Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 1 of 11 PageID #: 7488
`
`
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`GUARDANT HEALTH, INC.,
`
`
`Plaintiff,
`
`
`
`
`
`C.A. No. 20-1580 (LPS)
`
`
`
`
`
`
`)))))))))
`
`
`
`
`FOUNDATION MEDICINE, INC.,
`
`
`v.
`
`Defendant.
`
`
`
`
`
`
`FOUNDATION MEDICINE INC.’S APPENDIX IN SUPPORT OF
`BRIEF IN OPPOSITION TO GUARDANT HEALTH, INC.’S
`MOTION FOR A PRELIMINARY INJUNCTION
`
`VOLUME 1 OF 4 (EXHIBITS 1-50)
`
`MORRIS, NICHOLS, ARSHT & TUNNELL LLP
`Karen Jacobs (#2881)
`Jeremy A. Tigan (#5239)
`1201 North Market Street
`P.O. Box 1347
`Wilmington, DE 19899
`(302) 658-9200
`kjacobs@morrisnichols.com
`jtigan@morrisnichols.com
`
`Attorneys for Foundation Medicine, Inc.
`
`
`
`
`
`
`
`
`
`OF COUNSEL:
`
`Eric J. Marandett
`G. Mark Edgarton
`Sophie F. Wang
`Diane Seol
`CHOATE HALL & STEWART LLP
`Two International Place
`Boston, MA 02110
`(617) 248-5000
`
`
`
`
`
`PUBLIC VERSION
`
`Confidential Version Filed: February 26, 2021
`
`Public Version Filed: March 5, 2021
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 2 of 11 PageID #: 7489
`
`
`
`INDEX TO APPENDIX
`
`Ex.
`
`Date
`
`Document Description
`
`Feb. 26,
`2021
`Aug. 1,
`2020
`
`
`
`
`
` Oct. 1,
`2020
`Oct. 26,
`2020
`
`
`
`Nov. 1,
`2020
`
`Nov. 6,
`2020
`Nov. 9,
`2020
`
`
`
`
`
`
`
` Dec. 1,
`2020
`Feb. 4,
`2021
`
`
`
`1
`
`2
`
`3
`
`4
`
`5
`
`6
`
`7
`
`8
`
`9
`
`10 Oct. 1,
`2016
`11 June 1,
`2018
`12 May 1,
`2019
`13 Sept. 1,
`2020
`14 Dec. 1,
`2020
`Jan. 26,
`2007
`
`15
`
`Declaration of Jeremy A. Tigan in Support of Foundation Medicine, Inc.’s
`Brief in Opposition to Guardant’s Motion for a Preliminary Injunction
`Guardant360 CDx Technical Information
`Simon Exhibit 3
`(produced version available at, e.g., GHFMI-1580_0031841-GHFMI-
`1580_0031903)
`Rubraca® Label
`
`FoundationOne® Liquid CDx Summary of Safety and Effectiveness Data
`(SSED)
`FM1580-00006828-FM1580-00006891
`FoundationOne® Liquid CDx Technical Information – RAL-0035-03
`(FDA Label)
`Simon Exhibit 4
`(produced version available at FM1580-00005351-FM1580-00005396)
`FDA Letter Re: P200016 FoundationOne® Liquid CDx available at
`https://www.accessdata.fda.gov/cdrh_docs/pdf20/P200016A.pdf
`Foundation Medicine Press Release, “Foundation Medicine Expands
`Indication for FoundationOne® Liquid CDx to be used as a Companion
`Diagnostic for LYNPARZA®”
`FM1580-00045681-FM1580-00045685
`Lynparza® Label
`
`FDA, List of Cleared or Approved Companion Diagnostic Devices (In
`Vitro and Imaging Tools) available at
`https://www.fda.gov/medical-devices/vitro-diagnostics/list-cleared-or-
`approved-companion-diagnostic-devices-vitro-and-imaging-tools
`Tarceva® Label
`
`Alecensa® Label
`
`Iressa® Label
`
`Piqray® Label
`
`Tagrisso® Label
`
`Schindl et al., “Overexpression of the Human Homologue for
`Caenorhabditis elegans cul-4 gene is Associated with Poor Outcome in
`Node-negative Breast Cancer,” Anticancer Research (2007) 27:949-952
`
`- 1 -
`
`Appendix
`Page
`Numbers
`A0001-
`A0002
`A0003-
`A0065
`
`A0066-
`A0087
`A0088-
`A0151
`
`A0152-
`A0197
`
`A0198-
`A0205
`A0206-
`A0210
`
`A0211-
`A0228
`A0229-
`A0241
`
`A0242-
`A0260
`A0261-
`A0282
`A0283-
`A0289
`A0290-
`A0311
`A0312-
`A0323
`A0324-
`A0327
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 3 of 11 PageID #: 7490
`
`
`
`Ex.
