0001714899-21-000106 | 10-Q | XBRL Viewer

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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2021	Oct. 29, 2021
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2021
Document Transition Report	false
Entity File Number	001-38311
Entity Registrant Name	Denali Therapeutics Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	46-3872213
Entity Address, Address Line One	161 Oyster Point Blvd
Entity Address, City or Town	South San Francisco
Entity Address, State or Province	CA
Entity Address, Postal Zip Code	94080
City Area Code	650
Local Phone Number	866-8548
Title of 12(b) Security	Common Stock, par value $0.01 per share
Trading Symbol	DNLI
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding (shares)		122,125,581
Document Fiscal Year Focus	2021
Document Fiscal Period Focus	Q3
Amendment Flag	false
Entity Central Index Key	0001714899
Current Fiscal Year End Date	--12-31

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Current assets:
Cash and cash equivalents	$ 394,553	$ 507,144
Short-term marketable securities	644,622	962,553
Cost sharing reimbursements due from related party	1,194	5,674
Prepaid expenses and other current assets	15,140	20,284
Total current assets	1,055,509	1,495,655
Long-term marketable securities	319,472	32,699
Property and equipment, net	40,012	40,846
Operating lease right-of-use asset	31,196	32,618
Other non-current assets	3,777	2,462
Total assets	1,449,966	1,604,280
Current liabilities:
Accounts payable	4,817	1,071
Accrued compensation	10,534	20,503
Accrued manufacturing costs	13,142	7,140
Accrued clinical and other research & development costs	13,380	11,775
Other accrued costs and current liabilities	2,364	3,037
Operating lease liability, current	5,252	4,690
Related party contract liability, current	3,438	3,569
Contract liabilities, current	1,324	19,914
Total current liabilities	54,251	71,699
Related party contract liability, less current portion	291,434	293,849
Contract liabilities, less current portion	31,313	23,325
Operating lease liability, less current portion	59,990	64,175
Other non-current liabilities	701	701
Total liabilities	437,689	453,749
Commitments and contingencies (Note 7)
Stockholders' equity:
Convertible preferred stock, $0.01 par value; 40,000,000 shares authorized as of September 30, 2021 and December 31, 2020; 0 shares issued and outstanding as of September 30, 2021 and December 31, 2020	0	0
Common stock, $0.01 par value; 400,000,000 shares authorized as of September 30, 2021 and December 31, 2020; 122,011,151 shares and 120,531,333 shares issued and outstanding as of September 30, 2021 and December 31, 2020, respectively	1,545	1,531
Additional paid-in capital	1,580,988	1,503,660
Accumulated other comprehensive loss	(521)	(245)
Accumulated deficit	(569,735)	(354,415)
Total stockholders' equity	1,012,277	1,150,531
Total liabilities and stockholders’ equity	$ 1,449,966	$ 1,604,280

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2021	Dec. 31, 2020
Statement of Financial Position [Abstract]
Convertible preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Convertible preferred stock, shares authorized (in shares)	40,000,000	40,000,000
Convertible preferred stock, shares issued (in shares)	0	0
Convertible preferred stock, shares outstanding (in shares)	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized (in shares)	400,000,000	400,000,000
Common stock, shares issued (in shares)	122,011,151	120,531,333
Common stock, shares outstanding (in shares)	122,011,151	120,531,333

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($)
$ in Thousands

3 Months Ended

9 Months Ended

Sep. 30, 2021

Sep. 30, 2020

Sep. 30, 2021

Sep. 30, 2020

Collaboration revenue:

Collaboration revenue from customers

$ 5,285

^[1]

$ 9,388

$ 36,143

^[1]

$ 18,751

Other collaboration revenue

Total collaboration revenue

5,285

9,393

36,147

18,844

Operating expenses:

Research and development

71,559

^[2]

53,704

197,477

^[2]

157,872

General and administrative

19,319

15,805

57,300

42,332

Total operating expenses

90,878

69,509

254,777

200,204

Loss from operations

(85,593)

(60,116)

(218,630)

(181,360)

Interest and other income, net

1,005

1,944

3,310

7,611

Loss before income taxes

(84,588)

(58,172)

(215,320)

(173,749)

Income tax expense

(56)

Net loss

(84,588)

(58,228)

(215,320)

(173,749)

Other comprehensive loss:

Net unrealized loss on marketable securities, net of tax

(153)

(540)

(276)

(339)

Comprehensive loss

$ (84,741)

$ (58,768)

$ (215,596)

$ (174,088)

Net loss per share, basic (usd per share)

$ (0.69)

$ (0.54)

$ (1.77)

$ (1.65)

Net loss per share, diluted (usd per share)

$ (0.69)

$ (0.54)

$ (1.77)

$ (1.65)

Weighted average number of shares outstanding, basic (in shares)

121,742,067

107,490,702

121,309,197

105,217,770

Weighted average number of shares outstanding, diluted (in shares)

121,742,067

107,490,702

121,309,197

105,217,770

[1]	Includes related party collaboration revenue from a customer of $0.9 million and $2.5 million for the three and nine months ended September 30, 2021, respectively.
[2]	Includes an offset to expense from related party cost reimbursement of $1.2 million and $5.3 million for the three and nine months ended September 30, 2021, respectively.

Condensed Consolidated Statements of Operations and Comprehensive Loss (Parenthetical) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2021
Income Statement [Abstract]
Collaboration revenue from customers, related party	$ 0.9	$ 2.5
Offset to research and development expense, related party cost reimbursement	$ 1.2	$ 5.3

- Definition

Amount of revenue, fees and commissions earned from transactions between (a) a parent company and its subsidiaries; (b) subsidiaries of a common parent; (c) an entity and trusts for the benefit of employees, for example, but not limited to, pension and profit-sharing trusts that are managed by or under the trusteeship of the entity's management; (d) an entity and its principal, owners, management, or members of their immediate families; and (e) affiliates.

+ References

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+ Details

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Beginning balance (in shares) at Dec. 31, 2019		96,189,935
Beginning balance at Dec. 31, 2019	$ 394,890	$ 1,288	$ 818,803	$ 350	$ (425,551)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock upon public offering, net of issuance costs of $632 (in shares)		9,000,000
Issuance of common stock upon public offering, net of issuance costs of $632	193,948	$ 90	193,858
Issuance of common stock in connection with the Biogen Stock Purchase Agreement (in shares)		13,310,243
Issuance of common stock in connection with the Biogen Stock Purchase Agreement	420,146	$ 133	420,013
Issuances under equity incentive plans (in shares)		1,001,905
Issuances under equity incentive plans	11,133	$ 10	11,123
Vesting of restricted stock units (in shares)		293,133
Vesting of restricted stock units	0	$ 3	(3)
Stock-based compensation	36,521		36,521
Net loss	(173,749)				(173,749)
Other comprehensive loss	(339)			(339)
Ending balance (in shares) at Sep. 30, 2020		119,795,216
Ending balance at Sep. 30, 2020	882,550	$ 1,524	1,480,315	11	(599,300)
Beginning balance (in shares) at Jun. 30, 2020		105,897,872
Beginning balance at Jun. 30, 2020	502,167	$ 1,385	1,041,303	551	(541,072)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock in connection with the Biogen Stock Purchase Agreement (in shares)		13,310,243
Issuance of common stock in connection with the Biogen Stock Purchase Agreement	420,146	$ 133	420,013
Issuances under equity incentive plans (in shares)		412,389
Issuances under equity incentive plans	5,753	$ 4	5,749
Vesting of restricted stock units (in shares)		174,712
Vesting of restricted stock units	0	$ 2	(2)
Stock-based compensation	13,252		13,252
Net loss	(58,228)				(58,228)
Other comprehensive loss	(540)			(540)
Ending balance (in shares) at Sep. 30, 2020		119,795,216
Ending balance at Sep. 30, 2020	$ 882,550	$ 1,524	1,480,315	11	(599,300)
Beginning balance (in shares) at Dec. 31, 2020	120,531,333	120,531,333
Beginning balance at Dec. 31, 2020	$ 1,150,531	$ 1,531	1,503,660	(245)	(354,415)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		880,560
Issuances under equity incentive plans	14,180	$ 8	14,172
Vesting of restricted stock units (in shares)		599,258
Vesting of restricted stock units	0	$ 6	(6)
Stock-based compensation	63,162		63,162
Net loss	(215,320)				(215,320)
Other comprehensive loss	$ (276)			(276)
Ending balance (in shares) at Sep. 30, 2021	122,011,151	122,011,151
Ending balance at Sep. 30, 2021	$ 1,012,277	$ 1,545	1,580,988	(521)	(569,735)
Beginning balance (in shares) at Jun. 30, 2021		121,531,952
Beginning balance at Jun. 30, 2021	1,072,705	$ 1,541	1,556,679	(368)	(485,147)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuances under equity incentive plans (in shares)		228,048
Issuances under equity incentive plans	3,315	$ 2	3,313
Vesting of restricted stock units (in shares)		251,151
Vesting of restricted stock units	0	$ 2	(2)
Stock-based compensation	20,998		20,998
Net loss	(84,588)				(84,588)
Other comprehensive loss	$ (153)			(153)
Ending balance (in shares) at Sep. 30, 2021	122,011,151	122,011,151
Ending balance at Sep. 30, 2021	$ 1,012,277	$ 1,545	$ 1,580,988	$ (521)	$ (569,735)

Condensed Consolidated Statements of Stockholders' Equity (Parenthetical) $ in Thousands	9 Months Ended
	Sep. 30, 2020 USD ($)
Common Stock
Common stock issuance costs	$ 632

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Operating activities
Net loss	$ (215,320)	$ (173,749)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	6,499	6,410
Stock–based compensation expense	63,162	36,521
Net amortization of premiums (discounts) on marketable securities	6,316	(1,074)
Non-cash adjustment to operating lease expense	(2,201)	(1,669)
Other non-cash items	0	18
Changes in operating assets and liabilities:
Prepaid expenses and other assets	8,049	3,819
Accounts payable	3,783	147
Accruals and other current liabilities	(3,036)	4,880
Contract liabilities	(10,601)	(17,920)
Related party contract liability	(2,546)	44,854
Net cash used in operating activities	(145,895)	(97,763)
Investing activities
Purchases of marketable securities	(1,191,491)	(687,523)
Purchases of property and equipment	(5,447)	(1,900)
Maturities and sales of marketable securities	1,216,062	433,557
Net cash provided by (used in) investing activities	19,124	(255,866)
Financing activities
Proceeds from issuance of common stock in connection with Collaboration Agreements	0	420,146
Proceeds from public offering of common stock, net of issuance costs	0	193,948
Proceeds from exercise of awards under equity incentive plans	14,180	11,133
Net cash provided by financing activities	14,180	625,227
Net increase (decrease) in cash, cash equivalents and restricted cash	(112,591)	271,598
Cash, cash equivalents and restricted cash at beginning of period	508,644	80,949
Cash, cash equivalents and restricted cash at end of period	396,053	352,547
Supplemental disclosures of cash flow information
Property and equipment purchases accrued but not yet paid	$ 29	$ 32

