Foundation Medicine, Inc. v. Caris MPI, Inc.
`
`Case Nos. IPR2019-00164 (U.S. Patent No. 8,880,350),
`IPR2019-00170 (U.S. Patent No. 9,372,193), and
`IPR2019-00171 (U.S. Patent No. 9,383,365)
`
`PETITIONER’S ORAL ARGUMENT
`
`1
`
`FMI v. Caris MPI
`Exhibit 1167
`IPR2019-00170
`
`
`
`Case Nos. IPR2019-00164 (U.S. Patent No. 8,880,350),
`IPR2019-00170 (U.S. Patent No. 9,372,193), and
`IPR2019-00171 (U.S. Patent No. 9,383,365)
`
`PETITIONER’S ORAL ARGUMENT
`
`1
`
`FMI v. Caris MPI
`Exhibit 1167
`IPR2019-00170
`
`
`
`Summary of Argument
`
`• Elements of the claimed system were all known
`
`• No basis to import “lineage independence” limitation, particularly under
`BRI standard and in view of prosecution history
`
`• Even under Patent Owner’s flawed construction, the prior art renders the
`challenged claims obvious
`• Lu discloses a general system for identifying a therapeutic agent based on a
`patient’s genotype
`• Illumina discloses a panel of targets from a wide variety of cancers,
`including all of the molecular targets in the claims
`
`Paper 3 at 4-9, 19-21 (Petition); Ex. 1002 ¶¶ 34-66, 68-82, 100-101, 105, 107 (Spellman Decl.);
`Paper 12 at 13, 26 (Institution Decision); Paper 42 at 8 (Petitioner’s Reply)
`
`2
`
`
`
`Agenda
`
`Technology Background
`
`Prior Art References
`
`The Challenged Patents
`
`Obviousness Grounds
`
`Claim Construction
`
`Contested Issues
`
`3
`
`
`
`Technology Background
`
`4
`
`
`
`Ex. 1004, Fig. 4 (Lu)
`
`Cancer Therapies Targeting
`Genes Were Well Known
`Known Approved Drugs and
`Known Molecular
`Drugs in Clinical Trials
`Targets
`
`ABL
`KIT
`PDFGR
`
`Known
`
`Imatinib (Gleevec®)
`
`HER2 (neu)
`
`Known
`
`Trastuzumab (Herceptin®)
`
`EGFR
`
`Known
`
`Gefitinib (Iressa®) (ZD-1839)
`Erlotinib (Tarceva®) (CP-358,774)
`
`Paper 3 at 6-7 (Petition); Ex. 1002 ¶¶ 44-60 (Spellman Decl.);
`Ex. 1009 at 294; Ex. 1059 at 107; Ex. 1012 at 9-10
`
`* All cites are to IPR2019-00164, unless otherwise noted
`
`Paper 3 at 23-38 (Petition);
`Ex. 1002 ¶¶ 125-145
`(Spellman Decl.)
`
`5
`
`
`
`Cancer Therapies Targeting Genes Were Well Known
`
`Ex. 1059 at 97, 107 (Febbo); Paper 3 at 5-7 (Petition);
`Ex. 1002 ¶¶ 44-46 (Spellman Decl.)
`
`6
`
`
`
`Cancer Therapies Targeting Genes Were Well Known
`
`• Published in 2005
`
`c
`
`Ex. 1059 at 97, 107 (Febbo); Paper 3 at 5-7 (Petition);
`Ex. 1002 ¶¶ 44-46 (Spellman Decl.)
`
`7
`
`
`
`Investigating New Uses of Known Therapies Was
`Well Known
`
`c
`
`Ex. 1030 at 1 (ONCOMINE); Paper 3 at 7-8 (Petition); Ex. 1002 ¶¶ 68-72
`(Spellman Decl.); Paper 42 at 13-15 (Petitioner’s Reply);
`Ex. 1120 ¶¶ 27, 53-54 (Spellman Reply Decl.)
`
`8
`
`
`
`Using a Database to Develop New Uses of Known
`Therapies Was Well Known
`
`Ex. 1030 at 3 (ONCOMINE); Paper 3 at 7-8 (Petition); Ex. 1002 ¶¶ 68-72
`(Spellman Decl.); Paper 42 at 13-15 (Petitioner’s Reply);
`Ex. 1120 ¶¶ 27, 53-54 (Spellman Reply Decl.)
`
`9
`
`
`
`The Elements of the Claimed System Were All Known
`in the Art
`
`• Testing patient specimens for genomic alterations
`associated with cancer
`
`• Therapies targeting cancers associated with
`those alterations
`
`• A database associating the genomic alterations with
`associated targeted therapies
`
`Paper 3 at 4-9; Ex. 1002 ¶¶ 34-66, 68-82 (Spellman Decl.)