`
`Date
`
`Apr. 21,
`2015
`
`Feb. 15,
`2018
`
`16
`
`17
`
`18 Mar. 30,
`2018
`19 Apr. 25,
`2018
`Apr. 26,
`2018
`
`20
`
`Sept. 27,
`2018
`
`21
`
`22 Dec. 20,
`2018
`23 Dec. 20,
`2018
`24 July 20,
`2020
`Aug. 26,
`2020
`
`25
`
`
`
`26
`
`1948
`
`March
`1977
`
`27
`
`28
`
`Document Description
`
`Salvi et al., “Circulating cell-free AR and CYP17A1 copy number
`variations may associate with outcome of metastatic castration-resistant
`prostate cancer patients treated with abiraterone,” BJC (2015) 112, 1717-
`1724
`Press Release, “The Guardant360 Assay Receives Expedited Access
`Pathway Designation for Breakthrough Devices from FDA” available at
`https://investors.guardanthealth.com/press-releases/press-
`releases/2018/The-Guardant360-Assay-Receives-Expedited-Access-
`Pathway-Designation-for-Breakthrough-Devices-from-FDA/default.aspx
`FM1580-00007608-FM1580-00007616
`
`FM1580-00007616-FM1580-00007619
`
`Foundation Medicine Press Release, “Foundation Medicine’s New Liquid
`Biopsy Assay Granted Breakthrough Device Designation by U.S. Food and
`Drug Administration” available at
`https://www.foundationmedicine.com/press-releases/991ce685-7dbf-400a-
`aa33-eb4f9d411ed3
`FDA Guidance on Laboratory Developed Tests available at
`https://www.fda.gov/medical-devices/vitro-diagnostics/laboratory-
`developed-tests
`FM1580-00008092-FM1580-00008095
`
`FM1580-00008063
`
`FM1580-00051364-FM1580-00051365
`
`Foundation Medicine Press Release, “FDA Approves Foundation
`Medicine’s FoundationOne® Liquid CDx, a Comprehensive Pan-Tumor
`Liquid Biopsy Test with Multiple Companion Diagnostic Indications for
`Patients with Advanced Cancer” available at
`https://www.foundationmedicine.com/press-releases/445c1f9e-6cbb-488b-
`84ad-5f133612b721
`FM1580-00046212-FM1580-00046217
`FMI Gene Comparison Spreadsheet
`(produced contemporaneously herewith)
`P. Mandel, P. Métais, “Les acides nucléiques du plasma sanguin chez
`l’homme.” C. R. Seances Soc. Biol. Ses Fil. 1948, 142, 241–243
`FM1616-00510603-FM1616-00510605
`Leon et al., “Free DNA in the Serum of Cancer Patients and the Effect of
`Therapy,” Cancer Research 1977, 37, 646-650
`
`- 2 -
`
`Appendix
`Page
`Numbers
`A0328-
`A0335
`
`A0336-
`A0337
`
`A0338-
`A0346
`A0347-
`A0349
`A0350-
`A0354
`
`A0355-
`A0356
`
`A0357-
`A0360
`A0361
`
`A0362-
`A0363
`A0364-
`A0369
`
`A0370-
`A0374
`A0375-
`A0377
`
`A0378-
`A0383
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 4 of 11 PageID #: 7491
`
`
`
`Ex.
`
`Date
`
`Document Description
`
`June
`1987
`Sept.
`1996
`
`29
`
`30
`
`April 1,
`1998
`
`31
`
`32 2002
`Nov. 8,
`2005
`
`33
`
`Nov. 23,
`2006
`
`34
`
`2007
`
`35
`
`36 July 23,
`2008
`Aug.
