Ultragenyx Pharmaceutical (RARE) 10-K 17 Feb 17 2016 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($) $ in Billions	12 Months Ended
	Dec. 31, 2016	Feb. 13, 2017	Jun. 30, 2016
Document And Entity Information [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	FY
Trading Symbol	RARE
Entity Registrant Name	Ultragenyx Pharmaceutical Inc.
Entity Central Index Key	1,515,673
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	Yes
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		41,726,736
Entity Public Float			$ 1.9

CONSOLIDATED BALANCE SHEETS

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 161,120	$ 93,569
Short-term investments	219,028	343,428
Restricted cash	1,411	150
Prepaid expenses and other current assets	20,136	13,060
Total current assets	401,695	450,207
Property and equipment, net	17,055	7,373
Restricted cash	2,076	2,135
Long-term investments	117,963	99,259
Other assets	1,837	595
Total assets	540,626	559,569
Current liabilities:
Accounts payable	5,364	2,942
Accrued liabilities	54,554	24,784
Deferred rent—current portion	341	192
Total current liabilities	60,259	27,918
Other liabilities	6,393	561
Total liabilities	66,652	28,479
Commitments and contingencies (Note 10)
Stockholders’ equity:
Preferred stock, par value of $0.001 per share—25,000,000 shares authorized; nil outstanding as of December 31, 2016 and 2015
Common stock, par value of $0.001 per share—250,000,000 shares authorized; 41,240,230 and 38,882,394 shares issued and outstanding as of December 31, 2016 and 2015	41	39
Additional paid-in capital	1,003,561	816,578
Accumulated other comprehensive income (loss)	905	(868)
Accumulated deficit	(530,533)	(284,659)
Total stockholders’ equity	473,974	531,090
Total liabilities and stockholders’ equity	$ 540,626	$ 559,569

CONSOLIDATED BALANCE SHEETS (Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Dec. 31, 2016	Dec. 31, 2015
Statement Of Financial Position [Abstract]
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	25,000,000	25,000,000
Preferred stock, shares outstanding	0	0
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	250,000,000	250,000,000
Common stock, shares issued	41,240,230	38,882,394
Common stock, shares outstanding	41,240,230	38,882,394

CONSOLIDATED STATEMENTS OF OPER

CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Statement [Abstract]
Revenue	$ 133
Operating expenses:
Research and development	183,204	$ 114,737	$ 45,967
General and administrative	64,936	33,001	10,811
Total operating expenses	248,140	147,738	56,778
Loss from operations	(248,007)	(147,738)	(56,778)
Other income (expense), net:
Interest income	3,789	2,320	608
Other expense, net	(1,621)	(200)	(3,632)
Total other income (expense), net	2,168	2,120	(3,024)
Loss before income taxes	(245,839)	(145,618)	(59,802)
Income tax provision	(35)
Net loss	(245,874)	(145,618)	(59,802)
Net loss attributable to common stockholders	$ (245,874)	$ (145,618)	$ (64,610)
Net loss per share attributable to common stockholders, basic and diluted	$ (6.21)	$ (3.96)	$ (2.25)
Shares used in computing net loss per share attributable to common stockholders, basic and diluted	39,586,908	36,782,603	28,755,758

CONSOLIDATED STATEMENTS OF COMP

CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Statement Of Income And Comprehensive Income [Abstract]
Net loss	$ (245,874)	$ (145,618)	$ (59,802)
Other comprehensive income (loss):
Foreign currency translation adjustments	1,322
Unrealized gain (loss) on available-for-sale securities	451	(694)	(185)
Other comprehensive income (loss):	1,773	(694)	(185)
Total comprehensive loss	$ (244,101)	$ (146,312)	$ (59,987)

CONSOLIDATED STATEMENTS OF CONV

CONSOLIDATED STATEMENTS OF CONVERTIBLE PREFERRED STOCK AND SHAREHOLDERS' EQUITY (DEFICIT) - USD ($) $ in Thousands	Total	Series A Redeemable Convertible Preferred Stock	Series B Convertible Preferred Stock	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Beginning balance at Dec. 31, 2013	$ (74,821)			$ 4		$ 11	$ (74,836)
Beginning balance, shares at Dec. 31, 2013				3,766,289
Beginning balance at Dec. 31, 2013		$ 51,001	$ 73,929
Beginning balance, shares at Dec. 31, 2013		34,349,894	27,081,680
Accretion on convertible preferred stock		$ 4,430
Accretion on convertible preferred stock	(4,430)				$ (27)		(4,403)
Conversion of convertible preferred stock to common stock	129,360	$ (55,431)	$ (73,929)	$ 19	129,341
Conversion of convertible preferred stock to common stock, shares		(34,349,894)	(27,081,680)	19,598,486
Reclassification of preferred stock warrant liability	6,743				6,743
Issuance of common stock in connection with initial public offering, net of issuance costs and preferred stock dividend	121,711			$ 7	121,704
Issuance of common stock in connection with initial public offering, net of issuance costs and preferred stock dividend, shares				6,624,423
Issuance of common stock in connection with underwritten public offering, net of issuance costs	60,239			$ 2	60,237
Issuance of common stock in connection with underwritten public offering, net of issuance costs, shares				1,613,879
Employee stock-based compensation	5,394				5,394
Issuance of common stock upon exercise of stock options and warrants	$ 736				736
Issuance of common stock upon exercise of stock options and warrants, shares	305,090			331,605
Other comprehensive income (loss)	$ (185)					(185)
Net loss	(59,802)						(59,802)
Ending balance at Dec. 31, 2014	184,945			$ 32	324,128	(174)	(139,041)
Ending balance, shares at Dec. 31, 2014				31,934,682
Issuance of common stock in connection with underwritten public offering, net of issuance costs	461,136			$ 6	461,130
Issuance of common stock in connection with underwritten public offering, net of issuance costs, shares				5,980,000
Employee stock-based compensation	24,884				24,884
Issuance of common stock upon exercise of stock options and warrants	$ 7,355			$ 1	7,354
Issuance of common stock upon exercise of stock options and warrants, shares	795,825			957,587
Restricted stock units vested during the period, net	$ (918)				(918)
Restricted stock units vested during the period, net of shares				10,125
Other comprehensive income (loss)	(694)					(694)
Net loss	(145,618)						(145,618)
Ending balance at Dec. 31, 2015	$ 531,090			$ 39	816,578	(868)	(284,659)
Ending balance, shares at Dec. 31, 2015	38,882,394			38,882,394
Issuance of common stock in connection with at-the-market offering, net of issuance costs	$ 79,486			$ 1	79,485
Issuance of common stock in connection with at-the-market offering, net of issuance costs, shares				1,159,415
Issuance of common stock in connection with collaboration agreement, net of issuance costs	52,272			$ 1	52,271
Issuance of common stock in connection with collaboration agreement, net of issuance costs, shares				727,120
Put option grant in connection with collaboration agreement	(916)				(916)
Employee stock-based compensation	48,309				48,309
Issuance of common stock upon exercise of stock options and warrants	$ 9,096				9,096
Issuance of common stock upon exercise of stock options and warrants, shares	425,922			438,811
Restricted stock units vested during the period, net	$ (1,262)				(1,262)
Restricted stock units vested during the period, net of shares				32,490
Other comprehensive income (loss)	1,773					1,773
Net loss	(245,874)						(245,874)
Ending balance at Dec. 31, 2016	$ 473,974			$ 41	$ 1,003,561	$ 905	$ (530,533)
Ending balance, shares at Dec. 31, 2016	41,240,230			41,240,230

CONSOLIDATED STATEMENTS OF CASH

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Operating activities:
Net loss	$ (245,874)	$ (145,618)	$ (59,802)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	48,309	24,884	5,394
Amortization of premium on investment securities, net	4,842	5,637	3,600
Depreciation and amortization	3,424	1,384	684
Revaluation of convertible preferred stock warrant liability	0	0	3,324
Foreign currency remeasurement loss	1,322
Non-cash license fee from collaboration arrangement	700
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(7,147)	(7,131)	(4,081)
Other assets	(1,242)	179	(411)
Accounts payable	2,502	(1,982)	3,177
Accrued liabilities and other liabilities	32,189	16,670	3,481
Net cash used in operating activities	(160,975)	(105,977)	(44,634)
Investing activities:
Purchase of property and equipment	(10,188)	(4,955)	(2,149)
Purchase of investments	(442,490)	(624,226)	(208,972)
Proceeds from sale of investments	140,556	89,321	5,002
Proceeds from maturities of investments	403,239	249,050	82,972
Increase in restricted cash	(1,202)	(1,541)	(293)
Net cash provided by (used in) investing activities	89,915	(292,351)	(123,440)
Financing activities:
Proceeds from the issuance of common stock in connection with underwritten public offerings, net		461,136	188,581
Proceeds from the issuance of common stock in connection with at-the-market offering, net	79,486
Proceeds from the issuance of common stock in connection with collaboration agreement, net	51,356
Proceeds from the issuance of common stock from equity awards, net	7,834	6,437	736
Payment of preferred stock dividend			(4,346)
Net cash provided by financing activities	138,676	467,573	184,971
Effect of exchange rate changes on cash	(65)
Net increase in cash and cash equivalents	67,551	69,245	16,897
Cash and cash equivalents at beginning of year	93,569	24,324	7,427
Cash and cash equivalents at end of year	161,120	93,569	24,324
Supplemental disclosures of non-cash investing and financing information:
Costs of property and equipment included in accounts payable and accrued liabilities	147	$ 769	243
Tenant improvement allowance	$ 3,467
Reclassification of warrant liability to equity upon conversion to common stock warrants			6,743
Conversion of Series A and Series B preferred stock to common stock			$ 129,360

Organization and Basis of Prese

Organization and Basis of Presentation	12 Months Ended
	Dec. 31, 2016
Organization Consolidation And Presentation Of Financial Statements [Abstract]
Organization and Basis of Presentation	1. Organization and Basis of Presentation Ultragenyx Pharmaceutical Inc. (the Company) is a biopharmaceutical company and was 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 rare and ultra-rare diseases, with a focus on serious, debilitating genetic diseases. The Company is currently conducting a Phase 3 study of aceneuramic acid extended-release (Ace-ER) in patients with GNE myopathy, which is also known as hereditary inclusion body myopathy, a progressive muscle-wasting disorder; a Phase 3 study of recombinant human beta-glucuronidase (rhGUS) in patients with mucopolysaccharidosis 7 (MPS 7), a rare lysosomal storage disease; a Phase 2 clinical study for UX007 in patients with glucose transporter type-1 deficiency syndrome (Glut1 DS), a brain energy deficiency; a Phase 2 clinical study of UX007 in patients severely affected by long-chain fatty acid oxidation disorders (LC-FAOD), a genetic disorder in which the body is unable to convert long chain fatty acids into energy; and Phase 2 and Phase 3 studies of KRN23, an antibody targeting fibroblast growth factor 23, or FGF23, in patients with X-linked hypophosphatemia (XLH) and tumor-induced osteomalacia (TIO), both rare diseases that impair bone mineralization. The Company operates as one reportable segment. In the course of its research activities, the Company has sustained operating losses and expects such losses to continue over the next several years. The Company’s ultimate success depends on the outcome of its research and development activities. Management expects to incur additional losses in the future to conduct product research and development and recognizes the need to raise additional capital to fully implement its business plan. Through December 31, 2016, the Company has relied primarily on the proceeds from equity offerings to finance its operations. The Company intends to 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 will need to reevaluate its operating plans.

Summary of Significant Accounti

Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Basis of Consolidation The consolidated financial statements include the accounts of Ultragenyx Pharmaceutical Inc. and our wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated. Use of Estimates The accompanying consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“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, and stock-based compensation. 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 and Cash Equivalents 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 primarily of amounts invested in money market accounts and corporate bonds. Investments All investments have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities. Management determines the appropriate classification of its investments in debt securities at the time of purchase and reevaluates such designation as of each balance sheet date. Investments with a maturity of one year or less from the balance sheet date are reported as short-term investments and investments with a maturity of greater than one year from the balance sheet date are reported as long-term investments. Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive loss. Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in other expense, net. The cost of securities sold is based on the specific-identification method. Interest on investments is included in interest income. Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents, and investments. The Company’s cash, cash equivalents, and investments are held by financial institutions that management believes are of high credit quality. The Company’s investment policy limits investments to fixed income securities denominated and payable in U.S. dollars such as U.S. government obligations, money market instruments and funds, corporate bonds, and asset-backed securities and places restrictions on maturities and concentrations by type and issuer. Such deposits may, at times, exceed federally insured limits. The Company has not experienced any losses on its deposits of cash and cash equivalents and its accounts are monitored by management to mitigate risk. The Company is exposed to credit risk in the event of default by the financial institutions holding its cash and cash equivalents, corporate bond issuers and other financial instruments to the extent recorded in the balance sheets . Property and Equipment Property and equipment are stated at cost, less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the respective assets. Depreciation and amortization begins at the time the asset is placed in service. Maintenance and repairs are charged to operations as incurred. Upon sale or retirement of assets, the cost and related accumulated depreciation are removed from the balance sheet and the resulting gain or loss, if any, is reflected in operations. The useful lives of the property and equipment are as follows: Research and development equipment 5 years Furniture and office equipment 5 years Computer equipment 3 years Software 3-5 years Leasehold improvements Shorter of lease term or estimated useful life Impairment of Long-Lived Assets The Company evaluates its long-lived assets, including property and equipment, for impairment whenever events or changes in circumstances indicate that the carrying value of these assets may not be recoverable. Recoverability of these assets is measured by comparison of the carrying amount of each asset to the future undiscounted cash flows expected to result from the use of the asset and its eventual disposition. If the asset is considered to be impaired, the amount of any impairment is measured as the difference between the carrying value and the fair value of the impaired asset. The Company has not recorded impairment of any long-lived assets since inception. Restricted Cash Restricted cash primarily consists of money market accounts as collateral for its obligations under its facility leases of the Company’s corporate headquarters in Novato, California and for its facilities in Brisbane, California. Accruals of Research and Development Costs The Company records accruals for estimated costs of research, preclinical and clinical studies and manufacturing development. These costs are a significant component of the Company’s research and development expenses. A substantial portion of the Company’s ongoing research and development activities are conducted by third-party service providers, including contract research organizations. The Company accrues the costs incurred under its agreements with these third parties based on actual work completed in accordance with agreements established with these third parties. The Company determines the actual costs through discussions with internal personnel and external service providers as to the progress or stage of completion of the services and the agreed-upon fee to be paid for such services. The Company makes significant judgments and estimates in determining the accrual balance in each reporting period. As actual costs become known, the Company adjusts its accruals. The Company has not experienced any material deviations between accrued clinical trial expenses and actual clinical trial expenses. However, actual services performed, number of patients enrolled, and the rate of patient enrollment may vary from the Company’s estimates, resulting in adjustments to clinical trial expense in future periods. Changes in these estimates that result in material changes to the Company’s accruals could materially affect the Company’s results of operations. Revenue The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred, the price is fixed or determinable, and collectability is reasonably assured. Revenue is recognized once all revenue recognition criteria are met. During the year ended December 31, 2016, the Company recognized revenue from sales of rhGUS (UX003) on a “named patient” basis which are allowed in certain European countries prior to the commercial approval of the product in the territory. Due to the Company’s limited sales and collection history to date, revenue has been recognized upon receipt of payment. Leases The Company enters into lease agreements for its office and laboratory facilities. These leases are classified as operating leases. Rent expense is recognized on a straight-line basis over the term of the lease and, accordingly, the Company records the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Incentives granted under the Company’s facilities leases, including allowances to fund leasehold improvements, are deferred and are recognized as adjustments to rental expense on a straight-line basis over the term of the lease. Comprehensive Loss Comprehensive loss is the change in stockholders’ equity from transactions and other events and circumstances other than those resulting from investments by stockholders and distributions to stockholders. The Company’s other comprehensive loss is comprised of unrealized gains and losses on investments in available-for-sale securities and foreign currency translation adjustments. Research and Development Research and development costs are expensed as incurred and consist of salaries and benefits, stock-based compensation expense, lab supplies and facility costs, as well as fees paid to other nonemployees and entities that conduct certain research and development activities on the Company’s behalf. Amounts incurred in connection with license agreements are also included in research and development expense. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are deferred and capitalized. The capitalized amounts are expensed as the related goods are delivered or the services are performed. Stock-Based Compensation Stock-based awards issued to employees, including stock options and restricted stock units (RSUs), are recorded at fair value as of the grant date and recognized as expense on a straight-line basis over the employee’s requisite service period (generally the vesting period). Because noncash stock compensation expense is based on awards ultimately expected to vest, it is reduced by an estimate for future forfeitures. Forfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from estimates. Income Taxes The Company uses the liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on the differences between the financial reporting and the tax bases of assets and liabilities and are measured using the enacted tax rates and laws that will be in effect when the differences are expected to reverse. The Company must then assess the likelihood that the resulting deferred tax assets will be realized. A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized. Due to the Company’s lack of earnings history, the net deferred tax assets have been fully offset by a valuation allowance. The Company recognizes benefits of uncertain tax positions if it is more likely than not that such positions will be sustained upon examination based solely on their technical merits, as the largest amount of benefit that is more likely than not to be realized upon the ultimate settlement. The Company’s policy is to recognize interest and penalties related to the underpayment of income taxes as a component of income tax expense or benefit. To date, there have been no interest or penalties charged in relation to the unrecognized tax benefits. Foreign Currency Assets and liabilities of non-U.S. subsidiaries that operate in a local currency environment, where that local currency is the functional currency, are translated to U.S. dollars at exchange rates in effect at the balance sheet date, with the resulting translation adjustments directly recorded to a separate component of accumulated other comprehensive loss. Income and expense accounts are translated at average exchange rates for the period. Remeasurement adjustments are recorded in other income (expense), net. Net Loss per Share Attributable to Common Stockholders Basic net loss per share attributable to common stockholders is calculated by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share attributable to common stockholders is the same as basic net loss per share attributable to common stockholders, since the effects of potentially dilutive securities are antidilutive. In periods when we have incurred a net loss, convertible preferred stock, options and warrants to purchase common stock and convertible preferred stock warrants are considered common stock equivalents, but have been excluded from the calculation of diluted net loss per share attributable to common stockholders, as their effect is antidilutive. Recent Accounting Pronouncements In May 2014, the FASB, issued ASU 2014-09, Revenue from Contracts with Customers (Topic 606) Revenue from Contracts with Customers: Principal versus Agent Considerations Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients to provide supplemental adoption guidance and clarification to ASU 2014-09 Technical Corrections and Improvements to Topic 606, Revenue from Contracts with Customers In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842), which requires an entity that is a lessee to record a right of use asset and a corresponding lease liability on the balance sheet for all leases with terms longer than 12 months. This guidance also requires disclosures about the amount, timing, and uncertainty of cash flows arising from leases. This guidance is effective for annual reporting periods beginning after December 15, 2018, and interim periods within those annual periods, using a modified retrospective approach, and early adoption is permitted. The Company is evaluating the effect that this guidance will have on its Consolidated Financial Statements and related disclosures. In March 2016, the FASB issued ASU 2016-09, Compensation — Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting accounting for employee share-based payments, including income tax consequences, application of award forfeitures to expense, classification on the statement of cash flows, and classification of awards as either equity or liabilities. This guidance is effective for annual reporting periods beginning after December 15, 2016, and interim periods within those annual periods. In October 2016, the FASB issued ASU 2016-16, Income Taxes - Intra-Entity Transfers of Assets Other Than Inventory

Fair Value Measurements

Fair Value Measurements	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	3. Fair Value Measurements Financial assets and liabilities are recorded at fair value. The carrying amount of certain financial instruments, including cash and cash equivalents, 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. The Company’s financial instruments consist of Level 1 and Level 2 assets. Where quoted prices are available in an active market, securities are classified as Level 1. Money market funds are classified as Level 1. Level 2 assets consist primarily of corporate bonds, asset backed securities, commercial paper and U.S. Government agency securities based upon quoted market prices for similar movements in active markets, quoted prices for identical or similar instruments in markets that are not active and model-based valuation techniques for which all significant inputs are observable in the market or can be corroborated by observable market data for substantially the full term of the assets. Where applicable these models project future cash flows and discount the future amounts to a present value using market-based observable inputs obtained from various third party data providers, including but not limited to, benchmark yields, interest rate curves, reported trades, broker/dealer quotes and reference data. The following table sets forth the fair value of the Company’s financial assets and liabilities remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands): December 31, 2016 Level 1 Level 2 Level 3 Total Financial Assets: Money market funds $ 123,536 $ — $ — $ 123,536 Corporate bonds — 207,726 — 207,726 Commercial paper — 11,970 — 11,970 Asset-backed securities — 27,713 — 27,713 U.S. Government Treasury and agency securities — 111,931 — 111,931 Total financial assets $ 123,536 $ 359,340 $ — $ 482,876 December 31, 2015 Level 1 Level 2 Level 3 Total Financial Assets: Money market funds $ 53,254 $ — $ — $ 53,254 Corporate bonds — 370,445 — 370,445 Commercial paper — 13,887 — 13,887 Asset-backed securities — 29,302 — 29,302 U.S. Government Treasury and agency securities — 47,452 — 47,452 Total financial assets $ 53,254 $ 461,086 $ — $ 514,340

Balance Sheet Components

Balance Sheet Components	12 Months Ended
	Dec. 31, 2016
Investments Debt And Equity Securities [Abstract]
Balance Sheet Components	4. Balance Sheet Components Cash Equivalents and Investments The fair values of cash equivalents, short-term investments, and long-term investments classified as available-for-sale securities, consisted of the following (in thousands): December 31, 2016 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 123,536 $ — $ — $ 123,536 Corporate bonds 207,909 14 (197 ) 207,726 Commercial paper 11,970 — — 11,970 Asset-backed securities 27,712 3 (2 ) 27,713 U.S. Government Treasury and agency securities 112,166 10 (245 ) 111,931 Total $ 483,293 $ 27 $ (444 ) $ 482,876 December 31, 2015 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 53,254 $ — $ — $ 53,254 Corporate bonds 371,098 11 (664 ) 370,445 Commercial paper 13,887 — — 13,887 Asset-backed securities 29,356 — (54 ) 29,302 U.S. Government Treasury and agency securities 47,613 — (161 ) 47,452 Total $ 515,208 $ 11 $ (879 ) $ 514,340 At December 31, 2016, the remaining contractual maturities of available-for-sale securities were less than two years. There have been no significant realized gains or losses on available-for-sale securities for the periods presented. All marketable securities with unrealized losses at December 31, 2016 have been in a loss position for less than twelve months or the loss is not material and were temporary in nature. We do not intend to sell the investments that are in an unrealized loss position before recovery of their amortized cost basis. Property and Equipment, net Property and equipment, net consists of the following (in thousands): December 31, 2016 2015 Research and development equipment $ 2,154 $ 1,302 Furniture and office equipment 2,595 944 Computer equipment 2,013 628 Software 3,931 1,622 Leasehold improvements 12,486 3,466 Construction-in-progress 37 2,276 Property and equipment, gross 23,216 10,238 Less accumulated depreciation (6,161 ) (2,865 ) Property and equipment, net $ 17,055 $ 7,373 Depreciation expense for the years ended December 31, 2016, 2015 and 2014 was $3.4 million, $1.4 million and $0.7 million respectively. Amortization of leasehold improvements and software is included in depreciation expense. Accrued Liabilities Accrued liabilities consist of the following (in thousands): December 31, 2016 2015 Research and clinical study expenses $ 18,593 $ 9,764 Payroll and related expenses 17,226 9,423 Repayment liability under collaboration agreement 13,650 — Other 5,085 5,597 Total accrued liabilities $ 54,554 $ 24,784

License and Research Agreements

License and Research Agreements	12 Months Ended
	Dec. 31, 2016
Research Grant Agreement [Abstract]
License and Research Agreements	5. License and Research Agreements Nobelpharma License Agreement In September 2010, the Company entered into a collaboration and license agreement with Nobelpharma Co., Ltd. (Nobelpharma), which was amended in August 2015. Under the terms of this collaboration and license agreement, each party granted the other party a worldwide exclusive license under certain of that party’s intellectual property related to the compound identified as N-acetylneuraminic acid, also known as sialic acid, to develop, manufacture, and commercialize products. Nobelpharma’s licensed territory includes Japan and certain other Asian countries, and the Company’s licensed territory includes the rest of the world. The Company is required to make certain payments to Nobelpharma based upon achievement of certain development and approval milestones. The Company may make future payments that aggregate up to 200 million Yen (approximately $1.7 million based on the exchange rate at December 31, 2016) that are contingent upon attainment of various development and approval milestones. The Company will pay a mid-single digit royalty on net sales in the Company’s territory and will receive a mid-single digit royalty on net sales in the Nobelpharma territory, excluding Japan, if such product sales are ever achieved. Saint Louis University License Agreement In November 2010, the Company entered into a license agreement with Saint Louis University (SLU). Under the terms of this license agreement, SLU granted the Company an exclusive worldwide license to make, have made, use, import, offer for sale, and sell therapeutics related to SLU’s beta-glucuronidase product for use in the treatment of human diseases. The Company will be required to make a milestone payment of $0.1 million upon approval of a glucuronidase-based enzyme therapy for treatment of MPS 7. Additionally, upon reaching a certain level of cumulative worldwide sales of the product, the Company will be required to pay to SLU a low single-digit royalty on net sales of the licensed products in any country or region, if such product sales are ever achieved. Alcami Corporation License Agreement In March 2011, the Company entered into a license agreement with Alcami Corporation (Alcami). Under the terms of this license agreement, Alcami granted the Company a fully paid-up, royalty-free, exclusive, perpetual, and irrevocable license to research, develop, make, have made, use, import, offer for sale, and sell products incorporating Alcami’s controlled release matrix solid dose oral tablet. Under the license agreement, the Company will pay a mid-single digit percentage of any sublicense revenue received by Ultragenyx related to the sublicense of Alcami technology that had been initially licensed by Ultragenyx. HIBM Research Group In April 2012, the Company entered into an exclusive license agreement with HIBM Research Group (HRG). Under the terms of this license agreement, HRG granted the Company an exclusive worldwide license to certain intellectual property related to the treatment of HIBM. The Company may make future payments that aggregate up to $0.3 million that are contingent upon attainment of various development and approval milestones. Additionally, the Company will pay to HRG a royalty of less than 1% of net sales of the licensed products in the licensed territories, if such product sales are ever achieved. St. Jude Children’s Research Hospital License Agreement In September 2012, the Company entered into a license agreement with St. Jude Children’s Research Hospital (St. Jude). Under the terms of this license agreement, St. Jude granted the Company an exclusive license under certain know-how to research, develop, make, use, offer to sell, import, and otherwise commercialize and exploit St. Jude’s protective protein, cathepsin, a protein product to treat, prevent, and/or diagnose galactosialidosis and other monogenetic diseases. The Company will pay to St. Jude a royalty of less than 1% on net sales of the licensed products in the licensed territories, if such product sales are ever achieved. Baylor Research Institute License Agreement In September 2012, the Company entered into a license agreement with Baylor Research Institute (BRI). Under the terms of this license agreement, BRI exclusively licensed to the Company certain intellectual property related to triheptanoin for North America. In June 2013, the Company notified BRI that it was exercising its option pursuant to the agreement to license the rights to triheptanoin in all territories outside of the United States, Canada and Mexico and paid the option exercise fee of $0.8 million. The Company may make future payments of up to $10.5 million contingent upon attainment of various development milestones and $7.5 million contingent upon attainment of various sales milestones. Additionally, the Company will pay to BRI a mid-single digit royalty on net sales of the licensed product in the licensed territories, if such product sales are ever achieved. Kyowa Hakko Kirin Collaboration and License Agreement In August 2013, the Company entered into a collaboration and license agreement with Kyowa Hakko Kirin Co., Ltd. (KHK). Under the terms of this collaboration and license agreement, as amended, the Company and KHK will collaborate on the development and commercialization of certain products containing KRN23 in the field of orphan diseases in the United States and Canada, or the profit share territory, and in the European Union, Switzerland, and Turkey, or the European territory, and the Company will have the right to develop and commercialize such products in the field of orphan diseases in Mexico and Central and South America, or Latin America. In the field of orphan diseases, and except for ongoing studies being conducted by KHK, the Company will be the lead party for development activities in the profit share territory and in the European territory until the applicable transition date; the Company will also be 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 KHK. The Company will share 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 KHK, and KHK shall be responsible for 100% of the costs for development activities in Japan and Korea. On the applicable transition date in the profit share territory and the European territory, KHK 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 KHK. The Company has the primary responsibility for conducting certain research and development services. The Company is obligated to provide assistance in accordance with the agreed upon development plan as well as participate on various committees. If KRN23 is approved, the Company and KHK will share commercial responsibilities and profits in the profit share territory until the applicable transition date, KHK will commercialize KRN23 in the European territory, and the Company will develop and commercialize KRN23 in Latin America. KHK will manufacture and supply KRN23 for clinical use globally and will manufacture and supply KRN23 for commercial use in the profit share territory and Latin America. The remaining profit or loss from commercializing products in the profit-share territory, until the applicable transition date, will be shared between the Company and KHK on a 50/50 basis. Thereafter, the Company will be entitled to receive a tiered double-digit revenue share in the mid-to-high 20% range in the profit share territory, intended to approximate the profit share. The Company will also be entitled to receive a royalty of up to 10% on net sales in the European territory. In Latin America, the Company will pay to KHK a low single-digit royalty on net sales. The Company is accounting for the agreement as a collaboration arrangement as defined in ASC 808, Collaborative Agreements. As of December 31, 2016 and 2015, the Company had receivables in the amount of $8.6 million and $3.8 million, respectively, for this collaboration arrangement. Arcturus Research Collaboration and License Agreement In October 2015, the Company entered into a Research Collaboration and License Agreement with Arcturus Therapeutics, Inc. (Arcturus). The Company and Arcturus will collaborate on the research and development of therapies for select rare diseases. As consideration for entering into the arrangement, the Company paid Arcturus an upfront fee of $10.0 million. Arcturus will have the primary responsibility for conducting certain research services, funded by the Company, and the Company will be responsible for development and commercialization costs. Takeda License and Collaboration and Purchase Agreements In June 2016, the Company executed a collaboration and license agreement with Takeda Pharmaceutical Company Limited (Takeda). Pursuant to the agreement, which became effective in July 2016, the Company obtained an exclusive license for a pre-clinical compound from Takeda in a pre-determined field of use, which includes an option to an additional field of use for this product with the terms to be negotiated, and an option to a specified product candidate (identified option product). The Company is responsible for the development costs for the pre-clinical compound and the identified option product pursuant to an initial development plan. Because the license to the pre-clinical compound has no alternative future use, the estimated fair value of $0.7 million was recorded as a research and development expense upon acquisition. Under the license for the pre-clinical compound, the Company may be required to make future milestone payments to Takeda of up to $7.5 million if certain development milestones are met, $75.0 million if certain regulatory milestones are met, and $150.0 million if certain commercial milestones are met, as well as royalties with respect to net sales in the high-single digits to low-teens. Any products resulting from the pre-clinical compound or the identified option product is referred to in this report as the “licensed product.” A s part of the agreement, the Company and Takeda established a five-year research collaboration whereby the parties may mutually agree to add additional option products candidates to the collaboration, in which case the Company will bear the cost of the development activities, with certain exceptions. In July 2016, the Company consummated a common stock purchase agreement, executed in conjunction with the collaboration and license agreement, whereby Takeda purchased 374,590 shares of the Company’s common stock for $40.0 million in cash. The fair market value of the common stock issued to Takeda was $27.3 million, based on the closing stock price of $72.95 on the date of issuance, resulting in a $12.7 million premium paid to the Company. The Company also received a put option to require Takeda to purchase an additional $25.0 million in shares of the Company’s common stock at the then-current 30-day volume-weighted average price (VWAP). The put option was exercised in October 2016, whereby Takeda purchased 352,530 shares of the Company’s common stock for $25.0 million in cash. The Company also received a second put option, which is contingent upon meeting certain development milestones on the identified option product, to require Takeda to purchase an additional $10.0 million in shares of the Company’s common stock at the then-current 30-day VWAP. Takeda was subject to a 180-day lock-up provision as a result of the initial purchase of common stock, and a 90-day lock-up provision as a result of its purchase under the first put option, is subject to a five-year standstill (subject to customary exceptions or release), and has registration rights for purchases of common stock. The Company estimated the fair value of the put options to be $0.9 million and recorded the put options in additional paid-in capital. The valuation was performed using a Monte Carlo simulation approach using the term of the put options and an equity volatility of approximately 70%. The Company also granted Takeda an exclusive option for Asian rights, for a limited period, to any licensed products and any additional products resulting from the collaboration, as well as an option to exclusively license one of the Company’s products for development and commercialization in Japan. If Takeda exercises any of its option rights to license a product pursuant to the agreement, Takeda will pay for the development costs within the licensed territory, will share in a portion of the global development costs, and will make a milestone payment upon regulatory approval. Takeda will also owe royalties on net sales in the licensed territory for any licensed product, depending on the development stage when the product is licensed as well as sales levels. The royalties related to the option to license the Company’s product, as well as the additional product are subject to future good faith negotiations at the time that the option is exercised. The research and license agreement and the stock purchase agreement are being accounted for as one arrangement because they were entered into at the same time. The arrangements were evaluated pursuant to ASC 605-25, Multiple-Element Arrangements In January 2017, the Company terminated the option to the identified option product. As a result, the second put option to require Takeda to purchase an additional $10.0 million in shares of the Company’s common stock was terminated.

Equity

Equity	12 Months Ended
	Dec. 31, 2016
Equity [Abstract]
Equity	6. Equity Equity Transactions In July 2016, the Company entered into an At-The-Market (ATM) sales agreement, with Cowen and Company, LLC (Cowen), whereby the Company may sell up to $150.0 million in aggregate proceeds of common stock from time to time, through Cowen as our sales agent. During the year ended December 31, 2016, the Company sold 1,159,415 shares of common stock, resulting in net proceeds of approximately $79.5 million, after commissions and other offering costs. During the period of January 1, 2017 through February 15, 2017, the Company sold an additional 658,532 shares of common stock, resulting in net proceeds of approximately $48.4 million, after commissions and other offering costs. Common Stock Warrants In connection with various financing activities, the Company issued preferred stock warrants. The fair value ascribed to these warrants upon their issuance was $0.2 million, which was determined using an option-pricing method to allocate the equity value of the Company to the warrants based on the Company’s capital structure. Upon the closing of the Company’s IPO in February 2014, the warrants were converted into warrants to purchase common stock. Accordingly, the warrants were reclassified from a liability to permanent equity and were no longer subject to remeasurement. As of December 31, 2016 and 2015, there were 83,167 and 66,533 common stock warrants outstanding that were issued in June 2010 and June 2011, respectively, with a contractual term of 10 years and an exercise price of $3.006.

Stock-Based Awards

Stock-Based Awards	12 Months Ended
	Dec. 31, 2016
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Stock-Based Awards	7. Stock-Based Awards Equity Plan Awards In 2011, the Company adopted the 2011 Equity Incentive Plan (the 2011 Plan). The 2011 Plan provides for the granting of stock-based awards to employees, directors, and consultants under terms and provisions established by the board of directors. In 2014, the Company adopted the 2014 Incentive Plan (the 2014 Plan), which became effective upon the closing of the Company’s IPO in February 2014. The 2014 Plan had 2,250,000 shares of common stock available for future issuance at the time of its inception, which included 655,038 shares available under the 2011 Plan, which were transferred to the 2014 Plan upon adoption. No further grants subsequent to the IPO were made under the 2011 Plan. The 2014 Plan provides for automatic annual increases in shares available for grant, beginning on January 1, 2015 through January 1, 2024. Under the terms of the 2014 Plan, awards may be granted at an exercise price not less than fair market value. For employees holding more than 10% of the voting rights of all classes of stock, the exercise prices for awards must be at least 110% of fair market of the common stock on the grant date, as determined by the board of directors. The term of an award granted under the 2014 Plan may not exceed ten years. Typically, the vesting schedule for option grants to the employees provides that 1/4 of the grant vests upon the first anniversary of the date of grant, with the remainder of the shares vesting monthly thereafter at a rate of 1/48 of the total shares subject to the option. The vesting schedule for RSU grants provides that 1/4 of the grant vests upon the annual anniversary of the date of grant over the period of four years. As of December 31, 2016, an aggregate of 7,478,107 shares of common stock have been authorized for issuance under all equity award plans. Stock Option Activity The following table summarizes activity under the Company’s stock option plans, including the 2011 Plan and the 2014 Plan and related information: Options Outstanding Number of Options Weighted- Average Exercise Weighted-Average Remaining Contractual Term Aggregate Intrinsic Value (In Outstanding — December 31, 2013 2,228,883 $ 3.41 8.91 $ 19,468 Options granted 932,555 41.12 Options exercised (305,090 ) 2.14 Options cancelled (116,873 ) 8.92 Outstanding — December 31, 2014 2,739,475 $ 16.15 8.43 $ 79,840 Options granted 2,013,350 90.60 Options exercised (795,825 ) 8.65 Options cancelled (130,037 ) 31.49 Outstanding — December 31, 2015 3,826,963 $ 56.36 8.58 $ 217,386 Options granted 1,435,995 67.00 Options exercised (425,922 ) 21.21 Options cancelled (407,564 ) 70.87 Outstanding — December 31, 2016 4,429,472 $ 61.85 8.22 $ 79,135 Vested and exercisable — December 31, 2016 1,620,443 $ 44.96 7.24 $ 55,537 Vested and expected to vest — December 31, 2016 4,264,788 $ 61.33 8.18 $ 78,412 The aggregate intrinsic values of options outstanding, vested and exercisable, and vested and expected to vest were calculated as the difference between the exercise price of the options and the fair value of the Company’s common stock. The total intrinsic value of options exercised during the years ended December 31, 2016, 2015, and 2014 was $22.2 million, $59.0 million and $12.1 million, respectively. Cash received from the exercise of options was $9.0 The weighted-average estimated fair value of stock options granted was $40.49, $54.90 and $26.58 per share of the Company’s common stock during the years ended December 31, 2016, 2015, and 2014, respectively. The total estimated fair value of options vested during the years ended December 31, 2016, 2015, and 2014 was $43.8 million, $10.7 million, and $2.0 million, respectively. Restricted Stock Units The following table summarizes activity under the Company’s Restricted Stock Units (RSUs) from the 2014 Plan and related information: RSUs Outstanding Number of Shares Weighted- Average Grant Date Fair Value Unvested — December 31, 2013 — $ — RSUs granted 31,000 53.23 Unvested — December 31, 2014 31,000 $ 53.23 RSUs granted 187,260 89.67 RSUs released (18,209 ) 54.72 RSUs cancelled (2,900 ) 84.89 Unvested — December 31, 2015 197,151 $ 87.24 RSUs granted 477,816 66.83 RSUs released (52,273 ) 82.59 RSUs cancelled (48,950 ) 78.04 Unvested — December 31, 2016 573,744 $ 71.45 The fair value of the RSUs is determined on the grant date based on the fair value of the Company’s common stock. The fair value of the RSUs is recognized as expense ratably over the vesting period of one to four years. The total fair value of the 52,273 shares vested during 2016 was approximately $4.3 million with an aggregate intrinsic value of the shares of $3.3 million. Employee Stock Purchase Plan In January 2014, the Company adopted the 2014 Employee Stock Purchase Plan (ESPP) which became effective upon the closing of our IPO in February 2014. The Company had reserved a total of 600,000 shares of common stock for issuance under the ESPP. The ESPP provides for automatic annual increases in shares available for grant, beginning on January 1, 2015 through January 1, 2024. Eligible employees may purchase common stock at 85% of the lesser of the fair market value of common stock on the offering date or the purchase date with a six-month look-back feature. ESPP purchases are settled with common stock from the ESPP’s previously authorized and available pool of shares. Stock-Based Compensation Expense Total stock-based compensation recognized was as follows (in thousands): Year Ended December 31, 2016 2015 2014 Research and development $ 29,412 $ 17,100 $ 4,116 General and administrative 18,897 7,784 1,278 Total stock-based compensation expense $ 48,309 $ 24,884 $ 5,394 As of December 31, 2016, the total unrecognized compensation expense related to unvested equity awards, net of estimated forfeitures, was $136.5 million, which the Company expects to recognize over an estimated weighted-average period of 2.78 years. In determining the estimated fair value of the stock-based awards, the Company uses the Black-Scholes option-pricing model and assumptions discussed below. Each of these inputs is subjective and generally requires significant judgment to determine. Expected Term —The Company’s expected term represents the period that the Company’s stock-based awards are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). Expected Volatility —As the Company does not have sufficient historical stock price information from the Company to meet the expected life of the stock-based awards, our approach to estimating expected volatility is to phase in our own common stock trading history and supplement the remaining historical information with a blended volatility from the trading history from the common stock of the set of comparable publicly traded biopharmaceutical companies. When selecting comparable publicly traded biopharmaceutical companies on which to base the expected stock price volatility, we selected companies with comparable characteristics to it, including enterprise value, risk profiles, position within the industry, and with historical share price information sufficient to meet the expected life of the stock-based awards. The historical volatility data was computed using the daily closing prices for the selected companies’ shares during the equivalent period of the calculated expected term of the stock-based awards. The average volatility for comparable publicly traded biopharmaceutical companies over a period equal to the expected term of the stock option grants is used to supplement the Company’s historical volatility. We will continue to apply this process until a sufficient amount of historical information regarding the volatility of our own stock price becomes available. Risk-Free Interest Rate —The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of option. Expected Dividend —The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock. Therefore, the Company used an expected dividend yield of zero. The fair value of stock option awards was estimated at the date of grant using a Black-Scholes option-pricing model with the following weighted-average assumptions: Options Year Ended December 31, 2016 2015 2014 Expected term (years) 6.23 6.23 6.23 Expected volatility 65% 65% 70% Risk-free interest rate 1.5% 1.8% 1.9% Expected dividend rate 0.0% 0.0% 0.0%

