1 2 3 4 5 UNITED STATES DISTRICT COURT 6 NORTHERN DISTRICT OF CALIFORNIA 7 SAN JOSE DIVISION 8 9 IN RE CHROMACODE LITIGATION Case No. 23-cv-04823-EKL (VKD)

10 ORDER GRANTING IN PART AND 11 DENYING IN PART CHROMACODE’S MOTION FOR LEAVE TO AMEND 12 INFRINGEMENT CONTENTIONS 13 Re: Dkt. No. 128

14 15 Plaintiffs California Institute of Technology and ChromaCode, Inc. (collectively, 16 “ChromaCode”) move for leave to amend their infringement contentions for two patents asserted 17 against defendant Bio-Rad Laboratories, Inc. (“Bio-Rad”). Dkt. No. 128. Bio-Rad opposes the 18 motion. Dkt. No. 132. The Court held a hearing on this matter on September 16, 2025. Dkt. Nos. 19 147, 150 (transcript). 20 For the reasons explained below, the Court grants in part and denies in part ChromaCode’s 21 motion for leave to amend its infringement contentions. 22 I. BACKGROUND 23 In this consolidated action, ChromaCode asserts that Bio-Rad infringes

10,068,051 (“the ’051 patent”), U.S. Patent No 10,770,170 (“the ’170 patent”), and U.S. Patent 25 No. 11,827,921 (“the ’921 patent”). See Dkt. No. 111 at 3. 26 On March 21, 2024, ChromaCode served its Patent Local Rule 3-1 infringement 27 contentions for all three asserted patents. Dkt. No. 128 at 4. On September 16, 2024, Bio-Rad 1 ChromaCode’s contentions for the ’921 patent in this action.

Meanwhile, the parties briefed 2 questions of claim construction in this action, and the presiding judge issued a claim construction 3 order on July 22, 2025. See Dkt. No. 125. That order found the asserted claims of the ’051 patent 4 indefinite and construed disputed claim terms for the other two patents.

5 On May 30, 2025, ChromaCode asked Bio-Rad to stipulate to proposed amendments to 6 ChromaCode’s infringement contentions. Dkt. No. 128 at 9. Over the next few weeks, the parties 7 conferred and ChromaCode provided additional information.

On June 27, 2025, Bio-Rad 8 responded that it opposed the proposed amendments.

9 ChromaCode filed this motion for leave to amend its infringement contentions on July 29, 10 2025. 11 II. LEGAL STANDARD 12 A party may amend its infringement contentions “only by order of the Court upon a timely 13 showing of good cause,” such as the “[r]ecent discovery of nonpublic information about the 14 Accused Instrumentality.” Patent L.R. 3-6. In assessing whether good cause exists, the Court first 15 considers whether the moving party was diligent in seeking to amend its contentions, and then 16 whether the non-moving party would suffer prejudice if the amendment were permitted. Apple 17 Inc. v. Samsung Elecs. Co., No. 12-cv-00630 LHK,

, at *2 (N.D. Cal. Nov. 15, 18 2012) (citation omitted). 19 Whether a party has been diligent encompasses two considerations: (1) diligence in 20 discovering the basis for amendment, and (2) diligence in seeking amendment once the basis for 21 amendment has been discovered. Monolithic Power Sys., Inc. v. Silergy Corp., No. 14-cv-01745- 22 VC (KAW),

, at *2 (N.D. Cal. Sept. 15, 2015) (citing Positive Techs., Inc. v. 23 Sony Elecs., Inc., No. 11-cv-2226 SI,

, at *2 (N.D. Cal. Jan. 28, 2013)). The 24 party seeking leave to amend carries the burden of establishing diligence.

(citing Radware Ltd. 25 v. F5 Networks, Inc., No. 13-cv-02021-RMW,

, at *1 (N.D. Cal. July 28, 26 2014)). “Diligence is a fact intensive inquiry, and courts do not apply a mechanical rule in 27 assessing a party's diligence but instead consider the factual circumstances in total.” Word to Info 1 “If the court determines that the moving party was not diligent, the inquiry may end there.” 2 Twilio, Inc. v. TeleSign Corp., No. 16-cv-06925-LHK (SVK),

, at *2 (N.D. Cal. 3 Aug. 18, 2017) (citation omitted). “However, the court retains discretion to grant leave to amend 4 in the absence of diligence where there is no prejudice to the opposing party.”

