[10-Q] VERACYTE, INC. Quarterly Earnings Report

Rhea-AI Filing Summary

Veracyte, Inc. reported stronger Q3 2025 results, with total revenue of $131.9 million, up from $115.9 million a year ago. Testing revenue rose to $127.8 million, while product revenue was $3.3 million and biopharmaceutical and other revenue was $0.8 million. Gross profit increased to $91.3 million. Net income was $19.1 million versus $15.2 million last year, and diluted EPS was $0.24 versus $0.19.

Operating expenses were $68.3 million. Other income (loss), net was a loss of $4.1 million, reflecting a $6.7 million loss on deconsolidation of the French subsidiary in August 2025. For the nine months, operating cash flow was $83.7 million, up from $50.6 million. The balance sheet showed cash and cash equivalents of $315.6 million, short‑term investments of $50.9 million, and stockholders’ equity of $1.26 billion as of September 30, 2025. Medicare and UnitedHealthcare represented 33% and 14% of Q3 revenue, respectively. Shares outstanding were 79,049,173 as of October 31, 2025.

Insights

Equity analyst – diagnostics

Q3 showed double‑digit revenue growth and solid profitability.

Veracyte delivered Q3 revenue of $131.9M with higher testing revenue and gross profit of $91.3M. Operating expenses were stable relative to growth, supporting net income of $19.1M and diluted EPS of $0.24.

Below the line, other income turned negative due to a $6.7M loss on deconsolidation of the French subsidiary, partially offset by interest income. The nine‑month operating cash flow of $83.7M and cash and cash equivalents of $315.6M bolster liquidity.

Revenue concentration remained with Medicare at 33% and UnitedHealthcare at 14% in Q3. The enacted OBBBA tax changes benefited the effective tax rate in 2025. Subsequent filings may provide more detail on post‑deconsolidation cost structure.

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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q

(Mark One)

☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

 

For the quarterly period ended September 30, 2025

OR 

☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from             to            

Commission File Number 001-36156

VERACYTE, INC.

(Exact name of registrant as specified in its charter)

Delaware

20-5455398

(State or other jurisdiction of

(I.R.S. Employer

incorporation or organization)

Identification No.)

6000 Shoreline Court, Suite 300

South San Francisco, California 94080

(Address of principal executive offices, zip code)

(650)  243-6300

(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class

Trading Symbol(s)

Name of each exchange on which registered

Common Stock, par value, $0.001 per share

VCYT

The Nasdaq Stock Market LLC

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x No ¨

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes x No ¨

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Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of "large accelerated filer," "accelerated filer," "smaller reporting company," and "emerging growth company" in Rule 12b-2 of the Exchange Act.

Large accelerated filer

x

Accelerated filer

¨

Non-accelerated filer

¨

Smaller reporting company

☐

Emerging growth company

☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ¨

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐

No x

As of October 31, 2025, there were 79,049,173 shares of common stock, par value $0.001 per share, outstanding.

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VERACYTE, INC.

INDEX

						Page No.
PART I. — FINANCIAL INFORMATION
Item 1. Condensed Consolidated Financial Statements (Unaudited)						1
Condensed Consolidated Balance Sheets as of September 30, 2025 and December 31, 2024						1
Condensed Consolidated Statements of Operations for the Three and Nine Month Periods Ended September 30, 2025 and 2024						2
Condensed Consolidated Statements of Comprehensive Income (Loss) for the Three and Nine Month Periods Ended September 30, 2025 and 2024						3
Condensed Consolidated Statements of Stockholders' Equity for the Three and Nine Month Periods Ended September 30, 2025 and 2024						4
Condensed Consolidated Statements of Cash Flows for the Nine Month Periods Ended September 30, 2025 and 2024						6
Notes to Condensed Consolidated Financial Statements						7
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations						22
Item 3. Quantitative and Qualitative Disclosures About Market Risk						34
Item 4. Controls and Procedures						35
PART II. — OTHER INFORMATION
Item 1. Legal Proceedings						36
Item 1A. Risk Factors						36
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds						36
Item 3. Defaults Upon Senior Securities						36
Item 4. Mine Safety Disclosures						36
Item 5. Other Information						36
Item 6. Exhibits						37
SIGNATURES						38

i

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VERACYTE, INC.

SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS

This Quarterly Report on Form 10-Q, or this report, contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. All statements contained in this report other than statements of historical fact, including statements concerning our business strategy and plans, future operating results and financial position, as well as our objectives and expectations for our future operations, are forward-looking statements.

In some cases, you can identify forward-looking statements by such terminology as “believe,” “may,” “will,” “potentially,” “expect,” “estimate,” “continue,” “ongoing,” “anticipate,” “intend,” “could,” “would,” “project,” “plan,” “expect” and similar expressions that convey uncertainty of future events or outcomes, although not all forward-looking statements contain these words. These are statements that relate to future events and include, but are not limited to, statements about:

•the factors that may impact our financial results;

•our expectations regarding total revenue and total test volume;

•our expectations with respect to our future research and development, general and administrative and selling and marketing expenses and our anticipated uses of our funds;

•the impact of inflation, volatile interest rates and foreign exchange fluctuations, as well as regional conflicts globally, including the war in Ukraine, the ongoing conflict in the Middle East, any impacts of the policies and legislation enacted by the current administration, energy, trade and supply chain disruptions, and market volatility resulting from the above on our business;

•the effects of evolving international trade policies and government actions relating to tariffs;

•our beliefs with respect to importance of maintaining libraries of clinical evidence;

•our expectations regarding the Percepta Nasal Swab classifier for early lung cancer classification and the Prosigna breast cancer assay;

•our expectations regarding the addition of minimal residual detection capabilities to our diagnostics platform;

•our expectations regarding the timing and success of our transition to offering more of our tests as in vitro diagnostic tests on multiple platforms worldwide;

•our ability to continue to receive quality reagents and other raw materials from certain single source suppliers, including our in vitro diagnostics, or IVD, products;

•our ability to successfully integrate C2i Genomics, Inc., or C2i, and Decipher Biosciences into our business and our ability to develop and launch tests, and enter into supply agreements, with manufacturers of alternative systems;

•our expectations regarding our partnerships and agreements;

•our expectations regarding capital expenditures, our anticipated cash needs and our estimates regarding our capital requirements and profitability;

•our business strategy and our ability to execute on our strategy;

•our ability to obtain and maintain Medicare, other government payer, and other commercial third-party payer reimbursement at acceptable levels and our expectations regarding the timing of reimbursement;

•our expectations with regard to the estimated number of patients eligible for our tests and the attributes and potential benefits of our tests and any future tests we may develop to patients, physicians, and payers;

•our expectations on our ability to drive demand for and reimbursement of our tests;

•our sales, marketing and distribution capabilities and strategy;

•our intellectual property position;

•the impact of government laws and regulations, policies, guidance agency interpretations and judicial decisions; and

•our beliefs in our competitive position.

We caution you that the foregoing list does not contain all of the forward-looking statements made in this report. We have based these forward-looking statements largely on our current expectations and projections about future events and trends that we believe may affect our business, financial condition, results of operations, prospects, and financial needs. These forward-looking statements speak only as of the date of this report and are subject to a number of risks, uncertainties and assumptions described in the section titled “Risk Factors” in Part II, Item 1A and elsewhere in this report and in the section titled “Risk Factors” in Part I, Item 1A of our Annual Report on Form 10-K for the year ended December 31, 2024. Because forward-looking statements are inherently subject to risks and uncertainties, some of which cannot be predicted or quantified, you should not rely on these forward-looking statements as predictions of future events. The events and circumstances reflected in our forward-looking statements may not be achieved or occur and actual results could differ materially from those projected in

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the forward-looking statements. We disclaim any intention or obligation to publicly update or revise any forward-looking statements for any reason or to conform such statements to actual results or revised expectations, except as required by law.

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PART I. — FINANCIAL INFORMATION

Item 1. Condensed Consolidated Financial Statements-(Unaudited)

VERACYTE, INC. 

Condensed Consolidated Balance Sheets 

(unaudited)

(In thousands, except share and par value amounts)

			September 30, 2025						December 31, 2024
Assets
Current assets:
Cash and cash equivalents			$	315,573					$	239,087
Short-term investments			50,855						50,354
Accounts receivable			47,826						46,525
Supplies and inventory			20,327						21,750
Prepaid expenses and other current assets			14,643						14,551
Total current assets			449,224						372,267
Property, plant and equipment, net			18,900						22,953
Right-of-use assets, operating leases			37,301						48,189
Intangible assets, net			92,477						102,301
Goodwill			767,154						745,800
Restricted cash			1,637						1,544
Other assets			1,094						6,981
Total assets			$	1,367,787					$	1,300,035
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable			$	5,509					$	8,634
Accrued liabilities			48,373						43,826
Current portion of deferred revenue			417						1,673
Current portion of acquisition-related contingent consideration			13,571						16,981
Current portion of operating lease liabilities			4,282						7,500
Current portion of other liabilities			—						19
Total current liabilities			72,152						78,633
Deferred tax liabilities			1,214						1,227
Acquisition-related contingent consideration, net of current portion			583						561
Operating lease liabilities, net of current portion			36,171						43,237
Other liabilities			—						411
Total liabilities			110,120						124,069
Commitments and contingencies
Stockholders’ equity:
Preferred stock, $0.001 par value; 5,000,000 shares authorized, no shares issued and outstanding as of September 30, 2025 and December 31, 2024			—						—
Common stock, $0.001 par value; 125,000,000 shares authorized, 79,034,078 and 77,772,678 shares issued and outstanding as of September 30, 2025 and December 31, 2024, respectively			79						78
Additional paid-in capital			1,684,587						1,655,961
Accumulated deficit			(418,779)						(443,983)
Accumulated other comprehensive loss			(8,220)						(36,090)
Total stockholders’ equity			1,257,667						1,175,966
Total liabilities and stockholders’ equity			$	1,367,787					$	1,300,035

 

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERACYTE, INC.

 Condensed Consolidated Statements of Operations

 (Unaudited)

 (In thousands, except share and per share amounts)

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Revenue:
Testing revenue			$	127,756					$	109,536					$	357,328					$	306,809
Product revenue			3,301						3,188						10,479						10,631
Biopharmaceutical and other revenue			815						3,136						8,702						9,692
Total revenue			131,872						115,860						376,509						327,132
Cost of revenue:
Cost of testing revenue			33,777						29,029						94,444						82,928
Cost of product revenue			3,015						1,792						6,186						6,310
Cost of biopharmaceutical and other revenue			1,091						3,112						7,361						9,762
Intangible asset amortization - cost of revenue			2,707						2,917						7,959						8,741
Total cost of revenue			40,590						36,850						115,950						107,741
Gross profit			91,282						79,010						260,559						219,391
Operating expenses:
Research and development			15,981						17,574						49,965						50,004
Selling and marketing			24,455						22,612						74,225						70,610
General and administrative			27,278						25,742						93,417						83,697
Impairment of assets			—						185						20,505						614
Intangible asset amortization - operating expenses			622						880						1,865						2,499
Total operating expenses			68,336						66,993						239,977						207,424
Income from operations			22,946						12,017						20,582						11,967
Other income (loss), net			(4,057)						4,831						6,985						10,334
Income before income taxes			18,889						16,848						27,567						22,301
Income tax (benefit) provision			(248)						1,693						2,363						3,276
Net income			$	19,137					$	15,155					$	25,204					$	19,025
Earnings per share:
Basic			$	0.24					$	0.20					$	0.32					$	0.25
Diluted			$	0.24					$	0.19					$	0.32					$	0.25
Shares used to compute earnings per common share:
Basic			78,725,139						77,013,831						78,384,184						76,107,302
Diluted			79,691,703						78,464,654						79,946,386						77,339,897

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERACYTE, INC.

 Condensed Consolidated Statements of Comprehensive Income (Loss)

 (Unaudited)

 (In thousands)

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Net income			$	19,137					$	15,155					$	25,204					$	19,025
Other comprehensive income (loss):
Change in currency translation adjustments			(4,556)						9,328						19,575						2,736
Release of accumulated translation adjustment			8,295						—						8,295						—
Other comprehensive income			3,739						9,328						27,870						2,736
Net comprehensive income			$	22,876					$	24,483					$	53,074					$	21,761

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERACYTE, INC.