Significant Accounting Policies	9 Months Ended
Significant Accounting Policies	Sep. 30, 2021
Accounting Policies [Abstract]
Significant Accounting Policies	Significant Accounting Policies Organization and Description of Business Denali Therapeutics Inc. ("Denali" or the “Company”) is a biopharmaceutical company, incorporated in Delaware, that discovers and develops therapeutics to defeat neurodegenerative diseases. The Company is headquartered in South San Francisco, California. Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) for interim financial information and the instructions to Form 10-Q and Article 10 of SEC Regulation S-X for interim financial information. These unaudited condensed consolidated financial statements and notes should be read in conjunction with the audited consolidated financial statements and notes thereto contained in the Annual Report on Form 10-K for the year ended December 31, 2020, as filed with the Securities and Exchange Commission on February 26, 2021 (the "2020 Annual Report on Form 10-K"). The Condensed Consolidated Balance Sheet as of December 31, 2020 was derived from the audited annual consolidated financial statements as of and for the period then ended. Certain information and footnote disclosures typically included in the Company's annual consolidated financial statements have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements reflect all adjustments that, in the opinion of management, are necessary for a fair statement of the results of the interim periods presented. All such adjustments are of a normal recurring nature except for the impacts of adopting new accounting standards, if any, discussed below. These interim financial results are not necessarily indicative of results expected for the full fiscal year or for any subsequent interim period. During the nine months ended September 30, 2021, except as discussed below in the section titled "Recently Adopted Accounting Pronouncement," there were no material changes to the Company's significant accounting and financial reporting policies from those reflected in the 2020 Annual Report on Form 10-K. For further information with regard to the Company’s Significant Accounting Policies, please refer to Note 1, "Significant Accounting Policies," to the Company’s Consolidated Financial Statements included in the 2020 Annual Report on Form 10-K. Principles of Consolidation These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. For the Company and its subsidiaries, the functional currency has been determined to be U.S. dollars. Monetary assets and liabilities denominated in foreign currency are remeasured at period-end exchange rates. Non-monetary assets and liabilities denominated in foreign currencies are remeasured at historical rates. Foreign currency transaction gains and losses resulting from remeasurement are recognized in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires the Company to make certain estimates, judgments and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, as well as the reported amounts of expenses during the reporting period. Actual results could differ from those estimates, and such differences could be material to the Condensed Consolidated Balance Sheets and Statements of Operations and Comprehensive Loss. Reclassifications Certain amounts in prior period financial statements have been reclassified to conform to the current period presentation. Such reclassifications have not materially affected previously reported amounts. Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash, cash equivalents, marketable securities and forward foreign currency exchange contracts. Substantially all of the Company’s cash and cash equivalents are deposited in accounts with financial institutions that management believes are of high credit quality. Such deposits have and will continue to exceed federally insured limits. The Company maintains its cash with accredited financial institutions and accordingly, such funds are subject to minimal credit risk. The Company’s investment policy limits investments to certain types of securities issued by the U.S. government, its agencies and institutions with investment-grade credit ratings and places restrictions on maturities and concentration by type and issuer. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash, cash equivalents and marketable securities and issuers of marketable securities to the extent recorded on the Condensed Consolidated Balance Sheets. As of September 30, 2021 and December 31, 2020, the Company had no off balance sheet concentrations of credit risk. The Company is exposed to counterparty credit risk on all of its derivative financial instruments. The Company has established and maintains strict counterparty credit guidelines and enters into hedges only with financial institutions that are investment grade or better to minimize the Company’s exposure to potential defaults. The Company does not require collateral to be pledged under these agreements. The Company is subject to a number of risks similar to other early-stage biopharmaceutical companies, including, but not limited to, the need to obtain adequate additional funding, possible failure of current or future preclinical testing or clinical trials, its reliance on third parties to conduct its clinical trials, the need to obtain regulatory and marketing approvals for its product candidates, competitors developing new technological innovations, the need to successfully commercialize and gain market acceptance of the Company’s product candidates, its right to develop and commercialize its product candidates pursuant to the terms and conditions of the licenses granted to the Company, protection of proprietary technology, the ability to make milestone, royalty or other payments due under any license or collaboration agreements, and the need to secure and maintain adequate manufacturing arrangements with third parties. If the Company does not successfully commercialize or partner any of its product candidates, it will be unable to generate product revenue or achieve profitability. The COVID-19 pandemic has caused increased risk and uncertainty for the Company. Credit risk associated with investments in securities may increase if any institution with which the Company has an investment is significantly impacted by the COVID-19 pandemic. As of September 30, 2021, the Company has not realized any losses on its cash deposits or investments. COVID-19 may impact the timelines and progress of the Company's preclinical activities and clinical trials, and may impact its ability to raise capital in the near term. Segments The Company has one operating segment. The Company’s chief operating decision maker, its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of allocating resources. Cash, Cash Equivalents and Restricted Cash The Company considers all highly liquid investments with original maturities of 90 days or less at the date of purchase to be cash and cash equivalents. Cash equivalents are reported at fair value. Cash, cash equivalents, and restricted cash reported within the Condensed Consolidated Statements of Cash Flows is composed of Cash and Cash equivalents reported in the Condensed Consolidated Balance Sheets and $1.5 million of restricted cash for the letter of credit for the Company’s headquarters building lease, which is included within other non-current assets in the Condensed Consolidated Balance Sheets. Marketable Securities The Company generally invests its excess cash in money market funds and investment grade short to intermediate-term fixed income securities. Such investments are included in cash and cash equivalents, short-term marketable securities, or long-term marketable securities on the Condensed Consolidated Balance Sheets, are considered available-for-sale, and reported at fair value with net unrealized gains and losses included as a component of stockholders’ equity. The Company classifies investments in securities with remaining maturities of less than one year, or where its intent is to use the investments to fund current operations or to make them available for current operations, as short-term investments. The Company classifies investments in securities with remaining maturities of over one year as long-term investments. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Realized gains and losses and declines in value determined to be due to credit losses on marketable securities, if any, are included in interest and other income, net. The Company periodically evaluates the need for an allowance for credit losses. This evaluation includes consideration of several qualitative and quantitative factors, including whether it has plans to sell the security, whether it is more likely than not it will be required to sell any marketable securities before recovery of its amortized cost basis, and if the entity has the ability and intent to hold the security to maturity, and the portion of any unrealized loss that is the result of a credit loss. Factors considered in making these evaluations include quoted market prices, recent financial results and operating trends, implied values from any recent transactions or offers of investee securities, credit quality of debt instrument issuers, expected cash flows from securities, other publicly available information that may affect the value of the marketable security, duration and severity of the decline in value, and the Company's strategy and intentions for holding the marketable security. Accounts Receivable Accounts receivable are included within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheets. The accounts receivable balance represents amounts receivable from the Company's collaboration partners, excluding related parties, net of an allowance for credit losses, if required. Derivatives and Hedging Activities The Company measures its derivative instruments at fair value, and accounts for them as either assets or liabilities included within Prepaid expenses and other current assets and Other accruals and other current liabilities, respectively, on the Condensed Consolidated Balance Sheets. Derivatives are adjusted to fair value through interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Leases The Company leases real estate, and certain equipment for use in its operations. A determination is made as to whether an arrangement is a lease at inception. A right-of-use (“ROU”) asset and operating lease liability is recognized for identified operating leases in the Condensed Consolidated Balance Sheets. The changes in operating lease ROU assets and operating lease liabilities are presented net within non-cash adjustment to operating lease expense in the Condensed Consolidated Statements of Cash Flows. ROU assets represent the Company’s right to use the underlying asset for the lease term and lease liabilities represent the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments due over the lease term, with the ROU assets adjusted for lease incentives received. When determining the present value of lease payments, the Company uses its incremental borrowing rate on the date of lease commencement, or the rate implicit in the lease, if known. The Company does not assume renewals in its determination of the lease term unless the renewals are deemed by management to be reasonably certain at lease inception. Leases with an initial term of 12 months or less are not recorded on the balance sheet, unless they include an option to purchase the underlying asset that the Company is reasonably certain to exercise. The Company recognizes lease expenses on a straight-line basis over the lease term. The Company has leases with lease and non-lease components, which the Company has elected to account for as a single lease component. Revenue Recognition License and Collaboration Revenue The Company analyzes its collaboration arrangements to assess whether they are within the scope of ASC 808, Collaborative Arrangements (“ASC 808”) to determine whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. For collaboration arrangements within the scope of ASC 808 that contain multiple elements, the Company first determines which elements of the collaboration are deemed to be within the scope of ASC 808 and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of Topic 606. For elements of collaboration arrangements that are accounted for pursuant to ASC 808, an appropriate recognition method is determined and applied consistently, generally by analogy to Topic 606. The accounting treatment pursuant to Topic 606 is outlined below. The terms of licensing and collaboration agreements entered into typically include payment of one or more of the following: non-refundable, up-front license fees; development, regulatory and commercial milestone payments; payments for manufacturing supply and research and development services and royalties on net sales of licensed products. Each of these payments results in license, collaboration and other revenue, except for revenues from royalties on net sales of licensed products, which are classified as royalty revenue. The core principle of Topic 606 is to recognize revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received in exchange for those goods or services. The Company may also receive reimbursement or make payments to a collaboration partner to satisfy cost sharing requirements. These payments are accounted for pursuant to ASC 808 and are recorded as an offset or increase to research and development expenses, respectively. In determining the appropriate amount of revenue to be recognized as the Company fulfills its obligations under each of its agreements, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. Amounts received prior to satisfying the revenue recognition criteria are recorded as contract liabilities in the Company’s Condensed Consolidated Balance Sheets. If the related performance obligation is expected to be satisfied within the next twelve months this will be classified in current liabilities. Amounts recognized as revenue prior to the Company having an unconditional right (other than a right that is conditioned only on the passage of time) to receipt are recorded as contract assets in the Company's Condensed Consolidated Balance Sheets. If the Company expects to have an unconditional right to receive the consideration in the next twelve months, this will be classified in current assets. A net contract asset or liability is presented for each contract with a customer. At contract inception, the Company assesses the goods or services promised in a contract with a customer and identifies those distinct goods and services that represent a performance obligation. A promised good or service may not be identified as a performance obligation if it is immaterial in the context of the contract with the customer, if it is not separately identifiable from other promises in the contract (either because it is not capable of being separated or because it is not separable in the context of the contract), or if the promised good or service does not provide the customer with a material right. The Company considers the terms of the contract to determine the transaction price. The transaction price is the amount of consideration to which the Company expects to be entitled in exchange for transferring promised goods or services to a customer. The consideration promised in a contract with a customer may include fixed amounts, variable amounts, or both. Variable consideration will only be included in the transaction price when it is not considered constrained, which is when it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur. If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling prices ("SSP"). The relative SSP for each deliverable is estimated using external sourced evidence if it is available. If external sourced evidence is not available, the Company uses its best estimate of the SSP for the deliverable. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring a promised good or service to a customer. An asset is transferred when, or as, the customer obtains control of that asset, which for a service is considered to be as the services are received and used. The Company recognizes revenue over time by measuring the progress toward complete satisfaction of the relevant performance obligation using an appropriate input or output method based on the nature of the service promised to the customer. After contract inception, the transaction price is reassessed at every period end and updated for changes such as resolution of uncertain events. Any change in the transaction price is allocated to the performance obligations on the same basis as at contract inception, or to a single performance obligation as applicable. Management may be required to exercise considerable judgment in estimating revenue to be recognized. Judgment is required in identifying performance obligations, estimating the transaction price, estimating the SSP of identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations. Comprehensive Loss Comprehensive loss is composed of net loss and certain changes in stockholders’ equity that are excluded from net loss, primarily unrealized gains or losses on the Company’s marketable securities. Net Loss per Share Basic net loss per share is calculated by dividing the net loss 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 is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive given the net loss for each period presented. Recently Adopted Accounting Pronouncement In December 2019, the Financial Accounting Standards Board ("FASB") issued ASU No. 2019-12, Income Taxes (Topic 740) Simplifying the Accounting for Income Taxes. ASU No. 2019-12 modifies ASC 740 to simplify several aspects of accounting for income taxes, including eliminating certain exceptions to the guidance in ASC 740 related to the approach for intraperiod tax allocation. The guidance is effective for fiscal years beginning after December 15, 2020 and interim periods within those fiscal years, with early adoption permitted, and is required to be adopted prospectively, with the exception of certain specific amendments, which were not applicable to the Company. The Company adopted this standard as of January 1, 2021 using a prospective approach. Adoption of the standard did not have a material impact on its Condensed Consolidated Financial Statements.

