0001558370-20-013395 | 10-Q | XBRL Viewer

Commitments and contingencies - Termination of Agreement (Details) - Termination Agreement - Sanofi Genzyme $ in Millions	Jun. 14, 2019 USD ($) item
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
AAV capsids to license \| item	2
Number of non central nervous system \| item	2
Up-front payment made	$ 10.0
Milestone payment agreed to be paid	$ 10.0
Period in which milestone payment will be made of filing of investigational new drug	15 days
Percentage of threshold sublicensing income agreed to be paid	50.00%
Unused in-kind services waived	$ 0.4
Threshold number of capsids having exclusive options to evaluate for no consideration \| item	4
Threshold additional number of capsids having options to evaluate for low six-figure payment per capsid \| item	2
Threshold number of capsids that has right to obtain an exclusive license \| item	2
Option exercise fee	$ 1.0
Development and regulatory milestones
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone payable upon achievement	15.0
Sales milestone
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone payable upon achievement	$ 20.0

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Current assets:
Cash and cash equivalents	$ 147,447	$ 86,042
Marketable securities, current	52,571	195,491
Related party collaboration receivable	12,689	18,496
Prepaid expenses and other current assets	3,606	4,630
Total current assets	216,313	304,659
Property and equipment, net	23,212	17,986
Deposits and other non-current assets	1,917	1,723
Marketable securities, non-current	2,184	1,920
Operating lease, right-of-use asset	26,131	28,472
Total assets	269,757	354,760
Current liabilities:
Accounts payable	3,386	4,070
Accrued expenses	21,665	21,516
Other current liabilities	3,539	3,193
Deferred revenue, current	13,462	47,233
Total current liabilities	42,052	76,012
Deferred revenue, non-current	32,209	147,260
Other non-current liabilities	29,260	31,976
Total liabilities	103,521	255,248
Commitments and contingencies (see note 8)
Stockholders' equity:
Preferred stock $0.001 par value: 5,000,000 shares authorized at September 30, 2020 and December 31, 2019; no shares issued and outstanding at September 30, 2020 and December 31, 2019
Common stock, $0.001 par value: 120,000,000 shares authorized at September 30, 2020 and December 31, 2019; 37,262,703 and 36,865,116 shares issued and outstanding at September 30, 2020 and December 31, 2019, respectively	37	37
Additional paid-in capital	426,240	412,227
Accumulated other comprehensive loss	(60)	(104)
Accumulated deficit	(259,981)	(312,648)
Total stockholders' equity	166,236	99,512
Total liabilities and stockholders' equity	$ 269,757	$ 354,760