Condensed Consolidated Statements of Stockholders' Equity

(Unaudited)

(In thousands)

			Common Stock												Additional Paid-in Capital						Accumulated Deficit						Accumulated Other Comprehensive Loss						Total Stockholders' Equity
			Shares						Amount
Balance at June 30, 2025			78,599						$	79					$	1,670,853					$	(437,916)					$	(11,959)					$	1,221,057
Issuance of common stock on exercise of stock options and vesting of restricted stock units			363						—						4,386						—						—						4,386
Issuance of common stock under employee stock purchase plan (ESPP)			72						—						1,405						—						—						1,405
Tax portion of vested restricted stock units			—						—						(2,814)						—						—						(2,814)
Stock-based compensation expense (employee)			—						—						10,398						—						—						10,398
Stock-based compensation expense (ESPP)			—						—						359						—						—						359
Net income			—						—						—						19,137						—						19,137
Currency translation adjustments			—						—						—						—						(4,556)						(4,556)
Release of accumulated translation adjustment			—						—						—						—						8,295						8,295
Balance at September 30, 2025			79,034						$	79					$	1,684,587					$	(418,779)					$	(8,220)					$	1,257,667
Balance at December 31, 2024			77,773						$	78					$	1,655,961					$	(443,983)					$	(36,090)					$	1,175,966
Issuance of common stock upon exercise of stock options and vesting of restricted stock units			1,105						1						7,519						—						—						7,520
Issuance of common stock under ESPP			156						—						3,052						—						—						3,052
Tax portion of vested restricted stock units			—						—						(14,645)						—						—						(14,645)
Stock-based compensation expense (employee)			—						—						31,866						—						—						31,866
Stock-based compensation expense (ESPP)			—						—						834						—						—						834
Net income			—						—						—						25,204						—						25,204
Currency translation adjustments			—						—						—						—						19,575						19,575
Release of accumulated translation adjustment			—						—						—						—						8,295						8,295
Balance at September 30, 2025			79,034						$	79					$	1,684,587					$	(418,779)					$	(8,220)					$	1,257,667

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			Common Stock												Additional Paid-in Capital						Accumulated Deficit						Accumulated Other Comprehensive Loss						Total Stockholders' Equity
			Shares						Amount
Balance at June 30, 2024			76,744						$	77					$	1,627,307					$	(464,251)					$	(30,610)					$	1,132,523
Issuance of common stock on exercise of stock options and vesting of restricted stock units			689						—						11,281						—						—						11,281
Issuance of common stock under ESPP			58						—						1,190						—						—						1,190
Tax portion of vested restricted stock units			—						—						(2,182)						—						—						(2,182)
Stock-based compensation expense (employee)			—						—						8,335						—						—						8,335
Stock-based compensation expense (ESPP)			—						—						412						—						—						412
Net income			—						—						—						15,155						—						15,155
Currency translation adjustments			—						—						—						—						9,328						9,328
Balance at September 30, 2024			77,491						$	77					$	1,646,343					$	(449,096)					$	(21,282)					$	1,176,042
Balance at December 31, 2023			73,265						$	73					$	1,536,168					$	(468,121)					$	(24,018)					$	1,044,102
Issuance of common stock and options for acquisition			2,698						3						74,142						—						—						74,145
Issuance of common stock upon exercise of stock options and vesting of restricted stock units			1,390						1						13,842						—						—						13,843
Issuance of common stock under ESPP			138						—						2,886						—						—						2,886
Tax portion of vested restricted stock units			—						—						(7,315)						—						—						(7,315)
Stock-based compensation expense (employee)			—						—						25,636						—						—						25,636
Stock-based compensation expense (ESPP)			—						—						984						—						—						984
Net income			—						—						—						19,025						—						19,025
Currency translation adjustments			—						—						—						—						2,736						2,736
Balance at September 30, 2024			77,491						$	77					$	1,646,343					$	(449,096)					$	(21,282)					$	1,176,042

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERACYTE, INC.  

Condensed Consolidated Statements of Cash Flows 

(Unaudited) 

(In thousands)

			Nine Months Ended September 30,
			2025						2024
Operating activities
Net income			$	25,204					$	19,025
Adjustments to reconcile net income to net cash provided by operating activities:
Depreciation and amortization			16,117						17,206
Loss on disposal of property, plant and equipment			15						131
Stock-based compensation			32,700						26,620
Deferred income taxes			(13)						10
Noncash lease expense			2,289						3,628
Revaluation of acquisition-related contingent consideration			(2,713)						1,242
Effect of foreign currency on operations			(3,845)						(785)
Amortization of discount on short-term investments			(2,619)						—
Impairment loss			20,505						614
Non-cash loss on deconsolidation of subsidiary			3,863						—
Changes in operating assets and liabilities:
Accounts receivable			(3,858)						(8,396)
Supplies and inventory			(2,642)						(4,175)
Prepaid expenses and other current assets			(6,416)						149
Other assets			331						(1,710)
Operating lease liabilities			(1,681)						(3,929)
Accounts payable			(547)						(2,950)
Accrued liabilities and deferred revenue			7,034						3,892
Net cash provided by operating activities			83,724						50,572
Investing activities
Acquisition of C2i, net of cash acquired			—						5,012
Purchase of short-term investments			(99,998)						—
Proceeds from maturity of short-term investments			102,116						—
Purchases of property, plant and equipment			(5,897)						(7,146)
Net cash used in investing activities			(3,779)						(2,134)
Financing activities
Payment of taxes on vested restricted stock units			(14,645)						(7,315)
Proceeds from the exercise of common stock options and employee stock purchases			10,572						16,729
Net cash (used in) provided by financing activities			(4,073)						9,414
Increase in cash, cash equivalents and restricted cash			75,872						57,852
Effect of foreign currency on cash, cash equivalents and restricted cash			707						(23)
Net increase in cash, cash equivalents and restricted cash			76,579						57,829
Cash, cash equivalents and restricted cash at beginning of period			240,631						217,330
Cash, cash equivalents and restricted cash at end of period			$	317,210					$	275,159
Supplementary cash flow information:
Purchases of property, plant and equipment included in accounts payable and accrued liability			$	828					$	552
Cash paid for tax			$	2,388					$	1,205

Cash, Cash Equivalents and Restricted Cash:

			September 30, 2025						December 31, 2024
Cash and cash equivalents			$	315,573					$	239,087
Restricted cash			1,637						1,544
Total cash, cash equivalents and restricted cash			$	317,210					$	240,631

The accompanying notes are an integral part of these condensed consolidated financial statements.

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

1. Organization, Description of Business and Summary of Significant Accounting Policies

Veracyte, Inc., or Veracyte, or the Company, is a global diagnostics company that provides clinicians with tests for patients with, or potentially facing, a cancer diagnosis. Veracyte's tests are used by clinicians for diagnostic, prognostic and treatment decisions.

Veracyte was incorporated in the state of Delaware on August 15, 2006, as Calderome, Inc. Calderome, Inc. operated as an incubator until early 2008. On March 4, 2008, the Company changed its name to Veracyte, Inc. The Company’s headquarters are in South San Francisco, California, and it also has operations in San Diego, California, Austin, Texas, and Haifa, Israel.

The Company currently offers tests in prostate cancer (Decipher Prostate); thyroid cancer (Afirma); breast cancer (Prosigna); and bladder cancer (Decipher Bladder). In addition, the Company’s Percepta Nasal Swab test is being run in its Clinical Laboratory Improvement Amendments of 1988, or CLIA, certified lab in support of clinical studies.

The Company serves global markets with two complementary models. In the United States, it offers laboratory developed tests, or LDTs, through its centralized, CLIA certified laboratories in South San Francisco and San Diego, California, supported by its cytopathology expertise in Austin, Texas. Additionally, primarily outside of the United States, the Company provides its Prosigna test to patients through distribution to laboratories and hospitals that can perform the tests locally as an in vitro diagnostics, or IVD, test.

In February 2024, the Company acquired C2i Genomics, Inc., or C2i, a minimal residual disease, or MRD, detection company. Refer to Note 4, Business Combination, for additional information.

Basis of Presentation

The Company’s condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States, or GAAP. Certain information and note disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to such rules and regulations. The condensed consolidated balance sheet as of September 30, 2025, the condensed consolidated statements of operations for the three and nine months ended September 30, 2025 and 2024, the condensed consolidated statements of comprehensive income (loss) for the three and nine months ended September 30, 2025 and 2024, the condensed consolidated statements of stockholders' equity for the three and nine months ended September 30, 2025 and 2024, and the condensed consolidated statements of cash flows for the nine months ended September 30, 2025 and 2024 are unaudited, but include all adjustments, consisting only of normal recurring adjustments, which the Company considers necessary for a fair presentation of its financial position, operating results, stockholders' equity and cash flows for the periods presented. The condensed consolidated balance sheet as of December 31, 2024 has been derived from audited financial statements. The results for the three and nine months ended September 30, 2025 are not indicative of the results expected for the full year or any other period. The condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation. The Company operates in one segment.

Effective August 1, 2025, the Company ceased to have a controlling financial interest in its wholly-owned French subsidiary, Veracyte SAS. Accordingly, the Company derecognized the related assets and liabilities from its condensed consolidated financial statements. Prior to deconsolidation, the operating results and cash flows of Veracyte SAS were included in the Company’s condensed consolidated financial statements. Refer to Note 3, Balance Sheet Components, for additional information.

The accompanying interim period condensed consolidated financial statements and related financial information included in this Quarterly Report on Form 10-Q should be read in conjunction with the audited financial statements and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024.

Use of Estimates

The preparation of unaudited interim financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent liabilities as of

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

the date of the financial statements and the reported amounts of revenue and expenses during the reporting period. Significant items subject to such estimates include: revenue recognition; the useful lives of property, plant and equipment; the recoverability of long-lived assets; the incremental borrowing rates for leases; the estimation of the fair value of intangible assets and contingent consideration; stock-based compensation; income tax uncertainties, including a valuation allowance for deferred tax assets; credit related losses on investments; and allowance for credit losses and contingencies. The Company bases these estimates on historical and anticipated results, trends, and various other assumptions that the Company believes are reasonable under the circumstances, including assumptions as to future events. These estimates form the basis for making judgments about the carrying values of assets and liabilities and recorded revenue and expenses that are not readily apparent from other sources. Actual results could differ from those estimates and assumptions.

Concentrations of Credit Risk and Other Risks and Uncertainties

The majority of the Company’s cash and cash equivalents are deposited with three major financial institutions in the United States. Deposits in these institutions may exceed the amount of insurance provided on such deposits. The Company has not realized any losses on its deposits of cash and cash equivalents other than exchange rate losses related to foreign currency denominated accounts.

Several of the components of the Company’s sample collection kits and CLIA test reagents, IVD products and associated systems, as well as the systems service and service kits, are obtained from single-source suppliers. If these single-source suppliers fail to satisfy the Company’s requirements on a timely basis, or are unable to provide the Company with reagents that perform to specifications, the Company could suffer delays in being able to deliver its diagnostic solutions, suffer a possible loss of revenue, or incur higher costs, any of which could adversely affect its operating results.

Through September 30, 2025, the Company has derived most of its revenue from the sale of Decipher Prostate and Afirma testing. To date, Decipher Prostate and Afirma testing have been delivered primarily to physicians in the United States.

The Company is also subject to credit risk from its accounts receivable related to its sales. Credit risk for accounts receivable from testing revenue is incorporated in testing revenue accrual rates as the Company assesses historical collection rates and current developments to determine accrual rates and amounts the Company will ultimately collect. The Company generally does not perform evaluations of customers’ financial condition for testing revenue and generally does not require collateral. The Company assesses credit risk and the amount of accounts receivable the Company will ultimately collect for product, biopharmaceutical and other revenue based on collection history, current developments and credit worthiness of the customer. The estimate of credit losses is not material as of September 30, 2025.

The Company’s total third-party payers and other customers in excess of 10% of total revenue and their related revenue as a percentage of total revenue were as follows:

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Medicare			33		%				31		%				33		%				31		%
UnitedHealthcare			14		%				13		%				14		%				14		%
			47		%				44		%				47		%				45		%

The Company's significant third-party payers in excess of 10% of total accounts receivable and their related accounts receivable balance as a percentage of total accounts receivable were as follows:

			September 30, 2025						December 31, 2024
Medicare			22		%				16		%
UnitedHealthcare			12		%				12		%

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

Cash and Cash Equivalents

The Company considers demand deposits in a bank, money market funds and highly liquid investments with maturities at the time of purchase of three months or less to be cash equivalents.

Short-Term Investments

The Company's short-term investments consist of United States treasury securities and time deposits with a bank with maturities at the time of purchase that were between three months and one year. The Company classifies these investments as held-to-maturity debt securities, which are reported at amortized cost. Discounts or premiums from the purchase of the securities are recognized as a component of interest income in other income, net in the consolidated statements of operations. Investments are initially recorded net of an allowance for expected credit losses, if any, which are remeasured each period and any impairments are recognized as an expense. Unrealized gains and losses are not recognized in income. As of both September 30, 2025 and December 31, 2024, no allowances for expected credit losses had been recorded and there have been no impairment or credit losses on the Company's short-term investments.

Restricted Cash

The Company had deposits of $1.6 million and $1.5 million included in long-term assets as of September 30, 2025 and December 31, 2024, respectively, restricted from withdrawal and held by banks in the form of collateral for irrevocable standby letters of credit held as security for the Company's leases.

Revenue Recognition

The Company recognizes revenue in accordance with the provisions of the Financial Accounting Standards Board, or FASB, Accounting Standards Codification, or ASC, 606, Revenue from Contracts with Customers, or ASC 606. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue when the performance obligations have been satisfied. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer either on its own or together with other resources that are readily available to the customer and is separately identified in the contract. Performance obligations are considered satisfied once the Company has completed a service or transferred control of a product to the customer.

In arrangements involving more than one service or good, each required service or good is evaluated to determine whether it qualifies as a distinct performance obligation based on whether (i) the customer can benefit from the service or good either on its own or together with other resources that are readily available and (ii) the service or good is separately identifiable from other promises in the contract. The consideration under the arrangement is then allocated to each separate distinct performance obligation based on its respective relative stand-alone selling price. The estimated selling price of each deliverable reflects the Company's best estimate of what the selling price would be if the deliverable was regularly sold by the Company on a stand-alone basis or using an adjusted market assessment approach if selling price on a stand-alone basis is not available. The consideration allocated to each distinct performance obligation is recognized as revenue when control is transferred which may be at a point in time or over time.

