Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 1 of 33 PageID #: 7455
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`GUARDANT HEALTH, INC.,
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`Plaintiff,
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`v.
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`FOUNDATION MEDICINE, INC.,
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`Defendant.
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`C.A. No. 20-1580 (LPS)
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`FOUNDATION MEDICINE, INC.’S ANSWERING BRIEF IN OPPOSITION TO
`PLAINTIFF GUARDANT HEALTH, INC.’S MOTION
`FOR PRELIMINARY INJUNCTION
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`OF COUNSEL:
`
`Eric J. Marandett
`G. Mark Edgarton
`Sophie F. Wang
`Diane C. Seol
`CHOATE HALL & STEWART LLP
`Two International Place
`Boston, MA 02110
`(617) 248-5000
`
`
`
`MORRIS, NICHOLS, ARSHT & TUNNELL LLP
`Karen Jacobs (#2881)
`Jeremy A. Tigan (#5239)
`Sarah E. Simonetti (#6698)
`1201 North Market Street
`P.O. Box 1347
`Wilmington, DE 19899
`(302) 658-9200
`kjacobs@morrisnichols.com
`jtigan@morrisnichols.com
`ssimonetti@morrisnichols.com
`
`Attorneys for Defendant
`Foundation Medicine, Inc.
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`Confidential Version Filed: February 26, 2021
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`Public Version Filed: March 5, 2021
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 2 of 33 PageID #: 7456
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`TABLE OF CONTENTS
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`INTRODUCTION AND NATURE AND STAGE OF THE PROCEEDINGS ............................ 1
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`SUMMARY OF ARGUMENT ...................................................................................................... 2
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`ARGUMENT AND STATEMENT OF FACTS ............................................................................ 3
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`I.
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`GUARDANT CANNOT SHOW LIKELIHOOD OF SUCCESS ON THE
`MERITS .............................................................................................................................. 3
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`A.
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`FMI Does Not Infringe the Asserted Claims .......................................................... 3
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`1.
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`FMI Does Not Perform the “Grouping” Steps of the Asserted
`Claims ......................................................................................................... 4
`
`B.
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`The Asserted Claims Are Invalid ............................................................................ 6
`
`1.
`
`2.
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`The Asserted Claims Are Obvious Over the Prior Art ............................... 8
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`The Asserted Claims Are Invalid Under 35 U.S.C. § 112 .......................... 9
`
`C.
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`The Asserted Claims Are Not Enforceable ........................................................... 14
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`1.
`
`2.
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`The Asserted Claims Are Unenforceable Due to Inequitable
`Conduct ..................................................................................................... 14
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`Guardant’s Unclean Hands Further Raise a Substantial Question
`Regarding Enforceability of the Asserted Patents .................................... 18
`
`II.
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`GUARDANT CANNOT DEMONSTRATE THAT IT IS AT RISK OF ANY
`IRREPARABLE HARM .................................................................................................. 18
`
`A.
`
`B.
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`Guardant’s Alleged “Irreparable Harms” Are Conclusory and/or
`Adequately Addressed by Money Damages ......................................................... 19
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`Guardant’s Significant Delay Weighs Strongly Against Irreparable Harm.......... 21
`
`III.
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`IV.
