GeneDx Holdings Corp. 10-K

Item 8. Financial Statements and Supplementary Data Report of Independent Registered Public Accounting Firm (PCAOB ID 42 ) 66 Consolidated Financial Statements: Consolidated Balance Sheets 67 Consolidated Statements of Operations and Comprehensive Loss 68 Consolidated Statements of Stockholders' Equity 69 Consolidated Statements of Cash Flows 70 Notes to Consolidated Financial Statements 71 65 Table of Contents Report of Independent Registered Public Accounting Firm To the Stockholders and the Board of Directors of GeneDx Holdings Corp. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of GeneDx Holdings Corp. (the Company) as of December 31, 2024 and 2023, the related consolidated statements of operations and comprehensive loss, stockholders’ equity and cash flows for each of the two years in the period ended December 31, 2024, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2024 and 2023, and the results of its operations and its cash flows for each of the two years in the period ended December 31, 2024, in conformity with U.S. generally accepted accounting principles. Basis for Opinion These financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company’s financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Company is not required to have, nor were we engaged to perform, an audit of its internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Company’s internal control over financial reporting. Accordingly, we express no such opinion. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion. /s/ ERNST & YOUNG LLP We have served as the Company’s auditor since 2018. New York, New York February 20, 2025 66 Table of Contents GeneDx Holdings Corp. Consolidated Balance Sheets (in thousands, except share and per share amounts) December 31, 2024 2023 Assets Current assets: Cash and cash equivalents $ 85,212 $ 99,681 Marketable securities 55,973 30,467 Accounts receivable 37,426 32,371 Due from related parties 203 445 Inventory, net 10,650 8,777 Prepaid expenses and other current assets 8,504 10,598 Total current assets 197,968 182,339 Operating lease right-of-use assets 25,613 26,900 Property and equipment, net 32,893 32,479 Intangible assets, net 158,600 172,625 Other assets 4,306 4,413 Total assets $ 419,380 $ 418,756 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable and accrued expenses $ 30,044 $ 37,456 Due to related parties 1,607 1,379 Short-term lease liabilities 3,336 3,647 Other current liabilities 19,830 16,336 Total current liabilities 54,817 58,818 Long-term debt, net of current portion 51,913 52,688 Long-term lease liabilities 60,919 62,938 Other liabilities 5,519 14,735 Deferred taxes 965 1,560 Total liabilities 174,133 190,739 Purchase commitments and contingencies (Note 10) Stockholders’ Equity: Preferred Stock, $ 0.0001 par value: 1,000,000 shares authorized, 0 shares issued and outstanding at December 31, 2024 and December 31, 2023, respectively — — Class A common stock, $ 0.0001 par value: 1,000,000,000 shares authorized, 28,016,545 and 25,978,863 shares issued and outstanding at December 31, 2024 and December 31, 2023, respectively 2 2 Additional paid-in capital 1,596,889 1,527,778 Accumulated deficit ( 1,352,474 ) ( 1,300,188 ) Accumulated other comprehensive income 830 425 Total stockholders’ equity 245,247 228,017 Total liabilities and stockholders’ equity $ 419,380 $ 418,756 The accompanying notes are an integral part of these consolidated financial statements. 67 Table of Contents GeneDx Holdings Corp. Consolidated Statements of Operations and Comprehensive Loss (in thousands, except per share and share amounts) Year Ended December 31, 2024 2023 Revenue Diagnostic test revenue $ 302,157 $ 195,654 Other revenue 3,293 6,912 Total revenue 305,450 202,566 Cost of services 111,053 112,560 Gross profit 194,397 90,006 Research and development 45,722 58,266 Selling and marketing 67,371 60,956 General and administrative 101,110 133,755 Impairment loss — 10,402 Other operating expenses, net 3,407 7,223 Loss from operations ( 23,213 ) ( 180,596 ) Non-operating (expenses) income, net Change in fair value of warrants and contingent liabilities ( 13,370 ) 1,170 Interest (expense) income, net ( 3,032 ) 1,114 Other (expense) income, net ( 13,014 ) 1,619 Total non-operating (expense) income, net ( 29,416 ) 3,903 Loss before income taxes ( 52,629 ) ( 176,693 ) Income tax benefit 343 926 Net loss $ ( 52,286 ) $ ( 175,767 ) Other comprehensive income, net of tax Unrealized gain related to available for sale securities, net 405 425 Comprehensive loss $ ( 51,881 ) $ ( 175,342 ) Weighted average shares outstanding of Class A common stock 26,891,213 24,311,989 Basic and diluted net loss per share, Class A common stock $ ( 1.94 ) $ ( 7.23 ) The accompanying notes are an integral part of these consolidated financial statements. 68 Table of Contents GeneDx Holdings Corp. Consolidated Statements of Stockholders’ Equity (in thousands, except share amounts) Class A Common Stock Additional paid-in capital Accumulated deficit Accumulated other comprehensive income Total stockholders’ equity Shares Par Value Balance at December 31, 2022 11,773,065 $ 1 $ 1,378,125 $ ( 1,124,421 ) — $ 253,705 Net loss — — — ( 175,767 ) — ( 175,767 ) Common stock issued pursuant to stock option exercises 50,444 — 285 — — 285 Stock-based compensation expense — — ( 326 ) — — ( 326 ) Vested restricted stock units converted to common stock 431,671 — — — — — Other comprehensive income, net of tax — — — — 425 425 Issuance of common stock in registered direct offering, net of issuance costs 676,868 — 7,564 — — 7,564 Issuance of common stock for first Milestone Payment 701,460 — 6,692 — — 6,692 Fractional shares issued upon reverse stock split 29,603 — — — — — Issuance of common stock in underwritten public offering, net of issuance costs 12,315,752 1 135,438 — — 135,439 Balance at December 31, 2023 25,978,863 $ 2 $ 1,527,778 $ ( 1,300,188 ) $ 425 $ 228,017 Net loss — — — ( 52,286 ) — ( 52,286 ) Common stock issued pursuant to stock option exercises 68,453 — 394 — — 394 Common stock issued pursuant to Perceptive warrant exercise 645,414 — 12,586 — — 12,586 Stock-based compensation expense — — 9,138 — — 9,138 Other comprehensive income, net of tax — — — — 405 405 Vested restricted stock units converted to common stock 471,663 — — — — — Issuance of common stock in ATM offering, net of issuance costs 825,379 — 46,496 — — 46,496 Common stock issued pursuant to employee stock purchase plan 26,773 — 497 — — 497 Balance at December 31, 2024 28,016,545 $ 2 $ 1,596,889 $ ( 1,352,474 ) $ 830 $ 245,247 The accompanying notes are an integral part of these consolidated financial statements. 69 Table of Contents GeneDx Holdings Corp. Consolidated Statements of Cash Flows (in thousands) Year Ended December 31, 2024 2023 Operating activities Net loss $ ( 52,286 ) $ ( 175,767 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization expense 21,953 33,734 Stock-based compensation expense 9,138 ( 326 ) Change in fair value of warrants and contingent liabilities 13,370 ( 1,170 ) Deferred tax benefit ( 343 ) ( 926 ) Provision for excess and obsolete inventory 180 3,913 Change in third party payor reserves 607 ( 9,745 ) Gain on sale of assets — ( 1,677 ) Gain on debt forgiveness — ( 2,750 ) Impairment loss — 10,402 Other 3,630 2,406 Change in operating assets and liabilities: Accounts receivable ( 5,421 ) 10,263 Inventory ( 2,585 ) 975 Accounts payable and accrued expenses ( 20,461 ) ( 46,953 ) Other assets and liabilities 3,722 ( 2,526 ) Net cash used in operating activities ( 28,496 ) ( 180,147 ) Investing activities Proceeds from maturities of marketable securities 41,060 17,765 Purchases of marketable securities ( 66,302 ) ( 47,670 ) Purchases of property and equipment ( 5,491 ) ( 5,250 ) Proceeds from sales of marketable securities 601 — Consideration on escrow paid for Legacy GeneDx acquisition — ( 12,144 ) Proceeds from sales of assets — 4,034 Development of internal-use software assets — ( 461 ) Net cash used in investing activities ( 30,132 ) ( 43,726 ) Financing activities Proceeds from offerings, net of issuance costs 46,496 143,002 Exercise of stock options 394 285 Issuance of stock pursuant to employee stock purchase plan 497 — Long-term debt principal payments ( 497 ) ( 2,000 ) Finance lease payoff and principal payments ( 2,728 ) ( 3,598 ) Proceeds from long-term debt — 48,549 Net cash provided by financing activities 44,162 186,238 Net decrease in cash, cash equivalents and restricted cash ( 14,466 ) ( 37,635 ) Cash, cash equivalents and restricted cash, at beginning of year 100,668 138,303 Cash, cash equivalents and restricted cash, at end of year $ 86,202 $ 100,668 Supplemental disclosures of cash flow information Stock consideration paid pursuant to exercise of Perceptive warrant $ 12,586 $ — Cash paid for interest $ 6,677 $ 3,041 Purchases of property and equipment in accounts payable and accrued expenses $ 2,597 $ 134 Cash paid for taxes $ 1,167 $ 1,465 Assets acquired under capital leases obligations $ 689 $ — Issuance of common stock for first Milestone Payment $ — $ 6,692 Lease liability from obtaining right-of-use asset $ — $ 637 The accompanying notes are an integral part of these consolidated financial statements. 70 Table of Contents GeneDx Holdings Corp. Notes to Consolidated Financial Statements 1. Organization and Description of Business GeneDx Holdings Corp., through its subsidiary GeneDx, LLC, is a leading genomics company—one that sits at the intersection of diagnostics and data science, pairing decades of genomic expertise with an ability to interpret clinical data at scale. The Company believes that everyone deserves personalized, targeted medical care—and that it all begins with a genetic diagnosis. Fueled by one of the world’s largest rare disease data sets, the Company’s industry-leading exome and genome tests translate complex genomic data into clinical answers that unlock personalized health plans, accelerate drug discovery, and improve health system efficiencies. The Company operates with conviction that what is best for patients must be embedded in every aspect of our work. In support of these beliefs, we value equitability, simplicity and transparency. Unless otherwise stated herein or unless the context otherwise requires, references in these notes to : • “GeneDx Holdings” refer to GeneDx Holdings Corp., a Delaware corporation; • “Legacy GeneDx” refer to GeneDx, LLC, a Delaware limited liability company, which we acquired on April 29, 2022 (the “Acquisition”); • “Legacy Sema4” refer to Sema4 OpCo Inc., a Delaware corporation, which consummated the business combination with CM Life Sciences, Inc. (“CMLS”) on July 22, 2021 (the “Business Combination”); and • “we,” “us” and “our,” the “Company” and “GeneDx” refer, as the context requires, to GeneDx Holdings and its consolidated subsidiaries. 2. Summary of Significant Accounting Policies Basis of Presentation The accompanying consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States (“U.S. GAAP”). These financial statements consolidate the operations and accounts of the Company and its wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated. Unless otherwise noted, all tabular dollars are in thousands, except per share amounts. Emerging Growth Company The Company is an “emerging growth company” as defined in the Jumpstart Our Business Startups Act of 2012. In addition, the Company was previously a “smaller reporting company”, as defined in Item 10(f)(1) of the SEC’s Regulation S-K and currently takes advantage of certain of the scaled disclosures available to smaller reporting companies. As such, the Company is eligible for exemptions from various reporting requirements applicable to other public companies that are not emerging growth companies, including reduced reporting, including the reporting of two fiscal years of financial statements, not being required to provide an auditor attestation of internal control over financial reporting under Section 404 of the Sarbanes-Oxley Act, and extended transition periods to comply with new or revised accounting standards for public business entities. The Company has elected to avail itself of this exemption and, therefore, will not be subject to the same new or revised accounting standards as other public companies that are not emerging growth companies. Use of Estimates The preparation of the Company’s consolidated financial statements in conformity with U.S. GAAP requires management to make certain estimates, judgments and assumptions that affect the reported amounts of assets and liabilities and the related disclosures at the date of the consolidated financial statements as well as the reported amounts of revenues and expenses during the periods presented. The Company bases these estimates on current facts, historical and anticipated results, trends and various other assumptions that it believes are reasonable in the circumstances, including assumptions as to future events. These estimates include, but are not limited to, the transaction price for certain contracts with customers, potential or actual claims for recoupment from third-party payors, the valuation of stock-based awards, the valuation of warrant liabilities and income taxes. Actual results could differ materially from those estimates, judgments and assumptions. Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to concentrations of credit risk consist primarily of cash and cash equivalents, marketable securities and accounts receivable. The majority of the Company’s cash, cash equivalents and restricted cash are uninsured with account balances in excess of the Federal Deposit Insurance Company limits. 71 Table of Contents The Company’s cash, cash equivalents and marketable securities are deposited with high-quality financial institutions. Management believes these financial institutions are financially sound and, accordingly, that minimal credit risk exists. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash in excess of government insured limits and in the event of default by corporations and governments in which it holds investments in cash equivalents and short-term debt securities, to the extent recorded on the consolidated balance sheet. The Company has not experienced any losses on its deposits of cash and cash equivalents. The Company assesses both the self-pay patient and the third-party payor that reimburses the Company on the patient’s behalf and, institutional billed clients when evaluating concentration of credit risk from customers. Significant patients and payors are those that represent more than 10% of the Company’s total annual revenues or accounts receivable balance at each respective balance sheet date. The significant concentrations of accounts receivable as of December 31, 2024 and 2023 were primarily from large managed care insurance companies, institutional billed accounts, and data arrangements. There was no individual patient or client that accounted for 10% or more of revenue or accounts receivable for any of the years presented. The Company does not require collateral as a means to mitigate customer credit risk. For each significant payor, revenue as a percentage of total revenues and accounts receivable as a percentage of total accounts receivable are as follows: Revenue Accounts Receivable Year Ended December 31, As of December 31, 2024 2023 2024 2023 Payor A (1) 22 % 18 % 13 % * Payor B 32 % 28 % 11 % 10 % __________________ * less than 10% (1) This payor group includes multiple individual plans and the Company calculates and presents the aggregated value from all plans, which is consistent with the Company’s portfolio approach used in accounting for diagnostic test revenue. The Company is subject to a concentration of risk from a limited number of suppliers for certain reagents and laboratory supplies. One supplier accounted for approximately 13 % and 11 % of purchases for the years ended December 31, 2024 and 2023, respectively. Another supplier accounted for approximately 10 % and 11 % of purchases for the years ended December 31, 2024 and 2023, respectively. This risk is managed by maintaining a target quantity of surplus stock. Alternative suppliers are available for some or all of these reagents and supplies. Revenue Recognition The Company recognizes revenue when control of the promised goods or services is transferred to the customer in an amount that reflects the consideration which the Company expects to be entitled to in exchange for those goods or services. If any changes in customer credit issues are identified which were not assessed at the date of service, provisions for credit losses are recognized and recorded. Diagnostic test revenue The Company’s diagnostic test revenue contracts typically consist of a single performance obligation to deliver diagnostic testing services to the ordering facility or patient and therefore allocation of the contract transaction price is not applicable. Control over diagnostic testing services is generally transferred at a point in time when the customer obtains control of the promised service which is upon delivery of the test. Diagnostic test revenues consist primarily of services reimbursed by third-party insurance payors. Third-party insurance payors include managed care health plans and commercial insurance companies, including plans offered through the health insurance exchanges, and employers. In arrangements with third-party insurance payors, the transaction price is stated within the contract, however, the Company accepts payments from third-party payors that are less than the contractually stated price and is therefore variable consideration and the transaction price is estimated. When determining the transaction price, the Company uses a portfolio approach as a practical expedient to account for categories of diagnostic test contracts as collective groups rather than on an individual contract basis. The portfolio consists of major payor classes based on third-party payors. Based on historical collection trends and other analyses, the Company believes that revenue recognized by utilizing the portfolio approach approximates the revenue that would have been recognized if an individual contract approach was used. 72 Table of Contents Estimates of allowances for third-party insurance payors that impact the estimated transaction price are based upon the pricing and payment terms specified in the related contractual agreements. Contractual pricing and payment terms in third-party insurance agreements are generally based upon predetermined rates per diagnosis, per diem rates or discounted fee-for-service rates. In addition, for third-party payors in general, the estimated transaction price is impacted by factors such as historical collection experience, contractual provisions and insurance reimbursement policies, payor mix, and other relevant information for applicable payor portfolios. For institutional clients, the customer is the institution. The Company determines the transaction price associated with services rendered in accordance with the contractual rates established with each customer. Payment terms and conditions vary by contract and customer, however standard payment terms are generally less than 60 days from the invoice date. In instances where the timing of the Company’s revenue recognition differs from the timing of its invoicing, the Company does not assess whether a contract has a significant financing component if the expectation at contract inception is such that the period between payment by the customer and the transfer of the promised services to the customer will be one year or less. Other revenue The Company enters into both short-term and long-term project-based collaboration and service agreements with customers. Certain of these contracts include a license to directly access the Company’s intellectual property or participation by the Company on joint steering committees with the customer, which was considered to be immaterial in the context of the contract. The Company concludes that the goods and services transferred to our customers pursuant to these agreements generally comprise a single performance obligation on the basis that such goods and services are not distinct within the context of the contract. This is because the goods and services are highly interdependent and interrelated such that the Company would not be able to fulfill its underlying promise to our customers by transferring each good or service independently. Certain of these contracts include non-refundable upfront payments and variable payments based upon the achievement of certain milestones or fixed monthly payments during the contract term. Non-refundable upfront payments received prior to the Company performing performance obligation are recorded as a contract liability upon receipt. Milestone payments are included in the transaction price only when it is probable that doing so will not result in a significant reversal of cumulative revenue recognized when the uncertainty associated with the milestone is subsequently resolved. For longer-term contracts, the Company does not account for a significant financing component since a substantial amount of the consideration promised by the customer is variable and the amount or timing of that consideration varies on the basis of a future event that is not substantially within the control of either party. The Company satisfies its performance obligation generally over time if the customer simultaneously receives and consumes the benefits provided by the Company’s services as the Company performs those services. The Company recognizes revenue over time using an input measure based on costs incurred on the basis that this measure best reflects the pattern of transfer of control of the services to the customer. In some contracts, the Company subcontracts certain services to other parties for which the Company is ultimately responsible. Costs incurred for such subcontracted services are included in the Company’s measure of progress for satisfying its performance obligation and are recorded in cost of services in the consolidated statements of operations and comprehensive loss. Changes in the total estimated costs to be incurred in measuring the Company’s progress toward satisfying its performance obligation may result in adjustments to cumulative revenue recognized at the time the change in estimate occurs. See Note 3, “ Revenue Recognition ” for more information. Cash, Cash Equivalents and Restricted Cash The Company considers all highly liquid investments with original maturities of three months or less from the date of purchase to be cash equivalents. Cash equivalents consist of amounts invested in money market funds and debt securities. Carrying values of cash equivalents approximate fair value due to the short-term nature of these instruments. The current and long-term portions of restricted cash are included within prepaid expenses and other current assets and other assets. Marketable Securities Marketable securities are classified as current assets as these investments are intended to be available to the Company for use in funding current operations. Unrealized gains and losses on available for sale securities are deemed temporary and are classified in accumulated other comprehensive income within stockholders’ equity. Changes in the fair value of available for sale securities impact earnings only when such securities are sold, or an allowance for expected credit losses or impairment is recognized. The cost of marketable securities sold is based on the specific identification method. We regularly evaluate our portfolio of marketable securities for expected credit losses and impairment for any decline in fair value determined to be other-than-temporary. In 73 Table of Contents making this judgement, we evaluate, among other things, the extent to which the fair value of a security is less than its amortized cost; the financial condition of the issuer, including the credit quality, and any changes thereto; and our intent to sell, or whether we will more likely than not be required to sell, the security before recovery of its amortized cost basis. Our assessment of whether a marketable security has a credit loss or is impaired could change in the future due to new developments or changes in assumptions related to any particular security. See Note 4, “ Fair Value Measurements ” for more information. Accounts Receivable Accounts receivable consists of amounts due from customers and third-party payors for services performed and reflect the consideration to which the Company expects to be entitled in exchange for providing those services. Accounts receivable is estimated and recorded in the period the related revenue is recorded. During the years ended December 31, 2024 and 2023, the Company did not record provisions for credit losses. The Company wrote off $ 0.4 million of accounts receivable balances for the year ended December 31, 2024 and none for the year