(citations 5 omitted); see also Karl Storz Endoscopy-Am., Inc. v. Stryker Corp., No. 14-cv-00876-RS (JSC), 6

, at *7 (N.D. Cal. May 13, 2016) (collecting cases). 7 III. DISCUSSION 8 ChromaCode’s proposed amendments concern its infringement contentions for the ’170 9 patent and the ’921 patent. See Dkt. No. 150 at 3:7-9, 22:12-16, 37:3-5. The amendments fall into 10 four categories that ChromaCode describes as follows: (1) “single sample volume”; (2) coding 11 tables; (3) accused assays; and (4) insertion of Bates numbers. Dkt. No. 128 at 1-2. ChromaCode 12 characterizes its proposed amendments as either narrowing or clarifying its existing contentions. 13

Bio-Rad does not object to the fourth category of proposed amendments—insertion of Bates 14 numbers—but it characterizes the other amendments as adding new theories of infringement and 15 new accused products. Dkt. No. 132 at 1, 6 n.6. Bio-Rad objects to these proposed amendments, 16 citing both diligence and prejudice concerns.

. 17 As there is no dispute regarding ChromaCode’s proposal to amend its infringement 18 contentions to substitute citations to Bates numbered documents for existing citations to 19 documents at their URL addresses, see Dkt. No. 132 at 6 n.6, the Court grants this portion of 20 ChromaCode’s motion as unopposed. The Court addresses the proposed amendments that are 21 disputed below. 22 A. Single sample volume 23 “Single sample volume” is a claim term that appears in the asserted claims of the ’921 24 patent. ChromaCode, Inc. et al. v. Bio-Rad Laboratories, Inc., No. 23-cv-06360-EKL, Dkt. No. 25 54-3 at 48. In its original infringement contentions for limitation 1(c) of claim 1 of the ’921 26 patent, ChromaCode asserted, in relevant part: 27 For all of Bio-Rad’s infringing ddPCR assays and kits, the detection partitioned into multiple droplets. 1

2 [Image] 3 See Dkt. No. 127-3 at ECF 377; see also

at ECF 374-382. Further, with respect to limitation 4 1(e) of the same claim, ChromaCode asserted: 5 The analytes are amplified in the single sample volume. For 6 example, the single sample is partitioned into individual droplets:

7 [Image]

8 . . . Following droplet generation, the sample is amplified in a 9 thermal cycler:

at ECF 384-385. 10 ChromaCode proposes to amend its “single sample volume” contentions by deleting the 11 clause “the detection is performed in a single sample volume that is subsequently partitioned into 12 multiple droplets” and replacing it with the clause “[t]he analytes are amplified in the single 13 sample volume, such as in a droplet or well.” Dkt. No. 128 at 7. ChromaCode’s redline shows the 14 pertinent changes to its contentions for limitation 1(c) of claim 1 of the ’921 patent as follows: 15 16 For all of Bio-Rad’s infringing ddPCR assays and kits, the detection is performed in a single sample volume that is subsequently 17 partitioned into multiple droplets.

18 The analytes are amplified in the single sample volume, such as in a droplet or a well: 19 . . . 20 Following droplet generation, the sample is amplified in a thermal 21 cycler: . . . 22

23 Following amplification, each droplet is analyzed individually for color detection. 24 Dkt. No. 127-6 at ECF 581-582; see also

at ECF 577-606. Similarly, ChromaCode’s redline 25 shows the pertinent changes to its contentions for limitation 1(e) of the same claim as follows: 26 27 The analytes are amplified in the single sample volume. For example, the single sample is partitioned into individual droplets, . . . 1

2 Following droplet generation, the sample is amplified in a thermal cycler: 3 . . .

4 Following amplification, each droplet is analyzed individually for color detection. 5

at ECF 609-610. 6 ChromaCode describes these proposed amendments as narrowing its contentions regarding 7 the “single sample volume” limitation. Dkt. No. 128 at 4, 7. According to ChromaCode, its 8 original contentions asserted that a single sample volume could be either: (1) a droplet, or (2) the 9 solution before being partitioned into droplets.

