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Guardant Health, Inc. v. Foundation Medicine, Inc.

United States District Court, D. Delaware

September 6, 2019

GUARDANT HEALTH, INC., Plaintiff,
v.
FOUNDATION MEDICINE, INC., Defendant. GUARD ANT HEALTH, INC., Plaintiff,
v.
PERSONAL GENOME DIAGNOSTICS, INC., Defendant. Term Plaintiffs Proposed Construction Defendants' Proposed Construction Term Plaintiffs Proposed Construction Defendants' Proposed Construction Term Plaintiffs Proposed Construction Defendants' Proposed Construction

          REPORT AND RECOMMENDATION

          CHRISTOPHER J. BURKE UNITED STATES MAGISTRATE JUDGE

         In these two related actions filed by Plaintiff Guardant Health, Inc. ("Guardant" or "Plaintiff) against Defendants Foundation Medicine, Inc. ("FMI") and Personal Genome Diagnostics, Inc. ("PGDx" and collectively with FMI, "Defendants"), Guardant alleges infringement of United States 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" and collectively with the other patents, "the asserted patents"). Presently before the Court is the matter of claim construction. The Court recommends that the District Court adopt the constructions as set forth below.

         I. BACKGROUND

         Guardant commenced these actions on November 9, 2017. (Civil Action No. 17-1616-LPS-CJB, D.I. 1; Civil Action No. 17-1623-LPS-CJB, D.I. 1) The cases were thereafter referred to the Court to hear and resolve all pretrial matters, up to and including case-dispositive motions. (Civil Action No. 17-1616-LPS-CJB, D.I. 5; Civil Action No. 17-1623-LPS-CJB, D.I. 4)

         In the currently-operative Third Amended Complaints, Guardant alleges that Defendants' liquid biopsy tests infringe claims of the asserted patents. (Civil Action No. 17-1616-LPS-CJB, D.I. 149 at ¶¶ 4, 14-24; Civil Action No. 17-1623-LPS-CJB, D.I. 280 at ¶¶ 6, 17-28) The asserted patents relate to methods for identifying genetic material harboring cancer-causing mutations from a patient's blood. (See D.I. 59 at l)[1] Each of the patents is titled "Systems and Methods to Detect Rare Mutations and Copy Number Variation." (D.I. 53, exs. C-F)[2] The '731 patent, '822 patent and the '743 patent share a common specification ("the specification"), and the '992 patent has a similar specification. (See D.I. 75, ex. 1 at Slide 4)

         The parties completed initial briefing on claim construction on November 16, 2018. (D.I. 59; D.I. 68; D.I. 72; D.I. 74)[3] The Court held a Markman hearing on December 14, 2018. (D.I. 85 (hereinafter, "Tr.")) Following the hearing, Defendants submitted a supplemental letter brief relating to a new argument asserted by Guardant during the Markman hearing. (D.I. 84) And the parties thereafter submitted supplemental briefs relating to inter partes review proceedings with respect to the '731 patent, which the parties assert have relevance to the construction of certain disputed terms. (D.I. 88; D.I. 90; D.I. 136; D.I. 139; D.I. 162; D.I. 173; D.I. 283; D.I. 286; D.I. 351)

         II. STANDARD OF REVIEW

         It is well-understood that "[a] claim in a patent provides the metes and bounds of the right which the patent confers on the patentee to exclude others from making, using, or selling the protected invention." Corning Glass Works v. Sumitomo Elec. U.S.A., Inc., 868 F.2d 1251, 1257 (Fed. Cir. 1989). Claim construction is a generally a question of law, although subsidiary fact finding is sometimes necessary. Teva Pharms. USA, Inc. v. Sandoz, Inc., 135 S.Ct. 831, 837-38 (2015).

         The Court should typically assign claim terms their "ordinary and customary meaning[, ]" which is "the meaning that the term[s] would have to a person of ordinary skill in the art ['POSITA'] in question at the time of the invention, i.e., as of the effective filing date of the patent application." Phillips v. AWH Corp., 415 F.3d 1303, 1312-13 (Fed. Cir. 2005). However, when determining the ordinary meaning of claim terms, the Court should not extract and isolate those terms from the context of the patent; rather it should endeavor to reflect their "meaning to the ordinary artisan after reading the entire patent." Id. at 1321; see also Eon Corp. IP Holdings LLC v. Silver Spring Networks, Inc., 815 F.3d 1314, 1320 (Fed. Cir. 2016).

