`
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF MASSACHUSETTS
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`CARIS MPI, INC.,
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`Plaintiff,
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`v.
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`FOUNDATION MEDICINE, INC.
`
`Defendant.
`___________________________________
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`
`C.A. No. 1:17-cv-12194
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`
`
`MEMORANDUM IN SUPPORT OF
`FOUNDATION MEDICINE’S MOTION TO DISMISS FOR
`LACK OF PATENTABLE SUBJECT MATTER AND WRITTEN DESCRIPTION
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 2 of 26
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`Table of Contents
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`I.
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`Introduction and Summary of Argument ............................................................................... 1
`
`II. Applicable Legal Standard ..................................................................................................... 3
`
`III. The Patents-in-Suit Are Invalid for Claiming an Abstract Idea Based on the Application of
`a Law of Nature ..................................................................................................................... 4
`
`A. The Claimed Invention Rests Upon an Abstract Idea ...................................................... 5
`
`1.
`
`The Patents-in-Suit Are Directed to the Abstract Idea of Recommending a
`Treatment Based on a Patient’s Molecular Profile ................................................... 5
`
`B. The Claims Contain No Inventive Concept Beyond the Abstract Idea ........................... 7
`
`1.
`
`2.
`
`3.
`
`The Significance of an Individual’s Molecular Profile for Cancer Therapies Was
`Well-Known ............................................................................................................. 7
`
`The Asserted Claims Rely on the Application of Laws of Nature that Are Not
`Patentable and Were Not Discovered by the Caris Inventors .................................. 9
`
`The Three “Early Caris Patents” .......................................................................... 9
`a)
`b) The Two “Later Caris Patents” .......................................................................... 10
`c) Molecular Correlations Are Not Patentable and Cannot Qualify as Significantly
`More than the Judicial Exception ...................................................................... 11
`The Asserted Claims Recite Unspecified Generic Assays and Conventional
`Databases and Software Performing Their Most Basic Functions ......................... 13
`
`C. The Caris Patents Tie Up the Development of Targeted Cancer Therapies .................. 14
`
`D. Caris Repeatedly Abandoned Patent Applications Subject to Patentable Subject Matter
`Rejections During Prosecution ...................................................................................... 15
`
`IV. The Asserted Patents Are Invalid for Lack of Written Description ..................................... 17
`
`A. The Three “Early Caris Patents” .................................................................................... 17
`
`B. The Two “Later Caris Patents” ...................................................................................... 18
`
`V. This Court Should Resolve These Questions of Patent Eligibility Now ............................. 19
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 3 of 26
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`TABLE OF AUTHORITIES
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`CASES
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`Page(s)
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`Alice Corp. v. CLS Bank Int’l, 134 S. Ct. 2347 (2014) ....................................2, 3, 4, 5, 7, 9, 13, 16
`
`Alice. Esoterix Genetic Labs. LLC v. Qiagen, Inc., 133 F. Supp. 3d 349 (D. Mass.
`2015) ..................................................................................................................................11
`
`Alice. Genetic Techs. Ltd. v. Lab. Corp. of Am. Holdings, No. 12-cv-01736-LPS,
`2014 WL 4379587 (D. Del. Sept. 3, 2014) ..................................................................12, 13
`
`Ashcroft v. Iqbal, 556 U.S. 662 (2009) ............................................................................................3
`
`Ass’n for Mol. Pathology v. Myriad Genetics, Inc., 569 U.S. 576 (2013) ...................................2, 4
`
`AstraZeneca Pharm. LP v. Apotex Corp., 669 F.3d 1370 (Fed. Cir. 2012) .....................................4
`
`Bell Atl. Corp. v. Twombly, 550 U.S. 544 (2007) ..........................................................................19
`
`CLS Bank Int’l v. Alice, 717 F.3d 1269 (Fed. Cir. 2013).................................................................7
`
`Content Extraction & Transmission LLC v. Wells Fargo Bank, Nat. Ass’n, 776
`F.3d 1343 (Fed. Cir. 2014)...................................................................................................7
`
`DDR Holdings, LLC v. Hotels.Com, L.P., 773 F.3d 1245 (Fed. Cir. 2017) ....................................7
`
`Fujikawa v. Wattanasin, 93 F.3d 1559 (Fed. Cir. 1996) ...............................................................17
`
`In re Bendamustine Consol. Cases, No. 13-cv-2046-GMS, 2015 WL 1951399 (D.