`2008
`
`37
`
`Sept.
`2008
`
`38
`
`Oct. 21,
`2008
`
`39
`
`Nov. 25,
`2008
`
`40
`
`41 Mar. 8,
`2009
`July 15,
`2009
`
`42
`
`Stroun et al., “Isolation and Characterization of DNA from the Plasma of
`Cancer Patients,” Eur. J. Cancer Clin. Oncol. 1987, 23(6), 707-712
`Nawroz et al., “Microsatellite alterations in serum DNA of head and neck
`cancer patients,” Nature Medicine 1996, 2(9), 1035-1037
`FM1616-00510735-FM1616-00510737
`Lo et al., “Quantitative Analysis of Fetal DNA in Maternal Plasma and
`Serum: Implications for Noninvasive Prenatal Diagnosis,” Am. J. Hum.
`Genet. 1998, 62, 768-775
`FM1616-00510584-FM1616-00510591
`Brown, Genomes (2d ed. 2002)
`
`Diehl et al., “Detection and quantification of mutations in the plasma of
`patients with colorectal tumors,” Proc. Natl. Acad. Sci. 2005, 102(45),
`16368-16373 (“Diehl 2005”)
`FM1616-00510031-FM1616-00510036
`Redon et al., “Global variation in copy number in the human genome,”
`Nature 2006, 444-454 (“Redon”)
`FM1616-00510778-FM1616-00510788
`Illumina publication Preparing Samples for Sequencing Genomic DNA
`Using the Genomic DNA Sample Prep Oligo Only Kit, Revision A
`(“Illumina Kit Instructions”)
`ILL_GUARD0000002-ILL_GUARD0000008
`
`Gahan and Swaminathan, “Circulating Nucleic Acids in Plasma and
`Serum: Recent Developments,” Ann. N.Y. Acad. Sci. 2008, 1137:1-6
`(“Gahan”)
`FM1616-00510183-FM1616-00510188
`Diehl et al., “Circulating mutant DNA to assess tumor dynamics,” Nat.
`Med. 2008, 14(9), 985-990 (“Diehl 2008”)
`FM1616-00510017-FM1616-00510030
`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”)
`FM1616-00510063-FM1616-00510077
`Quail et al., “A large genome center’s improvements to the Illumina
`sequencing system,” Nature Methods 2008, 5(12), 1005-1010
`FM1616-00510772-FM1616-00510777
`ILL_GUARD0000015-ILL_GUARD0000021
`
`Li, H. and Durbin, R., “Fast and accurate short read alignment with
`Burrows—Wheeler transform, ” Bioinformatics 2009, 25 (14), 1754-1760
`(“Li and Durbin”)
`FM1616-00510559-FM1616-00510565
`
`- 3 -
`
`Appendix
`Page
`Numbers
`A0384-
`A0389
`A0390-
`A0392
`
`A0393-
`A0400
`
`A0401-
`A0432
`A0433-
`A0438
`
`A0439-
`A0449
`
`A0450-
`A0467
`
`A0468-
`A0474
`A0475-
`A0480
`
`A0481-
`A0494
`
`A0495-
`A0509
`
`A0510-
`A0515
`
`A0516-
`A0522
`A0523-
`A0529
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 5 of 11 PageID #: 7492
`
`
`
`Ex.
