TwinStrand BioScis. v. Guardant Health, Inc.

Decision Date29 December 2022
Docket NumberCivil Action 21-1126-GBW-SRF
PartiesTWINSTRAND BIOSCIENCES, INC. & UNIVERSITY OF WASHINGTON, Plaintiffs and Counterclaim Defendants, v. GUARDANT HEALTH, INC., Defendant and Counterclaim Plaintiff.
CourtU.S. District Court — District of Delaware

TWINSTRAND BIOSCIENCES, INC. & UNIVERSITY OF WASHINGTON, Plaintiffs and Counterclaim Defendants,
v.
GUARDANT HEALTH, INC., Defendant and Counterclaim Plaintiff.

Civil Action No. 21-1126-GBW-SRF

United States District Court, D. Delaware

December 29, 2022


REPORT AND RECOMMENDATION

SHERRY R. FALLON, UNITED STATES MAGISTRATE JUDGE.

Pending before the court are the parties' claim construction disputes. Plaintiffs TwinStrand Biosciences, Inc. and the University of Washington (“Plaintiffs”) assert four patents against defendant Guardant Health, Inc. (“Defendant”): United States Patent Nos. 10,287,631 (“the '631 patent”), 10,689,699 (“the '699 patent”), 10,752,951 (“the '951 patent”), and 10,760,127 (“the '127 patent”). (D.I. 1 at ¶ 1) In its counterclaims, Defendant asserts four patents against Plaintiffs: United States Patent Nos. 10,801,063 (“the '063 patent”), 10,889,858 (“the '858 patent”), 11,118,221 (“the '221 patent”), and 11,149,306 (“the '306 patent”). (D.I. 30 at ¶¶ 130-33) All of the asserted patents generally relate to similar methods of error-correcting DNA sequencing. This decision sets forth the court's recommendations of constructions following a review of the parties' joint claim construction brief and consideration of the arguments presented at the Markman hearing held on December 6, 2022. (D.I. 129)

The joint claim construction brief confirms that the parties have agreed upon constructions for ten claim terms. I recommend that the court adopt the parties' agreed-upon constructions as follows:

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Term

Recommended Construction

“uniquely labels” '631 patent, claim 1

Plain and ordinary meaning

“Quantifying at least two of (i) said paired sequence reads, (ii) said unpaired sequence reads, (iii) read depth of said paired sequence reads, and (iv) read depth of said unpaired sequence reads” '951 patent, claim 1

Plain and ordinary meaning

“partially single-stranded adapters”' 127 patent, claim 22

Plain and ordinary meaning with the understanding that the term can include both Y-shaped and U-shaped adaptors

“partially complementary, asymmetrical double-stranded adapter-DNA molecules”' 127 patent, claim 1

Plain and ordinary meaning with the understanding that the term can include both Y-shaped and U-shaped adaptors

“other fragment regions” '631 patent, claim 18

Plain and ordinary meaning

“circulating DNA molecule(s)”

'699 patent, claims 1, 8, 9, 12, 17-20, 24,

25

DNA molecules that circulate within the circulatory system, which can include cell-free DNA and cellular DNA

“double-stranded circulating nucleic acid molecules”

'951 patent, claims 11, 12, 15, 16, 18

Double-stranded nucleic acid molecules that circulate within the circulatory system, which can include cell-free DNA and cellular DNA

“cell-free deoxyribonucleic acid

(cfDNA)”

'063 patent, claims 15, 24

'858 patent, claims 1, 3, 5

'221 patent, claims 1-5

'306 patent, claims 17, 19, 20

DNA that exist(s) outside of a cell while in the body, including in blood, plasma, serum, urine, saliva, mucosal excretions, sputum, stool, cerebral spinal fluid, or tears

“a family of the families” '063 patent, claim 17

A single family from the plurality of families

“a subject having cancer” '221 patent, claim 2

Plain and ordinary meaning

2

Eleven terms remain in dispute. For the reasons set forth below, I recommend that the court adopt the following constructions for the parties' disputed terms:

Term

Recommended Construction

“non-uniquely tagged parent polynucleotide(s)”

'699 patent, claims 1, 18

A population of parent polynucleotide molecules affixed to polynucleotide barcodes, wherein the same polynucleotide barcode sequence is affixed to multiple parent polynucleotide molecules in the [population / sample], and wherein the polynucleotide barcode sequence serves as a molecular identifier only when combined with other information from the tagged parent polynucleotide molecule

“non-unique tag”