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit	Total
Stockholders' Equity, Beginning Balance at Dec. 31, 2018	$ 32	$ 315,598	$ (133)	$ (269,051)	$ 46,446
Shares, Outstanding, Beginning Balance at Dec. 31, 2018	32,364,895
Exercises of vested stock options	$ 1	283			284
Exercises of vested stock options (in shares)	31,360
Issuance of common stock in connection with Neurocrine Collaboration Agreement	$ 4	77,613			77,617
Issuance of common stock in connection with Neurocrine Collaboration Agreement (in shares)	4,179,728
Stock based compensation expense		3,459			3,459
Unrealized gain (loss) on available for-sale securities, net of tax			58		58
Net (loss) income				(27,170)	(27,170)
Stockholders' Equity, Ending Balance at Mar. 31, 2019	$ 37	396,953	(75)	(296,221)	100,694
Shares, Outstanding, Ending Balance at Mar. 31, 2019	36,575,983
Stockholders' Equity, Beginning Balance at Dec. 31, 2018	$ 32	315,598	(133)	(269,051)	46,446
Shares, Outstanding, Beginning Balance at Dec. 31, 2018	32,364,895
Unrealized gain (loss) on available for-sale securities, net of tax					118
Net (loss) income					(31,023)
Stockholders' Equity, Ending Balance at Sep. 30, 2019	$ 37	408,208	(15)	(300,074)	108,156
Shares, Outstanding, Ending Balance at Sep. 30, 2019	36,828,123
Stockholders' Equity, Beginning Balance at Mar. 31, 2019	$ 37	396,953	(75)	(296,221)	100,694
Shares, Outstanding, Beginning Balance at Mar. 31, 2019	36,575,983
Exercises of vested stock options		714			714
Exercises of vested stock options (in shares)	57,461
Issuance of common stock under ESPP		471			471
Issuance of common stock under ESPP (in shares)	44,164
Stock based compensation expense		5,196			5,196
Unrealized gain (loss) on available for-sale securities, net of tax			176		176
Net (loss) income				11,153	11,153
Stockholders' Equity, Ending Balance at Jun. 30, 2019	$ 37	403,334	101	(285,068)	118,404
Shares, Outstanding, Ending Balance at Jun. 30, 2019	36,677,608
Exercises of vested stock options		1,608			1,608
Exercises of vested stock options (in shares)	150,515
Stock based compensation expense		3,266			3,266
Unrealized gain (loss) on available for-sale securities, net of tax			(116)		(116)
Net (loss) income				(15,006)	(15,006)
Stockholders' Equity, Ending Balance at Sep. 30, 2019	$ 37	408,208	(15)	(300,074)	108,156
Shares, Outstanding, Ending Balance at Sep. 30, 2019	36,828,123
Stockholders' Equity, Beginning Balance at Dec. 31, 2019	$ 37	412,227	(104)	(312,648)	99,512
Shares, Outstanding, Beginning Balance at Dec. 31, 2019	36,865,116
Exercises of vested stock options		34			34
Exercises of vested stock options (in shares)	3,035
Vesting of restricted stock units (in shares)	108,600
Stock based compensation expense		3,949			3,949
Unrealized gain (loss) on available for-sale securities, net of tax			525		525
Net (loss) income				(24,263)	(24,263)
Stockholders' Equity, Ending Balance at Mar. 31, 2020	$ 37	416,210	421	(336,911)	79,757
Shares, Outstanding, Ending Balance at Mar. 31, 2020	36,976,751
Stockholders' Equity, Beginning Balance at Dec. 31, 2019	$ 37	412,227	(104)	(312,648)	$ 99,512
Shares, Outstanding, Beginning Balance at Dec. 31, 2019	36,865,116
Exercises of vested stock options (in shares)					214,287
Unrealized gain (loss) on available for-sale securities, net of tax					$ 44
Net (loss) income					52,667
Stockholders' Equity, Ending Balance at Sep. 30, 2020	$ 37	426,240	(60)	(259,981)	166,236
Shares, Outstanding, Ending Balance at Sep. 30, 2020	37,262,703
Stockholders' Equity, Beginning Balance at Mar. 31, 2020	$ 37	416,210	421	(336,911)	79,757
Shares, Outstanding, Beginning Balance at Mar. 31, 2020	36,976,751
Exercises of vested stock options		1,651			1,651
Exercises of vested stock options (in shares)	160,478
Vesting of restricted stock units (in shares)	21,403
Issuance of common stock under ESPP		638			638
Issuance of common stock under ESPP (in shares)	44,995
Stock based compensation expense		3,795			3,795
Unrealized gain (loss) on available for-sale securities, net of tax			(276)		(276)
Net (loss) income				(8,681)	(8,681)
Stockholders' Equity, Ending Balance at Jun. 30, 2020	$ 37	422,294	145	(345,592)	76,884
Shares, Outstanding, Ending Balance at Jun. 30, 2020	37,203,627
Exercises of vested stock options		510			510
Exercises of vested stock options (in shares)	50,774
Vesting of restricted stock units (in shares)	8,302
Stock based compensation expense		3,436			3,436
Unrealized gain (loss) on available for-sale securities, net of tax			(205)		(205)
Net (loss) income				85,611	85,611
Stockholders' Equity, Ending Balance at Sep. 30, 2020	$ 37	$ 426,240	$ (60)	$ (259,981)	$ 166,236
Shares, Outstanding, Ending Balance at Sep. 30, 2020	37,262,703

Summary of significant accounting policies and basis of presentation

9 Months Ended

Sep. 30, 2020

Summary of significant accounting policies and basis of presentation

Summary of significant accounting policies and basis of presentation

2. Summary of significant accounting policies and basis of presentation

Basis of presentation

The accompanying unaudited condensed consolidated financial statements of the Company have been prepared in accordance with accounting principles generally accepted in the United States (“GAAP”) for interim financial reporting and as required by Regulation S-X, Rule 10-01. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. For further information, refer to the consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2019 as filed with the Securities and Exchange Commission (“SEC”) on March 3, 2020. These interim condensed consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the Company’s financial position and results of operations for the periods presented. Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). See “Recently Adopted Accounting Pronouncements” below for discussion of the Company’s adoption of new guidance effective January 1, 2020. All amounts and disclosures set forth in this Quarterly Report on Form 10-Q reflect adoption of these changes.