Testing Revenue

The Company recognizes testing revenue from the sale of tests performed for customers, including patients and institutions, at the time test results are reported to physicians. Most tests requested by customers are sold without a written agreement; however, the Company determines that an implied contract exists with its customers for whom a physician will order the test. The Company identifies each sale of its test to a customer as a single performance obligation. A stated contract price does not exist and the transaction price for each implied contract with a customer represents variable consideration. The Company estimates the variable consideration under the portfolio approach and considers the historical reimbursement data from third-party commercial and governmental payers and patients, as well as known or anticipated reimbursement trends not reflected in the historical data. The Company monitors the estimated amount to be collected in the portfolio at each reporting period based on actual cash collections in order to assess whether a revision to the estimate is required. Both the estimate and any subsequent revision contain uncertainty and require the use of significant judgment in the estimation of the variable consideration and application of the constraint for such variable consideration. The Company analyzes its actual cash

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

collections over the expected reimbursement period and compares it with the estimated variable consideration for each payer group and any difference is recognized as an adjustment to estimated revenue after the expected reimbursement period, subject to assessment of the risk of future revenue reversal. For the three and nine months ended September 30, 2025, the Company recorded $1.5 million and $3.7 million as revenue, respectively, and for the three and nine months ended September 30, 2024, the Company recorded $3.1 million and $10.0 million, respectively, resulting from cash collections exceeding the estimated variable consideration related to tests reported in previous years, including revenue received from successful appeals of reimbursement denials, net of recoupments.

Product Revenue

The Company's product revenue primarily consists of the Prosigna IVD breast cancer assay, related diagnostic kits and services. Product revenue from diagnostic kits is generally recognized upon shipment from the contract manufacturer. Shipping and handling costs incurred for product shipments are included in product revenue. Revenue is presented net of the taxes that are collected from customers and remitted to governmental authorities.

Biopharmaceutical and Other Revenue

From time to time, the Company enters into arrangements to license or provide access to its assets or services, including clinical and testing services, research and development, as well as other services, which are classified under biopharmaceutical and other revenue. Such arrangements may require the Company to deliver various rights, data, test results, services and/or samples, including intellectual property rights/licenses and biopharmaceutical research and development services. The Company receives consideration in the form of upfront license fees; payments on delivery of data or test results; costs of service plus margin; and development and commercial performance milestone payments.

The Company develops estimates and assumptions that require judgment to determine the underlying stand-alone selling price for each performance obligation which determines how the transaction price is allocated among the performance obligations. The estimation of the stand-alone selling price may include independent evidence of market price, forecasted revenue or costs, development timelines, discount rates, and probabilities of technical and regulatory success. The Company evaluates each performance obligation to determine if the obligation can be satisfied at a point in time or over time, and it measures the services delivered to the collaborative partner which are periodically reviewed based on the progress of the related program. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time. The effect of any change made to an estimated input component and, therefore revenue or expense recognized, would be recorded as a change in estimate. In addition, variable consideration must be evaluated to determine if it is constrained and, therefore, excluded from the transaction price.

At the inception of each arrangement that includes milestone payments (variable consideration), the Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price. Milestone payments that are not within either party’s control, such as non-operational developmental and regulatory approvals, are generally not considered probable of being achieved until those approvals are received. At the end of each reporting period, the Company re-evaluates the probability of achievement of milestones that are within either party’s control, such as operational developmental milestones and any related constraint, and if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenue and earnings in the period of adjustment. Revisions to the Company’s estimate of the transaction price may also result in negative revenue and earnings in the period of adjustment. One collaboration arrangement with milestone payments falls under the scope of ASC Topic 808, Collaborative Arrangements, or ASC 808. These milestone payments are recognized in the same manner as milestone payments from customers and are classified under biopharmaceutical and other revenue.

Accounts receivable from biopharmaceutical and other revenue was $2.5 million at September 30, 2025 and $3.8 million at December 31, 2024. Deferred revenue related to these agreements was $0.4 million at September 30, 2025 and $1.7 million

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

at December 31, 2024. Revenue included in biopharmaceutical and other revenue for the three and nine months ended September 30, 2025 and 2024 was as follows (in thousands of dollars):

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Biopharmaceutical revenue			$	646					$	2,041					$	5,573					$	5,962
Contract manufacturing and testing			169						1,095						3,129						3,730
Total			$	815					$	3,136					$	8,702					$	9,692

Cost of Testing Revenue

The components of the Company's cost of testing revenue are laboratory expenses, sample collection expenses, compensation expense, license fees and royalties, depreciation, other expenses such as equipment and laboratory supplies, and allocations of facility and information technology expenses. Costs associated with performing tests are expensed as the test is processed regardless of whether and when revenue is recognized with respect to that test.

Cost of Product Revenue

Cost of product revenue consists primarily of costs of diagnostic kit components and reagents, labor, delivery costs and royalties for licensed technologies included in our products. Subsequent to the restructuring proceedings affecting Veracyte SAS in August 2025, these costs are paid to a third-party contract manufacturer. The cost of the finished product is recognized in the period the related revenue is recognized.

Cost of Biopharmaceutical and Other Revenue

Cost of biopharmaceutical and other revenue consists of costs of performing activities under arrangements that require the Company to license or provide access to its assets or laboratory testing services, as well as cost incurred in providing contracted research and development and manufacturing activities. These costs are mainly composed of compensation, manufacturing and laboratory supplies, and pass-through costs. Subsequent to the restructuring proceedings affecting Veracyte SAS beginning in August 2025 Veracyte SAS no longer performs biopharmaceutical services, contract manufacturing or contract development services.

Recent Accounting Pronouncements

In December 2023, the FASB issued Accounting Standards Update, or ASU, No. 2023-09, Improvements to Income Tax Disclosures (Topic 740). This update requires disaggregated information about a reporting entity’s effective tax rate reconciliation as well as additional information on income taxes paid. This ASU is effective on a prospective basis for annual periods beginning after December 15, 2024. Early adoption is also permitted for annual financial statements that have not yet been issued or made available for issuance. This ASU will result in the required additional disclosures being included in the Company's annual disclosures.

In November 2024, the FASB issued ASU 2024-03, Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses. ASU 2024-03 will require public business entities to disclose in the notes to the financial statements, at each interim and annual reporting period, specific information about certain costs and expenses, including purchases of inventory, employee compensation, depreciation, and intangible asset amortization included in each expense caption presented on the face of the income statement, and the total amount of an entity's selling expenses. ASU 2024-03 is effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027, and may be applied either prospectively or retrospectively. Early adoption is permitted. The Company is currently evaluating the impact of adopting this guidance on the consolidated financial statements.

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

2. Net Income (Loss) Per Common Share

Basic earnings (loss) per share, or EPS, is computed based on the weighted average number of common shares outstanding during the period. Diluted EPS is computed based on the sum of the weighted average number of common shares and potentially dilutive common shares outstanding during the period. In loss periods, basic and diluted loss per share are identical since the effect of potentially dilutive common shares is antidilutive and therefore excluded. Potentially dilutive common shares from equity awards are determined using the average share price for each period under the treasury stock method. In addition, proceeds from exercises of equity awards and the average amount of unrecognized compensation expense for equity awards are assumed to be used to repurchase shares. The following table sets forth the computation of basic and diluted EPS (in thousands, except per-share amounts):

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Numerator for basic and diluted EPS — net income (A)			$	19,137					$	15,155					$	25,204					$	19,025
Denominator for basic EPS — weighted average shares (B)			78,725						77,014						78,384						76,107
Effect of potentially dilutive common stock from:
Shares of common stock subject to outstanding options			333						511						438						503
Restricted stock units			595						907						1,081						696
Employee stock purchase plan			39						33						43						34
Dilutive potential common shares			967						1,451						1,562						1,233
Denominator for diluted EPS — adjusted weighted average shares and assumed conversions (C)			79,692						78,465						79,946						77,340
Basic EPS (A / B)			$	0.24					$	0.20					$	0.32					$	0.25
Diluted EPS (A / C)			$	0.24					$	0.19					$	0.32					$	0.25
Common stock equivalent shares excluded from the dilutive calculation due to antidilutive effect:
Shares of common stock subject to outstanding options			1,057						1,769						544						2,341
Restricted stock units			930						104						129						140
Anti-dilutive potential common shares			1,987						1,873						673						2,481

3. Balance Sheet Components

Goodwill

Goodwill was $767.2 million and $745.8 million as of September 30, 2025 and December 31, 2024, respectively. The changes in the carrying amounts of goodwill during the three and nine months ended September 30, 2025 were due to foreign currency translation. The Company has not recorded any impairment related to goodwill.

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Intangible Assets, Net

Intangible assets include finite-lived product technology, customer relationships, licenses and trade names and indefinite-lived in-process research and development. Intangible assets consisted of the following (in thousands of dollars):

			September 30, 2025																		December 31, 2024																		Weighted Average Remaining Amortization Period (Years)
			Gross Carrying Amount						Accumulated Amortization						Net Carrying Amount						Gross Carrying Amount						Accumulated Amortization						Net Carrying Amount
Percepta product technology			$	16,000					$	(11,200)					$	4,800					$	16,000					$	(10,400)					$	5,600					4.5
Prosigna product technology			4,120						(1,602)						2,518						4,120						(1,396)						2,724						9.2
Decipher product technology			97,300						(41,187)						56,113						90,000						(34,234)						55,766						6.6
Decipher trade names			4,000						(3,643)						357						4,000						(3,043)						957						0.5
C2i developed technology			25,300						(2,811)						22,489						25,300						(1,546)						23,754						13.3
Total finite-lived intangibles			146,720						(60,443)						86,277						139,420						(50,619)						88,801						8.3
In-process research and development			6,200						—						6,200						13,500						—						13,500
Total intangible assets			$	152,920					$	(60,443)					$	92,477					$	152,920					$	(50,619)					$	102,301

Acquisition-related intangibles are generally finite-lived and are carried at cost less accumulated amortization. Amortization of the finite-lived intangible assets is recognized on a straight-line basis over their estimated lives, which approximates the pattern in which the economic benefits of the intangible assets are expected to be realized.

Amortization expense of $3.3 million and $3.8 million was recognized for the three months ended September 30, 2025 and 2024, respectively, and an expense of $9.8 million and $11.2 million was recognized for the nine months ended September 30, 2025 and 2024, respectively.

The estimated future aggregate amortization expense as of September 30, 2025 is as follows (in thousands of dollars):

Year Ending December 31,			Amounts
2025 remainder of year			$	3,329
2026			12,672
2027			12,515
2028			12,515
2029			12,515
Thereafter			32,731
Total			$	86,277

 

Supplies and Inventory

Supplies consisted of lab supplies and reagents to be used in the performance of testing services. Inventory related to finished and semi-finished goods used in the assembly of diagnostic kits related to product sales as well as raw materials consumed in the contract manufacturing process. Subsequent to the restructuring proceedings affecting Veracyte SAS in August 2025, the Company no longer maintains inventory associated with product sales or contract manufacturing.

As of September 30, 2025 and December 31, 2024, supplies and inventory consisted of the following (in thousands of dollars):

			September 30, 2025						December 31, 2024
Supplies			$	20,327					$	17,876
Inventory			—						3,874
Total supplies and inventory			$	20,327					$	21,750

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Impairment of Assets

On July 16, 2025, the Marseille Commercial Court published a decision approving the divestiture of the contract manufacturing portion of the Company's French subsidiary, Veracyte SAS, to Helio Diagnostics SAS, effective August 1, 2025. The remaining assets of Veracyte SAS will be managed by the judicial administrator until such time that the Marseille Commercial Court appoints a judicial liquidator to solely initiate and manage liquidation proceedings. Effective August 1, 2025, the Company ceased to have a controlling interest in Veracyte SAS. As the Company began judicial restructuring proceedings affecting Veracyte SAS with the Marseille Commercial Court in the second quarter of 2025, the Company evaluated whether the associated assets of Veracyte SAS were impaired. The Company concluded, during the second quarter of 2025, that the long-lived assets of the Veracyte SAS asset group were not recoverable. As a result, the Company recorded a $20.5 million non-cash impairment charge during the three months ended June 30, 2025. The impairment related primarily to the Company's right-of-use assets; property, plant, and equipment; and certain tax credits. The impairment is included within the impairment of assets in the condensed consolidated statement of operations. The divestiture did not meet the criteria for discontinued operations under ASC 205-20 as the Company concluded it does not represent a strategic shift in the Company’s operations.

Deconsolidation of Wholly-Owned Subsidiary

Effective August 1, 2025, the Company ceased to have a controlling interest in its wholly-owned French subsidiary, Veracyte SAS. Accordingly, the Company derecognized the related assets and liabilities from its condensed consolidated financial statements. Prior to deconsolidation, the operating results and cash flows of Veracyte SAS were included in the Company’s condensed consolidated financial statements. The Company has no continuing involvement with Veracyte SAS and has entered into a contract manufacturing agreement with Helio Diagnostics SAS, an unrelated party, for the manufacture of certain IVD products.

In accordance with ASC 810, Consolidation, the Company recognized a loss on deconsolidation of approximately $6.7 million, which is included in other income, net in the condensed consolidated statements of operations for the three months ended September 30, 2025. The Company recognized outstanding accounts payable to the subsidiary at the time of deconsolidation for intercompany purchases from the subsidiary. The functional currency of Veracyte SAS is the Euro. With the deconsolidation of Veracyte SAS, the Company released the related accumulated foreign currency translation adjustment from accumulated other comprehensive income into earnings. The loss on deconsolidation was calculated as the carrying amount of the former subsidiary’s net liabilities as of the deconsolidation date less the release of the accumulated foreign currency translation, recording of accounts payable and other expenses. The deconsolidation did not have a material effect on the Company’s ongoing operations or liquidity. The fair market value of Veracyte SAS was deemed to be zero consequently no goodwill was allocated.