ended December 31, 2023. Inventory, net Inventory, net, which primarily consists of finished goods such as testing supplies and reagents, is capitalized when purchased and expensed when used in performing services. Inventory is stated at the lower of cost or net realizable value. Cost is determined using actual costs on a first-in, first-out basis. The Company periodically performs obsolescence assessments and writes off any inventory that is no longer usable. Any write-down of inventory to net realizable value creates a new cost basis. Property and Equipment, net Property and equipment, net are stated at cost less accumulated depreciation and amortization. Equipment includes assets under finance lease. Improvements are capitalized, while maintenance and repairs are expensed as incurred. When assets are retired or otherwise disposed of, the cost and accumulated depreciation and amortization are removed from the consolidated balance sheets and any resulting gain or loss is reflected in the consolidated statements of operations and comprehensive loss in the period realized. Finance leases and leasehold improvements are amortized straight-line over the shorter of the term of the lease or the estimated useful life. All other property and equipment assets are depreciated using the straight-line method over the estimated useful life of the asset, which ranges from three to five years . The Company reviews the recoverability of its long-lived assets when events or changes in circumstances occur that indicate that the carrying value of the asset or asset group may not be recoverable. An impairment loss is recognized when the total estimated future undiscounted cash flows expected to result from the use of the asset and its eventual disposition are less than its carrying amount. Impairment, if any, is assessed using discounted cash flows or other appropriate measures of fair value. See Note 5, “ Property and Equipment ”. Intangible Assets, Net Amortizable intangible assets include trade names and trademarks, developed technology and customer relationships acquired as part of business combinations. Intangible assets are amortized on a straight-line basis. All intangible assets subject to amortization are reviewed for impairment in accordance with ASC Topic 360, Property, Plant and Equipment . There were no impairment losses recorded on intangible assets for any periods presented. See Note 6, “ Intangible Assets ” for more information. Fair Value Measurements Financial assets and liabilities are recorded at fair value. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The Company determines the fair value of its financial instruments based on assumptions that market participants would use in pricing an asset or liability in the principal or most advantageous market. The following hierarchy lists three levels of fair value based on the extent to which inputs used in measuring fair value are observable in the market: Level 1 : Observable inputs such as quoted prices (unadjusted) in active markets that are accessible at the measurement date for identical assets or liabilities. 74 Table of Contents Level 2 : Observable inputs such as quoted prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active or model-derived valuations whose significant inputs are observable. Level 3 : Unobservable inputs that are significant to the measurement of fair value but are supported by little to no market data. The Company’s financial assets and liabilities consist of cash and cash equivalents, marketable securities, accounts receivable, other current assets, accounts payable and accrued expenses, other current liabilities, and long-term debt. The Company’s carrying value of cash and cash equivalents, accounts receivable, other current assets, accounts payable, accrued expenses and other current liabilities approximate their fair value due to the relatively short-term nature of these accounts. See Note 4, “ Fair Value Measurements ” for more information. Warrant Liability The Company accounts for warrants as liability-classified instruments based on an assessment of the warrant terms and applicable authoritative guidance in accordance with ASC Topic 480, Distinguishing Liabilities from Equity (“ASC 480”) and ASC Topic 815, Derivatives and Hedging (“ASC 815”). The assessment considers whether the warrants are freestanding financial instruments pursuant to ASC 480, whether the warrants meet the definition of a liability pursuant to ASC 480, and whether the warrants meet all of the requirements for equity classification under ASC 815. This assessment is conducted at the time of warrant issuance. The warrant liabilities are recorded on the consolidated balance sheets at fair value on their respective issuance dates, with subsequent changes in respective fair values recognized on the consolidated statements of operations and comprehensive loss at each reporting date. See Note 4, “ Fair Value Measurements ” for more information. Stock-Based Compensation The Company measures stock-based compensation at the grant date based on the fair value of the award and recognizes stock-based compensation expense over the requisite service period for each separate vesting portion of the award on a straight-line basis. The Company uses the Black-Scholes option-pricing model to estimate the fair value of its stock option awards. Determining the fair value of stock option awards requires judgment, including estimating expected stock price volatility and expected option term. The Company estimates a volatility factor for the Company’s options based on analysis of historical share prices of a peer group of public companies, the historical share prices of the Company, and the implied volatility of the Company’s call options. The Company estimates the expected term of options granted using the “simplified method,” which is the mid-point between the vesting date and the ending date of the contractual term. The Company does not rely on the historical holding periods of the Company’s options due to the limited availability of exercise data. The Company uses a risk-free interest rate based on the U.S. Treasury yield curve in effect for bonds with maturities consistent with the expected term of the option. Expected dividend yield is based on the fact that the Company has never paid dividends. Restricted stock awards are valued based on the fair value of the stock on the grant date. The Company issues new shares upon share option exercise and vesting of a restricted share unit. Forfeitures of stock-based compensation are recognized as they occur. See Note 11, “ Stock-Based Compensation ” for more information. Income Taxes The Company accounts for income taxes using the asset and liability method and deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying values of existing assets and liabilities and their respective tax bases. Deferred tax assets and liabilities are measured using enacted tax rates in effect for the year in which those temporary differences are expected to be recovered or settled. A valuation allowance is established when it is more likely than not that some or all of the deferred tax assets will not be realized. Based on the Company’s historical operating losses, the Company has recorded a valuation allowance to reduce deferred tax assets to the amount that is more likely than not to be realized. The Company recognizes tax benefits from uncertain tax positions only if it is more likely than not, based on technical merits, that the position will be sustained upon examination by the appropriate taxing authorities. The amount of tax benefit recognized for an uncertain tax position is the largest that is more than 50 percent likelihood to be realized upon ultimate settlement. The Company records interest and penalties related to tax uncertainties, where appropriate, in income tax expense. 75 Table of Contents See Note 12, “ Income Taxes ” for more information. Leases Under the accounting standards update (“ASU”) 2016-02, Leases to ASC Topic 842, the Company determines if an arrangement is or contains a lease at inception. A lease qualifies as a finance lease if any of the following criteria are met at the inception of the lease: (i) there is a transfer of ownership of the leased asset to the Company by the end of the lease term, (ii) the Company holds an option to purchase the leased asset that the Company is reasonably certain to exercise, (iii) the lease term is for a major part of the remaining economic life of the leased asset, (iv) the present value of the sum of lease payments equals or exceeds substantially all of the fair value of the leased asset, or (v) the nature of the leased asset is specialized to the point that it is expected to provide the lessor no alternative use at the end of the lease term. All other leases are classified as operating leases. Right-of-use assets (“ROU assets”) represent the Company’s right to use an underlying asset for the lease term and lease liabilities represent the Company’s obligation to make lease payments arising from the lease. Operating and finance lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of remaining future minimum lease payments over the lease term. The Company does not recognize a ROU asset or lease liability for leases with a term of 12 months or less and does not include variable costs, which are based on actual usage, in the measurement of ROU assets and lease liabilities. The ROU assets include any lease payments made prior to the commencement date and initial direct costs incurred and excludes lease incentives received. ROU assets are subsequently assessed for impairment in accordance with the Company’s accounting policy for long-lived assets. All lease liabilities are measured at the present value of the associated payments, discounted using the Company’s incremental borrowing rate determined based on the rate of interest that the Company would pay to borrow on a collateralized basis an amount equal to the lease payments for similar term and in a similar economic environment on a collateralized basis, unless there is a rate implicit in the lease that is readily determinable. The lease liabilities are classified as current or non-current based on the expected timing of payments. The Company recognizes lease expense for operating leases on a straight-line basis over the lease term, which may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise such options. Variable costs are expensed when the event determining the amount of variable consideration to be paid occurs. Interest expense for finance leases is recognized based on the accretion of the lease liability. The Company has operating and finance lease arrangements with lease and non-lease components. The Company accounts for lease and non-lease components as a single lease component for all leases. See Note 9, “ Leases ” for more information. Recently Issued Accounting Pronouncements Not Yet Adopted Changes to U.S. GAAP are established by the Financial Accounting Standards Board (the “FASB”) in the form of ASUs to the FASB’s ASC. The Company considers the applicability and impact of all ASUs. ASUs not included in the disclosures in this report were assessed and determined to be either not applicable or are not expected to have a material impact on the consolidated financial statements. In December 2023, the FASB issued ASU 2023-09, Income Taxes – Improvements to Income Tax Disclosures (“ASU 2023-09”). The standard requires additional disclosures around disaggregated information about a reporting entity’s effective tax rate reconciliation as well as information on income taxes paid. ASU 2023-09 will be effective for annual periods beginning after December 15, 2024, with early adoption permitted. The guidance will be applied on a prospective basis with the option to apply the standard retrospectively. The Company does not expect the adoption of ASU 2023-09 to have a material impact on its consolidated financial statements and related disclosures. In November 2024, the FASB issued ASU 2024-03, Disaggregation of Income Statement Expenses (“ASU 2024-03”). The standard requires public business entities to disclose additional information about specific expense categories in the notes to financial statements at interim and annual reporting periods. ASU 2024-03 will be effective for annual periods beginning after December 15, 2026, and interim periods beginning after December 15, 2027, with early adoption permitted. The guidance will be applied on a prospective basis with the option to apply the standard retrospectively. The Company is currently evaluating the impact of the new guidance on its consolidated financial statements and related disclosures. Recently Adopted Accounting Pronouncements In November 2023, the FASB issued ASU 2023-07, Improvements to Reportable Segment Disclosures (“ASU 2023-07”). The standard requires enhanced segment reporting disclosures, including significant segment expenses and other segment items. 