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

United States District Court, D. Delaware

September 11, 2019

GUARDANT HEALTH, INC., Plaintiff,
v.
FOUNDATION MEDICINE, INC., Defendant. GUARD ANT HEALTH, INC., Plaintiff,
v.
PERSONAL GENOME DIAGNOSTICS, INC., Defendant.

          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 claim construction-related decisions set forth below.

         I. BACKGROUND AND STANDARD OF REVIEW

         The Court hereby incorporates by reference the summary of the background of this matter set out in its September 6, 2019 Report and Recommendation ("September 6 R&R"). (D.I. 354 at 1-3)[1] It additionally incorporates by reference the legal principles regarding claim construction set out in the September 6 R&R. (Id. at 3-5)

         II. DISCUSSION

         The parties had claim construction disputes regarding 13 terms or sets of terms (hereinafter, "terms"). The Court has addressed three of these terms in the September 6 R&R. The Court addresses two of the remaining 10 terms herein.

         A. "consensus sequence"

         The claim term "consensus sequence" appears in claim 1 of the 731 patent. (D.I. 53, ex. B at 13) This claim is 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 each other 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 in said cell-free DNA from said subject.

         (731 patent, col. 62:8-54 (emphasis added)) The parties' competing proposed constructions for "consensus ...


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