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The following table summarizes the major classes of assets and liabilities of Veracyte SAS that were deconsolidated as of August 1, 2025 (in thousands of dollars):

						Amounts
Current assets:
Cash and cash equivalents						$	2,845
Accounts receivable						2,087
Supplies and inventory						4,318
Prepaid expenses and other current assets						3,751
Total current assets						13,001
Property, plant and equipment, net						804
Right-of-use assets, operating leases						673
Total assets deconsolidated						14,478
Current liabilities:
Accounts payable						(3,171)
Accrued Liabilities						(6,004)
Total current liabilities						(9,175)
Operating lease liabilities						(9,459)
Total liabilities deconsolidated						(18,634)
Net liabilities deconsolidated						$	(4,156)

The loss on deconsolidation was calculated as follows (in thousands of dollars):

						Nine Months Ended September 30,
Net liabilities deconsolidated						$	(4,156)
Release of accumulated translation adjustment						8,295
Recording of accounts payable to subsidiary						769
Other expenses						1,800
Net loss on deconsolidation						$	6,708

Net cash outflows arising from the deconsolidation of the subsidiary was $2.9 million during the nine months ended September 30, 2025 related to the balance of cash and cash equivalents deconsolidated.

Accrued Liabilities

Accrued liabilities consisted of the following (in thousands of dollars):

			September 30, 2025						December 31, 2024
Accrued compensation expenses			$	26,952					$	30,595
Accrued other			21,421						13,231
Total accrued liabilities			$	48,373					$	43,826

4. Business Combination

On February 5, 2024, or the Closing Date, the Company acquired 100% of the outstanding equity interests of C2i, or the C2i Acquisition. C2i was a privately-held company that developed a novel method for estimating tumor burden in cancer

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

patients by analyzing a patient’s cell free DNA sequence and offered post-treatment monitoring of cancer recurrence and progression by analyzing subtle changes in the pattern of the tumor’s DNA. The consideration to acquire C2i was $100.2 million, comprised of $73.3 million in the form of approximately 2.7 million shares of the Company’s common stock based on the Company's share price on the Closing Date, $0.8 million of pre-combination portion of replacement stock options issued to C2i’s continuing employees, $17.2 million of contingent consideration that was agreed to be paid on achievement of certain milestones and the remainder in cash.

Assets acquired and liabilities assumed were recorded based on valuations derived from estimated fair value assessments and assumptions used by the Company. The measurement period concluded in February 2025, and no adjustments were recorded during the measurement period.

5. Fair Value Measurements

The Company records certain of its financial assets and liabilities at fair value. The accounting guidance for fair value provides a framework for measuring fair value and clarifies the definition of fair value. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The accounting guidance establishes a three-tiered hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value as follows:

•Level I: Inputs which include quoted prices in active markets for identical assets and liabilities;

•Level II: Inputs other than Level I that are observable, either directly or indirectly, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities; and

•Level III: Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.

The carrying amounts of certain financial instruments of the Company, including cash and cash equivalents, prepaid expenses and other current assets, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities. The fair value of the Company’s financial assets include treasury bills, money market funds and deposits for leases of the Company's facilities. Included in cash and cash equivalents as of December 31, 2024 were $50.4 million of treasury bills with maturities at the time of purchase of three months or less, which are Level I assets as described above. Money market funds, included in cash and cash equivalents, were $2.8 million and $1.6 million as of September 30, 2025 and December 31, 2024, respectively, and are Level I assets as described above. The deposits for the leases, included in restricted cash, were $1.6 million and $1.5 million as of September 30, 2025 and December 31, 2024, respectively, and are Level I assets as described above. There were no transfers between Levels 1, 2 or 3 for the nine months ended September 30, 2025 and 2024.

As part of the Company’s agreement to acquire the exclusive global diagnostic license to the nCounter Analysis System, the Company may pay up to an additional $10.0 million in cash, contingent upon first achievement or occurrence, by or on behalf of the Company, of the commercial launch of the first, second and third diagnostic tests for use on the nCounter multiplex analysis system. This contingency was valued at $6.1 million as of the acquisition date and is remeasured to fair value at each reporting date until the contingent consideration is settled, with the corresponding changes included in general and administrative expense in the Company's condensed consolidated statements of operations. As of September 30, 2025 and December 31, 2024, this contingency was remeasured to $2.3 million and $3.3 million, respectively. For the three and nine months ended September 30, 2025, reversal of expense of zero and $1.0 million, respectively, was recorded, and for the three and nine months ended September 30, 2024, expense of zero and $0.1 million, respectively, was recorded. As of September 30, 2025, the achievement of one of the milestones is forecasted to occur within the next 12 months. As a result, $1.7 million of the contingent consideration is included in short term liabilities at September 30, 2025.

The contingent consideration related to the C2i Acquisition as discussed in Note 4, is dependent on the achievement of certain milestones and is payable in cash or shares of the Company’s common stock, at the Company’s election, of up to $25 million and was valued at $17.2 million. The fair value of the contingent consideration related to the C2i Acquisition will be remeasured to fair value at each reporting date until the contingent consideration is settled, with the corresponding changes included in general and administrative expense. As of September 30, 2025 and December 31, 2024, this contingency was remeasured to $11.9 million and $14.3 million, respectively. For the three and nine months ended September 30, 2025, an expense of $0.1 million and a reversal of expense of $1.7 million, respectively, were recorded. For the three and nine months

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

ended September 30, 2024, an expense of $0.4 million and $1.2 million, respectively, was recorded. As of September 30, 2025, the achievement of all of the remaining milestones is forecasted to occur within the next 12 months. As a result, the contingent consideration is included in short term liabilities at September 30, 2025. During the year ended December 31, 2024, one of the milestones was achieved resulting in the payment of $5.0 million in cash and, during the nine months ended September 30, 2025, one of the milestones was achieved resulting in the payment of $0.7 million in cash.

The fair value of contingent consideration includes inputs that are not observable in the market and thus represents a Level III financial liability. The estimation of the fair value of the contingent consideration is based on the present value of the expected payments calculated by assessing the likelihood of when the related milestones would be achieved and estimating the Company's borrowing rate. These estimates form the basis for making judgments about the carrying value of the contingent consideration that are not readily apparent from other sources. Changes to the forecasts for the achievement of the milestones and the borrowing rate can significantly affect the estimated fair value of the contingent consideration. As of September 30, 2025 and December 31, 2024, the Company calculated the estimated fair value of the milestones using the following significant unobservable inputs:

						Value or Range (Weighted-Average)
Unobservable input						September 30, 2025						December 31, 2024
Discount rate						4.4% - 5.0% (4.5%)						5.1% - 6.2% (5.3%)
Probability of achievement						10% - 90% (72%)						10% - 90% (86%)

Short-Term Investments Held-to-Maturity

The Company's short-term investments consist of United States treasury securities with maturities, at the time of purchase, that were between three months and one year. The Company classifies these investments as held-to-maturity debt securities, which are reported at amortized cost, and are Level I assets as described above. As of September 30, 2025 and December 31, 2024, short-term investments comprised United States treasury bills recorded at amortized cost of $50.9 million and $50.4 million, respectively, with fair values of approximately $50.9 million and $50.4 million, respectively. As of September 30, 2025, gross unrealized gains or losses on short-term investments were insignificant.

6. Commitments and Contingencies

Operating Leases

The Company leases office and laboratory facilities in the U.S., including in South San Francisco and San Diego, California and Austin, Texas, and, prior to August 2025, in Marseille, France, and leases certain equipment under various non-cancelable lease agreements. Effective August 2025, in connection with the restructuring proceeding in Veracyte SAS, the Company is no longer a party to the lease in Marseille, France. The lease terms of the Company’s leases as of September 30, 2025 extend to March 2040 and contain extension of lease terms and expansion options. The leases have a weighted average remaining lease term of 11.3 years as of September 30, 2025. The Company had deposits of $1.6 million and $1.5 million included in long-term assets as of September 30, 2025 and December 31, 2024, respectively, restricted from withdrawal and held by banks in the form of collateral for irrevocable standby letters of credit held as security for the leases.

The Company determined its operating lease liabilities using payments through their current expiration dates and a weighted average discount rate of 11.4% based on the rate that the Company would have to pay to borrow, on a collateralized basis, an amount equal to the lease payments in a similar economic environment. Operating lease liabilities along with the associated right-of-use assets are disclosed in the accompanying condensed consolidated balance sheets. After the adoption of ASC 842, Leases, or ASC 842, the Company classified its deferred rent for tenant improvements with its operating lease right-of-use assets on the consolidated balance sheets.

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VERACYTE, INC.

Notes to Financial Statements

(unaudited)

Future minimum lease payments under non-cancelable operating leases as of September 30, 2025 are as follows (in thousands of dollars):

Year Ending December 31,			Amounts
Remainder of 2025			$	1,877
2026			4,314
2027			6,999
2028			7,173
2029			6,858
Thereafter			47,461
Total future minimum lease payments			74,682
Less: amount representing interest			34,229
Present value of future lease payments			40,453
Less: short-term lease liabilities			4,282
Long-term lease liabilities			$	36,171

The Company recognizes operating lease expense on a straight-line basis over the non-cancelable lease period. The following table summarizes operating lease expense and cash paid for amounts included in the measurement of lease liabilities (in thousands of dollars):

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Operating lease expense			$	1,912					$	1,824					$	6,274					$	4,914
Cash paid for amounts included in the measurement of lease liabilities			$	1,722					$	1,967					$	5,620					$	5,274

Contingencies

From time to time, the Company may be involved in various legal proceedings and claims arising in the ordinary course of business. Although the outcomes of such matters cannot be predicted with certainty, the Company believes there is no litigation pending that could have, either individually or in the aggregate, a material adverse impact on the Company's consolidated financial statements.

On May 1, 2025, the Company filed a complaint in federal court in the Eastern District of Texas alleging that Sonic Healthcare USA, Inc., the healthcare company that is believed to offer ThyroSeq v3, is infringing three of the Company’s patents related to molecular testing of thyroid nodules. The complaint seeks treble damages, attorneys’ fees and costs as well as injunctive relief. On June 4, 2025, the Company filed an amended complaint asserting two additional patents. On July 21, 2025, Sonic Healthcare USA, Inc. filed an answer and a motion to dismiss. The Company filed its opposition to the motion to dismiss on October 31, 2025. The jury trial is currently scheduled for January 25, 2027.

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7. Stockholders’ Equity

Common Stock

The Company had reserved shares of common stock for issuance as follows:

			September 30, 2025						December 31, 2024
Stock options and restricted stock units issued and outstanding			5,170,600						5,773,382
Stock options and restricted stock units available for grant under stock option plans			10,899,141						8,971,566
Common stock available for the Employee Stock Purchase Plan			895,255						1,051,407
Total			16,964,996						15,796,355

8. Components of Other Income

Other income, net consists of the following (in thousands of dollars):

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Interest income			$	3,482					$	2,898					$	9,181					$	8,293
Loss on deconsolidation of subsidiary			(6,708)						—						(6,708)						—
Interest expense			—						(1)						(1)						(2)
Gain (loss) on currency revaluation			(832)						1,487						4,062						756
Other			1						447						451						1,287
Total			$	(4,057)					$	4,831					$	6,985					$	10,334

9. Segment

The chief operating decision maker for the Company is the Chief Executive Officer, who reviews financial information presented on a consolidated basis for purposes of allocating resources and assessing financial performance. The Company has a single reporting unit associated with the development and commercialization of diagnostic tests and biopharmaceutical services. The accounting policies of the Company's single segment are the same as those described in the summary of significant accounting policies in Note 1, Organization, Description of Business and Summary of Significant Accounting Policies. The chief operating decision maker assesses performance of the Company's single segment and decides how to allocate resources based on consolidated net income. Under the current organizational structure, this measure is not discreetly available or required individually for any of the Company’s business activities and is only available at the consolidated level. The monitoring of budgeted versus actual results are used in assessing performance of the Company's single segment, allocating resources and in establishing management’s compensation. The Company's chief operating decision maker intends for all revenue generating activities to rely on cross-functional activities across the consolidated entity in order to operate. No individual besides the chief operating decision maker has been tasked with reviewing discreet operating results of the business activities, nor is there any intent to bifurcate the overall business review process to produce discreet operating results specific to any of the Company's business activities. The measure of segment assets is reported on the consolidated balance sheet as total consolidated assets. Consolidated revenue does not include any inter-segment sales or transfers.

