Ultragenyx Pharmaceutical Inc. 10-Q

Item 1. Financial Statements ULTRAGENYX PHARMACEUTICAL INC. CONDENSED CONSOLIDATED BALANCE SHEETS (Unaudited) (In thousands, except share amounts) June 30, December 31, 2020 2019 Assets Current assets: Cash and cash equivalents $ 335,639 $ 433,584 Short-term investments 477,777 321,646 Receivable related to Daiichi Sankyo license agreements 8,473 — Accounts receivable, net 14,893 32,844 Inventory 11,061 11,546 Prepaid expenses and other current assets 58,196 51,397 Total current assets 906,039 851,017 Property and equipment, net 48,339 44,348 Investment in Arcturus equity securities 140,220 27,752 Long-term investments 4,068 5,174 Right-of-use assets 37,067 30,328 Intangible assets, net 131,275 129,000 Goodwill 44,406 44,406 Other assets 2,627 3,471 Total assets $ 1,314,041 $ 1,135,496 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 9,014 $ 12,871 Accrued liabilities 71,887 83,194 Short-term contract liability 131,570 — Short-term lease liabilities 7,258 7,235 Total current liabilities 219,729 103,300 Long-term contract liability 3,328 — Long-term lease liabilities 36,308 29,757 Deferred tax liabilities 33,306 33,306 Liability related to the sale of future royalties 325,783 315,369 Total liabilities 618,454 481,732 Stockholders’ equity: Preferred stock — 25,000,000 shares authorized; nil outstanding as of June 30, 2020 and December 31, 2019 — — Common stock — 250,000,000 shares authorized; 60,413,756 and 57,838,220 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively 60 58 Additional paid-in capital 2,220,963 2,086,863 Accumulated other comprehensive income (loss) 1,284 ( 147 ) Accumulated deficit ( 1,526,720 ) ( 1,433,010 ) Total stockholders’ equity 695,587 653,764 Total liabilities and stockholders’ equity $ 1,314,041 $ 1,135,496 See accompanying notes. 2 ULTRAGENYX PHARMACEUTICAL INC. CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (Unaudited) (In thousands, except share and per share amounts) Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Revenues: Collaboration and license $ 50,161 $ 19,247 $ 77,376 $ 33,485 Product sales 8,066 4,902 14,545 8,836 Non-cash collaboration royalty revenue 3,482 — 6,097 — Total revenues 61,709 24,149 98,018 42,321 Operating expenses: Cost of sales 1,803 766 ( 1,700 ) 1,218 Research and development 80,709 96,045 193,670 174,150 Selling, general and administrative 42,252 39,812 89,768 78,641 Total operating expenses 124,764 136,623 281,738 254,009 Loss from operations ( 63,055 ) ( 112,474 ) ( 183,720 ) ( 211,688 ) Interest income 1,797 4,063 4,716 7,149 Change in fair value of investment in Arcturus equity securities 95,200 9,828 102,868 9,828 Non-cash interest expense on liability related to the sale of future royalties ( 8,429 ) — ( 16,511 ) — Other income (expense) 217 ( 376 ) ( 239 ) ( 788 ) Income (loss) before income taxes 25,730 ( 98,959 ) ( 92,886 ) ( 195,499 ) Provision for income taxes ( 415 ) ( 213 ) ( 824 ) ( 429 ) Net income (loss) $ 25,315 $ ( 99,172 ) $ ( 93,710 ) $ ( 195,928 ) Net income (loss) per share: Basic $ 0.42 $ ( 1.72 ) $ ( 1.59 ) $ ( 3.54 ) Diluted $ 0.41 $ ( 1.72 ) $ ( 1.59 ) $ ( 3.54 ) Weighted-average shares used in computing net income (loss) per share: Basic 59,995,617 57,519,308 58,996,278 55,376,336 Diluted 61,146,231 57,519,308 58,996,278 55,376,336 See accompanying notes. 3 ULTRAGENYX PHARMACEUTICAL INC. CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (Unaudited) (In thousands) Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Net income (loss) $ 25,315 $ ( 99,172 ) $ ( 93,710 ) $ ( 195,928 ) Other comprehensive income: Foreign currency translation adjustments 89 26 40 155 Unrealized gain on available-for-sale securities 2,740 377 1,391 733 Other comprehensive income 2,829 403 1,431 888 Total comprehensive income (loss) $ 28,144 $ ( 98,769 ) $ ( 92,279 ) $ ( 195,040 ) See accompanying notes. 4 ULTRAGENYX PHARMACEUTICAL INC. CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (Unaudited) (In thousands, except share amounts) Common Stock Additional Paid-In Accumulated Other Comprehensive Accumulated Total Stockholders' Shares Amount Capital Income (Loss) Deficit Equity Balance as of March 31, 2020 59,488,873 $ 59 $ 2,162,667 $ ( 1,545 ) $ ( 1,552,035 ) $ 609,146 Issuance of common stock in connection with at-the-market offering, net of issuance costs 283,333 — 20,391 — — 20,391 Employee stock-based compensation — — 22,428 — — 22,428 Issuance of common stock under equity plan awards, net of tax 641,550 1 15,477 — — 15,478 Other comprehensive income — — — 2,829 — 2,829 Net income — — — — 25,315 25,315 Balance as of June 30, 2020 60,413,756 $ 60 $ 2,220,963 $ 1,284 $ ( 1,526,720 ) $ 695,587 Common Stock Additional Paid-In Accumulated Other Comprehensive Accumulated Total Stockholders' Shares Amount Capital Income (Loss) Deficit Equity Balance as of December 31, 2019 57,838,220 $ 58 $ 2,086,863 $ ( 147 ) $ ( 1,433,010 ) $ 653,764 Issuance of common stock in connection with license agreement, net of issuance costs 1,243,913 1 55,267 — — 55,268 Issuance of common stock in connection with at-the-market offering, net of issuance costs 283,333 — 20,391 — — 20,391 Employee stock-based compensation — — 42,585 — — 42,585 Issuance of common stock upon exercise of warrants and under equity plan awards, net of tax 1,048,290 1 15,857 — — 15,858 Other comprehensive income — — — 1,431 — 1,431 Net loss — — — — ( 93,710 ) ( 93,710 ) Balance as of June 30, 2020 60,413,756 $ 60 $ 2,220,963 $ 1,284 $ ( 1,526,720 ) $ 695,587 Common Stock Additional Paid-In Accumulated Other Comprehensive Accumulated Total Stockholders' Shares Amount Capital Income (Loss) Deficit Equity Balance as of March 31, 2019 57,303,888 $ 57 $ 2,013,859 $ ( 148 ) $ ( 1,127,039 ) $ 886,729 Issuance of common stock in connection with at-the-market offering, net of issuance costs 88,978 — 5,523 — — 5,523 Employee stock-based compensation — — 22,490 — — 22,490 Issuance of common stock under equity plan awards, net of tax 272,509 1 3,813 — — 3,814 Other comprehensive income — — — 403 — 403 Net loss — — — — ( 99,172 ) ( 99,172 ) Balance as of June 30, 2019 57,665,375 $ 58 $ 2,045,685 $ 255 $ ( 1,226,211 ) $ 819,787 5 ULTRAGENYX PHARMACEUTICAL INC. CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (Unaudited) (In thousands, except share amounts) Common Stock Additional Paid-In Accumulated Other Comprehensive Accumulated Total Stockholders' Shares Amount Capital Income (Loss) Deficit Equity Balance as of December 31, 2018 50,860,588 $ 51 $ 1,639,773 $ ( 633 ) $ ( 1,030,283 ) $ 608,908 Issuance of common stock in connection with underwritten public offering, net of issuance costs 5,833,333 6 330,409 — — 330,415 Issuance of common stock in connection with at-the-market offering, net of issuance costs 468,685 — 24,828 — — 24,828 Employee stock-based compensation — — 42,960 — — 42,960 Issuance of common stock under equity plan awards, net of tax 502,769 1 7,715 — — 7,716 Other comprehensive income — — — 888 — 888 Net loss — — — — ( 195,928 ) ( 195,928 ) Balance as of June 30, 2019 57,665,375 $ 58 $ 2,045,685 $ 255 $ ( 1,226,211 ) $ 819,787 See accompanying notes. 