`
`10
`
`
`
`
`
`Prior Art References
`
`Prior Art References
`
`11
`
`
`
`
`
`Lu Discloses a System for Selecting Cancer Treatment
`
`• Not considered by the examiner
`
`Ex. 1004, ¶ [0001] (Lu); Paper 3 at 17-20 (Petition); Ex. 1002 ¶¶ 99-105 (Spellman Decl.);
`Paper 42 at 16-19 (Petitioner’s Reply); Ex. 1120 ¶¶ 55-56, 62 (Spellman Reply Decl.)
`
`12
`
`
`
`Lu Discloses the Components
`of the Claimed System
`
`• Discloses a system that
`
`(1) analyzes a sample using a
`molecular assay;
`
`(2) compares a patient’s molecular
`profile to a database; and
`
`(3) generates a report identifying a
`recommended therapeutic agent
`
`Ex. 1004 ¶¶ [0034]-[0037], [0040]-[0045], Fig. 4 (Lu); Paper 3 at 17-20 (Petition);
`Ex. 1002 ¶¶ 99-105 (Spellman Decl.); Ex. 1120 ¶ 75 (Spellman Reply Decl.)
`
`13
`
`
`
`Lu Discloses Identifying Treatments Based on an
`Individual’s Molecular Profile
`• Discloses generally applicable system for
`identifying treatments for cancer based on
`“patient genotype”
`
`Ex. 1004 ¶ [0056], Claim 2 (Lu); Paper 3 at 17-20 (Petition); Ex. 1002 ¶¶ 118, 193 (Spellman Decl.);
`Paper 42 at 16-19 (Petitioner’s Reply); Ex. 1120 ¶¶ 55-63 (Spellman Reply Decl.)
`
`14
`
`
`
`Illumina Describes a Sensitive, Reproducible, and
`Clinically Reliable DASL Gene Expression Assay
`
`• Published on November 16, 2005
`• Not considered by examiner
`
`Ex. 1005 at 4 (Illumina); Paper 3 at 20-21 (Petition);
`Ex. 1002 ¶¶ 106-107 (Spellman Decl.); Paper 42 at
`22-23 (Petitioner’s Reply); Ex. 1120 ¶¶ 70-74
`(Spellman Reply Decl.)
`
`15
`
`
`
`Illumina Discloses a High-Throughput Assay
`
`• DASL cancer panel
`simultaneously assays
`502 gene targets,
`including each of the
`seven targets recited
`in each of the
`challenged patents
`
`Ex. 1005 at 4 (Illumina); Paper 3 at 20-21 (Petition); Ex. 1002 ¶¶ 106-107 (Spellman Decl.)
`
`16
`
`
`
`The Challenged Patents
`
`17
`
`
`
`The Challenged Patents
`
`Paper 3 at 4 (Petition); Ex. 1002 ¶¶ 19, 31 (Spellman Decl.)
`
`18
`
`
`
`’350 Patent, Claim 1
`
`System for generating a report identifying at
`least one therapeutic agent for an individual
`with a cancer comprising:
`• Assaying plurality of molecular targets
`including EGFR, KIT, TOP1, MLH1, PTEN,
`PDGFRA, and ESR1
`• Database with targets and genes
`• Software to compare test values
`• Software to identify and report target and
`corresponding therapeutic agent associated
`with likely benefit
`
`Ex. 1001 (’350 Patent); Paper 3 at 10-12 (Petition); Ex. 1002 ¶¶ 83-87 (Spellman Decl.)
`
`19
`
`
`
`Illumina and Lu Disclose Claim 1 Limitations
`
`Illumina DASL
`Cancer Panel
`Ex. 1005
`
`Lu
`Ex. 1004
`
`1. A system for generating a report identifying at least one therapeutic agent for
`an individual with a cancer comprising:
`a. at least one device configured to assay a plurality of molecular targets
`in a biological sample to determine individualized molecular profile test values for
`the plurality of molecular targets, wherein the molecular targets comprise EGFR,
`KIT, TOP1, MLH1, PTEN, PDGFRA, and ESR1;
`b. at least one computer database comprising: i. a reference value for the
`plurality of molecular targets; ii. a listing of available therapeutic agents for said
`plurality of molecular targets;
`c. a computer-readable program code comprising instructions to input the
`individualized molecular profile test values and to compare said test values with
`a corresponding reference value in (b)(i);
`d. a computer-readable program code comprising instructions to access
`the at least one computer database and to identify at least one therapeutic agent
`from the listing of available therapeutic agents for the plurality of molecular targets
`wherein said comparison to said reference in (c) indicates a likely benefit of the at
`least one therapeutic agent; and
`e. a computer-readable program code comprising instructions to generate
`a report that comprises a listing of the molecular targets wherein said comparison
`to said reference indicated a likely benefit of the at least one therapeutic agent in
`(d) along with the at least one therapeutic agent identified in (d).