Principles of consolidation

The unaudited interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiary as disclosed in Note 2, Summary of Significant Accounting Policies and Basis of Presentation, within the “Notes to Consolidated Financial Statements” accompanying the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2019. Intercompany accounts and transactions have been eliminated.

Use of estimates

The preparation of consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. On an ongoing basis, the Company’s management evaluates its estimates, which include, but are not limited to, estimates related to revenue recognition, accrued expenses, stock-based compensation expense, and income taxes. The Company bases its estimates on historical experience and other market specific or other relevant assumptions that it believes to be reasonable under the circumstances. Actual results may differ from those estimates or assumptions. Certain reclassifications have been made to prior periods to conform to current period presentation.

Net Income (Loss) per Share

Basic net income (loss) per share is computed by dividing net income (loss) by the weighted-average number of common shares and restricted stock unit awards outstanding during the period. Diluted net income (loss) per share is computed using the weighted-average number of common shares and restricted stock unit awards outstanding during the period and, if dilutive, the weighted-average number of potential shares of common stock and restricted stock unit awards.

Summary of Significant Accounting Policies

There have been no changes in the Company's significant accounting policies as described in, Summary of Significant Accounting Policies to the consolidated financial statements in its Annual Report on Form 10-K for the year ended December 31, 2019.

Recently Adopted Accounting Pronouncements

In 2016, the FASB issued ASU 2016-13, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”), which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available-for-sale debt securities. The Company adopted the standard on January 1, 2020. Based on the composition of the Company's investment portfolio, current market conditions, and historical credit loss activity, the adoption of this standard did not have a material impact on the Company's consolidated financial statements and related disclosures.

In August 2018, the FASB issued ASU No. 2018-13, Disclosure Framework - Changes to the Disclosure Requirements for Fair Value Measurement (“ASU 2018-13”). This standard eliminates, adds and modifies certain disclosure requirements for fair value measurements as part of its disclosure framework project. The Company adopted the standard on the required effective date of January 1, 2020. The adoption of this standard did not have a material impact on the Company’s consolidated financial statements and related disclosures.

Related party transactions (Details) $ in Thousands	3 Months Ended		9 Months Ended
Related party transactions (Details) $ in Thousands	Sep. 30, 2020 USD ($) individual	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($) individual	Sep. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)
Related party transactions
Related party collaboration receivable	$ 12,689		$ 12,689		$ 18,496
Former Executives \| Board and scientific advisory services
Related party transactions
Number of individuals providing services \| individual	2		2
Dr. Steven M Paul \| Board and scientific advisory services
Related party transactions
Expense recognized	$ 50	$ 200	$ 50	$ 200
Sah \| Board and scientific advisory services
Related party transactions
Expense recognized	200		300
Neurocrine \| Collaboration arrangement
Related party transactions
Related party collaboration receivable	$ 12,700		$ 12,700

Stock based compensation

9 Months Ended

Sep. 30, 2020

Stock based compensation

Stock based compensation

9. Stock-based compensation

Stock-Based Compensation Expense

Total compensation cost recognized for all stock-based compensation awards in the condensed consolidated statements of operations and comprehensive income (loss) is as follows:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2020		2019		2020		2019

	(in thousands)
Research and development	$	1,524	$	1,304	$	4,973	$	5,975
General and administrative		2,008		2,045		6,459		6,145
Total stock-based compensation expense	$	3,532	$	3,349	$	11,432	$	12,120

Stock-based compensation expense by type of award included within the condensed consolidated statements of operations and comprehensive income (loss) was as follows:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2020		2019		2020		2019

	(in thousands)
Stock options	$	2,696	$	3,008	$	8,834	$	10,312
Restricted stock awards and units		740		259		2,345		1,609
Employee stock purchase plan awards		96		82		252		199
Total stock-based compensation expense	$	3,532	$	3,349		11,432		12,120

Restricted Stock Units

A summary of the status of and changes in unvested restricted stock unit activity under the Company’s equity award plans for the nine months ended September 30, 2020 was as follows:


		Weighted
		Average
		Grant Date
		Fair Value
	Units	Per Unit
Unvested restricted stock units as of December 31, 2019	455,404		12.16
Granted	455,284	$	12.83
Vested	(138,305)		11.77
Forfeited	(128,376)	$	11.14
Unvested restricted stock units as of September 30, 2020	644,007	$	12.92

Stock-based compensation of restricted stock units is based on the fair value of the Company’s common stock on the date of grant and is recognized over the vesting period. The weighted average fair value of restricted stock units granted to employees during the three and nine months ended September 30, 2020 was $13.34 and $12.83 per share, respectively. The weighted average fair value of restricted stock units granted to employees during the three and nine months ended September 30, 2019 was $25.40 and $11.65 per share, respectively. The restricted stock units granted in the three and nine months ended September 30, 2020 vest in equal amounts, annually over three years. The expense related to restricted stock units granted to employees was $0.6 million and $2.1 million for the three and nine months ended September 30, 2020, respectively. The expense related to restricted stock units granted to employees was $0.3 million and $1.6 million for the three and nine months ended September 30, 2019, respectively.