6 ULTRAGENYX PHARMACEUTICAL INC. CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) (In thousands) Six Months Ended June 30, 2020 2019 Operating activities: Net loss $ ( 93,710 ) $ ( 195,928 ) Adjustments to reconcile net loss to net cash used in operating activities: Stock-based compensation 42,558 42,428 Amortization of discount on investment securities, net ( 149 ) ( 2,960 ) Depreciation and amortization 6,036 4,225 Foreign currency remeasurement (gain) loss 25 567 Change in fair value of investment in Arcturus equity securities ( 102,868 ) ( 9,828 ) Non-cash collaboration royalty revenue ( 6,097 ) — Non-cash interest expense on liability related to the sale of future royalties 16,511 — Other 34 ( 132 ) Changes in operating assets and liabilities: Accounts receivable 17,955 ( 8,161 ) Inventory 521 ( 6,040 ) Prepaid expenses and other assets ( 6,136 ) ( 3,255 ) Receivable related to the Daiichi Sankyo license agreement ( 8,473 ) — Right-of-use assets ( 6,753 ) ( 17,200 ) Accounts payable, accrued, and other liabilities ( 8,833 ) ( 7,076 ) Contract liabilities 134,898 — Lease liabilities 6,680 18,522 Net cash used in operating activities ( 7,801 ) ( 184,838 ) Investing activities: Purchase of property and equipment ( 18,179 ) ( 8,299 ) Purchase of investments ( 456,331 ) ( 461,088 ) Purchase of investment in Arcturus equity securities ( 9,600 ) ( 14,339 ) Proceeds from the sale of investments 28,850 22,600 Proceeds from maturities of investments 273,996 301,507 Net cash used in investing activities ( 181,264 ) ( 159,619 ) Financing activities: Proceeds from the issuance of common stock in connection with the license agreement, net 55,268 — Proceeds from the issuance of common stock in connection with underwritten public offerings, net — 330,415 Proceeds from the issuance of common stock in connection with at-the-market offering, net 20,391 24,828 Proceeds from the issuance of common stock from exercise of warrants and equity plan awards, net 15,858 7,716 Principal repayments of financing leases ( 91 ) — Net cash provided by financing activities 91,426 362,959 Effect of exchange rate changes on cash ( 198 ) ( 30 ) Net increase (decrease) in cash, cash equivalents and restricted cash ( 97,837 ) 18,472 Cash, cash equivalents and restricted cash at beginning of period 436,244 115,525 Cash, cash equivalents and restricted cash at end of period $ 338,407 $ 133,997 Supplemental disclosures of non-cash information: Acquired lease liabilities arising from obtaining right-of-use assets $ 3,462 $ 21,515 See accompanying notes. 7 ULTRAGENYX PHARMACEUTICAL INC. Notes to Condensed Consolidated Financial Statements 1. Organization Ultragenyx Pharmaceutical Inc. (the Company) is a biopharmaceutical company incorporated in California on April 22, 2010. The Company subsequently reincorporated in the state of Delaware in June 2011. The Company is focused on the identification, acquisition, development, and commercialization of novel products for the treatment of serious rare and ultra-rare genetic diseases. The Company has four approved therapies. Crysvita ® (burosumab) is approved in the United States by the U.S. Food and Drug Administration (FDA) and in Canada for the treatment of X-linked hypophosphatemia (XLH) in adult and pediatric patients one year of age and older, and has received European conditional marketing authorization for the treatment of XLH with radiographic evidence of bone disease in children one year of age and older and adolescents with growing skeletons. In Brazil, Crysvita is approved for treatment of XLH in adult and pediatric patients one year of age and older. Crysvita was approved by the FDA on June 18, 2020 for the treatment of FGF23-related hypophosphatemia in tumor-induced osteomalacia (TIO), associated with phosphaturic mesenchymal tumors that cannot be curatively resected or localized in adults and pediatric patients 2 years of age and older. The Company has also received FDA approval for Mepsevii™ (vestronidase alfa), the first medicine approved for the treatment of children and adults with mucopolysaccharidosis VII (MPS VII), also known as Sly syndrome. In the European Union and the United Kingdom, Mepsevii is approved under exceptional circumstances for patients of all ages for the treatment of non-neurological manifestations of MPS VII. In Brazil, Mepsevii is approved for the treatment of MPS VII for patients of all ages. Dojolvi, formerly known as UX007, was approved by FDA on June 30, 2020 for the treatment of pediatric and adult patients severely affected by long-chain fatty acid oxidation disorders (LC-FAOD). In addition to the approved treatments, the Company has two ongoing clinical development programs. DTX301 is an adeno-associated virus 8 (AAV8) gene therapy product candidate in development for the treatment of patients with ornithine transcarbamylase (OTC) deficiency, the most common urea cycle disorder; and DTX401 is an AAV8 gene therapy product candidate for the treatment of patients with glycogen storage disease type Ia (GSDIa). The Company operates as one reportable segment. The Company has sustained operating losses and expects such annual losses to continue over the next several years. The Company’s ultimate success depends on the outcome of its research and development and commercialization activities, for which it expects to incur additional losses in the future. Management recognizes that we will likely need to raise additional capital to fully implement its business plans. Through June 30, 2020, the Company has relied primarily on the proceeds from equity offerings and its sale of future royalties to finance its operations. The Company will likely raise additional capital through the issuance of equity, borrowings, or strategic alliances with partner companies. However, if such financing is not available at adequate levels, the Company would need to reevaluate its operating plans. 2. Summary of Significant Accounting Policies Basis of Presentation The accompanying unaudited Condensed Consolidated Financial Statements include the accounts of the Company and its wholly-owned subsidiaries and have been prepared in accordance with U.S. generally accepted accounting principles (GAAP) for interim financial information and in accordance with the instructions to Form 10-Q and Rule 10-01 of Regulation S-X. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. The unaudited interim consolidated financial statements have been prepared on the same basis as the annual financial statements. In the opinion of management, the accompanying unaudited Condensed Consolidated financial Statements reflect all adjustments (consisting only of normal recurring adjustments) considered necessary for a fair presentation. These financial statements should be read in conjunction with the audited financial statements and notes thereto for the preceding fiscal year contained in the Company’s Annual Report on Form 10-K filed on February 14, 2020 with the United States Securities and Exchange Commission (SEC). The results of operations for the three and six months ended June 30, 2020 are not necessarily indicative of the results to be expected for the year ending December 31, 2020. The Condensed Consolidated Balance Sheet as of December 31, 2019 has been derived from audited financial statements at that date, but does not include all of the information required by GAAP for complete financial statements. 