Illumina, Inc. et al v. BGI Genomics Co., Ltd et al

Filing 424

ORDER GRANTING MOTION FOR SUMMARY JUDGMENT AND GRANTING IN PART AND DENYING IN PART MOTION TO STRIKE OPINIONS OF DR. JOSEPH PUGLISI by Judge William H. Orrick. (jmdS, COURT STAFF) (Filed on 9/9/2021)

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 1 of 33

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UNITED STATES DISTRICT COURT

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NORTHERN DISTRICT OF CALIFORNIA

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ORDER GRANTING MOTION FOR
SUMMARY JUDGMENT AND
GRANTING IN PART AND DENYING IN
PART MOTION TO STRIKE OPINIONS
OF DR. JOSEPH PUGLISI

ILLUMINA, INC., et al.,

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Plaintiffs,

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United States District Court
Northern District of California

Case No. 19-cv-03770-WHO
Re: Dkt. Nos. 376, 377, 378, 379, 386, 387,
399, 412

v.

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Case No. 20-cv-01465-WHO
Re: Dkt. Nos. 406, 407, 421, 433, 448

BGI GENOMICS CO., LTD, et al.,

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Defendants.

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Plaintiffs Illumina Inc. and Illumina Cambridge Ltd. (collectively, “Illumina”) move for

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summary judgment on defendants BGI Genomics Co., Ltd., BGI Americas Corp., MGI Tech Co., Ltd.,

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MGI Americas, Inc., and Complete Genomics, Inc.’s (collectively, “BGI”) counterclaims for

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infringement under its U.S. Patent No. 9,944,984 (“’984 Patent”). Illumina also moves to strike

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portions of BGI’s infringement expert, Dr. Puglisi’s report. For the reasons explained below,

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Illumina’s motion to strike portions of the Puglisi Report is GRANTED in part and DENIED in

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part. Illumina’s motion for summary judgment related to (1) the noninfringement of the ’984

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Patent; (2) BGI’s doctrine of equivalents theory under the ’984 Patent; (3) BGI’s “inequitable

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conduct” defense; and (4) BGI’s other uncontested defenses is GRANTED.
BACKGROUND

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I.

PROCEDURAL BACKGROUND
Illumina filed the complaint in this matter on June 27, 2019.1 Dkt. No. 1. It alleges that BGI

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This matter (“Illumina I”) is related to Illumina Inc., et al., v. BGI Genomics Co., Ltd., et al., Case
No. 20-cv-1465 (N.D. Cal.) (“Illumina II”), in which Illumina alleges that BGI infringes different
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infringes U.S. Patent No. 9,410,200 (the “’200 Patent”) and 7,566,537 (the “’537 Patent”) (“Asserted

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Patents”) by selling its sequencers and related reagents. Id. ¶¶ 2, 33–44. Illumina asserts that BGI’s

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sequencers infringe claim 1 of the ’537 Patent and claim 1 of the ’200 Patent. Id. ¶¶ 35, 37, 41. BGI

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filed counterclaims, alleging that Illumina’s DNA sequencing systems (“Accused Products”) infringe

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claims 1–3 and 5 of its’984 Patent. Dkt. No. 94 (“First Amended Answer” or “FAA”) ¶ 10. On June

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26, 2020, I entered a claim construction order (“Claim Construction Order”) on terms in Illumina’s

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’537 and ’200 Patents as well as BGI’s ’984 Patent. Dkt. No. 190 (“Order”).

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Illumina emailed BGI on June 30, 2020, and asked it to drop its infringement contentions

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in light of the Claim Construction Order. Dkt. No. 379-6 at 7. On July 16, 2020, BGI responded
that its infringement contentions under the ’984 Patent were sufficient. Id. After the email

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United States District Court
Northern District of California

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exchange, Illumina did not respond and BGI did not amend its infringement contentions. Dkt. No.

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379 (“MTS Mot.”) at 15. Illumina also informed BGI that its infringement contentions were

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deficient in its October 13, 2020, and December 7, 2020, interrogatory responses but responded to

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them. See Dkt. No. 387-6 at 8; Dkt. No. 387-8 at 6.

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Fact discovery closed on March 26, 2021 and expert discovery closed on May 28, 2021.

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Illumina II, Dkt. No. 249 at 2. On June 16, 2021, Illumina filed a motion for summary judgment on

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BGI’s counterclaims. Dkt. No. 377 (“Mot.”); see also Illumina II, Dkt. No. 407. On the same day,

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Illumina also filed a motion to strike the expert opinions of BGI’s technical expert, Dr. Joseph Puglisi.

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Dkt. No. 379.

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II.

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PATENTS
Further background of the ’984 Patent is discussed in the Claim Construction Order. Order

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at 15–16. The ’984 Patent involves an “array,” or mechanism for analyzing multiple DNA

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fragments, that aims to increase the accuracy and efficiency of sequencing and thereby lower the

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cost. ’984 Patent at 3:44-53; 8:4-40. Target DNA is copied and modified prior to introduction to

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the array so that it will bind with the capture oligonucleotides on the array. See, e.g., id. at

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patents by making, selling, and using a different set of products. Further background in this matter is
discussed in Illumina Inc., et al., v. BGI Genomics Co., Ltd., et al., Case No. 19-cv-3770, Dkt. No.
185. (N.D. Cal.).
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6:17-30. It is then introduced to the array and binds to the capture oligonucleotides, and the target

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DNA can be sequenced by measuring signals or labels on the array. Id. at 3:44–4:23, 17:30-18:33.

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The target DNA fragments are first amplified so that multiple copies of the same fragment are

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present in one large macromolecule (as opposed to one single DNA fragment). Id. at 11:7-11.

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Amplification is generally understood to allow for stronger signal detection. Id. at 2:36-40. After

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the DNA fragment circles are formed, they are bound together into larger molecules, called

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“concatemers,” containing multiple copies of the same circular DNA fragments, usually in a process

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called rolling circle replication (“RCR”). Id. 11:45-58. Because there will be multiple copies of the

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same DNA fragment present at a particular binding site, the detection and sequencing of that fragment

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will be improved.

LEGAL STANDARD

United States District Court
Northern District of California

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I.

SUMMARY JUDGMENT
A party is entitled to summary judgment where it “shows that there is no genuine dispute

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as to any material fact and [it] is entitled to judgment as a matter of law.” FED. R. CIV. P. 56(a). A

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dispute is genuine if it could reasonably be resolved in favor of the nonmoving party. Anderson v.

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Liberty Lobby, Inc., 477 U.S. 242, 248 (1986). A fact is material where it could affect the

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outcome of the case. Id.

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The moving party has the initial burden of informing the court of the basis for its motion

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and identifying those portions of the record that demonstrate the absence of a genuine dispute of

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material fact. See Celotex Corp. v. Catrett, 477 U.S. 317, 323–24 (1986). Once the movant has

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made this showing, the burden shifts to the nonmoving party to identify specific evidence showing

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that a material factual issue remains for trial. Id. The nonmoving party may not rest on mere

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allegations or denials from its pleadings but must “cit[e] to particular parts of materials in the

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record” demonstrating the presence of a material factual dispute. FED. R. CIV. P. 56(c)(1)(A); see

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also Liberty Lobby, 477 U.S. at 248. The nonmoving party need not show that the issue will be

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conclusively resolved in its favor. Id. at 248–49. All that is required is the identification of

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sufficient evidence to create a genuine dispute of material fact, thereby “requir[ing] a jury or judge

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to resolve the parties' differing versions of the truth at trial.” Id. (internal quotation marks
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omitted). If the nonmoving party cannot produce such evidence, the movant “is entitled

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to . . . judgment as a matter of law because the nonmoving party has failed to make a sufficient

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showing on an essential element of her case.” Celotex, 477 U.S. at 323.
On summary judgment, the court draws all reasonable factual inferences in favor of the

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nonmoving party. Liberty Lobby, 477 U.S. at 255. “Credibility determinations, the weighing of

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the evidence, and the drawing of legitimate inferences from the facts are jury functions, not those

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of a judge.” Id. However, conclusory and speculative testimony does not raise a genuine factual

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dispute and is insufficient to defeat summary judgment. See Thornhill Publ'g Co., Inc. v. GTE

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Corp., 594 F.2d 730, 738–39 (9th Cir. 1979).

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II.

Patent Local Rule 3 “requires patent disclosures early in a case and streamlines discovery

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United States District Court
Northern District of California

MOTION TO STRIKE

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by replacing the series of interrogatories that parties would likely have propounded without it.”

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ASUS Computer Int'l v. Round Rock Research, LLC, No. 12-CV-02099-JST, 2014 WL 1463609,

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at *1 (N.D. Cal. Apr. 11, 2014) (internal quotation marks and modifications omitted). Patent

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Local Rule (“Patent L.R.”) 3-1 requires that a party claiming patent infringement serve a

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“Disclosure of Asserted Claims and Infringement Contentions” that includes “[e]ach claim of each

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patent in suit that is allegedly infringed by each opposing party, including for each claim the

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applicable statutory subsections of 35 U.S.C. § 271 asserted.” Patent L.R. 3-1(a). This requires “a

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limitation-by-limitation analysis, not a boilerplate reservation.” Rambus Inc. v. Hynix

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Semiconductor Inc., No. 05-CV-00334-RMW, 2008 WL 5411564, at *3 (N.D. Cal. Dec. 29,

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2008).

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Given the purpose of the Patent Local Rules, “a party may not use an expert report to

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introduce new infringement theories, new infringing instrumentalities, new invalidity theories, or

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new prior art references not disclosed in the parties' infringement contentions or invalidity

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contentions.” Verinata Health, Inc. v. Sequenom, Inc., No. 12-CV-00865-SI, 2014 WL 4100638,

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at *3 (N.D. Cal. Aug. 20, 2014) (internal quotation marks omitted). In determining whether to

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strike some or all of an expert report for failure to comply with the patent local rules, courts in this

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district have asked, “[W]ill striking the report result in not just a trial, but an overall litigation, that
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is more fair, or less?” Apple Inc. v. Samsung Electronics Co., No. 11-CV-01846-PSG, 2012 WL

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2499929, at *1 (N.D. Cal. June 27, 2012).
DISCUSSION

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I.