Fair Value Measurements

9 Months Ended

Sep. 30, 2021

Fair Value Disclosures [Abstract]

Fair Value Measurements

Assets and liabilities measured at fair value at each balance sheet date are as follows (in thousands):


	September 30, 2021
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	350,803	$	—	$	—	$	350,803
U.S. government treasuries	24,998		—		—		24,998

Short-term marketable securities:
U.S. government treasuries	472,214		—		—		472,214
U.S. government agency securities	—		15,003		—		15,003
Corporate debt securities	—		61,182		—		61,182
Commercial paper	—		96,223		—		96,223
Long-term marketable securities:
U.S. government treasuries	299,069		—		—		299,069

Corporate debt securities	—		20,403		—		20,403

Total	$	1,147,084	$	192,811	$	—	$	1,339,895
Liabilities:
Foreign currency derivative contracts	$	—	$	201	$	—	$	201
Total	$	—	$	201	$	—	$	201


	December 31, 2020
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	335,284	$	—	$	—	$	335,284
U.S. government treasuries	149,997		—		—		149,997
Short-term marketable securities:
U.S. government treasuries	878,938		—		—		878,938
U.S. government agency securities	—		25,217		—		25,217
Corporate debt securities	—		27,180		—		27,180
Commercial paper	—		31,218		—		31,218
Long-term marketable securities:
U.S. government treasuries	2,561		—		—		2,561
Corporate debt securities	—		30,138		—		30,138
Foreign currency derivative contracts	—		185		—		185
Total	$	1,366,780	$	113,938	$	—	$	1,480,718
Liabilities:
Foreign currency derivative contracts	$	—	$	11	$	—	$	11
Total	$	—	$	11	$	—	$	11

The carrying amounts of cost sharing reimbursements due from related party, prepaid expenses and other current assets, accounts payable and accrued liabilities approximate their fair values due to their short-term maturities.

The Company’s Level 2 securities are valued using third-party pricing sources. The pricing services utilize industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly.

The company has not transferred any assets or liabilities between the fair value measurement levels.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Marketable Securities

9 Months Ended

Sep. 30, 2021

Investments, Debt and Equity Securities [Abstract]

Marketable Securities

All marketable securities were considered available-for-sale at September 30, 2021 and December 31, 2020. On a recurring basis, the Company records its marketable securities at fair value using Level 1 or Level 2 inputs as discussed in Note 2, "Fair Value Measurements". The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands):


	September 30, 2021
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	472,214	$	13	$	(13)	$	472,214
U.S. government agency securities	15,003		—		—		15,003
Corporate debt securities(2)	61,187		5		(10)		61,182
Commercial paper	96,223		—		—		96,223
Total short-term marketable securities	644,627		18		(23)		644,622
Long-term marketable securities:
U.S. government treasuries(3)	299,225		17		(173)		299,069

Corporate debt securities(4)	20,413		2		(12)		20,403
Total long-term marketable securities	319,638		19		(185)		319,472
Total	$	964,265	$	37	$	(208)	$	964,094

__________________________________________________

(1)Unrealized holding losses on 7 securities with an aggregate fair value of $271.8 million.

(2)Unrealized holding losses on 8 securities with an aggregate fair value of $27.8 million.

(3)Unrealized holding losses on 11 securities with an aggregate fair value of $251.5 million.

(4)Unrealized holding losses on 5 securities with an aggregate fair value of $16.8 million.


	December 31, 2020
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	878,906	$	44	$	(12)	$	878,938
U.S. government agency securities(2)	25,214		5		(2)		25,217
Corporate debt securities	27,101		79		—		27,180
Commercial paper	31,218		—		—		31,218
Total short-term marketable securities	962,439		128		(14)		962,553
Long-term marketable securities:
U.S. government treasuries	2,561		—		—		2,561

Corporate debt securities(3)	30,147		2		(11)		30,138
Total long-term marketable securities	32,708		2		(11)		32,699
Total	$	995,147	$	130	$	(25)	$	995,252

__________________________________________________

(1)Unrealized holding losses on 19 securities with an aggregate fair value of $369.9 million.

(2)Unrealized holding losses on 2 securities with an aggregate fair value of $10.1 million.

(3)Unrealized holding losses on 1 security with an aggregate fair value of $20.1 million.

As of September 30, 2021 and December 31, 2020, some of the Company's marketable securities were in an unrealized loss position. The Company has not recognized an allowance for credit losses as of September 30, 2021 or December 31, 2020. The Company determined that it had the ability and intent to hold all marketable securities that have been in a continuous loss position until maturity or recovery. Further, these marketable securities were initially, and continue to be, held with investment grade, high credit quality institutions. All marketable securities with unrealized losses as of each balance sheet date have been in a loss position for less than twelve months or the loss is not material.

All of the Company’s marketable securities have an effective maturity of less than two years.

Derivative Financial Instruments

9 Months Ended

Sep. 30, 2021

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Derivative Financial Instruments

Foreign Currency Exchange Rate Exposure

The Company uses forward foreign currency exchange contracts to hedge certain operational exposures resulting from potential changes in foreign currency exchange rates. Such exposures result from portions of the Company’s forecasted cash flows being denominated in currencies other than the U.S. dollar, primarily the Euro and British Pound. The derivative instruments the Company uses to hedge this exposure are not designated as cash flow hedges, and as a result, changes in their fair value are recorded in interest and other income, net, on the Company's Condensed Consolidated Statements of Operations and Comprehensive Loss.

The fair values of forward foreign currency exchange contracts are estimated using current exchange rates and interest rates and take into consideration the current creditworthiness of the counterparties. Information regarding the specific instruments used by the Company to hedge its exposure to foreign currency exchange rate fluctuations is provided below.

The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of September 30, 2021 and December 31, 2020, respectively (notional amounts in thousands):


Foreign Exchange Contracts	Number of Contracts	Aggregate Notional(1) Amount in Foreign Currency	Maturity
Euros	12	1,700	Oct 2021 - Jun 2022
British Pounds	11	1,725	Oct 2021 - Jun 2022
Total at September 30, 2021	23
Euros	26	3,855	Jan 2021 - Nov 2021
British Pounds	21	2,658	Jan 2021 - Nov 2021
Total at December 31, 2020	47

_________________________________________________

(1) The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts.

Collaboration Agreements

9 Months Ended

Sep. 30, 2021

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaboration Agreements

Biogen

On August 5, 2020, the Company entered into a binding Provisional Collaboration and License Agreement (“Provisional Biogen Collaboration Agreement”) with Biogen Inc.’s subsidiaries, Biogen MA Inc. (“BIMA”) and Biogen International GmbH (“BIG”) (BIMA and BIG, collectively, “Biogen”), which expired in October 2020 upon the execution of a Definitive LRRK2 Collaboration and License Agreement (“LRRK2 Agreement”) with Biogen on October 4, 2020 and a Right of First Negotiation, Option and License Agreement (the “ROFN and Option Agreement”) on October 6, 2020 (collectively, the "Biogen Collaboration Agreement"). The details of the Provisional Biogen Collaboration Agreement and the Biogen Collaboration Agreement and the payments the Company has received, and is entitled to receive, are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K. During the third quarter of 2021, there were no changes to the terms of the Company’s collaboration agreement with Biogen, and no change in the transaction price for the Biogen Collaboration Agreement has been recorded during the three and nine months ended September 30, 2021.

A related party contract liability of $294.9 million was recorded on the Consolidated Balance Sheet as of September 30, 2021. Approximately $288.9 million of this contract liability relates to the revenue allocated to the material right for an option under the ROFN and Option Agreement which is being deferred until resolution of the option, which is expected to be at least a year from the balance sheet date, and $6.0 million of this contract liability relates to the portion of the Option Research Services performance obligation yet to be satisfied, with such amount to be recognized over the estimated period of the services, which is expected to be several years. The Company recorded $1.2 million and $5.3 million of cost sharing reimbursements for LRRK2 Development Activities as an offset to research and development expenses in the Condensed Consolidated Statement of Operations and Comprehensive Loss for the three and nine months ended September 30, 2021, respectively. The Company recorded cost sharing reimbursements due from related party on the Condensed Consolidated Balance Sheet as of September 30, 2021 and December 31, 2020 of $1.2 million and $5.7 million, respectively.

As of September 30, 2021, the Company had not achieved any milestones or recorded any product sales under the Biogen Collaboration Agreement.