`
`Date
`
`Document Description
`
`Appendix
`Page
`Numbers
`A0530-
`A0545
`
`A0546-
`A0553
`A0554-
`A0565
`
`A0566-
`A0574
`
`A0575-
`A0586
`
`A0587-
`A0598
`
`A0599-
`A0614
`
`A0615-
`A0622
`
`A0623-
`A0731
`A0732-
`A0744
`
`A0745-
`A0783
`A0784-
`A0802
`
`A0803-
`A0817
`
`43
`
`44
`
`45
`
`46
`
`47
`
`48
`
`49
`
`50
`
`Dec. 14,
`2010
`
`2011
`
`June
`2011
`
`June 7,
`2011
`
`51 July 28,
`2011
`Nov. 26,
`2011
`
`52
`
`Jan. 2010 Metzker, “Sequencing Technologies – the next generation,” Nature
`Reviews Genetics (2010) 11:31-46 (“Metzker”)
`FM1616-00510667-FM1616-00510510682
`Bainbridge et al., “Whole exome capture in solution with 3 Gbp of data,”
`June 17,
`2010
`Genome Biology 2010, 11:R62
`Oct. 2010 Meyerson et al., “Advances in understanding cancer genomes through
`second-generation sequencing,” Nature Review Genetics 2010, Vol. 11,
`685-696 (“Meyerson”)
`FM1616-00510703-FM1616-00510714
`Chiu et al., “Non-invasive prenatal assessment of trisomy 21 by
`multiplexed maternal plasma DNA sequencing: large scale validity study,”
`BMJ 2011, 1-9
`FM1616-00509967-FM1616-00509975
`“An Introduction to Next-Generation Sequencing Technology,” Illumina
`(February 28, 2012)
`https://www.illumina.com/Documents/products/Illumina_Sequencing_Intr
`oduction.pdf (“Intro to NGS”)
`FM1616-00510427-FM1616-00510438
`Schwarzenbach et al., “Cell-free nucleic acids as biomarkers in cancer
`patients,” Nature Reviews Cancer 2011, 11, 426-437 (“Schwarzenbach”)
`FM1616-00510978-FM1616-00510989
`Kinde et al., “Detection and quantification of rare mutations with
`massively parallel sequencing,” PNAS 2011, 108(23), 9530-9535 (“Kinde
`2011”)
`FM1616-00510489-FM1616-00510504
`July 2011 Sehnert et al., “Optimal Detection of Fetal Chromosomal Abnormalities by
`Massively Parallel DNA Sequencing of Cell-free DNA from Maternal
`Blood,” Clinical Chemistry 2011, 57:7, 1042-1049 (“Sehnert”)
`FM1616-00510997-FM1616-00511004
`Int. Pub. No. WO 2011/091046 A1 (“Rava ’046”)
`
`Mertes et al., “Targeted enrichment of genomic DNA regions for next-
`generation sequencing,” Briefings in Functional Genomics 2011, 10(6),
`374-386
`FM1616-00510644-FM1616-00510656
`Sambrook, “Molecular Cloning: A Laboratory Manual” (“Sambrook”)
`
`53 2012
`Jan. 2012 Kivioja et al., “Counting absolute numbers of molecules using unique
`molecular identifiers,” Nature Methods 2012, 9(1) (“Kivioja”)
`FM1616-00510515-FM1616-00510533
`Gordon et al., “Causes and consequences of aneuploidy in cancer,” Nature
`Reviews 2012, 13, 189-203 (“Gordon”)
`FM1616-00510189-FM1616-00510203
`
`54
`
`Jan. 24,
`2012
`
`55
`
`- 4 -
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 6 of 11 PageID #: 7493
`
`
`
`Ex.
`
`Date
`
`56 Feb. 8,
`2012
`57 Apr. 5,
`2012
`58 Apr. 22,
`2012
`May 30,
`2012
`
`59
`
`June
`2012
`
`60
`
`61
`
`June
`2012
`June 26,
`62
`2012
`63 June 27,
`2012
`64 June 28,
`2012
`65 June 28,
`2012
`66 June 28,
`2012
`67 July 2,
`2012
`68 July 5,
`2012
`July 15,
`2012
`
`69
`
`July 18,
`2012
`
`70
`
`71 July 23,
`2012
`72 July 26,
`2012
`73 July 29,
`2012
`
`Document Description
`
`GUARDFM00927449-GUARDFM00927456
`
`Int. Pub. No. WO 2012/042374 A2 (“Taipale”)
`FM1616-00511053-FM1616-00511117
`GUARDFM00927783-GUARDFM00927786
`
`Forshew et al., “Noninvasive Identification and Monitoring of Cancer
`Mutations by Targeted Deep Sequencing of Plasma DNA,” Sci. Transl.
