What changed in this filing

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Item 1. Financial Statements

2025-11-06 compared with 2025-08-07 · 101 added, 94 removed, 687 unchanged (22% of the section changed)

2 unchanged sentences

CONDENSED CONSOLIDATED BALANCE SHEETS

(In thousands, except par value) June 30,

(In thousands, except par value) September 30,

2025 December 31,

35 unchanged sentences

Authorized 1,000,000 shares;

issued and outstanding 300,350 and 294,418 shares at June 30, 2025 and December 31, 2024, respectively

issued and outstanding 301,853 and 294,418 shares at September 30, 2025 and December 31, 2024, respectively

Additional paid-in capital 2,690,304 2,654,804

7 unchanged sentences

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands, except per share amounts) 2025 2024 2025 2024

23 unchanged sentences

( 37,617 ) ( 60,725 ) ( 505,889 ) ( 312,222 )

Income tax provision (benefit)

35 — ( 267 ) —

Income tax provision

Net loss ( 38,000 ) ( 60,725 ) ( 506,005 ) ( 312,222 )

Other comprehensive income:

Unrealized loss on investments

Unrealized gain (loss) on investments

148 2,076 ( 7 ) 1,334

10 unchanged sentences

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY

Three Months Ended June 30, 2025

Three Months Ended September 30, 2025

Common Stock Additional

5 unchanged sentences

Shares Amount

Balance at March 31, 2025 300,041 $ 300 $ 2,665,958 $ 381 $ ( 2,575,001 ) $ 91,638

Balance at June 30, 2025 300,350 $ 300 $ 2,677,853 $ 267 $ ( 2,616,931 ) $ 61,489

Net loss — — — — ( 38,000 ) ( 38,000 )

Other comprehensive loss — — — ( 114 ) — ( 114 )

Other comprehensive income

— — — 148 — 148

Issuance of common stock in conjunction with equity plans 1,503 2 1,467 — — 1,469

Share-based compensation expense — — 10,984 — — 10,984

Balance at June 30, 2025 300,350 $ 300 $ 2,677,853 $ 267 $ ( 2,616,931 ) $ 61,489

Six Months Ended June 30, 2025

Balance at September 30, 2025 301,853 $ 302 $ 2,690,304 $ 415 $ ( 2,654,931 ) $ 36,090

Nine Months Ended September 30, 2025

Common Stock Additional

11 unchanged sentences

Share-based compensation expense — — 32,080 — — 32,080

Balance at June 30, 2025 300,350 $ 300 $ 2,677,853 $ 267 $ ( 2,616,931 ) $ 61,489

Three Months Ended June 30, 2024

Balance at September 30, 2025 301,853 $ 302 $ 2,690,304 $ 415 $ ( 2,654,931 ) $ 36,090

Three Months Ended September 30, 2024

Common Stock Additional

1 unchanged sentence

Comprehensive

(Loss) Income

Deficit Total

2 unchanged sentences

Shares Amount

Balance at March 31, 2024 272,280 $ 272 $ 2,566,304 $ ( 306 ) $ ( 1,917,253 ) $ 649,017

Balance at June 30, 2024 272,491 $ 272 $ 2,583,523 $ ( 523 ) $ ( 2,090,572 ) $ 492,700

Net loss — — — — ( 60,725 ) ( 60,725 )

Other comprehensive loss — — — ( 217 ) — ( 217 )

Other comprehensive income

— — — 2,076 — 2,076

Issuance of common stock in conjunction with equity plans 1,321 2 810 — — 812

Share-based compensation expense — — 18,259 — — 18,259

Balance at June 30, 2024 272,491 $ 272 $ 2,583,523 $ ( 523 ) $ ( 2,090,572 ) $ 492,700

Six Months Ended June 30, 2024

Balance at September 30, 2024 273,812 $ 274 $ 2,602,592 $ 1,553 $ ( 2,151,297 ) $ 453,122

Nine Months Ended September 30, 2024

Common Stock Additional

Capital Accumulated

Comprehensive Income (Loss)

Comprehensive Income

Deficit Total

3 unchanged sentences

Net loss — — — — ( 312,222 ) ( 312,222 )

Other comprehensive loss — — — ( 742 ) — ( 742 )

Other comprehensive income

— — — 1,334 — 1,334

Issuance of common stock in conjunction with equity plans 6,068 6 7,697 — — 7,703

Share-based compensation expense — — 55,003 — — 55,003

Balance at June 30, 2024 272,491 $ 272 $ 2,583,523 $ ( 523 ) $ ( 2,090,572 ) $ 492,700

Balance at September 30, 2024 273,812 $ 274 $ 2,602,592 $ 1,553 $ ( 2,151,297 ) $ 453,122

See accompanying notes to the condensed consolidated financial statements.