. It explains that the proposed 10 amendments rely exclusively on the “single droplet theory” and eliminate the “alternative theory 11 based on a single sample volume being the original sample that is subsequently partitioned into 12 droplets.” Dkt. No. 128 at 4, 10-11. 13 Bio-Rad characterizes the proposed amendments differently. According to Bio-Rad, after 14 originally contending that the “single sample volume” could be a volume of liquid that is 15 subsequently partitioned into droplets, ChromaCode now seeks to amend its contentions to specify 16 that the “single sample volume” is limited to liquid volumes that have already been partitioned 17 into droplets. Dkt. No. 132 at 4. Bio-Rad argues that the proposed amendments represent a 18 fundamental change in ChromaCode’s infringement theory based on a new claim construction that 19 was never briefed by the parties or resolved by the district court.1

; see also Dkt. No. 20 150 at 50:9-51:6. 21 Infringement contentions are not merely a vehicle for the disclosure of evidence; they force 22 patentees to crystallize their theories of infringement and adhere to those theories after they have 23 been disclosed. Alberta Telecomms. Rsch. Ctr. v. Rambus Inc., No. 06-cv-02595 RMW (RS), 24

, at *1 (N.D. Cal. Nov. 19, 2007) (“Patent Local Rule 3-1 requires parties to 25 crystallize their theories of the case early in the litigation and to adhere to those theories once they 26 have been disclosed.”) (internal quotations and revisions omitted). However, nothing in the Patent 27 1 Local Rules requires a patentee to continue to press a theory of infringement that it has concluded 2 is not supported by the evidence. 3 During the hearing on this motion, the Court and the parties addressed at length the nature 4 of ChromaCode’s proposed amendments. Both sides appear to agree that ChromaCode’s original 5 contentions do encompass both the single droplet theory and the alternative pre-partition theory of 6 infringement for the single sample volume limitation. See Dkt. No. 128 at 1, 4, 7; Dkt. No. 132 at 7 3 (Bio-Rad summarizing PTAB characterization of the parties’ interpretation of the scope of 8 “sample volume”); Dkt. No. 150 at 10:17-11:24, 14:18-15:7. Despite some ambiguity in its 9 moving papers regarding the basis for amendment, ChromaCode clarified during the hearing that it 10 lacks evidentiary support for its contention that Bio-Rad meets the single sample volume 11 limitation under the alternative pre-partition theory, and so ChromaCode no longer wishes to 12 pursue that theory of infringement. Dkt. No. 150 at 12:16-13:5, 14:14-15:23. Moreover, 13 ChromaCode conceded that the claim language can be interpreted to encompass both of its 14 original theories of infringement, and it affirmed that it is not advocating a narrower claim 15 construction—i.e. one that is limited to the single droplet theory. See

, 19:23- 16 20:19, 21:24-22:8, 56:14-21. In these circumstances, the Court agrees that ChromaCode’s 17 proposed amendments are correctly understood as eliminating one of two disclosed theories of 18 infringement, without implying any change to the broader claim construction on which 19 ChromaCode relied when it served its original contentions. 20 Diligence. ChromaCode does not address the question of diligence in its opening motion, 21 except to emphasize that it is not adding any new contentions but merely eliminating one of two 22 previously disclosed contentions. While it remains unclear to the Court when ChromaCode 23 determined its alternative pre-partition theory of infringement lacked evidentiary support, and 24 whether it should have amended its contentions at an earlier date, the Court is not persuaded that 25 delay in making this kind of amendment—eliminating a previously disclosed theory of 26 infringement without changing the underlying claim construction—presents the same concerns as 27 a failure to disclose a contention in the first instance. Indeed, parties typically stipulate to such 1 diligent in discovering the basis for the amendments and seeking to make the amendments, the 2 || proposed narrowing amendments are permissible, absent prejudice to Bio-Rad. 3 Prejudice. Bio-Rad’s principal objection to the proposed amendments is that ChromaCode 4 || is not merely narrowing its infringement theories but also changing the underlying claim 5 || construction, and this change prejudices Bio-Rad’s ability to sustain arguments it has already 6 || made in a pending IPR before the PTAB based on ChromaCode’s original infringement 7 contentions. Dkt. No. 132 at 8-9. In addition, Bio-Rad argues that because ChromaCode waited 8 || until after claim construction in this action had been briefed and argued before disclosing its 9 || proposed amendments, Bio-Rad did not have an opportunity to take the proposed amendments 10 || into account in deciding whether to seek construction of the claim term “single sample volume.” 11