76 Table of Contents Additionally, the standard requires public entities to provide in interim periods all disclosures about a reportable segment’s profit or loss and assets that are currently required annually. The guidance will be applied retrospectively to all periods presented in financial statements unless it is impractical to do so. The Company adopted ASU 2023-07 effective December 31, 2024 and it did not have a material impact on its consolidated financial statements and related disclosures. 3. Revenue Recognition Disaggregated Revenue The following table summarizes the Company’s disaggregated revenue by payor category: Year ended December 31, 2024 2023 GeneDx Other 1 Total GeneDx Other 1 Total Diagnostic test revenue: Patients with third-party insurance $ 231,542 $ 3,157 $ 234,699 $ 126,265 $ 8,226 $ 134,491 Institutional customers 65,115 — 65,115 59,497 — 59,497 Self-pay patients 2,343 — 2,343 1,702 ( 36 ) 1,666 Total diagnostic test revenue 299,000 3,157 302,157 187,464 8,190 195,654 Other revenue 3,293 — 3,293 6,912 — 6,912 Total $ 302,293 $ 3,157 $ 305,450 $ 194,376 $ 8,190 $ 202,566 __________________ (1) Other represents revenues associated with the Legacy Sema4 diagnostic testing business. Reassessment of Variable Consideration Subsequent changes to the estimate of the transaction price, determined on a portfolio basis when applicable, are generally recorded as adjustments to revenue in the period of the change. The Company updates estimated variable consideration quarterly. For the years ended December 31, 2024 and December 31, 2023, the total change in estimate resulted in a net increase to revenue of $ 15.1 million and $ 8.8 million respectively, resulting from changes in the estimated transaction price due to contractual adjustments, obtaining updated information from payors and patients that was unknown at the time the performance obligation was met and potential and actual settlements with third party payors. The change in estimate also included an increase in revenue related to the release of a previously established payor reserve, as further disclosed in the “Certain Payor Matters” section below. During the year ended December 31, 2024, the Company recorded a discrete benefit of $ 6.8 million in connection with a multi-year appeal recovery from a single third-party payor. Certain Payor Matters As noted above, third-party payors, including government programs, may decide to deny payment or seek to recoup payments for tests performed by the Company that they contend were improperly billed, not medically necessary or against their coverage determinations, or for which they believe they have otherwise overpaid, including as a result of their own error. As a result, the Company may be required to refund payments already received, and the Company’s revenues may be subject to retroactive adjustment as a result of these factors among others, including without limitation, differing interpretations of billing and coding guidance, and changes by government agencies and payors in interpretations, requirements, policies and/or “conditions of participation” in various programs. The Company processes requests for recoupment from third-party payors in the ordinary course of its business, and it is likely that the Company will continue to do so in the future. If a third-party payor denies payment for testing or recoups money from the Company in a later period, reimbursement and the associated recognition of revenue for the Company’s testing services could decline. From time to time, the Company may have an obligation to reimburse Medicare, Medicaid, and third-party payors for overpayments regardless of fault. Settlements with third-party payors for retroactive adjustments due to audits, reviews, or investigations are considered variable consideration and are included in the determination of the estimated transaction price for providing services. These settlements are estimated based on the terms of the payment agreement with the payor, correspondence from the payor, the Company’s historical settlement activity (if any), and the Company’s assessment of the probability a significant reversal of cumulative revenue recognized will occur when the uncertainty is subsequently resolved. Estimated settlements are adjusted in future periods as such adjustments become known (that is, if new information becomes available), or as years are settled or are no longer subject to such audits, reviews, and investigations. 77 Table of Contents On December 30, 2022, the Company entered into a settlement agreement with one of its third-party payors (the “Payor”) in order to settle the claims related to coverage and billing matters allegedly resulting in the overpayments by the Payor to Legacy Sema4 (the “Disputed Claims”). Under the settlement agreement, $ 42.0 million is to be paid by the Company to the Payor in a series of payments each year through June 30, 2026. The first installment payment of $ 15.0 million was made on December 31, 2022, the second installment of $ 5.0 million was made on December 27, 2023, and the third installment of $ 10.0 million was made on December 31, 2024. As of December 31, 2024, $ 12.0 million in scheduled payments under the agreement remain, with $ 10.0 million due in December 2025 and $ 2.0 million in 2026. In consideration for these payments, the Payor provided releases of the Disputed Claims, effective March 31, 2023. As a result of this matter, and in connection with a review of certain billing policies and procedures undertaken by management, the Company considered the need to establish reserves for potential recoupments of payments previously made by third-party payors. As of December 31, 2024 and December 31, 2023, $ 12.6 million and $ 27.0 million of liabilities were recorded in accounts payable and accrued expenses and other liabilities, respectively. The Company uses estimates, judgments, and assumptions to assess whether it is probable that a significant reversal in the amount of cumulative revenue may occur in future periods, based upon information presently available. These estimates are subject to change. In addition, as discussed above, the Company has made certain adjustments to its estimated variable consideration as result of this matter and other potential settlements with payors. 4. Fair Value Measurements Financial assets and liabilities are recorded at fair value on the consolidated balance sheets on a recurring basis. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. For further information regarding the Company’s fair value measurements, see Note 2, “ Summary of Significant Accounting Policies ” included within this Annual Report. The following tables set forth the fair value of financial instruments that were measured at fair value on a recurring basis: December 31, 2024 Total Level 1 Level 2 Level 3 Financial Assets: Money market funds $ 57,907 $ 57,907 $ — $ — U.S. treasury bonds 30,990 — 30,990 — Corporate and municipal bonds 25,679 — 25,679 — Total financial assets $ 114,576 $ 57,907 $ 56,669 $ — Financial Liabilities: Public warrant liability $ 2,415 $ 2,415 $ — $ — Private warrant liability 1,104 — 1,104 — Total financial liabilities $ 3,519 $ 2,415 $ 1,104 $ — December 31, 2023 Total Level 1 Level 2 Level 3 Financial Assets: Money market funds $ 92,702 $ 92,702 $ — $ — U.S. treasury bonds 6,128 — 6,128 — Corporate and municipal bonds 24,098 — 24,098 — Total financial assets $ 122,928 $ 92,702 $ 30,226 $ — Financial Liabilities: Public warrant liability $ 149 $ 149 $ — $ — Private warrant liability 71 — 71 — Perceptive warrant liability 2,515 — — 2,515 Total financial liabilities $ 2,735 $ 149 $ 71 $ 2,515 78 Table of Contents There were no transfers between Level 1, Level 2 and Level 3 during the years ended December 31, 2024 or December 31, 2023. The Company’s financial assets include investments in money market funds, U.S. treasury bonds, and corporate and municipal bonds. Investments in money market funds are classified within Level 1 of the fair value hierarchy as they are based on quoted prices in active markets. Investments in U.S. treasury bonds and corporate and municipal bonds are classified within Level 2 of the fair value hierarchy as they are based on quoted bid prices for comparable securities in the marketplace and broker/dealer quotes in active markets. The Company’s marketable securities presented in the consolidated balance sheet at December 31, 2024 have maturity dates ranging from 2025 through 2027 and are classified as current assets as these investments are intended to be readily available to fund current operations. The differences between the fair value and amortized cost basis of each security are the unrealized gains or losses recorded in accumulated other comprehensive income. As of December 31, 2024, the amortized cost for maturities less than one year and greater than one year were $ 36.6 million and $ 18.3 million, respectively. Public and Private Warrants As of the consummation of the CMLS and Legacy Sema4 Business Combination in July 2021, there were 666,516 warrants to purchase shares of Class A common stock outstanding, including 447,223 public warrants and 219,293 private placement warrants. As of December 31, 2024, there were 666,515 warrants to purchase shares of Class A common stock outstanding, including 457,323 public warrants and 209,192 private placement warrants outstanding. Each warrant expires five years after the Business Combination or earlier upon redemption or liquidation, and entitles the holder to purchase one share of Class A common stock at an exercise price of $ 379.50 per share, subject to adjustment, at any time commencing on September 4, 2021. The Company may redeem the outstanding public warrants if the price per share of the Class A common stock equals or exceeds $ 594.00 as described below: • in whole and not in part; • at a price of $ 0.33 per public warrant; • upon not less than 30 days’ prior written notice of redemption to each warrant holder; and • if, and only if, the closing price of the Class A common stock equals or exceeds $ 594.00 per share (as adjusted) for any 20 trading days within a 30 -trading day period ending three trading days before sending the notice of redemption to warrant holders. The Company may redeem the outstanding public warrants if the price per share of the Class A common stock equals or exceeds $ 330.00 as described below: • in whole and not in part; • at $ 3.30 per warrant upon a minimum of 30 days’ prior written notice of redemption provided that holders will be able to exercise their warrants on a cashless basis prior to redemption and receive that number of shares based on the redemption date and the fair market value of the common stock; • if, and only if, the closing price of the Class A common stock equals or exceeds $ 330.00 per share (as adjusted) for any 20 trading days within the 30 -trading day period ending three trading days before the Company sends the notice of redemption to the warrant holders; and • if the closing price of the common stock for any 20 trading days within a 30 -trading day period ending three trading days before the Company sends notice of redemption to the warrant holders is less than $ 594.00 per share (as adjusted), the private placement warrants must also be concurrently called for redemption on the same terms as the outstanding public warrants, as described above. The private placement warrants were issued to CMLS Holdings, LLC, Mr. Munib Islam, Dr. Emily Leproust and Mr. Nat Turner, and are identical to the public warrants underlying the units sold in the initial public offering, except that (1) the private placement warrants and the common stock issuable upon the exercise of the private placement warrants would not be transferable, assignable or salable until 30 days after the completion of a Business Combination, subject to certain limited exceptions, (2) the private placement warrants are exercisable on a cashless basis, (3) the private placement warrants are non-redeemable (except as described above, upon