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Information about reported segment revenue, measures of segment profit or loss, significant segment expenses and reconciliation to income from operations was as follows (in thousands):

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Revenue:
Testing revenue			$	127,756					$	109,536					$	357,328					$	306,809
Product revenue			3,301						3,188						10,479						10,631
Biopharmaceutical and other revenue			815						3,136						8,702						9,692
Total revenue			131,872						115,860						376,509						327,132
Cost of revenue:
Cost of testing revenue:
Laboratory supplies and reagents expense			14,766						13,887						43,134						39,131
Sample collection expense			3,078						3,663						9,398						9,884
Compensation expense			6,273						5,743						17,906						16,097
Other cost of testing revenue (1)			6,456						2,797						14,017						9,122
Allocation of facilities and IT expenses			3,204						2,939						9,989						8,694
Total cost of testing revenue			33,777						29,029						94,444						82,928
Cost of product revenue:
Product costs			1,050						545						1,864						2,436
License fees and royalties			257						270						888						1,021
Other cost of product revenue (2)			1,672						750						2,980						2,372
Allocation of facilities and IT expenses			36						227						454						481
Total cost of product revenue			3,015						1,792						6,186						6,310
Cost of biopharmaceutical and other revenue:
Compensation expense			426						1,424						3,318						4,958
Other cost of biopharmaceutical and other revenue (3)			612						1,024						3,118						3,244
Allocation of facilities and IT expenses			53						664						925						1,560
Total cost of biopharmaceutical and other revenue			1,091						3,112						7,361						9,762
Intangible asset amortization - cost of revenue			2,707						2,917						7,959						8,741
Gross profit			91,282						79,010						260,559						219,391
Operating expenses:
Research and development:
Compensation expense			9,028						8,906						27,840						26,356
Direct research and development expense			3,512						5,479						10,946						14,596
Other research and development expenses (4)			1,586						1,338						5,278						4,195
Allocation of facilities and IT expenses			1,855						1,851						5,901						4,857
Total research and development			15,981						17,574						49,965						50,004
Selling and marketing:
Compensation expense			16,977						15,814						52,214						50,517
Direct marketing expense			1,376						1,427						3,564						4,613
Other selling and marketing expenses (5)			3,332						3,271						10,880						9,897
Allocation of facilities and IT expenses			2,770						2,100						7,567						5,583
Total selling and marketing			24,455						22,612						74,225						70,610
General and administrative:
Compensation expense			20,688						18,958						62,121						59,824
Other general and administrative expenses (6)			14,508						14,565						56,132						45,048
Allocation of facilities and IT expenses			(7,918)						(7,781)						(24,836)						(21,175)
Total general and administrative			27,278						25,742						93,417						83,697
Impairment of assets			—						185						20,505						614
Intangible asset amortization - operating expenses			622						880						1,865						2,499
Other income, net			4,057						(4,831)						(6,985)						(10,334)
Income tax (benefit) provision			(248)						1,693						2,363						3,276
Net income			$	19,137					$	15,155					$	25,204					$	19,025

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________________

(1)Other cost of testing revenue includes cytopathology services, depreciation and amortization and other expenses.

(2)Other cost of product revenue includes contract manufacturing fees, license fees and royalties, depreciation and amortization and other expenses.

(3)Other cost of biopharmaceutical and other revenue includes license fees and royalties, depreciation and amortization and other expenses.

(4)Other research and development expenses includes depreciation and amortization and other expenses.

(5)Other selling and marketing expenses includes travel, entertainment, conference and other expenses.

(6)Other general and administrative expenses includes professional fees, information technology expense, occupancy costs, depreciation and amortization, contingent consideration and other expenses.

10. Income Taxes

The provision for income taxes is based on the current estimate of the annual effective tax rate applied to the Company’s year to date income and is adjusted for discrete items recorded in the period. For the three months ended September 30, 2025 and 2024, the Company’s effective tax rate was (1.3)% and 10.0%, respectively. For the nine months ended September 30, 2025 and 2024, the Company’s effective tax rate was 8.6% and 14.7%, respectively. For the nine months ended September 30, 2025, the primary difference between the effective tax rate and the federal statutory rate is driven by unfavorable permanent differences, offset by benefits from the One Big Beautiful Bill Act, or the OBBBA, and the full valuation allowance the Company has established on its federal, state and foreign net operating losses and credits. For the nine months ended September 30, 2024, the primary difference between the effective tax rate and the federal statutory rate is driven by unfavorable permanent differences and foreign and state taxes offset by the full valuation allowance the Company has established on its federal, state and foreign net operating losses and credits.

The Company recorded income tax benefit of $0.2 million and expense of $1.7 million for the three months ended September 30, 2025 and 2024, respectively, and recorded income tax expense of $2.4 million and $3.3 million for the nine months ended September 30, 2025 and 2024, respectively. The benefit and provision for income taxes recorded in the three and nine months ended September 30, 2025 and 2024 consists primarily of state income taxes incurred by a subsidiary associated with the Company's Decipher product line.

On July 4, 2025, the U.S. government enacted the OBBBA, which includes numerous changes to existing tax law including extending or making permanent certain business and international tax measures initially established under the 2017 Tax Cuts and Jobs Act, which were set to expire. The OBBBA permanently eliminates the requirement to capitalize and amortize U.S.-based research and experimental expenditures over five years, making these expenditures fully deductible in the period incurred. The OBBBA also permanently extends the full expensing of qualifying assets through accelerated bonus depreciation in the period acquired. The OBBBA has multiple effective dates, with certain provisions effective in 2025 and others to be implemented through 2027. The enactment of certain provisions in the period ending September 30, 2025 resulted in a reduction of current income tax liabilities and a corresponding reduction to income tax expense.

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Item 2.  Management’s Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis of our financial condition and results of operations should be read together with our unaudited condensed consolidated financial statements and the related notes and other financial information included elsewhere in this Quarterly Report on Form 10-Q and with our audited consolidated financial statements and the notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2024, or our Annual Report.

As discussed in the section titled “Special Note Regarding Forward-Looking Statements,” the following discussion and analysis contains forward-looking statements that involve risks and uncertainties. Our actual results and the timing of selected events could differ materially from those discussed below. Factors that could cause or contribute to such differences include, but are not limited to, those identified below and those set forth herein under the heading “Special Note Regarding Forward-Looking Statements” and in the section titled “Risk Factors” under Part II, Item 1A of this report and under Part I, Item 1A of our Annual Report. Historical results are not necessarily indicative of future results.

When used in this report, all references to "Veracyte," the "company," "we," "our" and "us" refer to Veracyte, Inc., together with its consolidated subsidiaries, unless otherwise noted.

The following is a non-exhaustive list of Veracyte and its affiliates’ trademarks and/or registered trademarks in the United States and certain other countries: Afirma, Decipher, Envisia, GenomeDx, GRID, Percepta, Prosigna, TrueMRD, Veracyte, and the Veracyte logo. nCounter is the registered trademark of Bruker Spatial Biology, Inc. and used by Veracyte under license.

Overview

We are a global diagnostics company that empowers clinicians with the high-value insights they need to guide and assure patients at pivotal moments in the race to diagnose and treat cancer. Our high-performing tests enable clinicians to make more confident diagnostic, prognostic and treatment decisions. Insights from these tests help patients avoid unnecessary procedures and interventions and accelerate time to appropriate treatment, thereby improving outcomes for patients in our global markets.

In the United States, we currently offer tests in prostate cancer (Decipher Prostate), thyroid cancer (Afirma), breast cancer (Prosigna), and bladder cancer (Decipher Bladder). In addition, our Percepta Nasal Swab test is being run in our Clinical Laboratory Improvement Amendments of 1988, or CLIA, certified labs in support of clinical studies.

We serve global markets with two complementary models. In the United States, we offer laboratory developed tests through our centralized CLIA certified laboratories in South San Francisco and San Diego, California, supported by our cytopathology expertise in Austin, Texas. Additionally, primarily outside of the United States, we provide in vitro diagnostics, or IVD, tests to patients through distribution to laboratories and hospitals that can perform the tests locally. Our international distribution of IVDs is currently limited to our Prosigna test, however, in the future, we intend to offer Decipher Prostate and Percepta Nasal Swab as IVD tests. We believe our broad menu of advanced diagnostic tests, combined with our ability to deliver them globally, differentiates us in the diagnostics industry.

We are aiming to expand our role across the cancer continuum with the addition of minimal residual disease, or MRD assays. This will broaden our portfolio of tests to help monitor the success of a therapeutic or surgical intervention, and support the determination of the best course of action for each patient.

Macroeconomic Factors

Recent macroeconomic factors, such as interest rate fluctuations and inflation in the United States and other markets, evolving international trade policies and government actions relating to tariffs, as well as volatility in the global banking and finance systems, have resulted in volatility in the capital and credit markets globally. Moreover, the continued fluctuation and reduced valuation of the U.S. dollar compared to other currencies has impacted and may continue to impact our results of operations. Further, the U.S. federal government has been shut down since October 1, 2025, and the impact of a prolonged government shutdown on business and economic conditions generally, and our results of operations, is uncertain. We intend to continue to monitor macroeconomic conditions closely and may determine to take certain financial or operational actions in response to such conditions as appropriate. In addition, regional conflicts like those between Russia and Ukraine and in Israel may adversely impact our business and operating results. Finally, the ongoing conflict in the Middle East and related political, military and security conditions in and around Israel may disrupt our Israel business operations and employees that we acquired through the Company’s acquisition of 100% of the outstanding equity interests of C2i, or the C2i Acquisition.

The extent of the impact of macroeconomic factors on our future liquidity and operational performance will depend on future developments and their impact on our customers' operations and our sales and renewal cycles. We may also be adversely

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affected by further changes in central bank policies and fluctuations in interest rates, rates of inflation, and changes in foreign currency exchange rates. See "Risk Factors" for further discussion.

Factors Affecting Our Performance

Reported Total Test Volume

Our performance currently depends on the number of tests that we perform and report as completed in our CLIA-certified laboratories and the number of tests purchased by our customers, which we refer to as our reported total test volume. Factors impacting our reported total test volume include, but are not limited to:

•the number of samples that we receive that meet the medical indication for each test performed;

•the quantity and quality of the sample received;

•receipt of the necessary documentation, such as physician order and patient consent, required to perform, bill and collect for our tests;

•the patient's ability to pay or provide necessary insurance coverage for the tests performed;

•the time it takes us or our customers to perform our tests and report the results, including as a result of supply chain challenges (including quality of single-source reagents);

•the seasonality inherent in our business, such as the impact of workdays per period, timing of industry conferences and timing of when patient deductibles are exceeded, which also impacts the reimbursement we receive from insurers;

•fluctuations in demand for our product test kits, including as a result of higher average selling prices and overall spending constraints across our industry; and

•our ability to obtain prior authorization or meet other requirements instituted by payers, benefit managers, or regulators necessary to be paid for our tests.

Continued Adoption of and Reimbursement for our Products

Revenue growth depends on our ability to secure coverage decisions, achieve broader reimbursement from third-party payers, obtain prior authorization, expand our base of prescribing physicians and increase our penetration in existing accounts. Because some payers consider our products experimental and investigational, we may not receive payment for tests and payments we receive may not be at acceptable levels. We expect our revenue growth to increase if more payers make a positive coverage decision and as payers enter into contracts with us, which should enhance our revenue and cash collections.

Our sales teams are aligned under our general manager-based structure to focus on specific products and global markets. If we are unable to expand the base of prescribing physicians and penetration within these accounts at an acceptable rate, or if we are not able to execute our strategy for increasing reimbursement and associated collections, we may not be able to effectively increase our revenue. We expect to continue to see pressure from payers to limit the utilization of tests, generally, and we believe more payers are deploying cost containment tactics, such as requiring prior authorization, reduction of the payer portion of reimbursement and employing laboratory benefit managers to reduce utilization rates. Revenue growth also depends on our ability to secure reimbursement from government payers at a reimbursement rate that is consistent with past reimbursement rates. Changes or implementation of government regulations or reimbursement policies, including under the Protecting Access to Medicare Act of 2014, or PAMA, could result in lower reimbursement rates for our tests. Any such reductions could negatively affect our revenues and margins.

Integrating Acquisitions

Revenue growth, operational results and advances to our test offering strategy depend on our ability to integrate any acquisitions into our existing business and effectively scale their operations. The integration of acquired assets and other strategic transactions that we may pursue may impact our revenue growth, increase the cost of operations or may require management resources that otherwise would be available for ongoing development of our existing business.

New Product Development

A significant aspect of our business is our investment in development activities, including activities related to the development of new tests and modifications and enhancements to our current tests, including the ongoing development of our IVD and MRD strategies. In addition to these development activities, we also perform clinical evidence studies which are critical to gaining clinician adoption of our tests, driving favorable coverage decisions by payers, as well as gaining guideline inclusion for such tests.

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How We Recognize Revenue

We recognize revenue in accordance with the provisions of the Financial Accounting Standards Board, or FASB, Accounting Standards Codification, or ASC, 606, Revenue from Contracts with Customers, or ASC 606. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue when the performance obligations have been satisfied.  

Testing Revenue

We generally bill for testing services at the time of test completion, upon delivery of a patient report to the prescribing physician. We recognize revenue based on estimates of the cash amount that will ultimately be collected. In determining the amount to accrue for a delivered test, we consider factors such as payment history, payer coverage, whether there is a reimbursement contract between the payer and us, payment as a percentage of agreed upon rate (if applicable), amount paid per test and any current developments or changes that could impact reimbursement. These estimates require significant judgment by management. Actual results could differ from those estimates and assumptions. Upon ultimate collection, the amount received is compared to previous estimates and the amount accrued is adjusted accordingly.

Generally, cash we receive is collected within 12 months of the date the test is billed. We cannot provide any assurance as to when, if ever, or to what extent, any of these amounts will be collected. Notwithstanding our efforts to obtain payment for these tests, payers may deny our claims, in whole or in part, and we may never receive payment for these tests. Our ability to increase our testing revenue will depend on our ability to penetrate the market, obtain positive coverage policies from additional third-party payers, obtain reimbursement and/or enter into contracts with additional third-party payers for our current and new tests, and increase reimbursement rates for tests performed. Finally, should the judgments underlying our estimated reimbursement change, our accrued revenue and financial results could be negatively impacted in future periods.

We bill list price regardless of contract rate, but only recognize revenue from amounts that we estimate are collectible and meet our revenue recognition criteria. Revenue may not be equal to the billed amount due to a number of factors that we consider when determining revenue accrual rates, including differences in reimbursement rates, the amounts of patient co-payments and co-insurance, the existence of secondary payers, claims denials and the amount we expect to ultimately collect. Finally, when we increase our list price, it will increase the cumulative amounts billed but not positively impact accrued revenue. In addition, payer contracts generally include the right of offset and payers may offset payments prior to resolving disputes over tests performed.