MOTION TO STRIKE OPINIONS OF DR. JOSEPH PUGLISI
Illumina moves to strike portions of the opening infringement report of BGI’s technical

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expert, Dr. Joseph Puglisi (“Puglisi Report”) because BGI allegedly proffered new theories, which

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it had not disclosed before. MTS Mot. at 1, 18 (moving to strike section VII.A.6 and ¶¶ 165–68,

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170–71, 176, and 178–79). The claim limitation at issue is the requirement that “more than 50%

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of the DNA binding regions in the array have multiple copies of one single DNA of said more

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United States District Court
Northern District of California

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than 105 different DNAs.” ’984 Patent 75:26-28.
Some background is necessary to understand this dispute. According to Illumina, BGI’s

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infringement theory “was based on the erroneous belief that all that is required by this limitation is

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that 50% of the binding regions comprise multiple copies of a DNA molecule, regardless of

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whether there are other molecules or other sequences in the same binding region.” MTS Mot. at 7.

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Illumina asserts that BGI’s sole infringement theory was that Illumina’s “finished clusters, which

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are generated by clonally amplifying template DNA until the cluster has ~1000 copies, satisfy the

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limitation because they include multiple copies of a DNA sequence.” Id. at 10. In my Claim

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Construction Order, however, I construed the claim limitation to require that “more than 50% of

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the DNA binding regions in the array are occupied by a single DNA molecule comprising multiple

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copies of only one” DNA sequence. Claim Construction Order at 17.

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In light of the Order, Illumina emailed BGI on June 30, 2020, and asked it to drop its

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infringement contentions because BGI “has no basis . . . to contend that more than 50% of the

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nanowells in Illumina’s accused products are either (a) ‘occupied by a single DNA molecule’ or

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(b) comprise ‘multiple copies of only one of the more than 100,000 genomic DNA sequences’ as

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required by the Court’s Order.” Dkt. No. 379-6 at 7. On July 16, 2020, BGI responded that its

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infringement claims under the ’984 Patent “continue to be well founded even after the Court’s

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claim construction” in part because as BGI “pointed out in its complaint and its infringement

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contentions, the cluster generation process . . . begins with a single target template.” Id. at 2. BGI
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further explained,
“(A) This single template is formed by a single fragment of DNA that
is bound in the nanowell. Polymerase then converts the single
stranded portion of that fragment into double stranded DNA. That
double stranded molecule contains two copies for the same DNA
sequence. This molecule satisfies the elements [Illumina contends]
are absent. (B) Additionally, after the first double stranded molecule
containing multiple copies of the same DNA is denatured, and the
remaining strand goes through bridge amplification, the resulting
double stranded molecule also satisfies the claim elements [Illumina
contends] are missing.”

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Id. After the email exchange, Illumina did not respond and BGI did not amend its infringement
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contentions. MTS Mot. at 15. Illumina also informed BGI that its infringement contentions were
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deficient but responded to them in its October 13, 2020, and December 7, 2020, interrogatory
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United States District Court
Northern District of California

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responses. Dkt. No. 401 (“MTS Reply”) at 2; Dkt. No. 387-6 at 8 (referring to the July 16, 2020,
email and asserting that “CGI argued a new infringement theory that is both wrong in substance
and unsupported by CGI’s infringement contentions”); Dkt. No. 387-8 at 6 (same).

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In considering Illumina’s motion to strike, I look at two issues: disclosure and fairness. I
conclude that BGI failed to properly disclose the three allegedly “new” theories found in the
Puglisi Report: (1) that the intermediate structures, as opposed to the final clusters, such as “a
double-stranded DNA fragment is a ‘single DNA molecule comprising multiple copies of only
one’ genomic DNA sequence that occupies a binding region as required by claim limitation 1(g)”
(“Double-Stranded DNA theory”); (2) “that the number of nanowells that pass filter shows that
greater than 50% of the nanowells meet the requirements of [the] claim limitation” (“Pass Filter
theory”); and (3) that claim 1 is infringed under DOE. Id. at 12. However, because Illumina

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waited more than a year until after fact discovery closed to challenge the first two, I will not strike
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them. The DOE theory is different—it was first disclosed in the Puglisi Report, and it will be
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struck.
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A.

Disclosure

BGI argues that its infringement contentions fully comply with the disclosure requirements
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under Patent L.R. 3-1 and that Illumina was put on notice about what was accused. Dkt. No. 389
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(“MTS Opp.”) at 4, 11. I disagree.

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Double-Stranded DNA Theory

First, BGI argues that it did not solely disclose that Illumina’s “finished clusters” infringed,
but that it also asserted the Double-Stranded DNA theory accusing Illumina’s cluster generation
process “based on the formation of infringing DNA molecules during the process of exclusion
amplification.” MTS Opp. at 13. It points to its Patent L.R. 3-1 Disclosures, where it stated that
the “‘DNA array’ claimed by the ’984 Patent is generated during the use of, and/or present in,
each of the Accused Illumina Systems.” Dkt. No. 389-2 (“BGI’s Patent L.R. 3-1 Disclosures”) at
2 (emphasis added); see also Dkt. No. 54 (“Counterclaims”) ¶¶ 50–52.

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BGI also asserts that if it had not been accusing the intermediate structures, and only the
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final clusters, then it would not have included contentions regarding the process for cluster
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United States District Court
Northern District of California

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formation in its Patent L.R. 3-1 Disclosures. MTS Opp. at 13–14. For example, BGI’s
infringement analysis described the steps of Illumina’s ExAmp process for cluster generation in

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detail, including the formation of the exact double-stranded DNA molecules accused of
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infringement. See, e.g., BGI’s Patent L.R. 3-1 Disclosures, Ex. A (“’984 Claim Chart”) at 4, 45
(“By enabling simultaneous seeding (landing of the DNA strand in the nanowell) and

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amplification, exclusion amplification promotes monoclonal cluster generation within the
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nanowells.”); id. at 69 (“After strand capture, the complementary strand is generated using
polymerase, thereby resulting in an immobilized template strand.”); id. at 70 (“Following bridge

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formation, the complementary strand is generated by a polymerase, resulting in a second
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nucleotide template strand.”). As a result, it argues that the “theories” in the Puglisi Report, which
Illumina asserts should have been cited in BGI’s contentions, are merely additional details and are

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proper because they do not constitute a new theory of infringement but rather elaborate on the
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previously disclosed theory. See Finjan, Inc. v. Blue Coat Sys., Inc., No. 13-CV-03999-BLF,
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2015 WL 3640694, at *2 (N.D. Cal. June 11, 2015) (“[T]he Patent Local Rules do not require
perfect clarity, only reasonable notice that is ‘as specific as possible’ given the information of
which a plaintiff is aware.”).
Illumina contends, correctly, that none of BGI’s statements provide notice that BGI “was
accusing a particular ‘intermediate structure’ (i.e., the double-stranded DNA)” of infringing the

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claim limitation. MTS Reply at 5. While BGI claims that it discusses the cluster generation

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process in its contentions only because it was accusing the double-stranded DNA of infringement,

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Illumina points out that BGI could also discuss the process to support its original theory, that each

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of the “~1000 copies” has the same sequence—a theory which fails in light of the Claim

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Construction Order. Id. at 4. Similarly, Illumina asserts that BGI contended that “the ‘DNA

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array’ claimed by the ’984 Patent is generated during the use of, and/or present, in each of the

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Accused Illumina Systems” to show that infringement occurs by “making” the claimed DNA

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arrays and not to accuse transient, intermediate structures “that exist only momentarily and are not

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even found in the finished array.” Id.

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BGI’s Double-Stranded DNA theory was not explicitly disclosed under the Patent Local

United States District Court
Northern District of California

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Rules and cannot be implicitly disclosed. See Thought, Inc. v. Oracle Corp., No.

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12-CV-05601-WHO, 2016 WL 3230696, at *6 (N.D. Cal. June 13, 2016), aff'd, 698 Fed. Appx.

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1028 (Fed. Cir. 2017) (unpublished) (rejecting an argument that an infringement theory was

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“implicitly” disclosed because the “purpose of requiring parties to disclose the basis for their

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contentions is to make them explicit and streamline patent litigation.”); see also DCG Sys. v.

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Checkpoint Techs., LLC, No. C 11-03792 PSG, 2012 WL 1309161, at *2 (N.D. Cal. Apr. 16,

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2012) (a patentee must “disclose what in each accused instrumentality it contends practices each

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and every limitation of each asserted claim to the extent appropriate information is reasonably

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available to it.”); Finjan, Inc. v. Proofpoint, Inc., No. 13-CV-05808-HSG, 2015 WL 1517920, at

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*7 (N.D. Cal. Apr. 2, 2015) (“if [plaintiff] believes that the first and second functions are

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contained within the obfuscated scripts, it was obligated to say so explicitly in its infringement

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contentions. Neither the Court nor the Defendants should be required to guess which aspects of

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the accused products allegedly infringe each claim element.”).

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2.

Pass Filter Theory

Second, BGI asserts that the “pass filter” data from Illumina’s sequencing is evidence in

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support of infringement under the Double-Stranded DNA theory and not a new theory. MTS Opp.

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at 16; see Blue Coat, 2015 WL 3640694, at *2 (“[t]he dispositive inquiry in a motion to strike is []

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whether the allegedly undisclosed ‘theory’ is in fact a new theory . . . or whether the ‘theory’ is
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instead the identification of additional evidentiary proof showing that the accused element did in

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fact practice the limitation.”). Though it does not dispute that it does not discuss the Pass Filter

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theory in its infringement contentions, it argues that the “passing filter statistics from Illumina’s

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sequencing runs is evidence to show that 50% threshold of the disputed element in the asserted

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claims is met.” MTS Opp. at 17; see also Dkt. No. 387-12 (“Puglisi Rep.”) ¶¶ 129–34. For

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example, Puglisi explains that “the intermediate DNA molecules that infringe the ‘more than 50%’

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element are necessarily formed in the nanowells on Illumina’s accused flow cells that ‘pass

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filter.’” MTS Opp. at 16; Puglisi Rep. ¶ 134.