As of September 30, 2020, the Company had unrecognized stock-based compensation expense related to its unvested restricted stock units of $6.3 million, which is expected to be recognized over the remaining average vesting period of 2.0 years.

Stock Options

The following is a summary of stock option activity for the nine months ended September 30, 2020:


		Weighted		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value
	Shares	Price		(in years)	(in thousands)
Outstanding at December 31, 2019	5,317,326	$	15.98
Granted	1,388,135	$	12.07
Exercised	(214,287)	$	10.24
Cancelled or forfeited	(837,339)	$	16.99
Outstanding at September 30, 2020	5,653,835	$	15.09	7.6	$	2,078
Exercisable at September 30, 2020	2,997,805	$	15.50	6.5	$	1,312

As of September 30, 2020, the Company had unrecognized stock-based compensation expense related to its unvested stock options of $23.4 million which is expected to be recognized over the remaining weighted-average vesting period of 2.6 years.

Commitments and contingencies (Tables)

9 Months Ended

Sep. 30, 2020

Schedule of collaboration receivables and contract liabilities


	Balance at						Balance at
	December 31, 2019		Additions		Deductions		September 30, 2020

		(in thousands)
Related party collaboration receivable	$	18,496	$	29,152	$	(34,959)	$	12,689

Contract liabilities:
Deferred revenue	$	70,040	$		$	(24,369)	$	45,671

AbbVie Tau Collaboration Agreement

Schedule of allocation of transaction price


Performance Obligation	Amount
	(in thousands)
Research Services	$	34,482
First Development Option Material Right		34,518
Total	$	69,000

AbbVie Alpha Synuclein Collaboration Agreement

Schedule of allocation of transaction price


Performance Obligation	Amount
	(in thousands)
ASN Research Services	$	23,768
ASN First Development Option Material Right		41,232
Total	$	65,000

Neurocrine Collaboration Agreement

Schedule of allocation of variable consideration


Performance Obligation	Amount
	(in thousands)
Variable Consideration
VY-AADC Program	$	83,983
FA Program		113,033
Discovery Program 1		72,164
Discovery Program 2		71,262
Total	$	340,442

Schedule of allocation of fixed consideration


Performance Obligation	Amount
	(in thousands)
Fixed Consideration
VY-AADC Program	$	80,373
FA Program		6,005
Discovery Program 1		3,002
Discovery Program 2		3,002
Total	$	92,382

Stock based compensation - Stock Options - (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Outstanding, beginning balance (in shares)			5,317,326
Granted (in shares)			1,388,135
Exercised (in shares)			(214,287)
Cancelled or forfeited (in shares)			(837,339)
Outstanding, ending balance (in shares)	5,653,835		5,653,835
Exercisable (in shares)	2,997,805		2,997,805
Weighted Average Exercise Price
Outstanding (in dollars per share)			$ 15.98
Granted (in dollars per share)			12.07
Exercised (in dollars per share)			10.24
Cancelled or forfeited (in dollars per share)			16.99
Outstanding (in dollars per share)	$ 15.09		15.09
Exercisable (in dollars per share)	$ 15.50		$ 15.50
Remaining Contractual Life
Outstanding			7 years 7 months 6 days
Exercisable			6 years 6 months
Aggregate Intrinsic Value
Outstanding	$ 2,078		$ 2,078
Exercisable	1,312		1,312
Options disclosures
Stock-based compensation	3,532	$ 3,349	11,432	$ 12,120
Outstanding stock options
Options disclosures
Stock-based compensation	$ 2,696	$ 3,008	$ 8,834	$ 10,312

Other liabilities (Tables)

9 Months Ended

Sep. 30, 2020

Other liabilities

Summary of other current and non-current liabilities


	As of September 30,		As of December 31,
	2020		2019

	(in thousands)
Other current liabilities
Lease liability		3,539		3,193
Total other current liabilities	$	3,539	$	3,193

Other non-current liabilities
Lease liability	$	28,259	$	30,975
Other		1,001		1,001
Total other non-current liabilities	$	29,260	$	31,976