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`THE BALANCE OF THE HARMS DOES NOT FAVOR A PRELIMINARY
`INJUNCTION ................................................................................................................... 22
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`A PRELIMINARY INJUNCTION IS CONTRARY TO THE PUBLIC
`INTEREST ........................................................................................................................ 22
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`CONCLUSION ............................................................................................................................. 25
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 3 of 33 PageID #: 7457
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`
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`
`
`Cases
`
`TABLE OF AUTHORITIES
`
`
`
`Page(s)
`
`Abbott Cardiovascular Sys. v. Edwards Lifesciences Corp.,
`2019 WL 2521305 (D. Del. June 6, 2019) .........................................................................20, 23
`
`Abbott Labs v. Sandoz, Inc.,
`544 F.3d 1341 (Fed. Cir. 2008)................................................................................................21
`
`Agfa Corp. v. Creo Prods., Inc.,
`451 F.3d 1366 (Fed. Cir. 2006)................................................................................................15
`
`Andover Healthcare, Inc. v. 3M Co.,
`2016 WL 6404111 (D. Del. Oct. 27, 2016) ...............................................................................8
`
`Apple, Inc. v. Samsung Elecs. Co.,
`678 F.3d 1314 (Fed. Cir. 2012)................................................................................................21
`
`Ariad Pharms., Inc. v. Eli Lilly & Co.,
`598 F.3d 1336 (Fed. Cir. 2010)................................................................................................10
`
`Atari Games Corp. v. Nintendo of Am., Inc.,
`897 F.2d 1572 (Fed. Cir. 1990)..................................................................................................2
`
`Auburn Univ. v. IBM,
`2012 WL 3151545 (M.D. Ala. Aug. 2, 2012)............................................................................5
`
`Baxalta Inc. v. Genentech, Inc.,
`2018 WL 3742610 (D. Del. Aug. 7, 2018) ................................................................................6
`
`Bd. of Regents of the Univ. of Tex. Sys. v. BENQ Am. Corp.,
`533 F.3d 1362 (Fed. Cir. 2008)................................................................................................12
`
`BICC plc v. Focas, Inc.,
`1991 U.S. Dist. LEXIS 11924 (D. Del. Aug. 7, 1991) ............................................................22
`
`Butamax Advanced Biofuels LLC v. Gevo, Inc.,
`117 F. Supp. 3d 632 (D. Del. 2015) .........................................................................................10
`
`Celsis in Vitro, Inc. v. CellzDirect, Inc.,
`664 F.3d 922 (Fed. Cir. 2012)..................................................................................................21
`
`
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`- ii -
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`

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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 4 of 33 PageID #: 7458
`
`
`
`Chestnut Hill Sound, Inc. v. Apple Inc.,
`2015 WL 6870037 (D. Del. Nov. 6, 2015) ..................................................................18, 19, 22
`
`Cochlear Bone Anchored Sols. AB v. Oticon Med. AB,
`958 F.3d 1348 (Fed. Cir. 2020)................................................................................................10
`
`Consol. Aluminum Corp. v. Foseco Int’l, Ltd.,
`910 F.2d 804 (Fed. Cir. 1990)..................................................................................................15
`
`Cordis Corp. v. Boston Sci. Corp.,
`99 Fed. App’x 928 (Fed. Cir. 2004) ...................................................................................22, 23
`
`D Three Enters., LLC v. SunModo Corp.,
`890 F.3d 1042 (Fed. Cir. 2018)................................................................................................12
`
`Douglas Dynamics, LLC v. Buyers Prods. Co.,
`717 F.3d 1336 (Fed. Cir. 2013)................................................................................................21
`
`Entegris, Inc. v. Pall Corp.,
`490 F.3d 1340 (Fed. Cir. 2007)..................................................................................................3
`
`Erico Int’l Corp. v. Vutec Corp.,
`516 F.3d 1350 (Fed. Cir. 2008)..................................................................................................6
`
`eSpeed, Inc. v. Brokertec USA, L.L.C.,
`417 F. Supp. 2d 580 (D. Del. 2006) .........................................................................................18
`
`Genentech, Inc. v. Novo Nordisk A/S,
`108 F.3d 1361 (Fed. Cir. 1997)..................................................................................................3
`
`Geneva Pharms., Inc. v. GlaxoSmithKline PLC,
`349 F.3d 1373 (Fed. Cir. 2003)..........................................................................................11, 14
`
`Geospan Corp. v. Pictometry Int’l Corp.,