Defined Contribution Plan

Defined Contribution Plan	12 Months Ended
	Dec. 31, 2016
Defined Contribution Pension And Other Postretirement Plans Disclosure [Abstract]
Defined Contribution Plan	8. Defined Contribution Plan In March 2013, the Company began to sponsor a 401(k) retirement plan, in which substantially all of its full-time employees are eligible to participate. Eligible participants may contribute a percentage of their annual compensation to this plan, subject to statutory limitations. Prior to 2015, the Company had not provided any contributions to the plan. In 2015, the Company began to make contributions to the Plan for eligible participants, and recorded $1.5 million and $0.6 million and as contribution expenses for the years ended December 31, 2016 and 2015, respectively.

Income Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Income Taxes	9. Income Taxes The components of the Company’s loss before income taxes were as follows (in thousands): Year Ended December 31, 2016 2015 2014 Domestic $ 192,287 $ 145,618 $ 59,802 Foreign 53,552 — — Total loss before income taxes $ 245,839 $ 145,618 $ 59,802 The components of the Company’s income tax provision were as follows (in thousands): Year Ended December 31, 2016 2015 2014 Federal $ — $ — $ — State — — — International 35 — — Total income tax provision $ 35 $ — $ — The Company has incurred net operating losses since inception. The Company has not reflected any benefit of such net operating loss carryforwards in the accompanying financial statements. The Company has established a full valuation allowance against its deferred tax assets due to the uncertainty surrounding the realization of such assets. The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows: Year Ended December 31, 2016 2015 2014 Federal statutory income tax rate 34.0 % 34.0 % 34.0 % State income taxes, net of federal benefit 1.3 7.5 4.6 Federal tax credits 13.7 5.9 6.7 Other (0.3 ) 0.8 — Nondeductible permanent items — — (1.2 ) Stock-based compensation (1.4 ) (1.3 ) (1.4 ) Uncertain tax positions 2.0 (7.7 ) — Change in valuation allowance (41.9 ) (39.2 ) (42.7 ) Foreign rate differential (7.4 ) — — Provision for income taxes — — — The tax effect of temporary differences that give rise to significant portions of the deferred tax assets is presented below (in thousands): Year Ended December 31, 2016 2015 Deferred tax assets: Net operating loss carryforwards $ 102,960 $ 61,503 Tax credits 78,324 33,881 Stock options 16,084 6,680 Accruals and reserves 10,039 2,541 Fixed assets and intangibles 3,014 4,442 Other 1,950 432 Total deferred tax assets 212,371 109,479 Valuation allowance (212,371 ) (109,479 ) Net deferred tax assets $ — $ — As of December 31, 2016 and 2015, the Company had approximately $315.5 million and $225.5 million of federal net operating loss carryforwards available to reduce future taxable income that will begin to expire in 2030. As of December 31, 2016 and 2015, the Company had approximately $259.8 million and $255.0 million of state net operating loss carryforwards available to reduce future taxable income that will begin to expire in 2030. As of December 31, 2016 and 2015, the Company had federal research tax credit carryforwards of approximately $2.5 million and $1.7 million available to reduce future tax liabilities that will begin to expire in 2030. As of December 31, 2016 and 2015, the Company had state research credit carryforwards of approximately $6.7 million and $4.3 million available to reduce future tax liabilities that will be carried forward indefinitely. As of December 31, 2016 and 2015, the Company had federal Orphan Drug Credits of approximately $84.3 million and $35.2 million available to reduce future tax liabilities that will begin to expire in 2031. The Company’s ability to use net operating loss and tax credit carryforwards to reduce future taxable income and liabilities may be subject to annual limitations pursuant to Internal Revenue Code Sections 382 and 383 as a result of ownership changes in the past and future. As a result of ownership changes in 2012 and 2011, $3.6 million of federal net operating loss carryforwards, $3.6 million of state net operating loss carryforwards, and $0.2 million of federal tax credits are permanently limited. Deferred tax assets for net operating losses and tax credits have been reduced and a corresponding adjustment to the valuation allowance has been recorded. The valuation allowance increased by $102.9 million and $58.1 million during the year ended December 31, 2016 and 2015, respectively. The Company recorded unrecognized tax benefits for uncertainties in income taxes. A reconciliation of the Company’s unrecognized tax benefits for the years ended December 31, 2016, 2015, and 2014 is as follows (in thousands): December 31, 2016 2015 2014 Balance at beginning of year $ 24,010 $ 7,275 $ 3,725 Additions based on tax positions related to current year 6,777 15,628 3,550 Additions for tax positions of prior years 877 5,505 — Reductions for tax positions of prior years (18,159 ) (4,398 ) — Balance at end of year $ 13,505 $ 24,010 $ 7,275 The entire amount of the unrecognized tax benefits would not impact the Company’s effective tax rate if recognized. The Company has elected to include interest and penalties as a component of tax expense. During the years ended December 31, 2016 and 2015, the Company did not recognize accrued interest and penalties related to unrecognized tax benefits. The Company does not anticipate that the amount of existing unrecognized tax benefits will significantly increase or decrease during the next 12 months. It is our intention to reinvest the earnings of our non-U.S. subsidiaries in their operations. As of December 31, 2016, the Company had not made a provision for U.S. income taxes or foreign withholding taxes on approximately $0.1 million of the excess of the amount of net income for financial reporting over the tax basis of investments in foreign subsidiaries that are essentially permanent in duration. Generally, such amounts become subject to U.S. taxation upon repatriation as dividends and under certain other circumstances. If these earnings were repatriated to the U.S., the deferred tax liability associated with these temporary differences would result in a nominal amount. The Company files income tax returns in the U.S. federal, California, and other state tax jurisdictions. The federal and state income tax returns from inception to December 31, 2016 remain subject to examination.

Commitments and Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2016
Commitments And Contingencies Disclosure [Abstract]
Commitments and Contingencies	10. Commitments and Contingencies Facilities In December 2015, the Company entered into a lease agreement for office facilities in Brisbane, California, which provided for a tenant improvement allowance of up to $3.7 million. This operating lease commenced in May 2016 and expires 122 months after the commencement date. At the end of the lease term, the Company has the option to extend the lease for two additional consecutive terms of five years each. As provided in the lease agreement, monthly lease payments are subject to annual increases as defined in the lease agreement. The Company leases office space and research, testing and manufacturing laboratory space in various facilities in Novato, California, under operating agreements expiring at various dates through 2020 and include tenant improvement allowance up to $1.5 million. Certain of the leases provide for options by the Company to extend the lease for multiple five-year renewal periods and also provide for annual minimum increases in rent, usually based on a consumer price index or annual minimum increases. The Company recognizes rent expense on a straight-line basis over the noncancelable term of its operating lease. Rent expense was $3.3 million, $1.4 million, and $0.6 million during the years ended December 31, 2016, 2015 and 2014, respectively. Other Commitments The Company has various manufacturing, clinical, research, and other contracts with vendors in the conduct of the normal course of its business. Other than as noted below, contracts are terminable, with varying provisions regarding termination. If a contract with a specific vendor were to be terminated, the Company would only be obligated for the products or services that the Company had received at the time the termination became effective. As of December 31, 2016, the aggregate future minimum lease payments under the noncancelable operating lease arrangements and future payments under contractually binding manufacturing and service agreements are as follows (in thousands): Year Ending December 31, Leases Manufacturing and Services 2017 $ 3,956 $ 1,956 2018 4,534 810 2019 3,553 265 2020 2,867 62 2021 2,346 — Thereafter 11,446 — $ 28,702 $ 3,093 Contingencies While there are no material legal proceedings the Company is aware of, the Company may become party to various claims and complaints arising in the ordinary course of business. Management does not believe that any ultimate liability resulting from any of these claims will have a material adverse effect on its results of operations, financial position, or liquidity. However, management cannot give any assurance regarding the ultimate outcome of these claims, and their resolution could be material to operating results for any particular period, depending upon the level of income for the period. Guarantees and Indemnifications The Company indemnifies each of its directors and officers for certain events or occurrences, subject to certain limits, while the director is or was serving at the Company’s request in such capacity, as permitted under Delaware law and in accordance with its certificate of incorporation and bylaws. The term of the indemnification period lasts as long as a director may be subject to any proceeding arising out of acts or omissions of such director in such capacity. The maximum amount of potential future indemnification is unlimited; however, the Company currently holds director liability insurance. This insurance allows the transfer of risk associated with the Company’s exposure and may enable it to recover a portion of any future amounts paid. The Company believes that the fair value of these indemnification obligations is minimal. Accordingly, it has not recognized any liabilities relating to these obligations for any period presented.