2 unchanged sentences

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

Six Months Ended June 30,

Nine Months Ended September 30,

(In thousands) 2025 2024

26 unchanged sentences

Purchases of investments ( 183,817 ) ( 418,164 )

Sales of investments — 8,061

Maturities of investments 280,089 480,440

4 unchanged sentences

Net cash provided by financing activities 3,428 7,213

Net decrease in cash, cash equivalents, and restricted cash ( 957 ) ( 80,843 )

Net increase (decrease) in cash, cash equivalents, and restricted cash

707 ( 102,429 )

Cash, cash equivalents, and restricted cash at beginning of period 57,592 182,633

24 unchanged sentences

All intercompany transactions and balances have been eliminated.

The financial statements should be read in conjunction with the audited consolidated financial statements and notes included in our Annual Report on Form 10-K for the year ended December 31, 2024 ("2024 Annual Report").

Use of Estimates

2 unchanged sentences

On an ongoing basis, we evaluate our significant estimates, including those relating to the valuation of inventory, fair value of contingent consideration, valuation of acquired intangible assets, useful lives assigned to finite-lived assets, asset impairment assessments, computation of provisions for income taxes, and valuations related to our convertible senior notes.

While the extent of the potential impact of current macroeconomic conditions on our business is highly uncertain, we considered information available related to assumptions and estimates used to determine the results reported and asset valuations as of June 30, 2025.

Actual results could differ materially from these estimates.

21 unchanged sentences

This new standard requires a company to expand its existing income tax disclosures, specifically related to the rate reconciliation and income taxes paid.

The standard is effective for annual periods beginning in 2025.

The new standard is expected to be applied prospectively, but retrospective application is permitted.

We are currently evaluating the impact of ASU 2023-09 on the consolidated financial statements and related disclosures.

The standard is effective for annual periods beginning in 2025 and is expected to be applied retrospectively.

We expect that the adoption of this new standard will result in incremental income tax related disclosures to the notes to the consolidated financial statements but will not have a material impact on the consolidated financial statements.

In November 2024, the FASB issued ASU 2024-04, Debt—Debt With Conversion and Other Options (Subtopic 470-20):

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The new standard is expected to be applied prospectively, but retrospective application is permitted.

We are currently evaluating the impact of ASU 2024-04 on the consolidated financial statements and related disclosures.

We do not expect the adoption of this new standard to have a material impact on the consolidated financial statements and related disclosures.

In November 2024, the FASB issued ASU 2024-03, Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40):

4 unchanged sentences

We are currently evaluating the impact of ASU 2024-03 on the consolidated financial statements and related disclosures.

In September 2025, the FASB issued ASU 2025-06, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40):

Targeted Improvements to the Accounting for Internal-Use Software.

This new standard clarifies and modernizes the recognition and disclosure framework for capitalized internal-use software costs by removing all references to project stages and introduces a more judgment-based approach.

The standard also clarifies the threshold to be applied to begin capitalizing.

The standard will be effective for us beginning in the first quarter of 2028, with early adoption permitted, and can be applied using a prospective, retrospective, or modified transition approach.

We are currently evaluating the impact of ASU 2025-06 on the consolidated financial statements and related disclosures.

Q3 Fiscal 2025 Form 10-Q

Significant Accounting Policies

There have been no changes to our significant accounting policies as disclosed in our 2024 Annual Report.

Q2 Fiscal 2025 Form 10-Q

FINANCIAL INSTRUMENTS

19 unchanged sentences

The following table sets forth the fair value of our financial assets and liabilities that were measured on a recurring basis:

June 30, 2025 December 31, 2024

September 30, 2025 December 31, 2024

(In thousands)

9 unchanged sentences

Total liabilities measured at fair value $ — $ — $ — $ — $ — $ — $ 18,700 $ 18,700

During the six months ended June 30, 2025, there were no transfers between Level 1, Level 2, or Level 3 assets or liabilities reported at fair value on a recurring basis, and our valuation techniques did not change compared to the prior year.