`Med. 2012, 4(136), 1-12 (“Forshew”)
`FM1616-00510149-FM1616-00510182
`Bianchi et al., “Genome-Wide Fetal Aneuploidy Detection by Maternal
`Plasma DNA Sequencing,” Obstetrics & Gynecology 2012, 119(5), 1-12
`(“Bianchi”)
`FM1616-00509923-FM1616-00509935
`NEBNext® DNA Library Prep Reagent Set for Illumina®: Instruction
`Manual, NEB (June 2012)
`GUARDFM00968319-GUARDFM00968320
`ILL_GUARD0062597-ILL_GUARD0062598
`GUARDFM00276786-GUARDFM00276787
`
`GUARDFM00278365-GUARDFM00278366
`
`GUARDFM00913980-GUARDFM00913982
`
`GUARDFM00278367-GUARDFM00278368
`
`GUARDFM00770831-GUARDFM00770832
`
`GUARDFM00929064-GUARDFM00929066
`
`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 (“Narayan”)
`FM1616-00510715
`Kinde et. al., “FAST-SeqS: A Simple and Efficient Method for the
`Detection of Aneuploidy by Massively Parallel Sequencing,” PLoS ONE
`(2012), 7(7) (“Kinde 2012”)
`FM1616-00510505-FM1616-00510512
`GUARDFM00914093
`
`Int. Pub. No. WO 2012/099832 A2 (“Hendricks”)
`
`GUARDFM00914102
`
`- 5 -
`
`Appendix
`Page
`Numbers
`A0818-
`A0825
`A0826-
`A0890
`A0891-
`A0894
`A0895-
`A0928
`
`A0929-
`A0941
`
`A0942-
`A0973
`A0974-
`A0975
`A0976-
`A0977
`A0978-
`A0979
`A0980-
`A0982
`A0983-
`A0984
`A0985-
`A0986
`A0987-
`A0989
`A0990-
`A0997
`
`A0998-
`A1005
`
`A1006-
`A1006
`A1007-
`A1085
`A1086-
`A1086
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 7 of 11 PageID #: 7494
`
`
`
`Ex.
`
`Date
`
`Document Description
`
`74 July 30,
`2012
`75 Aug. 4,
`2012
`76 Aug. 9,
`2012
`77 Aug. 20,
`2012
`Sept. 4,
`2012
`
`78
`
`Sept. 4,
`2012
`
`79
`
`81
`
`80
`Oct. 8,
`2012 –
`Feb. 8,
`2013
`82 Oct. 11,
`2012
`83 Feb. 21,
`2013
`Mar. 14,
`2013
`
`84
`
`85
`
`Feb. 6,
`2015
`Oct. 16,
`86
`2015
`87 Apr. 19,
`2016
`88 Apr. 26,
`2016
`89
`Feb. 9,
`90
`2017
`91 Apr. 19,
`2017
`May 9,
`2017
`
`92
`
`GUARDFM00482826-GUARDFM00482827
`
`GUARDFM00935286
`
`GUARDFM00914128-GUARDFM00914134
`
`GUARDFM00914161
`
`Kirsch and Klein, “Sequence error storms and the landscape of mutations
`in caner,” PNAS 2012, 109(36), 14289-14290
`FM1616-00510513-FM1616-00510514
`Schmitt et al., “Detection of ultra-rare mutations by next-generation
`sequencing,” PNAS 2012, 109(36), 14508-14513 (“Schmitt 2012”)
`FM1616-00510854-FM1616-00510865
`INTENTIONALLY OMMITTED
`
`Excerpt of GUARDFM00148276-GUARDFM00148375 Dragan
`Sebisanovic Lab Notebook
`
`GUARDFM00770579-GUARDFM00770586
`
`GUARDFM00275643-GUARDFM00275644
`
`Gansauge and Meyer, “Single-stranded DNA library preparation for the
`sequencing of ancient or damaged DNA,” Nature Protocols 2013, 8(4),
`737-748
`GUARDFM00131259-GUARDFM00131275
`Cooper Exhibit 10 (INF-SOP-001)
`Supplemental Figure 2 to Exhibit 5 of the Declaration of Gregory Cooper,
`Ph.D. (D.I. 10, Ex. 5)
`GHFMI-1580_0030277-GHFMI-1580_0030282
`
`U.S. Patent No. 9,323,888 B2 (“Rava ’888”)
`
`Bioo Scientific, “Optimizing Library Preparation: Enhanced Adapter
`Ligation Technology”
`U.S. Patent App. No. 15/076,565 (U.S. Patent No. 9,902,992), Non-Final
`Rejection
`Declaration of Stefanie Mortimer Pursuant to 37 CFR §1.132, U.S. Patent
`App. No. 14/855,301
`U.S. Patent App. No. 15/076,565 (U.S. Patent No. 9,902,992), Amendment
`and Response to Non-Final Office Action
`
`- 6 -
`
`Appendix
`Page
`Numbers
`A1087-
`A0188
`A1089-
`A1089
`A1090-
`A1096
`A1097-
`A1097
`A1098-
`A1099
`
`A1100-
`A1111
`
`A1112-
`A1114
`A1115-
`A1117
`
`A1118-
`A1125
`A1126-
`A1127
`A1128-
`A1140
`
`A1141-
`A1157
`A1158-
`A1158
`A1159-
`A1164
`A1165-
`A1373
`A1374-
`A1376
`A1377-
`A1398
`A1399-
`A1402
`A1403-
`A1427
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 8 of 11 PageID #: 7495
`
`
`
`Ex.