`
`Paper 3 at 23-58 (Petition); Ex. 1002 ¶¶ 112-187 (Spellman Decl.)
`
`20
`
`
`
`Illumina Teaches All Molecular Targets in ’350 Patent
`
`• DASL panel
`simultaneously
`assays 502 genes,
`including each
`gene target found
`in claim 1 of the
`’350 patent
`
`Ex. 1005 at 4 (Illumina); Paper 3, IPR2019-00164, at 20-21 (Petition)
`Ex. 1002, IPR2019-00164, ¶¶ 106-107 (Spellman Decl.)
`
`21
`
`
`
`’193 & ’365 Patents Recite the Same System
`With Different Molecular Targets
`’193 Patent, Claim 1
`
`’365 Patent, Claim 1
`
`22
`
`
`
`Illumina Teaches All Molecular Targets in ’193 Patent
`
`• DASL panel
`simultaneously
`assays 502 genes,
`including each gene
`target found in claim
`1 of the ’193 patent
`
` ERBB2 is synonymous
`with HER2
`
`Ex. 1005 at 4 (Illumina); Paper 3, IPR2019-00170, 20 (Petition)
`Ex. 1002, IPR2019-00170, ¶¶ 105-106 (Spellman Decl.)
`
`23
`
`
`
`Illumina Teaches All Molecular Targets in ’365 Patent
`
`• DASL panel
`simultaneously
`assays 502 genes,
`including each gene
`target found in claim
`1 of the ’365 patent
`
`Ex. 1005 at 4 (Illumina); Paper 3, IPR2019-00171, 21 (Petition)
`Ex. 1002, IPR2019-00171, ¶¶ 105-106 (Spellman Decl.)
`
`24
`
`
`
`The Specification Describes
`Well Known Technology
`• Using individual’s molecular profile to identify potential
`therapies was known
`Ex. 1001, 1:42-49
`
`• Targeted anticancer agents were known
`Ex. 1001, 2:13-14
`
`• Discloses both lineage dependent and lineage
`independent embodiments
`Ex. 1001, 3:49-67, 4:1-33, 4:63-67, 5:1-4
`
`• No description of specific panel of genes recited
`in the claims
`
`• Except for EGFR and AR, the patents do not disclose
`any treatment associated with the genes listed in the
`claimed panels
`
`Ex. 1001 (’350 Patent); Paper 3 at 12-13 (Petition); Ex. 1002 ¶¶ 89-93 (Spellman Decl.)
`
`25
`
`Ex. 1001, 1:42-49
`
`Ex. 1001, 2:10-16
`
`Ex. 1001, 14:1-19
`
`
`
`Summary of the File History
`
`• The Examiner allowed the challenged claims
`because “the prior art does not disclose the
`panel of molecular targets as in claim 1”
`
`Illumina DASL Cancer Panel
`Ex. 1005
`
`• However, the Examiner did not consider
`Illumina’s DASL panel during prosecution
`Ex. 1003 at 23 (’350 File History); Paper 3 at 14-16 (Petition); Ex. 1002 ¶¶ 94-98 (Spellman Decl.);
`Paper 49 at 13-15 (Patent Owner’s Reply); Ex. 1003, IPR2019-00170, 29 (’193 File History);
`Ex. 1003, IPR2019-00171, 35 (’365 File History);
`
`26
`
`
`
`
`
`Obviousness Grounds
`
`Obviousness Grounds
`
`27
`
`rat FOUNDATION
`
`MEDICINE
`
`
`
`Obviousness Grounds
`’350 Patent
`
`’193 Patent
`
`Paper 3, IPR2019-00164, at 4 (Petition)
`’365 Patent
`
`Paper 3, IPR2019-00170, at 3 (Petition)
`
`Paper 3, IPR2019-00171, at 4 (Petition)
`
`28
`
`
`
`
`
`Claim Construction
`
`Claim Construction
`
`29
`
`eats FOUNDATION
`
`MEDICINE
`
`
`
`Testing for “Lineage Independence” Cannot Be
`the Broadest Reasonable Interpretation
`
`“[U]nder the broadest reasonable construction standard, where two claim
`constructions are reasonable, the broader construction governs.”