Sanofi

In October 2018, the Company entered into a Collaboration and License Agreement ("Sanofi Collaboration Agreement") with Genzyme Corporation, a wholly owned subsidiary of Sanofi S.A. ("Sanofi"). The details of the Sanofi Collaboration Agreement and the payments the Company has received, and is entitled to receive, are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K. During the third quarter of 2021, there were no changes to the terms of the Company’s collaboration agreement with Sanofi.

The transaction price of the Sanofi Collaboration Agreement did not change in the three months ended September 30, 2021, and increased by $15.0 million in the nine months ended September 30, 2021. This increase related to the $15.0 million milestone triggered in June 2021 upon first patient in a Phase 2 study of DNL758 (SAR443122) in patients with cutaneous lupus erythematosus. The transaction price increased by $0.1 million and $0.9 million for the three and nine months ended September 30, 2020, respectively, related to costs incurred for Retained Activities that were no longer constrained.

A contract liability of $3.4 million was recorded on the Condensed Consolidated Balance Sheets as of both September 30, 2021 and December 31, 2020. This contract liability relates to the portion of the Alzheimer's Disease Services performance obligation yet to be satisfied, with such amounts to be recognized over the estimated period of the services, which is expected to be several years. The Company recorded no receivable and a receivable of $44,303 associated with the Sanofi Collaboration Agreement on the Condensed Consolidated Balance Sheets as of September 30, 2021 and December 31, 2020, respectively.

Through September 30, 2021, the Company has earned milestone payments of $25.0 million, and the Company has not recorded any product sales under the Sanofi Collaboration Agreement.

Takeda

In January 2018, the Company entered into a Collaboration and Option Agreement ("Takeda Collaboration Agreement") with Takeda Pharmaceutical Company Limited ("Takeda"). The details of the Takeda Collaboration Agreement and the payments the Company has received, and is entitled to receive, are further described in Note 6, Collaboration Agreements, to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K. During the third quarter of 2021, there were no changes to the terms of the Company’s collaboration agreement with Takeda, and no change in the transaction price for the Takeda Collaboration Agreement has been recorded during the three and nine months ended September 30, 2021.

Revenue is recognized under the Takeda Collaboration Agreement when, or as, the Company satisfies its performance obligations by transferring the promised services to Takeda. Revenue is being recognized over time using the input method, based on costs incurred to perform the research services, since the level of costs incurred over time is thought to best reflect the transfer of services to Takeda. There were no material changes in estimates during the three and nine months ended September 30, 2021 or September 30, 2020.

A contract liability of $29.2 million and $39.8 million was recorded on the Condensed Consolidated Balance Sheets as of September 30, 2021 and December 31, 2020, respectively. This contract liability relates to the three performance obligations identified, with such amounts to be recognized over the estimated period of the pre-IND research services, which is expected to be up to several years. There was no receivable as of September 30, 2021 and a receivable of $8.0 million for a preclinical milestone as of December 31, 2020.

Through September 30, 2021, the Company has earned $31.0 million in preclinical milestone payments from Takeda, and has not recorded any product sales under the Takeda Collaboration Agreement.

Collaboration Revenue

Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2021		2020		2021		2020
Takeda Collaboration Agreement(1)	$	4,425	$	9,271	$	18,597	$	17,826
Sanofi Collaboration Agreement

Peripheral Program License	—		—		15,000		—
Retained Activities	—		117		—		925
Alzheimer's Disease Services(2)	—		5		4		93
Total Sanofi Collaboration Revenue	—		122		15,004		1,018
Biogen Collaboration Agreement



Option Research Services(2)	860		—		2,546		—
Total Biogen Collaboration Revenue	$	860	$	—	$	2,546	$	—
Total Collaboration Revenue	$	5,285	$	9,393	$	36,147	$	18,844

_________________________________________________

(1)$15.6 million of revenue for the nine months ended September 30, 2021 was included in the contract liability balance at the beginning of the period. All revenue for the three months ended September 30, 2021 and the three and nine months ended September 30, 2020 was included in the contract liability balance at the beginning of the period.

(2)Revenue for the three and nine months ended September 30, 2021 and September 30, 2020, where applicable, represent amounts that were included in the contract liability balance at the beginning of the respective period.

License Agreements	9 Months Ended
License Agreements	Sep. 30, 2021
Organization, Consolidation and Presentation of Financial Statements [Abstract]
License Agreements	License Agreements Genentech In June 2016, the Company entered into an Exclusive License Agreement with Genentech, Inc. (“Genentech”). The details of the Genentech License Agreement are further described in Note 7, License Agreements, to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K. No expenses were recorded associated with the Genentech License Agreement in the three and nine months ended September 30, 2021 or 2020.

Commitments and Contingencies

9 Months Ended

Sep. 30, 2021

Commitments and Contingencies Disclosure [Abstract]

Commitments and Contingencies

Lease Obligations

In May 2018, the Company entered into an operating lease for its corporate headquarters in South San Francisco (the "Headquarters Lease"). The details of the Headquarters Lease are further described in Note 9, Commitments and Contingencies, to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K. During the third quarter of 2021, there were no changes to the terms of the Headquarters Lease.

In August 2021, the Company entered into an operating lease for approximately 50,000 square feet of laboratory, office and warehouse premises in Salt Lake City, Utah (“SLC Lease”), with a contractual term of approximately 8.4 years which will commence upon completion of certain improvements by the landlord and the Company, and future undiscounted lease payments totaling approximately $12.5 million. For accounting purposes, the lease has not yet commenced as the landlord has not yet made the underlying asset available for use by Denali, and as such, no lease liability or ROU asset is recorded on the condensed consolidated balance sheet as of September 30, 2021, and no operating lease expense has been recorded for the three and nine months ended September 30, 2021.

Management exercised judgment in applying the requirements of ASC 842, including the determination as to whether certain contracts contain a lease and for the headquarters lease, the discount rate used to determine the measurement of the lease liability. The discount rate of our headquarters lease is an approximation of the Company's incremental borrowing rate and is dependent upon the term and economics of the agreement. To estimate the incremental borrowing rate, management considered observable debt yields of comparable market instruments, as well as benchmarks within the headquarters lease agreement that may be indicative of the rate implicit in the lease.

The following table contains a summary of the lease costs recognized under ASC 842 and other information pertaining to the Company’s operating leases for the periods presented (in thousands):


	Three Months Ended September 30,					Nine Months Ended September 30,
	2021		2020			2021		2020
Operating lease cost (1)	$	2,863	$	2,833		$	8,429	$	8,341
Cash paid for amounts included in measurement of lease liability	$	2,618	$	2,536		$	7,717	$	7,202

	As of September 30,
	2021					2020
Weighted average remaining lease term	7.6 years					8.6 years
Weighted average discount rate	9				%	9				%

__________________________________________________

(1)Including variable and short-term lease costs

The following table reconciles the undiscounted cash flows for the next five years and total of the remaining years to the operating lease liability recorded in the Condensed Consolidated Balance Sheet as of September 30, 2021 (in thousands):


Year Ended December 31:
2021 (three months)	$	2,618
2022	10,702
2023	11,053
2024	11,417
2025	11,793
Thereafter	42,148
Total undiscounted lease payments	89,731
Present value adjustment	(24,489)
Net operating lease liabilities	$	65,242

Sublease

In October 2018, the Company entered into a sublease agreement ("Sublease Agreement") for space in the corporate headquarters. The details of the Sublease Agreement are further described in Note 9, Commitments and Contingencies, to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K. During the third quarter of 2021, there were no changes to the terms of the Sublease Agreement. Total sublease income, including rent and variable sublease cost reimbursements, was $1.0 million and $0.9 million for the three months ended September 30, 2021 and 2020, respectively, and $2.9 million and $2.8 million for the nine months ended September 30, 2021 and 2020, respectively.

The following table details the future undiscounted cash inflows relating to the Sublease Agreement as of September 30, 2021 (in thousands):


Year Ended December 31:
2021 (three months)	$	737
2022	3,009
2023	3,096
2024	876

Total undiscounted sublease receipts	$	7,718

Indemnification

In the ordinary course of business, the Company may provide indemnifications of varying scope and terms to vendors, lessors, business partners, board members, officers, and other parties with respect to certain matters, including, but not limited to, losses arising out of breach of such agreements, services to be provided by the Company, negligence or willful misconduct of the Company, violations of law by the Company, or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with directors and certain officers and employees that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors, officers or employees. No demands have been made upon the Company to provide indemnification under such agreements, and thus, there are no claims that the Company is aware of that could have a material effect on the Company’s Condensed Consolidated Balance Sheets, Condensed Consolidated Statements of Operations and Comprehensive Loss, or Condensed Consolidated Statements of Cash Flows.

Commitments

Effective September 2017, the Company entered into a Development and Manufacturing Services Agreement as amended (“DMSA”) with Lonza Sales AG (“Lonza”) for the development and manufacture of biologic products. Under the DMSA, the Company will execute purchase orders based on project plans authorizing Lonza to provide development and manufacturing services with respect to certain of the Company's antibody and enzyme products, and will pay for the services provided and batches delivered in accordance with the DMSA and project plan. Unless earlier terminated, the DMSA will expire on September 6, 2022.

As of September 30, 2021 and December 31, 2020, the Company had open purchase orders for biological product development and manufacturing costs totaling $42.0 million and $33.0 million, respectively. The activities under these purchase orders are expected to be completed by July 2027. As of September 30, 2021 and December 31, 2020, the Company had total non-cancellable purchase commitments under the DMSA of $27.6 million and $27.1 million, respectively, under the DMSA.

During the three months ended September 30, 2021 and 2020, the Company incurred costs of $5.8 million and $1.4 million, respectively, and made payments of $4.0 million and $0.8 million, respectively, for the development and manufacturing services rendered under the DMSA. During the nine months ended September 30, 2021 and 2020, the Company incurred costs of $14.2 million and $6.2 million, respectively, and made payments of $10.4 million and $6.0 million, respectively, for the development and manufacturing services rendered under the DMSA.

Contingencies

From time to time, the Company may be involved in lawsuits, arbitration, claims, investigations and proceedings consisting of intellectual property, employment and other matters which arise in the ordinary course of business. The Company records accruals for loss contingencies to the extent that the Company concludes that it is probable that a liability has been incurred and the amount of the related loss can be reasonably estimated.

Stock-Based Awards

9 Months Ended

Sep. 30, 2021

Share-based Payment Arrangement [Abstract]

Stock-Based Awards

The Company has issued stock-based awards from various equity incentive and stock purchase plans, as more fully described in Note 10, "Stock-Based Awards" to the consolidated financial statements in the Company's 2020 Annual Report on Form 10-K.