`
`Date
`
`Document Description
`
`Sep. 5,
`93
`2017
`94 Apr. 26,
`2018
`Apr. 26,
`2018
`May 9,
`2018
`
`95
`
`96
`
`97 June 4,
`2018
`Aug. 22,
`2018
`
`98
`
`Aug. 22,
`2018
`
`99
`
`Sept. 10,
`100
`2018
`101 Sep. 20,
`2018
`Feb. 26,
`2019
`
`102
`
`Feb. 26,
`2019
`
`103
`
`Mar. 5,
`2019
`
`Mar. 20,
`2019
`April 8,
`2019
`
`April 30,
`2019
`
`104
`
`105
`
`106
`
`107
`
`U.S. Patent No. 9,752,188 B2 (“Schmitt ’188)
`FM1616-00510944
`GUARDFM00569762-GUARDFM00569764
`
`GUARDFM00610204-GUARDFM00610206
`Simon Exhibit 6
`Castro-Giner et al., “Cancer Diagnosis Using a Liquid Biopsy: Challenges
`and Expectations,” Diagnostics 2018, 8(31) (“Castro-Giner”)
`FM1616-00509945-FM1616-00509962
`GUARDFM00394668-GUARDFM00394674
`
`U.S. Department of Veterans Affairs Contract with Foundation Medicine,
`Inc.: “Genomic Sequencing Testing Services”
`FM1616-00507056-FM1616-00507095
`(Exhibit Reproduced in PDF Format)
`U.S. Department of Veterans Affairs Contract with Foundation Medicine,
`Inc.: “Genomic Sequencing Testing Services” Request for Proposal (RFP)
`(Exhibit Reproduced in PDF Format; produced contemporaneously
`herewith)
`Application Data Sheet, U.S. Application No. 15/076,565 (U.S. Patent No.
`9,902,992)
`GHFMI-1580_0049013-GHFMI-1580_0049026
`
`Excerpt of AM Transcript of the Deposition of Stefanie Mortimer, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`Excerpt of PM Transcript of the Deposition of Stefanie Mortimer, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`Saarenheimo et al., “The Value of Liquid Biopsies for Guiding Therapy
`Decisions in Non-small Cell Lung Cancer,” Frontiers in Oncology 2019,
`Vol. 9, Article 129
`FM1616-00510826-FM1616-00510836
`GUARDFM00868161
`(Exhibit Reproduced in PDF Format)
`Excerpt of Transcript of the Deposition of Helmy Eltoukhy, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`Excerpt of Transcript of the Deposition of AmirAli Talasaz, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`
`- 7 -
`
`Appendix
`Page
`Numbers
`A1428-
`A1461
`A1462-
`A1464
`A1465-
`A1467
`A1468-
`A1485
`
`A1486-
`A1492
`A1493-
`A1532
`
`A1533-
`A1600
`
`A1601-
`A1610
`A1611-
`A1624
`A1625-
`A1628
`
`A1629-
`A1633
`
`A1634-
`A1644
`
`A1645-
`A1646
`A1647-
`A1652
`
`A1653-
`A1656
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 9 of 11 PageID #: 7496
`
`
`
`Ex.