. However, as ChromaCode concedes that it does not advocate a narrower claim 12 || construction, but only a narrower infringement theory, the proposed amendments will not have 13 any impact on claim construction in this action, nor should they have any impact on proceedings 14 || before the PTAB. 3 15 Accordingly, the Court concludes that ChromaCode may amend its infringement 16 || contentions to eliminate its alternative pre-partition theory of infringement for the single sample 3 17 || volume limitation of claim 1 the ’921 patent, while retaining the previously-disclosed single 18 droplet theory of infringement. 19 B. Coding tables 20 ChromaCode proposes to amend its infringement contentions for the °170 patent and the 21 °921 patent by deleting the original “exemplary coding tables,” which use integers to represent 22 || different thresholds (e.g., image at left below), and replacing them with different coding tables, 23 which use decimals to represent different thresholds (e.g., image at right below):

25 Ni 1 0 N2? 1 O01 *° MHV oO 1 MHV 0 1 27 Dkt. No. 128 at 8, 11; compare original contentions at Dkt. No. 127-3 at ECF 368 with proposed

1 amended contentions at Dkt. No. 127-6 at ECF 538. ChromaCode explains that the coding tables 2 are meant to be a descriptive of the chromatogram cluster plots generated using data from Bio- 3 Rad’s accused assays. Dkt. No. 128 at 2, 5. Although ChromaCode’s original contentions state 4 the accused assays meet the claim limitations of the asserted patents that require a “non- 5 degenerate” coding scheme capable of yielding a definitive result, see, e.g., Dkt. No. 127-3 at ECF 6 3952, ChromaCode acknowledges that the coding tables accompanying those contentions reflect a 7 degenerate coding scheme, not a non-degenerate coding scheme.3 Dkt. No. 128 at 5-6 & n.4. 8 According to ChromaCode, the purpose of the proposed amendments is to “correct the exemplary 9 coding tables to be non-degenerate and [to] more directly map to non-degenerate chromatogram 10 cluster plots, removing any inadvertent suggestion that Plaintiffs construed the accused kits or 11 assays to be degenerate . . . .”

; see also

; Dkt. No. 150 at 26:19-27:12, 29:2-12. 12 Again, Bio-Rad characterizes ChromaCode’s proposed amendments differently. 13 According to Bio-Rad, the proposed amendments introduce new coding schemes that “raise 14 entirely new issues relating to the acceptable tolerances of signals that are considered non- 15 degenerate.” Dkt. No. 132 at 12. Bio-Rad emphasizes that it relied on ChromaCode’s original 16 contentions, including its integer-based coding tables, since those contentions were served in 17 March 2024 to develop its non-infringement and invalidity arguments in this action and its 18 invalidity arguments in the co-pending IPR proceeding.