8 Use of Estimates The accompanying consolidated financial statements have been prepared in accordance with GAAP. The preparation of the consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent liabilities and the reported amounts of expenses in the consolidated financial statements and the accompanying notes. On an ongoing basis, management evaluates its estimates, including those related to clinical trial accruals, fair value of assets and liabilities, income taxes, stock-based compensation, and the liability related to the sale of future royalties. Management bases its estimates on historical experience and on various other market-specific and relevant assumptions that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Cash, Cash Equivalents and Restricted Cash Restricted cash primarily consists of money market accounts as collateral for the Company’s obligations under its facility leases. The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheets that sum to the total of the same such amounts shown in the consolidated statement of cash flows (in thousands): June 30, 2020 2019 Cash and cash equivalents $ 335,639 $ 131,337 Restricted cash included in prepaid expenses and other current assets 847 161 Restricted cash included in other assets 1,921 2,499 Total cash, cash equivalents, and restricted cash shown in the statements of cash flows $ 338,407 $ 133,997 Credit Losses Effective January 1, 2020, the Company adopted Accounting Standards Update (ASU) 2016-13, Financial Instruments — Credit Losses, (Topic 326): Measurement of Credit Losses on Financial Instruments, which changed the impairment model for most financial assets and certain other instruments. For trade receivables and other instruments, the Company uses a new forward-looking expected loss model that generally results in the earlier recognition of allowances for losses. For available-for-sale debt securities with unrealized losses, the losses are recognized as allowances rather than as reductions in the amortized cost of the securities. The Company is exposed to credit losses primarily through receivables from customers and collaborators and through its available-for-sale debt securities. The Company’s expected loss allowance methodology for the receivables is developed using historical collection experience, current and future economic market conditions, a review of the current aging status and financial condition of the entities. Specific allowance amounts are established to record the appropriate allowance for customers that have a higher probability of default. Balances are written off when determined to be uncollectible. The Company’s expected loss allowance methodology for the debt securities is developed by reviewing the extent of the unrealized loss, the size, term, geographical location, and industry of the issuer, the issuers’ credit ratings and any changes in those ratings, as well as reviewing current and future economic market conditions and the issuers’ current status and financial condition. The Company considered the current and expected future economic and market conditions surrounding the novel coronavirus (COVID-19) pandemic and determined that the estimate of credit losses was not significantly impacted. The adoption of ASU 2016-13 did not have a material impact on the Condensed Consolidated Financial Statements and related disclosures and there was no allowance for losses on available-for-sale debt securities which were attributable to credit risk for the three and six months ended June 30, 2020. Revenue Recognition Collaboration and license revenue The Company has certain license and collaboration agreements that are within the scope of Accounting Standards Codification (ASC) 808, Collaborative Agreements , which provides guidance on the presentation and disclosure of collaborative arrangements. Generally, the classification of the transactions under the collaborative arrangements is determined based on the nature of contractual terms of the arrangement, along with the nature of the operations of the participants. The Company records its share of collaboration revenue, net of transfer pricing related to net sales in the period in which such sales occur, if the Company is considered as an agent in the arrangement. The Company is considered an agent when the collaboration partner controls the product before transfer to the customers and has the ability to direct the use of and obtain substantially all of the remaining benefits from the product. Funding received related to research and development services and commercialization costs is generally classified as a reduction of research and development expenses and selling, general and administrative expenses, respectively, in the consolidated statement of operations, because the provision of such services for collaborative partners are not considered to be part of the Company’s ongoing major or central operations. 9 The Company also re cords royalty revenues under certain of the Company’s license or collaboration agreements in exchange for license of intellectual property. If the Company does not have any future performance obligations for these license or collaboration agreements, royalty revenue is recorded as the underlying sales occur. In order to record collaboration revenue, the Company utilizes certain information from its collaboration partners , including revenue from the sale of the product, associated reserves on revenue, and costs incurred for development and sales activities. For the periods covered in the financial statements presented, there have been no material changes to prior period estimates of revenues and expenses. The terms of the Company’s collaboration and license agreements may contain multiple performance obligations, which may include licenses and research and development activities. The Company evaluates these agreements under ASC 606, Revenue from Contracts with Customers (ASC 606), to determine the distinct performance obligations. The Company analogizes to ASC 606 for the accounting for distinct performance obligations for which there is a customer relationship. Prior to recognizing revenue, the Company makes estimates of the transaction price, including variable consideration that is subject to a constraint. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Total consideration may include nonrefundable upfront license fees, payments for research and development activities, reimbursement of certain third-party costs, payments based upon the achievement of specified milestones, and royalty payments based on product sales derived from the collaboration. If there are multiple distinct performance obligations, the Company allocates the transaction price to each distinct performance obligation based on its relative standalone selling price. The standalone selling price is generally determined based on the prices charged to customers or using expected cost-plus margin. The Company estimates the efforts needed to complete the performance obligations and recognizes revenue by measuring the progress towards complete satisfaction of the performance obligations using input measures. Product sales The Company sells its approved products through a limited number of distributors. Under ASC 606, revenue from product sales is recognized at the point in time when the delivery is made and when title and risk of loss transfers to these distributors. The Company also recognizes revenue from sales of certain products on a “named patient” basis, which are allowed in certain countries prior to the commercial approval of the product. Prior to recognizing revenue, the Company makes estimates of the transaction price, including any variable consideration that is subject to a constraint. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Product sales are recorded net of estimated government-mandated rebates and chargebacks, estimated product returns, and other deductions. Provisions for returns and other adjustments are provided for in the period the related revenue is recorded, as estimated by management. These reserves are based on estimates of the amounts earned or to be claimed on the related sales and are reviewed periodically and adjusted as necessary. If actual results vary, the Company may need to adjust these estimates, which could have an effect on earnings in the period of the adjustment. Non-cash collaboration royalty revenue Effective January 1, 2020, the Company sold the right to receive certain royalty payments from net sales of Crysvita to RPI Finance Trust (RPI), an affiliate of Royalty Pharma, as further described in Note 7. The Company records the royalty revenue from the net sales of Crysvita in the applicable European territories on a prospective basis as non-cash royalty revenue in the Consolidated Statements of Operations over the term of the arrangement. 3. Financial Instruments Financial assets and liabilities are recorded at fair value. The carrying amount of certain financial instruments, including cash and cash equivalents, accounts receivable, accounts payable and accrued liabilities approximate fair value due to their relatively short maturities. Assets and liabilities recorded at fair value on a recurring basis in the balance sheets are categorized based upon the level of judgment associated with the inputs used to measure their fair values. Fair value is defined as the exchange price that would be received for an asset or an exit price that would be paid to transfer a liability in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. The authoritative guidance on fair value measurements establishes a three-tier fair value hierarchy for disclosure of fair value measurements as follows: Level 1 —Inputs are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date; Level 2 —Inputs are observable, unadjusted quoted prices in active markets for similar assets or liabilities, unadjusted quoted prices for identical or similar assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the related assets or liabilities; and Level 3 —Unobservable inputs that are significant to the measurement of the fair value of the assets or liabilities that are supported by little or no market data. 10 The following tables set forth the fair value of the Company’s financial assets remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands): June 30, 2020 Level 1 Level 2 Level 3 Total Money market funds $ 297,003 $ — $ — $ 297,003 Time deposits — 10,000 — 10,000 Corporate bonds — 215,486 — 215,486 Commercial paper — 98,233 — 98,233 Asset-backed securities — 15,183 — 15,183 U.S. Government Treasury and agency securities 104,924 48,019 — 152,943 Investment in Arcturus equity security 140,220 — — 140,220 Total $ 542,147 $ 386,921 $ — $ 929,068 December 31, 2019 Level 1 Level 2 Level 3 Total Money market funds $ 293,309 $ — $ — $ 293,309 Repurchase agreements — 100,000 — 100,000 Time deposits — 10,000 — 10,000 Corporate bonds — 77,026 — 77,026 Commercial paper — 80,119 — 80,119 Asset-backed securities — 30,406 — 30,406 U.S. Government Treasury and agency securities 96,329 53,979 — 150,308 Investment in Arcturus equity securities 26,088 — 1,664 27,752 Total $ 415,726 $ 351,530 $ 1,664 $ 768,920 The Company determined the fair value of the Arcturus Therapeutics Holdings Inc. (Arcturus) common stock by using the quoted market price on June 30, 2020, which is a Level 1 fair value measurement. T he fair value of the option to purchase additional shares of Arcturus common stock was based on unobservable inputs that are significant to the measurement of the fair value of the asset and is supported by little or no market data; accordingly, the fair value of the option is considered a Level 3 financial asset. The Company measured the fair value of the option by applying the Black-Scholes option pricing method and utilizing the following inputs: stock price, strike price, volatility, risk-free interest rate, and expected term. The expected term was the Company’s estimated period to purchase additional stock. In May 2020, the Company exercised its option to purchase additional shares of Arcturus common stock. See Note 6 for additional details on the Arcturus transaction. 4. Balance Sheet Components Cash Equivalents and Investments The fair values of cash equivalents and investments classified as available-for-sale securities consisted of the following (in thousands): June 30, 2020 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 297,003 $ — $ — $ 297,003 Time deposits 10,000 — — 10,000 Corporate bonds 214,224 1,266 ( 4 ) 215,486 Commercial paper 98,233 — — 98,233 Asset-backed securities 15,151 32 — 15,183 U.S. Government Treasury and agency securities 152,687 264 ( 8 ) 152,943 Total $ 787,298 $ 1,562 $ ( 12 ) $ 788,848 11 December 31, 2019 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 293,309 $ — $ — $ 293,309 Repurchase agreements 100,000 — — 100,000 Time deposits 10,000 — — 10,000 Corporate bonds 77,022 17 ( 13 ) 77,026 Commercial paper 80,119 — — 80,119 Asset-backed securities 30,375 31 — 30,406 U.S. Government Treasury and agency securities 150,184 124 — 150,308 Total $ 741,009 $ 172 $ ( 13 ) $ 741,168 At June 30, 2020, the remaining contractual maturities of available-for-sale securities were less than two years . There have been no realized gains or losses on available-for-sale securities for the three and six months ended June 30, 2020 and 2019. All marketable securities with unrealized losses at June 30, 2020 have been in a loss position for less than twelve months. Based on the Company’s application of its expected loss allowance methodology, it is probable that the principal and interest will be collected in accordance with the contractual terms, and that the unrealized loss on these securities were not attributable to credit risk. Inventory Inventory consists of the following (in thousands): June 30, December 31, 2020 2019 Work-in-process $ 7,677 $ 8,191 Finished goods 3,384 3,355 Total inventory $ 11,061 $ 11,546 Accrued Liabilities Accrued liabilities consist of the following (in thousands): June 30, December 31, 2020 2019 Research, clinical study, and manufacturing expenses $ 21,719 $ 22,894 Payroll and related expenses 35,836 41,324 Other 14,332 18,976 Total accrued liabilities $ 71,887 $ 83,194 5. Revenue The following table disaggregates total revenues from customers (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Collaboration and license revenue: Crysvita collaboration revenue in profit- share territory $ 29,806 $ 17,248 $ 57,021 $ 29,187 Royalty revenue in European territory 1,498 1,931 1,498 $ 3,946 Daiichi Sankyo 18,857 — 18,857 — Bayer — 68 — 352 Total collaboration and license revenue 50,161 19,247 77,376 33,485 Product sales: Crysvita 2,549 1,006 4,159 1,594 Mepsevii 4,185 3,240 7,610 5,913 UX007 1,332 656 2,776 1,329 Total product sales 8,066 4,902 14,545 8,836 Non-cash collaboration royalty revenue 3,482 — 6,097 — Total revenues $ 61,709 $ 24,149 $ 98,018 $ 42,321 12 The following table disaggregates total revenues based on geographic location (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 United States $ 51,931 $ 20,163 $ 82,288 $ 34,618 Europe 6,548 2,821 10,705 5,732 All other 3,230 1,165 5,025 1,971 Total revenues $ 61,709 $ 24,149 $ 98,018 $ 42,321 The following table presents changes in the contract assets (liabilities) (in thousands): Six Months Ended June 30, 2020 2019 Balance of contract assets (liabilities) at beginning of period $ — $ 2,979 Additions ( 153,755 ) 352 Deductions 18,857 ( 3,386 ) Balance of contract liabilities at end of period $ ( 134,898 ) $ ( 55 ) See Note 6 for additional details on contract assets (liabilities) activities. The Company’s largest accounts receivable balance accounted for 79 % and 87 % of the total accounts receivable balance as of June 30, 2020 and December 31, 2019, respectively, and was due from a collaboration partner. 