`Google LLC v. Network-1 Techs., Inc., 726 F. App’x 779, 785 (Fed. Cir. 2018).
`
`Paper 42 at 10 (Petitioner’s Reply)
`• Reading the claims to require this narrowing limitation cannot be the broadest
`reasonable interpretation
`Paper 42 at 6 (Petitioner’s Reply); Paper 49 at 8 (Patent Owner’s Sur-Reply) (citing 37 C.F.R. § 42.100(b))
`
`• Patent Owner’s non-obviousness position is predicated on its unsupported
`lineage independence construction
`Paper 32 at 46-48 (Patent Owner’s Response); Paper 49 at 25 (Patent Owner’s Sur-Reply)
`
`30
`
`
`
`Patent Owner Provides No Basis to
`Import “Lineage Independence”
`
`Paper 32 at 27 (Patent Owner’s Response)
`
`Paper 49 at 9 (Patent Owner’s Sur-Reply)
`
`• No specific claim language for
`construction identified
`
`•
`
`Inferring “lineage independence”
`limitation based on disparate claim
`elements
`
`• Renishaw PLC v. Marposs Societa’
`per Azioni, 158 F.3d 1243, 1248
`(Fed. Cir. 1998) (“a claim must explicitly
`recite a term in need of definition before
`a definition may enter the claim from the
`written description”)
`Paper 42 at 6-8 (Petitioner’s Reply)
`
`31
`
`
`
`Prosecution History Confirms That Patent Owner
`Knew How to Claim “Lineage Independence”
`
`• U.S. Provisional Patent Application No. 60/747,645
`(filed May 18, 2006) included explicit lineage independent
`limitations, which were amended and removed during
`prosecution
`
`Ex. 1140 at 9 (U.S. Patent Application No. 2008/0014146);
`Ex. 1139 at 26 (U.S. Provisional Patent Application No. 60/747,645);
`Paper 42 at 8-9 (Petitioner’s Reply); Ex. 1120 ¶¶ 44-46 (Spellman Reply Decl.)
`32
`
`
`
`Prosecution History Confirms That Patent Owner
`Knew How to Claim Lineage Independent Limitation
`
`• During prosecution of U.S.
`Application No. 11/750,721
`(Filed May 18, 2007), other
`lineage independent
`limitations were introduced
`• All lineage independent
`limitations were removed
`before allowance
`
`Paper 42 at 9 (Petitioner’s Reply);
`Ex. 1120 ¶¶ 44-46 (Spellman Reply Decl.)
`
`Ex. 1141 at 531, 121, 133 (File History of U.S. Patent Application No. 11/750,721)
`
`33
`
`
`
`Whether a System is “Lineage Dependent” or
`“Lineage Independent” Changes Over Time, Based
`on Level of Clinical Proof
`
`Dr. O’Shaughnessy
`
`***
`
`Paper 42 at 11 (Petitioner’s Reply)
`
`Ex. 1119, 320:2-321:6 (O’Shaughnessy Dep.)
`
`34
`
`Ex. 1119, 330:21-331:14 (O’Shaughnessy Dep.)
`
`
`
`’350 Patent, Limitation 1(d) Does Not Require a
`Therapeutic Agent Directed to a Claimed Target
`• 1(d) does not require a therapeutic
`agent directed to a claimed target
`• The “plurality of molecular targets”
`of element 1(a) “comprise” the
`named targets
`• No construction needed for purposes
`of this proceeding
`• Does not require identifying “all”
`therapeutic agents
`Paper 3 at 34-35 (Petition); Ex. 1002 ¶ 142 (Spellman Decl.);
`Paper 42 at 12 (Petitioner’s Reply);
`Ex. 1120 ¶ 48 (Spellman Reply Decl.);
`Paper 32 at 31 (Patent Owner‘s Response);
`Paper 49 at 10 (Patent Owner‘s Sur-Reply)
`
`Ex. 1001, claim 1(a), 1(d) (’350 Patent)
`
`***
`
`35
`
`
`
`
`
`Contested Issues
`
`Contested Issues
`
`36
`
`coma FOUNDATION
`
`MEDICINE
`
`
`
`Contested Issues
`
`1. Obviousness Analysis Under Patent Owner’s
`Lineage Independence Construction
`
`2. Motivation to Combine Lu with Illumina
`
`3. POSA Definition
`
`4. Secondary Considerations
`
`37
`
`
`
`Lu Discloses a General System for Identifying a
`Therapeutic Agent Based on a Patient’s Genotype
`
`Ex. 1004 ¶ [0056] (Lu)
`
`Paper 3 at 17-20 (Petition); Ex. 1002 ¶¶ 99-105, 118 (Spellman Decl.);
`Paper 42 at 15-19 (Petitioner’s Reply); Ex. 1120 ¶¶ 55-63 (Spellman Reply Decl.)