Net income (loss) per share (Details) - shares	9 Months Ended
Net income (loss) per share (Details) - shares	Sep. 30, 2020	Sep. 30, 2019
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	4,130,891	5,892,024
Unvested restricted common stock awards
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	117,647	235,294
Restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities		421,182
Outstanding stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities	4,013,244	5,235,548

Summary of significant accounting policies and basis of presentation (Policies)	9 Months Ended
	Sep. 30, 2020
Summary of significant accounting policies and basis of presentation
Basis of presentation	Basis of presentation The accompanying unaudited condensed consolidated financial statements of the Company have been prepared in accordance with accounting principles generally accepted in the United States (“GAAP”) for interim financial reporting and as required by Regulation S-X, Rule 10-01. Accordingly, they do not include all of the information and footnotes required by GAAP for complete financial statements. For further information, refer to the consolidated financial statements and footnotes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2019 as filed with the Securities and Exchange Commission (“SEC”) on March 3, 2020. These interim condensed consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the Company’s financial position and results of operations for the periods presented. Any reference in these notes to applicable guidance is meant to refer to the authoritative United States generally accepted accounting principles as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASU”) of the Financial Accounting Standards Board (“FASB”). See “Recently Adopted Accounting Pronouncements” below for discussion of the Company’s adoption of new guidance effective January 1, 2020. All amounts and disclosures set forth in this Quarterly Report on Form 10-Q reflect adoption of these changes.
Principles of Consolidation	Principles of consolidation The unaudited interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiary as disclosed in Note 2, Summary of Significant Accounting Policies and Basis of Presentation, within the “Notes to Consolidated Financial Statements” accompanying the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2019. Intercompany accounts and transactions have been eliminated.
Use of estimates	Use of estimates The preparation of consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. On an ongoing basis, the Company’s management evaluates its estimates, which include, but are not limited to, estimates related to revenue recognition, accrued expenses, stock-based compensation expense, and income taxes. The Company bases its estimates on historical experience and other market specific or other relevant assumptions that it believes to be reasonable under the circumstances. Actual results may differ from those estimates or assumptions. Certain reclassifications have been made to prior periods to conform to current period presentation.
Net Income (Loss) Per Share	Net Income (Loss) per Share Basic net income (loss) per share is computed by dividing net income (loss) by the weighted-average number of common shares and restricted stock unit awards outstanding during the period. Diluted net income (loss) per share is computed using the weighted-average number of common shares and restricted stock unit awards outstanding during the period and, if dilutive, the weighted-average number of potential shares of common stock and restricted stock unit awards.
Summary of Significant Accounting Policies and Recently Adopted Accounting Pronouncements	Summary of Significant Accounting Policies There have been no changes in the Company's significant accounting policies as described in, Summary of Significant Accounting Policies to the consolidated financial statements in its Annual Report on Form 10-K for the year ended December 31, 2019. Recently Adopted Accounting Pronouncements In 2016, the FASB issued ASU 2016-13, Financial Instruments-Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”), which amends the impairment model by requiring entities to use a forward-looking approach based on expected losses to estimate credit losses on certain types of financial instruments, including trade receivables and available-for-sale debt securities. The Company adopted the standard on January 1, 2020. Based on the composition of the Company's investment portfolio, current market conditions, and historical credit loss activity, the adoption of this standard did not have a material impact on the Company's consolidated financial statements and related disclosures. In August 2018, the FASB issued ASU No. 2018-13, Disclosure Framework - Changes to the Disclosure Requirements for Fair Value Measurement (“ASU 2018-13”). This standard eliminates, adds and modifies certain disclosure requirements for fair value measurements as part of its disclosure framework project. The Company adopted the standard on the required effective date of January 1, 2020. The adoption of this standard did not have a material impact on the Company’s consolidated financial statements and related disclosures.

Net income (loss) per share - Basic and diluted weighted average shares outstanding (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Numerator:
Net income (loss)	$ 85,611	$ (15,006)	$ 52,667	$ (31,023)
Denominator for basic net income (loss) per share:
Weighted average shares outstanding	37,242,504	36,742,993	37,079,242	35,581,408
Denominator for diluted net income (loss) per share:
Weighted average shares outstanding	37,242,504	36,742,993	37,079,242	35,581,408
Common stock options and restricted stock units	429,824		420,913
Weighted average shares and conversions	37,672,328	36,742,993	37,500,155	35,581,408

- Definition

Amount, after deduction of tax, noncontrolling interests, dividends on preferred stock and participating securities; of income (loss) available to common shareholders.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22595-107794