6. License and Research Agreements Kyowa Kirin Collaboration and License Agreement In August 2013, the Company entered into a collaboration and license agreement with Kyowa Kirin Co., Ltd. (KKC or formerly Kyowa Hakko Kirin Co., Ltd. or KHK). Under the terms of this collaboration and license agreement, as amended, the Company and KKC collaborate on the development and commercialization of Crysvita in the field of orphan diseases in the United States and Canada, or the profit-share territory, and in the European Union, United Kingdom, and Switzerland, or the European territory, and the Company has the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America. Development Activities In the field of orphan diseases, and except for ongoing studies being conducted by KKC, the Company is the lead party for development activities in the profit-share territory and in the European territory until the applicable transition date; the Company is also the lead party for core development activities conducted in Japan and Korea, for which the core development plan is limited to clinical trials mutually agreed to by the Company and KKC. The Company shares the costs for development activities in the profit-share territory and the European territory conducted pursuant to the development plan before the applicable transition date equally with KKC. KKC is responsible for 100 % of the costs for development activities in Japan and Korea. In April 2023, which is the transition date for the profit-share territory, and on the applicable transition date for the European territory, KKC will become the lead party and be responsible for the costs of the development activities. However, the Company will continue to share the costs of the studies commenced prior to the applicable transition date equally with KKC. Crysvita was approved in the European Union and United Kingdom in February 2018 and was approved by the FDA in April 2018. The collaboration and license agreements are within the scope of ASC 808, which provides guidance on the presentation and disclosure of collaborative arrangements. Collaboration revenue related to sales in profit-share territory The Company and KKC share commercial responsibilities and profits in the profit-share territory until April 2023. Under the collaboration agreement, KKC manufactures and supplies Crysvita for commercial use in the profit-share territory and charges the Company the transfer price of 35 % of net sales through December 31, 2022, and 30 % thereafter. The remaining profit or loss after supply costs from commercializing products in the profit-share territory are shared between the Company and KKC on a 50 /50 basis until April 2023. Thereafter, the Company will be entitled to receive a tiered double-digit revenue share in the mid-to-high 20 % range. As KKC is the principal in the sale transaction with the customer, the Company recognizes a pro-rata share of collaboration revenue, net of transfer pricing, in the period the sale occurs. The Company concluded that its portion of KKC’s sales in the profit-share territory is analogous to a royalty and therefore recorded its share as collaboration revenue, similar to a royalty. Royalty revenue related to sales in European territory 13 KKC has the commercial responsibility for Crysvita in the European territory. In December 2019, the Company sold its right to receive royalty payments based on sales in the European territory to Royalty Pharma, effective January 1, 2020, as further described in Note 7. Prior to the Company’s sale of the royalty, the Company received a royalty of up to 10 % on net sales in the European territory, which was recognized as the underlying sales occur. Beginning in 2020, the Company records the royalty revenue as non-cash royalty revenues. During the three months ended June 30, 2020, there was a change in estimate of the revenue reserves related to sales made prior to January 1, 2020, as a result of which, the Company recorded $ 1.5 million as royalty revenue in European territory. The Company’s share of collaboration and royalty revenue related to Crysvita was as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Company's share of revenue in profit- share territory $ 29,806 $ 17,248 $ 57,021 $ 29,187 Royalty revenue in European territory 1,498 1,931 1,498 3,946 Non-cash royalty revenue in European territory 3,482 — 6,097 — Total $ 34,786 $ 19,179 $ 64,616 $ 33,133 Product revenue related to sales in other territories The Company is responsible for commercializing Crysvita in Latin America and Turkey. The Company is considered the principal in these territories as the Company controls the product before it is transferred to the customer. Accordingly, the Company records revenue on a gross basis related to the sale of Crysvita once the product is delivered and the risk and title of the product is transferred to the distributor. The Company recorded product sales of $ 2.5 million and $ 4.2 million for the three and six months ended June 30, 2020, respectively, and $ 1.0 million and $ 1.6 million for the three and six months ended June 30, 2019, respectively, net of estimated product returns and other deductions. KKC has the option to assume responsibility for commercialization efforts in Turkey from the Company, after a certain minimum period. Under the collaboration agreement, KKC manufactures and supplies Crysvita, which is purchased by the Company for sales in the above territories and is based on 35 % of the net sales through December 31, 2022 and 30 % thereafter. The Company also pays to KKC a low single-digit royalty on net sales in Latin America . Cost sharing payments Under the collaboration agreement, KKC and the Company share certain development and commercialization costs. As a result, the Company was reimbursed for these costs and operating expenses were reduced as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Research and development $ 5,168 $ 5,895 $ 10,658 $ 12,994 Selling, general and administrative 5,965 5,163 13,017 10,376 Total $ 11,133 $ 11,058 $ 23,675 $ 23,370 Collaboration receivable The Company had accounts receivable from KKC in the amount of $ 11.8 million and $ 28.5 million from profit-share revenue and royalties and other receivables recorded in prepaid and other current assets of $ 8.2 million and $ 17.8 million and accrued liabilities of $ 1.3 million and $ 0.9 million from commercial and development activity reimbursements, as of June 30, 2020 and December 31, 2019, respectively. Bayer HealthCare LLC The Company has an agreement with Bayer Healthcare LLC (Bayer) to research, develop and commercialize AAV gene therapy products for the treatment of hemophilia A (DTX 201). Under this agreement, Bayer has been granted an exclusive license to develop and commercialize one or more novel gene therapies for hemophilia A. The agreement requires that Bayer use commercially reasonable efforts to conduct and fund a proof-of-concept (POC) clinical trial and any subsequent clinical trials and commercialization of gene therapy products for treatment of hemophilia A. Bayer will have worldwide rights to commercialize the potential future product. Bayer is responsible for funding certain research and development services performed by the Company in the performance of its obligations under the annual research plan and budget. Under the terms of the agreement with Bayer, the Company is eligible to receive development and commercialization milestone payments of up to $ 232.0 million, as well as, royalty payments ranging in the high single-digit to low double-digit percentages, not exceeding the mid-teens, of net sales of licensed products. The Company achieved the first milestone in December 2017, the second milestone in April 2018, and has received $ 15.0 million for such milestones to date. 14 The Company’s obligations under the contract were completed by end of December 31, 2019 and as a result, no revenue was recorded for the three and six months ended June 30, 2020. The Company recorded revenue of $ 0.1 million and $ 0.4 million for the three and six months ended June 30, 2019, respectively. The Company may record future milestone payments as revenue, if it becomes probable that a significant reversal in the amount of revenue recognized will not occur and when the uncertainty associated with the variable consideration is subsequently resolved. Arcturus The Company has a Research Collaboration and License Agreement with Arcturus to research and develop therapies for select rare diseases. Pursuant to the agreement, the Company incurred $ 0.4 million and $ 0.6 million for the three and six months ended June 30, 2019, respectively, in research and development expense for the funding of certain research services received from Arcturus. No research and development expenses were recognized in 2020 related to the Arcturus agreement. In May 2020, the Company exercised an option to purchase 600,000 shares of Arcturus’ common stock at $ 16.00 per share, or a total purchase price of $ 9.6 million. Accordingly, after the exercise of the option, the Company owned 3,000,000 shares, or 14.6 %, of Arcturus’ then outstanding common stock. The purchase was made pursuant to the equity purchase agreement between the parties entered into in June 2019 in connection with the amendment to the research collaboration and license agreement. The Arcturus common stock is restricted from sale or transfer by the Company for six months from the exercise date, subject to certain conditions. The Company has elected to apply the fair value option to account for the equity investment in Arcturus. The Company had accounted for the option to purchase additional shares of Arcturus common stock at fair value based on the Black-Scholes option pricing method. The changes in the fair value of the Company’s investment in Arcturus securities were as follows (in thousands): Arcturus common stock Fair value of option to purchase additional shares of Arcturus common stock Total Acquisition of investment in Arcturus securities in June 2019 $ 13,872 $ 467 $ 14,339 Change in fair value 12,216 1,197 13,413 December 31, 2019 26,088 1,664 27,752 Change in fair value 78,920 23,948 102,868 Transfer of value upon option exercise 35,212 ( 25,612 ) 9,600 June 30, 2020 $ 140,220 $ — $ 140,220 GeneTx In August 2019, the Company entered into a Program Agreement and a Unitholder Option Agreement with GeneTx Biotherapeutics, LLC (GeneTx) to collaborate on the development of GeneTx’s GTX-102, an antisense oligonucleotide (ASO) for the treatment of Angelman syndrome. Pursuant to the terms of the Unitholder Option Agreement, the Company made an upfront payment of $ 20.0 million for an exclusive option to acquire GeneTx, which was exercisable any time prior to 30 days following FDA acceptance of the IND for GTX-102. Pursuant to the agreement, upon acceptance of IND, the Company elected to extend the option period by paying an option extension payment of $ 25.0 million (option extension premium) during the prior quarter ended March 31, 2020. The Company has a right to acquire GeneTx for a payment of $ 125.0 million, at any time, until the earlier of 30 months from the first dosing of a patient in a planned Phase 1/2 study (subject to extensions) or 90 days after results are available from that study. This exclusive option to acquire GeneTx can be extended under certain circumstances, by up to four additional three-month periods, by paying an additional extension fee for each three-month period. During the exclusive option period, GeneTx is responsible for conducting the program based on the development plan agreed between the parties and, subject to the terms in the Program Agreement, has the decision-making authority on all matters in connection with the research, development, manufacturing and regulatory activities with respect to the Program. The Company will provide support, at its discretion, including strategic guidance and clinical expertise. The Company and GeneTx will collaborate on the submission of the IND and management of the Phase 1/2 study in patients with Angelman syndrome. If the Company acquires GeneTx, the Company will then be responsible for all development and commercialization activities from the date of acquisition. The Company would also be required to make payments upon achievement of certain development and commercial milestones, as well as royalties, depending upon the success of the program. Although GeneTx is a variable interest entity, the Company is not the primary beneficiary as it currently does not have the power to direct the activities that would most significantly impact the economic performance of GeneTx. Prior to product regulatory approval, all consideration paid to GeneTx represents rights to potential future benefits associated with GeneTx’s in-process research and development activities, which have not reached technological feasibility and have no alternative future use. Accordingly, for the three and six months ended June 30, 2020, the Company recorded the option extension payment of none and $ 25.0 million as an in-process research and development expense. 