`
`Ex. 1004 ¶ [0003] (Lu)
`
`38
`
`
`
`Lu Discloses a General System for Identifying a
`Therapeutic Agent Based on a Patient’s Genotype
`
`Ex. 1004 at 15, Claim 2 (Lu); Paper 42 at 18 (Petitioner‘s Reply)
`
`39
`
`
`
`Lu Discloses a General System for Identifying a
`Therapeutic Agent Based on a Patient’s Genotype
`
`Paper 12 at 26-27 (Institution Decision); Paper 42 at 16 (Petitioner’s Reply);
`Ex. 1120 ¶ 55 (Spellman Reply Decl.)
`
`40
`
`
`
`Lu Discloses a “Lineage Independent” Panel Under
`Patent Owner’s Expert’s Analysis
`
`• O’Shaughnessy: Assaying EGFR in any cancer other than lung
`cancer was lineage independent
`
`Dr. O’Shaughnessy
`
`Ex. 1119, 320:2-20 (O’Shaughnessy Dep.); Paper 42 at 15-16 (Petitioner’s Reply)
`
`41
`
`
`
`Lu Discloses a “Lineage Independent” Panel Under
`Patent Owner’s Expert’s Analysis
`
`• O’Shaughnessy: Assaying EGFR in breast cancer is
`lineage independent
`
`Dr. O’Shaughnessy
`
`Ex. 1119, 324:2-14 (O’Shaughnessy Dep.); Paper 42 at 15-16 (Petitioner’s Reply)
`
`42
`
`
`
`O’Shaughnessy: Lu’s “Breast Cancer” Targets
`Include EGFR
`
`Dr. O’Shaughnessy
`
`Ex. 1004 ¶ [0051] (Lu)
`
`Ex. 1119, 399:5-16
`(O’Shaughnessy Dep.)
`
`Paper 3 at 18, 26 (Petition);
`Ex. 1002 ¶¶ 101, 105, 126
`(Spellman Decl.);
`Paper 42 at 15-16 (Petitioner’s Reply);
`Ex. 1120 ¶ 58 (Spellman Reply Decl.)
`
`43
`
`
`
`Lu Describes Assays Targeting Markers Associated
`with Multiple Cancers
`
`Ex. 1004 ¶ [0052] (Lu)
`
`Ex. 1004 ¶ [0054] (Lu)
`
`• BCL-2 was associated with NSCLC,
`follicular and B-cell lymphomas, chronic
`lymphocytic leukemias, and breast and
`prostate cancers
`
`• DPD was associated with bladder,
`breast, cervical, colorectal, esophageal,
`gastric, hepatic, pancreatic, prostate,
`and renal cancers
`
`Ex. 1007 at 142; Ex. 2022 at 61-62; Ex. 2052 at 282;
`Ex. 1118, 174:4-12 (O’Shaughnessy Dep.); Ex. 1100 at 8
`
`Ex. 1121 at 33
`
`Ex. 1120 ¶¶ 57, 59-60, 63 (Spellman Reply Decl.); Paper 42 at 17-18 (Petitioner’s Reply)
`
`44
`
`
`
`Lu’s System Describes the Use of Non-Disease
`Specific Treatments
`
`Ex. 1004 ¶ [0054] (Lu)
`
`Ex. 1144 at 2248; Ex. 1145 at 330; Ex. 1146 at 2;
`Ex. 1120 ¶ 63 (Spellman Reply Decl.); Paper 42 at 19 (Petitioner’s Reply)
`
`45
`
`
`
`Illumina Discloses a Lineage-Independent Panel
`of Targets
`
`Ex. 1119, 426:16-21 (O’Shaughnessy Dep.)
`
`Dr. O’Shaughnessy
`
`Ex. 1005 at 4 (Illumina)
`
`Paper 3 at 20-21, 25, 31 (Petition);
`Ex. 1002 ¶¶ 107, 127, 134-135 (Spellman Decl.);
`Paper 42 at 19-20 (Petitioner’s Reply);
`Ex. 1120 ¶¶ 65-66 (Spellman Reply Decl.)