         In proceeding with claim construction, the Court should look first and foremost to the language of the claims themselves, because "[i]t is a bedrock principle of patent law that the claims of a patent define the invention to which the patentee is entitled the right to exclude." Phillips, 415 F.3d at 1312 (internal quotation marks and citations omitted). For example, the context in which a term is used in a claim may be "highly instructive." Id. at 1314. In addition, "[o]ther claims of the patent in question, both asserted and unasserted, can . .. be valuable" in discerning the meaning of a particular claim term. Id. This is "[b]ecause claim terms are normally used consistently throughout the patent, [and so] the usage of a term in one claim can often illuminate the meaning of the same term in other claims." Id. Moreover, "[differences among claims can also be a useful guide[, ]" as when "the presence of a dependent claim that adds a particular limitation gives rise to a presumption that the limitation in question is not present in the independent claim." Id. at 1314-15.

         In addition to the words of the claims, the Court should look to other intrinsic evidence. For example, the Court should analyze the patent specification, which "may reveal a special definition given to a claim term . . . that differs from the meaning [that term] would otherwise possess" or may reveal an intentional disclaimer of claim scope. Id., at 1316. Even if the specification does not contain such revelations, it "is always highly relevant to the claim construction analysis. Usually, it is dispositive; it is the single best guide to the meaning of a disputed term." Id. at 1315 (internal quotation marks and citation omitted). That said, however, the specification "is not a substitute for, nor can it be used to rewrite, the chosen claim language." SuperGuide Corp. v. DirecTV Enters., Inc., 358 F.3d 870, 875 (Fed. Cir. 2004). And a court should also consider the patent's prosecution history, if it is in evidence, because it "can often inform the meaning of the claim language by demonstrating how the inventor understood the invention and whether the inventor limited the invention in the course of prosecution[.]" Phillips, 415 F.3d at 1317.

         Extrinsic evidence, "including expert and inventor testimony, dictionaries, and learned treatises[, ]" can also "shed useful light on the relevant art[.]" Id. (internal quotation marks and citations omitted). Overall, while extrinsic evidence may be useful, it is "less significant than the intrinsic record in determining the legally operative meaning of claim language." Id. (internal quotation marks and citations omitted); accord Markman v. Westview Instruments, Inc., 52 F.3d 967, 981 (Fed. Cir. 1995).

         In utilizing these resources during claim construction, courts should keep in mind that "[t]he construction that stays true to the claim language and most naturally aligns with the patent's description of the invention will be, in the end, the correct construction." Renishaw PLC v. Marposs Societa'per Azioni, 158 F.3d 1243, 1250 (Fed. Cir. 1998).

         III. DISCUSSION

         The parties currently have disputes regarding 13 terms or sets of terms (hereinafter, "terms"). This Report and Recommendation addresses three such terms. The other terms will be addressed in one or more forthcoming Report and Recommendations.

         A. "sequence read"

         The claim term "sequence read" appears in certain claims of all four asserted patents. (D.I. 53, ex. B at 4-5) The use of the disputed term in claim 1 of the 731 patent and claim 1 of the 743 patent is representative. (See Defendants' Markman Presentation, Slide 3; Guardant's Markman Presentation, Slide 7) Accordingly, these claims are reproduced below, with the disputed term highlighted:

1. A method for quantifying single nucleotide variant tumor markers in cell-free DNA from a subject, comprising:
(a) providing at least 10 ng of cell-free DNA obtained from a bodily sample of the subject;
(b) attaching tags comprising barcodes having from 5 to 1000 distinct barcode sequences to said cell-free DNA obtained from said bodily sample of the subject, to generate non-uniquely tagged parent polynucleotides, wherein each barcode sequence is at least 5 nucleotides in length;
(c) amplifying the non-uniquely tagged parent polynucleotides to produce amplified non-uniquely tagged progeny polynucleotides;
(d) sequencing the amplified non-uniquely tagged progeny polynucleotides to produce a plurality of sequence reads from each parent polynucleotide, wherein each sequence read comprises a barcode sequence and a sequence derived from cell-free DNA;
(e) grouping the plurality of sequence reads produced from each non-uniquely tagged parent polynucleotide into families based on i) the barcode sequence and ii) at least one of: sequence information at a beginning of the sequence derived from cell-free DNA, sequence information at an end of the sequence derived from cell-free DNA, and length of the sequence read, whereby each family comprises sequence reads of non-uniquely tagged progeny polynucleotides amplified from a unique polynucleotide among the non-uniquely tagged parent polynucleotides;
(f) comparing the sequence reads grouped within each family to determine consensus sequences for each family, wherein each of the consensus sequences corresponds to a unique polynucleotide among the non-uniquely tagged parent polynucleotides;
(g) providing one or more reference sequences from a human genome, said one or more reference sequences comprising one or more loci of reported tumor markers, wherein each of the reported tumor markers is a single nucleotide variant;
(h) identifying consensus sequences that map to a given locus of said one or more loci of reported tumor markers; and
(i) calculating a number of consensus sequences that map to the given locus that include the single nucleotide variant thereby quantifying single nucleotide variant tumor markers ...

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