`Del. Apr. 29, 2015) ..............................................................................................................4
`
`In re Ruschig, 379 F.2d 990 (C.C.P.A. 1967) ................................................................................17
`
`Intellectual Ventures I LLC v. Symantec Corp., 838 F.3d 1307 (Fed. Cir. 2016) ...........................5
`
`Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66 (2012) ....................4, 5, 12, 13
`
`Mayo. Return Mail, Inc. v. United States Postal Serv., 868 F.3d 1350 (Fed. Cir.
`2017) ..................................................................................................................................13
`
`Netflix, Inc. v. Rovi Corp., 114 F. Supp. 3d 927, 947 (N.D. Cal. 2015), aff’d, 670
`F. App’x 704 (Fed. Cir. 2016) .............................................................................................7
`
`Par Pharm., Inc. v. Luitpold Pharm., Inc., No. 16-cv-02290-WHW, 2017 WL
`452003 (D.N.J. Feb. 2, 2017)...............................................................................................4
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 4 of 26
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`Presqriber, LLC v. Advanced Data Sys. Advanced Corp., No. 6:14-cv-859, 2015
`WL 11170154 (E.D. Tex. June 29, 2015) ............................................................................7
`
`Secured Mail Sols. LLC v. Universal Wilde, Inc., 873 F.3d 905 (Fed. Cir. 2017) ........................20
`
`Shaw v. Digital Equip. Corp., 82 F.3d 1194 (1st Cir. 1996) ...........................................................3
`
`Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709 (Fed. Cir. 2014) .....................................3, 9, 19, 20
`
`Union Oil Co. of Cal. v. Atl. Richfield Co., 208 F.3d 989 (Fed. Cir. 2000) ..................................17
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 5 of 26
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`I.
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`Introduction and Summary of Argument
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`In the 1990s, scientists discovered that certain cancers were associated with specific
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`changes in the molecular expression of specific genes and/or production of proteins controlled by
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`gene expression (i.e., “a molecular abnormality”) and set out to develop cancer treatments
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`targeting those molecular abnormalities. Targeted treatments represented an attractive
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`alternative to non-selective, toxic, and debilitating chemotherapy, which was the prior standard
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`of care for many cancers. These efforts ushered in a new era of personalized medicine with
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`drugs designed to treat individuals with specific molecular profiles. For example, in 1998,
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`Herceptin® (trastuzumab) was approved by the FDA for treatment of patients with metastatic
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`breast cancer whose tumors overexpress the HER2 protein. Additional targeted cancer therapies
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`were subsequently identified for the treatment of patients with specific molecular abnormalities.
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`The patents asserted by Plaintiff Caris MPI, Inc. (“Caris”),1 which claim priority to a
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`provisional application filed May 18, 2006, generally claim a system for identifying potential
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`cancer therapeutics that could be effective based on an individual’s molecular profile.2 The
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`Patents-in-Suit do not disclose a new or improved method for performing molecular profiling to
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`identify genetic alterations that may be associated with particular cancers, nor do they identify or
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`disclose any new correlation between a specific cancer, gene, or drug. Instead, the patents
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`purport to claim an abstract approach for matching individuals possessing one of a handful of
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`genetic mutations associated with cancer to existing therapies that are known in the prior art to
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`
`1 Caris has asserted infringement of U.S. Patent Nos. 8,880,350 (the “’350 Patent”); 9,092,392
`(the “’392 Patent”); 9,292,660 (the “’660 Patent”); 9,372,193 (the “’193 Patent”), and 9,383,365
`(the “’365 Patent) (collectively, the “asserted patents” or “Patents-in-Suit”).
`
`2 In the Patents-in-Suit, a “molecular profile” refers to a comparison of genes, proteins,
`molecular mechanisms, and combinations thereof with a reference sample and therefore
`encompasses molecular, genomic, and proteomic findings. See, e.g., Dkt. No. 1-1, Abstract.