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=121326447&loc=d3e1448-109256

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 11
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22694-107794

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=121326447&loc=d3e1377-109256

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (a)
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 22
-URI http://asc.fasb.org/extlink&oid=120311839&loc=d3e8736-108599

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 250
-SubTopic 10
-Section 50
-Paragraph 11
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=109234566&loc=d3e22694-107794

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Publisher FASB
-Name Accounting Standards Codification
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-Publisher FASB
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+ Details

Other liabilities

9 Months Ended

Sep. 30, 2020

Other liabilities

Other liabilities

7. Other liabilities

As of September 30, 2020 and December 31, 2019, other current and non-current liabilities consisted of the following:


	As of September 30,		As of December 31,
	2020		2019

	(in thousands)
Other current liabilities
Lease liability		3,539		3,193
Total other current liabilities	$	3,539	$	3,193

Other non-current liabilities
Lease liability	$	28,259	$	30,975
Other		1,001		1,001
Total other non-current liabilities	$	29,260	$	31,976

Accrued expenses (Tables)

9 Months Ended

Sep. 30, 2020

Accrued expenses

Schedule of accrued expenses


	As of September 30,		As of December 31,
	2020		2019

	(in thousands)
Research and development costs	$	9,353	$	13,248
Employee compensation costs		6,649		5,733
Accrued goods and services		4,608		1,386
Professional services		976		897
Other		79		252
Total	$	21,665	$	21,516

Commitments and contingencies

9 Months Ended

Sep. 30, 2020

Commitments and contingencies

Commitments and contingencies

8. Commitments and contingencies

Significant Agreements

Sanofi Genzyme Collaboration Agreement

Summary of Agreement

In February 2015, the Company entered into a collaboration agreement with Sanofi Genzyme (the “Sanofi Genzyme Collaboration Agreement”) which included a non-refundable upfront payment of $65.0 million to the Company. In addition, contemporaneous with entering into the Sanofi Genzyme Collaboration Agreement, Sanofi Genzyme entered into a Series B Stock Purchase Agreement with the Company, under which Sanofi Genzyme purchased 10,000,000 shares of the Company’s Series B Preferred Stock for $30.0 million. The fair value of the Series B Preferred Stock at the time of issuance was approximately $25.0 million. The $5.0 million premium over the fair value is accounted for as additional consideration under the Sanofi Genzyme Collaboration Agreement.

Under the Sanofi Genzyme Collaboration Agreement, the Company granted Sanofi Genzyme an exclusive option to license, develop and commercialize (i) ex-U.S. rights to the following programs, which are referred to as Split Territory Programs; VY-AADC (NBIb-1817) for Parkinson’s disease (the “VY-AADC Program”), VY-FXN01 for Friedreich’s ataxia (the “FA Program”), a future program to be designated by Sanofi Genzyme (the “Future Program”), and VY-HTT01 for Huntington’s disease (the “Huntington’s Program”), with an incremental option to co-commercialize VY-HTT01 in the United States and (ii) worldwide rights to VY-SMN101 (the “Spinal Muscular Atrophy Program”). Sanofi Genzyme’s option for the Split Territory Programs and the Spinal Muscular Atrophy Program is triggered following the completion of the first proof-of-principle human clinical study (“POP Study”), on a program by program basis.

The Company was solely responsible for all costs incurred in connection with the development of the Split Territory Programs and the Spinal Muscular Atrophy Program prior to the exercise of an option by Sanofi Genzyme with the exception of the following: (i) at the Company’s request and upon mutual agreement, Sanofi Genzyme would provide “in-kind” services valued at up to $5.0 million and (ii) Sanofi Genzyme would be responsible for the costs and expenses of activities under the Huntington’s Program development plan to the extent such activities were covered by financial support Sanofi Genzyme is entitled to receive from a patient advocacy group.

Termination of Agreement

On June 14, 2019 (the “Termination Date”), the Company and Sanofi Genzyme executed a termination agreement to terminate the Sanofi Genzyme Collaboration Agreement (the “Sanofi Genzyme Termination Agreement”). Under the terms of the Sanofi Genzyme Termination Agreement, Sanofi Genzyme relinquished its rights to the exclusive license options to the Huntington’s Program, the FA Program and the Future Program. The Company has been relieved of its obligations to perform the research and development services under those programs through completion of the respective POP Studies. As a result, the Company gained worldwide rights to the Huntington’s Program and ex-U.S. rights to the FA Program. The ex-U.S. rights to the FA Program have been, in turn, transferred from the Company to Neurocrine Biosciences pursuant to the collaboration and option agreement with Neurocrine Biosciences. Additionally, the Company and Sanofi Genzyme entered into an Amended and Restated Option and License Agreement related to AAV capsids (the “Amended Capsid Agreement”). Under the Amended Capsid Agreement, Sanofi Genzyme has obtained exclusive option rights to exclusively license up to two select novel AAV capsids owned or controlled by the Company for exclusive use for up to two non-central nervous system (“non-CNS”) indications.

