`
`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
`_____________________
`
`EXHIBIT LIST
`
`
`
`
`
`
`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)
`
`
`
`
`
`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”)
`
`
`
`
`
`1026
`
`1027
`
`1028
`
`1029
`
`1030
`
`1031
`
`1032
`
`1033
`
`1034
`
`1035
`
`1036
`
`1037
`
`1038
`
`1039
`
`1040
`
`1041
`
`1042
`
`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
`
`
`
`
`
`1043
`
`1044
`
`1045
`
`Sparks et al., “Selective analysis of cell-free DNA in maternal blood
`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
`
`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”)
`
`
`
`
`
`1054
`
`1055
`
`1056
`
`1057
`
`1058
`
`1059
`
`1060
`
`Schwarzenbach et al., “Cell-free nucleic acids as biomarkers in cancer
`patients,” Nat. Rev. Cancer 2011, 11(6), 426-437 (“Schwarzenbach”)
`
`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
`
`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”)
`
`
`
`
`
`1067
`
`Schweiger et al., “Genome-wide massively parallel sequencing of
`formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for
`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
`
`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
`
`
`
`
`
`1078
`
`1079
`
`1080
`
`1081
`
`1082
`
`1083
`
`1084
`
`1085
`
`1086
`
`1087
`
`1088
`
`1089
`
`1090
`
`1091
`
`1092
`
`1093
`
`1094
`
`Arneson et al., “Whole-Genome Amplification by Adaptor-Ligation
`PCR of Randomly Sheared Genomic DNA (PRSG),” CSH Protocols,
`2008, 3(1) (“Arneson”)
`
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`Intentionally Left Blank
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`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”)
`
`1095
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`Transcript of July 19, 2019 Teleconference
`
`
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`
`
`
`
`Respectfully submitted,
`
`Date: August 5, 2019
`
`By: /Rolando Medina/
`
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`Rolando Medina, Reg. No. 54,756
`Eric J. Marandett, pro hac vice to be filed
`Margaret E. Ives, pro hac vice to be filed
`Matthew S. Barrett, pro hac vice to be filed
`Stephanie L. Schonewald, Reg. No. 72,452
`CHOATE, HALL & STEWART LLP
`Two International Place
`Boston, MA 02110
`617-248-5000
`Attorneys for Petitioner
`
`
`
`
`
`
`
`
`
`
`
`
`CERTIFICATE OF SERVICE
`
`The undersigned hereby certifies that the foregoing Exhibit List and
`
`EX1095 were served in their entirety on August 5, 2019 via electronic mail to the
`
`following attorneys of record:
`
` mrosato@wsgr.com
` sparmelee@wsgr.com
` sgerrard@wsgr.com
`
`
`
`
`
`
`
`Respectfully submitted,
`
`Date: August 5, 2019
`
`By: /Rolando Medina/
`
`
`
`
`
`
`Rolando Medina, Reg. No. 54,756
`Eric J. Marandett, pro hac vice to be filed
`Margaret E. Ives, pro hac vice to be filed
`Matthew S. Barrett, pro hac vice to be filed
`Stephanie L. Schonewald, Reg. No. 72,452
`CHOATE, HALL & STEWART LLP
`Two International Place
`Boston, MA 02110
`617-248-5000
`Attorneys for Petitioner
`
`
`
`
`
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