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 6 of 26
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`be effective against one or more of those mutations.
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`Defendant Foundation Medicine, Inc. (“FMI”) is a leader in personalized medicine focused
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`on fundamentally changing the way cancer patients are treated. FMI develops genomic testing
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`products providing comprehensive information about each patient’s individual cancer, enabling
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`physicians to optimize treatment in clinical practice and biopharmaceutical companies to develop
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`targeted oncology therapies more effectively and rapidly by identifying patient populations who
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`will benefit from these therapies and finding patients who are eligible to be enrolled in clinical
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`trials for these therapies. FMI’s tests leverage proprietary methods and algorithms for analyzing
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`patient samples across all types of cancer. FMI’s diagnostic testing products meet the oncology
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`community’s need for comprehensive molecular information about genomic alterations in
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`hundreds of genes known to be biologically or clinically relevant to cancer in a concise and
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`actionable format that informs the treating physician about targeted therapies and clinical trials
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`that correspond to each individual patient’s genomic alterations.
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`This case should be dismissed because each of Caris’s claims is premised on the abstract
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`idea of identifying a potential therapy based on the comparison of a patient’s molecular profile
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`with known databases of potentially correlated therapeutics and genes. The claimed system
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`relies exclusively on the application of laws of nature, which are not sufficiently described in the
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`patent specifications and are themselves patent ineligible. Controlling precedent is clear:
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`Abstract ideas and laws of nature are not patentable unless the claims amount to “significantly
`
`more” than the patent ineligible subject matter. Alice Corp. v. CLS Bank Int’l, 134 S. Ct. 2347,
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`2355 (2014); Ass’n for Mol. Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 589-90 (2013).
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`The limitations of the claims asserted in this case, whether viewed individually or as part of an
`
`ordered combination, do not contain “‘an inventive concept’ sufficient to ‘transform’ the claimed
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 7 of 26
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`abstract idea into a patent-eligible application.” Alice, 134 S. Ct. at 2357. The Patents-in-Suit
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`are therefore invalid and this case should be dismissed. This determination can be made now,
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`based on the language of the asserted patents themselves, without the need for any discovery.
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`The Patents-in-Suit are invalid for a second, independent reason: They do not satisfy the
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`written description requirement, which requires a patentee to demonstrate possession of the
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`invention. The asserted claims cover a general system of identifying a cancer treatment from
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`which an individual would “likely benefit” based on the individual’s molecular profile across a
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`panel of genes. Specifically, each of the asserted claims requires “a plurality of molecular
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`targets” comprising four to seven genes. Although the Patents-in-Suit disclose hundreds of
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`genes, the specifications contain no support for the specific gene panels claimed. Each of the
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`Patents-in-Suit is therefore invalid for lack of written description. As with invalidity on the
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`patent ineligibility grounds above, this determination can be made now, without discovery.
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`II. Applicable Legal Standard
`A motion to dismiss tests the legal sufficiency of the complaint. See Ashcroft v. Iqbal, 556
`
`U.S. 662, 678-679 (2009). A district court considering a Rule 12(b)(6) motion must accept all
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`non-conclusory, well-pleaded allegations in the complaint as true and view them in the light
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`most favorable to the non-moving party. Id. Patent eligibility is readily amenable to resolution
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`under Rule 12(b)(6). Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709, 712, 718 (Fed. Cir. 2014).
`
`Although in evaluating a motion to dismiss the Court may not consider matters extraneous
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`to the pleadings, the Court “may properly consider the relevant entirety of a document integral to
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`or explicitly relied upon in the complaint, even though not attached to the complaint, without
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`converting the motion into one for summary judgment.” Shaw v. Digital Equip. Corp., 82 F.3d
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`1194, 1220 (1st Cir. 1996). For example, the Court is permitted to examine the asserted patents
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`and their file histories in resolving a motion to dismiss. See, e.g., Par Pharm., Inc. v. Luitpold
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 8 of 26
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`
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`Pharm., Inc., No. 16-cv-02290-WHW, 2017 WL 452003, at *4 (D.N.J. Feb. 2, 2017); In re
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`Bendamustine Consol. Cases, No. 13-cv-2046-GMS, 2015 WL 1951399, at *1 (D. Del. Apr. 29,
`
`2015); see also AstraZeneca Pharm. LP v. Apotex Corp., 669 F.3d 1370, 1378 n.5 (Fed. Cir.