During the nine months ended September 30, 2025, there were no transfers between Level 1, Level 2, or Level 3 assets or liabilities reported at fair value on a recurring basis, and our valuation techniques did not change compared to the prior year.

Contingent Consideration

9 unchanged sentences

The key input used in the determination of the fair value included projected revenues of the high-throughput short-read products and services leveraging Apton's technology.

Primarily due to management's decision to cease development of the high-throughput short-read system, and the resulting changes in the expected future revenues, among other factors, and as the milestone event must occur prior to the five-year anniversary of the closing date of the acquisition, the estimated fair value of the contingent consideration liability was $ 0 .

An increase in the fair value of the liability may result from an acceleration in the timing of or increase in projected revenues and from a

1 unchanged sentence

decrease in discount rates, including the risk-free rate and estimated subordinated credit spread for a CCC credit rating.

Changes in the estimated fair value of the contingent consideration liability during the six months ended June 30, 2025 were as follows:

Changes in the estimated fair value of the contingent consideration liability during the nine months ended September 30, 2025 were as follows:

(In thousands)

1 unchanged sentence

Change in estimated fair value ( 18,700 )

Ending balance as of June 30, 2025 $ —

Ending balance as of September 30, 2025 $ —

Changes to the fair value are recorded as change in fair value of contingent consideration in the condensed consolidated statements of operations and comprehensive loss.

1 unchanged sentence

The following tables summarize our cash, cash equivalents, restricted cash, and investments:

As of June 30, 2025

As of September 30, 2025

(In thousands)

16 unchanged sentences

Q3 Fiscal 2025 Form 10-Q

The following table summarizes the contractual maturities of our cash equivalents and available-for-sale investments, excluding money market funds, as of June 30, 2025:

The following table summarizes the contractual maturities of our cash equivalents and available-for-sale investments, excluding money market funds, as of September 30, 2025:

(In thousands)

3 unchanged sentences

Actual maturities may differ from contractual maturities because issuers may have the right to call or prepay obligations without call or prepayment penalties.

Investment income included in other income, net on the condensed consolidated statements of operations and comprehensive loss was $ 3.4 million and $ 7.3 million for the three and six months ended June 30, 2025, respectively, and $ 6.5 million and $ 13.8 million for the three and six months ended June 30, 2024, respectively.

Investment income included in other income, net on the condensed consolidated statements of operations and comprehensive loss was $ 3.1 million and $ 10.4 million for the three and nine months ended September 30, 2025, respectively, and $ 6.0 million and $ 19.8 million for the three and nine months ended September 30, 2024, respectively.

BALANCE SHEET COMPONENTS

2 unchanged sentences

(In thousands)

September 30,

2025 December 31,

21 unchanged sentences

The decline in the fair value of the IPR&D below its carrying amount as of March 31, 2025 resulted primarily from changes in the timing of expected future cash flows as compared to the fair value as of December 31, 2024, driven by the restructuring initiatives that prioritize the adoption of HiFi sequencing.

The impairment charge is included in our consolidated statements of operations and comprehensive loss for the six months ended June 30, 2025.

The impairment charge is included in our consolidated statements of operations and comprehensive loss for the nine months ended September 30, 2025.

Significant estimates and assumptions used in the income approach include timing of future cash flows, revenue growth assumptions, a selected discount rate of 14.0 %, and a selected obsolescence factor of 11 years.

3 unchanged sentences

A decrease of 200 basis points to the discount rate used in our analysis would have resulted in an increase in the estimated fair value of the IPR&D of approximately $ 3 million, and an increase of one year to the obsolescence factor used in our analysis would have resulted in an increase in the estimated fair value of the IPR&D of approximately $ 3 million.

Changes to IPR&D during the six months ended June 30, 2025 were as follows:

Changes to IPR&D during the nine months ended September 30, 2025 were as follows:

(In thousands)

1 unchanged sentence

Impairment charge ( 15,000 )

Balance as of June 30, 2025

Balance as of September 30, 2025

Restructuring for additional information on costs incurred in connection with our current year restructuring activities.