`
`Date
`
`May 1,
`2019
`
`108
`
`109 June 20,
`2019
`July 24,
`2019
`
`110
`
`July 24,
`111
`2019
`112 July 29,
`2019
`Aug. 5,
`113
`2019
`114 Aug. 22,
`2019
`Sept. 6,
`2019
`Oct. 16,
`2019
`
`115
`
`116
`
`Dec. 5,
`117
`2019
`118 Dec. 20,
`2019
`Jan. 23,
`119
`2020
`120 Mar. 31,
`2020
`121 Jun. 23,
`2020
`122 Aug. 2,
`2020
`Aug. 7,
`2020
`
`123
`
`Aug. 18,
`124
`2020
`125 Aug. 25,
`2020
`126 Aug. 27,
`2020
`
`Document Description
`
`Excerpt of Transcript of the Deposition of AmirAli Talasaz, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`Sequence Alignment/Map Format Specification
`
`Excerpt of the Expert Report of Stephen L. Becker, Ph.D. with regard to
`Foundation Medicine, Inc., Guardant Health, Inc. v. Foundation Medicine,
`Inc., C.A. No. 17-01616-LPS-CJB
`Excerpt of the Expert Report of Gregory Cooper, Ph.D., Guardant Health,
`Inc. v. Foundation Medicine, Inc., C.A. No. 17-01616-LPS-CJB
`GHFMI-1580_0007477-GHFMI-1580_0007575
`
`Discovery Dispute Teleconference Transcript, Guardant Health, Inc. v.
`Foundation Medicine, Inc., C.A. No. 17-cv-1616-LPS-CJB
`GHFMI-1580_0030391-GHFMI-1580_0030410
`
`Rebuttal Expert Report of Michael L. Metzker, Ph.D., Guardant Health,
`Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-LPS-CJB
`Excerpt of Transcript of the Deposition of Gregory Cooper, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`Foundation Medicine, Inc. v. Guardant Health, Inc., Case No. IPR2019-
`00652, Paper 26, Patent Owner Response
`INTENTIONALLY OMMITTED
`
`Excerpt of Summary Judgment Hearing Transcript, Guardant Health, Inc.
`v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-LPS-CJB
`U.S. Patent No. 10,604,804 B2 (“Salk ’804”)
`
`U.S. Patent No. 10,689,699 B2 (“Salk ’699”)
`
`GHFMI-1580_0038766-GHFMI-1580_0038767
`
`Guardant360 CDx Summary of Safety and Effectiveness Data available at
`https://www.fda.gov/medical-devices/recently-approved-
`devices/guardant360-cdx-p200010
`Foundation Medicine, Inc. v. Guardant Health, Inc., Case No. IPR2019-
`00652, Paper 47, Final Written Decision
`U.S. Patent No. US 10,752,951 B2 (“Salk ’951”)
`
`GHFMI-1580_0041208-GHFMI-1580_0041219
`
`
`- 8 -
`
`Appendix
`Page
`Numbers
`A1657-
`A1662
`
`A1663-
`A1683
`A1684-
`A1688
`
`A1689-
`A1698
`A1699-
`A1797
`A1798-
`A1848
`A1849-
`A1868
`A1869-
`A1890
`A1891-
`A1893
`
`A1894-
`A1964
`A1965-
`A1966
`A1967-
`A1971
`A1972-
`A2008
`A2009-
`A2044
`A2045-
`A2046
`A2047-
`A2121
`
`A2122-
`A2189
`A2190-
`A2226
`A2227-
`A2238
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 10 of 11 PageID #: 7497
`
`
`
`Ex.
`
`Date
`
`127 Sep. 1,
`2020
`Sept. 18,
`2020
`
`128
`
`Oct. 26,
`2020
`
`129
`
`Oct. 31,
`2020
`
`130
`
`133
`
`134
`
`Dec. 31,
`131
`2020
`132 Jan. 12,
`2021
`Jan. 27,
`2021
`Jan. 28,
`2021
`Feb. 22,
`2021
`Aug. 26,
`2020
`Oct. 27,
`2020
`
`135
`
`136
`
`137
`
`Nov. 6,
`2020
`June
`2010
`
`138
`
`139
`
`140
`
`May 29,
`2013 –
`Aug. 9,
`2013
`
`
`141
`142 May 29,
`2018
`
`Document Description
`
`U.S. Patent No. 10,760,127 B2 (“Salk ’127”)
`
`Excerpt of Transcript of the Deposition of Helmy Eltoukhy, Ph.D.,
`Guardant Health, Inc. v. Foundation Medicine, Inc., C.A. No. 17-cv-1616-
`LPS-CJB
`FDA Premarket Approval letter for the FoundationOne Liquid CDx for
`certain indications
`FM1580-00049089-FM1580-00049097
`Fourth Supplemental Report of Stephen L. Becker, Ph.D. with regard to
`Foundation Medicine Inc., Guardant Health Inc. v. Foundation Medicine,
`Inc., C.A. No. 17-01616-LPS-CJB
`GHFMI-1580_0041125
`(Exhibit Reproduced in PDF Format)
`GHFMI-1580_0041201
`
`Transcript of the Deposition of Daniel Simon, Guardant Health, Inc. v.