Generally, we determine accrual rates by calculating an average of reimbursement from all payers for tests performed over a four-quarter period as it reduces the effects of temporary volatility and seasonality. The periods selected to determine accrual rates typically are at least six months old because it takes a significant period of time to collect from some payers. We may also determine accrual rates based on other factors such as coverage decisions, contracts, or more recent reimbursement data as appropriate.

The average test reimbursement rates will change over time due to a number of factors, including medical coverage decisions by payers, the effects of contracts signed with payers, changes in allowed amounts by payers, our ability to successfully win appeals for payment, and our ability to collect cash payments from third-party payers and individual patients. Historical average reimbursement is not necessarily indicative of future average reimbursement.

We incur expense for tests in the period in which the test is conducted and recognize revenue for tests in the period in which our revenue recognition criteria are met.

Product Revenue

Our product revenue consists primarily of sales of the Prosigna breast cancer IVD and related diagnostic kits, and services. We recognize product revenue when control of the promised goods is transferred to our customers, in an amount that reflects the consideration expected to be received in exchange for those products. This process involves identifying the contract with a customer, determining the performance obligations in the contract, determining the contract price, allocating the contract price to the distinct performance obligations in the contract, and recognizing revenue when the performance obligations have been satisfied. A performance obligation is considered distinct from other obligations in a contract when it provides a benefit to the customer, either on its own or together with other resources that are readily available to the customer, and is separately identified in the contract. Performance obligations are considered satisfied once we have transferred control of a product to the

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customer, meaning the customer has the ability to use and obtain the benefit of the product. We recognize product revenue for satisfied performance obligations only when there are no uncertainties regarding payment terms or transfer of control. Shipping and handling costs incurred for product shipments are charged to our customers and included in product revenue. Revenue is presented net of the taxes that are collected from customers and remitted to governmental authorities.

Biopharmaceutical and Other Revenue

We enter into arrangements to license or provide access to our assets or services to third parties, including clinical and testing services, research and development, as well as other services. Such arrangements may require us to deliver various rights, data, services, access and/or testing services to partner biopharmaceutical and other companies. The underlying terms of these arrangements generally provide for consideration paid to us in the form of nonrefundable fees; payments on delivery of data or test results; costs of service plus margin; performance milestone payments; expense reimbursements and possibly royalty and/or other payments. Net sales of data or other services to our customers are recognized in accordance with ASC 606 and are classified under biopharmaceutical and other revenue. Payments received that are not related to sales or services to a customer are recorded as offsets against research and development expense or cost of biopharmaceutical and other revenue in our consolidated statements of operations.

In arrangements involving more than one good or service delivered to a customer, each good or service is evaluated to determine whether it qualifies as a distinct performance obligation based on whether (i) the customer can benefit from the good or service either on its own or together with other resources that are readily available and (ii) the good or service is separately identifiable from other promises in the contract. The consideration under the arrangement is then allocated to each separate distinct performance obligation based on its respective relative stand-alone selling price. The estimated selling price of each deliverable reflects our best estimate of what the selling price would be if the deliverable was regularly sold by us on a stand-alone basis or using an adjusted market assessment approach if the selling price on a stand-alone basis is not available.

The consideration allocated to each distinct performance obligation is recognized as revenue when control is transferred which may be at a point in time or over time. Consideration associated with at-risk substantive performance milestones is recognized as revenue when it is probable that a significant reversal of the cumulative revenue recognized will not occur. Should there be royalties, we utilize the sales and usage-based royalty exception in arrangements that resulted from the license of intellectual property, recognizing revenue generated from royalties or profit sharing as the underlying sales occur.

Timing of Our Research and Development Expenses

We deploy state-of-the-art and costly genomic technologies in our discovery and development experiments. Further, we conduct clinical studies to validate our new products, as well as on-going clinical studies to further the published evidence to support our commercialized tests. The timing of these research and development activities is difficult to predict, as is the timing of clinical trial enrollments and sample acquisitions. Therefore, spending on research and development may vary significantly by quarter depending on the timing of these various expenses.

Financial Overview

Revenue

Through September 30, 2025, we derived the majority of our revenue as testing revenue from the sale of Decipher Prostate and Afirma tests, delivered primarily to physicians in the United States. We generally invoice third-party payers upon delivery of a patient report to the prescribing physician. As such, we take the assignment of benefits and the risk of cash collection from the third-party payer and individual patients. Third-party payers and other customers in excess of 10% of total revenue and their related revenue as a percentage of total revenue were as follows for the periods presented:

			Three Months Ended September 30,												Nine Months Ended September 30,
			2025						2024						2025						2024
Medicare			33		%				31		%				33		%				31		%
UnitedHealthcare			14		%				13		%				14		%				14		%
			47		%				44		%				47		%				45		%

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Cost of Testing Revenue

The components of our cost of testing revenue are sample collection kit costs, reagent expenses, compensation expense, license fees and royalties, depreciation, other expenses such as equipment and laboratory supplies, and allocations of facility and information technology expenses. We expect cost of testing revenue in absolute dollars to increase as the number of tests we perform increases. However, we expect that the cost per test will decrease over time due to leveraging fixed costs, efficiencies we may gain as test volume increases and process enhancements such as automation, and other cost reductions. As we introduce new tests, initially our cost per test will be high as we expect to run suboptimal batch sizes, quality control batches, test batches, registry samples, and generally incur costs that may suppress or reduce gross margins. This will disproportionately increase our aggregate cost of testing revenue until we achieve processing efficiencies.

Cost of Product Revenue

Our cost of product revenue consists primarily of costs of diagnostic kit components and reagents, labor, delivery costs and royalties for licensed technologies included in our products. Subsequent to the restructuring proceedings affecting Veracyte SAS in August 2025, these costs are paid to a third-party contract manufacturer. As our Prosigna test kits are sold in various configurations with different numbers of tests, our product cost per test will continue to vary based on the specific kit configuration purchased by customers.

Cost of Biopharmaceutical and Other Revenue

Our cost of biopharmaceutical and other revenue consists of costs of performing activities under arrangements that require us to license or provide access to our assets or laboratory testing services, as well as cost incurred in providing contracted research and development and manufacturing activities. These costs are mainly composed of compensation, manufacturing and laboratory supplies, and pass-through costs. Subsequent to the to the restructuring proceedings affecting Veracyte SAS in August 2025, Veracyte SAS will no longer perform biopharmaceutical services, and contract manufacturing and development services.

Intangible Asset Amortization - Cost of Revenue

Our finite-lived intangible assets, acquired in business combinations, are being amortized over 10 to 15 years, using the straight-line method. Intangible asset amortization - cost of revenue includes amortization of finite-lived intangible assets related to developed and product technology utilized in our current product and service offerings and customer backlog.

Research and Development

Research and development expenses include expenses incurred to collect clinical samples and conduct clinical studies to develop and support our products and pipeline, as well as develop future technology. These expenses consist of compensation expenses, direct research and development expenses such as laboratory supplies and costs associated with setting up and conducting clinical studies at domestic and international sites, professional fees, depreciation and amortization, other miscellaneous expenses and allocation of facility and information technology expenses. We expense all research and development costs in the periods in which they are incurred. We incurred a majority of our research and development expenses in the nine months ended September 30, 2025 and the year ended December 31, 2024 in support of our early-stage products, including Percepta Nasal Swab, support for the development and validation of our MRD tests, and the development of new IVD products and discovery. Going forward, we expect to incur significant expense as we invest in the continued development of our innovation engine, early-stage products including our MRD tests, required clinical studies and the development of current IVD tests.

Selling and Marketing

Selling and marketing expenses consist of compensation expenses, direct marketing expenses, professional fees, other expenses such as travel and communications costs, as well as allocation of facility and information technology expenses. Our sales team of approximately 110 representatives is organized by business unit in the U.S., with separate teams calling on thyroid cancer and urologic cancer physicians. The business units have dedicated marketing support, as well as a marketing operations team that serves the commercial organization broadly. Prosigna sales outside of the U.S. are led by country managers and sales teams that call on laboratories and breast cancer oncologists.

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General and Administrative

General and administrative expenses include compensation expenses for executive officers and administrative, billing and client service personnel, professional fees for legal and audit services, occupancy costs, depreciation and amortization, and other expenses such as information technology, acquisition related costs and miscellaneous expenses, offset by allocation of facility and information technology expenses to other functions. We expect general and administrative expenses to continue to increase as we build our infrastructure to scale revenue growth, and to decline as a percentage of revenue thereafter.

Intangible Asset Amortization - Operating Expenses

Our finite-lived intangible assets, acquired in business combinations, are being amortized over 5 to 15 years, using the straight-line method. Intangible asset amortization - operating expenses includes amortization of finite-lived intangible assets related to developed technology utilized in the development of future product and service offerings, trade names and customer relationships.

Other Income (Loss), Net

Other income (loss), net consists primarily of interest income from our cash held in interest bearing accounts, realized and unrealized gains and losses on foreign currency transactions and loss on the deconsolidation of Veracyte SAS.

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Results of Operations

Comparison of the three and nine months ended September 30, 2025 and 2024 (in thousands of dollars, except percentages and test volume):

			Three Months Ended September 30,																								Nine Months Ended September 30,
			2025						2024						Change						%						2025						2024						Change						%
Revenue:
Testing revenue			$	127,756					$	109,536					$	18,220					17%						$	357,328					$	306,809					$	50,519					16%
Product revenue			3,301						3,188						113						4%						10,479						10,631						(152)						(1)%
Biopharmaceutical and other revenue			815						3,136						(2,321)						(74)%						8,702						9,692						(990)						(10)%
Total revenue			131,872						115,860						16,012						14%						376,509						327,132						49,377						15%
Cost of revenue:
Cost of testing revenue			33,777						29,029						4,748						16%						94,444						82,928						11,516						14%
Cost of product revenue			3,015						1,792						1,223						68%						6,186						6,310						(124)						(2)%
Cost of biopharmaceutical and other revenue			1,091						3,112						(2,021)						(65)%						7,361						9,762						(2,401)						(25)%
Intangible asset amortization - cost of revenue			2,707						2,917						(210)						(7)%						7,959						8,741						(782)						(9)%
Total cost of revenue			40,590						36,850						3,740						10%						115,950						107,741						8,209						8%
Gross profit			91,282						79,010						12,272						16%						260,559						219,391						41,168						19%
Operating expenses:
Research and development			15,981						17,574						(1,593)						(9)%						49,965						50,004						(39)						—%
Selling and marketing			24,455						22,612						1,843						8%						74,225						70,610						3,615						5%
General and administrative			27,278						25,742						1,536						6%						93,417						83,697						9,720						12%
Impairment of assets			—						185						(185)						(100)%						20,505						614						19,891						3240%
Intangible asset amortization - operating expenses			622						880						(258)						(29)%						1,865						2,499						(634)						(25)%
Total operating expenses			68,336						66,993						1,343						2%						239,977						207,424						32,553						16%
Income from operations			22,946						12,017						10,929						91%						20,582						11,967						8,615						72%
Other income (loss), net			(4,057)						4,831						(8,888)						(184)%						6,985						10,334						(3,349)						(32)%
Income before income taxes			18,889						16,848						2,041						12%						27,567						22,301						5,266						24%
Income tax (benefit) provision			(248)						1,693						(1,941)						(115)%						2,363						3,276						(913)						(28)%
Net income			$	19,137					$	15,155					$	3,982					26%						$	25,204					$	19,025					$	6,179					32%
Other Operating Data:
Diagnostic tests reported			43,679						36,792						6,887						19%						124,198						103,818						20,380						20%
Product tests sold			2,209						2,240						(31)						(1)%						7,311						7,661						(350)						(5)%
Total test volume			45,888						39,032						6,856						18%						131,509						111,479						20,030						18%
Depreciation and amortization expense			$	5,267					$	5,878					$	(611)					(10)%						$	16,117					$	17,206					$	(1,089)					(6)%
Stock-based compensation expense			$	10,757					$	8,747					$	2,010					23%						$	32,700					$	26,620					$	6,080					23%

Revenue

Revenue increased $16.0 million for the three months ended September 30, 2025 compared to the same period in 2024. This was primarily due to a $18.2 million increase in testing revenue partially offset by a $2.3 million decrease in our biopharmaceutical and other revenue. The $2.3 million decrease was due to continued decline in the biopharma business conducted in France and the ultimate deconsolidation of Veracyte SAS in August 2025. The 17% growth in testing revenue was primarily driven by a 19% volume increase, partially offset by lower prior period collections compared to the prior year period.

Revenue increased $49.4 million for the nine months ended September 30, 2025 compared to the same period in 2024. This was primarily due to a $50.5 million increase in testing revenue and a $1.0 million decrease in our biopharmaceutical and other revenue. The 16% growth in testing revenue was primarily driven by a 20% volume increase, partially offset by lower prior period collections compared to the prior year and the decision to stop marketing Envisia. The Biopharmaceutical and other revenue decrease was driven primarily by a continued decline in biopharmaceutical services, as well as contract development and manufacturing services projects as a result of the restructuring proceedings affecting Veracyte SAS that were underway throughout 2025.

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Product revenue was flat for the three and nine months ended September 30, 2025 compared to the same periods in 2024.