`
`46
`
`
`
`The Illumina Panel Is Lineage Independent Under
`Patent Owner’s Definition
`
`Dr. O’Shaughnessy
`• The targets in Claim 1 of ’365 patent
`include EGFR, KIT, TOP1, MLH1,
`PTEN, PDGFRA, and ERRB2
`
`Ex. 1005, IPR2019-00171, 4 (Illumina),
`Ex. 1001, IPR2019-00171, 17:10-12 (’365 Patent, claim 1)
`
`Ex. 1119, IPR2019-00171, 333:12-20 (O’Shaughnessy Dep.);
`Ex. 1120, IPR2019-00171, ¶ 66 (Spellman Reply Decl.);
`Paper 43, IPR2019-00171, at 20 (Petitioner’s Reply)
`
`47
`
`
`
`Contested Issues
`
`1. Obviousness Analysis Under Patent Owner’s
`Lineage Independence Construction
`
`2. Motivation to Combine Lu with Illumina
`
`3. POSA Definition
`
`4. Secondary Considerations
`
`48
`
`
`
`A POSA Would Have Been Motivated to Combine
`Lu with Illumina
`
`• Claims do not require treating a patient – they only require:
`1) a system for determining a molecular profile; and
`2) generating a report of possible therapeutic agents
`Paper 3 at 10-11 (Petition); Ex. 1002 ¶¶ 86-88 (Spellman Decl.); Paper 42 at 2 (Petitioner’s Reply);
`Ex. 1120 ¶ 9 (Spellman Reply Decl.)
`
`O’Shaughnessy: Claim 1 “doesn’t say you have to treat the
`patient with these therapies”
`Ex. 1118, 83:9-84:3 (O’Shaughnessy Dep.)
`
`Dr. O’Shaughnessy
`
`49
`
`
`
`Modifying Lu with Illumina Results in Substantial
`Throughput and Cost-Saving Advantages
`
`Ex. 1005 at 3 (Illumina); Paper 3 at 51-54 (Petition); Ex. 1002 ¶¶ 117-122 (Spellman Decl.)
`
`• Lu: Discloses screening select genes using low-throughput RT-PCR assays to
`identify effective cancer therapies
`Ex. 1004 ¶¶ [0022], [0034]-[0038], [0050]-[0056] (Lu)
`
`•
`
`Illumina: Discloses that DASL (a high-throughput assay) can be used clinically to
`screen 500+ cancer genes simultaneously
`Ex. 1005 at 1, 4, 8 (Illumina)
`
`Paper 3 at 24-25, 48-54 (Petition); Ex. 1002 ¶¶ 112-123 (Spellman Decl.); Paper 42 at 21-23 (Petitioner’s Reply);
`Ex. 1120 ¶¶ 68-76 (Spellman Reply Decl.)
`
`50
`
`
`
`Contested Issues
`
`1. Obviousness Analysis Under Patent Owner’s
`Lineage Independence Construction
`
`2. Motivation to Combine Lu with Illumina
`
`3. POSA Definition
`
`4. Secondary Considerations
`
`51
`
`
`
`The Record Supports Petitioner’s POSA Definition
`Dr. Spellman
`
`Dr. O’Shaughnessy
`
`• Ph.D. with research experience in
`cancer genomics
`Ex. 1002 ¶ 32 (Spellman Decl.); Paper 3 at 16 (Petition);
`Ex. 1120 ¶¶ 8-17 (Spellman Reply Decl.);
`Paper 42 at 2-5 (Petitioner’s Reply)
`
`• M.D. oncologist with clinical
`experience treating cancer patients
`Ex. 2021 ¶ 14 (O’Shaughnessy Decl.);
`Paper 32 at 4 (Patent Owner’s Response)
`
`Patent Owner’s Definition Does Not
`Require the POSA to Be a “Practicing
`Academic Medical Oncologist” with
`“Translational Clinical Experience”
`
`Paper 32 at 4
`(Patent Owner’s Response)
`
`52
`
`
`
`Specification Explains that POSAs Would Have Been
`Familiar with Assays and System Technologies
`
`Ex. 1001, 10:65-11:3 (’350 Patent)
`
`Ex. 1001, 13:21-31 (’350 Patent)
`
`Ex. 1001, 13:48-52 (’350 Patent)
`
`Ex. 1001 (’350 Patent); Paper 42 at 3-4 (Petitioner’s Reply); Ex. 1120 ¶¶ 11-14 (Spellman Reply Decl.)
`
`53
`
`
`
`Specification Equates “Treating Physicians”
`with “End Users” and “Participants”
`
`Ex. 1001, 10:15-21 (’350 Patent); Paper 42 at 3-4 (Petitioner’s Reply);
`Ex. 1120 ¶ 13 (Spellman Reply Decl.)