`2011 WL 1261583 (D. Minn. Mar. 31, 2011) ...........................................................................5
`
`Gilead Sciences, Inc. v. Merck & Co.,
`888 F.3d 1231 (Fed. Cir. 2018)................................................................................................18
`
`GOLO, LLC v. Goli Nutrition Inc.,
`2020 WL 5203601 (D. Del. Sept. 1, 2020) ..............................................................................19
`
`HZNP Meds. LLC v. Actavis Labs. UT, Inc.,
`940 F.3d 680 (Fed. Cir. 2019)............................................................................................11, 13
`
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`- iii -
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 5 of 33 PageID #: 7459
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`
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`Icon Health & Fitness, Inc. v. Polar Electro Oy,
`656 Fed. App’x 1008 (Fed. Cir. 2016) .....................................................................................10
`
`ICU Med., Inc. v. Alaris Med. Sys., Inc.,
`2004 WL 1874992 (C.D. Cal. Aug. 2, 2004) ...........................................................................22
`
`Ingevity Corp. v. BASF Corp.,
`2019 WL 2356978 (D. Del. June 4, 2019) ...........................................................................3, 13
`
`Integra LifeScience Corp. v. HyperBranch Med. Tech., Inc.,
`2016 WL 4770244 (D. Del. Aug. 12, 2016) ......................................................................22, 23
`
`Intel Corp. v. ULSI Sys. Tech., Inc.,
`995 F.2d 1566 (Fed. Cir. 1993)..................................................................................................2
`
`Keystone Driller Co. v. General Excavator Co.,
`290 U.S. 240 (1933) .................................................................................................................18
`
`KSR Int’l Co. v. Teleflex Inc.,
`550 U.S. 398 (2007) ...................................................................................................................8
`
`Litton Sys. v. Sundstrand Corp.,
`750 F.2d 952 (Fed. Cir. 1984)..................................................................................................22
`
`Minton v. NASD, Inc.,
`336 F.3d 1373 (Fed. Cir. 2003)..................................................................................................9
`
`Nat’l Steel Car, Ltd. v. Canadian Pac. Ry., Ltd.,
`357 F.3d 1319 (Fed. Cir. 2004)..................................................................................................6
`
`Nautilus, Inc. v. Biosig Instruments, Inc.,
`572 U.S. 898 (2014) .................................................................................................................10
`
`Neology, Inc. v. Fed. Signal Corp.,
`2012 WL 2308202 (D. Del. June 18, 2012), adopted by 2012 WL 3236718 (D.
`Del. Aug. 2, 2012)....................................................................................................................19
`
`Nutrition 21 v. United States,
`930 F.2d 867 (Fed. Cir. 1991)....................................................................................................3
`
`Otsuka Pharm. Co., LTD v. Torrent Pharms. Ltd., Inc.,
`99 F. Supp. 3d 461 (D.N.J. 2015) ............................................................................................19
`
`PerSeptive Biosystems, Inc. v. Pharmacia Biotech, Inc.,
`225 F.3d 1315 (Fed. Cir. 2000)..........................................................................................15, 16
`
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`- iv -
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 6 of 33 PageID #: 7460
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`
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`Power Integrations, Inc. v. BCD Semiconductor Corp.,
`2008 WL 5069784 (D. Del. Nov. 19, 2008) ............................................................................19
`
`QBAS Co. v. C Walters Intercoastal Corp.,
`2010 WL 7785955 (C.D. Cal. Dec. 16, 2010) .........................................................................21
`
`Regeneron Pharms., Inc. v. Merus N.V.,
`864 F.3d 1343 (Fed. Cir. 2017)................................................................................................17
`
`Saso Golf, Inc. v. Nike, Inc.,
`2021 WL 486578 (Fed. Cir. Feb. 10, 2021) ............................................................................10
`
`Sebela Int’l Ltd. v. Actavis Labs. FL, Inc.,
`2017 WL 4782807 (D.N.J. Oct. 20, 2017)...............................................................................22
`
`Siemens Postal, Parcel & Airport Logistics LLC v. Pteris Global (USA) Inc.,
`2019 WL 6247898 (W.D.N.C. Nov. 21, 2019)........................................................................20
`
`SimpleAir, Inc. v. Sony Ericsson Mobile Commc’ns AB,
`820 F.3d 419 (Fed. Cir. 2016)..................................................................................................12
`
`Sofamor Danek Grp., Inc. v. DePuy-Motech, Inc.,
`74 F.3d 1216 (Fed. Cir. 1996)....................................................................................................4
`