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Illumina responds that the Pass Filter theory is a new theory because prior to the Claim
Construction Order, “whether nanowells ‘pass filter’ was irrelevant to BGI’s original infringement

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United States District Court
Northern District of California

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theory,” which was based on the belief that the claim limitation could be satisfied “regardless of

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whether there were multiple sequences or multiple molecules in the same nanowell.” Mot. at 16.

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Furthermore, because the “only theory of infringement to which BGI links the ‘pass filter’ data” is

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the Double-Stranded DNA theory, the Pass Filter theory is also unsupported in BGI’s

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infringement contentions. MTS Reply at 9. For those reasons, I agree with Illumina that BGI’s

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Pass Filter theory was not properly disclosed in its infringement contentions.

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3.

Doctrine of Equivalents

Finally, BGI argues that contrary to Illumina’s assertion, it preserved its arguments under

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DOE. MTS Opp. at 17–19. Illumina points out that the only reference to DOE in BGI’s

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infringement contentions is a general boilerplate statement that “[t]o the extent that any limitation

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of any asserted claim is not literally present in the Accused Illumina Systems, any such limitations

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are present under the DOE.” Claim Chart at 1; MTS Mot. at 17. Courts in this district have

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rejected such boilerplate language. See, e.g., ASUS, 2014 WL 1463609, at *3 (granting motion to

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strike portions of expert reports opining on DOE where the DOE theory was placeholder language:

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“to the extent that any claim element is found not to be literally embodied in the Accused

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Instrumentalities, Round Rock contends that the Accused Instrumentalities embody such claim

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elements under the doctrine of equivalents.”) (collecting cases); OptimumPath, LLC v. Belkin Int'l,

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Inc., No. 09-CV-01398 CW, 2011 WL 1399257, at *8 (N.D. Cal. Apr. 12, 2011), aff'd, 466 F.
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App'x 904 (Fed. Cir. 2012) (noting that “judges of this court have rejected plaintiffs’ attempts to

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assert claims under the doctrine of equivalents with blanket statements.”).

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BGI contends that Puglisi’s opinions on the DOE are in response to Illumina’s arguments

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on noninfringement in Illumina’s interrogatory response. MTS Opp. at 18. Specifically, Illumina

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identified another mechanism for the ExAmp process, where “the result of cluster generation is

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multiple different single-stranded DNA molecules that each have at most one copy of a particular

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sequence.” MTS Mot. at 7. In these “polyclonal nanowells,” “a single sequence can be detected

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by filtering out the sequencing data from non-dominant clusters and using only the sequencing

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data from the dominant cluster.” Id. This is contrary to Illumina’s other explanation of its flow
wells—that the cluster generation results in “monoclonal” clusters. MTS Opp. at 18.

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United States District Court
Northern District of California

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Consequently, BGI asserts that Puglisi should be permitted to testify regarding infringement under

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the DOE in response to Illumina’s competing explanations.

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The two cases on which BGI relies are distinguishable. The courts in Finjan, Inc. v.

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Symantec Corp., No. 14-CV-02998-HSG (JSC), 2017 WL 4025219, at *4 (N.D. Cal. Sept. 13, 2017)

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and Accord Facebook, Inc. v. BlackBerry Ltd., No. 18-CV-05434-JSW (JSC), 2019 WL 8013872, at

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*9 (N.D. Cal. Sept. 17, 2019) found good cause for the patentee to amend its DOE theories where

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the defendant had provided new information regarding its noninfringement arguments. Here, the

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question is not whether BGI has “good cause” to amend its DOE theories but whether it

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adequately disclosed its DOE theories in the first place. Because BGI’s DOE theory is merely

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boilerplate language, it should be rejected. See Blue Coat, 2015 WL 3640694, at *5 (finding that

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the plaintiff’s “boilerplate and generic” DOE disclosures did not satisfy plaintiff’s “obligation to

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provide a limitation-by-limitation analysis of its theory of infringement” and “[h]ad Defendant

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earlier moved to strike those embryonic disclosures, they would likely have been stricken as

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violative of the Patent Local Rules.”).

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Furthermore, Illumina points out that it served the interrogatory response—that BGI refers

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to as the “previously undisclosed mechanism for exclusion amplification”—on October 13, 2020,

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five months before fact discovery closed. Dkt. No. 387-6 at 7–8. BGI had ample time to respond

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during fact discovery and to seek leave to amend its DOE contentions. It cannot justify adding
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new theories to its boilerplate DOE arguments in the Puglisi Report as a response to Illumina’s

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allegedly new noninfringement arguments that were served seven months earlier. See Dynetix

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Design Sols., Inc. v. Synopsys, Inc., No. 11-CV5973-PSG, 2013 WL 4537838, at *1 (N.D. Cal. Aug.

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22, 2013) (“By failing to give Synopsys adequate notice of these theories during fact discovery,

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Dynetix severely prejudiced Synopsys’ ability to refute any DOE theories.”). “In sum, while

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equivalents theories can serve as ‘Plan B’ to literal infringement theories, if our local rules are to have

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any teeth, they must be adequately disclosed and supplemented along the way, should new evidence

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arise in discovery.” Id.

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B.

Fairness

Although I have determined that all three theories should have been disclosed, that does

United States District Court
Northern District of California

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not establish that I should strike them from the Puglisi Report. In deciding whether to strike some

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or all of an expert report for failure to comply with the Patent Local Rules, I have to consider

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whether striking the expert report will result in a fairer litigation. Apple, 2012 WL 2499929, at *1.

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Illumina argues that it suffered prejudice from the lack of disclosure because it “never had the

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opportunity to review and evaluate BGI’s actual infringement theories during fact discovery;

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instead, it had to guess about what infringement theory BGI might pursue until BGI served expert

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reports.” MTS Reply at 14. BGI contends that Illumina’s motion to strike Puglisi’s report a year

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after fact discovery closed and a few weeks after expert discovery closed is untimely, although

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Illumina says that BGI was aware that Illumina believed its infringement contentions to be new

20

theories and that BGI was obliged to seek amendment for its infringement contentions. In short,

21

the parties dispute whether Illumina should have compelled BGI to amend its infringement

22

contentions or whether BGI should have amended its infringement contentions after receiving

23

notice from Illumina about the alleged deficiencies.

24

Two cases from this District are applicable. The first is Blue Coat, on which both parties

25

rely. There, the court found that the plaintiff’s DOE disclosures were boilerplate and generic, like

26

BGI’s here. Blue Coat, 2015 WL 3640694, at *5. Had the defendant moved earlier to strike the

27

DOE disclosures, the court acknowledged that it likely would have struck the disclosures as

28

violative of the Patent Local Rules. Id. But the defendant did not move to strike and the court
11

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1

suspected that it may not have because the plaintiff would then “have had the opportunity to seek

2

leave to re-assert the theory with proper factually-based contentions.” Id. As a result, the court

3

could not “overlook the timing” of the defendants’ motion, which came “after the close of

4

discovery,” similar to Illumina’s motion. Id. The defendant explained that because the plaintiff

5

did not supplement its infringement contentions even after it received its confidential information,

6

it understood that the plaintiff would not pursue a theory of infringement under DOE. Id. But the

7

court rejected this explanation and held that the defendant should have provided some notice of

8

the deficiencies in the plaintiff’s disclosures so that the plaintiff “would be on notice of the

9

deficiency and would fail to supplement at its own risk. Instead, Defendant played the

10

United States District Court
Northern District of California

11

(apocryphal) ostrich, burying its head in the sand until it was safe to raise the issue.” Id.
The second case is Verinata Health, where the court found that the defendant should have

12

expressly stated in its infringement contentions what obviousness combinations it was asserting,

13

even though it was clear from the claim charts that the prior art reference was part of the obvious

14

combination. Verinata Health, 2014 WL 4100638, at *6. The court, however, held that “if the

15

claim charts caused [the plaintiff] to suffer any confusion as to what particular obviousness

16

combinations were being asserted, then the proper recourse would have been for [the plaintiff] to

17

compel [the defendant] to amend its invalidity contentions, not for [the plaintiff] to wait until

18

expert discovery and then move to strike the expert report.” Id.

19

Illumina contends that it had repeatedly told BGI that it believed BGI’s infringement

20

theories were “new” and therefore BGI “failed to supplement [its disclosures] at its own risk.” See

21

Blue Coat, 2015 WL 3640694, at *5. Blue Coat, however, does not address the situation where

22

the moving party had provided notice about the allegedly inadequate infringement contentions but

23

the non-moving party had refused to acknowledge that its disclosures were insufficient. Verinata

24

Health is more analogous. If Illumina suffered any confusion concerning what infringement

25

contentions were being asserted, then “the proper recourse” would have been for Illumina to

26

compel BGI to amend its infringement contentions, not to wait until after expert discovery to

27

move to strike the Puglisi Report. See Verinata Health, 2014 WL 4100638, at *6. Illumina knew

28

of the Double-Stranded DNA theory in July 2020. Although the Pass Filter theory was not
12

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1

disclosed in the July 2020 email, it is linked to the Double-Stranded DNA theory as “additional

2

evidentiary proof showing that the accused element did in fact practice the limitation,” Blue Coat

3

2015 WL 3640694, at *2.
Illumina’s motion to strike the Double-Stranded DNA theory and the Pass Filter theory

4

after the close of fact and expert discovery is untimely. Fact discovery closed on March 26, 2021

6

and expert discovery closed on May 28, 2021. Illumina II, Dkt. No. 249 at 2. Illumina did not file

7

the present motion until June 16, 2021. Although it asserted that BGI’s theories were allegedly

8

new in its interrogatory responses, it never sought supplemental briefing or clarification nor

9

moved to compel BGI to amend its contentions. See MTS Opp. at 8. It notified BGI that it

10

intended to move to strike the Puglisi Report in April 2021, but it did not move to strike then

11

United States District Court
Northern District of California

5

either. Dkt. No. 389-10 (“Sawyer April 19, 2021 Email”); see also Dkt. No. 389-11 (“Tigchelaar

12

April 22, 2021 Email”) (BGI responding that its infringement contentions were sufficient and

13

pointing Illumina to the July 2020 email exchange). It waited a full year after the close of fact

14

discovery and a few weeks after the close of expert discovery to file its motion to strike, burying

15

its head in the sand until it was safe to raise the issue of the Double-Stranded DNA and Pass Filter

16

theories with the court. See Blue Coat, 2015 WL 3640694, at *5. I will not strike those theories

17

from the Puglisi Report. 2
As for the DOE theories, BGI argues that the present case is analogous to Blue Coat and

18
19

that because Illumina did not object to the adequacy of BGI’s DOE contentions, Illumina’s motion

20

should be denied. MTS Opp. at 19. But as Illumina contends, it “did put BGI on notice that it had

21

set forth no viable doctrine of equivalents theory” in its June 30, 2020, email, which “applied to

22

the entire infringement theory set forth in BGI infringement contentions.” MTS Reply at 401.