`
`2012).
`
`III. The Patents-in-Suit Are Invalid for Claiming an Abstract Idea Based on the
`Application of a Law of Nature
`
`The Supreme Court has long held that “abstract ideas are not patentable.” Alice, 134 S. Ct.
`
`at 2354 (quoting Myriad, 569 U.S. at 589). This principle recognizes that abstract ideas
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`comprise “the basic tools of scientific and technological work,” Myriad, 569 U.S. at 589, and
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`that “monopolization of those tools through the grant of a patent might tend to impede
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`innovation more than it would tend to promote it,” Mayo Collaborative Servs. v. Prometheus
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`Labs., Inc., 566 U.S. 66, 71 (2012). The Supreme Court has repeatedly articulated its concern
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`that “patent law not inhibit further discovery by improperly tying up the future use of [the]
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`building blocks of human ingenuity.” Alice, 134 S. Ct. at 2354 (quoting Mayo, 566 U.S. at 85).
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`The two-step framework set forth in Alice distinguishes patents that claim those “building
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`blocks of human ingenuity” from patents that “integrate the building blocks into something
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`more.” Alice, 134 S. Ct. at 2354 (internal quotation marks and alterations omitted). Under Step
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`One of Alice, a court must determine whether the claims at issue are directed to an abstract idea.
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`Alice, 134 S. Ct. at 2355. If a court determines that the claims are directed to an abstract idea,
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`the court must next consider at Step Two of Alice “the elements of each claim both individually
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`and ‘as an ordered combination’” to determine whether the additional elements provide an
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`“inventive concept”—i.e., whether they “‘transform the nature of the claim’ into a patent-eligible
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`application.” Alice, 134 S. Ct. at 2355 (quoting Mayo, 566 U.S. at 78, 79). Only “an element or
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`[a] combination of elements that is ‘sufficient to ensure that the patent in practice amounts to
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 9 of 26
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`significantly more than a patent upon the [ineligible concept] itself’” demonstrates an inventive
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`concept. Id. (quoting Mayo, 566 U.S. at 73). “‘Simply appending conventional steps, specified
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`at a high level of generality,’ which are ‘well known in the art’ and consist of ‘well-understood,
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`routine, conventional activit[ies]’” is insufficient. Intellectual Ventures I LLC v. Symantec
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`Corp., 838 F.3d 1307, 1313 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2357, 2359).
`
`A. The Claimed Invention Rests Upon an Abstract Idea
`1. The Patents-in-Suit Are Directed to the Abstract Idea of Recommending a
`Treatment Based on a Patient’s Molecular Profile
`
`A stated purpose of the Patents-in-Suit is the determination of “individualized medical
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`intervention” based on “molecular profiling.” Dkt. No. 1-1, ’350 Patent, Abstract. Claim 1 of
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`the ’350 Patent is representative. See Ex. 1 at 2. Claim 1 recites:
`
`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; and
`b.
`at least one computer database comprising:
`i.
`a reference value for the plurality of molecular targets;
`and
`a listing of available therapeutic agents for said
`ii.
`plurality of molecular targets;
`a computer-readable program code comprising instructions to
`c.
`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
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 10 of 26
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`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).
`
`Dkt. No. 1-1, ’350 Patent cols. 16:64-17:27. The asserted claims thus generally cover a system
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`for identifying a cancer therapy comprising: (1) a device to analyze an individual’s molecular
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`profile with respect to a limited set of genes (i.e., targets) that are believed to be associated with
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`particular cancers; (2) a database that contains information about what the standard (or
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`“reference value”) is for each target and information about available therapies associated with
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`each of those targets; (3) software for comparing the individual’s molecular profile with the
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`reference to determine if a mutation is present; (4) software to match the individual with known
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`therapies where the aforementioned comparison indicates that a mutation is present at one of the
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`targets; and (5) software to generate a report identifying any such mutation and the associated
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`therapy. See Ex. 1 (illustrating parallel structure of Patents-in-Suit). Each of the Patents-in-Suit
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`claims a different gene panel, and two of the Patents-in-Suit recite a specific cancer.3 All of the
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`asserted claims are open-ended and require a “plurality” of molecular targets that “comprise” a
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`small set of four to seven genes.