Stock Option Activity

The following table summarizes stock option activity for the nine months ended September 30, 2021:


	Number of Options	Weighted-Average Exercise Price
Balance at December 31, 2020	12,959,926	$	16.31
Granted	1,944,717	73.31
Exercised	(831,207)	14.27
Forfeited	(259,060)	34.89
Balance at September 30, 2021	13,814,376	$	24.11
Vested and expected to vest at September 30, 2021	12,078,689	$	27.48
Exercisable at September 30, 2021	7,856,046	$	15.22

The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions:


	Nine Months Ended September 30,
	2021	2020
Expected term (in years)	5.50 - 6.08	5.50 - 6.08
Volatility	62.2% - 63.7%	65.2% - 67.1%
Risk-free interest rate	0.5% - 1.2%	0.3% - 1.7%
Dividend yield	—	—

Restricted Stock Activity

The following table summarizes restricted stock unit ("RSU") activity for the nine months ended September 30, 2021:


	Number of RSU shares	Weighted-Average Fair Value at Date of Grant per Share
Unvested at December 31, 2020	2,301,679	$	27.08
Granted	1,046,259	69.50
Vested and released	(599,258)	25.63
Forfeited	(126,827)	60.92
Unvested at September 30, 2021	2,621,853	$	43.83
Expected to vest at September 30, 2021	2,621,853	$	43.83

Stock-Based Compensation Expense

The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2021		2020		2021		2020
Research and development	$	12,174	$	7,781	$	36,997	$	20,981
General and administrative	8,824		5,471		26,165		15,540
Total	$	20,998	$	13,252	$	63,162	$	36,521

Net Loss Per Share

9 Months Ended

Sep. 30, 2021

Earnings Per Share [Abstract]

Net Loss Per Share

Since the Company was in a loss position for all periods presented, basic net loss per share is the same as diluted net loss per share for all periods as the inclusion of all potential shares of common stock outstanding would have been anti-dilutive.

Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:


	Three and Nine Months Ended September 30,
	2021	2020
Options issued and outstanding and ESPP shares issuable	13,877,115	13,680,889
Restricted shares subject to future vesting	2,621,853	2,269,897

Total	16,498,968	15,950,786

Significant Accounting Policies (Policies)	9 Months Ended
Significant Accounting Policies (Policies)	Sep. 30, 2021
Accounting Policies [Abstract]
Organization and Description of Business	Organization and Description of Business Denali Therapeutics Inc. ("Denali" or the “Company”) is a biopharmaceutical company, incorporated in Delaware, that discovers and develops therapeutics to defeat neurodegenerative diseases. The Company is headquartered in South San Francisco, California.
Basis of Presentation	Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) for interim financial information and the instructions to Form 10-Q and Article 10 of SEC Regulation S-X for interim financial information. These unaudited condensed consolidated financial statements and notes should be read in conjunction with the audited consolidated financial statements and notes thereto contained in the Annual Report on Form 10-K for the year ended December 31, 2020, as filed with the Securities and Exchange Commission on February 26, 2021 (the "2020 Annual Report on Form 10-K"). The Condensed Consolidated Balance Sheet as of December 31, 2020 was derived from the audited annual consolidated financial statements as of and for the period then ended. Certain information and footnote disclosures typically included in the Company's annual consolidated financial statements have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements reflect all adjustments that, in the opinion of management, are necessary for a fair statement of the results of the interim periods presented. All such adjustments are of a normal recurring nature except for the impacts of adopting new accounting standards, if any, discussed below. These interim financial results are not necessarily indicative of results expected for the full fiscal year or for any subsequent interim period.
Principles of Consolidation	Principles of Consolidation These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. For the Company and its subsidiaries, the functional currency has been determined to be U.S. dollars. Monetary assets and liabilities denominated in foreign currency are remeasured at period-end exchange rates. Non-monetary assets and liabilities denominated in foreign currencies are remeasured at historical rates. Foreign currency transaction gains and losses resulting from remeasurement are recognized in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires the Company to make certain estimates, judgments and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, as well as the reported amounts of expenses during the reporting period. Actual results could differ from those estimates, and such differences could be material to the Condensed Consolidated Balance Sheets and Statements of Operations and Comprehensive Loss.
Reclassifications	Reclassifications Certain amounts in prior period financial statements have been reclassified to conform to the current period presentation. Such reclassifications have not materially affected previously reported amounts.
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 significant concentrations of credit risk consist primarily of cash, cash equivalents, marketable securities and forward foreign currency exchange contracts. Substantially all of the Company’s cash and cash equivalents are deposited in accounts with financial institutions that management believes are of high credit quality. Such deposits have and will continue to exceed federally insured limits. The Company maintains its cash with accredited financial institutions and accordingly, such funds are subject to minimal credit risk. The Company’s investment policy limits investments to certain types of securities issued by the U.S. government, its agencies and institutions with investment-grade credit ratings and places restrictions on maturities and concentration by type and issuer. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash, cash equivalents and marketable securities and issuers of marketable securities to the extent recorded on the Condensed Consolidated Balance Sheets. As of September 30, 2021 and December 31, 2020, the Company had no off balance sheet concentrations of credit risk. The Company is exposed to counterparty credit risk on all of its derivative financial instruments. The Company has established and maintains strict counterparty credit guidelines and enters into hedges only with financial institutions that are investment grade or better to minimize the Company’s exposure to potential defaults. The Company does not require collateral to be pledged under these agreements. The Company is subject to a number of risks similar to other early-stage biopharmaceutical companies, including, but not limited to, the need to obtain adequate additional funding, possible failure of current or future preclinical testing or clinical trials, its reliance on third parties to conduct its clinical trials, the need to obtain regulatory and marketing approvals for its product candidates, competitors developing new technological innovations, the need to successfully commercialize and gain market acceptance of the Company’s product candidates, its right to develop and commercialize its product candidates pursuant to the terms and conditions of the licenses granted to the Company, protection of proprietary technology, the ability to make milestone, royalty or other payments due under any license or collaboration agreements, and the need to secure and maintain adequate manufacturing arrangements with third parties. If the Company does not successfully commercialize or partner any of its product candidates, it will be unable to generate product revenue or achieve profitability. The COVID-19 pandemic has caused increased risk and uncertainty for the Company. Credit risk associated with investments in securities may increase if any institution with which the Company has an investment is significantly impacted by the COVID-19 pandemic.
Segments	Segments The Company has one operating segment. The Company’s chief operating decision maker, its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of allocating resources.
Cash, Cash Equivalents and Restricted Cash	Cash, Cash Equivalents and Restricted Cash The Company considers all highly liquid investments with original maturities of 90 days or less at the date of purchase to be cash and cash equivalents. Cash equivalents are reported at fair value. Cash, cash equivalents, and restricted cash reported within the Condensed Consolidated Statements of Cash Flows is composed of Cash and Cash equivalents reported in the Condensed Consolidated Balance Sheets and $1.5 million of restricted cash for the letter of credit for the Company’s headquarters building lease, which is included within other non-current assets in the Condensed Consolidated Balance Sheets.
Marketable Securities	Marketable Securities The Company generally invests its excess cash in money market funds and investment grade short to intermediate-term fixed income securities. Such investments are included in cash and cash equivalents, short-term marketable securities, or long-term marketable securities on the Condensed Consolidated Balance Sheets, are considered available-for-sale, and reported at fair value with net unrealized gains and losses included as a component of stockholders’ equity. The Company classifies investments in securities with remaining maturities of less than one year, or where its intent is to use the investments to fund current operations or to make them available for current operations, as short-term investments. The Company classifies investments in securities with remaining maturities of over one year as long-term investments. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Realized gains and losses and declines in value determined to be due to credit losses on marketable securities, if any, are included in interest and other income, net. The Company periodically evaluates the need for an allowance for credit losses. This evaluation includes consideration of several qualitative and quantitative factors, including whether it has plans to sell the security, whether it is more likely than not it will be required to sell any marketable securities before recovery of its amortized cost basis, and if the entity has the ability and intent to hold the security to maturity, and the portion of any unrealized loss that is the result of a credit loss. Factors considered in making these evaluations include quoted market prices, recent financial results and operating trends, implied values from any recent transactions or offers of investee securities, credit quality of debt instrument issuers, expected cash flows from securities, other publicly available information that may affect the value of the marketable security, duration and severity of the decline in value, and the Company's strategy and intentions for holding the marketable security.
Accounts Receivable	Accounts Receivable Accounts receivable are included within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheets. The accounts receivable balance represents amounts receivable from the Company's collaboration partners, excluding related parties, net of an allowance for credit losses, if required.
Derivatives and Hedging Activities	Derivatives and Hedging ActivitiesThe Company measures its derivative instruments at fair value, and accounts for them as either assets or liabilities included within Prepaid expenses and other current assets and Other accruals and other current liabilities, respectively, on the Condensed Consolidated Balance Sheets. Derivatives are adjusted to fair value through interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss.
Leases	Leases The Company leases real estate, and certain equipment for use in its operations. A determination is made as to whether an arrangement is a lease at inception. A right-of-use (“ROU”) asset and operating lease liability is recognized for identified operating leases in the Condensed Consolidated Balance Sheets. The changes in operating lease ROU assets and operating lease liabilities are presented net within non-cash adjustment to operating lease expense in the Condensed Consolidated Statements of Cash Flows. ROU assets represent the Company’s right to use the underlying asset for the lease term and lease liabilities represent the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments due over the lease term, with the ROU assets adjusted for lease incentives received. When determining the present value of lease payments, the Company uses its incremental borrowing rate on the date of lease commencement, or the rate implicit in the lease, if known. The Company does not assume renewals in its determination of the lease term unless the renewals are deemed by management to be reasonably certain at lease inception. Leases with an initial term of 12 months or less are not recorded on the balance sheet, unless they include an option to purchase the underlying asset that the Company is reasonably certain to exercise. The Company recognizes lease expenses on a straight-line basis over the lease term. The Company has leases with lease and non-lease components, which the Company has elected to account for as a single lease component.
Revenue Recognition	Revenue Recognition License and Collaboration Revenue The Company analyzes its collaboration arrangements to assess whether they are within the scope of ASC 808, Collaborative Arrangements (“ASC 808”) to determine whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. For collaboration arrangements within the scope of ASC 808 that contain multiple elements, the Company first determines which elements of the collaboration are deemed to be within the scope of ASC 808 and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of Topic 606. For elements of collaboration arrangements that are accounted for pursuant to ASC 808, an appropriate recognition method is determined and applied consistently, generally by analogy to Topic 606. The accounting treatment pursuant to Topic 606 is outlined below. The terms of licensing and collaboration agreements entered into typically include payment of one or more of the following: non-refundable, up-front license fees; development, regulatory and commercial milestone payments; payments for manufacturing supply and research and development services and royalties on net sales of licensed products. Each of these payments results in license, collaboration and other revenue, except for revenues from royalties on net sales of licensed products, which are classified as royalty revenue. The core principle of Topic 606 is to recognize revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received in exchange for those goods or services. The Company may also receive reimbursement or make payments to a collaboration partner to satisfy cost sharing requirements. These payments are accounted for pursuant to ASC 808 and are recorded as an offset or increase to research and development expenses, respectively. In determining the appropriate amount of revenue to be recognized as the Company fulfills its obligations under each of its agreements, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. Amounts received prior to satisfying the revenue recognition criteria are recorded as contract liabilities in the Company’s Condensed Consolidated Balance Sheets. If the related performance obligation is expected to be satisfied within the next twelve months this will be classified in current liabilities. Amounts recognized as revenue prior to the Company having an unconditional right (other than a right that is conditioned only on the passage of time) to receipt are recorded as contract assets in the Company's Condensed Consolidated Balance Sheets. If the Company expects to have an unconditional right to receive the consideration in the next twelve months, this will be classified in current assets. A net contract asset or liability is presented for each contract with a customer. At contract inception, the Company assesses the goods or services promised in a contract with a customer and identifies those distinct goods and services that represent a performance obligation. A promised good or service may not be identified as a performance obligation if it is immaterial in the context of the contract with the customer, if it is not separately identifiable from other promises in the contract (either because it is not capable of being separated or because it is not separable in the context of the contract), or if the promised good or service does not provide the customer with a material right. The Company considers the terms of the contract to determine the transaction price. The transaction price is the amount of consideration to which the Company expects to be entitled in exchange for transferring promised goods or services to a customer. The consideration promised in a contract with a customer may include fixed amounts, variable amounts, or both. Variable consideration will only be included in the transaction price when it is not considered constrained, which is when it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur. If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling prices ("SSP"). The relative SSP for each deliverable is estimated using external sourced evidence if it is available. If external sourced evidence is not available, the Company uses its best estimate of the SSP for the deliverable. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring a promised good or service to a customer. An asset is transferred when, or as, the customer obtains control of that asset, which for a service is considered to be as the services are received and used. The Company recognizes revenue over time by measuring the progress toward complete satisfaction of the relevant performance obligation using an appropriate input or output method based on the nature of the service promised to the customer. After contract inception, the transaction price is reassessed at every period end and updated for changes such as resolution of uncertain events. Any change in the transaction price is allocated to the performance obligations on the same basis as at contract inception, or to a single performance obligation as applicable. Management may be required to exercise considerable judgment in estimating revenue to be recognized. Judgment is required in identifying performance obligations, estimating the transaction price, estimating the SSP of identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations.
Comprehensive Loss	Comprehensive Loss Comprehensive loss is composed of net loss and certain changes in stockholders’ equity that are excluded from net loss, primarily unrealized gains or losses on the Company’s marketable securities.
Net Loss per Share	Net Loss per Share Basic net loss per share is calculated by dividing the net loss 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 is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive given the net loss for each period presented.
Recently Adopted Accounting Pronouncement	Recently Adopted Accounting Pronouncement In December 2019, the Financial Accounting Standards Board ("FASB") issued ASU No. 2019-12, Income Taxes (Topic 740) Simplifying the Accounting for Income Taxes. ASU No. 2019-12 modifies ASC 740 to simplify several aspects of accounting for income taxes, including eliminating certain exceptions to the guidance in ASC 740 related to the approach for intraperiod tax allocation. The guidance is effective for fiscal years beginning after December 15, 2020 and interim periods within those fiscal years, with early adoption permitted, and is required to be adopted prospectively, with the exception of certain specific amendments, which were not applicable to the Company. The Company adopted this standard as of January 1, 2021 using a prospective approach. Adoption of the standard did not have a material impact on its Condensed Consolidated Financial Statements.

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2021

Fair Value Disclosures [Abstract]

Schedule of Assets and Liabilities Measured at Fair Value

Assets and liabilities measured at fair value at each balance sheet date are as follows (in thousands):


	September 30, 2021
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	350,803	$	—	$	—	$	350,803
U.S. government treasuries	24,998		—		—		24,998

Short-term marketable securities:
U.S. government treasuries	472,214		—		—		472,214
U.S. government agency securities	—		15,003		—		15,003
Corporate debt securities	—		61,182		—		61,182
Commercial paper	—		96,223		—		96,223
Long-term marketable securities:
U.S. government treasuries	299,069		—		—		299,069

Corporate debt securities	—		20,403		—		20,403

Total	$	1,147,084	$	192,811	$	—	$	1,339,895
Liabilities:
Foreign currency derivative contracts	$	—	$	201	$	—	$	201
Total	$	—	$	201	$	—	$	201


	December 31, 2020
	Level 1		Level 2		Level 3		Total
Assets:
Cash equivalents:
Money market funds	$	335,284	$	—	$	—	$	335,284
U.S. government treasuries	149,997		—		—		149,997
Short-term marketable securities:
U.S. government treasuries	878,938		—		—		878,938
U.S. government agency securities	—		25,217		—		25,217
Corporate debt securities	—		27,180		—		27,180
Commercial paper	—		31,218		—		31,218
Long-term marketable securities:
U.S. government treasuries	2,561		—		—		2,561
Corporate debt securities	—		30,138		—		30,138
Foreign currency derivative contracts	—		185		—		185
Total	$	1,366,780	$	113,938	$	—	$	1,480,718
Liabilities:
Foreign currency derivative contracts	$	—	$	11	$	—	$	11
Total	$	—	$	11	$	—	$	11

Marketable Securities (Tables)

9 Months Ended

Sep. 30, 2021

Investments, Debt and Equity Securities [Abstract]

Summary of Available for Sale Securities

The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands):


	September 30, 2021
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	472,214	$	13	$	(13)	$	472,214
U.S. government agency securities	15,003		—		—		15,003
Corporate debt securities(2)	61,187		5		(10)		61,182
Commercial paper	96,223		—		—		96,223
Total short-term marketable securities	644,627		18		(23)		644,622
Long-term marketable securities:
U.S. government treasuries(3)	299,225		17		(173)		299,069

Corporate debt securities(4)	20,413		2		(12)		20,403
Total long-term marketable securities	319,638		19		(185)		319,472
Total	$	964,265	$	37	$	(208)	$	964,094

__________________________________________________

(1)Unrealized holding losses on 7 securities with an aggregate fair value of $271.8 million.

(2)Unrealized holding losses on 8 securities with an aggregate fair value of $27.8 million.

(3)Unrealized holding losses on 11 securities with an aggregate fair value of $251.5 million.

(4)Unrealized holding losses on 5 securities with an aggregate fair value of $16.8 million.


	December 31, 2020
	Amortized Cost		Unrealized Holding Gains		Unrealized Holding Losses		Aggregate Fair Value
Short-term marketable securities:
U.S. government treasuries(1)	$	878,906	$	44	$	(12)	$	878,938
U.S. government agency securities(2)	25,214		5		(2)		25,217
Corporate debt securities	27,101		79		—		27,180
Commercial paper	31,218		—		—		31,218
Total short-term marketable securities	962,439		128		(14)		962,553
Long-term marketable securities:
U.S. government treasuries	2,561		—		—		2,561

Corporate debt securities(3)	30,147		2		(11)		30,138
Total long-term marketable securities	32,708		2		(11)		32,699
Total	$	995,147	$	130	$	(25)	$	995,252

__________________________________________________

(1)Unrealized holding losses on 19 securities with an aggregate fair value of $369.9 million.

(2)Unrealized holding losses on 2 securities with an aggregate fair value of $10.1 million.

(3)Unrealized holding losses on 1 security with an aggregate fair value of $20.1 million.

Derivative Financial Instruments (Tables)

9 Months Ended

Sep. 30, 2021

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Summary of Forward Foreign Currency Exchange Contracts Outstanding

The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of September 30, 2021 and December 31, 2020, respectively (notional amounts in thousands):


Foreign Exchange Contracts	Number of Contracts	Aggregate Notional(1) Amount in Foreign Currency	Maturity
Euros	12	1,700	Oct 2021 - Jun 2022
British Pounds	11	1,725	Oct 2021 - Jun 2022
Total at September 30, 2021	23
Euros	26	3,855	Jan 2021 - Nov 2021
British Pounds	21	2,658	Jan 2021 - Nov 2021
Total at December 31, 2020	47

_________________________________________________

(1) The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts.

- Definition

Tabular disclosure of pertinent information about a derivative or group of derivatives on a disaggregated basis, such as for individual instruments, or small groups of similar instruments. May include a combination of the type of instrument, risks being hedged, notional amount, hedge designation, related hedged item, inception date, maturity date, or other relevant item.

+ References

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+ Details

Collaboration Agreements (Tables)

9 Months Ended

Sep. 30, 2021

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Summary of Collaboration Revenue

Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2021		2020		2021		2020
Takeda Collaboration Agreement(1)	$	4,425	$	9,271	$	18,597	$	17,826
Sanofi Collaboration Agreement

Peripheral Program License	—		—		15,000		—
Retained Activities	—		117		—		925
Alzheimer's Disease Services(2)	—		5		4		93
Total Sanofi Collaboration Revenue	—		122		15,004		1,018
Biogen Collaboration Agreement



Option Research Services(2)	860		—		2,546		—
Total Biogen Collaboration Revenue	$	860	$	—	$	2,546	$	—
Total Collaboration Revenue	$	5,285	$	9,393	$	36,147	$	18,844

_________________________________________________

Commitments and Contingencies (Tables)

9 Months Ended

Sep. 30, 2021

Commitments and Contingencies Disclosure [Abstract]

Summary of Supplemental Information for Lease Amounts Recognized

The following table contains a summary of the lease costs recognized under ASC 842 and other information pertaining to the Company’s operating leases for the periods presented (in thousands):


	Three Months Ended September 30,					Nine Months Ended September 30,
	2021		2020			2021		2020
Operating lease cost (1)	$	2,863	$	2,833		$	8,429	$	8,341
Cash paid for amounts included in measurement of lease liability	$	2,618	$	2,536		$	7,717	$	7,202

	As of September 30,
	2021					2020
Weighted average remaining lease term	7.6 years					8.6 years
Weighted average discount rate	9				%	9				%

__________________________________________________

(1)Including variable and short-term lease costs

Summary of Future Minimum Lease Commitments


Year Ended December 31:
2021 (three months)	$	2,618
2022	10,702
2023	11,053
2024	11,417
2025	11,793
Thereafter	42,148
Total undiscounted lease payments	89,731
Present value adjustment	(24,489)
Net operating lease liabilities	$	65,242

Summary of Future Minimum Lease Receivables

The following table details the future undiscounted cash inflows relating to the Sublease Agreement as of September 30, 2021 (in thousands):


Year Ended December 31:
2021 (three months)	$	737
2022	3,009
2023	3,096
2024	876

Total undiscounted sublease receipts	$	7,718

Stock-Based Awards (Tables)

9 Months Ended

Sep. 30, 2021

Share-based Payment Arrangement [Abstract]

Summary of Stock Option Activity

The following table summarizes stock option activity for the nine months ended September 30, 2021:


	Number of Options	Weighted-Average Exercise Price
Balance at December 31, 2020	12,959,926	$	16.31
Granted	1,944,717	73.31
Exercised	(831,207)	14.27
Forfeited	(259,060)	34.89
Balance at September 30, 2021	13,814,376	$	24.11
Vested and expected to vest at September 30, 2021	12,078,689	$	27.48
Exercisable at September 30, 2021	7,856,046	$	15.22

Summary of Assumptions Used for Estimating the Fair Value of Stock Granted

The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions:


	Nine Months Ended September 30,
	2021	2020
Expected term (in years)	5.50 - 6.08	5.50 - 6.08
Volatility	62.2% - 63.7%	65.2% - 67.1%
Risk-free interest rate	0.5% - 1.2%	0.3% - 1.7%
Dividend yield	—	—

Summary of Restricted Stock Activity

The following table summarizes restricted stock unit ("RSU") activity for the nine months ended September 30, 2021:


	Number of RSU shares	Weighted-Average Fair Value at Date of Grant per Share
Unvested at December 31, 2020	2,301,679	$	27.08
Granted	1,046,259	69.50
Vested and released	(599,258)	25.63
Forfeited	(126,827)	60.92
Unvested at September 30, 2021	2,621,853	$	43.83
Expected to vest at September 30, 2021	2,621,853	$	43.83

Summary of Stock-Based Compensation Expense

The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2021		2020		2021		2020
Research and development	$	12,174	$	7,781	$	36,997	$	20,981
General and administrative	8,824		5,471		26,165		15,540
Total	$	20,998	$	13,252	$	63,162	$	36,521

Net Loss Per Share (Tables)

9 Months Ended

Sep. 30, 2021

Earnings Per Share [Abstract]

Schedule of Dilutive Securities Not Included in Diluted Per Share Calculations

Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows:


	Three and Nine Months Ended September 30,
	2021	2020
Options issued and outstanding and ESPP shares issuable	13,877,115	13,680,889
Restricted shares subject to future vesting	2,621,853	2,269,897

Total	16,498,968	15,950,786

Significant Accounting Policies - Narrative (Details) $ in Millions	9 Months Ended
	Sep. 30, 2021 USD ($) Segment
Accounting Policies [Abstract]
Number of operating segments \| Segment	1
Restricted cash \| $	$ 1.5

Fair Value Measurements - Schedule of Assets and Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2021	Dec. 31, 2020
Assets:
Fair value	$ 964,094	$ 995,252
Foreign currency derivative contracts		185
Total	1,339,895	1,480,718
Liabilities:
Foreign currency derivative contracts	201	11
Total	201	11
Money market funds
Assets:
Cash equivalents	350,803	335,284
U.S. government treasuries
Assets:
Cash equivalents	24,998	149,997
Short-term marketable securities \| U.S. government treasuries
Assets:
Fair value	472,214	878,938
Short-term marketable securities \| U.S. government agency securities
Assets:
Fair value	15,003	25,217
Short-term marketable securities \| Corporate debt securities
Assets:
Fair value	61,182	27,180
Short-term marketable securities \| Commercial paper
Assets:
Fair value	96,223	31,218
Long-term marketable securities \| U.S. government treasuries
Assets:
Fair value	299,069	2,561
Long-term marketable securities \| Corporate debt securities
Assets:
Fair value	20,403	30,138
Level 1
Assets:
Foreign currency derivative contracts		0
Total	1,147,084	1,366,780
Liabilities:
Foreign currency derivative contracts	0	0
Total	0	0
Level 1 \| Money market funds
Assets:
Cash equivalents	350,803	335,284
Level 1 \| U.S. government treasuries
Assets:
Cash equivalents	24,998	149,997
Level 1 \| Short-term marketable securities \| U.S. government treasuries
Assets:
Fair value	472,214	878,938
Level 1 \| Short-term marketable securities \| U.S. government agency securities
Assets:
Fair value	0	0
Level 1 \| Short-term marketable securities \| Corporate debt securities
Assets:
Fair value	0	0
Level 1 \| Short-term marketable securities \| Commercial paper
Assets:
Fair value	0	0
Level 1 \| Long-term marketable securities \| U.S. government treasuries
Assets:
Fair value	299,069	2,561
Level 1 \| Long-term marketable securities \| Corporate debt securities
Assets:
Fair value	0	0
Level 2
Assets:
Foreign currency derivative contracts		185
Total	192,811	113,938
Liabilities:
Foreign currency derivative contracts	201	11
Total	201	11
Level 2 \| Money market funds
Assets:
Cash equivalents	0	0
Level 2 \| U.S. government treasuries
Assets:
Cash equivalents	0	0
Level 2 \| Short-term marketable securities \| U.S. government treasuries
Assets:
Fair value	0	0
Level 2 \| Short-term marketable securities \| U.S. government agency securities
Assets:
Fair value	15,003	25,217
Level 2 \| Short-term marketable securities \| Corporate debt securities
Assets:
Fair value	61,182	27,180
Level 2 \| Short-term marketable securities \| Commercial paper
Assets:
Fair value	96,223	31,218
Level 2 \| Long-term marketable securities \| U.S. government treasuries
Assets:
Fair value	0	0
Level 2 \| Long-term marketable securities \| Corporate debt securities
Assets:
Fair value	20,403	30,138
Level 3
Assets:
Foreign currency derivative contracts		0
Total	0	0
Liabilities:
Foreign currency derivative contracts	0	0
Total	0	0
Level 3 \| Money market funds
Assets:
Cash equivalents	0	0
Level 3 \| U.S. government treasuries
Assets:
Cash equivalents	0	0
Level 3 \| Short-term marketable securities \| U.S. government treasuries
Assets:
Fair value	0	0
Level 3 \| Short-term marketable securities \| U.S. government agency securities
Assets:
Fair value	0	0
Level 3 \| Short-term marketable securities \| Corporate debt securities
Assets:
Fair value	0	0
Level 3 \| Short-term marketable securities \| Commercial paper
Assets:
Fair value	0	0
Level 3 \| Long-term marketable securities \| U.S. government treasuries
Assets:
Fair value	0	0
Level 3 \| Long-term marketable securities \| Corporate debt securities
Assets:
Fair value	$ 0	$ 0

Marketable Securities - Summary of Available for Sale Securities (Details) $ in Thousands	Sep. 30, 2021 USD ($) security	Dec. 31, 2020 USD ($) security
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 964,265	$ 995,147
Unrealized Holding Gains	37	130
Unrealized Holding Losses	(208)	(25)
Aggregate Fair Value	964,094	995,252
Short-term marketable securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	644,627	962,439
Unrealized Holding Gains	18	128
Unrealized Holding Losses	(23)	(14)
Aggregate Fair Value	644,622	962,553
Short-term marketable securities \| U.S. government treasuries
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	472,214	878,906
Unrealized Holding Gains	13	44
Unrealized Holding Losses	(13)	(12)
Aggregate Fair Value	$ 472,214	$ 878,938
Number of securities held in unrealized holding loss position \| security	7	19
Aggregate fair value, unrealized holding loss position	$ 271,800	$ 369,900
Short-term marketable securities \| U.S. government agency securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	15,003	25,214
Unrealized Holding Gains	0	5
Unrealized Holding Losses	0	(2)
Aggregate Fair Value	15,003	$ 25,217
Number of securities held in unrealized holding loss position \| security		2
Aggregate fair value, unrealized holding loss position		$ 10,100
Short-term marketable securities \| Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	61,187	27,101
Unrealized Holding Gains	5	79
Unrealized Holding Losses	(10)	0
Aggregate Fair Value	$ 61,182	27,180
Number of securities held in unrealized holding loss position \| security	8
Aggregate fair value, unrealized holding loss position	$ 27,800
Short-term marketable securities \| Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	96,223	31,218
Unrealized Holding Gains	0	0
Unrealized Holding Losses	0	0
Aggregate Fair Value	96,223	31,218
Long-term marketable securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	319,638	32,708
Unrealized Holding Gains	19	2
Unrealized Holding Losses	(185)	(11)
Aggregate Fair Value	319,472	32,699
Long-term marketable securities \| U.S. government treasuries
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	299,225	2,561
Unrealized Holding Gains	17	0
Unrealized Holding Losses	(173)	0
Aggregate Fair Value	$ 299,069	2,561
Number of securities held in unrealized holding loss position \| security	11
Aggregate fair value, unrealized holding loss position	$ 251,500
Long-term marketable securities \| Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	20,413	30,147
Unrealized Holding Gains	2	2
Unrealized Holding Losses	(12)	(11)
Aggregate Fair Value	$ 20,403	$ 30,138
Number of securities held in unrealized holding loss position \| security	5	1
Aggregate fair value, unrealized holding loss position	$ 16,800	$ 20,100

Marketable Securities - Narrative (Details) - USD ($)	Sep. 30, 2021	Dec. 31, 2020
Investments, Debt and Equity Securities [Abstract]
Allowance for credit losses	$ 0	$ 0
Effective maturity (less than)	2 years

Derivative Financial Instruments - Summary of Forward Foreign Currency Exchange Contracts Outstanding (Details) - Designated as Hedging Instrument € in Thousands, £ in Thousands	Sep. 30, 2021 EUR (€) derivative_instrument	Sep. 30, 2021 GBP (£) derivative_instrument	Dec. 31, 2020 EUR (€) derivative_instrument	Dec. 31, 2020 GBP (£) derivative_instrument
Euros
Derivative [Line Items]
Number of Contracts	12	12	26	26
Aggregate Notional Amount in Foreign Currency \| €	€ 1,700		€ 3,855
British Pounds
Derivative [Line Items]
Number of Contracts	11	11	21	21
Aggregate Notional Amount in Foreign Currency \| £		£ 1,725		£ 2,658
Foreign Exchange Contracts
Derivative [Line Items]
Number of Contracts	23	23	47	47

Collaboration Agreements - Biogen (Details)

3 Months Ended

9 Months Ended

Sep. 30, 2021

USD ($)

milestone

Sep. 30, 2020

USD ($)

Sep. 30, 2021

USD ($)

milestone

Sep. 30, 2020

USD ($)

Dec. 31, 2020

USD ($)

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Offset to research and development expense, related party cost reimbursement

$ 1,200,000

$ 5,300,000

Cost sharing reimbursements due from related party

1,194,000

$ 5,674,000

Collaboration revenue from customers

5,285,000

^[1]

$ 9,388,000

36,143,000

^[1]

$ 18,751,000

Biogen Collaboration Agreement | Related Party

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Contract liability

294,900,000

Biogen Collaborative Arrangement | Biogen Collaboration Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Transaction price, change

Offset to research and development expense, related party cost reimbursement

1,200,000

5,300,000

Cost sharing reimbursements due from related party

$ 1,200,000

$ 5,700,000

Number of milestones achieved | milestone

Biogen Collaborative Arrangement | Biogen Collaboration Agreement | Option Research Services | Related Party

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Contract liability

$ 6,000,000.0

Biogen Collaborative Arrangement | Biogen Collaboration Agreement | Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaboration revenue from customers

ROFN and Option Agreement | Biogen Collaboration Agreement | Related Party

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Contract liability

$ 288,900,000

[1]	Includes related party collaboration revenue from a customer of $0.9 million and $2.5 million for the three and nine months ended September 30, 2021, respectively.