; see also Dkt. No. 150 at 19 61:23-64:8, 65:4-66:9. In addition, Bio-Rad argues that because ChromaCode waited until after 20 claim construction in this action had been briefed and argued before disclosing its proposed 21 amendments, Bio-Rad did not have an opportunity to take the proposed amendments into account 22 in developing its claim construction positions. Dkt. No. 132 at 12. 23 The Court agrees with Bio-Rad that ChromaCode’s proposed amendments, swapping out 24 integer-based coding tables and replacing them with decimal-based coding tables, are more than 25 an immaterial clarification or correction of its original contentions. ChromaCode argues that the 26 2 The same text appears, for example, in the proposed amendments at Dkt. No. 127-6 at ECF 650. 27 1 chromatogram cluster plots included in its original contentions and retained in the proposed 2 amended contentions show that the accused assays “are clearly non-degenerate.” Dkt. No. 138 at 3 10. But that validity of that assertion is not-self-evident, and it is contested by ChromaCode. 4 While the proposed amended contentions retain some of the same text and material as the original 5 contentions, the coding table changes reflect changes in ChromaCode’s view of how it believes the 6 accused Bio-Rad assays infringed the asserted claims of the ’170 patent and the ’921 patent. 7 Diligence. ChromaCode does not address the question of diligence in its opening motion, 8 except to emphasize that it is not adding any new contentions but merely “clarifying” its existing 9 contentions. See Dkt. No. 128 at 11; Dkt. No. 138 at 8-9. When pressed to address the question 10 of diligence in more detail at the hearing, ChromaCode eventually explained that it discovered the 11 “error” while reviewing its contentions in connection with the proposed amendments regarding the 12 “single sample volume” limitations. Dkt. No. 150 at 30:2-21. This explanation is not persuasive. 13 Because the proposed amendments to the coding tables represent a material change in 14 ChromaCode’s contentions about how it believes the Bio-Rad accused assays infringe, 15 ChromaCode’s failure to show, let alone address, the question of diligence in its motion papers is 16 fatal here. On the record presented, the Court concludes that, at a minimum, ChromaCode was not 17 diligent in discovering the basis for the proposed amendments. 18 Prejudice. Because the Court concludes that ChromaCode has not acted diligently with 19 respect to amending its contentions regarding the coding scheme, it need not reach the question of 20 whether Bio-Rad would suffer prejudice if the amendments were permitted. O2 Micro Int’l Ltd. v. 21 Monolithic Power Sys., Inc.,

, 1368 (Fed. Cir. 2006); Synopsys, Inc. v. ATopTech, 22 Inc., No. 13-cv-02965-MMC (DMR),

, at *4-5 (N.D. Cal. Nov. 9, 2016). 23 Nevertheless, the Court agrees with Bio-Rad that if the amendments were permitted, Bio-Rad 24 would be prejudiced in its ability to timely develop claim construction, non-infringement, and 25 invalidity positions responsive to ChromaCode’s changed infringement theory regarding how the 26 accused assays satisfy the claim limitations requiring a non-degenerate coding scheme. 27 Accordingly, the Court denies ChromaCode’s motion for leave to amend its infringement 1 proposed new coding tables. 2 C. Accused assays 3 ChromaCode proposes to amend its infringement contentions for the ’170 patent and the 4 ’921 patent to add three new accused instrumentalities: (1) Bio-Rad assay 3542 (“3542 assay”), 5 and (2) two assays performed by non-party Verily Life Sciences (“Verily assays”). Dkt. No. 128 6 at 2. ChromaCode explains that it learned of these three additional assays during discovery after 7 serving its original infringement contentions.

. ChromaCode emphasizes that it 8 relies on the same infringement theories for these three new assays as it does for the assays 9 identified in its original infringement contentions.

. Bio-Rad opposes the proposed 10 amendments principally on the ground that ChromaCode was not diligent in discovering the bases 11 for the amendments or seeking leave to amend.4 Dkt. No. 132 at 5, 14. 12 Diligence. In its opening motion, ChromaCode does not explain when or how it 13 discovered the 3542 assay, or otherwise address the question of diligence. However, in its reply, 14 ChromaCode claims that it discovered the 3542 assay after taking discovery of a non-party in 15 March of 2025. Dkt. No. 138 at 12-13. It argues that it would have learned of this assay sooner 16 had Bio-Rad not failed to disclose it in response to an interrogatory.