15 REGENXBIO, Inc. In March 2020, the Company executed a License Agreement with REGENXBIO, Inc. (REGENEX), for an exclusive, sublicensable, worldwide license to REGENX’s NAV AAV8 and AAV9 Vectors for the development and commercialization of gene therapy treatments for a rare metabolic disorder. In return for these rights, the Company made an upfront payment of $ 7.0 million, which was recorded as an in-process research and development expense during the prior quarter ended March 31, 2020. The Company will pay certain annual fees of $ 0.1 million, milestone payments of up to $ 14.0 million, and royalties on any net sales of products incorporating the licensed intellectual property that range from a high single-digit to low double-digit royalty . Daiichi Sankyo In March 2020, the Company executed a License and Technology Access Agreement (the License Agreement) with Daiichi Sankyo Co., Ltd. (Daiichi Sankyo). Pursuant to the License Agreement, the Company granted Daiichi Sankyo a non-exclusive license to intellectual property, including know-how and patent applications, with respect to its HeLa PCL and HEK293 transient transfection manufacturing technology platforms for AAV-based gene therapy products. The Company retains the exclusive right to use the manufacturing technology for its current target indications and additional indications identified now and in the future. The Company will provide certain technical assistance and technology transfer services during the technology transfer period of three years to enable Daiichi Sankyo to use the technologies for its internal gene therapy programs. Daiichi Sankyo has an option to extend the technology transfer period including know-how improvements by two additional one-year periods by paying a fixed amount for each additional year. Daiichi Sankyo will be responsible for the manufacturing, development, and commercialization of products manufactured with the licensed technology; however, the Company has the option to co-develop and co-commercialize rare disease products at the IND stage. Ultragenyx may also provide strategic consultation to Daiichi Sankyo on the development of both AAV-based gene therapy products and other products for rare diseases. Under the terms of the License Agreement, Daiichi Sankyo made an upfront payment of $ 125.0 million and will pay an additional $ 25.0 million upon completion of the technology transfer of the HeLa PCL and HEK293 platforms, as well as single-digit royalties on net sales of products manufactured in either system. Daiichi Sankyo will reimburse the Company for all costs associated with the transfer of the manufacturing technology. The Company also entered into a Stock Purchase Agreement (SPA) with Daiichi Sankyo, pursuant to which Daiichi Sankyo purchased 1,243,913 shares in exchange for $ 75.0 million in cash during the first quarter of 2020. The fair market value of the common stock issued to Daiichi Sankyo was $ 55.3 million based on the stock price of $ 44.43 on the date of issuance, resulting in a $ 19.7 million premium on the SPA. Daiichi Sankyo is also subject to a three-year standstill and restrictions on sale of the shares (subject to customary exceptions or release). In June 2020, the Company executed a subsequent license agreement (the Sublicense Agreement) with Daiichi Sankyo for transfer of certain technology in consideration for an upfront payment of $ 8.0 million and annual maintenance fees, milestone payments, and royalties on any net sales of products incorporating the licensed intellectual property. The License Agreement, the Sublicense Agreement, and the SPA are being accounted for as one arrangement because they were entered into at or near the same time and negotiated in contemplation of one another. The Company evaluated the License Agreement and the Sublicense Agreement under ASC 606 and determined that the performance obligations under the agreements are (i) intellectual property with respect to its HeLa PCL and HEK293 transient transfection manufacturing technology platforms together with the initial technical assistance and technology transfer services, which are expected to be completed over a period of 18 months, and (ii) the transfer of any know-how and improvements after the completion of the initial technology transfer through the end of the three year technology transfer period. The Company determined that the total transaction price of the License Agreement was $ 183.8 million which was comprised of the $ 19.7 million premium from the SPA, the $ 125.0 million upfront payment, the $ 25.0 million in unconstrained milestone payments, $ 8.0 million from the Sublicense Agreement, and the $ 5.5 million estimated reimbursement amount for delivering the license and technology services. The Company allocated the total transaction price to the two performance obligations on a relative stand-alone selling price basis. Revenue allocated to the intellectual property and the technology transfer services will be recognized over an initial estimated period of 18 to 21 months, measuring the progress toward complete satisfaction of the individual performance obligation using an input measure. Revenue for know-how and improvements after the completion of technology transfer will be recognized over the remaining technology transfer period (i.e., months 19-36) on a straight-line basis, as it is expected that Daiichi Sankyo will receive and consume the benefits consistently throughout the period. The performance obligations are estimated to be substantially complete by March 2023. The estimated period to complete the technology transfer services and the related milestones payments, if any, are subject to revised estimates which could be impacted by limitations or delays from the COVID-19 pandemic, successful scale-up of the manufacturing, and other changes that may impact timing. Royalties from commercial sales will be accounted for as revenue upon achievement of such sales, assuming all other revenue recognition criteria are met. 16 The technology transfer services were initiated during the second quarter of 2020, as such the Company began recognizing revenue during the period. For the three and six months ended June 30, 2020, the Company recognized $ 18.9 million in revenue related to this arrangement. Accordingly, the Company had recorded $ 131.6 million as short-term contract liability and $ 3.3 million as long- term contract liability as of June 30, 2020. The Company had a receivable related to the above agreements of $ 8.5 million as of June 30, 2020. 7. Liability Related to the Sale of Future Royalties In December 2019, the Company entered into a Royalty Purchase Agreement with RPI. Pursuant to the agreement, RPI paid $ 320.0 million to the Company in consideration for the right to receive royalty payments effective January 1, 2020, arising from the net sales of Crysvita in the European Union, the United Kingdom, and Switzerland under the terms of the Company’s Collaboration and License Agreement with KKC dated August 29, 2013, as amended. The agreement with RPI will automatically terminate, and the payment of royalties to RPI will cease, in the event aggregate royalty payments received by RPI are equal to or greater than $ 608.0 million prior to December 31, 2030, or in the event aggregate royalty payments received by RPI are less than $ 608.0 million prior to December 31, 2030, when aggregate royalty payments received by RPI are equal to $ 800.0 million. As RPI’s rate of return is explicitly limited due to the cap on royalties they may receive, proceeds from the transaction were recorded as a liability (liability related to sale of future royalties on the Consolidated Balance Sheets). The Company amortizes $ 320.0 million, net of transaction cost of $ 5.8 million using the effective interest method over the estimated life of the arrangement. In order to determine the amortization of the liability, the Company is required to estimate the total