In addition to IPR&D, we had the following acquired finite-lived intangible assets:

As of June 30, 2025 As of December 31, 2024

As of September 30, 2025 As of December 31, 2024

(In thousands, except years)

8 unchanged sentences

Total $ 421,539 $ ( 405,396 ) $ 16,143 $ 411,539 $ ( 36,967 ) $ 374,572

Q3 Fiscal 2025 Form 10-Q

The estimated future amortization expense of intangible assets with finite lives is as follows:

3 unchanged sentences

Total $ 16,143

Q2 Fiscal 2025 Form 10-Q

Amortization of acquired intangible assets is included within our cost of revenue if the costs and expenses related to the intangible assets are attributable to revenue generating activities.

6 unchanged sentences

As a result of the change in estimate, during the three months ended March 31, 2025, we recognized accelerated amortization of $ 359.3 million within amortization of acquired intangible assets in operating expenses, reflecting our revised estimate that the asset will no longer generate economic benefit beyond March 31, 2025.

This expense had a negative impact on basic and diluted net loss per share of $ 1.20 for the six months ended June 30, 2025.

This expense had a negative impact on basic and diluted net loss per share of $ 1.20 for the nine months ended September 30, 2025.

We review finite-lived intangible assets for impairment when indication of potential impairment exists, such as a significant reduction in cash flows associated with the assets.

3 unchanged sentences

Both the acquired technology and license are classified as intangible assets and are being amortized over an estimated useful life of three years .

As of June 30, 2025, $ 5.0 million of these intangible assets remained unpaid.

As of September 30, 2025, $ 5.0 million of these intangible assets remained unpaid.

This amount is included in accrued liabilities on the condensed consolidated balance sheets and is expected to be paid in 2026.

1 unchanged sentence

Deferred Revenue

As of June 30, 2025, we had a total of $ 20.6 million of deferred revenue, $ 14.9 million of which was recorded as deferred revenue, current, and $ 5.7 million of which was recorded as deferred revenue, non-current, which primarily relates to deferred service contract revenues and is scheduled to be recognized in the next four years .

Revenue recorded in the three and six months ended June 30, 2025 includes $ 4.8 million and $ 9.4 million, respectively, that was included in deferred revenue as of December 31, 2024.

As of September 30, 2025, we had a total of $ 20.4 million of deferred revenue, $ 16.0 million of which was recorded as deferred revenue, current, and $ 4.4 million of which was recorded as deferred revenue, non-current, which primarily relates to deferred service contract revenues and is scheduled to be recognized in the next four years .

Revenue recorded in the three and nine months ended September 30, 2025 includes $ 2.4 million and $ 10.5 million, respectively, that was included in deferred revenue as of December 31, 2024.

Q3 Fiscal 2025 Form 10-Q

Performance Obligations

4 unchanged sentences

Most performance obligations are generally satisfied within a year of the contract execution date.

As of June 30, 2025, the aggregate amount of the transaction price allocated to remaining performance obligations was $ 56.6 million, of which approximately 72 % is expected to be converted to revenue over the next twelve months , approximately 22 % in the following twelve months , and the remainder thereafter.

Q2 Fiscal 2025 Form 10-Q

As of September 30, 2025, the aggregate amount of the transaction price allocated to remaining performance obligations was $ 48.7 million, of which approximately 72 % is expected to be converted to revenue over the next twelve months , approximately 23 % in the following twelve months , and the remainder thereafter.

Product Warranties

6 unchanged sentences

Changes in the reserve for product warranties were as follows for the periods indicated:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands)

15 unchanged sentences

The 2029 Notes will mature on August 15, 2029, subject to earlier conversion, redemption or repurchase.

Q3 Fiscal 2025 Form 10-Q

The 2029 Notes are convertible at the option of the holder at any time from the expiration of the Lock-Up Period until the second scheduled trading day prior to the maturity date, including in connection with a redemption by the Company.

1 unchanged sentence

Upon conversion of the 2029 Notes, we may elect to settle such conversion obligation in cash, shares of our common stock, or a combination of cash and shares of our common stock.

Q2 Fiscal 2025 Form 10-Q

on, and including, the trading day immediately preceding the date on which we provide the redemption notice at a redemption price of 100 % of the principal amount of such 2029 Notes, plus accrued and unpaid interest up to, but excluding, the redemption date.