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`The specifications of the Patents-in-Suit are not limited to a specific gene panel or cancer.
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`In fact, the three dozen-plus applications filed in the patent family of the Patents-in-Suit claim a
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`range of gene panels and cancers. Moreover, the patents’ solution of identifying potential
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`treatments based on an individual’s molecular profile is not rooted in a specific diagnostic
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`method or system. The expansive scope of the issued and pending claims thus threatens to
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`“preempt” use of any diagnostic method or system that generates molecular or genomic profiles
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`3 The ’392 Patent and ’660 Patent claim the identification of a therapeutic for an individual with
`colorectal and lung cancer, respectively). See Ex. 1 at 4, 8.
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 11 of 26
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`and associates those profiles with potential cancer therapies. See Netflix, Inc. v. Rovi Corp., 114
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`F. Supp. 3d 927, 947 (N.D. Cal. 2015), aff’d, 670 F. App’x 704 (Fed. Cir. 2016) (invalidating
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`claims that “seek to preempt all applications of the abstract idea”).
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`At bottom, the claimed invention is directed to a health care provider’s task of identifying a
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`treatment for a particular medical condition, which is akin to a “fundamental economic and
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`conventional business practice.” DDR Holdings, LLC v. Hotels.Com, L.P., 773 F.3d 1245, 1256
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`(Fed. Cir. 2017); see also Presqriber, LLC v. Advanced Data Sys. Advanced Corp., No. 6:14-cv-
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`859, 2015 WL 11170154, at *4 (E.D. Tex. June 29, 2015). Therefore, the claimed invention
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`rests upon an abstract idea.4
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`B. The Claims Contain No Inventive Concept Beyond the Abstract Idea
`Step 2 of Alice requires the Court to determine whether the asserted claims—when viewed
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`individually and as an ordered combination—contain “an inventive concept sufficient to
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`transform the claimed abstract idea into a patent-eligible application.” Alice, 134 S. Ct. at
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`2357 (internal quotation marks omitted). A claim to an abstract idea contains an inventive
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`concept only if it “include[s] additional features” that are more than “well-understood, routine,
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`conventional activities.” Id. at 2357, 2359 (internal quotation marks, brackets, and citations
`
`omitted). The asserted claims do not contain any inventive concept sufficient to transform the
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`claimed abstract idea into patent-eligible subject matter.
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`1. The Significance of an Individual’s Molecular Profile for Cancer Therapies
`
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`4 The parallel claims of the Patents-in-Suit are appropriately evaluated together. See CLS Bank
`Int’l v. Alice, 717 F.3d 1269, 1288 (Fed. Cir. 2013) (parallel claims warrant similar substantive
`treatment); Content Extraction & Transmission LLC v. Wells Fargo Bank, Nat. Ass’n, 776 F.3d
`1343, 1348 (Fed. Cir. 2014) (same). While each of the Patents-in-Suit recites a different gene
`panel and two of the patents recite a specific cancer to be treated, the claims cover the same
`abstract system for identifying a potentially beneficial cancer treatment based on an individual’s
`molecular profile. See Ex. 1.
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 12 of 26
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`Was Well-Known
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`The Patents-in-Suit fail Step Two of the Alice analysis and are thus unpatentable. Well
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`before the earliest provisional application to which the Patents-in-Suit claim priority was filed in
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`2006, oncologists were obtaining information about individuals’ molecular profiles and using
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`that information to identify possible therapies indicated to be beneficial where particular genetic
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`alterations were present. Indeed, as the specifications of the Patents-in-Suit make clear, “the
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`molecular mechanisms behind various disease states have been the subject of studies for years”
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`and “treatment regimens have been determined using molecular profiling in combination with
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`clinical characterization” of a patient. Dkt. No. 1-1, ’350 Patent col. 1:42-49. Moreover, the
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`specifications acknowledge the “explosion of interest in developing new anticancer agents that
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`are more targeted against a cell surface receptor or an up regulated or amplified gene product.”