`Sunoco Partners Mktg. & Terminals L.P. v. Powder Springs Logistics, LLC,
`2018 WL 395750 (D. Del. Jan 8, 2018) .............................................................................18, 20
`
`Takeda Pharm. Co. v. Actavis Labs. FL, Inc.,
`2016 WL 3193188 (D. Del. June 6, 2016) .................................................................................9
`
`Therasense, Inc. v. Becton, Dickinson & Co.,
`649 F.3d 1276 (Fed. Cir. 2011)................................................................................................15
`
`Truinject Corp. v. Galderma,
`2020 WL 3287047 (D. Del. June 18, 2020) .............................................................................13
`
`Turn-Key-Tech, LLC v. Nat’l Film Lab, Inc.,
`74 F. App’x 58 (Fed. Cir. 2003) ................................................................................................6
`
`U-Fuel, Inc. (NV) v. Highland Tank & Mfg. Co.,
`228 F. Supp. 2d 597 (E.D. Pa. 2002) .......................................................................................22
`
`Waters Corp. v. Agilent Techs., Inc.,
`410 F. Supp. 3d 702 (D. Del. 2019) ...............................................................................2, 15, 23
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 7 of 33 PageID #: 7461
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`Other Authorities
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` LR 7.1.3(c)(2) .................................................................................................................................4
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 8 of 33 PageID #: 7462
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`INTRODUCTION AND NATURE AND STAGE OF THE PROCEEDINGS
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`In 2012, Defendant Foundation Medicine, Inc. (“FMI”) launched FoundationOne®, the
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`first comprehensive genomic profiling (“CGP”) test capable of detecting mutations in hundreds of
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`cancer genes, and providing patients, doctors, and researchers with a wealth of clinically actionable
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`information in the fight against cancer. Because its revolutionary assay design allowed for the
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`detection of multiple classes of genomic alterations in a single test, FoundationOne® enabled, for
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`the first time, truly personalized cancer therapy. Building on FoundationOne®’s next-generation
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`sequencing (“NGS”) platform, FMI developed additional CGP tests, including its current, FDA-
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`approved liquid biopsy test, FoundationOne® Liquid CDx (“F1LCDx”). Due to FMI’s innovative
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`technology and rigorous validation efforts, FDA approved F1LCDx as being safe and effective for
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`detecting mutations in over 300 cancer genes. It is also the only liquid biopsy test that is FDA-
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`approved for six therapies targeting lung, prostate, ovarian, and breast cancer.
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`In contrast, Guardant360® CDx (“G360CDx”) is approved by FDA for detecting
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`mutations in only 55 genes and for only one therapy targeting a single cancer type. Yet Guardant’s
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`Motion seeks to eliminate FMI’s life-saving test. It should be denied.
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`After a series of setbacks in Guardant’s first lawsuit against FMI and related IPR
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`proceedings1, Guardant filed this action asserting that F1LCDx infringes seven related patents.
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`D.I. 1.2 Guardant was aware of FMI’s planned launch of F1LCDx and considered it “a real and
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`imminent” threat since at least 2018. Ex. 95, 204. Although Guardant never took steps in the three
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`years since it first sued FMI to prevent what its Motion calls irreparable harm, Guardant now seeks
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`a preliminary injunction to remove what it describes as “the only FDA-approved liquid biopsy that
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`1 See Guardant Health Inc. v. Foundation Medicine, Inc., No. 17-1616-LPS-CJB (“the 1616
`Action”). The 1616 Action involved U.S. Patent Nos. 9,598,731 (the “’731 patent”), 9,834,822
`(the “’822 patent”), 9,840,743 (the “’743 patent”), and 9,902,992 (the “’992 patent”).
`2 “D.I.” cites herein refer to this action. Cites to the 1616 Action are denoted as “1616, D.I. #.”
`For purposes of its Motion, Guardant asserts only Claim 1 of each of U.S. Patent Nos. 10,704,085
`and 10,704,086 (the “Asserted Patents” or “Asserted Claims”) (D.I. 9, Exs. 4-5). D.I. 8, at 1.