On or after August 20, 2027, and prior to the 31st scheduled trading day immediately preceding the maturity date, the 2029 Notes will be redeemable by the Company in the event that the closing sale price of our common stock has been at least 150 % of the conversion price then in effect for at least 20 trading days (whether or not consecutive) during any 30 consecutive trading day period (including the last trading day of such period) ending on, and including, the trading day immediately preceding the date on which we provide the redemption notice at a redemption price of 100 % of the principal amount of such 2029 Notes, plus accrued and unpaid interest up to, but excluding, the redemption date.

Upon the occurrence of a Fundamental Change (as defined in the 2029 Indenture), the holders of the 2029 Notes may require that we repurchase all or part of the principal amount of the 2029 Notes at a purchase price of par plus unpaid interest up to, but excluding, the maturity date.

13 unchanged sentences

However, due to the nature and terms of the reporting obligations, the value of the embedded derivative is immaterial.

Q3 Fiscal 2025 Form 10-Q

The exchange qualified as a troubled debt restructuring under ASC 470-60 – Troubled Debt Restructurings by Debtors .

3 unchanged sentences

The gain was calculated as the difference between the carrying amount of the old debt and the carrying amount of the new debt, adjusted for debt issuance costs.

We incurred issuance costs related to the 2029 Notes of approximately $ 3.1 million, including $ 0.2 million of lender fees, which were recorded as a reduction to the gain on debt restructuring in our consolidated

Q2 Fiscal 2025 Form 10-Q

statements of operations and comprehensive loss.

We also paid accrued but unpaid interest of $ 1.8 million on the 2028 Notes in connection with the 2024 Exchange Transaction.

2 unchanged sentences

Following the closing of the 2024 Exchange Transaction, no amounts were outstanding on the 2028 Notes.

The carrying amount of the liability for the 2029 Notes as of June 30, 2025 is $ 213.5 million, of which $ 210.5 million is included as convertible senior notes, net, non-current, and $ 3.0 million is included as accrued expenses on our consolidated balance sheets.

Changes to the 2029 Notes during the six months ended June 30, 2025 were as follows:

The carrying amount of the liability for the 2029 Notes as of September 30, 2025 is $ 212.0 million, of which $ 209.0 million is included as convertible senior notes, net, non-current, and $ 3.0 million is included as accrued expenses on our consolidated balance sheets.

Changes to the 2029 Notes during the nine months ended September 30, 2025 were as follows:

(In thousands)

1 unchanged sentence

Contractual interest expense ( 2,200 )

Carrying amount as of June 30, 2025

As of June 30, 2025, the estimated fair value (Level 2) of the 2029 Notes was $ 161.9 million.

Carrying amount as of September 30, 2025

As of September 30, 2025, the estimated fair value (Level 2) of the 2029 Notes was $ 169.4 million.

The fair value of the 2029 Notes is estimated using a binomial lattice model that is primarily affected by the trading price of our common stock, market interest rates and volatility.

10 unchanged sentences

Upon conversion of the 2030 Notes, we may elect to settle such conversion obligation in cash, shares of our common stock, or a combination of cash and shares of our common stock.

On or after June 20, 2028, and prior to the 31st scheduled trading day immediately preceding the maturity date, the 2030 Notes will be redeemable by the Company in the event that the closing sale price of our common stock has been at least 150 % of the conversion price then in effect for at least 20 trading days (whether or not consecutive) during any 30 consecutive trading day period (including the last trading day of such period) ending on, and including, the trading day immediately preceding the date on which we provide the redemption notice at a redemption price of 100 % of the principal amount of such 2030 Notes, plus accrued and unpaid interest up to, but excluding, the redemption date.

Upon the occurrence of a Fundamental Change (as defined in the 2030 Indenture), the holders of the 2030 Notes may require that we repurchase all or part of the principal amount of the 2030 Notes at a purchase price equal to 100 % of the principal amount of the notes to be repurchased, plus any accrued and unpaid interest up to, but excluding, the fundamental change repurchase date, and all unpaid interest from the fundamental change repurchase date thereon, but excluding, the maturity date.

Q3 Fiscal 2025 Form 10-Q

consecutive) during any 30 consecutive trading day period (including the last trading day of such period) ending on, and including, the trading day immediately preceding the date on which we provide the redemption notice at a redemption price of 100 % of the principal amount of such 2030 Notes, plus accrued and unpaid interest up to, but excluding, the redemption date.