Net Loss per Share Attributable

Net Loss per Share Attributable to Common Stockholders	12 Months Ended
	Dec. 31, 2016
Earnings Per Share [Abstract]
Net Loss per Share Attributable to Common Stockholders	11. Net Loss per Share Attributable to Common Stockholders The following table sets forth the computation of the basic and diluted net loss per share attributable to common stockholders during the years ended December 31, 2016, 2015 and 2014 (in thousands, except share and per share data): Year Ended December 31, 2016 2015 2014 Numerator: Net loss $ (245,874 ) $ (145,618 ) $ (59,802 ) Accretion and dividends on convertible preferred stock — — (4,808 ) Net loss attributable to common stockholders $ (245,874 ) $ (145,618 ) $ (64,610 ) Denominator: Weighted-average shares used to compute net loss per share attributable to common stockholders, basic and diluted 39,586,908 36,782,603 28,755,758 Net loss per share attributable to common stockholders, basic and diluted $ (6.21 ) $ (3.96 ) $ (2.25 ) The following weighted-average outstanding common stock equivalents were excluded from the computation of diluted net loss per share attributable to common stockholders for the periods presented because including them would have been antidilutive: Year Ended December 31, 2016 2015 2014 Convertible preferred stock — — 1,610,834 Options to purchase common stock and RSUs 4,699,111 3,368,507 2,582,444 Convertible preferred stock warrants — — 29,051 Employee stock purchase plan 7,933 — — Common stock warrants 149,700 195,762 318,666 4,856,744 3,564,269 4,540,995

Accumulated Other Comprehensive

Accumulated Other Comprehensive Income (Loss)	12 Months Ended
	Dec. 31, 2016
Other Comprehensive Income Loss Net Of Tax Period Increase Decrease [Abstract]
Accumulated Other Comprehensive Income (Loss)	12. Accumulated Other Comprehensive Income (Loss) Total accumulated other comprehensive income (loss) consisted of the following (in thousands) : Unrealized Gain (Loss) on Securities Available-for-Sale Foreign Currency Translation Adjustments Accumulated Other Comprehensive Income (Loss) December 31, 2013 $ 11 $ — $ 11 Current period other comprehensive loss (185 ) — (185 ) December 31, 2014 (174 ) — (174 ) Current period other comprehensive loss (694 ) — (694 ) December 31, 2015 (868 ) — (868 ) Current period other comprehensive income 451 1,322 1,773 December 31, 2016 $ (417 ) $ 1,322 $ 905

Quarterly Financial Data (unaud

Quarterly Financial Data (unaudited)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Data [Abstract]
Quarterly Financial Data (unaudited)	13. Quarterly Financial Data (unaudited) The following table presents certain unaudited quarterly financial information. This information has been prepared on the same basis as the audited financial statements and includes all adjustments (consisting only of normal recurring adjustments) necessary to present fairly the unaudited quarterly results of operations set forth herein (in thousands, except share and per share data): 2016 March 31, June 30, September 30, December 31, Revenue $ — $ 17 $ 111 $ 5 Operating expenses 53,622 58,070 65,894 70,554 Net loss attributable to common stockholders (52,757 ) (56,923 ) (64,907 ) (71,287 ) Net loss per share attributable to common stockholders, basic and diluted $ (1.35 ) $ (1.46 ) $ (1.64 ) $ (1.75 ) 2015 March 31, June 30, September 30, December Operating expenses $ 21,502 $ 30,142 $ 39,936 $ 56,158 Net loss attributable to common stockholders (21,379 ) (29,787 ) (39,232 ) (55,220 ) Net loss per share attributable to common stockholders, basic and diluted $ (0.63 ) $ (0.83 ) $ (1.03 ) $ (1.42 )

Summary of Significant Accoun21

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Basis of Consolidation	Basis of Consolidation The consolidated financial statements include the accounts of Ultragenyx Pharmaceutical Inc. and our wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated.
Use of Estimates	Use of Estimates The accompanying consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (“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, and stock-based compensation. 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 and Cash Equivalents	Cash and Cash Equivalents 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 primarily of amounts invested in money market accounts and corporate bonds.
Investments	Investments All investments have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities. Management determines the appropriate classification of its investments in debt securities at the time of purchase and reevaluates such designation as of each balance sheet date. Investments with a maturity of one year or less from the balance sheet date are reported as short-term investments and investments with a maturity of greater than one year from the balance sheet date are reported as long-term investments. Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive loss. Realized gains and losses and declines in fair value judged to be other than temporary, if any, on available-for-sale securities are included in other expense, net. The cost of securities sold is based on the specific-identification method. Interest on investments is included in interest income.
Concentration of Credit Risk and Other Risks and Uncertainties	Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents, and investments. The Company’s cash, cash equivalents, and investments are held by financial institutions that management believes are of high credit quality. The Company’s investment policy limits investments to fixed income securities denominated and payable in U.S. dollars such as U.S. government obligations, money market instruments and funds, corporate bonds, and asset-backed securities and places restrictions on maturities and concentrations by type and issuer. Such deposits may, at times, exceed federally insured limits. The Company has not experienced any losses on its deposits of cash and cash equivalents and its accounts are monitored by management to mitigate risk. The Company is exposed to credit risk in the event of default by the financial institutions holding its cash and cash equivalents, corporate bond issuers and other financial instruments to the extent recorded in the balance sheets .
Property and Equipment	Property and Equipment Property and equipment are stated at cost, less accumulated depreciation and amortization. Depreciation and amortization is computed using the straight-line method over the estimated useful lives of the respective assets. Depreciation and amortization begins at the time the asset is placed in service. Maintenance and repairs are charged to operations as incurred. Upon sale or retirement of assets, the cost and related accumulated depreciation are removed from the balance sheet and the resulting gain or loss, if any, is reflected in operations. The useful lives of the property and equipment are as follows: Research and development equipment 5 years Furniture and office equipment 5 years Computer equipment 3 years Software 3-5 years Leasehold improvements Shorter of lease term or estimated useful life
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets The Company evaluates its long-lived assets, including property and equipment, for impairment whenever events or changes in circumstances indicate that the carrying value of these assets may not be recoverable. Recoverability of these assets is measured by comparison of the carrying amount of each asset to the future undiscounted cash flows expected to result from the use of the asset and its eventual disposition. If the asset is considered to be impaired, the amount of any impairment is measured as the difference between the carrying value and the fair value of the impaired asset. The Company has not recorded impairment of any long-lived assets since inception.
Restricted Cash	Restricted Cash Restricted cash primarily consists of money market accounts as collateral for its obligations under its facility leases of the Company’s corporate headquarters in Novato, California and for its facilities in Brisbane, California.
Accruals of Research and Development Costs	Accruals of Research and Development Costs The Company records accruals for estimated costs of research, preclinical and clinical studies and manufacturing development. These costs are a significant component of the Company’s research and development expenses. A substantial portion of the Company’s ongoing research and development activities are conducted by third-party service providers, including contract research organizations. The Company accrues the costs incurred under its agreements with these third parties based on actual work completed in accordance with agreements established with these third parties. The Company determines the actual costs through discussions with internal personnel and external service providers as to the progress or stage of completion of the services and the agreed-upon fee to be paid for such services. The Company makes significant judgments and estimates in determining the accrual balance in each reporting period. As actual costs become known, the Company adjusts its accruals. The Company has not experienced any material deviations between accrued clinical trial expenses and actual clinical trial expenses. However, actual services performed, number of patients enrolled, and the rate of patient enrollment may vary from the Company’s estimates, resulting in adjustments to clinical trial expense in future periods. Changes in these estimates that result in material changes to the Company’s accruals could materially affect the Company’s results of operations.
Revenue	Revenue The Company recognizes revenue when persuasive evidence of an arrangement exists, delivery has occurred, the price is fixed or determinable, and collectability is reasonably assured. Revenue is recognized once all revenue recognition criteria are met. During the year ended December 31, 2016, the Company recognized revenue from sales of rhGUS (UX003) on a “named patient” basis which are allowed in certain European countries prior to the commercial approval of the product in the territory. Due to the Company’s limited sales and collection history to date, revenue has been recognized upon receipt of payment.
Leases	Leases The Company enters into lease agreements for its office and laboratory facilities. These leases are classified as operating leases. Rent expense is recognized on a straight-line basis over the term of the lease and, accordingly, the Company records the difference between cash rent payments and the recognition of rent expense as a deferred rent liability. Incentives granted under the Company’s facilities leases, including allowances to fund leasehold improvements, are deferred and are recognized as adjustments to rental expense on a straight-line basis over the term of the lease.
Comprehensive Loss	Comprehensive Loss Comprehensive loss is the change in stockholders’ equity from transactions and other events and circumstances other than those resulting from investments by stockholders and distributions to stockholders. The Company’s other comprehensive loss is comprised of unrealized gains and losses on investments in available-for-sale securities and foreign currency translation adjustments.
Research and Development	Research and Development Research and development costs are expensed as incurred and consist of salaries and benefits, stock-based compensation expense, lab supplies and facility costs, as well as fees paid to other nonemployees and entities that conduct certain research and development activities on the Company’s behalf. Amounts incurred in connection with license agreements are also included in research and development expense. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are deferred and capitalized. The capitalized amounts are expensed as the related goods are delivered or the services are performed.
Stock-Based Compensation	Stock-Based Compensation Stock-based awards issued to employees, including stock options and restricted stock units (RSUs), are recorded at fair value as of the grant date and recognized as expense on a straight-line basis over the employee’s requisite service period (generally the vesting period). Because noncash stock compensation expense is based on awards ultimately expected to vest, it is reduced by an estimate for future forfeitures. Forfeitures are estimated at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from estimates.
Income Taxes	Income Taxes The Company uses the liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on the differences between the financial reporting and the tax bases of assets and liabilities and are measured using the enacted tax rates and laws that will be in effect when the differences are expected to reverse. The Company must then assess the likelihood that the resulting deferred tax assets will be realized. A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized. Due to the Company’s lack of earnings history, the net deferred tax assets have been fully offset by a valuation allowance. The Company recognizes benefits of uncertain tax positions if it is more likely than not that such positions will be sustained upon examination based solely on their technical merits, as the largest amount of benefit that is more likely than not to be realized upon the ultimate settlement. The Company’s policy is to recognize interest and penalties related to the underpayment of income taxes as a component of income tax expense or benefit. To date, there have been no interest or penalties charged in relation to the unrecognized tax benefits.
Foreign Currency	Foreign Currency Assets and liabilities of non-U.S. subsidiaries that operate in a local currency environment, where that local currency is the functional currency, are translated to U.S. dollars at exchange rates in effect at the balance sheet date, with the resulting translation adjustments directly recorded to a separate component of accumulated other comprehensive loss. Income and expense accounts are translated at average exchange rates for the period. Remeasurement adjustments are recorded in other income (expense), net.
Net Loss per Share Attributable to Common Stockholders	Net Loss per Share Attributable to Common Stockholders Basic net loss per share attributable to common stockholders is calculated by dividing the net loss attributable to common stockholders by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share attributable to common stockholders is the same as basic net loss per share attributable to common stockholders, since the effects of potentially dilutive securities are antidilutive. In periods when we have incurred a net loss, convertible preferred stock, options and warrants to purchase common stock and convertible preferred stock warrants are considered common stock equivalents, but have been excluded from the calculation of diluted net loss per share attributable to common stockholders, as their effect is antidilutive.
Recent Accounting Pronouncements	Recent Accounting Pronouncements In May 2014, the FASB, issued ASU 2014-09, Revenue from Contracts with Customers (Topic 606) Revenue from Contracts with Customers: Principal versus Agent Considerations Revenue from Contracts with Customers: Identifying Performance Obligations and Licensing Revenue from Contracts with Customers: Narrow-Scope Improvements and Practical Expedients to provide supplemental adoption guidance and clarification to ASU 2014-09 Technical Corrections and Improvements to Topic 606, Revenue from Contracts with Customers In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842), which requires an entity that is a lessee to record a right of use asset and a corresponding lease liability on the balance sheet for all leases with terms longer than 12 months. This guidance also requires disclosures about the amount, timing, and uncertainty of cash flows arising from leases. This guidance is effective for annual reporting periods beginning after December 15, 2018, and interim periods within those annual periods, using a modified retrospective approach, and early adoption is permitted. The Company is evaluating the effect that this guidance will have on its Consolidated Financial Statements and related disclosures. In March 2016, the FASB issued ASU 2016-09, Compensation — Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting accounting for employee share-based payments, including income tax consequences, application of award forfeitures to expense, classification on the statement of cash flows, and classification of awards as either equity or liabilities. This guidance is effective for annual reporting periods beginning after December 15, 2016, and interim periods within those annual periods. In October 2016, the FASB issued ASU 2016-16, Income Taxes - Intra-Entity Transfers of Assets Other Than Inventory

Summary of Significant Accoun22

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2016
Accounting Policies [Abstract]
Summary of Useful Lives of Property and Equipment	The useful lives of the property and equipment are as follows: Research and development equipment 5 years Furniture and office equipment 5 years Computer equipment 3 years Software 3-5 years Leasehold improvements Shorter of lease term or estimated useful life

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	12 Months Ended
	Dec. 31, 2016
Fair Value Disclosures [Abstract]
Summary of Financial Assets Measured on Recurring Basis	The following table sets forth the fair value of the Company’s financial assets and liabilities remeasured on a recurring basis based on the three-tier fair value hierarchy (in thousands): December 31, 2016 Level 1 Level 2 Level 3 Total Financial Assets: Money market funds $ 123,536 $ — $ — $ 123,536 Corporate bonds — 207,726 — 207,726 Commercial paper — 11,970 — 11,970 Asset-backed securities — 27,713 — 27,713 U.S. Government Treasury and agency securities — 111,931 — 111,931 Total financial assets $ 123,536 $ 359,340 $ — $ 482,876 December 31, 2015 Level 1 Level 2 Level 3 Total Financial Assets: Money market funds $ 53,254 $ — $ — $ 53,254 Corporate bonds — 370,445 — 370,445 Commercial paper — 13,887 — 13,887 Asset-backed securities — 29,302 — 29,302 U.S. Government Treasury and agency securities — 47,452 — 47,452 Total financial assets $ 53,254 $ 461,086 $ — $ 514,340

Balance Sheet Components (Table

Balance Sheet Components (Tables)	12 Months Ended
	Dec. 31, 2016
Investments Debt And Equity Securities [Abstract]
Summary of Fair Values of Cash Equivalents, Short-Term Investments and Long-Term Investments Classified as Available-for-Sale Securities	The fair values of cash equivalents, short-term investments, and long-term investments classified as available-for-sale securities, consisted of the following (in thousands): December 31, 2016 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 123,536 $ — $ — $ 123,536 Corporate bonds 207,909 14 (197 ) 207,726 Commercial paper 11,970 — — 11,970 Asset-backed securities 27,712 3 (2 ) 27,713 U.S. Government Treasury and agency securities 112,166 10 (245 ) 111,931 Total $ 483,293 $ 27 $ (444 ) $ 482,876 December 31, 2015 Gross Unrealized Amortized Cost Gains Losses Estimated Fair Value Money market funds $ 53,254 $ — $ — $ 53,254 Corporate bonds 371,098 11 (664 ) 370,445 Commercial paper 13,887 — — 13,887 Asset-backed securities 29,356 — (54 ) 29,302 U.S. Government Treasury and agency securities 47,613 — (161 ) 47,452 Total $ 515,208 $ 11 $ (879 ) $ 514,340
Summary of Property and Equipment	Property and equipment, net consists of the following (in thousands): December 31, 2016 2015 Research and development equipment $ 2,154 $ 1,302 Furniture and office equipment 2,595 944 Computer equipment 2,013 628 Software 3,931 1,622 Leasehold improvements 12,486 3,466 Construction-in-progress 37 2,276 Property and equipment, gross 23,216 10,238 Less accumulated depreciation (6,161 ) (2,865 ) Property and equipment, net $ 17,055 $ 7,373
Accrued Liabilities	Accrued liabilities consist of the following (in thousands): December 31, 2016 2015 Research and clinical study expenses $ 18,593 $ 9,764 Payroll and related expenses 17,226 9,423 Repayment liability under collaboration agreement 13,650 — Other 5,085 5,597 Total accrued liabilities $ 54,554 $ 24,784

Stock-Based Awards (Tables)

Stock-Based Awards (Tables)	12 Months Ended
	Dec. 31, 2016
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Summary of Activity Under Stock Option Plans Including 2011 Plan and 2014 Plan	Stock Option Activity The following table summarizes activity under the Company’s stock option plans, including the 2011 Plan and the 2014 Plan and related information: Options Outstanding Number of Options Weighted- Average Exercise Weighted-Average Remaining Contractual Term Aggregate Intrinsic Value (In Outstanding — December 31, 2013 2,228,883 $ 3.41 8.91 $ 19,468 Options granted 932,555 41.12 Options exercised (305,090 ) 2.14 Options cancelled (116,873 ) 8.92 Outstanding — December 31, 2014 2,739,475 $ 16.15 8.43 $ 79,840 Options granted 2,013,350 90.60 Options exercised (795,825 ) 8.65 Options cancelled (130,037 ) 31.49 Outstanding — December 31, 2015 3,826,963 $ 56.36 8.58 $ 217,386 Options granted 1,435,995 67.00 Options exercised (425,922 ) 21.21 Options cancelled (407,564 ) 70.87 Outstanding — December 31, 2016 4,429,472 $ 61.85 8.22 $ 79,135 Vested and exercisable — December 31, 2016 1,620,443 $ 44.96 7.24 $ 55,537 Vested and expected to vest — December 31, 2016 4,264,788 $ 61.33 8.18 $ 78,412
Summary of Activity Under Restricted Stock Units (RSUs) from 2014 Plan	The following table summarizes activity under the Company’s Restricted Stock Units (RSUs) from the 2014 Plan and related information: RSUs Outstanding Number of Shares Weighted- Average Grant Date Fair Value Unvested — December 31, 2013 — $ — RSUs granted 31,000 53.23 Unvested — December 31, 2014 31,000 $ 53.23 RSUs granted 187,260 89.67 RSUs released (18,209 ) 54.72 RSUs cancelled (2,900 ) 84.89 Unvested — December 31, 2015 197,151 $ 87.24 RSUs granted 477,816 66.83 RSUs released (52,273 ) 82.59 RSUs cancelled (48,950 ) 78.04 Unvested — December 31, 2016 573,744 $ 71.45
Summary of Stock-Based Compensation Recognized	Total stock-based compensation recognized was as follows (in thousands): Year Ended December 31, 2016 2015 2014 Research and development $ 29,412 $ 17,100 $ 4,116 General and administrative 18,897 7,784 1,278 Total stock-based compensation expense $ 48,309 $ 24,884 $ 5,394
Fair Value of Stock Option Awards Estimated Using Black-Scholes Option-Pricing Model	The fair value of stock option awards was estimated at the date of grant using a Black-Scholes option-pricing model with the following weighted-average assumptions: Options Year Ended December 31, 2016 2015 2014 Expected term (years) 6.23 6.23 6.23 Expected volatility 65% 65% 70% Risk-free interest rate 1.5% 1.8% 1.9% Expected dividend rate 0.0% 0.0% 0.0%

Income Taxes (Tables)

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2016
Income Tax Disclosure [Abstract]
Components of Company's Loss Before Income Taxes	The components of the Company’s loss before income taxes were as follows (in thousands): Year Ended December 31, 2016 2015 2014 Domestic $ 192,287 $ 145,618 $ 59,802 Foreign 53,552 — — Total loss before income taxes $ 245,839 $ 145,618 $ 59,802
Components of Company's Income Tax Provision	The components of the Company’s income tax provision were as follows (in thousands): Year Ended December 31, 2016 2015 2014 Federal $ — $ — $ — State — — — International 35 — — Total income tax provision $ 35 $ — $ —
Effective Tax Rate of Provision for Income Taxes from Federal Statutory Rate	The effective tax rate of our provision for income taxes differs from the federal statutory rate as follows: Year Ended December 31, 2016 2015 2014 Federal statutory income tax rate 34.0 % 34.0 % 34.0 % State income taxes, net of federal benefit 1.3 7.5 4.6 Federal tax credits 13.7 5.9 6.7 Other (0.3 ) 0.8 — Nondeductible permanent items — — (1.2 ) Stock-based compensation (1.4 ) (1.3 ) (1.4 ) Uncertain tax positions 2.0 (7.7 ) — Change in valuation allowance (41.9 ) (39.2 ) (42.7 ) Foreign rate differential (7.4 ) — — Provision for income taxes — — —
Schedule of Tax Effect of Temporary Differences to Significant Portions of Deferred Tax Assets	The tax effect of temporary differences that give rise to significant portions of the deferred tax assets is presented below (in thousands): Year Ended December 31, 2016 2015 Deferred tax assets: Net operating loss carryforwards $ 102,960 $ 61,503 Tax credits 78,324 33,881 Stock options 16,084 6,680 Accruals and reserves 10,039 2,541 Fixed assets and intangibles 3,014 4,442 Other 1,950 432 Total deferred tax assets 212,371 109,479 Valuation allowance (212,371 ) (109,479 ) Net deferred tax assets $ — $ —
Unrecognized Tax Benefits	A reconciliation of the Company’s unrecognized tax benefits for the years ended December 31, 2016, 2015, and 2014 is as follows (in thousands): December 31, 2016 2015 2014 Balance at beginning of year $ 24,010 $ 7,275 $ 3,725 Additions based on tax positions related to current year 6,777 15,628 3,550 Additions for tax positions of prior years 877 5,505 — Reductions for tax positions of prior years (18,159 ) (4,398 ) — Balance at end of year $ 13,505 $ 24,010 $ 7,275

Commitments and Contingencies (

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2016
Commitments And Contingencies Disclosure [Abstract]
Summary of Future Minimum Lease Payments under Non-Cancellable Operating Leases Arrangements and Future Payments under Contractually Binding Manufacturing and Service Agreements	As of December 31, 2016, the aggregate future minimum lease payments under the noncancelable operating lease arrangements and future payments under contractually binding manufacturing and service agreements are as follows (in thousands): Year Ending December 31, Leases Manufacturing and Services 2017 $ 3,956 $ 1,956 2018 4,534 810 2019 3,553 265 2020 2,867 62 2021 2,346 — Thereafter 11,446 — $ 28,702 $ 3,093

Net Loss per Share Attributab28

Net Loss per Share Attributable to Common Stockholders (Tables)	12 Months Ended
	Dec. 31, 2016
Earnings Per Share [Abstract]
Computation of Basic and Diluted Net Loss per Share	The following table sets forth the computation of the basic and diluted net loss per share attributable to common stockholders during the years ended December 31, 2016, 2015 and 2014 (in thousands, except share and per share data): Year Ended December 31, 2016 2015 2014 Numerator: Net loss $ (245,874 ) $ (145,618 ) $ (59,802 ) Accretion and dividends on convertible preferred stock — — (4,808 ) Net loss attributable to common stockholders $ (245,874 ) $ (145,618 ) $ (64,610 ) Denominator: Weighted-average shares used to compute net loss per share attributable to common stockholders, basic and diluted 39,586,908 36,782,603 28,755,758 Net loss per share attributable to common stockholders, basic and diluted $ (6.21 ) $ (3.96 ) $ (2.25 )
Outstanding Shares of Common Stock Equivalents Excluded from Computation of Diluted Net Loss per Share	The following weighted-average outstanding common stock equivalents were excluded from the computation of diluted net loss per share attributable to common stockholders for the periods presented because including them would have been antidilutive: Year Ended December 31, 2016 2015 2014 Convertible preferred stock — — 1,610,834 Options to purchase common stock and RSUs 4,699,111 3,368,507 2,582,444 Convertible preferred stock warrants — — 29,051 Employee stock purchase plan 7,933 — — Common stock warrants 149,700 195,762 318,666 4,856,744 3,564,269 4,540,995

Accumulated Other Comprehensi29

Accumulated Other Comprehensive Income (Loss) (Tables)	12 Months Ended
	Dec. 31, 2016
Other Comprehensive Income Loss Net Of Tax Period Increase Decrease [Abstract]
Schedule of Total Accumulated Other Comprehensive Income (Loss)	Total accumulated other comprehensive income (loss) consisted of the following (in thousands) : Unrealized Gain (Loss) on Securities Available-for-Sale Foreign Currency Translation Adjustments Accumulated Other Comprehensive Income (Loss) December 31, 2013 $ 11 $ — $ 11 Current period other comprehensive loss (185 ) — (185 ) December 31, 2014 (174 ) — (174 ) Current period other comprehensive loss (694 ) — (694 ) December 31, 2015 (868 ) — (868 ) Current period other comprehensive income 451 1,322 1,773 December 31, 2016 $ (417 ) $ 1,322 $ 905

Quarterly Financial Data (una30

Quarterly Financial Data (unaudited) (Tables)	12 Months Ended
	Dec. 31, 2016
Quarterly Financial Data [Abstract]
Summary of Unaudited Quarterly Financial Information	The following table presents certain unaudited quarterly financial information. This information has been prepared on the same basis as the audited financial statements and includes all adjustments (consisting only of normal recurring adjustments) necessary to present fairly the unaudited quarterly results of operations set forth herein (in thousands, except share and per share data): 2016 March 31, June 30, September 30, December 31, Revenue $ — $ 17 $ 111 $ 5 Operating expenses 53,622 58,070 65,894 70,554 Net loss attributable to common stockholders (52,757 ) (56,923 ) (64,907 ) (71,287 ) Net loss per share attributable to common stockholders, basic and diluted $ (1.35 ) $ (1.46 ) $ (1.64 ) $ (1.75 ) 2015 March 31, June 30, September 30, December Operating expenses $ 21,502 $ 30,142 $ 39,936 $ 56,158 Net loss attributable to common stockholders (21,379 ) (29,787 ) (39,232 ) (55,220 ) Net loss per share attributable to common stockholders, basic and diluted $ (0.63 ) $ (0.83 ) $ (1.03 ) $ (1.42 )

Organization and Basis of Pre31

Organization and Basis of Presentation - Additional Information (Details)	12 Months Ended
	Dec. 31, 2016Segment
United States of America
Organization And Nature Of Business [Line Items]
Number of reportable segments	1

Summary of Significant Accoun32

Summary of Significant Accounting Policies - Summary of Useful Lives of Property and Equipment (Details)	12 Months Ended
	Dec. 31, 2016
Research and Development Equipment
Property Plant And Equipment [Line Items]
Property plant and equipment useful life	5 years
Furniture and Office Equipment
Property Plant And Equipment [Line Items]
Property plant and equipment useful life	5 years
Computer Equipment
Property Plant And Equipment [Line Items]
Property plant and equipment useful life	3 years
Software | Minimum
Property Plant And Equipment [Line Items]
Property plant and equipment useful life	3 years
Software | Maximum
Property Plant And Equipment [Line Items]
Property plant and equipment useful life	5 years
Leasehold Improvements
Property Plant And Equipment [Line Items]
Property plant and equipment useful life	Shorter of lease term or estimated useful life

Summary of Significant Accoun33

Summary of Significant Accounting Policies - Additional Information (Details)	12 Months Ended
	Dec. 31, 2016USD ($)
Accounting Policies [Abstract]
Unrecognized tax benefits related to interest or penalties	$ 0