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`Dkt. No. 1-1, ’350 Patent col. 2:10-14. The specifications of the Patents-in-Suit also admit that
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`targeted anticancer agents designed to interact with specific receptors or gene products had been
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`developed by the priority filing date of the Patents-in-Suit including: “Herceptin against
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`HER2/neu in breast cancer cells,” “rituximab against CD20 in lymphoma cells,” “bevacizamab
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`against VEGF,” and “Cetuximab against EGFR, etc.” Dkt. No. 1-1, ’350 Patent col. 2:14-17.
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`Several additional “non-disease specific agents that have been found to interact with specific
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`targets found in different cancer patients” are also described in Table 1 of the specification of the
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`’350 Patent. Dkt. No. 1-1, ’350 Patent col. 14:5-19.
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`Against this backdrop of successful development of targeted cancer therapies, the claims
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`add no inventive concept beyond the application of unspecified molecular or genomic assays
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`(e.g., Dkt. No. 1-1, ’350 Patent col. 13:7-31), and computer and database technology (e.g., Dkt.
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`No. 1-1, ’350 Patent cols. 5:37-10:14, 11:32-52), to perform the analysis and comparisons that
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`doctors have performed manually for years. As a result, nothing in the claims rises to the level
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 13 of 26
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`of an inventive contribution sufficient to distinguish the Patents-in-Suit from the abstract idea.
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`See Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709, 716 (Fed. Cir. 2014) (quoting Alice, 134 S.
`
`Ct. at 2358) (“Narrowing the abstract idea” in “an ‘attempt[ ] to limit the use’ of the abstract idea
`
`‘to a particular technological environment,’ . . . is insufficient to save a claim.”).
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`Because the prescription of cancer treatments based on patient molecular profiles was
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`known and is described in the Background Section of the specifications of the Patents-in-Suit,
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`the asserted claims covering a system for identifying potential therapies based on individual
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`molecular profiles does not add significantly more than the patent ineligible abstract idea.
`
`2. The Asserted Claims Rely on the Application of Laws of Nature that Are Not
`Patentable and Were Not Discovered by the Caris Inventors
`a) The Three “Early Caris Patents”
`Three of the Patents-in-Suit claim priority to U.S. Prov. App. No. 60/747,645, filed on May
`
`18, 2006, and share a common specification with U.S. App. No. 11/750,721, filed on May 18,
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`2007.5 The common specification of these three patents (the “Early Caris Patents”) does not
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`describe the association of any cancer treatment with any molecular or genomic profile across
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`multiple genes. The common specification instead describes only six “non-disease specific
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`agents that have been found to interact with specific targets found in different cancer patients.”
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`Dkt. No. 1-1, ’350 Patent col. 14:5-19. The specification also does not describe the interaction
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`of any therapeutic agent or any cancer with the following seven genes, which are recited in the
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`claims of the Early Caris Patents: AR, ESR1, KIT, MLH1, PDGFRA, PTEN, and TOP1. See
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`Ex. 1 at 2, 12, 16. Because the specification does not describe the association of these seven
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`genes with any therapeutic or tumor type, the selection of the claimed gene panels is not an
`
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`5 The three Patents-in-Suit claiming priority to U.S. Prov. App. No. 60/747,645 through
`continuation applications are the ’350 patent, the ’193 patent, and the ’365 patent.
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 14 of 26
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`“inventive concept” sufficient to distinguish these patents from the abstract idea.
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`b) The Two “Later Caris Patents”
`The ’392 and ’660 patents (the “Later Caris Patents”), which claim priority to a series of
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`later provisional applications that add new matter to U.S. Prov. App. No. 60/747,645,6 describe
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`“the efficacy of various treatments particular for a target gene or gene product” in Tables 1 and 2
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`in a “rules database.” Dkt. No. 1-2, Ex. 2, ’392 Patent col. 5:39-43. The rules database tables
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`(Tables 1 and 2) were first described in U.S. App. No. 12/658,770, filed on February 12, 2010.