Cost of revenue

Comparison of the three and nine months ended September 30, 2025 and 2024 is as follows (in thousands of dollars, except percentages):

			Three Months Ended September 30,																								Nine Months Ended September 30,
			2025						2024						Change						%						2025						2024						Change						%
Cost of testing revenue:
Laboratory supplies and reagents expense			$	14,766					$	13,887					$	879					6		%				$	43,134					$	39,131					$	4,003					10		%
Sample collection expense			3,078						3,663						(585)						(16)		%				9,398						9,884						(486)						(5)		%
Compensation expense			6,273						5,743						530						9		%				17,906						16,097						1,809						11		%
Cytopathology services			1,629						1,518						111						7		%				4,700						4,386						314						7		%
Depreciation and amortization			501						360						141						39		%				1,487						1,216						271						22		%
Other expenses			4,326						919						3,407						371		%				7,830						3,520						4,310						122		%
Allocations			3,204						2,939						265						9		%				9,989						8,694						1,295						15		%
Total			$	33,777					$	29,029					$	4,748					16		%				$	94,444					$	82,928					$	11,516					14		%
Cost of product revenue:
Product costs			$	1,050					$	545					$	505					93		%				$	1,864					$	2,436					$	(572)					(23)		%
License fees and royalties			257						270						(13)						(5)		%				888						1,021						(133)						(13)		%
Depreciation and amortization			110						222						(112)						(50)		%				471						659						(188)						(29)		%
Other expenses			1,562						528						1,034						196		%				2,509						1,713						796						46		%
Allocations			36						227						(191)						(84)		%				454						481						(27)						(6)		%
Total			$	3,015					$	1,792					$	1,223					68		%				$	6,186					$	6,310					$	(124)					(2)		%
Cost of biopharmaceutical and other revenue:
Compensation expense			$	426					$	1,424					$	(998)					(70)		%				$	3,318					$	4,958					$	(1,640)					(33)		%
License fees and royalties			—						—						—						NM						—						150						(150)						(100)		%
Depreciation and amortization			10						48						(38)						(79)		%				109						172						(63)						(37)		%
Other expenses			602						976						(374)						(38)		%				3,009						2,922						87						3		%
Allocations			53						664						(611)						(92)		%				925						1,560						(635)						(41)		%
Total			$	1,091					$	3,112					$	(2,021)					(65)		%				$	7,361					$	9,762					$	(2,401)					(25)		%
Intangible asset amortization - cost of revenue			$	2,707					$	2,917					$	(210)					(7)		%				$	7,959					$	8,741					$	(782)					(9)		%

Cost of testing revenue increased $4.7 million, or 16%, for the three months ended September 30, 2025 compared to the same period in 2024. The increase in cost of testing revenue was due to increased volume in testing, higher staffing to support higher volume and the build out of infrastructure related to current and future growth expectations, primarily related to Decipher Prostate and Afirma tests, partially offset by lab efficiencies.

Cost of testing revenue increased $11.5 million, or 14%, for the nine months ended September 30, 2025 compared to the same period in 2024. The increase in cost of testing revenue was due to increased volume in testing, higher staffing to support higher volume and the build out of infrastructure related to current and future growth expectations, primarily related to Decipher Prostate and Afirma tests, partially offset by lab efficiencies.

Cost of product revenue increased $1.2 million, or 68%, for the three months ended September 30, 2025 and decreased $0.1 million, or 2%, for the nine months ended September 30, 2025 compared to the same periods in 2024. The increase for the three months ended September 30, 2025 is primarily related to one-time start-up costs associated with our new contract manufacturer of Prosigna kits.

Cost of biopharmaceutical and other revenue includes labor costs, laboratory supplies and pass-through expenses incurred. Cost of biopharmaceutical and other revenue for the three and nine months ended September 30, 2025 decreased by

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$2.0 million and $2.4 million, respectively, compared to the same periods in 2024, driven primarily by a continued decline in biopharmaceutical services, as well as contract development and manufacturing services projects as a result of the restructuring proceedings affecting Veracyte SAS that were underway throughout 2025.

Research and development

Comparison of the three and nine months ended September 30, 2025 and 2024 is as follows (in thousands of dollars, except percentages):

			Three Months Ended September 30,																								Nine Months Ended September 30,
			2025						2024						Change						%						2025						2024						Change						%
Research and development expense:
Compensation expense			$	9,028					$	8,906					$	122					1		%				$	27,840					$	26,356					$	1,484					6		%
Direct research and development expense			3,512						5,479						(1,967)						(36)		%				10,946						14,596						(3,650)						(25)		%
Depreciation and amortization			444						332						112						34		%				1,311						819						492						60		%
Other expenses			1,142						1,006						136						14		%				3,967						3,376						591						18		%
Allocations			1,855						1,851						4						—		%				5,901						4,857						1,044						21		%
Total			$	15,981					$	17,574					$	(1,593)					(9)		%				$	49,965					$	50,004					$	(39)					—		%

Research and development expense decreased $1.6 million, or 9%, for the three months ended September 30, 2025 compared to the same period in 2024. The decrease was primarily due the deconsolidation of Veracyte SAS and the timing of direct research and product development expense related to our on-going development costs for our IVD and MRD strategies, partially offset by increased headcount expenses.

Research and development expense for the nine months ended September 30, 2025 was unchanged compared to the same period in 2024. A decrease due to the timing of spend related to direct research and product development expense related to our on-going development costs for our U.S. CLIA, IVD and MRD strategies was offset by increases in annual compensation expense and our allocated costs from general and administrative expenses.

Selling and marketing

Comparison of the three and nine months ended September 30, 2025 and 2024 is as follows (in thousands of dollars, except percentages):

			Three Months Ended September 30,																								Nine Months Ended September 30,
			2025						2024						Change						%						2025						2024						Change						%
Selling and marketing expense:
Compensation expense			$	16,977					$	15,814					$	1,163					7		%				$	52,214					$	50,517					$	1,697					3		%
Direct marketing expense			1,376						1,427						(51)						(4)		%				3,564						4,613						(1,049)						(23)		%
Other expenses			3,332						3,271						61						2		%				10,880						9,897						983						10		%
Allocations			2,770						2,100						670						32		%				7,567						5,583						1,984						36		%
Total			$	24,455					$	22,612					$	1,843					8		%				$	74,225					$	70,610					$	3,615					5		%

Selling and marketing expense increased $1.8 million, or 8%, for the three months ended September 30, 2025 compared to the same period in 2024. The increase in compensation expense was primarily related to annual merit increases and headcount additions. Further, there was an increase in allocated costs from general and administrative expenses.

Selling and marketing expense increased $3.6 million, or 5%, for the nine months ended September 30, 2025 compared to the same period in 2024. The increase was primarily due to annual merit increases and headcount additions offset in part by the reduction of Envisia sales support and associated restructuring costs. Direct marketing expense decreased primarily due to the timing of trade show events. Further, there was an increase in allocated costs from general and administrative expenses.

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General and administrative

Comparison of the three and nine months ended September 30, 2025 and 2024 is as follows (in thousands of dollars, except percentages):

			Three Months Ended September 30,																								Nine Months Ended September 30,
			2025						2024						Change						%						2025						2024						Change						%
General and administrative expense:
Compensation expense			$	20,688					$	18,958					$	1,730					9		%				$	62,121					$	59,824					$	2,297					4		%
Professional fees			6,193						5,796						397						7		%				32,908						19,876						13,032						66		%
Information technology expense			3,794						3,057						737						24		%				11,019						8,887						2,132						24		%
Occupancy costs			2,565						2,736						(171)						(6)		%				8,482						7,828						654						8		%
Depreciation and amortization			861						1,105						(244)						(22)		%				2,876						3,070						(194)						(6)		%
Revaluation of acquisition-related contingent consideration			166						379						(213)						(56)		%				(2,713)						1,242						(3,955)						(318)		%
Other expenses			929						1,492						(563)						(38)		%				3,560						4,145						(585)						(14)		%
Allocations			(7,918)						(7,781)						(137)						2		%				(24,836)						(21,175)						(3,661)						17		%
Total			$	27,278					$	25,742					$	1,536					6		%				$	93,417					$	83,697					$	9,720					12		%

General and administrative expense increased by $1.5 million for the three months ended September 30, 2025, compared to the same period in 2024. The results were impacted primarily by an increase in stock-based compensation and professional fees, related to the Veracyte SAS collective proceedings petition filing, as well as information technology expense increases related to our cloud infrastructure and software development investments. These increases were offset by a favorable legal settlement associated with a vendor dispute. General and administrative expenses related to occupancy costs and information technology costs are allocated to general and administrative expense, selling and marketing expense, research and development expense, and cost of revenue based on the number of employees by location.

General and administrative expense increased by $9.7 million for the nine months ended September 30, 2025, compared to the same period in 2024. The results were impacted primarily by an increase of $8.6 million in professional fees related to the Veracyte SAS collective proceedings petition filing, as well as information technology expense increases related to our cloud infrastructure and software development investments. Compensation expense increased primarily due to annual merit increases, additional headcount and higher stock-based compensation and was partially offset by the prior year expense related to the voluntary exits related to our Veracyte SAS employees. These increases were offset by reductions in the revaluation of contingent consideration related to the acquisitions of C2i and nCounter diagnostic rights and the impact of the deconsolidation of Veracyte SAS. General and administrative expenses related to occupancy costs and information technology costs are allocated to general and administrative expense, selling and marketing expense, research and development expense, and cost of revenue based on the headcount and employee location.

Impairment of assets

On July 16, 2025, the Marseille Commercial Court published a decision approving the divestiture of the contract manufacturing portion of our French subsidiary, Veracyte SAS, to Helio Diagnostics SAS, effective August 1, 2025. The remaining assets of Veracyte SAS will be managed by the judicial administrator until such time that the Marseille Commercial Court appoints a judicial liquidator to solely initiate and manage liquidation proceedings. Effective August 1, 2025, we ceased to have a controlling interest in Veracyte SAS. As we began judicial restructuring proceedings affecting Veracyte SAS with the Marseille Commercial Court in the second quarter of 2025, we evaluated whether the associated assets of Veracyte SAS were impaired. We concluded, during the second quarter of 2025, that the long-lived assets of the Veracyte SAS asset group were not recoverable. As a result, we recorded a $20.5 million non-cash impairment charge during the three months ended June 30, 2025. The impairment related primarily to the Company's right-of-use assets; property, plant, and equipment; and certain tax credits.

Other income, net

Other income, net, decreased $8.9 million for the three months ended September 30, 2025 compared to the same period in 2024, primarily due to a loss of $6.7 million due to the deconsolidation of Veracyte SAS and a decrease of $2.3 million due to foreign currency revaluation, partially offset by an increase of $0.6 million from interest income.

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Other income, net, decreased $3.3 million for the nine months ended September 30, 2025 compared to the same period in 2024, primarily due to a loss of $6.7 million due to the deconsolidation of Veracyte SAS, partially offset by an increase of $3.3 million due to foreign currency revaluation and an increase of $0.9 million from interest income.

Income tax expense

We recorded income tax benefit of $0.2 million and expense of $1.7 million for the three months ended September 30, 2025 and 2024, respectively, and recorded income tax expense of $2.4 million and $3.3 million for the nine months ended September 30, 2025 and 2024, respectively.

Given our current earnings, we believe that, within the next two years, sufficient positive evidence may become available to allow us to reach a conclusion that a portion of the valuation allowance recorded against the deferred tax assets held may be reversed. A reversal would result in an income tax benefit for the quarterly and annual period in which we determine to release the valuation allowance. However, the exact timing and amount of a valuation allowance release are subject to change on the basis of the level of profitability that we actually achieve.

On July 4, 2025, the U.S. government enacted the One Big Beautiful Bill Act, or the OBBBA, which includes numerous changes to existing tax law including extending or making permanent certain business and international tax measures initially established under the 2017 Tax Cuts and Jobs Act, which were set to expire. The OBBBA permanently eliminates the requirement to capitalize and amortize U.S.-based research and experimental expenditures over five years, making these expenditures fully deductible in the period incurred. The OBBBA also permanently extends the full expensing of qualifying assets through accelerated bonus depreciation in the period acquired. The OBBBA has multiple effective dates, with certain provisions effective in 2025 and others to be implemented through 2027. The enactment of certain provisions in the period ending September 30, 2025 resulted in a reduction of current income tax liabilities and a corresponding reduction to income tax expense.

Liquidity and Capital Resources

As of September 30, 2025, we had cash and cash equivalents and short-term investments of $366.4 million. During the nine months ended September 30, 2025, our cash and cash equivalents and short-term investments increased by $77.0 million. Historically, we have obtained financing primarily through sales of our equity securities. Beginning in 2023, our operations have been financed primarily by cash flows generated by our revenue. For the nine months ended September 30, 2025, we had net income of $25.2 million, but we may not sustain profitability in the future. As of September 30, 2025, we had an accumulated deficit of $418.8 million.

We expect to continue to generate cash and our near- and longer-term liquidity requirements will continue to consist of costs to run our laboratories, research and development expenses, selling and marketing expenses, general and administrative expenses, working capital, capital expenditures, lease obligations, potential milestones associated with the C2i Acquisition, and general corporate expenses associated with the growth of our business. However, we may also use cash to acquire or invest in complementary businesses, technologies, services or products that would change our cash requirements. If we are not able to generate cash flows from our revenue to finance our cash requirements, we will need to finance future cash needs primarily through public or private equity offerings, debt financings, borrowings or strategic collaborations or licensing arrangements. If we are not able to secure additional financing when needed, or on terms that are favorable to us, we may have to delay, reduce the scope of or eliminate one or more research and development programs or selling and marketing initiatives, or forgo potential acquisitions or investments. In addition, we may have to work with a partner on one or more of our products or development programs, which could lower the economic value of those programs to us. Moreover, any instability in the global credit markets or the banking system may impact our liquidity both in the short term and long term.

Our material cash requirements include the following obligations:

Operating Leases

We lease office and laboratory facilities in the U.S., including in South San Francisco and San Diego, California and Austin, Texas, and lease certain equipment under various non-cancelable lease agreements. Effective August 2025, in connection with the restructuring proceeding in Veracyte SAS, we are no longer a party to the lease in Marseille, France. The lease terms of our leases as of September 30, 2025 extend to March 2040 and contain extension of lease term and expansion options. As of September 30, 2025, the leases have a weighted average remaining lease term of 11.3 years and total future minimum lease payments of $74.7 million.