Fair Value Measurements - Summa

Fair Value Measurements - Summary of Financial Assets and Liabilities Measured on Recurring Basis (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Financial Assets:
Fair value	$ 482,876	$ 514,340
Money Market Funds
Financial Assets:
Fair value	123,536	53,254
Asset Backed Securities
Financial Assets:
Fair value	27,713	29,302
Corporate Bonds
Financial Assets:
Fair value	207,726	370,445
Commercial Paper
Financial Assets:
Fair value	11,970	13,887
US Government Treasury and Agencies Securities
Financial Assets:
Fair value	111,931	47,452
Level 1
Financial Assets:
Fair value	123,536	53,254
Level 1 | Money Market Funds
Financial Assets:
Fair value	123,536	53,254
Level 2
Financial Assets:
Fair value	359,340	461,086
Level 2 | Asset Backed Securities
Financial Assets:
Fair value	27,713	29,302
Level 2 | Corporate Bonds
Financial Assets:
Fair value	207,726	370,445
Level 2 | Commercial Paper
Financial Assets:
Fair value	11,970	13,887
Level 2 | US Government Treasury and Agencies Securities
Financial Assets:
Fair value	$ 111,931	$ 47,452

Balance Sheet Components - Summ

Balance Sheet Components - Summary of Fair Values of Cash Equivalents, Short-Term Investments and Long-Term Investments Classified as Available-for-Sale Securities (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Schedule Of Available For Sale Securities [Line Items]
Amortized Cost	$ 483,293	$ 515,208
Gross Unrealized Gains	27	11
Gross Unrealized Losses	(444)	(879)
Estimated Fair Value	482,876	514,340
Money Market Funds
Schedule Of Available For Sale Securities [Line Items]
Amortized Cost	123,536	53,254
Estimated Fair Value	123,536	53,254
Commercial Paper
Schedule Of Available For Sale Securities [Line Items]
Amortized Cost	11,970	13,887
Estimated Fair Value	11,970	13,887
Corporate Bonds
Schedule Of Available For Sale Securities [Line Items]
Amortized Cost	207,909	371,098
Gross Unrealized Gains	14	11
Gross Unrealized Losses	(197)	(664)
Estimated Fair Value	207,726	370,445
Asset Backed Securities
Schedule Of Available For Sale Securities [Line Items]
Amortized Cost	27,712	29,356
Gross Unrealized Gains	3
Gross Unrealized Losses	(2)	(54)
Estimated Fair Value	27,713	29,302
U.S. Government Treasury and Agency Securities
Schedule Of Available For Sale Securities [Line Items]
Amortized Cost	112,166	47,613
Gross Unrealized Gains	10
Gross Unrealized Losses	(245)	(161)
Estimated Fair Value	$ 111,931	$ 47,452

Balance Sheet Components - Addi

Balance Sheet Components - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Schedule Of Available For Sale Securities [Line Items]
Significant realized gains or losses on available-for-sale securities	$ 0
Depreciation and amortization	$ 3,424,000	$ 1,384,000	$ 684,000
Maximum
Schedule Of Available For Sale Securities [Line Items]
Available-for-sale securities remaining contractual maturities	2 years

Balance Sheet Components - Su37

Balance Sheet Components - Summary of Property and Equipment (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Property Plant And Equipment [Line Items]
Property and equipment, gross	$ 23,216	$ 10,238
Less accumulated depreciation	(6,161)	(2,865)
Property and equipment, net	17,055	7,373
Research and Development Equipment
Property Plant And Equipment [Line Items]
Property and equipment, gross	2,154	1,302
Furniture and Office Equipment
Property Plant And Equipment [Line Items]
Property and equipment, gross	2,595	944
Computer Equipment
Property Plant And Equipment [Line Items]
Property and equipment, gross	2,013	628
Software
Property Plant And Equipment [Line Items]
Property and equipment, gross	3,931	1,622
Leasehold Improvements
Property Plant And Equipment [Line Items]
Property and equipment, gross	12,486	3,466
Construction-in-progress
Property Plant And Equipment [Line Items]
Property and equipment, gross	$ 37	$ 2,276

Balance Sheet Components - Accr

Balance Sheet Components - Accrued Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015
Payables And Accruals [Abstract]
Research and clinical study expenses	$ 18,593	$ 9,764
Payroll and related expenses	17,226	9,423
Repayment liability under collaboration agreement	13,650
Other	5,085	5,597
Total accrued liabilities	$ 54,554	$ 24,784

License and Research Agreemen39

License and Research Agreements - Additional Information (Details) $ / shares in Units, $ in Thousands, ¥ in Millions	1 Months Ended					12 Months Ended
	Oct. 31, 2016USD ($)shares	Jul. 31, 2016USD ($)$ / sharesshares	Jun. 30, 2016USD ($)	Oct. 31, 2015USD ($)	Jun. 30, 2013USD ($)	Dec. 31, 2016USD ($)shares	Dec. 31, 2015USD ($)shares	Dec. 31, 2014USD ($)shares	Jan. 31, 2017USD ($)	Dec. 31, 2016JPY (¥)shares
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Research and development						$ 183,204	$ 114,737	$ 45,967
Common stock purchased | shares						41,240,230	38,882,394			41,240,230
Common stock value								$ 121,711
Common stock issued upon option exercised in period, shares | shares						425,922	795,825	305,090
Common stock issued upon option exercised in period, value						$ 9,096	$ 7,355	$ 736
Liability under collaboration arrangement						$ 13,650
Common Stock
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Common stock value								$ 7
Common stock issued upon option exercised in period, shares | shares						438,811	957,587	331,605
Common stock issued upon option exercised in period, value							$ 1
Nobelpharma License Agreement | Maximum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Aggregate future payments						$ 1,700				¥ 200
Saint Louis University License Agreement
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments						100
H I B M Research Group License Agreement | Development and Approval Milestones
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments						$ 300
H I B M Research Group License Agreement | Maximum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Payments for royalty on net sales						1.00%
St. Jude Children's Research Hospital License Agreement | Maximum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Payments for royalty on net sales						1.00%
Baylor Research Institute License Agreement
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Payment of option exercise fee					$ 800
Baylor Research Institute License Agreement | Development Milestones
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments						$ 10,500
Baylor Research Institute License Agreement | Sales Milestones
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments						7,500
Kyowa Hakko Kirin Collaboration | License Agreement
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Reduction in research and development cost						26,800	10,800
License agreement receivable						$ 8,600	$ 3,800
Kyowa Hakko Kirin Collaboration | License Agreement | Profit Share Territory
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Remaining profit or loss share percentage on commercializing products						50.00%
Tiered double-digit revenue share percentage entitled to receive						20.00%
Kyowa Hakko Kirin Collaboration | Maximum | License Agreement | European Territory
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Percentage of royalty on net sales entitled to receive						10.00%
Arcturus Research Collaboration and License Agreement
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Research and development				$ 10,000
Takeda License and Collaboration and Purchase Agreements
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Estimated fair value of license recorded as research and development expense			$ 700
Research collaboration agreement, period			5 years
Common stock purchased | shares		374,590
Common stock value		$ 40,000
Common closing stock price per share | $ / shares		$ 72.95
Common stock shares issued premium amount		$ 12,700
Option to purchase additional common stock, value		$ 25,000
Volume weighted average price, period		30 days
Second option to purchase additional common stock, value		$ 10,000
Common stock purchase agreement, terms						Takeda was subject to a 180-day lock-up provision as a result of the initial purchase of common stock, and a 90-day lock-up provision as a result of its purchase under the first put option, is subject to a five-year standstill (subject to customary exceptions or release), and has registration rights for purchases of common stock.
Total arrangement consideration received		14,300
Initial development plan period						Approximately one and a half years
Liability under collaboration arrangement						$ 14,300
Takeda License and Collaboration and Purchase Agreements | Subsequent Event
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Second option to purchase additional common stock, value									$ 10,000
Takeda License and Collaboration and Purchase Agreements | Put Option
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Estimated fair value of future options		$ 900
Common stock issued upon option exercised in period, shares | shares	352,530
Common stock issued upon option exercised in period, value	$ 25,000
Takeda License and Collaboration and Purchase Agreements | Put Option | Monte Carlo Simulation
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Equity volatility percentage		70.00%
Takeda License and Collaboration and Purchase Agreements | Common Stock
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Fair market value of shares issued		$ 27,300
Takeda License and Collaboration and Purchase Agreements | Maximum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Estimated approximate cost for expected work performed		15,500
Takeda License and Collaboration and Purchase Agreements | Maximum | Development Milestones
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments			$ 7,500
Takeda License and Collaboration and Purchase Agreements | Maximum | Regulatory Milestones
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments			75,000
Takeda License and Collaboration and Purchase Agreements | Maximum | Commercial Milestones
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Future contingent milestone payments			$ 150,000
Takeda License and Collaboration and Purchase Agreements | Minimum
Collaborative Arrangements And Noncollaborative Arrangement Transactions [Line Items]
Estimated approximate cost for expected work performed		$ 10,000

Equity - Additional Information

Equity - Additional Information (Details) - USD ($)	1 Months Ended	2 Months Ended	12 Months Ended
	Jul. 31, 2016	Feb. 15, 2017	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Jan. 30, 2014	Jun. 30, 2011
Stockholders Equity [Line Items]
Net proceeds from sale of common stock				$ 461,136,000	$ 188,581,000
Fair value of warrants						$ 6,700,000	$ 200,000
Revaluation of convertible preferred stock warrant liability			$ 0	$ 0	$ 3,324,000
June 2010 Common Stock Warrant [Member]
Stockholders Equity [Line Items]
Common stock warrants outstanding			83,167	83,167
Common stock warrants, issued date			2010-06	2010-06
Common stock warrants, contractual term			10 years	10 years
Common stock warrants, exercise price			$ 3.006	$ 3.006
June 2011 Common Stock Warrant [Member]
Stockholders Equity [Line Items]
Common stock warrants outstanding			66,533	66,533
Common stock warrants, issued date			2011-06	2011-06
Common stock warrants, contractual term			10 years	10 years
Common stock warrants, exercise price			$ 3.006	$ 3.006
Subsequent Event
Stockholders Equity [Line Items]
Common stock shares sold		658,532
Net proceeds from sale of common stock		$ 48,400,000
ATM Sales Agreement
Stockholders Equity [Line Items]
Common stock shares sold			1,159,415
Net proceeds from sale of common stock			$ 79,500,000
Maximum | ATM Sales Agreement
Stockholders Equity [Line Items]
Option to sell common stock for cash	$ 150,000,000

Stock-Based Awards - Additional

Stock-Based Awards - Additional Information (Details) - USD ($) $ / shares in Units, $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Feb. 05, 2014
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Total intrinsic value of options exercised	$ 22.2	$ 59	$ 12.1
Cash received from exercise of options	$ 9	$ 6.9	$ 0.7
Weighted-average estimated fair value of stock option	$ 40.49	$ 54.90	$ 26.58
Total estimated fair value of options vested	$ 43.8	$ 10.7	$ 2
Total unrecognized compensation cost	$ 136.5
Weighted-average period to recognize cost	2 years 9 months 11 days
Restricted Stock Units
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Shares vested during the period	52,273	18,209
Total fair value of shares vested	$ 4.3
Aggregate intrinsic value	$ 3.3
Maximum | Restricted Stock Units
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Stock based awards vesting period	4 years
Minimum | Restricted Stock Units
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Stock based awards vesting period	1 year
2014 Incentive Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Share of common stock authorized for future issuance				2,250,000
Automatic increases in shares available for grant effective date	Jan. 1, 2015
Shares available for grant, ending date	Jan. 1, 2024
2014 Incentive Plan | Employee Stock Option
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Minimum percentage of voting rights of all classes of stock	10.00%
Percentage of statutory stock awards	110.00%
2014 Incentive Plan | Maximum | Employee Stock Option
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Award expiration period	10 years
2011 Equity Incentive Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Share of common stock authorized for future issuance				655,038
2011 Equity Incentive Plan | Restricted Stock Units
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Option vesting rights, percentage	25.00%
Stock based awards vesting period	4 years
2011 Equity Incentive Plan | First Anniversary | Employee Stock Option
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Option vesting rights, percentage	25.00%
2011 Equity Incentive Plan | Shares Vesting Monthly After First Anniversary | Employee Stock Option
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Option vesting rights, percentage	2.08%
2011 Equity Incentive Plan and 2014 Incentive Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Share of common stock authorized for future issuance	7,478,107
2014 Employee Stock Purchase Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Automatic increases in shares available for grant effective date	Jan. 1, 2015
Shares available for grant, ending date	Jan. 1, 2024
Percentage of statutory stock awards	85.00%
Share of common stock available for future issuance				600,000