The 2030 Indenture includes customary “events of default,” which may result in the acceleration of the maturity of the 2030 Notes under the 2030 Indenture.

18 unchanged sentences

In exchange for issuing the 2030 Notes pursuant to the 2023 Exchange Transaction, we received and cancelled the exchanged 2028 Notes.

Following the closing of the 2023 Exchange Transaction, $ 459.0 million in aggregate principal amount of 2028 Notes remained outstanding with terms unchanged.

Q3 Fiscal 2025 Form 10-Q

Following the closing of the 2023 Exchange Transaction, $ 459.0 million in aggregate principal amount of 2028 Notes remained outstanding with terms unchanged.

The net carrying amount of the liability for the 2030 Notes is included as convertible senior notes, net, non-current in the condensed consolidated balance sheets as follows:

(In thousands)

September 30,

2025 December 31,

4 unchanged sentences

Interest expense for the 2030 Notes was as follows:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands)

3 unchanged sentences

Total interest expense $ 1,757 $ 1,753 $ 5,268 $ 5,277

As of June 30, 2025, the estimated fair value (Level 2) of the 2030 Notes was $ 291.3 million.

As of September 30, 2025, the estimated fair value (Level 2) of the 2030 Notes was $ 314.5 million.

The fair value of the 2030 Notes is estimated using a binomial lattice model that is primarily affected by the trading price of our common stock, market interest rates and volatility.

9 unchanged sentences

Interest expense for the 2028 Notes was as follows:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(in thousands) 2025 2024 2025 2024

9 unchanged sentences

(In thousands)

Three Months Ended June 30, 2025 Cumulative amount incurred to date

Three Months Ended September 30, 2025 Cumulative amount incurred to date

Employee separation costs

$ 138 $ 4,787

Other costs 66 629

Total restructuring charges (1)

$ 701 $ 5,350

(1) Cumulative charges incurred to date include $ 3.3 million in sales, general and administrative expense and $ 2.1 million in research and development expense.

13 unchanged sentences

Amount recorded in current liabilities

as of June 30, 2025

$ 324 $ 563 $ 887

as of September 30, 2025 $ — $ 101 $ 101

Estimated total restructuring costs to still be incurred $ — $ — $ —

4 unchanged sentences

(In thousands)

Three Months Ended June 30, 2025 Cumulative amount incurred to date

Three Months Ended September 30, 2025 Cumulative amount incurred to date

Employee separation costs $ — $ 10,008

1 unchanged sentence

Total restructuring charges (1)

$ ( 87 ) $ 26,110

(1) Cumulative charges incurred to date include $ 15.8 million in sales, general and administrative expense;

13 unchanged sentences

Cash payments ( 1,058 ) ( 1,058 )

Amount recorded in current liabilities as of June 30, 2025

Amount recorded in current liabilities as of September 30, 2025

Estimated total restructuring costs to still be incurred $ — $ —

The table above excludes noncash activities and amounts incurred relating to the San Diego office lease liability.

The ending balance of the San Diego office lease liability as of June 30, 2025 is $ 0 .

The ending balance of the San Diego office lease liability was $ 0 at the end of the second quarter of 2025.

Q3 Fiscal 2025 Form 10-Q

16 unchanged sentences

To the extent that any such indemnification obligations apply to the lawsuits described above, any associated expenses incurred are included within the related accrued litigation expense amounts.

No additional liability associated with such indemnification obligations has been recorded as of June 30, 2025 and December 31, 2024.

No additional liability associated with such indemnification obligations has been recorded as of September 30, 2025 and December 31, 2024.

EQUITY PLANS AND SHARE-BASED COMPENSATION

As of June 30, 2025, the Company had share-based compensation awards outstanding under the 2020 Equity Incentive Plan (the “2020 Plan”), the 2020 Inducement Equity Incentive Plan (the “Inducement Plan”), the 2021 adopted Omniome Equity Incentive Plan of Pacific Biosciences of California, Inc.

As of September 30, 2025, the Company had share-based compensation awards outstanding under the 2020 Equity Incentive Plan (the “2020 Plan”), the 2020 Inducement Equity Incentive Plan (the “Inducement Plan”), the 2021 adopted Omniome Equity Incentive Plan of Pacific Biosciences of California, Inc.