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 9 of 33 PageID #: 7463
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`competes directly” with its products. D.I. 8, at 1. But a preliminary injunction is not, and should
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`not be, a competitive tactic, particularly when life-saving products are involved and where, as here,
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`the patentee’s case suffers from a series of substantial deficiencies on the merits. Rather, an
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`injunction is a drastic and “extraordinary” remedy that is only appropriate in “limited
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`circumstances.” Waters Corp. v. Agilent Techs., Inc., 410 F. Supp. 3d 702, 707 (D. Del. 2019)
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`(citation omitted); Intel Corp. v. ULSI Sys. Tech., Inc., 995 F.2d 1566, 1568 (Fed. Cir. 1993).
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`Guardant’s Motion fails to show that extraordinary relief is warranted.
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`SUMMARY OF ARGUMENT
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`(1) Guardant has not established likelihood of success on the merits. As explained below
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`and by FMI’s experts, Drs. Gabriel and Benson, FMI raises substantial questions that the Asserted
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`Claims are (1) not infringed; (2) invalid in view of at least U.S. Patent No. 9,752,188 (“Schmitt”)
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`combined with other prior art; (3) invalid for indefiniteness and lack of written description; and
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`(4) unenforceable due to Guardant’s inequitable conduct and unclean hands. Indeed, Guardant’s
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`Motion rests on inapplicable, preliminary PTAB findings and ignores the language of its new
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`claims, known prior art, and compelling evidence of inequitable conduct.
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`(2) Further, Guardant cannot show irreparable harm or that the balance of equities supports
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`an injunction. Guardant’s significant delay in seeking an injunction, availability of money
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`damages, speculative losses, and lack of nexus between any purported losses and FMI’s alleged
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`infringement defeats its claim of irreparable harm. The Court should also reject Guardant’s effort
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`to dramatically change the status quo based on unsupported assertions. Atari Games Corp. v.
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`Nintendo of Am., Inc., 897 F.2d 1572, 1575 (Fed. Cir. 1990) (courts “should be wary of issuing an
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`injunction based solely upon allegations and conclusory affidavits submitted by plaintiff.”).
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`(3) Finally, Guardant’s claim that “enjoining FMI will not harm cancer patients” is
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`contrary to the facts. D.I. 8, at 19. As shown by the multiple declarations submitted herewith from
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 10 of 33 PageID #: 7464
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`physicians and researchers who rely on F1LCDx, G360CDx is not a viable alternative at least
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`because it detects substantially fewer clinically relevant mutations and is not FDA-approved for
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`six of the seven therapies for which F1LCDx is approved. Thus, an injunction would have grave
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`consequences for patient treatment and cancer research. Guardant’s suggestion otherwise is, at
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`best, inaccurate and in reckless disregard for the concerns of the cancer community.
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`ARGUMENT AND STATEMENT OF FACTS3
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`GUARDANT CANNOT SHOW LIKELIHOOD OF SUCCESS ON THE MERITS
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`“[A]t the preliminary injunction stage, because of the extraordinary nature of the relief, the
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`I.
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`patentee carries the burden of showing likelihood of success on the merits with respect to the
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`patent’s validity, enforceability, and infringement.” Nutrition 21 v. United States, 930 F.2d 867,
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`869 (Fed. Cir. 1991) (emphasis in original).4 Guardant’s scant showing does not meet its burden
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`to show that it “will likely prove” infringement, or that the Asserted Claims “will likely withstand”
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`the significant challenges raised by FMI. Genentech, Inc. v. Novo Nordisk A/S, 108 F.3d 1361,
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`1364 (Fed. Cir. 1997); Ingevity Corp. v. BASF Corp., 2019 WL 2356978, at *2 (D. Del. June 4,
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`2019). Because Guardant cannot prove that FMI’s defenses lack “substantial merit,” its Motion
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`should be denied. Entegris, Inc. v. Pall Corp., 490 F.3d 1340, 1351 (Fed. Cir. 2007).
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`A.