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Acquisition-Related Contingent Consideration

C2i Acquisition Contingent Consideration

Pursuant to the Agreement and Plan of Merger, dated as of January 5, 2024, by and among the Company, C2i, Canary Merger Sub I, Inc., a Delaware corporation and wholly owned subsidiary of the Company, Veracyte Diagnostics, LLC, a Delaware limited liability company and a wholly owned subsidiary of the Company, and Fortis Advisors LLC, as the C2i securityholders’ agent, or the Merger Agreement, we may be required to pay to certain noteholders of C2i up to an additional $16.0 million in cash or shares of our common stock, at our election, upon the achievement of certain milestones. During the nine months ended September 30, 2025, one of the milestones was achieved resulting in the payment of $0.7 million. As of September 30, 2025, we expect to potentially achieve a portion of all of the remaining milestones contained in the Merger Agreement within the next 12 months, requiring payments totaling up to $16.0 million.

nCounter Analysis System Acquisition Contingent Consideration

As part of our agreement to acquire the exclusive global diagnostic license to the nCounter Analysis System, we may be required to pay up to an additional $10.0 million in cash, contingent upon first achievement or occurrence, by us or on our behalf, of the commercial launch of the first, second and third diagnostic tests for use on the nCounter multiplex analysis system. As of September 30, 2025, the achievement of one of the milestones is forecasted to occur within the next 12 months, requiring payments totaling $3.5 million.

Cash Flows

The following table summarizes our cash flows for the nine months ended September 30, 2025 and 2024 (in thousands of dollars): 

			Nine Months Ended September 30,
			2025						2024
Net cash provided by operating activities			$	83,724					$	50,572
Net cash used in investing activities			(3,779)						(2,134)
Net cash (used in) provided by financing activities			(4,073)						9,414

Cash Flows from Operating Activities

Cash provided by operating activities for the nine months ended September 30, 2025 was $83.7 million. Our net income of $25.2 million includes non-cash charges of $32.7 million of stock-based compensation expense, $16.1 million of depreciation and amortization, of which $9.8 million was related to intangible asset amortization, $20.5 million tied to the impairment of assets, $3.9 million loss on the deconsolidation of Veracyte SAS, non-cash lease expense of $2.3 million, non-cash gains of $2.7 million from the revaluation of contingent consideration, $3.8 million from the effect of foreign currency changes on operations and amortization of discount on short-term investments of $2.6 million. Cash used as a result of changes in operating assets and liabilities was $7.8 million, primarily composed of an increase in prepaid expenses and other current assets of $6.4 million, an increase in accounts receivable of $3.9 million, an increase in supplies and inventory of $2.6 million, a decrease in operating lease liabilities of $1.7 million, and an increase in accounts payable of $0.5 million, partially offset by an increase in accrued liabilities and deferred revenue of $7.0 million and a decrease in other assets of $0.3 million.

Cash provided by operating activities for the nine months ended September 30, 2024 was $50.6 million. Our net income of $19.0 million includes non-cash charges of $26.6 million of stock-based compensation expense, $17.2 million of depreciation and amortization, of which $11.2 million was related to intangible asset amortization, and the remainder was due to a non-cash lease expense of $3.6 million. Cash used as a result of changes in operating assets and liabilities was $17.1 million, primarily composed of an increase in accounts receivable of $8.4 million, an increase in supplies and inventory of $4.2 million, a decrease in operating lease liability of $3.9 million, a decrease in accounts payable of $3.0 million, and an increase in other assets of $1.7 million, partially offset by a decrease in accrued liabilities and deferred revenue of $3.9 million.

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Cash Flows from Investing Activities

Cash used in investing activities for the nine months ended September 30, 2025 was $3.8 million, consisting of $5.9 million used in the purchase of property, plant and equipment, partially offset by net proceeds of $2.1 million from the purchase and maturity of short-term investments.

Cash used in investing activities for the nine months ended September 30, 2024 was $2.1 million, consisting of $7.1 million used in the purchase of property, plant and equipment, partially offset by $5.0 million net cash acquired from C2i excluding post-close transactions costs.

Cash Flows from Financing Activities

Cash used in financing activities for the nine months ended September 30, 2025 was $4.1 million, consisting of $14.6 million in tax payments during the period related to the vesting of restricted stock units granted to employees, partially offset by $10.6 million in proceeds from the exercise of options to purchase our common stock and the purchase of stock under our Employee Stock Purchase Plan, or ESPP.

Cash provided by financing activities for the nine months ended September 30, 2024 was $9.4 million, consisting of $16.7 million in proceeds from the exercise of options to purchase our common stock and the purchase of stock under our ESPP, partially offset by $7.3 million in tax payments during the period related to the vesting of restricted stock units granted to employees.

Recent Accounting Pronouncements

For a discussion of recent accounting pronouncements, see Note 1, Organization, Description of Business and Summary of Significant Accounting Policies, in the notes to our condensed consolidated financial statements included elsewhere in this report.

Critical Accounting Policies and Estimates

Our management's discussion and analysis of our financial condition and results of operations is based on our condensed consolidated financial statements, which have been prepared in accordance with GAAP. The preparation of the condensed consolidated financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent liabilities at the date of the condensed consolidated financial statements, as well as the reported revenue generated and expenses incurred during the reporting periods. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions and any such differences may be material. We believe that the accounting policies discussed in our Annual Report are critical to understanding our historical and future performance, as these policies relate to the more significant areas involving management's judgments and estimates. There have been no material changes to our critical accounting policies and estimates as compared to the critical accounting policies and estimates disclosed in our Annual Report.

Item 3.  Quantitative and Qualitative Disclosure About Market Risk

Interest Rate Risk

We are exposed to market risks in the ordinary course of our business. These risks primarily relate to interest rates. We had cash and cash equivalents and short-term investments of $366.4 million as of September 30, 2025 which consisted of bank deposits, money market funds and United States treasury securities. Such interest-bearing instruments carry a degree of risk; however, a hypothetical 10% change in interest rates during any of the periods presented would not have had a material impact on our condensed consolidated financial statements. This analysis is based on a sensitivity model that measures market value changes when changes in interest rates occur. Any realized gains or losses resulting from such interest rate changes and from the current unrealized gains or losses would only occur if we sold the investments prior to maturity. We do not enter into investments for trading purposes and have not used any derivative financial instruments to manage our interest rate risk exposure.

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Foreign Currency Risk

As of September 30, 2025 we held $1.0 million of bank deposits denominated in Euros. Such Euro denominated deposits carry a degree of risk from changes in currency exchange rates as the gains or losses from changes in exchange rates are included in our net income and comprehensive income (loss). As of September 30, 2025 a hypothetical 10% appreciation or depreciation of the U.S. dollar relative to the Euro would not have had a material impact on our condensed consolidated financial statements. At this time, we have not entered into, but in the future we may enter into, derivatives or other financial instruments in an attempt to hedge our foreign currency risk.

Inflation Risk

We are facing inflation headwinds in compensation, travel, supply and inventory costs. However, we do not believe that inflation has had a material effect on our business, financial condition, or operating results to date.

Item 4.  Controls and Procedures

(a)Evaluation of Disclosure Controls and Procedures

We maintain “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or Exchange Act, which are designed to provide reasonable assurance that information required to be disclosed by us in reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in Securities and Exchange Commission rules and forms, and that such information is accumulated and communicated to our management, including our Chief Executive Officer and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. Management recognized that disclosure controls and procedures, no matter how well designed and operated, can provide only reasonable, not absolute, assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible disclosure controls and procedures.

Based on this evaluation, our Chief Executive Officer and Chief Financial Officer concluded that, our disclosure controls and procedures were effective as of September 30, 2025 at the reasonable assurance level.

(b)Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) that occurred during the three months ended September 30, 2025, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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PART II. — OTHER INFORMATION

Item 1.  Legal Proceedings

The information set forth in Note 6, Commitments and Contingencies, under the heading “Contingencies,” in the notes to our condensed consolidated financial statements included elsewhere in this report is incorporated herein by reference

Item 1A.  Risk Factors

Summary of Risk Factors

In addition to the information set forth in this report, you should consider carefully the factors and other cautionary statements discussed in the section titled “Risk Factors” in Part I, Item 1A of our Annual Report on Form 10-K. There have been no material changes in our risk factors from those described in our Annual Report.

Item 2. Unregistered Sales of Equity Securities and Use of Proceeds

None.

Item 3. Defaults Upon Senior Securities

None.

Item 4. Mine Safety Disclosures

Not applicable.

Item 5. Other Information

(C) Insider Trading Arrangements

During the three months ended September 30, 2025, the following officers and directors adopted, modified or terminated a “Rule 10b5-1 trading arrangement” (as defined in Item 408 of Regulation S-K of the Exchange Act). None of our other Section 16 officers or directors adopted, modified or terminated such “Rule 10b5-1 trading arrangements” during the three months ended September 30, 2025.

•Jens Holstein, Director, adopted a new trading plan on August 21, 2025 (with the first trade under the new plan scheduled for approximately November 20, 2025). The trading plan will be effective until August 21, 2026 to sell an aggregate of 10,000 shares of our common stock.

•Phil Febbo, Chief Scientific Officer and Chief Medical Officer, adopted a new trading plan on August 21, 2025 (with the first trade under the new plan scheduled for approximately February 28, 2026). The trading plan will be effective until November 27, 2026 to sell an aggregate of (i) 13,425 shares of our common stock, plus (ii) 100% of the net shares resulting from the vesting of 26,514 restricted stock units during the plan period (net shares are net of tax withholding).

•Rebecca Chambers, Chief Financial Officer, adopted a new trading plan on August 21, 2025 (with the first trade under the new plan scheduled for approximately November 20, 2025). The trading plan will be effective until December 11, 2026 to sell an aggregate of (i) 10,000 shares of our common stock, plus (ii) 100% of the net shares resulting from the vesting of 82,188 restricted stock units during the plan period (net shares are net of tax withholding).

•Annie McGuire, General Counsel and Chief People Officer, adopted a new trading plan on August 29, 2025 (with the first trade under the new plan scheduled for approximately November 28, 2025). The trading plan will be effective until December 18, 2026 to sell an aggregate of (i) 7,671 shares of our common stock, plus (ii) specified percentages ranging between 33% and 100% of the net shares resulting from the vesting of 179,803 restricted stock units during the plan period (net shares are net of tax withholding).

•Karin Eastham, Director, adopted a new trading plan on September 5, 2025 (with the first trade under the new plan scheduled for approximately December 5, 2025). The trading plan will be effective until November 20, 2026 to sell an aggregate of 29,533 shares of our common stock.

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Table of Contents

Item 6.  Exhibits

Incorporated by Reference

Exhibit Number

Description

Form

File No.

Exhibit

Filing Date

Filed Herewith

31.1

Certification of Principal Executive Officer pursuant to Rules 13a-14(a)/15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

X

31.2

Certification of Principal Financial Officer pursuant to Rule 13a-14(a)/15d-14(a), as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

X

32.1*

Certification of Principal Executive Officer pursuant to 18 U.S.C. § 1350 (Section 906 of the Sarbanes-Oxley Act of 2002)

X

32.2*

Certification of Principal Financial Officer pursuant to 18 U.S.C. § 1350 (Section 906 of the Sarbanes-Oxley Act of 2002)

X

101.INS

Inline XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL

X

101.SCH

Inline XBRL Taxonomy Extension Schema

X

101.CAL

Inline XBRL Taxonomy Extension Calculation Linkbase

X

101.DEF

Inline XBRL Taxonomy Extension Definition Linkbase

X

101.LAB

Inline XBRL Taxonomy Extension Label Linkbase

X

101.PRE

Inline XBRL Taxonomy Extension Presentation Linkbase

X

104

Cover Page Interactive Data File (embedded within the Inline XBRL and contained in Exhibit 101)

X

*

In accordance with Item 601(b)(32)(ii) of Regulation S-K and SEC Release No. 34-47986, the certifications furnished in Exhibits 32.1 and 32.2 hereto are deemed to accompany this Form 10-Q and will not be deemed “filed” for purposes of Section 18 of the Exchange Act or deemed to be incorporated by reference into any filing under the Exchange Act or the Securities Act except to the extent that the registrant specifically incorporates it by reference.

37

Table of Contents

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

Date: November 5, 2025

VERACYTE, INC.

By:

/s/ Rebecca Chambers

Rebecca Chambers Chief Financial Officer

38

FAQ

What were Veracyte (VCYT) Q3 2025 revenues and earnings?

Q3 2025 revenue was $131.9 million and net income was $19.1 million; diluted EPS was $0.24.

How did Veracyte’s revenue mix look in Q3 2025?

Testing revenue was $127.8 million, product revenue $3.3 million, and biopharma/other revenue $0.8 million.

What was Veracyte’s cash position at quarter-end?

As of September 30, 2025, cash and cash equivalents were $315.6 million; short-term investments were $50.9 million.

Did any one payer account for a large share of revenue?

Yes. In Q3, Medicare represented 33% of total revenue and UnitedHealthcare 14%.

What notable non-operating item affected Q3 results?

A $6.7 million loss on deconsolidation of the French subsidiary was recorded in other income (loss), net.

How much operating cash flow did Veracyte generate year-to-date?

For the nine months ended September 30, 2025, operating cash flow was $83.7 million.

How many shares of VCYT were outstanding?

There were 79,049,173 common shares outstanding as of October 31, 2025.