'951 patent, claim 25

A tag that is affixed to a parent polynucleotide molecule and having a nucleotide sequence, wherein the same tag nucleotide sequence is affixed to multiple parent polynucleotide molecules in the sample, and wherein the tag nucleotide sequence serves as a molecular identifier only when combined with other information from the tagged parent polynucleotide molecule

“substantially unique”

'699 patent, claims 1, 20

Plain and ordinary meaning; not indefinite

“degenerate . . . sequence(s)” '631 patent, claims 1, 12, 13, 15 '951 patent, claim 23

'127 patent, claim 13

A nucleotide sequence that is known or unknown in which every nucleotide position is unrestricted in its nucleotide variability

“semi-degenerate . . . sequence(s)” '631 patent, claims 1, 12, 13, 15 '951 patent, claim 23

'127 patent, claim 13

A nucleotide sequence that is known or unknown in which at least one, but not all, nucleotide positions are fixed or restricted in their nucleotide variability

“high accuracy consensus sequence read” '631 patent, claims 1, 4, 7, 16, 23

Plain and ordinary meaning; not indefinite

“fragment features”

'631 patent, claims 16, 18

Plain and ordinary meaning; not indefinite

“DNA fragment-specific information”' 127 patent, claim 22

Plain and ordinary meaning; not indefinite

“fragment ends” '631 patent, claim 1

Plain and ordinary meaning

“comprises between 1 nanogram (ng) and 100 ng of cfDNA molecules”

'221 patent, claim 3

'306 patent, claim 19

Plain and ordinary meaning

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I. LEGAL STANDARDS

A. Claim Construction

The purpose of the claim construction process is to “determin[e] the meaning and scope of the patent claims asserted to be infringed.” Markman v. Westview Instruments, Inc., 52 F.3d 967, 976 (Fed. Cir. 1995), aff'd, 517 U.S. 370, 388-90 (1996). Construing the claims of a patent presents 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) (citing Markman, 52 F.3d at 977-78). An actual dispute regarding the proper scope of a claim term must be resolved by a judge, as opposed to the jury. Markman, 52 F.3d at 979.

“[T]here is no magic formula or catechism for conducting claim construction.” Phillips v. AWH Corp., 415 F.3d 1303, 1324 (Fed. Cir. 2005). Instead, the court may attach the appropriate weight to appropriate sources “in light of the statutes and policies that inform patent law.” Id. The words of the claims “are generally given their ordinary and customary meaning,” which is “the meaning that the term would have to a person of ordinary skill in the art in question at the time of the invention, i.e., as of the effective filing date of the patent application.” Id. at 1312-13 (internal citations and quotation marks omitted). If the meaning of a claim term is not readily apparent, the court considers sources including “the words of the claims themselves, the remainder of the specification, the prosecution history, and extrinsic evidence concerning relevant scientific principles, the meaning of technical terms, and the state of the art.” Innova/Pure Water, Inc. v. Safari Water Filtration Sys., Inc., 381 F.3d 1111, 1116 (Fed. Cir. 2004).

“It 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 v. AWH Corp., 415 F.3d 1303, 1312 (Fed. Cir. 2005)

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(internal quotation marks omitted). Accordingly, “the claims themselves provide substantial guidance as to the meaning of particular claim terms.” Id. at 1314. Claim terms are typically used consistently throughout the patent, and “usage of a term in one claim can often illuminate the meaning of the same term in other claims.” Id. Also, “[d]ifferences among claims can also be a useful guide .... For example, 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 (internal citation omitted).

The claims must be read in view of the specification, which “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.” Vitronics Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1582 (Fed. Cir. 1996). “[T]he specification may reveal a special definition given to a claim term by the patentee that differs from the meaning it would otherwise possess. In such cases, the inventor's lexicography governs.” Phillips, 415 F.3d at 1316 (citing CCS Fitness, Inc. v. Brunswick Corp., 288 F.3d 1359, 1366 (Fed. Cir. 2002)). The specification may also contain a disclaimer or disavowal of claim scope. Id. However, “[e]ven when the specification describes only a single embodiment, the claims of the patent will not be read restrictively unless the patentee has demonstrated a clear intention to limit the claim scope using words or expressions of manifest exclusion or restriction.” Liebel-Flarsheim Co. v. Medrad, Inc., 358 F.3d 898, 906 (Fed. Cir. 2004) (internal quotation marks omitted). 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).

The court should also consider the patent's prosecution history, which is intrinsic evidence and “consists of the complete record of the proceedings before the [Patent and

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Trademark Office] and includes the prior art cited during the examination of the patent.” Phillips, 415 F.3d at 1317. “[T]he...

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