Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 1 of 11 PageID #: 12266
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` IN THE UNITED STATES DISTRICT COURT
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`FOR THE DISTRICT OF DELAWARE
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`GUARDANT HEALTH, INC.,
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`Plaintiff,
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`v.
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`FOUNDATION MEDICINE, INC.,
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`Defendant.
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`C.A. No. 1:20-cv-01580-LPS
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`FILED UNDER SEAL
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`DECLARATION OF GREGORY COOPER, PH.D.
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 2 of 11 PageID #: 12267
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`I.
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`Introduction and brief summary of opinions
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`1.
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`I have been asked by counsel for Guardant to provide this declaration in response
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`to certain of the opinions provided in the declaration of Gary Benson, Ph.D. which I understand
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`was submitted in opposition to Guardant’s motion for a preliminary injunction.
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`2.
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`I previously provided a declaration which I understand was filed with Guardant’s
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`Motion for Preliminary Injunction. My qualifications and compensation are explained in that
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`declaration so I have not repeated them here.
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`3.
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`In his declaration, Dr.Benson explains his opinion that the Accused Product,
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`FoundationOne Liquid CDx, does not infringe because the source code used by FMI to perform
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`the test does not perform the “grouping” limitations of claim 1 of the ’085 Patent and claim 1 of
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`the ’086 Patent, which I reproduce below, with the portions that Dr. Benson focuses on in bold:
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`’085 Patent
`(g) grouping a plurality of the
`sequencing reads into a plurality of
`families based at least on sequence
`information of the molecular barcodes, a
`start base position of a given sequencing
`read from among the sequencing reads at
`which the given sequencing read is
`determined to start aligning to the
`reference sequence, and a stop base
`position of the given sequencing read at
`which the given sequencing read is
`determined to stop aligning to the
`reference sequence, wherein a family of
`the plurality of families is representative of
`a cell-free nucleic acid molecule in the
`sample;
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`’086 Patent
`(e) grouping a plurality of the mapped
`sequencing reads into a plurality of
`families based on sequence information
`from the molecular barcodes and at least
`(1) a start base position of a given
`mapped sequencing read from among
`the mapped sequencing reads at which
`the given mapped sequencing read is
`determined to start mapping to the
`reference sequence and/or (2) a stop base
`position of the given mapped sequencing
`read at which the given mapped
`sequencing read is determined to stop
`mapping to the reference sequence;
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`4.
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`I disagree with Dr. Benson, and as I explain below, Dr. Benson’s own declaration
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`demonstrates that these limitations are met by the Accused Product’s source code, confirming my
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`opinion that the Accused Product infringes both claims.
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 3 of 11 PageID #: 12268
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`5.
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`Dr. Benson offers two reasons for his opinions that the Accused Product does not
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`infringe. First, Dr. Benson contends that the Accused Product does not practice the grouping
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`limitations of both claims because, he says,
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`6.
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`Second, Dr. Benson contends that the Accused Product does not meet the grouping
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`limitation of claim 1 of the ’085 Patent,
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`7.
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`I disagree with Dr. Benson. Further, the facts that Dr. Benson admits in his
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`declaration and deposition demonstrate that the Accused Product infringes both of the Asserted
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`Claims.
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`8.
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 4 of 11 PageID #: 12269
`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 4 of 11 PageID #: 12269
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`9.
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`Dr. Benson also offers opinions that the Asserted Claims are indefinite. Briefly,
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`his opinions are similar to saying that a sequence has a beginning and an end is indefinite because
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`either end could be the beginning. I disagree with these opinions as well and will explain them in
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`more detail below.
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`II.
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`Dr. Benson’s Declaration and Deposition Confirm That the Accused Product
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`Infringes Claim 1 of the 085 Patent and Claim 1 of the 086 Patent
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`A.
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`The Accused Products Group Sequences “Based On At Least” a Start Base
`Position
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 5 of 11 PageID #: 12270
`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 5 of 11 PageID #: 12270
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`Benson Decl. Fig. 1
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`[Benson Decl. 11 48]
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 6 of 11 PageID #: 12271
`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 6 of 11 PageID #: 12271
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`14.
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 7 of 11 PageID #: 12272
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`Benson Decl. Figure 2, Read Pair B
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`16.
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 8 of 11 PageID #: 12273
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`The Accused Products Group Sequences Based On A Start And A Stop Base
`Position
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`B.
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`N .0
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 9 of 11 PageID #: 12274
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`C.
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`The Grouping Limitations Are Not Indefinite and are Supported By
`Adequate Written Description In the Specification
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`22.
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`Dr. Benson contends that the “grouping” limitations of the Asserted Claims are
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`indefinite, because, in his view, the specification does not provide “useful guidance” as to how the
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`grouping terms should be understood. I disagree.
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`23.
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`The specification explains that the grouping step is performed to identify a family
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`of sequences generated from a unique tagged parent polynucleotide. See, e.g. Fig. 9 at 910 (“Group
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`sequence reads into families, each family generated from a unique tagged parent polynucleotide”);
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`Fig. 10 at 1010, Fig. 11 at 1110, Fig. 12 at 1210. To accomplish this grouping, the specification
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`describes “tagging parent molecules with a sufficient number of unique identifiers (e.g., the tag
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`count) such that there is a likelihood that two duplicate molecules, i.e., molecules having the same
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`start and stop positions, bear different unique identifiers so that sequence reads are traceable back
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`to particular parent molecules.” [’085 Patent at 41:4-9]. This is readily understandable to a person
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`of ordinary skill in the art.
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`24. While different aligning algorithms, including different configurations of the same
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`bwa aligner used in the Accused Product, may give slightly different alignments, a person of skill
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`in the art would have understood that aligned sequences have two ends, regardless of the alignment
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 10 of 11 PageID #: 12275
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`software or configuration used. The start and stop positions refer to those two ends. Aligning
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`algorithms were well-known in the art in 2014 when the application leading to the ’085 and ’086
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`Patents were filed, including the Burrows-Wheeler algorithm used in the Accused Product. [’085
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`Patent, p.8] (citing “Fast and accurate short read alignment with Burrows-Wheeler transform,”
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`Bioinformatics 2009, 25(14), 1754-1760”).
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`25.
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`Dr. Benson complains that which end is the start and which is the stop position is
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`indefinite, because sequences can be oriented in different directions. [Benson Decl. ¶ 73-77] This
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`is similar to saying that a person of ordinary skill in the art cannot tell where a ruler starts and stops
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`because it can be oriented in different directions. A person of ordinary skill would readily
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`understand what start and stop base positions refer to in the context of an alignment with a
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`reference sequence.
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`26.
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`Dr. Benson also contends that a person of ordinary skill would not understand a
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`position at which a given sequencing read aligns to a reference sequence to provide sequence
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`information as described in parts of the specification. [Benson Decl. ¶ 79-82] I disagree. A
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`reference sequence is a list of bases and their corresponding positions. A position at which a given
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`sequencing read starts or stops aligning to a reference sequence therefore comprises information
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`about both position and base identity. It is therefore sequence information as described in the
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`specification.
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`27.
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`For at least these reasons, I disagree with Dr. Benson’s opinions that the grouping
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`limitations are indefinite and lack written description.
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`Case 1:20-cv-01580-LPS Document 57 Filed 04/21/21 Page 11 of 11 PageID #: 12276
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`I declare under the penalty of perjury under the laws of the United States of America that
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`the foregoing is true and correct.
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`Executed on March 29, 2021 at Huntsville, AL.
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`Gregory Cooper, Ph.D.
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