a redemption of warrants when the price per share of Class A common stock equals or exceeds $ 330.00 ) so long as they are held by the initial purchasers or their permitted transferees, and (4) the holders of the private placement warrants and the common stock issuable upon the exercise of the private placement warrants have certain registration rights. If the private placement warrants are held by someone other than the initial purchasers or their permitted transferees, the private placement warrants will be redeemable by the Company and exercisable by such holders on the same basis as the public warrants. The public warrants are classified within Level 1 of the fair value hierarchy as they are traded in active markets and the fair value is determined on the basis of quoted market prices. The private placement warrants are classified within Level 2 of the fair value 79 Table of Contents hierarchy as management determined the fair value of each private placement warrant is the same as that of a public warrant because the terms are substantially the same. For the years ended December 31, 2024 and 2023, a loss of $ 3.3 million and gain of $ 0.2 million was recorded within the change in the change in fair market value of warrants and contingent liabilities in the consolidated statements of operations and comprehensive loss, respectively. Perceptive Warrant O n October 27, 2023 (the “Closing Date”), the Company entered into a Credit Agreement and Guaranty (the “Credit Agreement”) with Perceptive Credit Holdings IV, LP, as lender and administrative agent (“Perceptive”), which provides for a senior secured delayed draw term loan facility in an aggregate principal amount of up to $ 75.0 million (the “Perceptive Term Loan Facility”). As consideration for the Credit Agreement, the Company issued to Perceptive a warrant to purchase up to 1,200,000 shares (the “Perceptive Warrants”) of its Class A common stock. 800,000 warrant shares (the “Initial Warrant Shares”) vested and became exercisable on the Closing Date and 400,000 warrant shares (the “Additional Warrant Shares” and, together with the Initial Warrant Shares, the “Warrant Shares”) would have potentially vested and become exercisable on the Tranche B Borrowing Date, as defined in Note 8, “ Long-Term Debt ” included within this Annual Report. As the Company did not seek the additional funding from the Tranche B Loan, the Additional Warrant Shares did not vest and are not exercisable. On April 30, 2024 (the “Exercise Date”) Perceptive provided the Company with a notice to exercise the Initial Warrant Shares at an aggregate exercise price of $ 2.5 million and, as payment of the aggregate exercise price, instructed the Company to withhold a number of Initial Warrant Shares based on their aggregate fair market value as of the Exercise Date. The fair market value price of each Initial Warrant Share was equal to the 1-day volume weighted average price (the “ 1-day VWAP”) of the Company’s Class A common stock on the Exercise Date, or $ 16.4321 . As a result, the Company issued 645,414 shares of its Class A common stock to Perceptive in satisfaction of the cashless exercise in respect of the Initial Warrant Shares. See Note 8, “ Long-Term Debt ” included within this Annual Report for further information. For the year ended December 31, 2024, a loss of $ 10.1 million was recorded within the change in fair market value of warrants and contingent liabilities in the consolidated statements of operations and comprehensive loss based on re-measurement performed as of the Exercise Date. Contingent Consideration In connection with the Acquisition, up to $ 150.0 million of contingent payments was to be payable to OPKO Health, Inc. (“OPKO”), based upon achievement of 2022 and 2023 revenue milestones (the “Milestone Payments”) pursuant to the merger agreement (the “Acquisition Merger Agreement”). The first Milestone Payment was paid out in full in April 2023 and the second Milestone Payment was valued at zero as the milestone was not met during fiscal year 2023. During the year ended December 31, 2023, a gain of $ 0.9 million was recorded in the change in fair market value of warrants and contingent liabilities in the consolidated statements of operations and comprehensive loss. Connecticut Department of Economic and Community Development Funding Commitment The Company’s loan from the Connecticut Department of Economic and Community Development (“DECD”) is classified within Level 2 of the fair value hierarchy. The loan was recorded at its carrying value of $ 5.8 million and $ 6.3 million, respectively, at December 31, 2024 and December 31, 2023, with $ 1.2 million of recorded in other current liabilities on the consolidated balance sheets at December 31, 2024. The fair value was $ 4.9 million, which is estimated based on discounted cash flows using the yields of similar debt instruments of other companies with similar credit profiles. 80 Table of Contents 5. Property and Equipment Property and equipment consisted of the following: As of December 31, 2024 2023 Capitalized software $ 32,171 $ 32,171 Laboratory equipment 18,267 15,538 Leasehold improvements 14,655 14,614 Computer equipment 6,912 5,819 Building under finance lease 4,529 4,529 Equipment under finance leases 3,293 2,604 Furniture, fixtures and other equipment 584 550 Construction in-progress 4,960 3,106 Total property and equipment 85,371 78,931 Less: accumulated depreciation and amortization ( 52,478 ) ( 46,452 ) Property and equipment, net $ 32,893 $ 32,479 For the years ended December 31, 2024 and 2023, depreciation and amortization expense was $ 7.9 million and $ 19.7 million, respectively, which included software amortization expense of zero and $ 6.6 million for the years ended December 31, 2024 and 2023. For intangible amortization, see Note 6, “ Intangible Assets ”. For the year ended December 31, 2024, the Company recorded the following: • $ 0.6 million charge to accelerate the depreciation, net of trade-in credits, for certain lab equipment that was sold during the period as a trade-in associated with the purchase of new lab equipment; and • $ 0.3 million charge to accelerate the depreciation for certain lab equipment that was retired during the period. For the year ended December 31, 2023, the Company recorded the following: • $ 4.0 million charge to accelerate the amortization for certain capitalized software projects associated with Legacy Sema4 that were not expected to be utilized; • $ 9.9 million non-cash impairment charges (of which $ 5.6 million was allocated to the right-of-use asset associated with the sublease), driven by indicators of impairment related to the Icahn School of Medicine at Mount Sinai (“ISMMS“) sublease agreements during the first and third quarters of 2023; and • $ 1.7 million net gain on sale of assets primarily associated with the closure of Legacy Sema4 facilities. Depreciation and amortization expense is included within the statements of operations and comprehensive loss as follows: Year Ended December 31, 2024 2023 Cost of services $ 4,047 $ 4,350 Research and development 923 6,710 Selling and marketing — 2 General and administrative 2,958 8,647 Total depreciation and amortization expense $ 7,928 $ 19,709 81 Table of Contents 6. Intangible Assets The following table reflects, as of December 31, 2024 and December 31, 2023, the carrying values and remaining useful lives of acquired intangible assets: December 31, 2024 December 31, 2023 Weighted-Average Amortization Period (in years) Gross Carrying Amount Accumulated Amortization Net Carrying Value Gross Carrying Amount Accumulated Amortization Net Carrying Value Tradenames and trademarks $ 50,000 $ ( 8,333 ) $ 41,667 $ 50,000 $ ( 5,208 ) $ 44,792 13.3 Developed Technology 48,000 ( 16,000 ) 32,000 48,000 ( 10,000 ) 38,000 5.3 Customer Relationships 98,000 ( 13,067 ) 84,933 98,000 ( 8,167 ) 89,833 17.3 $ 196,000 $ ( 37,400 ) $ 158,600 $ 196,000 $ ( 23,375 ) $ 172,625 The following table summarizes the Company’s estimated future amortization expense of intangible assets with finite lives as of December 31, 2024: 2025 $ 14,025 2026 14,025 2027 14,025 2028 14,025 2029 14,025 Thereafter 88,475 Total estimated future amortization expense $ 158,600 Amortization expense for tradenames and trademarks and developed technology of $ 9.1 million was recorded in general and administrative expenses for each of the years ended December 31, 2024 and 2023, within the consolidated statements of operations and comprehensive loss. Amortization expense for customer relationships of $ 4.9 million was recorded in selling and marketing expenses for each of the years ended December 31, 2024 and 2023, within the consolidated statements of operations and comprehensive loss. 7. Related Party Transactions Related Party Revenues Total related party diagnostic testing revenues were $ 1.7 million and $ 3.2 million for the years ended December 31, 2024 and 2023, respectively. Related party revenues primarily include diagnostic testing revenues from a subsidiary of OPKO and the prices charged represent market rates. Related Party Expenses Total related party costs are included within cost of services and related party expenses in the consolidated statements of operations and comprehensive loss as follows: Year Ended December 31, 2024 2023 Costs of services $ 9,228 $ 4,338 General and administrative — 435 Other operating expenses, net 3,407 5,266 Total related party costs $ 12,635 $ 10,039 Expenses recognized pursuant to other service arrangements with ISMMS totaled $ 4.6 million and $ 6.8 million for the years ended December 31, 2024 and 2023, respectively. These amounts are included in either cost of services or other operating expenses, net on the consolidated statements of operations and comprehensive loss depending on the particular activity to which the costs relate. Payables due to ISMMS for the other service arrangements were $ 0.9 million and $ 1.0 million as of 82 Table of Contents December 31, 2024 and December 31, 2023, respectively. These amounts are included within due to related parties on the Company’s consolidated balance sheets. Additionally, the Company incurred $ 10.5 million and $ 3.4 million in purchases of diagnostic testing kits and materials and $ 8.1 million and $ 1.8 million was recorded in cost of services for the year ended December 31, 2024 and 2023, respectively, from an affiliate of a member of the Board of Directors who has served in the role since July 2021. The prices paid represent market rates. Payables due were $ 0.7 million and $ 0.4 million as of December 31, 2024 and 2023. Legacy GeneDx and OPKO entered into a Transition Services Agreement dated as of April 29, 2022 (the “OPKO TSA”) pursuant to which OPKO had agreed to provide services, at cost, subject to certain limited exceptions, in order to facilitate the transactions contemplated by the Acquisition Merger Agreement, including human resources, information technology support, and finance and accounting. Services in connection with the OPKO TSA were fully completed in October 2023. The Company recognized $ 1.6 million in costs for the year ended December 31, 2023 related to the agreement. 8. Long-Term Debt As of December 31, 2024, long-term debt matures as follows: 2025 $ 1,211 2026 1,235 2027 1,260 2028 51,285 2029 762 Total debt 55,753 Less: current portion of long-term debt ( 1,211 ) Less: long-term debt issuance costs ( 2,629 ) Total long-term debt, net of current portion and debt issuance costs $ 51,913 Perceptive Term Loan Facility O n October 27, 2023 (the “Closing Date”), the Company entered into the Perceptive Term Loan Facility. An initial tranche of $ 50.0 million (the “Tranche A Loan”) was funded under the Perceptive Term Loan Facility on the Closing Date. In addition to the Tranche A Loan, the Perceptive Term Loan Facility included an additional tranche of $ 25.0 million (the “Tranche B Loan,” and together with the Tranche A Loan, the “Term Loans”), which was accessible by the Company through December 31, 2024 so long as the Company satisfied certain customary conditions precedent, including a specified revenue milestone (the funding date of the Tranche B Loan, the “Tranche B Borrowing Date”). Although the requirements for the Tranche B funding were met, the Company did not seek the additional funding. The Perceptive Term Loan Facility has a maturity date of October 27, 2028 (the “Maturity Date”) and provides for an interest-only period during the term of the loan with principal due at the maturity date. The Company’s net proceeds from the Tranche A Loan were approximately $ 48.8 million, after deducting debt issuance costs and expenses. Interest Rate The Perceptive Term Loan Facility will accrue interest at an annual rate equal to the sum of (a) Term SOFR (as defined in the Credit Agreement) and (b) an applicable margin of 7.5 % (the “Applicable Margin”). Accrued interest on the Term Loans is payable monthly in arrears. Upon an Event of Default (as defined in the Credit Agreement), the Applicable Margin will automatically increase by an additional 4 % per annum. Amortization and Prepayment Prior to the Maturity Date, there will be no scheduled principal payments under the Perceptive Term Loan Facility. On the Maturity Date, the Company is required to pay Perceptive the aggregate outstanding principal amount of the Term Loans and all accrued and unpaid interest thereon. The Term Loans may be prepaid at any time, subject to a prepayment premium equal to 0 % to 10 % of the aggregate outstanding principal amount being prepaid, depending on the date of prepayment. 