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`FMI Does Not Infringe the Asserted Claims
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`Guardant attempts to shortcut a proper infringement analysis by arguing that (i) FMI only
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`asserted one basis for non-infringement in the 1616 Action against the parent ’992 patent, which
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`(ii) Guardant says does not apply to the Asserted Claims. D.I. 8, at 15-16. In fact, FMI asserted
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`multiple defenses in the 1616 Action,5 and indeed, some of the limitations Guardant added6 to the
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`3 The relevant facts are cited and addressed throughout the Argument section.
`4 All emphasis herein is added unless expressly noted otherwise.
`5 That FMI only moved on one non-infringement ground at summary judgment does not mean
`that FMI conceded infringement on all other bases. See, e.g., Ex. 119, at 133:22-25.
`6 For example, the claimed grouping by “start”/“stop” “positions”—which, as discussed below, is
`not even described in the specification—is an attempt to avoid FMI’s indefiniteness defenses
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 11 of 33 PageID #: 7465
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`Asserted Claims are thinly veiled attempts to escape FMI’s prior non-infringement and invalidity
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`defenses. These new limitations also provide new grounds for non-infringement, as demonstrated
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`by Dr. Benson’s analysis of FMI’s source code. Benson Dec. ¶¶34-69. Guardant’s own expert,
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`Dr. Cooper, admitted that FMI’s source code “controls” the bioanalytical steps of its tests. Ex.
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`116, at 799:6-14. In the face of the controlling source code, Guardant’s reliance on Dr. Cooper’s
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`conclusory assertions falls far short of meeting its burden to prove likelihood of success.7
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`1.
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`FMI Does Not Perform the “Grouping” Steps of the Asserted Claims
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`The Asserted Claims require grouping based on at least the “start” and/or “stop” base
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`positions of a given sequencing read or given mapped sequencing read that an aligner actually
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`“aligns” or “maps” to the reference sequence.8 See ’086 patent, 1(e); ’085 patent, 1(g). The
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`Asserted Claims use “aligning” and “mapping” interchangeably. See Ex. 134, at 237:20-238:5.
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`Dec. ¶¶41-69 and Figs. 1-5.
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`FMI does not perform the claimed “grouping” steps for at least two reasons. See Benson
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`against prior claims reciting grouping based on “sequence information” at “a beginning” or “an
`end” of the sequence read, and FMI’s prior non-infringement positions. Ex. 115, ¶¶116-132, 167.
`7 Dr. Cooper’s opinions are not based on source code. He also admitted that he did not consider
`(i) the proper scope of key limitations, (ii) material differences between the Asserted Claims, or
`(iii) the doctrine of equivalents (“DOE”). Ex. 134, at 14:15-15:5, 303:17-304:20, 200:7-201:1.
`Guardant could have, and should have, offered these opinions with its Motion, but it chose not to
`do so. It should not be permitted to remedy these deficiencies or wholesale change its theories on
`reply. D. Del. LR 7.1.3(c)(2).
`8 For purposes of the Motion, terms should be preliminarily construed consistent with their plain
`and ordinary meanings in view of the specification and prosecution history. See Sofamor Danek
`Grp., Inc. v. DePuy-Motech, Inc., 74 F.3d 1216, 1221 (Fed. Cir. 1996) (non-final claim
`constructions are appropriate at the preliminary injunction stage). FMI reserves the right to assert
`additional claim construction and/or non-infringement positions as discovery moves forward.
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 12 of 33 PageID #: 7466
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` See, e.g., Auburn Univ. v. IBM, Corp., 2012 WL 3151545, at
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`*12-14, 14 n.12 (M.D. Ala. Aug. 2, 2012) (accused calculation was not “based on” claimed
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`criterion even where criterion was “a necessary precondition” because that “that X is a necessary
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`precondition for Y does not necessarily mean that Y is ‘based on’ X.”).9
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`The differences between FMI’s grouping step and the Asserted Claims are substantial, as
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`evidenced by Dr. Cooper’s own explanation of how he believes Guardant’s products embody the
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`Asserted Claims. See, e.g., D.I. 10, ¶¶229, 251. As Dr. Cooper acknowledges, the purpose of the
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`claimed grouping, based on the actual aligned positions, is to address the fact that sequence reads
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`do not map perfectly to the reference sequence.11 Guardant’s products
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`9 See also Geospan Corp. v. Pictometry Int’l Corp., 2011 WL 1261583, at *3-4 (D. Minn. Mar.