`
`54
`
`
`
`Patent Owner’s Expert Agrees POSA Need Not Be
`Practicing Oncologist
`
`Dr. O’Shaughnessy
`
`• Daiichi Sankyo Co. v. Apotex, Inc., 501 F.3d
`1254, 1257 (Fed. Cir. 2007) (“while a general
`practitioner or pediatrician could (and would)
`prescribe the [claimed] invention … he would
`not have the training or knowledge to develop
`the claimed compound”)
`
`• Nat’l Oilwell Varco, L.P. v. Tech. Indus.,
`Inc., No. IPR2017-00648, 2018 WL 3494798,
`at *5 (July 18, 2018) (rejecting POSA
`definition “based on the faulty premise that an
`ordinarily skilled artisan would have been one
`who uses [the claimed techniques], rather
`than one who develops them”)
`
`Ex. 1118, 94:18-95:6, 97:2-11 (O’Shaughnessy Dep.);
`Paper 42 at 2-5 (Petitioner’s Reply); Paper 49 at 4-8 (Patent Owner’s Sur-Reply)
`
`55
`
`
`
`Contested Issues
`
`1. Obviousness Analysis Under Patent Owner’s
`Lineage Independence Construction
`
`2. Motivation to Combine Lu with Illumina
`
`3. POSA Definition
`
`4. Secondary Considerations
`
`56
`
`
`
`Doroshow Does Not Praise Alleged Invention
`
`• No nexus to “establishing a novel algorithm”
`Paper 42 at 24-25 (Petitioner’s Reply); Ex. 1120 ¶ 38 (Spellman Reply Decl.); Ex. 1118, 240:21-241:11
`(O’Shaughnessy Dep.) (the challenged patents do not claim using an algorithm to prioritize treatments)
`• No nexus to “novel approach” using N = 1 pilot studies relying on time
`to progression
`Paper 42 at 24-25 (Petitioner’s Reply); Ex. 1120 ¶¶ 21-38 (Spellman Reply Decl.)
`• Investigating new uses of known therapies was well known
`Paper 3 at 4-8 (Petition); Ex. 1002 ¶¶ 44-72 (Spellman Decl.); Paper 42 at 13-15 (Petitioner’s Reply);
`Ex. 1120 ¶¶ 27, 53-54 (Spellman Reply Decl.); Ex. 1016 at 81-85 (Scholl); Ex. 1064 at 33 (Cappuzzo);
`Ex. 1030 at 1, 3 (ONCOMINE)
`
`57
`
`
`
`Conducting Clinical Trials to Study New Uses of
`Known Therapies Was Known
`
`Dr. O’Shaughnessy
`
`Ex. 1016 at 1-5 (Scholl) (2001)
`
`Ex. 1118, 165:9-22 (O’Shaughnessy Dep.)
`
`Paper 3 at 4-8 (Petition); Ex. 1002 ¶¶ 44-72 (Spellman Decl.); Paper 42 at 13-15
`(Petitioner’s Reply); Ex. 1120 ¶¶ 27, 53-54 (Spellman Reply Decl.)
`
`Ex. 1064 at 33 (Cappuzzo) (2006)
`
`58
`
`
`
`Significant Study Limitations Preclude Surprising or
`Unexpected Results
`
`• Significant study limitations from lack of randomization create
`“worrisome potential biases”
`Paper 42 at 24-25 (Petitioner’s Reply); Ex. 2013 at 1, 5 (Bisgrove); Ex. 2014 at 2 (Doroshow)
`
`• Results not unexpected where 11 of 18 patients with
`PFS ratio of ≥ 1.3 were treated with approved drugs already
`associated with the target and cancer
`Paper 42 at 24-25 (Petitioner’s Reply); Ex. 1120 ¶¶ 32-35 (Spellman Reply Decl.); Ex. 2014 at 2 (Doroshow)
`
`59
`
`
`
`No Skepticism or Surprising Results from
`2006 Abstract
`• No third-party publications expressing skepticism
`Paper 42 at 24 n.14 (Petitioner’s Reply); Ex. 1118, 210:12-17 (O’Shaughnessy Dep.) (O'Shaughnessy not aware of third-party
`publications expressing skepticism about data in 2006 abstract)
`
`In re Ethicon, Inc., 844 F.3d 1344, 1352 (Fed. Cir. 2017)
`(affirming Board decision discounting secondary considerations argument
`supported by insufficient evidence and conclusory testimony)
`
`Paper 42 at 24-27 (Petitioner’s Reply (citing Ex. 2042 at 1-2))
`• Unsupported expert testimony not entitled to weight
`Paper 42 at 24-27
`• No nexus between 2006 abstract and the claims
`Paper 42 at 24 (Petitioner’s Reply); Ex. 1118, 195:2-6 (O’Shaughnessy Dep.) (O'Shaughnessy did not know whether the assays in
`2006 study would satisfy the claims)
`
`60
`
`
`
`No Satisfaction of Long-Felt Need for Improved Tools
`for Identifying Therapeutic Agents
`
`• No new technology disclosed
`Paper 3 at 10 (Petition); Ex. 1002 ¶ 84 (Spellman Decl.); Ex. 1120 ¶ 26 (Spellman Reply Decl.)