23
24
25
26
27
28

Illumina contends that no showing of prejudice is required “because prejudice is inherent in the
assertion of a new theory after discovery has closed.” Adobe Sys. Inc. v. Wowza Media Sys., No.
11-CV-02243-JST, 2014 WL 709865, at *15, n.7 (N.D. Cal. Feb. 23, 2014). But “the same does
not pertain to insufficiently supported but nevertheless previously disclosed theories.” Blue Coat,
2015 WL 3640694, at *6. Although BGI did not disclose its Double-Stranded DNA theory in its
original infringement contentions, it disclosed the theory to Illumina in the July 2020 email. As a
result, there is no prejudice to denying Illumina’s motion for the Double-Stranded DNA and Pass
Filter theories because Illumina had the full opportunity to depose Puglisi and respond to his
opinions through its expert Weinstock’s rebuttal report during expert discovery. See Dkt. No.
376-8 (“Weinstock Reb.”) ¶ 59.
13
2

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 14 of 33

1

Unlike with the Double-Stranded DNA theory, BGI did not respond that its DOE theories were

2

sufficient; Illumina was unaware of the DOE theories until the Puglisi Report. The DOE theories

3

are struck from Puglisi’s report. Accordingly, Illumina’s motion to strike is GRANTED in part

4

and DENIED in part.

5

II.

MOTION FOR SUMMARY JUDGMENT
Noninfringement of the ’984 Patent

6

A.

7

Illumina moves for summary judgment on BGI’s infringement claims against Illumina

8

under the ’984 Patent. “Summary judgment of no literal infringement is proper when, construing

9

the facts in a manner most favorable to the nonmovant, no reasonable jury could find that the
accused system meets every limitation recited in the properly construed claims.” Catalina

11

United States District Court
Northern District of California

10

Marketing Int'l, Inc. v. Coolsavings.com, Inc., 289 F.3d 801, 812 (Fed. Cir. 2002).

12

The only claim element at issue is the requirement that “more than 50% of the DNA

13

binding regions in the array have multiple copies of one single DNA of said more than 105

14

different DNAs.” ’984 Patent 75:26-28; Dkt. No. 388 (“Opp.”) at 3. Both parties agree that in my

15

Claim Construction Order I construed this element to require that “more than 50% of the DNA

16

binding regions in the array are occupied by a single DNA molecule comprising multiple copies of

17

only one” DNA sequence. Order at 17. BGI asserts that under this construction, this element has

18

two principal features: (1) the DNA binding region is occupied by a single DNA molecule having

19

multiple copies of only one DNA sequence; and (2) the DNA molecule having multiple copies is

20

found in more than 50% of the DNA binding regions. Opp. at 3.

21

Illumina argues that the evidence shows that no reasonable jury would find that Illumina

22

infringes either of these elements, both of which are independent reasons that preclude

23

infringement as a matter of law. Mot. at 6. BGI asserts that there is ample evidence for a jury to

24

conclude that Illumina infringed the ’984 Patent and at a minimum, that there are genuine disputes

25

of multiple facts. Opp. at 3.

26

1.

Illumina’s Two Different Mechanisms For its Accused Products

27

As a preliminary matter, BGI contends that Illumina has two distinct mechanisms for how

28

its Accused Products work and that there are factual disputes that are not appropriate to resolve at
14

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 15 of 33

1

the summary judgment stage. Opp. at 4. Under the first mechanism (the one that BGI emphasizes

2

and the one portrayed in Illumina’s public materials), during Illumina’s “exclusion amplification”

3

(“ExAmp”) process, individual DNA fragments are bound to the patterned flow cell and

4

amplified. Opp. at 4. During cluster generation, the ExAmp process involves a rapid

5

amplification as soon as the first template DNA seeds a particular nanowell. Id. Rapid

6

amplification of this single template DNA means that all of the oligonucleotides are quickly

7

saturated, thereby excluding other template DNAs from binding and amplifying in the same

8

nanowell. Id. BGI’s expert, Puglisi, explains that this exclusion process ensures that the number

9

of wells with “purely monoclonal” clusters generated from a single template DNA is maximized.

10

Opp. at 4 (citing Puglisi Rep. ¶ 156).

United States District Court
Northern District of California

11

Under the second mechanism (the one asserted in Illumina’s motion for summary

12

judgment), clusters of single-stranded DNA (“ssDNA”) molecules are generated in the nanowells

13

through in situ amplification of template DNA molecules that bind to oligonucleotide primers

14

attached to the surface of each nanowell.3 Mot. at 5. The process of in situ amplification includes

15

both: (1) “seeding” or the attachment of the ssDNA templates to the oligonucleotide primers on

16

the surface of the cell; and (2) “cluster generation” or the repeated process of generating a strand

17

complementary to the DNA template strand to create a double-stranded DNA (“dsDNA”) and

18

denaturing it to allow for the now two separate ssDNAs to then be further copied. Id. Once all of

19

the DNA is denatured and left single-stranded, the result is a “cluster” of ssDNA, which consists

20

of copies of any DNA template strands that were “seeded” in the nanowell and their

21

complementary strands. Id. This allows for sequencing by synthesis to be performed on the DNA

22

fragments within the nanowells. Id.
Most of the nanowells will contain several different sequences because multiple template

23
24

DNA strands were “seeded” during the initial step. Mot. at 5. This occurs because a single

25

dsDNA only binds to one of the many oligonucleotide primers in the nanowell and does not

26

exclude other template ssDNA strands from attaching to other oligonucleotide primers. Id. But

27
28

This is the noninfringement argument in Illumina’s October 13, 2020, interrogatory response that
BGI alleged was “new.” MTS Opp. at 18.
15
3

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 16 of 33

1

according to BGI’s expert, Puglisi, the results are “effectively monoclonal” clusters. Puglisi Rep.

2

¶ 129. “Clusters that are ‘effectively monoclonal’ may have a mixture of DNA template

3

sequences, but the amount of the minor DNA sequences is sufficiently low that it does not

4

interfere with the detection and analysis of the dominant sequence.” Puglisi Rep. ¶ 129.

5

Next, the original template DNA strands or their complementary strands that were created

6

as part of the amplification process are cleaved and washed away. Mot. at 5. This is done because

7

the template DNA and complementary copies have different sequences and would produce

8

interfering signals during the sequencing detection. Id. An algorithm is used to interpret the

9

mixed signals received from each nanowell, and determine whether there is a sufficiently
dominant signal among the different sequences from which a sequence can be determined. Id. If

11

United States District Court
Northern District of California

10

there is a sufficiently dominant signal determined from the nanowell after the algorithm processes

12

the data, the nanowell is determined to “pass filter” and the data is used to determine the sequence

13

of the dominant signal in the cluster. Id.

14
15

2.

BGI’s Infringement Arguments Under Both Mechanisms

Under the first mechanism, BGI contends that Illumina’s Accused Products infringe its

16

’984 Patent in two scenarios: (1) after the initial replication step; and (2) after replication through

17

bridge amplification. Opp. at 5. After the initial replication step, the cluster generation process

18

begins when a template DNA molecule is introduced into the nanowell and hybridizes to an

19

oligonucleotide present on the surface. Id. Polymerase copies the original template DNA to form

20

a dsDNA molecule that comprises two copies of one template sequence. Id. After the initial

21

replication step, the nanowell is occupied by a single DNA molecule comprising two copies of the

22

DNA template sequence and thereby infringes the ’984 Patent. Id.; ’984 Patent 75:26–27 (claim

23

limitation requires that “more than 50% of the DNA binding regions in the array are occupied by a

24

single DNA molecule comprising multiple copies of only one single DNA.”). After replication

25

through bridge amplification, a double stranded structure is formed, which is a single DNA

26

molecule comprising two copies of the DNA template sequence. Id. As a result, a high

27

percentage of nanowells are occupied by clusters originating from a single template. Id.

28

Under the second mechanism, BGI contends that the amplification progresses through the
16

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 17 of 33

1

same intermediate DNA molecules discussed above that have multiple copies of one DNA. Opp.

2

at 7. Rapid amplification of the first template DNA “out of the gate” means that copies of the first

3

DNA will rapidly bind to and saturate the oligonucleotides in the nanowell, thereby excluding

4

other DNA templates from amplifying in the same well. Id. During this process, the cluster

5

generation takes advantage of the “saturation/exclusion (single occupancy) principle” of the ’984

6

Patent, i.e., the rapid saturation of all of the oligonucleotide binding sites in a particular DNA

7

binding region ensuring that the DNA binding region will be occupied by a single DNA molecule.

8

Id.; see ’984 Patent at 16:27-29.

9

3.

10

Whether Illumina’s Accused Products Infringe the Following Claim
Element: “The DNA Binding Region is Occupied by a Single DNA
Molecule Having Multiple Copies of One DNA Sequence”

United States District Court
Northern District of California

11

The first dispute is whether the double-stranded DNA (“dsDNA”) in Illumina’s Accused

12

Products contains two different sequences or one single sequence. BGI only accuses the dsDNA

13

attached to the DNA binding region as infringing the “multiple copies of one single DNA”

14

limitation. Dkt. No. 377-4 (“Puglisi Tr.”) at 162:17-21. The Claim Construction Order explains

15

that the ’984 Patent requires only one DNA sequence under the claim limitation at issue, “more

16

than 50% of the DNA binding regions in the array have multiple copies of one single DNA”:

17
18
19
20

“The language ‘one single DNA’ indicates that one, and only one,
DNA sequence is present in each binding region. Were BGI’s
interpretation correct that additional, different DNAs could also be
present, the inventor could have written ‘one DNA’ or ‘at least one
DNA’ of the 100,000 or more different DNAs. The use of the term
‘one single’ is clear: only one DNA sequence is present.”
Order at 18 (emphasis in original).