83 Table of Contents Security Instruments and Warrant In connection with the Credit Agreement, the Company also entered into a Security Agreement, dated as of the Closing Date, with Perceptive, pursuant to which all of its obligations under the Credit Agreement are secured by a first lien perfected security interest on substantially all of its existing and after-acquired assets, subject to customary exceptions. On the Closing Date, as consideration for the Credit Agreement, the Company issued the Perceptive Warrant to Perceptive, which allowed them to purchase up to 1,200,000 Warrant Shares. The 800,000 Initial Warrant Shares vested and became exercisable on the Closing Date and 400,000 Additional Warrant Shares would have potentially vested and become exercisable on the Tranche B Borrowing Date. As the Company did not seek the additional funding from the Tranche B Loan, the Additional Warrant Shares did not vest and are not exercisable. The per share exercise price for the Initial Warrant Shares is $ 3.1752 (the “Initial Warrant Exercise Price”), which is equal to the 10-day volume weighted average price (the “ 10-day VWAP”) of the Company’s Class A common stock at the end of the business day immediately prior to the Closing Date, and the per share exercise price for the Additional Warrant Shares would have been equal to the lower of (a) the Initial Warrant Exercise Price or (b) the 10-day VWAP ending on the end of the business day immediately preceding the Tranche B Borrowing Date. The Perceptive Warrant will be exercisable, in whole or in part, until the 10 th anniversary of the applicable vesting date. On April 30, 2024, Perceptive provided the Company with a notice to exercise the Initial Warrant Shares at an aggregate exercise price of $ 2.5 million and instructed the Company to withhold a number of Initial Warrant Shares as payment for the aggregate exercise price. As a result, the Company issued 645,414 shares of its Class A common stock in satisfaction of the cashless exercise in respect of the Initial Warrant Shares. See Note 4, “ Fair Value Measurement ” for further information. Connecticut Department of Economic and Community Development Funding Commitment In June 2017, ISMMS assigned a loan funding commitment from the DECD to the Company (the “DECD Loan Agreement”) to support the Genetic Sequencing Laboratory Project in Branford, Connecticut, with funding based on the achievement of certain project development phases. The DECD Loan Agreement provided for a total loan commitment of $ 15.5 million at a fixed annual interest rate of 2.0 % for a term of 10 years. The Company was required to make interest-only payments through July 2023 and principal and interest payments commencing in August 2023. The final payment of principal and interest was due in July 2028. However, under the terms of the DECD Loan Agreement, the DECD granted a partial principal loan forgiveness of up to $ 12.3 million in the aggregate. Such forgiveness was contingent upon the Company achieving certain job creation and retention milestones and $ 4.5 million had been forgiven at December 31, 2022. This commitment was collateralized by a security interest in certain machinery and equipment the Company acquired from ISMMS, as defined in a separate security agreement. In January 2023, the Company amended the DECD Loan Agreement, which resulted in the Company agreeing to pay $ 2.0 million in principal, obtaining $ 2.8 million in debt forgiveness for achieving its Phase 2 job milestone, and agreeing to two new forgiveness milestone targets for its Phase 3 job milestone (eligible for $ 2.0 million in forgiveness) and a final phase job milestone (eligible for $ 1.0 million in forgiveness) (the “2022 Amended DECD Loan Agreement”). Upon execution of this amendment, the Company paid the $ 2.0 million in principal and received $ 2.8 million in debt forgiveness, and the Company recognized the debt forgiveness as other (expense) income, net in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2023. The terms of the 2022 Amended DECD Loan Agreement require the Company to make interest-only payments through July 2024 and requires the Company to make principal and interest payments commencing in August 2024 through July 2029 at the same fixed annual interest rate of 2.0 %. The other terms of the 2022 Amended DECD Loan Agreement remained the same. During the year ended December 31, 2024, the Company made principal payments totaling $ 0.5 million. The outstanding loan balance of the DECD loan was $ 5.8 million at December 31, 2024. 9. Leases The Company’s leases primarily consist of office and lab space, and equipment for use in its operations. Its leases generally have lease agreements which expire in 2026 to 2036, some with the option to extend. The Company includes extension options that are reasonably certain to be exercised as part of the lease terms. As of December 31, 2024, none of the Company’s lease terms included the extension option as the Company has determined that it is unlikely to exercise the extension option. Operating Leases The Company’s primary operating lease arrangements include leased properties for its corporate office and headquarters located in Stamford, Connecticut, its primary operating laboratory located in Gaithersburg, Maryland, and a satellite meeting space located in New York City. The lease agreements for these properties expire in 2034, 2031, and 2026, respectively. 84 Table of Contents The Company’s operating leases also include laboratories in Branford, Connecticut and Stamford, Connecticut, which as previously disclosed, have ceased operations as part of the Company’s announced exits in 2022 from reproductive health and somatic tumor testing. The lease agreements for these properties expire in 2030 and 2036, respectively. These facilities as well as a portion of its headquarters located in Stamford, Connecticut are actively being marketed for sublet; however, the outstanding lease obligations remain obligations. At inception of the lease for the laboratory in Stamford, Connecticut, the value of the land was determined to be more than 25% of the total value and therefore the building is accounted for as a finance lease and the land as an operating lease. Finance Leases In addition to its leased laboratory building in Stamford, Connecticut noted above, the Company routinely enters into various finance lease agreements to obtain laboratory equipment that contain bargain purchase commitments at the end of the lease term. The leases are secured by the underlying equipment. The tables below present financial information associated with the Company’s operating and finance leases as of, and for the year ended, December 31, 2024 and 2023: December 31, Classification 2024 2023 Assets Operating lease assets Operating lease right-of-use assets $ 25,613 $ 26,900 Finance lease assets Property and Equipment, net 3,173 3,440 Total lease assets $ 28,786 $ 30,340 Liabilities Current Operating Short-term lease liabilities $ 2,608 $ 2,331 Finance Short-term lease liabilities 728 1,316 Non-current Operating Long-term lease liabilities $ 42,698 $ 44,428 Finance Long-term lease liabilities 18,221 18,510 Total lease liabilities $ 64,255 $ 66,585 Year ended December 31, Lease cost 2024 2023 Operating lease cost Operating lease cost $ 5,637 $ 5,806 Short-term lease cost 314 745 Variable lease cost 1,140 659 Total operating lease cost $ 7,091 $ 7,210 Finance lease cost Depreciation and amortization of leased assets $ 647 $ 1,970 Interest on lease liabilities 1,460 1,041 Total finance lease cost $ 2,107 $ 3,011 Total lease cost $ 9,198 $ 10,221 85 Table of Contents Future minimum lease payments under non-cancellable leases as of December 31, 2024 are as follows: Maturity of lease liabilities Operating lease Finance lease Total 2025 $ 6,201 $ 2,670 $ 8,871 2026 6,292 2,003 8,295 2027 6,263 2,045 8,308 2028 6,447 2,107 8,554 2029 6,601 2,170 8,771 Thereafter 30,539 20,877 51,416 Total 62,343 31,872 $ 94,215 Less: imputed interest ( 17,037 ) ( 12,923 ) ( 29,960 ) Present value of lease liabilities $ 45,306 $ 18,949 $ 64,255 Other information related to leases as of and for the year ended December 31, 2024 and 2023 and are as follows: December 31, 2024 2023 Weighted-average remaining lease term (years) Operating leases 9.0 10.0 Finance leases 11.4 11.8 Weighted-average discount rate Operating leases 6.4 % 6.4 % Finance leases 8.4 % 8.1 % Cash paid for amounts included in the measurement of lease liabilities Operating cash flows from operating leases $ 5,231 $ 5,482 Operating cash flows from finance leases 3,029 1,874 Financing cash flows from finance lease 2,728 3,598 10. Purchase Commitments and Contingencies Purchase Commitments The following sets forth purchase commitments with software and equipment providers as of December 31, 2024 with a remaining term of at least one year: 2025 $ 15,699 2026 8,394 2027 4,592 2028 4,021 2029 3,914 Thereafter 978 Total purchase commitments $ 37,598 The Company enters into contracts with suppliers to purchase materials needed for diagnostic testing. These contracts generally do not require multi-year purchase commitments. For further information regarding the Company’s lease obligations, see Note 9, “ Leases ” included within this Annual Report. Contingencies The Company is or may become subject to various claims and legal actions arising in the ordinary course of business. The Company does not believe that the outcome of any existing matters will have a material effect on the Company’s consolidated 86 Table of Contents financial statements. However, no assurance can be given that the ultimate resolution of such proceedings will not materially impact the Company’s consolidated financial statements. Except as described below, the Company was not a party to any material legal proceedings as of December 31, 2024, nor is it a party to any material legal proceedings as of the date of issuance of these consolidated financial statements. On September 7, 2022, a shareholder class action lawsuit was filed in the United States District Court for the District of Connecticut, styled Helo v. Sema4 Holdings Corp., et al, 22-cv-1131 (D. Conn.) against the Company and certain of the Company’s current and former officers. Following the appointment of a lead plaintiff, an amended complaint was filed on January 30, 2023. The defendants moved to dismiss the amended complaint on August 21, 2023, and that motion was granted on July 31, 2024. A second amended complaint was filed on September 13, 2024. As amended, the complaint purports to bring suit on behalf of the stockholders who purchased the Company’s publicly traded securities between January 18, 2022 and August 15, 2022. The second amended complaint purports to allege that the defendants made false and misleading statements about the Company’s business, operations, and prospects in violation of Sections 10(b) and 20(a) of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), and seeks unspecified compensatory damages, fees, and costs. The Company believes the allegations and claims are without merit. On November 28, 2023, a stockholder filed a derivative suit, allegedly on behalf of the Company, based largely on the same allegations in the securities class action referenced above. The suit was filed in federal court in the District of Delaware, styled Ghazaleh v. Schadt, et al, 23-cv-01357 (D. Del.), and purports to assert claims against