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`The Later Caris Patents concede that the information in the rules database (i.e., the potential
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`correlation of a treatment with a gene or gene product) is not limited to information discovered
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`or “invented” by the Caris inventors; instead, the rules database “maps treatments and molecular
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`profiling results” and “the mapping is created by reviewing the literature for links between
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`biological agents and therapeutic agents.” Dkt. No. 1-2, Ex. 2, ’392 Patent col. 53:34-35, 53:45-
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`50. The Later Caris Patents even recommend that “a journal article, patent publication or patent
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`application publication, scientific presentation, etc[.] can be reviewed for potential mappings.”
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`Dkt. No. 1-2, Ex. 2, ’392 Patent col. 53:48-50.
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`Scraping together possible correlations between molecular abnormalities and therapeutic
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`agents from the scientific community’s published work to capture the inventive activity of
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`others, including by relying on what is described in public articles, presentations, and patent
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`filings, does not provide an “inventive concept” sufficient to distinguish the claims from the
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`patent ineligible abstract idea.
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`Furthermore, the rules database in the Later Caris Patents does not describe the association
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`6 The’392 and ’660 patents claim priority to a number of applications and are “continuation-in-
`part” applications of U.S. App. No. 11/750,721, filed on May 18, 2007. See Dkt. No. 1-2, Ex. 2
`(’392 Patent); Dkt. No. 1-5, Ex. 5 (’660 Patent).
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 15 of 26
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`of any therapeutic agent or cancer with PIK3CA and CTNNB1, even though those genes are
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`recited in the independent claims of the ’392 and ’660 patents, respectively. Because the
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`specification does not describe the association of those genes with any therapeutic or cancer, the
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`selection of the claimed gene panels is not an “inventive concept” that distinguishes the Later
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`Caris Patents from the patent ineligible abstract idea for this additional reason.
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`c) Molecular Correlations Are Not Patentable and Cannot Qualify as
`Significantly More than the Judicial Exception
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`The Patents-in-Suit claim a system for identifying a cancer therapy associated with a
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`“likely benefit” based on the comparison of an individual’s molecular or genomic information
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`with a reference database. The claims are directed to the abstract idea of identifying a potentially
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`useful cancer therapy based on an individual’s molecular characteristics relative to open-ended
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`gene panels. The correlation of genomic abnormalities and treatments associated with a “likely
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`benefit” for individuals with those abnormalities is not an inventive concept that distinguishes
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`the invention from the abstract idea because that correlation is an unpatentable law of nature.
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`In Esoterix Genetic Labs. LLC v. Qiagen, Inc., Judge Burroughs found factually analogous
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`claims patent ineligible under Mayo and Alice. Esoterix Genetic Labs. LLC v. Qiagen, Inc., 133
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`F. Supp. 3d 349 (D. Mass. 2015). In Esoterix, the inventors identified that there is “a positive
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`correlation between the existence of particular naturally-occurring nucleotide variations on a
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`person’s epidermal growth factor receptor (‘EGFR’) gene, and the likelihood that specific
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`pharmaceutical compounds (namely, gefitinib or erlotinib) will be effective in treating non-small
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`lung cancers in that person.” Id. at 351. The inventors claimed a method for “determining an
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`increased likelihood of pharmacological effectiveness of treatment by gefitinib or erlotinib” by
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`obtaining DNA from a tumor sample and determining the presence or absence of certain
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`mutations in the EGFR gene. Id. at 353. The Court held that the independent claim failed Alice
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`Case 1:17-cv-12194-MLW Document 23 Filed 01/16/18 Page 16 of 26
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`Step One because it was “directed to a law of nature” in that it merely described “the correlation
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`between a naturally-occurring mutation in a cancer cell, and the likelihood that a particular type
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`of known pharmaceutical compound will be effective in treating that type of cancer.” Id. at 358.
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`The Court held that the claim also failed Alice Step Two because nothing in the claim w
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