. The Court will not 17 consider ChromaCode’s belated arguments regarding diligence made for the first time in its reply. 18 See, e.g., United States v. Romm,

(9th Cir. 2006) (declining to consider an 19 argument first raised on reply because “arguments not raised by a party in its opening brief are 20 deemed waived”); Turtle Island Restoration Network v. U.S. Dep't of Com.,

, 1166 21 n.8 (9th Cir. 2012). However, because it appears that the 3542 assay is either part of or essentially 22 identical to an assay or kit that ChromaCode included in its original contentions, the Court 23 concludes that the proposed amendment adding the 3542 assay is permissible, absent prejudice to 24 Bio-Rad. 25 4 During the hearing, Bio-Rad argued that the Verily assays are distinct from other accused assays 26 because they are the only assays that are alleged to infringe the asserted method claims of the ’170 patent that require a minimum number of targets. Dkt. No. 150 at 70:17-71:9. Bio-Rad did not 27 make this argument in its opposition brief, and the Court will not consider it here. In any event, 1 With respect to the Verily assays, ChromaCode concedes that it learned of the Verily 2 assays in September 2024 and January 2025 when it received detailed documentation about 3 them—i.e. 4-8 months before it asked Bio-Rad to stipulate to the amendments, and 6-10 months 4 before it sought leave to amend. Dkt. No. 128 at 12; Dkt. No. 138 at 14 & n.4; see also Dkt. No. 5 127-7 (Verily production document). ChromaCode does not dispute that its proposed amendments 6 rely on this same documentation it has had since September 2024. See Dkt. No. 132 at 13; Dkt. 7 No. 138 at 14 & n.4. To the extent ChromaCode believed deposition testimony from non-party 8 Verily was necessary to developing its proposed amendments, the record does not reflect that it 9 was diligent in obtaining (or asking the Court to compel) such testimony. As to the Verily assays, 10 the Court concludes that ChromaCode was not diligent in seeking amendment once the basis for 11 amendment has been discovered. 12 Prejudice. With respect to the 3542 assay, Bio-Rad relies solely on a conclusory argument 13 that if the amendment is permitted it will not have an opportunity to consider this new assay in 14 developing its claim construction arguments. Dkt. No. 132 at 14-15. However, Bio-Rad does not 15 explain how the addition of a new assay that is not materially different from any of the other 16 accused Bio-Rad assays implicates any claim construction issues. Indeed, during the hearing, Bio- 17 Rad acknowledged it did not develop its argument regarding prejudice for this assay. Dkt. No. 18 150 at 69:7-12. The Court finds that Bio-Rad would not suffer prejudice if ChromaCode were 19 permitted to amend its contentions to add the 3542 assay. 20 With respect to the Verly assays, because the Court concludes that ChromaCode has not 21 acted diligently in seeking amendment with respect to the Verily assays, it need not reach the 22 question of whether Bio-Rad would suffer prejudice if the amendments were permitted. O2 23 Micro, 467 F.3d at 1368; Synopsys,

, at *4-5. However, the Court notes that 24 Bio-Rad also did not identify any concrete prejudice with respect to the Verily assays in its 25 opposition. 26 Accordingly, the Court grants ChromaCode’s motion for leave to amend its infringement 27 contentions to add the 3542 assay and denies its motion to add the Verily assays. IV. CONCLUSION In sum, the Court orders as follows with respect to the four categories of proposed 2 amendments at issue: 3 1. Single sample volume: ChromaCode’s motion is granted, as set forth above; 4 ChromaCode may amend its infringement contentions to eliminate its alternative pre- 5 partition theory of infringement for the single sample volume limitation of claim 1 the 6 °921 patent, while retaining the previously-disclosed single droplet theory of 4 infringement. 8 2. Coding tables: ChromaCode’s motion is denied. 9 3. Accused assays: ChromaCode’s motion is granted with respect to the 3542 assay, but 10 denied with respect to the Verily assays. 11 4. Insertion of Bates numbers: ChromaCode’s motion is granted. 12 ChromaCode shall serve its amended infringement contentions, in accordance with this 13 order, no later than October 23, 2025, unless the parties agree to a different date. 14 IT IS SO ORDERED. 15 Dated: October 9, 2025 16

= 17 . 28

Z 18 Virginia K. DeMarchi 19 United States Magistrate Judge 20 21 22 23 24 25 26 27 28