certain of the Company’s former and current officers and directors under Section 10(b) of the Exchange Act, and for breach of fiduciary duty, aiding and abetting breach of fiduciary duty, unjust enrichment and corporate waste. The Company is named only as a nominal defendant. The complaint seeks damages on the Company’s behalf, and seeks corporate governance and other relief. On March 11, 2024, the Court issued an order staying this suit pending resolution of the Helo class action referenced above. On June 25, 2024, a substantially similar stockholder derivative suit was filed in federal court in the District of Connecticut, styled Scinto v. Schadt, et al, 2:24-cv-01100 (D. Conn.). The suit, also purportedly brought on the Company’s behalf against certain of its former or current officers and directors, asserts claims for breach of fiduciary duty, unjust enrichment, corporate waste, and violations of Sections 10(b) and 14(a) of the Exchange Act. The Company is named only as a nominal defendant. The complaint seeks damages on the Company’s behalf, as well as corporate governance reforms and other relief. On August 8, 2024, the Court issued an order staying this suit until the earlier of a commencement of discovery, announcement of settlement, or dismissal with prejudice in the Helo class action referenced above. On February 7, 2023, a stockholder commenced a lawsuit in the Delaware Court of Chancery. The suit is brought as a class action on behalf of stockholders of CMLS who did not redeem their shares in connection with the Business Combination between CMLS and Legacy Sema4. The defendants named in the amended complaint include and directors of CMLS at the time of the transaction, including certain directors who continue to serve on the Company’s Board of Directors, as well as CMLS Holdings LLC, Corvex Management LP, and Casdin Capital, LLC. The Company is not named as a defendant. The complaint alleges that the July 2, 2021 proxy statement mailed to CMLS stockholders in connection with the transaction contained false and misleading statements, and purports to assert a claim of breach of fiduciary duty against all individual defendants, and a similar claim against CMLS Holdings LLC and certain individuals for breach of fiduciary duty as control persons. The suit seeks to recover unspecified damages on behalf of the alleged class, among other relief. After defendants moved to dismiss the case, the plaintiff filed an amended complaint on July 6, 2023, revising certain allegations and adding third parties as defendants. The defendants answered the amended complaint on September 15, 2023. The Company is subject to certain claims for advancement and indemnification by the individual defendants in this proceeding. During the second quarter of 2024, the parties reached an agreement in principle through mediation to resolve all claims for approximately $ 21 million, and during the third quarter of 2024, the parties executed a formal stipulation of settlement reflecting such agreement in principle. The settlement was paid into escrow on November 12, 2024 and was funded by the Company (based on its indemnification obligations), available insurance of approximately $ 10 million and proceeds of approximately $ 1.4 million from the insurance of a third-party defendant. The Delaware Court of Chancery approved the settlement on December 2, 2024. As of December 31, 2024, remaining unpaid litigation and indemnification costs were nominal. Defined Contribution Plan Substantially all of the Company’s employees in the U.S. are eligible to participate in the defined contribution plan the Company sponsors. The defined contribution plan allows employees to contribute a portion of their compensation in accordance with specified guidelines. The Company, at its discretion, makes matching contributions. The Company contributed $ 5.9 million and $ 6.5 million for the years ended December 31, 2024 and 2023, respectively. 87 Table of Contents 11. Stock-Based Compensation Stock-Based Compensation Expense Stock-based compensation expense is included within the consolidated statements of operations and comprehensive loss as follows: Year Ended December 31, 2024 2023 Cost of services $ 431 $ ( 1,217 ) Research and development 1,192 ( 2,585 ) Selling and marketing 1,089 ( 1,266 ) General and administrative 6,426 4,742 Total stock-based compensation expense 1,2 $ 9,138 $ ( 326 ) 1 The Company recorded an aggregate reversal of stock-based compensation of $ 3.9 million and $ 24.7 million during the years ended December 31, 2024 and 2023, respectively, due to forfeiture activities upon employee terminations. 2 Includes $ 0.6 million of expense related to the 2021 Employee Stock Purchase Plan during year ended December 31, 2024. Stock Incentive Plans The Company maintains the Amended and Restated 2021 Equity Incentive Plan (as amended and restated, the “2021 Plan”), which allows for grants of stock-based awards. No awards granted under the 2021 Plan are exercisable after 10 years from the date of grant, and the awards granted under the 2021 Plan generally vest over a four-year period on a graded vesting basis; however, the Company has also granted certain restricted stock units (“RSUs”) with vesting terms beginning 12 months from the grant date and vesting immediately on the grant date. On January 1 of each year through 2031, the aggregate number of shares of Class A common stock reserved for issuance under the 2021 Plan may be increased automatically by the number of shares equal to 5 % of the total number of shares of all classes of common stock issued and outstanding immediately preceding December 31. In January 2024, the number of Class A common stock reserved for future issuance under the 2021 Plan automatically increased by 1,298,943 shares. The Company also maintains the 2023 Equity Inducement Plan (the “Equity Inducement Plan”), which allows for grants of equity awards of the Company’s Class A common stock to individuals who were not previously an employee or director of the Company, or following a bona fide period of non-employment, as an inducement material to such persons entering into employment with the Company. As of December 31, 2024, there was an aggregate of 1,857,260 shares available for grants of stock options or other awards under the 2021 Plan and Equity Inducement Plan. In January 2025, the number of Class A common stock reserved for future issuance under the 2021 Plan automatically increased by 1,400,827 shares. Stock Option Activity All stock options granted under the 2021 Plan are accounted for as time-based equity awards. The following summarizes the stock option activity during the year ended December 31, 2024: Stock Options Outstanding Weighted Average Exercise Price Weighted Average Remaining Contractual Life (years) Aggregate Intrinsic Value Balance at December 31, 2023 497,976 $ 42.80 5.55 $ — Options granted — $ — Options exercised ( 68,453 ) $ 5.77 Options forfeited and canceled ( 88,243 ) $ 63.45 Balance at December 31, 2024 341,280 $ 44.83 5.99 $ 12,429 Options exercisable at December 31, 2024 290,963 $ 40.47 5.74 $ 11,799 Non-vested options outstanding at the end of the year were 50,317 with weighted average grant-date fair value of $ 14.52 . As of December 31, 2024, unrecognized stock-based compensation cost related to the unvested portion of the Company’s stock options was $ 0.5 million, which is expected to be recognized on a graded-vesting basis over a weighted-average period of 1.0 years. 88 Table of Contents The weighted-average grant-date fair value and total fair value of options with tranches vested was $ 34.42 and $ 0.7 million for the year ended December 31, 2024, respectively, and $ 25.07 and $ 1.5 million for the year ended December 31, 2023, respectively. The aggregate intrinsic value of exercised options was $ 2.3 million and $ 0.3 million in the years ended December 31, 2024 and 2023, respectively, and is calculated based on the difference between the exercise price and the fair value of the Company’s common stock as of the exercise date. The weighted-average grant-date fair value of options forfeited and canceled was $ 7.46 for the year ended December 31, 2024. There were no options granted during the year ended December 31, 2024. The fair value of the stock option awards granted during the year ended December 31, 2023 were estimated using the Black-Scholes option pricing model with the following assumptions: 2023 Expected volatility 105.0 % Weighted-average expected volatility 105.0 % Expected term (in years) 5.5 Risk-free interest rate 4.03 % Dividend yield — Fair value of Class A common stock $ 6.35 Restricted Stock Units (RSU) The Company issued time-based RSUs to employees under the 2021 Plan. The RSUs automatically convert to common stock on a one -for-one basis as the awards vest. The Company measures the value of RSUs at fair value based on the closing price of the underlying common stock on the grant date. The RSUs granted generally vest over a four-year vesting period from the grant date, however, the Company also granted certain RSUs with vesting term beginning 12 months from the grant date and vesting immediately on the grant date. The following table summarizes the activity related to the Company’s time-based RSUs: Restricted Stock Units Outstanding Weighted Average Grant Date Fair Value Per Unit Balance at December 31, 2023 1,507,877 $ 15.48 Restricted Stock Units granted 1,187,165 $ 11.37 Restricted Stock Units vested ( 471,663 ) $ 17.72 Restricted Stock Units forfeited ( 353,818 ) $ 15.63 Balance at December 31, 2024 1,869,561 $ 12.03 The total fair value of RSUs vested for the years ended December 31, 2024 and 2023 was $ 2.1 million and $ 6.6 million, respectively. As of December 31, 2024, unrecognized stock-based compensation cost related to the Company’s RSUs was $ 10.7 million, which is expected to be recognized on a graded-vesting basis over a weighted-average period of 1.8 years. Employee Stock Purchase Plan The 2021 Employee Stock Purchase Plan (the “2021 ESPP”) authorizes the issuance of shares of Class A common stock pursuant to purchase rights granted to employees. On January 1 of each year through 2031, the aggregate number of shares of Class A common stock reserved for issuance under the 2021 ESPP may be increased automatically by the number of shares equal to 1 % of the total number of shares of all classes of common stock issued and outstanding immediately preceding December 31. The 2021 ESPP became open for enrollment in April 2024. Under the 2021 ESPP, eligible employees may purchase shares of the Company’s Class A common stock at a discount through payroll deductions during each discrete six-month offering period. The purchase price under each discrete offering period is equal to 85 % of the lesser of the fair market value of the Class A common stock on the first and last day of the offering period. The first offering period was completed on October 31, 2024 and the Company issued 26,773 shares under the 2021 ESPP during the year ended December 31, 2024. A total of 569,831 shares of Class A common stock were reserved for future issuance under the 2021 ESPP as of December 31, 2024. In January 2025, the number of Class A common stock reserved for future issuance under the 2021 ESPP automatically increased by 280,165 shares. 