`
`• No new target-therapy correlations disclosed
`Paper 3 at 10 (Petition); Ex. 1002 ¶ 84 (Spellman Decl.); Ex. 1120 ¶ 26 (Spellman Reply Decl.)
`
`• No evidence of “changed paradigm” based on challenged patents
`Paper 32 at 13 (Patent Owner’s Response)
`• NCCN guidelines remain organized by cancer lineage
`Paper 32 at 9-10 (Patent Owner’s Response)
`
`61
`
`
`
`No Nexus with Awards for Unrelated Contributions
`
`Ex. 2012 at 1 (Karnofsky)
`
`Ex. 2017 at 1 (Scripps)
`
`Paper 42 at 25-27 (Petitioner’s Reply); Ex. 1120 ¶¶ 39-40 (Spellman Reply Decl.); Ex. 2012 at 1; Ex. 2017 at 1
`
`62
`
`
`
`Alleged Praise Based on Products Lacks Nexus
`
`Petitioner’s and Patent Owner’s Products
`• No showing that products practice challenged claims
`• Assertion that “FMI’s reports bear a striking similarity to the Caris reports”
`is misplaced; challenged claims do not relate to report’s visual appearance
`Paper 42 at 26-27 (Petitioner’s Reply); Paper 32 at 23, 50 (Patent Owner’s Response)
`
`Cited Evidence Not “Praise”
`• Advertisements “intended to generate interest” and not “prove [a product’s]
`superiority” are not persuasive secondary considerations evidence
`Paper 42 at 26-27 (Petitioner’s Reply);
`Richardson-Vicks Inc. v. UpJohn Co., 122 F.3d 1476, 1484 n.3 (Fed. Cir. 1997)
`
`63
`
`
`
`Summary of Argument
`
`• Elements of the claimed system were all known
`
`• No basis to import “lineage independence” limitation, particularly under
`BRI standard and in view of prosecution history
`
`• Even under Patent Owner’s flawed construction, the prior art renders the
`challenged claims obvious
`• Lu discloses a general system for identifying a therapeutic agent based on a
`patient’s genotype
`• Illumina discloses a panel of targets from a wide variety of cancers,
`including all of the molecular targets in the claims
`
`Paper 3 at 4-9, 19-21 (Petition); Ex. 1002 ¶¶ 34-66, 68-82, 100-101, 105, 107 (Spellman Decl.);
`Paper 12 at 13, 26 (Institution Decision); Paper 42 at 8 (Petitioner’s Reply)
`
`64
`
`
`
`Foundation Medicine, Inc. v. Caris MPI, Inc.
`
`Case Nos. IPR2019-00164 (U.S. Patent No. 8,880,350),
`IPR2019-00170 (U.S. Patent No. 9.372,193), and
`IPR2019-00171 (U.S. Patent No. 9,383,365)
`
`PETITIONER’S ORAL ARGUMENT
`
`65
`
`
`
`
`
`Appendix
`
`Appendix
`
`66
`
`66 al FOUNDATION
`
`MEDICINE
`
`
`
`Muraca
`
`• Describes inputting molecular profile test
`values remotely to a database or using
`the internet
`
`Ex. 1006 ¶¶ [0151], [0018] (Muraca); Paper 3 at 21-22, 58-61 (Petition);
`Ex. 1002 ¶¶ 108-109, 198-202 (Spellman Decl.)
`
`67
`
`
`
`McDoniels-Silvers
`
`• Published in 2002
`• Discloses determining individual’s test
`values after they receive cancer drug
`therapy; and after they failed to respond
`to a cancer therapeutic
`
`Ex. 1007 at Table 1 (McDoniels-Silvers); Paper 3 at 22-23, 64-66 (Petition);
`Ex. 1002 ¶¶ 110-111, 215, 218, 220-221 (Spellman Decl.)
`
`68
`
`
`
`Foundation Medicine, Inc. v. Caris MPI, Inc.
`
`Case Nos. IPR2019-00164 (U.S. Patent No. 8,880,350),
`IPR2019-00170 (U.S. Patent No. 9.372,193), and
`IPR2019-00171 (U.S. Patent No. 9,383,365)
`
`PETITIONER’S ORAL ARGUMENT
`
`69
`
`
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