Sanofi Genzyme has granted the Company exclusive, irrevocable, perpetual, royalty-free, fully-paid sublicensable (through multiple tiers), non-transferable, worldwide licenses in Sanofi Genzyme’s interests in the collaboration technology generated under or used in the Huntington’s Program and the FA Program with respect to those programs pursuant to the Sanofi Genzyme Collaboration Agreement. In addition, Sanofi Genzyme has granted the Company non-exclusive, irrevocable, perpetual, royalty-free, fully-paid, sublicensable (through multiple tiers), non-transferable, worldwide licenses to the Sanofi Genzyme technology that was contributed to the Sanofi Genzyme

Collaboration Agreement and was used in the development or manufacture of product candidates prior to the termination date.

Under the Sanofi Genzyme Termination Agreement, the Company made a $10.0 million upfront payment to Sanofi Genzyme and has agreed to make a $10.0 million milestone payment to Sanofi Genzyme within fifteen days of the filing of an investigational new drug (“IND”) application for a product candidate incorporating certain intellectual property rights developed under or substantially related to the Huntington’s Program (a “Post-Termination HD Product”). The Company has agreed to pay Sanofi Genzyme (i) 50% of any income received from sublicensing arrangements related to Post-Termination HD Products in excess of specified thresholds and entered into prior to (a) the filing of an IND application for a Post-Termination HD Product or (b) the dosing of the first patient in a clinical trial for a Post-Termination HD Product in the United States or certain European countries, respectively and (ii) a low-double digit percentage of any income received from sublicensing arrangements outside the United States related to products incorporating intellectual property rights developed under, or substantially related to, the FA Program (collectively, “Post-Termination FA Products”) that are in excess of a specified threshold and entered into prior to the dosing of the first patient in a clinical trial for a Post-Termination FA Product in the United States or certain European countries, in each case, subject to certain limitations. The Company has also agreed to pay low-single digit royalties on net sales of Post-Termination HD Products. Under the Sanofi Genzyme Collaboration Agreement, the Company had rights to certain in-kind services. As of the effective date of the Sanofi Genzyme Termination Agreement, the Company waived its right to approximately $0.4 million in unused in-kind services, relinquished its rights to the Spinal Muscular Atrophy Program, and no longer has the right to receive any option payments, regulatory or commercial milestone payments or royalties from Sanofi Genzyme under the Sanofi Genzyme Collaboration Agreement.

The Company has granted Sanofi Genzyme an exclusive royalty-free, fully-paid, sublicensable (through multiple tiers), non-transferable, worldwide license under the Company’s interest in the collaboration technology generated under or used in the Spinal Muscular Atrophy Program pursuant to the Sanofi Genzyme Collaboration Agreement to manufacture, develop, and commercialize any Spinal Muscular Atrophy product. Under the Amended Capsid Agreement, the Company has granted Sanofi Genzyme an exclusive option to evaluate up to four capsids for no consideration. During the capsid evaluation period, the Company has granted Sanofi Genzyme a non-exclusive license to the capsid intellectual property to conduct evaluation studies. In addition, Sanofi Genzyme is able to evaluate up to two additional capsids for a low six-figure payment per additional capsid. The Company is not obligated to perform any additional research on the capsids. Sanofi Genzyme shall have the right to obtain an exclusive license for up to two capsids, each in a specified non-CNS indication. At its discretion, Sanofi Genzyme may exercise both its options for the same capsid for different specified non-CNS indications. Upon its exercise of each option, Sanofi Genzyme has agreed to pay the Company a $1.0 million option exercise fee. Under the Amended Capsid Agreement, the Company is also entitled to receive potential development and regulatory milestone payments upon the achievement of certain milestone events for products containing licensed capsids (“Sanofi Licensed Products”) of up to an aggregate of $15.0 million per Sanofi Licensed Product. In addition, for each specified indication, Sanofi Genzyme has agreed to pay to the Company a one-time sales milestone payment of $20.0 million, if aggregate worldwide net sales for all Sanofi Licensed Products for such specified indication surpass a specified amount, and low-to-mid single-digit tiered royalty payments on worldwide net sales of Sanofi Licensed Products, on a Sanofi Licensed Product-by-Sanofi Licensed Product basis.