(the “Omniome Plan”) and the 2010 Employee Stock Purchase Plan, from which we issued equity awards and employee stock.

On June 4, 2025, our stockholders approved an amendment to the 2020 Plan to reserve an additional 23 million shares of our common stock for issuance pursuant to equity awards granted under the 2020 Plan.

As of June 30, 2025, we had 13.5 million shares remaining and available for future issuance under the 2020 Plan, Inducement Plan, and the Omniome Plan.

As of September 30, 2025, we had 37.8 million shares remaining and available for future issuance under the 2020 Plan, Inducement Plan, and the Omniome Plan.

Shares remaining and available for future issuance reflect shares that may become eligible to vest upon the achievement of maximum targets for certain equity awards.

10 unchanged sentences

Expired ( 376 ) 6.44

Outstanding at June 30, 2025 16,549 $ 6.57

Outstanding at September 30, 2025 15,922 $ 6.57

Restricted Stock Units ("RSU") and Performance Stock Units ("PSU")

We issue RSUs for which the respective shares vest when the requisite service period is achieved.

We issue PSUs for which the number of shares issuable is based on performance relative to specified revenue targets and continued employment through the vesting period.

We grant RSUs for which the respective shares vest when the requisite service period is achieved.

We granted PSUs during the first quarter of 2023 for which the number of shares issuable is based on performance relative to specified revenue targets and continued employment through the vesting period.

The PSUs are issuable following the third year of the performance period.

7 unchanged sentences

Forfeited ( 3,652 ) — 4.08 —

Outstanding at June 30, 2025 18,907 392 $ 3.67 $ 9.43

Outstanding at September 30, 2025 18,123 392 $ 3.55 $ 9.43

Employee Stock Purchase Plan ("ESPP")

Shares issued under our ESPP wer e 1,752,417 and 1,194,436 durin g the six months ended June 30, 2025 and 2024, respectively.

Shares issued under our ESPP wer e 3,102,930 and 1,906,529 durin g the nine months ended September 30, 2025 and 2024, respectively.

In the first quarter of 2025, an additional 4.0 million shares were reserved under the ESPP.

As of June 30, 2025, 16.5 million shares of our common stock remain avai lable for issuance under our ESPP.

As of September 30, 2025, 15.2 million shares of our common stock remain avai lable for issuance under our ESPP.

Share-based Compensation

The following table summarizes share-based compensation expense:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands)

18 unchanged sentences

The fair value of employee stock options was estimated using the following assumptions:

Six Months Ended June 30,

Nine Months Ended September 30,

Expected term in years 4.9 4.9

5 unchanged sentences

The fair value of shares to be issued under the ESPP was estimated using the following assumptions:

Six Months Ended June 30,

Nine Months Ended September 30,

Expected term in years 0.5 — 2.0

9 unchanged sentences

The following table presents the calculation of the basic and diluted net loss per share amounts presented in the condensed consolidated statements of operations and comprehensive loss:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands, except per share amounts) 2025 2024 2025 2024

7 unchanged sentences

The following shares issuable upon conversion of the Notes and outstanding equity awards were excluded from the computation of diluted net loss per share for the periods presented because the effect of including such shares would have been antidilutive:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands) 2025 2024 2025 2024

Shares issuable upon conversion of convertible senior notes 61,415 31,063 61,415 31,063

Shares issuable upon conversion of

convertible senior notes 61,415 31,063 61,415 31,063

Equity awards 42,599 36,496 42,599 36,496

13 unchanged sentences

A summary of the segment profit or loss, including significant segment expenses is as follows:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands) 2025 2024 2025 2024

9 unchanged sentences

1,260 3,352 6,775 9,063

Income tax provision (benefit)

35 — ( 267 ) —

Income tax provision

Consolidated net loss ( 38,000 ) ( 60,725 ) ( 506,005 ) ( 312,222 )

A summary of our revenue by geographic location is as follows:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands) 2025 2024 2025 2024

4 unchanged sentences

A summary of our revenue by category is as follows:

Three Months Ended June 30, Six Months Ended June 30,

Three Months Ended September 30, Nine Months Ended September 30,

(In thousands) 2025 2024 2025 2024

6 unchanged sentences

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements