42.6(e) ......................................................................... 75
`
`37 C.F.R. § 42.10(a) ……………………………………………………………..72
`37 C.F.R. §42.10(a) ....................................................................... 72
`
`37 C.F.R. § 42.24(a) ………………………………………………………….…..74
`37 C.F.R. § 42.24(a) ........................................................................ 74
`
`37 C.F.R. § 42.100(b) …………………………………………………………….18
`37 C.F.R. §42.100(b) ...................................................................... 18
`
`37 C.F.R. § 42.104(a) …………………………………………………………….73
`37 C.F.R. § 42.104(a) ...................................................................... 73
`
`37 C.F.R. § 42.105(a) …………………………………………………………….75
`37 C.F.R. §42.105(a) ...................................................................... 75
`
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`vi
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`Vi
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`

`

` 
`
`Exhibit
`No.
`1001
`
`1002
`
`1003
`
`1004
`
`EXHIBIT LIST
`
`Description
`
`U.S. Patent No. 9,902,992 (“the '992 patent”)
`
`Declaration of Dr. Stacey Gabriel (“Gabriel Declaration”)
`
`Curriculum Vitae of Dr. Stacey Gabriel
`
`Forshew et al., “Noninvasive Identification and Monitoring of Cancer
`Mutations by Targeted Deep Sequencing of Plasma DNA,” Science
`Translational Medicine, 2012, 4(136) (“Forshew”)
`
`1005 Meyerson et al., “Advances in understanding cancer genomes through
`second-generation sequencing,” Nature Review Genetics, Vol. 11
`(2010), 685-696 (“Meyerson”)
`
`1006 Williford and Betrán, “Gene Fusion,” eLS 2013, 1-8 (“Williford”)
`
`1007
`
`1008
`
`1009
`
`1010
`
`1011
`
`1012
`
`1013
`
`Ding et al., “Analysis of next-generation genomic data in cancer:
`accomplishments and challenges,” Hum. Mol. Genet. 2010 19(R2),
`R188-R196 (“Ding”)
`
`Sehnert et al., “Optimal Detection of Fetal Chromosomal
`Abnormalities by Massively Parallel DNA Sequencing of Cell-free
`Fetal DNA from Maternal Blood,” Clinical Chemistry 2011, 57:7,
`1042-1049 (“Sehnert”)
`
`Redon et al., “Global variation in copy number in the human
`genome,” Nature 2006 444(7118), 444-454 (“Redon”)
`
`Gordon et al., “Causes and consequences of aneuploidy in cancer,”
`Nat. Rev. Genet. 2012 13(3), 189-203 (“Gordon”)
`
`U.S. Patent No. 9,752,188 (“Schmitt”)
`
`U.S. Provisional Application 61/613,413 (“Schmitt '413 provisional”)
`
`Duncan and Patel, Diagnostic Molecular Pathology: A Guide to
`Applied Molecular Testing 25-33 (Coleman and Tsongalis eds., 1st
`ed. 2016)
`
`vii
`
`

`

` 
`
`1014
`
`1015
`
`1016
`
`1017
`
`1018
`
`1019
`
`1020
`
`1021
`
`1022
`
`Nielsen et al., “Genotype and SNP calling from next-generation
`sequencing data,” Nat. Rev. Genet. 2011 12(6), 443-451 (“Nielsen”)
`
`Shendure and Ji, “Next-generation DNA sequencing,” Nat.
`Biotechnol. 2008 26(10), 1135-1145 (“Shendure”)
`
`Kao et al., “BayesCall: A model-based base-calling algorithm for
`high-throughput short-read sequencing,” Genome Res. 2009 19(10),
`1884-1895 (“Kao”)
`
`Quinlan et al., “Pyrobayes: an improved base caller for SNP
`discovery in pyrosequences,” Nat. Methods 2008 5(2), 179-181
`(“Quinlan”)
`
`Liang et al., “Bayesian basecalling for DNA sequence analysis using
`hidden Markov models,” IEE/ACM Trans. Comput. Biol. Bioinform.
`2007 4(3), 430-440 (“Liang”)
`
`Ledergerber and Dessimoz, “Base-calling for next-generation
`sequencing platforms,” Brief Bioinform. 2011 12(5), 489-497
`(“Ledergerber”)
`
`Kircher et al., “Improved base calling for the Illumina Genome
`Analyzer using machine learning strategies,” Genome Biol. 2009,
`10(8), R83 (“Kircher”)
`
`U.S. Patent No. 6,582,908 (“Fodor”)
`
`U.S. Patent No. 9,476,095 (“Kinde”)
`
`1023 Metzker, “Sequencing technologies - the next generation,” 2010
`11(1), 31-46 (“Metzker”)
`
`1024
`
`1025
`
`Lo et al., “Quantitative analysis of fetal DNA in maternal plasma and
`serum: implications for noninvasive prenatal diagnosis,” Am. J. Hum.
`Genet. 1998, 62(4), 768-775 (“Lo”)
`
`Narayan et al., “Ultrasensitive Measurement of Hotspot Mutations in
`Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep
`Sequencing,” Cancer Res. 2012 72(14), 3492-3498 (published July
`15, 2012) (“Narayan”)
`
`viii
`
`

`

` 
`
`1026
`
`1027
`
`1028
`
`1029
`
`1030
`
`1031
`
`1032
`
`1033
`
`1034
`
`1035
`
`1036
`
`1037
`
`1038
`
`1039
`
`1040
`
`1041
`
`1042
`
`1043
`
`International Publication No. WO 2012/042374 A2 (“Taipale”)
`
`U.S. Patent Application No. 15/076,565 (the “'565 application”)
`
`U.S. Patent Application No. 15/076,565 March 21, 2016 TrackOne
`Request
`
`U.S. Patent Application No. 15/076,565 April 29, 2016 Application
`Data Sheet
`
`U.S. Patent Application No. 15/076,565 June 10, 2016 TrackOne
`Request Granted
`
`U.S. Patent Application No. 15/076,565 June 15, 2017 Notice of
`Allowance
`
`U.S. Patent Application No. 15/076,565 February 9, 2017 Non-Final
`Rejection
`
`U.S. Patent Application No. 15/076,565 February 9, 2017 List of
`References Cited by Examiner
`
`U.S. Patent Application No. 15/076,565 February 9, 2017 List of
`References Cited by Applicant and Considered by Examiner
`
`U.S. Patent Application No. 15/076,565 May 9, 2017 Amendment
`and Response to Non-Final Office Action
`
`U.S. Provisional 61/696,734
`
`U.S. Provisional 61/704,400
`
`U.S. Provisional 61/793,997
`
`U.S. Provisional 61/845,987
`
`PCT/US2013/058061
`
`U.S. Patent Application No. 13/969,260
`
`U.S. Provisional 61/948,530
`
`Sparks et al., “Selective analysis of cell-free DNA in maternal blood
`
`ix
`
`

`

` 
`
`1044
`
`1045
`
`for evaluation of fetal trisomy,” Prenat. Diagn. 2012, 32(1), 3-9
`(“Sparks”)
`
`U.S. Patent No. 8,209,130 (“Kennedy”)
`
`April 5, 2018 Memorandum from Deputy Commissioner for Patent
`Examination Policy to Patent Examining Corps
`
`1046 Mertes et al., “Targeted enrichment of genomic DNA regions for
`next-generation sequencing,” Brief Funct. Genomics 2011, 10(6),
`374-386 (“Mertes”)
`
`1047
`
`1048
`
`1049
`
`1050
`
`1051
`
`1052
`
`1053
`
`1054
`
`Schmitt et al., “Detection of ultra-rare mutations by next-generation
`sequencing,” Proc. Natl. Acad. Sci. USA 2012, 109(36), 14508-14513
`(“Schmitt 2012”)
`
`Fan et al., “Noninvasive diagnosis of fetal aneuploidy by shotgun
`sequencing DNA from maternal blood,” Proc. Natl. Acad. Sci. USA
`2008, 105(42), 16266-16271 (“Fan”)
`
`Kinde et al., “Detection and quantification of rare mutations with
`massively parallel sequencing,” Proc. Natl. Acad. Sci. USA 2011,
`108(23), 9530-9535 (“Kinde 2011”)
`
`Chiu et al., “Non-invasive prenatal assessment of trisomy 21 by
`multiplexed maternal plasma DNA sequencing: large scale validity
`study”, BMJ 2011;342, c7401 (“Chiu”)
`
`Diehl et al., “Detection and quantification of mutations in the plasma
`of patients with colorectal tumors,” Proc. Natl. Acad. Sci. USA 2005,
`102(45), 16368-16373 (“Diehl”)
`
`Liao et al., “Targeted massively parallel sequencing of maternal
`plasma DNA permits efficient and unbiased detection of fetal alleles,”
`Clin. Chem. 2011, 57(1), 92-101 (“Liao”)
`
`Vasyukhin et al., Challenges of Modern Medicine, 141-150 (Verna
`and Shamoo eds, 1994) (“Vasyukhin”)
`
`Schwarzenbach et al., “Cell-free nucleic acids as biomarkers in cancer
`patients,” Nat. Rev. Cancer 2011, 11(6), 426-437 (“Schwarzenbach”)
`
`x
`
`

`

` 
`
`1055
`
`1056
`
`1057
`
`1058
`
`1059
`
`1060
`
`Koboldt et al., “The next-generation sequencing revolution and its
`impact on genomics,” Cell 2013, 155(1), 27-38 (“Koboldt”)
`
`Kirsch and Klein, “Sequence error storms and the landscape of
`mutations in cancer,” Proc. Natl. Acad. Sci. USA 2012 109(36),
`14289-14290 (“Kirsch and Klein”)
`
`Kennedy et al., “Detecting ultralow-frequency mutations by Duplex
`Sequencing,” Nat. Protoc. 2014, 9(11), 2586-2606 (“Kennedy 2014”)
`
`Kivioja et al., “Counting absolute numbers of molecules using unique
`molecular identifiers,” Nat. Methods 2011, 9(1), 72-74 (“Kivioja”)
`
`Kinde et al., “FAST-SeqS: a simple and efficient method for the
`detection of aneuploidy by massively parallel sequencing,” PLoS One
`2012, 7(7), e41162 (“Kinde 2012”)
`
`Krimmel et al., “Ultra-deep sequencing detects ovarian cancer cells in
`peritoneal fluid and reveals somatic TP53 mutations in noncancerous
`tissues,” Proc. Natl. Acad. Sci. USA 2016, 113(21), 6005-6010
`(“Krimmel”)
`
`1061 Meyer and Kircher, “Illumina sequencing library preparation for
`highly multiplexed target capture and sequencing,” Cold Spring Harb.
`Protoc. 2010, (6), prot5448 (“Meyer and Kircher”)
`
`1062
`
`1063
`
`1064
`
`1065
`
`1066
`
`1067
`
`Quail et al., “A large genome center's improvements to the Illumina
`sequencing system,” Nat. Methods 2008, 5(12), 1005-1010 (“Quail”)
`
`Lohman, Efficient Adaptor Ligation for the Preparation of dsDNA
`Libraries using the Blunt/TA Ligase Master Mix (“Lohman”)
`
`U.S. Patent No. 8,865,410
`
`Ng et al., “Targeted capture and massively parallel sequencing of 12
`human exomes,” Nature 2009, 461(7261), 272-276 (“Ng”)
`
`Albert et al., “Direct selection of human genomic loci by microarray
`hybridization,” Nat. Methods 2007, 4(11), 903-905 (“Albert”)
`
`Schweiger et al., “Genome-wide massively parallel sequencing of
`formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for
`
`xi
`
`

`

` 
`
`copy-number- and mutation-analysis,” PLoS One 2009, 4(5), e5548
`(“Schweiger”)
`
`1068 McKernan et al., “Sequence and structural variation in a human
`genome uncovered by short-read, massively parallel ligation
`sequencing using two-base encoding,” Genome Res. 2009, 19(9),
`1527-1541 (“McKernan”)
`
`1069
`
`1070
`
`1071
`
`1072
`
`1073
`
`Ajay et al., “Accurate and comprehensive sequencing of personal
`genomes,” Genome Res. 2011, 21(9), 1498-1505 (“Ajay”)
`
`U.S. Patent Application No. 14/712,754 December 4, 2015 Office
`Action
`
`U.S. Patent No. 8,697,408 (“Kucera”)
`
`Nawroz et al., “Microsatellite alterations in serum DNA of head and
`neck cancer patients,” Nat. Med. 1996, 2(9), 1035-1037 (“Nawroz”)
`
`Korbel et al., “Paired-end mapping reveals extensive structural
`variation in the human genome,” Science 2007, 318(5849), 420-426
`(“Korbel”)
`
`1074 Wheeler et al., “The complete genome of an individual by massively
`parallel DNA sequencing,” Nature 2008, 452(7189), 872-876
`(“Wheeler”)
`
`1075 Mamanova et al., “Target-enrichment strategies for next-generation
`sequencing,” Nat. Methods 2010, 7(2), 111-118 (“Mamanova”)
`
`1076
`
`1077
`
`1078
`
`Parkinson et al., “Preparation of high-quality next-generation
`sequencing libraries from picogram quantities of target DNA,”
`Genome Res. 2012, 22(1), 125-133 (“Parkinson”)
`
`Li and Durbin, “Fast and accurate short read alignment with
`Burrows–Wheeler transform,” Bioinformatics 2009, 25(14), 1754-
`1760
`
`Arneson et al., “Whole-Genome Amplification by Adaptor-Ligation
`PCR of Randomly Sheared Genomic DNA (PRSG),” CSH Protocols,
`2008, 3(1) (“Arneson”)
`
`xii
`
`

`

` 
`
`1079
`
`1080
`
`1081
`
`1082
`
`1083
`
`1084
`
`1085
`
`1086
`
`1087
`
`1088
`
`1089
`
`1090
`
`1091
`
`1092
`
`1093
`
`1094
`
`Intentionally Left Blank
`
`Intentionally Left Blank
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`Intentionally Left Blank
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`Intentionally Left Blank
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`
`Intentionally Left Blank
`
`Intentionally Left Blank
`
`Intentionally Left Blank
`
`U.S. Provisional Application 61/625,319 (“Schmitt '319 provisional”)
`
`Intentionally Left Blank
`
`Bryzgunova et al., “A reliable method to concentrate circulating
`DNA,” Analytical Biochem., 2010, 408:354-356 (“Bryzgunova”)
`
`xiii
`
`

`

` 
`
`I.
`
`INTRODUCTION
`Pursuant to 35 U.S.C. § 311 and 37 C.F.R. § 42.100 et seq., Foundation
`
`Medicine, Inc. (“Petitioner”) hereby respectfully requests inter partes review of
`
`claims 1-11, 13, 15-26 of United States Patent No. 9,902,992 (“the ’992 patent”)
`
`(EX1001). The ’992 patent issued on February 27, 2018 and is assigned to
`
`Guardant Health, Inc. (“Patent Owner”). The ’992 patent is subject to the first
`
`inventor to file provisions of the AIA. EX1029, at 5. This Petition demonstrates
`
`by a preponderance of the evidence that it is more likely than not that claims 1-11,
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`13, and 15-26 of the ’992 patent are unpatentable over the prior art.
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`II. OVERVIEW
`The claims of the ’992 patent are directed to methods for detecting genetic
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`aberrations (i.e., genetic variations) in cell-free DNA, but merely recite producing
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`sequence reads using ordinary sequencing techniques and then sorting the
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`sequence reads into groups, to be compared to one another and to a known
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`reference to identify mutations. As described further below, a person of ordinary
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`skill in the art (“POSA”) would have found claims 1-11, 13, 15-26 to be obvious in
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`view of the prior art as of September 4, 2012, the earliest claimed priority date.
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`III. TECHNOLOGY BACKGROUND
`The claims of the ’992 patent are directed to methods for detecting genetic
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`aberrations in cell-free DNA. EX1001.
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`A. DNA and Cell-Free DNA
`DNA molecules consist of two strands, each of which is a linear
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`arrangement of repeating units called “nucleotides.” EX1002, ¶18. DNA is also
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`therefore referred to as a “polynucleotide.” Id. As illustrated below, four chemical
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`bases comprise the nucleotides of DNA: adenine (A), guanine (G), cytosine (C),
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`and thymine (T). Id., ¶19. The order of these bases—referred to as the
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`“sequence”—determines the information available for building and maintaining an
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`organism:
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`Id.
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`
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`DNA is typically present in cells, but in an organism, DNA may be released
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`from cells into the bloodstream. EX1002, ¶21. Once released, this DNA is called
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`“circulating cell-free DNA”—or sometimes simply “cell-free DNA” or
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`“circulating DNA.” Id. Tumor cell DNA that has been released into the
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`bloodstream is sometimes called “circulating tumor DNA” or “ctDNA.” Id. DNA
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`that has been released from circulating fetal cells into the bloodstream of pregnant
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`2
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`women is sometimes called “circulating fetal DNA” (“cfDNA”) or “cell-free fetal
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`DNA” (“cffDNA”). Id.; EX1004, 1 (citing publications).
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`B. Genetic Mutations
`DNA sometimes undergoes changes to its structure referred to as genetic
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`variations or mutations. EX1002, ¶22. Mutations can range in size, affecting
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`anywhere from a single base pair to a large segment of a chromosome. Id., ¶23.
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`Substitutions involving a single base pair are called “single nucleotide variants,”
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`and are the most common type of tumor-related genetic mutation. Id., ¶24;
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`EX1005, 690.
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`Another type of variation is a “gene fusion,” occurring when partial or
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`complete sequences of two or more distinct genes join together to form a chimeric
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`gene or “fusion gene.” EX1006, Abstract; EX1002, ¶25. Fusion genes may be
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`found in several types of cancer, including leukemia. EX1002, ¶25; EX1007,
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`R190.
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`Another common type of variation is known as “copy number variation,” or
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`CNV, occurring when copies of some section of the genome are either amplified or
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`lost. EX1002, ¶26. Such sections of the genome may include sections of genes,
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`entire genes, large portions of a chromosome, or entire chromosomes. Id.;
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`EX1008, 1048; EX1009, 444; EX1010, 189-191. For example, aneuploidy is a
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`type of CNV associated with the presence of an abnormal number of
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`3
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`chromosomes, and includes “trisomy” in which there are three copies of a
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`particular chromosome instead of the normal two. EX1002, ¶26. Trisomy 21
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`(“T21”), referring to the presence of all or part of a third copy of chromosome 21,
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`is also known as Down syndrome. Id.
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`Sequencing
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`C.
`One way to identify genetic variations in an individual’s DNA is through a
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`process called “sequencing,” which determines the order of nucleotides in a DNA
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`fragment. EX1002, ¶29. DNA fragments are read by a sequencer to produce
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`sequence reads, as illustrated below:
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`
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`Id., ¶30.
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`The sequencing technology employed today for mutation detection referred
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`to as Next Generation Sequencing, or NGS, is sometimes also called massively