`31, 2011) (“untenable” position “would render the phrase ‘based upon’ entirely meaningless”).
`10 As this Court has previously found in related contexts, the use of “a given [mapped] sequencing
`read” followed by “the given [mapped] sequencing read” reflects an intention to refer back to the
`“initial antecedent phrase,” i.e., the same read stated earlier in the claim. 1616, D.I. 260, at 20-22
`(citing cases); 1616, D.I. 404. Dr. Cooper agrees. See, e.g., Ex. 134, at 344:8-19, 232:12-20.
`11 Ex. 134, at 238:6-11 (“Do sequence reads always align or map perfectly to a reference
`sequence? . . . A: No. There are a variety of reasons why a read might have mismatches, indels, et
`cetera, in comparison to a reference.”); id. at 238:13-239:20; id. at 266:1-267:5 (“the read
`representing that fragment would align more poorly because it has these bases on the end that
`actually aren’t present in the sample”).
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 13 of 33 PageID #: 7467
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`FMI thus does not infringe the Asserted Claims either literally or under the DOE.13
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`B.
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`The Asserted Claims Are Invalid
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`Guardant’s Motion should also be denied because the Asserted Claims are “vulnerable” to
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`multiple and substantial questions of invalidity. Erico Int’l Corp. v. Vutec Corp., 516 F.3d 1350,
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`1356 (Fed. Cir. 2008); Baxalta Inc. v. Genentech, Inc., 2018 WL 3742610, at *8 (D. Del. Aug. 7,
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`2018); see also Nat’l Steel Car, Ltd. v. Canadian Pac. Ry., Ltd., 357 F.3d 1319, 1335 (Fed. Cir.
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`2004) (“[V]ulnerability is the issue at the preliminary injunction stage[.]”) (citation omitted).
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`Like the 1616 Action patent claims, the Asserted Claims are invalid because they are
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`directed to basic NGS methods that were well understood for years before the purported priority
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`date (March 5, 2014). See Gabriel Dec. ¶¶49-82. Indeed, Dr. Cooper admits, and the Asserted
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`12 See Ex. 134, at 283:17-284:8 (“[I]f my aligner determined that the read stops mapping at
`Position 99 because there is this indel in Position 100, then that is the stop base position that I
`would be using for this claim; is that correct? A: Right. Exactly.”); id. at 271:10-272:17, 275:12-
`276:22,; Ex. 85, at 268-69.
`13 See Turn-Key-Tech, LLC v. Nat'l Film Lab, Inc., 74 Fed. App’x 58, 61 (Fed. Cir. 2003).
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 14 of 33 PageID #: 7468
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`Patents show, that (i) POSAs have analyzed cfDNA since the 1940s; (ii) standard NGS methods
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`and bioinformatics tools were routinely applied, including for cancer research, by the early 2000s;
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`(iii) molecular barcoding was widely used by the 2000s and for error correction by at least 2012;
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`and (iv) techniques for achieving high ligation efficiencies were known by 2012. See, e.g., D.I.
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`10, ¶¶26-37; ’085 patent, 1:40-41, 30:12-16, 38:28-33, 38:49-61, 37:61-38:8.
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`In fact, two years before the alleged priority date of Guardant’s patents, Schmitt expressly
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`described methods of incorporating “tag-based error correction” techniques into standard NGS
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`workflows for “deep sequencing” to achieve improved detection of “minor variants within
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`heterogeneous mixtures” such as cfDNA by “reduc[ing] or eliminat[ing] artifactual mutations
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`arising from DNA damage, PCR errors, and sequencing errors.” Ex. 93, at 1:28-41, 2:56-59; see
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`also id. at 2:56-62 (describing detecting mutations “with unprecedented sensitivity”); Gabriel Dec.