`Foundation Medicine, Inc., C.A. No. 20-01580-LPS
`Transcript of the Deposition of Gregory Cooper, Ph.D., Guardant Health,
`Inc. v. Foundation Medicine, Inc., C.A. No. 20-01580-LPS
`Public PAIR Parent Continuity Data, U.S. Application No. 15/076,565
`(U.S. Patent No. 9,902,992)
`FDA Premarket Approval letter for the FoundationOne Liquid® CDx for
`certain indications
`Foundation Medicine Press Release, “FDA Approves New
`FoundationOne® Liquid CDx Companion Diagnostic Indications for Three
`Targeted Therapies That Treat Advanced Ovarian, Breast and Non-Small
`Cell Lung Cancer”
`FDA Premarket Approval letter for the FoundationOne Liquid® CDX for
`certain indication
`Meyer and Kircher, “Illumina Sequencing Library Preparation for Highly
`Multiplexed Target Capture and Sequencing,” Cold Spring Harbor
`Laboratory Press 2010, 2010(6).
`Excerpt of GUARDFM00148805-GUARDFM00148909 Stefanie
`Mortimer Lab Notebook (Exhibit 40)
`
`Kircher, “Chapter 23: Analysis of High-Throughput Ancient DNA
`Sequencing Data,” Methods in Molecular Biology 2012, Vol. 840.
`U.S. Patent No. 9,982,295 B2 (Talasaz)
`
`Appendix
`Page
`Numbers
`A2239-
`A2275
`A2276-
`A2287
`
`A2288-
`A2296
`
`A2297-
`A2339
`
`A2340-
`A2343
`A2344-
`A2344
`A2345-
`A2410
`A2411-
`A2503
`A2504-
`A2504
`A2505-
`A2512
`A2513-
`A2520
`
`A2521-
`A2528
`A2529-
`A2548
`
`A2549-
`A2561
`
`A2562-
`A2598
`A2599-
`A2658
`
`- 9 -
`
`

`

`Case 1:20-cv-01580-LPS Document 39 Filed 03/05/21 Page 11 of 11 PageID #: 7498
`
`
`
`
`
`Ex.
`
`Date
`
`Jan. 24,
`2012
`
`143
`
`144
`
`Oct. 4,
`2012
`May 31,
`145
`2011
`146 July 29,
`2008
`Mar.
`2011
`
`147
`
`Document Description
`
`Shiroguchi et al., “Digital RNA sequencing minimizes sequence-dependent
`bias and amplification noise with optimized single-molecule barcodes,”
`PNAS 2012 109(4) 1347-1352
`Excerpt of GUARDFM00147968-GUARDFM00148069
`Alain Mir Lab Notebook
`Fu et al., “Counting individual DNA molecules by the stochastic
`attachment of diverse labels,” PNAS 2011, 108(22), 9026-9031
`Mitchell, et al. “Circulating microRNAs as stable blood-based markers for
`cancer detection,” PNAS 2008; 105:10513-8
`Ehrich, et al. “Noninvasive detection of fetal trisomy 21 by sequencing of
`DNA in maternal blood: a study in a clinical setting,” Am. J. Obstetrics &
`Gynecology 2011; 204:205el-11.
`
`Appendix
`Page
`Numbers
`A2659-
`A2672
`
`A2673-
`A2681
`A2682-
`A2687
`A2688-
`A2693
`A2694-
`A2704
`
`- 10 -
`
`