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`parallel sequencing or high-throughput sequencing. Id., ¶32. NGS technologies
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`began to emerge in the mid-2000s and were in widespread use by no later than
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`September 2012. Id.; EX1011, 1:28-37; EX1012, [0002]. The specification of the
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`’992 patent acknowledges that the alleged invention includes “sequencing of cell
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`free polynucleotides by techniques known in the art,” EX1001, 30:21-22, and
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`identifies numerous methods of sequencing known in the art. Id., 37:66-38:11.
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`Identifying genomic variations through NGS can include making copies of
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`the DNA fragments of interest through a process called amplification. EX1002,
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`¶33. The ’992 patent explains that amplification can be performed using
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`polymerase chain reaction (“PCR,” developed in the 1980s). Id.; EX1001, 38:52-
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`64. PCR creates copies of DNA fragments exponentially as illustrated below:
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`
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`EX1002 ¶33. As described further below, the ’992 patent refers to the original
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`DNA fragments as “parent polynucleotides” and to the amplified copies as
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`“progeny polynucleotides.” EX1001, Figure 9.
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`5
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`Following amplification, each amplified copy is sequenced to produce a
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`“sequence read,” indicating the order of nucleotide bases in each amplified DNA
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`molecule. EX1002, ¶34; EX1011, 3:10-20; EX1012, [0009].
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`D. Base Calling
`The process by which the sequence read is converted into nucleotide bases is
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`called “base calling.” EX1013, 29. This process utilizes base calling algorithms,
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`which also assign a measure of the uncertainty (called a “quality score”) to each
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`base call. EX1014, 444. Base-calling procedures vary according to the sequencing
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`platform used and are prone to different types of errors. Id. The typical error rate
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`for different NGS platforms ranges from a few tenths of a percent to several
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`percent. Id. Reducing the error rate of base calls and improving the accuracy of
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`the per-base quality score is important for reliable post-sequencing analysis.
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`EX1002, ¶35. As of September 2012, several base-calling algorithms had been
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`developed that provided ~5–30% improvement in error rates. EX1002, ¶36;
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`EX1015; EX1016; EX1017; EX1018; EX1019. As the ’992 patent acknowledges,
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`such methods were known in the art. EX1001, 47:42-50.
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`E. Alignment/Mapping
`After sequence reads are generated, they typically are compared to a
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`reference sequence, in a process called “alignment” or “mapping.” EX1002, ¶37.
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`The reference sequence may consist of a sequence from the genome of an
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`6
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`individual known to be healthy. Id. As illustrated below, if a sequence read aligns
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`perfectly with the reference sequence, it does not contain a mutation, whereas if it
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`differs at one or more nucleotide bases, the sequence read is identified as
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`containing a mutation:
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`
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`Id.
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`Mapping a sequence read to a reference sequence is a necessary step in
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`identifying genetic mutations because a genetic variant can be identified only when
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`the sequence differs from the reference at one or more nucleotide positions.
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`EX1002, ¶37. Mapping sequence reads enables one to detect any number of
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`genetic mutations, including but not limited to, deletions, insertions, gene fusions,
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`and copy number variation. EX1002, ¶¶38-39, ¶38 (figure).
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`
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`Accordingly, as of September 2012, a POSA would have understood any
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`method of identifying rare mutations to include mapping sequence reads to a
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`reference genome. EX1002, ¶40. The ’992 patent explains that reference
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`sequences were readily available: “Human genome sequences useful as references
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`can include the hg19 assembly or any previous or available hg assembly. Such
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`7
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`sequences can be
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`interrogated using
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`the genome browser available at
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`genome.ucsc.edu/index.html.” EX1001, 35:35-40.
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`F. Error Correction and Molecular Barcodes
`Amplification and sequencing can produce errors. EX1002, ¶41. For
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`example, if the sequence of the original fragment is A-G-C-T-A-G, one of the
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`nucleotide bases may be miscopied during the amplification process, resulting in
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`an amplified copy with the sequence A-G-C-T-G-G. Id. The sequencer may also
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`misread one or more nucleotide bases.