21
Illumina asserts that the Accused dsDNA contains two different sequences, i.e., a template
22
23

sequence and its complementary sequence. Mot. at 6. For example, because adenine (“A”)
always pairs with thymine (“T”) and guanine (“G”) always pairs with cytosine (“C”), a template

24
sequence of A-G-G-T would have a complementary sequence T-C-C-A. According to Illumina,
25
26

“Whether one sequence could be generated or determined from its complementary sequence is
irrelevant. They are still different sequences.” Mot. at 7. It also explains that the Accused

27
dsDNA are only present during the intermediate steps before cluster generation is completed and
28
17

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 18 of 33

1

are not sequenced in the Accused Flow Cells because the dsDNA contain different sequences.

2

Mot. at 8. Otherwise, the presence of both strands of dsDNA, i.e., the different sequences, would

3

produce conflicting signals during sequencing. Id.
BGI contends that the question of whether dsDNA comprises of a single DNA sequence or

4
5

different DNA sequences is a genuine issue of material fact. Opp. at 8. According to BGI, a

6

person of ordinary skill in the art (“POSITA”) would understand that a dsDNA molecule includes

7

two complementary copies of a single DNA sequence and the claim element referring to “multiple

8

copies of one single DNA” encompasses such complementary copies. Id.; see Puglisi Rep.

9

¶¶ 172–74. But BGI’s infringement expert, Puglisi admitted during his deposition that the two

10

strands of dsDNA are different sequences:
“Q: Do you see the image on the left of the double-stranded DNA?”
A: Yes I do.
Q: Are those two sequences the same or different?
A: They’re complementary to one another.
Q: So would you say they are the same or different?
A: They are different sequences, but are complements of one another
through the rules of Watson-Crick base pair.
Q: So you agree with the text above the figure that says the
composition of the bases are different, correct?
A: In the two strands they are different.”

United States District Court
Northern District of California

11
12
13
14
15
16

Puglisi Tr. at 9:20–10:7.
17

Accordingly, even if I drew all reasonable inferences in BGI’s favor, there is no genuine

18
dispute of fact that the dsDNA comprises of two different sequences. Due to the presence of the
19
20

second strand in the dsDNA with a different, albeit complementary, sequence, Illumina’s Accused
Products cannot infringe this limitation in the ’984 Patent. Whether Illumina’s Accused Products

21
create a purely monoclonal cluster or an effectively monoclonal cluster under the first or second
22
mechanisms is also irrelevant because both mechanisms have the dsDNA with two different
23

sequences. See Dkt. No. 400 (“Reply”) at 6. Because all of BGI’s infringement theories rely on a

24
flawed opinion that the Accused dsDNA contain multiple copies of one single DNA sequence,
25

there is no evidence that Illumina’s Accused Products infringe the ’984 Patent.4 Mot. at 6; Dkt.

26
27
28

I will not address the disputes about the “occupied” requirement in the first element or about the
second element. Even if there were genuine disputes of fact, it would not change the
noninfringement conclusion because Illumina’s Accused Products cannot satisfy the “one DNA
18
4

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 19 of 33

1

No. 387-12 Puglisi Rep. ¶¶ 119–28. Illumina’s motion for summary judgment on the

2

noninfringement of the ’984 Patent is GRANTED.

3

B.

4

As established above, BGI has not preserved its DOE theories in its infringement

Doctrine of Equivalents

5

contentions and therefore there can be no infringement under DOE. See supra Part I.A.3. Even if

6

BGI had sufficiently disclosed its DOE theories, the DOE analysis is flawed because it fails to

7

compare the accused features to the claim limitations.5 See Warner-Jenkinson Co. v. Hilton Davis

8

Chem. Co., 520 U.S. 17, 21 (1997) (DOE requires showing “‘equivalence’ between the elements of the

9

accused product or process and the claimed elements of the patented invention.”). “If an asserted

claim does not literally read on an accused product, infringement may still occur under the

11

United States District Court
Northern District of California

10

doctrine of equivalents if there is not a substantial difference between the limitations of the claim

12

and the accused product.” Bayer AG v. Elan Pharm. Research Corp., 212 F.3d 1241, 1250 (Fed.

13

Cir. 2000). “Insubstantiality may be determined by whether the accused device ‘performs

14

substantially the same function in substantially the same way to obtain the same result’ as the

15

claim limitation.” Catalina Marketing, 289 F.3d at 813. “Such evidence must be presented on a

16

limitation-by-limitation basis. Generalized testimony as to the overall similarity between the

17

claims and the accused infringer's product or process will not suffice.” Texas Instruments Inc. v.

18

Cypress Semiconductor Corp., 90 F.3d 1558, 1567 (Fed. Cir. 1996).
Illumina asserts that BGI’s DOE analysis is untied to any claim element. Mot. at 14. In

19
20

the DOE analysis, Puglisi addresses Illumina’s contention that “effectively monoclonal” clusters

21

under the second mechanism do not infringe the “more than 50%” element of the asserted claims.

22

Opp. at 16; Puglisi Rep. ¶¶ 150, 165–68. He opines that “effectively monoclonal clusters are

23

insubstantially different from purely monoclonal clusters for purposes of DNA sequencing with

24

the claimed patterned flow cells” but the patent does not mention or encompass clusters whether

25
26
27
28

sequence” requirement in the first element.
5

Because I conclude that the DOE theories have not been sufficiently disclosed and are flawed, I
will not address the question of whether the DOE claim is barred as a matter of law by prosecution
history estoppel.
19

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 20 of 33

1

“purely monoclonal” or “effectively monoclonal.” Id.; see Puglisi Rep. ¶ 167. The Claim

2

Construction Order rejected BGI’s construction that “would contemplate clusters of the

3

macromolecules per binding site,” which would “diminish[] a key benefit of the high-density

4

array.” Claim Construction Order at 21.
In addition, the DOE analysis does not provide a limitation-by-limitation basis for the

5

alleged insubstantiality between the Accused Products and the claim limitation. The Puglisi

7

Report does not specifically address how “clusters” containing multiple molecules are equivalent

8

to a single molecule or the equivalency to the “occupied” limitation. Mot. at 14; Dkt. No. 407 at

9

32; see Puglisi Rep. ¶¶ 150, 165–68. Moreover, BGI’s literal infringement theory is based on the

10

transient “intermediate DNA structures” that are “formed during cluster generation,” and not the

11

United States District Court
Northern District of California

6

clusters themselves, but BGI does not have a DOE theory on these intermediate structures. See

12

Opp. at 5–6; Reply at 7. Accordingly, BGI’s DOE theories fail and there can be no infringement

13

of the ’984 Patent under DOE.6

14

C.

15

The parties contest whether two of Illumina’s inventors of the ’444 and ’973 patents, Dr.

Inequitable Conduct

16

Xiaohai Liu and Xiaolin Wu, deliberately concealed a reference (the “Kovács” reference) from the

17

Patent and Trademark Office (“PTO”) during the prosecution of the ’444 and ’973 Patents. “To

18

prevail on the defense of inequitable conduct, the accused infringer must prove that the applicant

19

misrepresented or omitted material information with the specific intent to deceive the PTO.”

20

Therasense, Inc. v. Becton, Dickinson & Co., 649 F.3d 1276, 1287 (Fed. Cir. 2011). In a case

21

involving nondisclosure of information, like the one here, “the accused infringer must prove by

22

clear and convincing evidence that the applicant knew of the reference, knew that it was material,

23

and made a deliberate decision to withhold it.” Id. at 1290. The evidence of intent “must be the

24

single most reasonable inference able to be drawn from the evidence.” Id. “[W]hen there are multiple

25

reasonable inferences that may be drawn, intent to deceive cannot be found . . . .” Id.

26
27
28

6

I will not address the royalty base dispute about whether there is evidence of infringement of
certain Accused Products included in BGI’s royalty base for damages because I conclude that
there can be no infringement under the ’984 Patent.
20

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 21 of 33

1

BGI alleges that Illumina intentionally withheld or failed to disclose a reference to a paper by

2

Terez Kovacs and Laslo Otvos titled Simple Synthesis of 5-Vinyl and 5-Ethynyl- 2’

3

Deoxyuridine-5’-Triphosphates, and published in Tetrahedron Letters, Vol. 29, pp 4525-4528, 1988

4

(“Kovacs”). See Dkt. No. 233-7 (“Kovács”). It states that Kovács discloses a methodology for

5

converting nucleosides to nucleotides that is very similar to the method that Liu and Wu were using to

6

create modified nucleotides. FAA ¶ 337. It claims that Liu and Wu copied the specific methodology

7

used in Kovács but did not disclose Kovács as relevant prior art. Id.

8
9

Illumina answers that BGI’s “inequitable conduct” defense fails as a matter of law because
there is no evidence that the inventors had specific intent to deceive the PTO. Mot. at 2–3. For
the reasons below, even if I drew all inferences in BGI’s favor, I cannot reasonably conclude that

11

United States District Court
Northern District of California

10

the inventors had specific intent to deceive the PTO and therefore BGI’s inequitable conduct

12

defense fails.

13
14

1.

Whether the ’984 Inventors Knew About the Kovács Reference

Notwithstanding Drs. Wu and Liu’s declarations that they did not know about the Kovács

15

reference, BGI contends that Dr. Sarah Lee, a colleague of the inventors, cited Kovács in a

16

notebook as the methodology that she and Drs. Liu and Wu used for phosphorylation. Opp. at 20.