Collaboration Agreements - Sanofi (Details) - USD ($)

1 Months Ended

3 Months Ended

9 Months Ended

36 Months Ended

Jun. 30, 2021

Sep. 30, 2021

Sep. 30, 2020

Sep. 30, 2021

Sep. 30, 2020

Sep. 30, 2021

Dec. 31, 2020

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaboration revenue from customers

$ 5,285,000

^[1]

$ 9,388,000

$ 36,143,000

^[1]

$ 18,751,000

Sanofi | Collaborative Arrangement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Receivable

$ 0

$ 44,303

Sanofi | Collaborative Arrangement | Milestone Triggered

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Transaction price increase

15,000,000

Collaboration revenue from customers

$ 15,000,000

25,000,000

Sanofi | Collaborative Arrangement | Milestone Triggered and Retained Activities

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Transaction price increase

$ 100,000

$ 900,000

Sanofi | Collaborative Arrangement | Alzheimer's Disease Services

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Contract liability

$ 3,400,000

3,400,000

$ 3,400,000

Sanofi | Collaborative Arrangement | Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaboration revenue from customers

$ 0

[1]	Includes related party collaboration revenue from a customer of $0.9 million and $2.5 million for the three and nine months ended September 30, 2021, respectively.

Collaboration Agreements - Takeda (Details)

3 Months Ended

9 Months Ended

45 Months Ended

Sep. 30, 2021

USD ($)

Sep. 30, 2020

USD ($)

Sep. 30, 2021

USD ($)

Sep. 30, 2020

USD ($)

Sep. 30, 2021

USD ($)

Dec. 31, 2020

USD ($)

Jan. 31, 2018

program

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaboration revenue from customers

$ 5,285,000

^[1]

$ 9,388,000

$ 36,143,000

^[1]

$ 18,751,000

Collaborative Arrangement | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Transaction price, change

Contract liability

29,200,000

$ 29,200,000

$ 39,800,000

Number of performance obligations | program

Preclinical milestone payment earned not yet received

$ 0

Collaborative Arrangement | Takeda Pharmaceutical Company Limited | Milestone Triggered

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaboration revenue from customers

31,000,000

Collaborative Arrangement | Takeda Pharmaceutical Company Limited | Product

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaboration revenue from customers

$ 0

Collaborative Arrangement, PTV:PGRN | Takeda Pharmaceutical Company Limited

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Preclinical milestone payment earned not yet received

$ 8,000,000

[1]	Includes related party collaboration revenue from a customer of $0.9 million and $2.5 million for the three and nine months ended September 30, 2021, respectively.

Collaboration Agreements - Summary of Collaboration Revenue (Details) - USD ($)
$ in Thousands

3 Months Ended

9 Months Ended

Sep. 30, 2021

Sep. 30, 2020

Sep. 30, 2021

Sep. 30, 2020

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

$ 5,285

^[1]

$ 9,388

$ 36,143

^[1]

$ 18,751

Collaborative revenue, excluding revenue from contract with customer

Total Collaboration Revenue

5,285

9,393

36,147

18,844

Takeda Collaboration Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

4,425

9,271

18,597

17,826

Revenue recognized included in the contract liability balance at the beginning of the year

15,600

Sanofi Collaboration Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Total Collaboration Revenue

122

15,004

1,018

Sanofi Collaboration Agreement | Peripheral Program License

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

15,000

Sanofi Collaboration Agreement | Retained Activities

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

117

925

Sanofi Collaboration Agreement | Alzheimer's Disease Services

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, excluding revenue from contract with customer

Biogen Collaboration Agreement

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Total Collaboration Revenue

860

2,546

Biogen Collaboration Agreement | Option Research Services

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Collaborative revenue, revenue from contract with customer

$ 860

$ 0

$ 2,546

$ 0

[1]	Includes related party collaboration revenue from a customer of $0.9 million and $2.5 million for the three and nine months ended September 30, 2021, respectively.

License Agreements - Narrative (Details) - USD ($)	3 Months Ended		9 Months Ended
License Agreements - Narrative (Details) - USD ($)	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Genentech Inc \| License Agreement \| Research and development
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Upfront fee paid	$ 0	$ 0	$ 0	$ 0

Commitments and Contingencies - Narrative (Details) ft² in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Aug. 31, 2021 USD ($) ft²	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2021 USD ($)	Sep. 30, 2020 USD ($)	Dec. 31, 2020 USD ($)
Loss Contingencies [Line Items]
Sublease income		$ 1,000,000.0	$ 900,000	$ 2,900,000	$ 2,800,000
DMSA
Loss Contingencies [Line Items]
Purchase order executed		42,000,000		42,000,000		$ 33,000,000
Non-refundable purchase commitments		27,600,000		27,600,000		$ 27,100,000
Costs incurred		5,800,000	1,400,000	14,200,000	6,200,000
Payments for development and manufacturing services		4,000,000	$ 800,000	10,400,000	$ 6,000,000
Operating Lease, 8 Year Lease Agreement \| Building
Loss Contingencies [Line Items]
Lease not yet commenced, area under lease \| ft²	50
Lease not yet commenced, period	8 years 4 months 24 days
Lease not yet commenced, undiscounted lease payments	$ 12,500,000
Lease not yet commenced, lease liability		0		0
Lease not yet commenced, ROU asset		0		0
Lease not yet commenced, operating lease expense		$ 0		$ 0

Commitments and Contingencies - Summary of Supplemental Lease Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Commitments and Contingencies Disclosure [Abstract]
Operating lease cost	$ 2,863	$ 2,833	$ 8,429	$ 8,341
Cash paid for amounts included in measurement of lease liability	$ 2,618	$ 2,536	$ 7,717	$ 7,202
Weighted average remaining lease term	7 years 7 months 6 days	8 years 7 months 6 days	7 years 7 months 6 days	8 years 7 months 6 days
Weighted average discount rate	9.00%	9.00%	9.00%	9.00%

Commitments and Contingencies - Summary of Company's Future Minimum Lease Commitments (Details) $ in Thousands	Sep. 30, 2021 USD ($)
Operating Lease Liabilities, Payments Due [Abstract]
2021 (three months)	$ 2,618
2022	10,702
2023	11,053
2024	11,417
2025	11,793
Thereafter	42,148
Total undiscounted lease payments	89,731
Present value adjustment	(24,489)
Net operating lease liabilities	$ 65,242

Commitments and Contingencies - Summary of Company's Future Minimum Lease Receivables (Details) $ in Thousands	Sep. 30, 2021 USD ($)
Commitments and Contingencies Disclosure [Abstract]
2021 (three months)	$ 737
2022	3,009
2023	3,096
2024	876
Total undiscounted sublease receipts	$ 7,718

Stock-Based Awards - Summary of Stock Option Activity (Details)	9 Months Ended
	Sep. 30, 2021 $ / shares shares
Number of Options
Beginning balance (in shares) \| shares	12,959,926
Granted (in shares) \| shares	1,944,717
Exercised (in shares) \| shares	(831,207)
Forfeited (in shares) \| shares	(259,060)
Ending balance (in shares) \| shares	13,814,376
Vested and expected to vest (in shares) \| shares	12,078,689
Exercisable (in shares) \| shares	7,856,046
Weighted-Average Exercise Price
Beginning balance (usd per share) \| $ / shares	$ 16.31
Granted (usd per share) \| $ / shares	73.31
Exercised (usd per share) \| $ / shares	14.27
Forfeited (usd per share) \| $ / shares	34.89
Ending balance (usd per share) \| $ / shares	24.11
Vested and expected to vest (usd per share) \| $ / shares	27.48
Exercisable (usd per share) \| $ / shares	$ 15.22

Stock-Based Awards - Summary of Assumptions Used for Estimating the Fair Value of Stock Options Granted (Details) - Stock Options	9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Volatility, minimum	62.20%	65.20%
Volatility, maximum	63.70%	67.10%
Risk-free interest rate, minimum	0.50%	0.30%
Risk-free interest rate, maximum	1.20%	1.70%
Dividend yield	0.00%	0.00%
Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (in years)	5 years 6 months	5 years 6 months
Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (in years)	6 years 29 days	6 years 29 days

Stock-Based Awards - Summary of Restricted Stock Activity (Details) - Restricted Stock Units (RSUs)	9 Months Ended
	Sep. 30, 2021 $ / shares shares
Number of RSU shares
Beginning balance (in shares) \| shares	2,301,679
Granted (in shares) \| shares	1,046,259
Vested and released (in shares) \| shares	(599,258)
Forfeited (in shares) \| shares	(126,827)
Ending balance (in shares) \| shares	2,621,853
Expected to vest (in shares) \| shares	2,621,853
Weighted-Average Fair Value at Date of Grant per Share
Beginning balance (usd per share) \| $ / shares	$ 27.08
Granted (usd per share) \| $ / shares	69.50
Vested and released (usd per share) \| $ / shares	25.63
Forfeited (usd per share) \| $ / shares	60.92
Ending balance (usd per share) \| $ / shares	43.83
Expected to vest (usd per share) \| $ / shares	$ 43.83

Stock-Based Awards - Summary of Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total	$ 20,998	$ 13,252	$ 63,162	$ 36,521
Research and development
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total	12,174	7,781	36,997	20,981
General and administrative
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Total	$ 8,824	$ 5,471	$ 26,165	$ 15,540

Net Loss Per Share - Schedule of Dilutive Securities Not Included in Diluted Per Share Calculations (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2021	Sep. 30, 2020	Sep. 30, 2021	Sep. 30, 2020
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	16,498,968	15,950,786	16,498,968	15,950,786
Options issued and outstanding and ESPP shares issuable
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	13,877,115	13,680,889	13,877,115	13,680,889
Restricted shares subject to future vesting
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total (in shares)	2,621,853	2,269,897	2,621,853	2,269,897