89 Table of Contents 12. Income Taxes The components of income before incomes taxes consisted of the following: Year Ended December 31, 2024 2023 Foreign $ 929 $ 623 Domestic ( 53,558 ) ( 177,316 ) Loss before income tax provision (benefit) ( 52,629 ) ( 176,693 ) Year Ended December 31, 2024 2023 Current Federal $ — $ — State and Local — — Foreign 241 164 Total Current $ 241 $ 164 Deferred Federal $ ( 229 ) $ 942 State and Local ( 355 ) ( 2,032 ) Foreign — — Total Deferred ( 584 ) ( 1,090 ) Total income tax provision (benefit) $ ( 343 ) $ ( 926 ) For the years ended December 31, 2024 and 2023, the Company recorded a total income tax benefit of $ 0.3 million and $ 0.9 million, respectively. Accordingly, the effective tax rate for the Company for the years ended December 31, 2024 and 2023 was 0.6 % and 0.5 %, respectively. A reconciliation of the anticipated income tax expense/(benefit) computed by applying the statutory federal income tax rate of 21% to loss before income taxes to the amount reported in the statement of operations and comprehensive loss is as follows: Year Ended December 31, 2024 2023 U.S. federal taxes at statutory rate 21.0 % 21.0 % State taxes (net of federal benefit) 0.6 1.1 Research and development tax credits — ( 0.8 ) Non-deductible stock-based compensation ( 3.8 ) ( 2.4 ) 162(m) limitation ( 2.7 ) ( 0.1 ) Permanent items ( 0.5 ) ( 0.1 ) Unrealized fair market value gain on warrants ( 5.4 ) 0.1 Goodwill impairment — ( 0.1 ) Change in valuation allowance ( 10.7 ) ( 18.4 ) Other 2.1 0.2 Effective tax rate 0.6 % 0.5 % 90 Table of Contents The tax effects of temporary differences and carryforwards that give rise to significant portions of the net deferred tax assets and liabilities were as follows: As of December 31, 2024 2023 Deferred tax assets: Net operating loss carryforwards $ 257,047 $ 257,960 Stock-based compensation 2,599 7,690 Accrued compensation 2,001 1,269 Accrued expenses 247 3,470 Research and development credits 6,477 6,374 Leases 14,801 14,054 Obsolete inventory reserve 12 136 Third party liability 2,971 7,514 Section 174 amortization 29,484 25,993 Capitalized software 766 1,211 Other 1,194 814 Total deferred tax assets 317,599 326,485 Valuation allowance ( 272,275 ) ( 271,567 ) Deferred tax assets, net of valuation allowance 45,324 54,918 Deferred tax liabilities: Property and equipment ( 1,013 ) ( 1,279 ) ROU asset ( 6,252 ) ( 7,353 ) Intangible amortization ( 39,024 ) ( 47,846 ) Total deferred tax liabilities ( 46,289 ) ( 56,478 ) Net deferred tax liability after valuation allowance $ ( 965 ) $ ( 1,560 ) As of December 31, 2024, the Company had the following tax net operating loss carryforwards available to reduce future federal and state taxable income, and tax credit carryforwards available to offset future federal and Connecticut income taxes: Amount Expiration period Tax net operating loss carryforwards: Federal (pre-2018 net operating losses) $ 33,056 2036-2037 Federal (post-2017 net operating losses) $ 871,367 No expiration State and Local $ 1,179,626 2027-2044 State and Local $ 100,363 No expiration Tax credit carryforwards: Federal research and development $ 5,460 2038-2041 Connecticut research and development $ 777 2036 Connecticut research and development $ 511 No expiration The Company had the following deferred tax valuation allowance balances: Year Balance at the Beginning of Period Additions Balance at the End of Period 2024 $ 271,567 708 $ 272,275 2023 $ 226,644 44,923 $ 271,567 Future realization of the tax benefits of existing temporary differences and carryforwards ultimately depends on the existence of sufficient taxable income within the carryforward period. As of December 31, 2024 and 2023 the Company performed an 91 Table of Contents evaluation to determine whether a valuation allowance was needed. Based on the Company’s analysis, which considered all available evidence, both positive and negative, the Company determined that it is more likely than not that a significant portion of its deferred tax assets will not be realized. Accordingly, the Company maintained a full valuation allowance as of December 31, 2024 and 2023. The valuation allowance increased by $ 0.7 million in 2024 and $ 44.9 million in 2023, primarily due to the increase in net operating loss carryforwards. Under Internal Revenue Code Section 382, if a corporation undergoes an “ownership change,” the corporation’s ability to use its pre-change NOL carryforwards and other pre-change tax attributes to offset its post-change income may be limited. Generally, an ownership change occurs when certain shareholders increase their aggregated ownership by more than 50 percentage points over their lowest ownership percentage in a testing period (typically three years). Future changes in stock ownership, which may be outside of the Company’s control, may trigger an ownership change. In addition, future equity offerings or acquisitions that have an equity component of the purchase price could result in an ownership change. If an ownership change has occurred or does occur in the future, utilization of the NOL carryforwards or other tax attributes may be limited. A reconciliation of the beginning and ending amounts of unrecognized tax benefits for the years ended December 31, 2024 and 2023 is as follows: As of December 31, 2024 2023 Unrecognized tax benefits – January 1 $ 718 $ 718 Gross increases – tax positions in current period — — Unrecognized tax benefits – December 31 $ 718 $ 718 To the extent penalties and interest would be assessed on any underpayment of income tax, the Company’s policy is that such amounts would be accrued and classified as a component of income tax expense in the financial statements. The Company had a nominal amount of accrued interest or penalties related to uncertain tax positions as of December 31, 2024 and 2023. The Company files income tax returns for U.S federal jurisdiction, various state jurisdictions, and various foreign countries. In the normal course of business, the Company is subject to examination by federal, state and foreign jurisdictions, where applicable. There are currently no pending federal, state or foreign income tax examinations. As a result of the Company’s net operating loss carryforwards, the Company’s federal and state statutes of limitations remain open from 2016 and forward until the net operating loss carryforwards are utilized or expire prior to utilization. 13. Net Loss per Share Basic net loss per share is computed by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock outstanding for the period. The following table sets forth the computation of basic and diluted net loss per share attributable to common stockholders: Year Ended December 31, 2024 2023 Numerator: Net loss attributable to common stockholders $ ( 52,286 ) $ ( 175,767 ) Denominator: Basic and diluted weighted-average common shares outstanding 26,891,213 24,311,989 Basic and diluted loss per share $ ( 1.94 ) $ ( 7.23 ) 92 Table of Contents The following tables summarize the outstanding shares of potentially dilutive securities that were excluded from the computation of diluted net loss per share attributable to common stockholders for the period presented because including them would have been anti-dilutive: Year Ended December 31, 2024 2023 Outstanding options and RSUs to purchase Class A common stock 2,210,841 2,005,853 Outstanding warrants 666,515 1,466,515 Outstanding 2021 ESPP shares 20,566 — Total 2,897,922 3,472,368 14. Restructuring Costs The table below provides certain information concerning restructuring activity during the year ended December 31, 2024 and December 31, 2023: Reserve Balance at December 31, 2023 Charged to Costs and Expenses Payments and Other Reserve Balance at December 31, 2024 Severance $ 1,853 $ 1,752 $ ( 2,859 ) $ 746 Reserve Balance at December 31, 2022 Charged to Costs and Expenses Payments and Other Reserve Balance at December 31, 2023 Severance $ 4,770 $ 6,514 $ ( 9,431 ) $ 1,853 Other 253 18 ( 271 ) — Total $ 5,023 $ 6,532 $ ( 9,702 ) $ 1,853 Expenses related to restructuring activities are included within the consolidated statements of operations and comprehensive loss as follows: Year Ended December 31, 2024 2023 Cost of services $ 54 $ 139 Research and development 151 3,176 Selling and marketing 548 1,371 General and administrative 999 1,846 Total restructuring expense $ 1,752 $ 6,532 On October 30, 2023, the Company announced a continued strategic realignment of its organization to key priorities which includes the elimination of approximately 50 positions impacted on August 23, 2023, and approximately 35 positions impacted on October 30, 2023. Together these actions reduced the size of the Company’s workforce by 10 % from the total number that existed at the time of the August reduction in force. 15. Supplemental Financial Information The following table provides a reconciliation of cash, cash equivalents and restricted cash reported on the consolidated balance sheets to the total of the same amounts shown on the consolidated statements of cash flows: As of December 31, 2024 2023 Cash and cash equivalents $ 85,212 $ 99,681 Restricted cash (included in other assets) 990 987 Total $ 86,202 $ 100,668 93 Table of Contents Restricted cash included in other assets as of December 31, 2024 and 2023 primarily consists of money market deposit accounts that secure an irrevocable standby letter of credit that serves as collateral for security deposit operating leases. Prepaid expenses and other current assets consisted of the following: As of December 31, 2024 2023 Prepaid expenses $ 7,425 $ 8,640 Other current assets 1,079 1,958 Total $ 8,504 $ 10,598 Accounts payable and accrued expenses consisted of the following: As of December 31, 2024 2023 Accounts payable $ 7,954 $ 10,238 Accrued expenses 11,504 12,179 Reserves for refunds to insurance carriers 10,586 15,039 Total $ 30,044 $ 37,456 Other current liabilities consisted of the following: As of December 31, 2024 2023 Accrued compensation $ 16,241 $ 12,465 Accrued severance 746 1,853 Other 2,843 2,018 Total $ 19,830 $ 16,336 Other liabilities consisted of the following: As of December 31, 2024 2023 Warrant liability $ 3,519 $ 2,735 Third party payor reserve 2,000 12,000 Total $ 5,519 $ 14,735 2023 Capital Raise On January 31, 2023, the Company raised approximately $ 150.0 million in gross proceeds and announced the closing of an underwritten public offering of 9,962,316 shares of its Class A common stock and a concurrent registered direct offering of 2,353,436 shares of its Class A common stock. The net offering proceeds received after deducting underwriters’ discounts and commissions payable by the Company were approximately $ 135.4 million. On April 17, 2023, following the Company’s receipt of stockholder approval for the issuance, the Company issued the remaining 676,868 shares of its Class A common stock to Corvex Select Equity Master Fund LP, Corvex Master Fund LP and Corvex Dynamic Equity Select Master Fund LP in its previously announced registered direct offering for gross proceeds of approximately $ 7.6 million. 2024 Sales Agreement The Company entered into a sales agreement (the “Sales Agreement”) with TD Securities (USA) LLC (“TD Cowen”) in April 2024, pursuant to which the Company may, but is not obligated to, offer and sell, from time to time, shares of its Class A common stock with an aggregate offering price up to $ 75.0 million through TD Cowen, as sales agent, subject to the terms and conditions described in the Sales Agreement and SEC rules and regulations (the “ATM offering”). During the year ended December 31, 2024, the Company issued 825,379 shares of its Class A common stock in connection with the ATM offering at an average price 94 Table of Contents of $ 58.41 per share. Proceeds received, net of agent fees and other offering expenses, were $ 46.5 million. As of December 31, 2024, approximately $ 26.8 million of capacity remained available under this ATM offering. 16. Segment Reporting The Company’s structure is aligned with how the chief operating decision maker (“CODM”) reviews the business, makes investing and resource allocation decisions and assesses operating performance. The Company’s CODM is its Chief Executive Officer. At December 31, 2024, the Company has identified one reportable segment: GeneDx inclusive of Legacy GeneDx and Legacy Sema4 data revenues and associated costs. The GeneDx segment primarily provides pediatric and rare disease diagnostics with a focus on whole exome and genome sequencing and, to a lesser extent, data and information services. Other represents the revenues and costs associated with the Legacy Sema4 diagnostics business which was completely shut down in 2023. The CODM evaluates segment performance based on revenue and adjusted gross profit. Year ended December 31, 2024 2023 GeneDx Other Total GeneDx Other Total Revenue $ 302,293 $ 3,157 $ 305,450 $ 194,376 $ 8,190 $ 202,566 Adjusted cost of services 106,376 145 106,521 106,983 2,305 109,288 Adjusted gross profit (1) 195,917 3,012 198,929 87,393 5,885 93,278 Reconciliations: Depreciation and amortization 4,047 4,350 Stock-based compensation 431 ( 1,217 ) Restructuring charges 54 139 Gross profit $ 194,397 $ 90,006 (1) Adjusted cost of services and adjusted gross profit exclude depreciation and amortization expense, stock-based compensation expense and restructuring costs. Management manages assets on a total company basis, not by reporting segment. The CODM does not regularly review any asset information by reporting segment and, accordingly, the Company does not report asset information by reporting segment. 95 Table of Contents Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosures None.