17

Because these three worked on the same phosphorylation methodology, “worked shoulder-to

18

shoulder at the lab bench,” and “talked every day about their work,” BGI argues that it is not the

19

“most reasonable to believe the inventors knew nothing about Kovács.” Id. But as Illumina

20

emphasizes, there are no citations to Kovács in any of the inventors’ lab notebooks. Mot. at 17.

21

Instead, the inventors have testified that they do not remember having ever seen the Kovács

22

reference; BGI’s experts admitted that there was no evidence that the inventors were aware of the

23

Kovács reference. See Dkt. No. 377-8 (“Wu Decl.”) ¶ 5; Dkt. No. 377-9 (“Liu Decl.”) ¶ 5; 1465 Dkt.

24

239-6 (“Wu Tr.”) at 287:14-20; Dkt. No. 377-11 (“Metzker Tr.”) at 245:19–246:4.

25

BGI contests Illumina’s defense that its inventors developed their phosphorylation method

26

from references other than Kovács. Opp. at 21. Its expert, Dr. Patrick Hrdlicka, compared the

27

chemical synthesis steps that Kovács teaches to phosphorylate nucleosides with what the inventors

28

used and disclosed in their patents and concluded that the inventors must have known about
21

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 22 of 33

1

Kovács. See Dkt. No. 386-46 (“Hrdlicka Rep.”) ¶¶ 208–39. According to BGI, “At the very least,

2

there is a dispute between the experts as to whether the similarities between Kovács and what the

3

inventors did and disclosed establishes that they knew about and used Kovács as a guide for their

4

work” rendering summary judgment inappropriate. Opp. at 22. But as Illumina correctly notes,

5

raising a factual dispute is not enough to foreclose the other reasonable inferences and prove that

6

intentional deceit is the single most reasonable inference. Reply at 12.

7

For example, Illumina asserts that another reasonable inference is that Lee could have

8

simply communicated “a common proton sponge protocol (what BGI calls the Kovács

9

methodology) to Drs. Wu and Liu without communicating where the proton sponge protocol was
published.” Reply at 10; Mot. at 17–18. BGI contends that this speculation is implausible

11

United States District Court
Northern District of California

10

because there “is no reason Dr. Lee would have concealed the copy of Kovacs she was referencing

12

from Drs. Wu and Liu, who were working right next to her.” Opp. at 21. Illumina responds that

13

at Lee’s previous job, Lee had performed extensive work on phosphorylation protocols similar to

14

the protocol in Kovács. Dkt. No. 377-15 (“Romesberg Rep.”) ¶ 355. Based on her prior

15

experience and publications, Lee could have explained the phosphorylation protocol to her

16

colleagues without needing to reference or share any specific literature. Id. Illumina argues that

17

this inference is more reasonable than BGI’s “speculation that the inventors would have seen all

18

literature cited in Dr. Lee’s lab notebook just because they were working in the same laboratory.”

19

Reply at 10.

20
21

2.

Whether the Inventors Thought the Kovács Reference Was Material

In addition, Illumina asserts that because there is no evidence that any inventor had ever

22

seen Kovács, BGI’s theory that the inventors believed that the reference was material to the

23

claimed invention is “even more far-fetched.” Mot. at 19. Even if the inventors had seen Kovács,

24

Illumina argues that there is no evidence to show that the inventors would have thought it was

25

material to the claims because (1) the fields of technology were different; (2) BGI itself did not

26

recognize the materiality of the Kovács reference; and (3) Kovács was merely cumulative of other

27

prior art. Mot. at 19–20. BGI contends that Kovács is material, as evidenced by the fact that Lee

28

cited to it in her lab notebook and that Kovács is more relevant than the other prior art references,
22

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 23 of 33

1

which Illumina did disclose. Opp. at 22–23. Illumina, however, maintains that Kovács “has

2

nothing to do with sequencing or the azido blocking group.” Reply at 11.

3
4

3.

Whether the Inventors Had Specific Intent to Deceive the PTO

Even if the inventors knew about Kovács and believed it was material, “[d]espite extensive

5

discovery that involved over 50 hours of inventor depositions and combing through over 300 lab

6

notebooks, BGI has no evidence from which a reasonable fact finder could conclude that the inventors

7

deliberately withheld Kovacs with a specific intent to deceive the PTO.” Mot. at 20. BGI’s experts

8

admitted this. Metzker Tr. at 414:6-14 (“I have no knowledge of the [sic] intentionability of any of

9

the inventors in this case. I don’t know what their intentions are. I’m not saying they had any malice
intentions”); id. at 417:1-14 (“I don’t have any knowledge of what they purposefully did or not

11

United States District Court
Northern District of California

10

purposefully did in the laboratory . . . whether they attempted to hide or not hide purposefully. I

12

wouldn’t know that”); Dkt. No. 377-12 (“Hrdlicka Tr.”) at 14:6–15:10 (“I have not formulated any

13

opinions or conclusions regarding whether or not the inventors had malicious intent in withholding

14

information from the patent office . . . I cannot speculate to what was going on in the mind of . . .

15

inventors”).

16

But “because direct evidence of deceptive intent is rare, a district court may infer intent from

17

indirect and circumstantial evidence, provided that such intent is the single reasonable inference.” Am.

18

Calcar, Inc. v. Am. Honda Motor Co., 768 F.3d 1185, 1190–91 (Fed. Cir. 2014). BGI contends that a

19

possible motive for withholding knowledge of the Kovács reference could have been to ensure that

20

they could still claim to be inventors and therefore this motive creates a reasonable inference that

21

the inventors did have a specific intent to deceive the PTO by withholding Kovács. Reply at 23.

22

According to BGI, Illumina’s witnesses are not credible, which is a “crucial” factor in finding

23

specific intent to deceive. See Opp. at 20; see Poller v. Columbia Broad. Sys., Inc., 368 U.S. 464,

24

473 (1962) (“[S]ummary judgement should be used sparingly where motive and intent play

25

leading roles” to allow credibility of witnesses to be examined on cross examination.). For

26

example, Drs. Wu and Liu, as well as the six other inventors, which Illumina hired as consultants,

27

testified that Dr. Wu came up with the idea to use the 3’-O azidomethyl block. Dkt. No. 386-38

28

(“Romesberg Reb.”) ¶¶ 266–69. But the one inventor who Illumina did not hire as a consultant,
23

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 24 of 33

1

Dr. Milton, testified that he was the one who came up with the idea. Dkt. No. 386-40 (“Milton

2

Tr.”) at 27:24–28:1.
BGI also asserts that Illumina’s reasons for not disclosing Kovács are “not credible and

3
4

part of the scheme to conceal its copying Zavgorodny,” a prior art reference which BGI had

5

accused Illumina of concealing until the patent examiner found the reference on his own. Opp. at

6

24; Illumina II, Dkt. No. 241-4 at 6. BGI emphasizes that Illumina has argued that Zavgorodny is

7

irrelevant to its invention. But when pressed, Dr. Liu testified that he found Zavgorodny “very

8

interesting because it had done what the Illumina inventors had done.” Opp. at 24; Dkt. No. 241-4

9

at 6. Illumina and its inventors also claim that they did not know about Zavgorodny before they
filed their patent applications but an email shows otherwise. See Dkt. No. 386-45. Because

11

United States District Court
Northern District of California

10

Illumina inventors had a motive to claim that they did not know about Kovács—in order to obtain

12

patent protection—BGI argues that “there is more than enough evidence, given the contradictory

13

facts Illumina relies on, to draw the reasonable inference that the Illumina inventors knew about

14

Kovács, knew it was material, and withheld it from the patent office with a specific intent to

15

deceive.” Opp. at 25.
As Illumina points out, nothing about the Zavgorodny reference was concealed; it was

16
17

fully disclosed and considered by the PTO. Reply at 13. And Milton’s testimony that he came up

18

with the idea to use a 3’-O azidomethyl blocking group, while it may (or may not) undermine the

19

credibility of Illumina’s witnesses, disproves BGI’s theory that the inventors copied the invention

20

from Zavgorodny. Id. Milton and the other inventors all testified that none of the inventors had

21

seen the Zavgorodny references before. Milton Tr. at 39:6–40:5; 30:22–31:2; 31:10-22; 34:4-7;

22

45:5-15; Romesberg Reb. ¶ 291. Given this record, drawing all reasonable inferences in BGI’s

23

favor, I cannot reasonably conclude that the single most reasonable inference for the failure to

24

disclose the Kovács reference to the PTO was to intentionally deceive the PTO. 7 Illumina’s

25
26
27
28

Because I reject BGI’s “inequitable conduct” defense, I will not address Illumina’s request to
strike portions of BGI’s expert reports that opine on the inventors’ states of mind. Mot. at 22; see,
e.g., Dkt. No. 377-14 (“Metzker Rep.”) ¶ 273 (opining that the inventors claimed to have not
known anything about [Kovacs], to gain some advantage in the patent prosecution context.”).
7

24

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 25 of 33

1

motion for summary judgment on BGI’s inequitable conduct defense is GRANTED.
BGI’s Other Defenses

2

D.

3

Finally, Illumina moves for summary judgment that (1) the Accused StandardMPS

4

products infringe all Asserted Claims of all Asserted Patents; (2) the Accused CoolMPS products

5

infringe the Asserted Claims of the ’973 and ’444 Patents;8 (3) the Asserted Claims are not

6

anticipated; and (4) the ’444 Patent is not invalid for lack of written description or enablement.

7

Mot. at 23–25. The first two issues are not rebutted by BGI’s expert opinions and BGI’s counsel

8

confirmed that its experts did not serve reports on these issues. Mot. at 24. In addition, BGI’s

9

expert does not assert that any Asserted Claim is anticipated or that the ’444 Patent is invalid. Id.
at 24–25. BGI does not contend that there is a genuine issue of material fact. BGI only asserts

11

United States District Court
Northern District of California

10

that Illumina failed to show there were no disputed issues of fact and that these issues are best

12

addressed during the preparation of pre-trial submissions. Opp. at 25. I disagree and GRANT

13

summary judgment in favor of Illumina on these four uncontested defenses.

14

III.