amount of future royalty payments to be received by the Company and paid to RPI, subject to the capped amount, over the life of the arrangement. The excess of future estimated royalty payments (subject to the capped amount), over the $ 314.2 million of net proceeds, is recorded as non-cash interest expense over the life of the arrangement. Consequently, the Company estimates an imputed interest on the unamortized portion of the liability and records interest expense relating to the transaction. The Company records the royalty revenue from the net sales of Crysvita in the applicable European territories as non-cash royalty revenue in the Consolidated Statements of Operations. The Company periodically assesses the expected royalty payments using a combination of historical results, internal projections and forecasts from external sources. To the extent such payments are greater or less than the Company’s initial estimates or the timing of such payments is materially different than its original estimates, the Company will prospectively adjust the amortization of the liability and the effective interest rate. The Company’s effective annual interest rate was approximately 10.3 % and 10.1 % as of June 30, 2020 and December 31, 2019, respectively. There are a number of factors that could materially affect the amount and timing of royalty payments from KKC in the applicable European territories, most of which are not within the Company’s control. Such factors include, but are not limited to, the success of KKC’s sales and promotion of Crysvita, changing standards of care, delays or disruptions related to the COVID-19 pandemic, the introduction of competing products, approval of label expansion for adults, pricing for reimbursement in various European territories, manufacturing or other delays, intellectual property matters, adverse events that result in governmental health authority imposed restrictions on the use of Crysvita, significant changes in foreign exchange rates as the royalty payments are made in U.S. dollars (USD) while significant portions of the underlying European sales of Crysvita are made in currencies other than USD, and other events or circumstances that could result in reduced royalty payments from European sales of Crysvita, all of which would result in a reduction of non-cash royalty revenue and the non-cash interest expense over the life of the arrangement. Conversely, if sales of Crysvita in Europe are more than expected, the non-cash royalty revenue and the non-cash interest expense recorded by the Company would be greater over the term of the arrangement. The following table shows the activity within the liability account (in thousands): Liability related to the sale of future royalties Proceeds from sale of future royalties in December 2019 $ 314,234 Non-cash interest expense 1,135 December 31, 2019 315,369 Non-cash collaboration royalty revenue ( 6,097 ) Non-cash interest expense 16,511 June 30, 2020 $ 325,783 8 . Stock-Based Awards The 2014 Incentive Plan (the 2014 Plan) provides for automatic annual increases in shares available for grant, beginning on January 1, 2015 through January 1, 2024 . As of June 30, 2020 , there were 3,304,531 shares reserved under the 2014 Plan for the future issuance of equity awards and 3,287,825 shares reserved for the 2014 Employee Stock Purchase Plan. 17 The table below sets forth the stock-based compensation expense for the periods presented (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Cost of sales $ 112 $ 51 $ 180 $ 85 Research and development 12,856 12,032 23,785 23,262 Selling, general and administrative 9,441 10,124 18,616 19,081 Total stock-based compensation expense $ 22,409 $ 22,207 $ 42,581 $ 42,428 9 . Net Income (Loss) Per Share Basic net income (loss) per share has been computed by dividing the net income (loss) by the weighted-average number of shares of common stock outstanding during the period. Diluted net income (loss) per share is calculated by dividing net income (loss) by the weighted-average number of shares of common stock and potential dilutive securities outstanding during the period. For the six months ended June 30, 2020 and the three and six months ended June 30, 2019, there were no differences between basic and diluted net loss per share since the effect of the dilutive securities would have been antidilutive and therefore were excluded from the diluted net loss per share calculation. The following table sets forth the computation of the basic and diluted net income (loss) per share (in thousands, except share and per share data): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Net income (loss), basic and diluted $ 25,315 $ ( 99,172 ) $ ( 93,710 ) $ ( 195,928 ) Weighted-average shares used in computing net income (loss) per share, basic 59,995,617 57,519,308 58,996,278 55,376,336 Weighted-average effect of dilutive securities: Options to purchase common stock and RSUs 1,150,614 — — — Weighted-average shares used in computing net income (loss) per share, diluted 61,146,231 57,519,308 58,996,278 55,376,336 Net income (loss) per share: Basic $ 0.42 $ ( 1.72 ) $ ( 1.59 ) $ ( 3.54 ) Diluted $ 0.41 $ ( 1.72 ) $ ( 1.59 ) $ ( 3.54 ) The following weighted-average outstanding common stock equivalents were excluded from the computation of diluted net income (loss) per share for the periods presented because including them would have been antidilutive: Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Options to purchase common stock and restricted stock units 5,204,036 8,220,733 8,643,439 7,825,615 Employee stock purchase plan 10,952 7,857 5,476 3,950 Common stock warrants — 149,700 59,222 149,700 5,214,988 8,378,290 8,708,137 7,979,265 10 . Equity Transactions In July 2017, the Company entered into an At-The-Market, or ATM, sales agreement with Cowen and Company, LLC (Cowen), whereby the Company could sell up to $ 150.0 million in aggregate proceeds of common stock from time to time, with Cowen as its sales agent. During the three and six months ended June 30, 2020, the Company sold 283,333 shares of common stock, resulting in net proceeds of $ 20.4 million, after commissions and other offering costs. During the three and six months ended June 30, 2019, the Company sold 88,978 and 468,685 shares of common stock, respectively, resulting in net proceeds of approximately $ 5.5 million and $ 24.8 million, respectively, after commissions and other offering costs. As of June 30, 2020 , the Company had completed the sale of all available amounts under the ATM facility. 18 In February 2019, the Company completed an underwritten public offering in which 5,833,333 shares of common stock were sold, which included 760,869 shares purchased by the underwriters pursuant to an option granted to them in connection with the offering, at a public offering price of $ 60.00 per share. The total proceeds that the Company received from the offering were approximately $ 330.4 million, net of underwriting discounts and commissions. 11 . Accumulated Other Comprehensive Income (Loss) Total accumulated other comprehensive income (loss) consisted of the following (in thousands): June 30, December 31, 2020 2019 Foreign currency translation adjustments $ ( 266 ) $ ( 306 ) Unrealized gain on securities available-for-sale 1,550 159 Total accumulated other comprehensive income (loss) $ 1,284 $ ( 147 ) 19