Stock-Based Awards - Summary of

Stock-Based Awards - Summary of Activity Under Stock Option Plans Including 2011 Plan and 2014 Plan (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Number of Options, Outstanding, Beginning Balance	3,826,963	2,739,475	2,228,883
Number of Options, Options granted	1,435,995	2,013,350	932,555
Number of Options, Options exercised	(425,922)	(795,825)	(305,090)
Number of Options, Options cancelled	(407,564)	(130,037)	(116,873)
Number of Options, Outstanding, Ending Balance	4,429,472	3,826,963	2,739,475	2,228,883
Number of Options, Vested and exercisable — December 31, 2016	1,620,443
Number of Options, Vested and expected to vest — December 31, 2016	4,264,788
Weighted Average Exercise Price, Outstanding, Beginning Balance	$ 56.36	$ 16.15	$ 3.41
Weighted Average Exercise Price, Options granted	67	90.60	41.12
Weighted Average Exercise Price, Options exercised	21.21	8.65	2.14
Weighted Average Exercise Price, Options cancelled	70.87	31.49	8.92
Weighted Average Exercise Price, Outstanding, Ending Balance	61.85	$ 56.36	$ 16.15	$ 3.41
Weighted Average Exercise Price, Vested and exercisable — December 31, 2016	44.96
Weighted Average Exercise Price, Vested and expected to vest — December 31, 2016	$ 61.33
Weighted Average Remaining Contractual Term (Years), Outstanding	8 years 2 months 19 days	8 years 6 months 29 days	8 years 5 months 5 days	8 years 10 months 28 days
Weighted Average Remaining Contractual Term (Years), Vested and exercisable — December 31, 2016	7 years 2 months 27 days
Weighted Average Remaining Contractual Term (Years), Vested and expected to vest — December 31, 2016	8 years 2 months 5 days
Aggregate Intrinsic Value, Outstanding	$ 79,135	$ 217,386	$ 79,840	$ 19,468
Aggregate Intrinsic Value, Vested and exercisable — December 31, 2016	55,537
Aggregate Intrinsic Value, Vested and expected to vest — December 31, 2016	$ 78,412

Stock-Based Awards - Summary 43

Stock-Based Awards - Summary of Activity Under Restricted Stock Units (RSUs) from 2014 Plan (Details) - Restricted Stock Units - $ / shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
RSUs Outstanding, Number of Shares, Unvested, Beginning Balance	197,151	31,000
Number of Shares, RSUs granted	477,816	187,260	31,000
Number of Shares, RSUs released	(52,273)	(18,209)
Number of Shares, RSUs cancelled	(48,950)	(2,900)
RSUs Outstanding, Number of Shares, Unvested, Ending Balance	573,744	197,151	31,000
RSUs Outstanding, Weighted-Average Grant Date Fair Value, Unvested, Beginning Balance	$ 87.24	$ 53.23
Weighted-Average Grant Date Fair Value, RSUs granted	66.83	89.67	$ 53.23
Weighted-Average Grant Date Fair Value, RSUs released	82.59	54.72
Weighted-Average Grant Date Fair Value, RSUs cancelled	78.04	84.89
RSUs Outstanding, Weighted-Average Grant Date Fair Value, Unvested, Ending Balance	$ 71.45	$ 87.24	$ 53.23

Stock-Based Awards - Summary 44

Stock-Based Awards - Summary of Stock-Based Compensation Recognized (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Employee Service Share Based Compensation Allocation Of Recognized Period Costs [Line Items]
Stock-based compensation expense	$ 48,309	$ 24,884	$ 5,394
Research and development
Employee Service Share Based Compensation Allocation Of Recognized Period Costs [Line Items]
Stock-based compensation expense	29,412	17,100	4,116
General and administrative
Employee Service Share Based Compensation Allocation Of Recognized Period Costs [Line Items]
Stock-based compensation expense	$ 18,897	$ 7,784	$ 1,278

Stock-Based Awards - Fair Value

Stock-Based Awards - Fair Value of Stock Option Awards Estimated Using Black-Scholes Option-Pricing Model (Details) - Employee Stock Option	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (years)	6 years 2 months 23 days	6 years 2 months 23 days	6 years 2 months 23 days
Expected volatility	65.00%	65.00%	70.00%
Risk-free interest rate	1.50%	1.80%	1.90%
Expected dividend rate	0.00%	0.00%	0.00%

Defined Contribution Plan - Add

Defined Contribution Plan - Additional Information (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015
Defined Contribution Pension And Other Postretirement Plans Disclosure [Abstract]
Contribution expenses	$ 1.5	$ 0.6

Income Taxes - Components of Co

Income Taxes - Components of Company's Loss Before Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Disclosure [Abstract]
Domestic	$ 192,287	$ 145,618	$ 59,802
Foreign	53,552
Total loss before income taxes	$ 245,839	$ 145,618	$ 59,802

Income Taxes - Components of 48

Income Taxes - Components of Company's Income Tax Provision (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2016USD ($)
Income Tax Disclosure [Abstract]
International	$ 35
Total income tax provision	$ 35

Income Taxes - Effective Tax Ra

Income Taxes - Effective Tax Rate of Provision for Income Taxes from Federal Statutory Rate (Details)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Effective Income Tax Rate Continuing Operations Tax Rate Reconciliation [Abstract]
Federal statutory income tax rate	34.00%	34.00%	34.00%
State income taxes, net of federal benefit	1.30%	7.50%	4.60%
Federal tax credits	13.70%	5.90%	6.70%
Other	(0.30%)	0.80%
Nondeductible permanent items			(1.20%)
Stock-based compensation	(1.40%)	(1.30%)	(1.40%)
Uncertain tax positions	2.00%	(7.70%)
Change in valuation allowance	(41.90%)	(39.20%)	(42.70%)
Foreign rate differential	(7.40%)

Income Taxes - Schedule of Tax

Income Taxes - Schedule of Tax Effect of Temporary Differences to Significant Portions of Deferred Tax Assets (Details) - USD ($) $ in Thousands	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2012	Dec. 31, 2011
Deferred tax assets:
Net operating loss carryforwards	$ 102,960	$ 61,503	$ 200	$ 200
Tax credits	78,324	33,881
Stock options	16,084	6,680
Accruals and reserves	10,039	2,541
Fixed assets and intangibles	3,014	4,442
Other	1,950	432
Total deferred tax assets	212,371	109,479
Valuation allowance	(212,371)	(109,479)
Net deferred tax assets	$ 0	$ 0

Income Taxes - Additional Infor

Income Taxes - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2012	Dec. 31, 2011
Tax Credit Carryforward [Line Items]
Deferred tax assets net operating loss carryforwards	$ 102,960,000	$ 61,503,000	$ 200,000	$ 200,000
Valuation allowance increased	102,900,000	58,100,000
Unrecognized tax benefits, income tax penalties and interest accrued	0	0
Undistributed earnings of foreign subsidiaries	100,000
Federal
Tax Credit Carryforward [Line Items]
Deferred tax assets operating loss carryforwards subject to expiration	$ 315,500,000	225,500,000
Operating loss carryforwards expiration year	2,030
Tax credit carryforwards	$ 2,500,000	1,700,000
Tax credit carryforwards expiration year	2,030
Deferred tax assets net operating loss carryforwards			3,600,000	3,600,000
Federal | Orphan Drug Credits [Member]
Tax Credit Carryforward [Line Items]
Deferred tax assets operating loss carryforwards subject to expiration	$ 84,300,000	35,200,000
Operating loss carryforwards expiration year	2,031
State
Tax Credit Carryforward [Line Items]
Deferred tax assets operating loss carryforwards subject to expiration	$ 259,800,000	255,000,000
Operating loss carryforwards expiration year	2,030
Tax credit carryforwards	$ 6,700,000	$ 4,300,000
Deferred tax assets net operating loss carryforwards			$ 3,600,000	$ 3,600,000

Income Taxes - Unrecognized Tax

Income Taxes - Unrecognized Tax Benefits (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Income Tax Disclosure [Abstract]
Balance at beginning of year	$ 24,010	$ 7,275	$ 3,725
Additions based on tax positions related to current year	6,777	15,628	3,550
Additions for tax positions of prior years	877	5,505
Reductions for tax positions of prior years	(18,159)	(4,398)
Balance at end of year	$ 13,505	$ 24,010	$ 7,275

Commitments and Contingencies -

Commitments and Contingencies - Additional Information (Details) $ in Thousands	1 Months Ended	12 Months Ended
	Dec. 31, 2015USD ($)Option	Dec. 31, 2016USD ($)	Dec. 31, 2015USD ($)	Dec. 31, 2014USD ($)
Disclosure Commitments And Contingencies Additional Information Details [Line Items]
Tenant improvement allowance		$ 3,467
Operating lease commencement date	2016-05
Rent expense		$ 3,300	$ 1,400	$ 600
Brisbane Office Facility
Disclosure Commitments And Contingencies Additional Information Details [Line Items]
Tenant improvement allowance	$ 3,700
Operating lease expiration period	122 months
Number of options to extend lease | Option	2
Lease renewal term	5 years
Novato Office Facility
Disclosure Commitments And Contingencies Additional Information Details [Line Items]
Tenant improvement allowance	$ 1,500
Lease renewal term	5 years
Operating lease expiration year		2,020

Commitments and Contingencies54

Commitments and Contingencies - Summary of Future Minimum Lease Payments under Non-Cancellable Operating Leases Arrangements and Future Payments under Contractually Binding Manufacturing and Service Agreements (Details) $ in Thousands	Dec. 31, 2016USD ($)
Commitments And Contingencies Disclosure [Abstract]
Leases, 2017	$ 3,956
Leases, 2018	4,534
Leases, 2019	3,553
Leases, 2020	2,867
Leases, 2021	2,346
Leases, Thereafter	11,446
Leases, Total	28,702
Manufacturing and Services, 2017	1,956
Manufacturing and Services, 2018	810
Manufacturing and Services, 2019	265
Manufacturing and Services, 2020	62
Manufacturing and Services, Total	$ 3,093

Net Loss per Share Attributab55

Net Loss per Share Attributable to Common Stockholders - Computation of Basic and Diluted Net Loss per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Numerator:
Net loss									$ (245,874)	$ (145,618)	$ (59,802)
Accretion and dividends on convertible preferred stock											(4,808)
Net loss attributable to common stockholders	$ (71,287)	$ (64,907)	$ (56,923)	$ (52,757)	$ (55,220)	$ (39,232)	$ (29,787)	$ (21,379)	$ (245,874)	$ (145,618)	$ (64,610)
Denominator:
Weighted-average shares used to compute net loss per share attributable to common stockholders, basic and diluted									39,586,908	36,782,603	28,755,758
Net loss per share attributable to common stockholders, basic and diluted	$ (1.75)	$ (1.64)	$ (1.46)	$ (1.35)	$ (1.42)	$ (1.03)	$ (0.83)	$ (0.63)	$ (6.21)	$ (3.96)	$ (2.25)

Net Loss per Share Attributab56

Net Loss per Share Attributable to Common Stockholders - Outstanding Shares of Common Stock Equivalents Excluded from Computation of Diluted Net Loss per Share (Details) - shares	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Common stock equivalents excluded from computation of diluted net loss per share	4,856,744	3,564,269	4,540,995
Convertible Preferred Stock
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Common stock equivalents excluded from computation of diluted net loss per share			1,610,834
Options to Purchase Common Stock and RSUs
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Common stock equivalents excluded from computation of diluted net loss per share	4,699,111	3,368,507	2,582,444
Convertible Preferred Stock Warrants
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Common stock equivalents excluded from computation of diluted net loss per share			29,051
Common Stock Warrants
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Common stock equivalents excluded from computation of diluted net loss per share	149,700	195,762	318,666
Employee Stock Purchase Plan
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Common stock equivalents excluded from computation of diluted net loss per share	7,933

Accumulated Other Comprehensi57

Accumulated Other Comprehensive Income (Loss) - Schedule of Total Accumulated Other Comprehensive Income (Loss) (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Accumulated Other Comprehensive Income (Loss) [Line Items]
Beginning balance	$ 531,090	$ 184,945	$ (74,821)
Current period other comprehensive income (loss)	1,773	(694)	(185)
Ending balance	473,974	531,090	184,945
Unrealized Gain (Loss) on Securities Available-for-Sale
Accumulated Other Comprehensive Income (Loss) [Line Items]
Beginning balance	(868)	(174)	11
Current period other comprehensive income (loss)	451	(694)	(185)
Ending balance	(417)	(868)	(174)
Foreign Currency Translation Adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Current period other comprehensive income (loss)	1,322
Ending balance	1,322
Accumulated Other Comprehensive Income (Loss)
Accumulated Other Comprehensive Income (Loss) [Line Items]
Beginning balance	(868)	(174)	11
Current period other comprehensive income (loss)	1,773	(694)	(185)
Ending balance	$ 905	$ (868)	$ (174)

Quarterly Financial Data (una58

Quarterly Financial Data (unaudited) - Summary of Unaudited Quarterly Financial Information (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2016	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015	Jun. 30, 2015	Mar. 31, 2015	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Selected Quarterly Financial Information [Abstract]
Revenue	$ 5	$ 111	$ 17						$ 133
Operating expenses	70,554	65,894	58,070	$ 53,622	$ 56,158	$ 39,936	$ 30,142	$ 21,502	248,140	$ 147,738	$ 56,778
Net loss attributable to common stockholders	$ (71,287)	$ (64,907)	$ (56,923)	$ (52,757)	$ (55,220)	$ (39,232)	$ (29,787)	$ (21,379)	$ (245,874)	$ (145,618)	$ (64,610)
Net loss per share attributable to common stockholders, basic and diluted	$ (1.75)	$ (1.64)	$ (1.46)	$ (1.35)	$ (1.42)	$ (1.03)	$ (0.83)	$ (0.63)	$ (6.21)	$ (3.96)	$ (2.25)