MOTIONS TO SEAL

15

The parties have filed ten motions to seal. See 1465 Dkt. Nos. 406, 421, 433, 448; 3770

16

Dkt. Nos. 376, 378, 386, 387, 399, 412. A party seeking to seal court records must overcome a

17

strong presumption in favor of the public’s right to access those records. See Ctr. for Auto Safety

18

v. Chrysler Grp., LLC, 809 F.3d 1092, 1096 (9th Cir. 2016), cert. denied sub nom. FCA U.S. LLC

19

v. Ctr. for Auto Safety, 137 S. Ct. 38 (2016). Here, the “compelling reasons” standard applies.

20

See id. at 1101. The Ninth Circuit has explained that examples of “compelling reasons” include

21

“the use of records to gratify private spite, promote public scandal, circulate libelous statements,

22

or release trade secrets.” Kamakana v. City & Cty. of Honolulu, 447 F.3d 1172, 1179 (9th Cir.

23

2006). Other examples include “sources of business information that might harm a litigant’s

24

competitive standing.” Ctr. for Auto Safety, 809 F.3d at 1097. For the reasons explained in the

25

table below, the following motions are GRANTED: 3770 Dkt. Nos. 376, 378, 399, 412 and 1465

26

Dkt. Nos. 406, 433, 448. The following motions are GRANTED in part and DENIED in part:

27
28

In a separate order, I rejected BGI’s argument that the ’973 Patent was invalid. See Illumina II,
Dkt. No. 469 at 5–9.
25
8

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 26 of 33

1

3770 Dkt. Nos. 386, 387 and 1465 Dkt. No. 421. The clerk shall UNSEAL 3770 Dkt. Nos.

2

386-20, 386-22, 386-24, 386-26, 386-28, 386-30, 386-36, 386-44, 387-4, 387-6, 387-8, 387-10

3

and 1465 Dkt. Nos. 421-20, 421-22, 421-24, 421-26, 421-28, 421-30, 421-36, 421-44.

4
5
6
7
8
9
10

United States District Court
Northern District of California

11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

Designatin
Portions to Be
Ruling
g
Filed Under
Party
Seal
3770 Dkt. No. 376 / 1465 Dkt. No. 406 – GRANTED
Illumina’s Motion for
2:13, 10:7
Illumina
GRANTED
Summary Judgment
(Discusses Illumina’s proprietary
product information and trade
secrets, which if made public
could cause harm to Illumina.
Dkt. No. 376-1 ¶ 6.)
¶¶127-128, 146, 165-167 Illumina
GRANTED
Exhibit 1 to the
(Discusses Illumina’s proprietary
Declaration of Andrew
product information and trade
Gesior in Support of
secrets, which if made public
Illumina’s Motion for
could cause harm to Illumina.
Summary Judgment
Dkt. No. 376-1 ¶ 6.)
(2021-04-12 Opening
Expert Report of Joseph
Puglisi
Ph.D.)
GRANTED
Exhibit 2 to the
¶¶ 37-41, 43-58, 59 n.7, Illumina
(Discusses Illumina’s proprietary
Declaration of Andrew 60-63
product information and trade
Gesior in Support of
secrets, which if made public
Illumina’s Motion for
could cause harm to Illumina.
Summary Judgment
Dkt. No. 376-1 ¶ 6.)
(2021-05-10 George
Weinstock’s Rebuttal
Report re
Noninfringement of U.S.
Patent No.
9,944,984)
Illumina
GRANTED
Exhibit 5 to the
111:9-15, 111:21-22,
(Discusses Illumina’s proprietary
112:13-14
Declaration of Andrew
product information and trade
Gesior in Support of
secrets, which if made public
Illumina’s Motion for
could cause harm to Illumina.
Summary Judgment
Dkt. No. 376-1 ¶ 6.)
(2021-01-22 Deposition
Transcript of Sergio
Peisajovic)
GRANTED
Exhibit 16 to the
¶¶ 63-66, 84-85, 93, 97, BGI
(Discusses BGI’s trade secrets
Declaration of Andrew 99, 110-111, 116-117,
and confidential information
Gesior in Support of
149-150, 154, 175, 183,
regarding its products, chemical
Illumina’s Motion for
reagents, and R&D, which if
Document

26

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 27 of 33

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2
3
4
5
6
7
8
9
10

United States District Court
Northern District of California

11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

Summary Judgment
(2021-04-12 Expert
Report of Floyd
Romesberg Ph.D. re
Infringement)

186-187, 196, 204, 207208, 234, 263, 266, 269,
272, 275, 278, 305, 318,
347, 363, 393, 407, 423,
427, 432, 440, 447, 457,
460-461, 464, and 469470, and n.10, n.13, and
n.15 (highlighted in
yellow)
BGI
¶ 10 (highlighted in
yellow)

Exhibit 17 to the
Declaration of Andrew
Gesior in Support of
Illumina’s Motion for
Summary Judgment
(2021-05-10 Rebuttal
Expert Report of Michael
Metzker Ph.D. re
Noninfringement)
¶ 95
Exhibit 18 to the
Declaration of Andrew
Gesior in Support of
Illumina’s Motion for
Summary Judgment
(2021-04-12 Opening
Expert Report of James
Kearl)

Illumina

made public could harm its
competitive standing. 3770 Dkt.
No. 383 ¶ 4.)

GRANTED
(Discusses BGI’s trade secrets
and confidential information
regarding its products, chemical
reagents, and R&D, which if
made public could harm its
competitive standing. 3770 Dkt.
No. 383 ¶ 4.)
GRANTED
(Discusses Illumina’s
confidential, non-public financial
information, such as sales and
revenue data, which if made
public could cause harm to
Illumina. Dkt. No. 376-1 ¶ 7.)

3770 Dkt. No. 386 / 1465 Dkt. No. 421 – GRANTED IN PART AND DENIED IN PART
GRANTED
Portions of p. 4 Illumina
Defendants’ Opposition •
(Discusses Illumina’s proprietary
•
Portions of p. 25
to
product information and trade
Illumina’s Motion for
secrets, which if made public
Summary Judgment
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)
•
Portions of ¶ 66 Illumina GRANTED
Ex. 2 - April 12, 2021
(Discusses Illumina’s
•
Portions of
Expert
confidential, non-public
¶¶ 70-71
Report of Joseph D.
information regarding its
•
Portions of ¶ 74
Puglisi, Ph.D.
third-party licensing agreements
•
Portions of ¶ 76
as well as its proprietary product
•
Portions of ¶ 80
information and trade secrets.
•
Portions of ¶ 83
3770 Dkt. No. 396 ¶¶ 7–8.)
•
Portions of
¶¶ 104-109
•
Portions of
¶¶ 127-128
•
Portions of ¶ 152
•
Portions of
¶¶ 159-160
•
Portions of
¶¶ 165-167
27

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 28 of 33

•
•

•
•
•
•

Portions of ¶ 171
Portions of
¶¶ 184-187
Portions of p. 4
Portions of p.
6-11
Portions of p.
18-21
Portion of p. 27
Portions of p.
29-32
p. 7:22
p. 66:16-24
p. 67:4-9; 12-14;
16-23; 25
p. 68:19-21;
23-25
p. 69:1-3; 5-6
p. 83:24-35
p. 84:1-13; 15-25
p. 85:1-14
p. 97:10-11;
13-25
p. 98:1-7; 9-11;
13-16; 18-20; 25
p. 101:2-5; 7-25
p. 102:2-5; 7-9;
11-17; 22-23
p. 103:13
p. 145: 1-7; 9-11;
18-21;25
p. 146: 1-2; 5-8;
10-19; 21-22;
24-25
p. 153: 1-4; 8-12;
14-20; 22-25
174:12-16
p. 9: 1-2
p. 95:2-16; 24-25
p. 96:1-6

Ex. 12 - Excerpts from
the May 25, 2021
deposition transcript of
Joseph D. Puglisi, Ph.D.

•
•
•
•

Illumina
p. 6:20
p. 171:9-16
p. 186:6-9; 15-17
p. 187:4-7

Ex. 14 - Excerpts
from the April 12,
2021 Expert Report

•

Portions of
¶¶ 54-62
Portions of

1
2
3

Ex. 3 - Ex. 3 to Puglisi
Report
(Claim Chart)

•
•

4

•

5

•
•

6
7
8
9

Ex. 4 - Excerpts from
the May 28, 2021
deposition transcript
of
George M. Weinstock,
Ph.D.

10

United States District Court
Northern District of California

11
12

•
•
•
•
•
•
•
•
•

13

•

14

•
•

15
16
17
18
19

Ex. 6 - Excerpts from
the January
22, 2021 deposition
transcript of Sergio
Peisajovich, Ph.D.

20
21
22
23
24
25

Ex. 7 - Excerpts
from the March 18,
2021 deposition
transcript of
Peter McInerney, Ph.D.

•
•
•
•
•

Illumina

GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)

Illumina

GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets and contains the home
addresses of third-party witnesses.
3770 Dkt. No. 396 ¶¶ 8–9.)

Illumina

GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)

Illumina

GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets and contains the home
addresses of third-party witnesses.
3770 Dkt. No. 396 ¶¶ 8–9.)
GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets and contains the home
addresses of third-party witnesses.
3770 Dkt. No. 396 ¶¶ 8–9.)
GRANTED
(Discusses Illumina’s
confidential, non-public financial

26
27
28

•

Illumina

28

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 29 of 33

1

of James
R. Kearl, Ph.D.

2
3
4
5
6
7
8
9
10

United States District Court
Northern District of California

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14
15
16
17
18
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20
21
22
23
24
25
26
27
28

•
•
•
•

information regarding its sales,
revenue data, IP portfolio, and
business development. Also
discusses its proprietary product
information and trade secrets.
3770 Dkt. No. 396 ¶¶ 7–8.)

¶¶ 64-65
Portions of ¶ 85
Portions of ¶ 95
Portions of fn.
128
Portions of fn.
135

Ex. 15 - Excerpts from
the May 10, 2021
Rebuttal Expert Report
of
George M. Weinstock,
Ph.D.
Ex. 18 - Excerpts of the
document
produced bearing
beginning Bates
numbers
ILMNBGI0207713
Ex. 19 - Excerpts of
the document
produced bearing
beginning Bates
numbers
ILMNBGI_NDCAL000
3471
Ex. 20 - Excerpts of
the document
produced bearing
beginning Bates
numbers
ILMNBGI0203644
Ex. 21 - Excerpts of
the document
produced bearing
beginning Bates
numbers
ILMNBGI0203857
Ex. 22 - Excerpts from
the January 7, 2021
deposition transcript of
Joseph Samuel Brennan,
Ph.D.