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`¶¶105-202. Schmitt also teaches using >30X molar excess of adaptors in its ligation reactions to
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`achieve high ligation efficiencies. See Ex. 93, at 19:65-67, 20:9-15, 22:53-56; Gabriel Dec. ¶¶126-
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`31. At best, Guardant’s patents are no more than an obvious application of Schmitt’s teachings.
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`Indeed, the U.S. Patent Office issued patents to Schmitt’s inventors directed to analyzing cfDNA
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`and the tagging, amplifying, sequencing, grouping, and detecting steps that Guardant argues are
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`novel aspects of its patents. These patents claim priority to Schmitt’s prior art patent applications,
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`confirming Schmitt’s earlier invention. See, e.g., Ex. 127; Ex. 125; Ex. 121; Ex. 120.
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`Guardant’s alleged inventors were, in fact, keenly aware of Schmitt’s teachings before they
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`filed their patent applications. Internal lab notebooks show that
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` Despite Guardant’s intimate familiarity with Schmitt’s inventions and a wealth of other prior
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`art, the Motion devotes less than a page to validity and relies solely on preliminary IPR decisions
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`Case 1:20-cv-01580-LPS Document 38 Filed 03/05/21 Page 15 of 33 PageID #: 7469
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`regarding the ’992 patent. See D.I. 8, at 16.14 At the same time, Guardant completely disregards
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`the PTAB’s other, final IPR decisions finding that “ordinarily skilled artisans knew that barcode-
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`based deep-sequencing techniques had been used to screen cfDNA for genetic defects,” such that
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`Guardant’s purported inventions reflect “the mere application of a known technique to a piece of
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`prior art ready for the improvement.” Ex. 124, 54, 55 (citing KSR Int’l Co. v. Teleflex Inc., 550
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`U.S. 398, 417 (2007)). Guardant’s selective reliance on preliminary PTAB decisions betrays the
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`weakness of its position. Finally, the Asserted Claims fail to distinguish the prior art and instead
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`add new limitations that render the claims indefinite and lacking written description.
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`1.
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`The Asserted Claims Are Obvious Over the Prior Art
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`As described in detail in Dr. Gabriel’s declaration, the Asserted Claims are obvious at least
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`from (i) Schmitt in view of common knowledge in the art (see Gabriel Dec. ¶¶104-241); (ii)
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`Schmitt in view of WO 2012/099832 (“Hendricks”) and common knowledge (id. ¶¶242-59); (iii)
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`Schmitt in view of Hendricks and Fan or Forshew (id. ¶¶260-85); and (iv) WO 2011/091046
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`(“Rava”), along with the New England Biolabs (NEB) Manual in view of Schmitt (id. ¶¶286-384).
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`A POSA would have been expressly motivated to combine Schmitt with any of these teachings,
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`and would have reasonably expected success. Id. ¶¶251-53, 258-59, 267-79, 284-85, 345-50, 382-
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`84. To the extent Guardant claims it is the recited 20% sample ligation efficiency15 and/or molar
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`excess limitations that are the novel features of the Asserted Claims (they are not)16, use of such
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`14 Notably, the PTAB did not have access to Guardant’s lab notebooks evidencing their own
`understanding of what was routine in the art before their alleged invention. Moreover, Guardant’s
`reliance on PTAB preliminary decisions is misplaced because they (1) were based on limited,
`different prior art and theories; (2) involved different claims; (3) turned on an unrelated question
`of inherency (not asserted here); (4) were discretionary and involved only a preliminary
`evidentiary assessment; and (5) have no estoppel effect. See, e.g., Andover Healthcare, Inc. v. 3M
`Co., 2016 WL 6404111, at *2 (D. Del. Oct. 27, 2016) (PTAB institution decision was “not a final
`decision on validity, is based on different legal standards, and has no estoppel effect”).
`15 Dr. Cooper agrees that “wherein at least 20% of the cfDNA molecules from the population of
`cfDNA molecules are attached to molecular barcodes” refers to a sample ligation efficiency of at
`least 20%.