N/A

Illumina

N/A

Illumina

N/A

Illumina

N/A

Illumina

N/A

Illumina

N/A

Illumina

Ex. 23 Excerpts from
the April 12, 2021
Opening Expert
Report of
Michael L. Metzker,
Ph.D.
Ex. 26 - Excerpts of the
document

•
•

Portions of ¶ 247 Illumina
Portions of ¶ 263

•

Illumina
Portions of p.
1979/ILMNBGI0
29

DENIED – The court shall
unseal 3770 Dkt. No. 386-20 and
1465 Dkt. No. 421-20.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-22 and
1465 Dkt. No. 421-22.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-24 and
1465 Dkt. No. 421-24.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-26 and
1465 Dkt. No. 421-26.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-28 and
1465 Dkt. No. 421-28.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-30 and
1465 Dkt. No. 421-30.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)
GRANTED
(Discusses Illumina’s proprietary

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 30 of 33

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6
7
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9
10

United States District Court
Northern District of California

11
12
13
14

produced bearing
beginning Bates
numbers
ILMNBGI0213690
Ex. 29 - Excerpts from
the May 24, 2021
deposition transcript of
Floyd
Romesberg, Ph.D.

•

product information and trade
secrets, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)

213692
Portions of p.
19811984/ILMNBGI0
213694-697
Illumina

N/A

Ex. 30 - Excerpts from N/A
the May 10, 2021
Expert Rebuttal Report
of Floyd Romesberg,
Ph.D. on
Validity
Ex. 31 - Excerpts from p. 8:3-4
the January 15, 2021
deposition transcript of
John Milton, Ph.D.
Ex. 32 - Exhibit 0075
Entire document
from the December 8,
2020 deposition of
Shankar
Balasubramanian, Ph.D.

Illumina

Ex. 33 - Excerpts from
the August 20, 2020
deposition transcript
of
Xiaohai Liu, Ph.D.

N/A

Illumina

Ex. 34 - Excerpts from
the April 12, 2021
Opening Expert Report
of
Professor Patrick J.
Hrdlicka
Ex. 35 - Document
produced bearing
Bates numbers
ILMNBGI1110437-52

•

Portions of p.
ILMNBGI1110437

Illumina

Ex. 36 - Excerpts from
the January
14, 2021 deposition
transcript of Harold P.
Swerdlow, Ph.D.

•

Illumina

Illumina

Illumina

15
16
17
18
19
20
21
22
23
24
25
26
27
28

•

•
•

Illumina
Portions of
¶¶ 176-179
Portions of fn. 43

Portions of p.
212:9-10: 14
Portions of p.
212:25-213:5
Portions of p.
213:9-10
30

DENIED – The court shall
unseal 3770 Dkt. No. 386-36 and
1465 Dkt. No. 421-36.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-38 and
1465 Dkt. No. 421-38.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
GRANTED
(Contains the home addresses of
third-party witnesses. 3770 Dkt.
No. 396 ¶ 9.)
GRANTED
(Discusses Illumina’s non-public
working draft regarding its
strategic publication of
information related to its
technology, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)
DENIED – The court shall
unseal 3770 Dkt. No. 386-44 and
1465 Dkt. No. 421-44.
(Illumina does not seek to seal
this document. 3770 Dkt. No.
396.)
GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)
GRANTED
(Discusses Illumina’s proprietary
product information and trade
secrets, which if made public
could harm Illumina. 3770 Dkt.
No. 396 ¶ 8.)
GRANTED
(Discusses Illumina’s
confidential, non-public financial
information regarding its sales,
revenue data, IP portfolio, and
business development. 3770 Dkt.

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 31 of 33

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United States District Court
Northern District of California

11
12
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14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

No. 396 ¶ 7.)
3770 Dkt. No. 399 / 1465 Dkt. No. 433 – GRANTED
Portions of page 5 and Illumina GRANTED
Illumina’s Reply in
(Discusses Illumina’s confidential
15
Support of Illumina’s
proprietary product information
Motion for Summary
and trade secrets, which if made
Judgment
public could cause harm to
Illumina. 3770 Dkt. No. 399-1
¶ 4.)
Exhibit 22 to the
Portions of ¶¶ 327-328 Illumina GRANTED
(Discusses Illumina’s confidential
p. 127, fn. 12
Supplemental
proprietary product information
Declaration of Andrew
and trade secrets, which if made
Gesior in Support of
public could cause harm to
Illumina’s Reply in
Illumina. 3770 Dkt. No. 399-1
Support of Illumina’s
¶ 4.)
Motion for Summary
Judgment (excerpts of the
Expert Report of Floyd
Romesberg, Ph. D. on
Validity served on May
10, 2021)
3770 Dkt. No. 412 / 1465 Dkt. No. 448 – GRANTED
Defendants GRANTED
BGI’s Prowse
Green highlighted
(Discusses BGI’s trade secrets
Presentation
portions
and confidential business
information regarding its ongoing
R&D activities and expenditures
that if made public would harm
BGI. 1465 Dkt. No. 448; Dkt.
No. 412).
Illumina GRANTED
BGI’s Opposition
Green highlighted
(Discusses Illumina’s proprietary
Presentation
portions of slide 12–13,
product information and trade
35
secrets. 3770 Dkt. No. 415; 1465
Dkt. No. 452.)
3770 Dkt. No. 378 – GRANTED
Exhibit 2 to the
¶¶ 37-41, 43, 47, 50-58, Illumina GRANTED
(Discusses confidential, non59 n.7, 60-63
Declaration of Audra
public information such as
Sawyer in Support of
Illumina’s proprietary product
Illumina’s Motion to
information and trade secrets.
Strike Expert Report of
Dkt. No. 378.)
Dr. Joseph Puglisi and
Preclude Defendants
From Relying On New
Infringement Theories
(2021-05-10 George
Weinstock’s Rebuttal
Report re
Noninfringement of U.S.
Patent No. 9,944,984)
31

Case 3:19-cv-03770-WHO Document 424 Filed 09/09/21 Page 32 of 33

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United States District Court
Northern District of California

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Illumina GRANTED
Exhibit 4 to the
¶¶127-128, 146,
(Discusses confidential,
Declaration of Audra
165-167, 171
non-public information such as
Sawyer in Support of
Illumina’s proprietary product
Illumina’s Motion to
information and trade secrets.
Strike Expert Report of
Dkt. No. 378.)
Dr. Joseph Puglisi and
Preclude Defendants
From Relying On New
Infringement Theories
(2021-04-12 Opening
Expert Report of Joseph
Puglisi Ph.D.)
Illumina GRANTED
Exhibit 6 to the
Entire document
(Discusses confidential,
Declaration of Audra
non-public information such as
Sawyer in Support of
Illumina’s proprietary product
Illumina’s Motion to
information and trade secrets.
Strike Expert Report of
Dkt. No. 378.)
Dr. Joseph Puglisi and
Preclude Defendants
From Relying On New
Infringement Theories
(excerpt of Illumina
Powerpoint presentation
entitled “ExAmp
Clustering”)
3770 Dkt. No. 387 – GRANTED IN PART AND DENIED IN PART
Illumina DENIED – The clerk shall
BGI’s Opposition to
N/A
UNSEAL Dkt. No. 387-4.
Illumina’s Motion to
(Illumina does not request this
Strike Puglisi’s Expert
document to be sealed. Dkt. No.
Opinion
395.)
Illumina DENIED – The clerk shall
N/A
Ex. 5 – Excerpts from
UNSEAL Dkt. No. 387-6.
Illumina’s
(Illumina does not request this
October 13, 2020
document to be sealed. Dkt. No.
Responses and
395.)
Objections to
Defendants’ Second
Set of Interrogatories
(Nos. 7-16)
Illumina DENIED – The clerk shall
N/A
Ex. 6 - Excerpts from
UNSEAL Dkt. No. 387-8.
Illumina’s
(Illumina does not request this
December 7, 2020
document to be sealed. Dkt. No.
Supplemental
395.)
Responses and
Objections to
Defendants’ Second Set
of
Interrogatories

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Ex. 7 - Excerpts from
Illumina’s
March 26, 2021 Second
Supplemental Responses
and
Objections to
Defendants’ Second
Set of Interrogatories
Ex. 8 - April 12, 2021
Expert Report of Dr.
Joseph D. Puglisi

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United States District Court
Northern District of California

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Ex. 12 - Excerpts from
the May 25,
2021 deposition transcript
of Dr.
Joseph D. Puglisi

•
•
•
•
•
•
•

Illumina
Portions of ¶ 66
Portions of ¶¶ 70-71
Portions of ¶ 74
Portions of ¶ 76
Portions of ¶ 80
Portions of ¶ 83
Portions of
¶¶ 104-109
• Portions of
¶¶ 127-128
• Portions of ¶ 152
• Portions of
¶¶ 159-160
• Portions of
¶¶ 165-167
• Portions of ¶ 171
• Portions of
¶¶ 184-187
Illumina
Portions of p. 6:20

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Illumina

N/A

DENIED – The clerk shall
UNSEAL Dkt. No. 387-10.
(Illumina does not request this
document to be sealed. Dkt. No.
395.)

GRANTED
(Discusses Illumina’s
confidential, non-public
information related to its thirdparty licensing agreements, tradesecrets, and proprietary
information, which if made public
could cause harm to Illumina.
Dkt. No. 395.)

GRANTED
(Proposed redacted language
concerns the home address of a
third-party witness. Dkt. No.
395.)

CONCLUSION
For the reasons explained above, Illumina’s motion to strike portions of the Puglisi Report
is GRANTED in part and DENIED in part. Illumina’s motion for summary judgment is
GRANTED.
IT IS SO ORDERED.
Dated: September 9, 2021

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William H. Orrick
United States District Judge

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