Accounting Analysis

The Sanofi Genzyme Termination Agreement modifies both the pricing and scope of the Sanofi Genzyme Collaboration Agreement. As the modification does not add distinct goods or services to the Sanofi Genzyme Collaboration Agreement, the agreement is considered a modification of the original contract.

The Sanofi Genzyme Termination Agreement includes the following performance obligations: (i) worldwide license to collaboration technology and Sanofi Genzyme technology for the development, manufacturing and commercialization of the Huntington’s Program and (ii) worldwide license to collaboration technology and Sanofi Genzyme technology for the development, manufacturing and commercialization for the FA Program. Such performance obligations were satisfied upon the Termination Date as control had transferred upon execution of the Sanofi Genzyme Termination Agreement. Therefore, the remainder of the transaction price under the Sanofi Genzyme Collaboration Agreement, which had not yet been recognized, was recognized as revenue upon the Termination Date.

The Company recognized $28.7 million of revenue upon the Termination Date. This amount consists of $48.7 million of deferred revenue related to the original agreement as of the Termination Date, offset by (x) $10.0 million related to the fee paid by the Company to Sanofi Genzyme on the Termination Date, and (y) $10.0 million related to the milestone payment paid to Sanofi Genzyme upon the Company’s filing in September 2020 of an IND application for VY-HTT01 for the treatment of Huntington’s disease. In October 2020, the U.S. Food and Drug Administration (“FDA”) placed a clinical hold on the Company’s IND application for VY-HTT01 pending the resolution of certain chemistry, manufacturing and controls information requests. The Company has subsequently received written feedback from the FDA requesting additional information on specific CMC topics, including drug device compatibility and drug substance and product characterization and plans to work closely with the FDA to resolve them in a timely manner. Subject to its resolution of the clinical hold and the clearance of its IND application, the Company expects to initiate its clinical evaluation of VY-HTT01.

The Company made the milestone payment related to the filing of the IND for VY-HTT01 in September 2020. The Company has recorded the payment as a reversal of deferred revenue The $20.0 million payable by the Company to Sanofi Genzyme in aggregate was treated as consideration payable to a customer and therefore accounted for as a reduction of the transaction price.

During the three and nine months ended September 30, 2019 the Company recognized $0.2 million and $31.8 million of revenue, respectively, associated with its collaboration with Sanofi Genzyme related to research and development services and committee obligations performed during the period. No amounts were recorded as revenue under the Sanofi Genzyme Collaboration Agreement in the three and nine months ended September 30, 2020. As of September 30, 2020, there was no remaining deferred revenue related to the Sanofi Genzyme Collaboration Agreement.

Costs incurred relating to the programs that Sanofi Genzyme had the option to license under the Sanofi Genzyme Collaboration Agreement consisted of internal and external research and development costs, which primarily included: salaries and benefits, lab supplies and preclinical research studies. These costs were included in research and development expenses in the Company’s condensed consolidated statement of operations during the three and nine months ended September 30, 2019.

AbbVie Tau Collaboration Agreement

Summary of Agreement

In February 2018, the Company entered into an exclusive collaboration and option agreement (the “AbbVie Tau Collaboration Agreement”) with AbbVie for the research, development and commercialization of AAV and other virus-based gene therapy products for the treatment of diseases of the central nervous system and other neurodegenerative diseases related to defective or excess aggregation of tau protein in the human brain, including Alzheimer’s disease. Under the AbbVie Tau Collaboration Agreement, the Company and AbbVie agreed to collaborate on the research and development of specified vectorized antibody compounds comprised of an AAV or other viral capsid and a virus vector genome that encodes one or more antibodies that target and bind to a tau protein. The collaboration was comprised of a research period (the “Research Period”), a development period (the “Development Period”), and an exclusive license option (the “License Option”). The AbbVie Tau Collaboration Agreement included a non-refundable upfront payment to the Company of $69.0 million for services during the Research Period.

During the Research Period, each party agreed to identify up to five antibodies for inclusion in the collaboration. Subject to certain conditions and exceptions, the parties agreed to select up to three antibodies (each, a “Research Antibody”) as candidates for creation of research compounds (each, a “Research Compound”), with AbbVie having the right to select two of the three Research Antibodies. The Company was required to use diligent efforts to conduct antibody engineering and other research activities to create Research Compounds and to develop product candidates containing or comprised of such Research Compounds (“Product Candidates”). The Company was solely responsible for its costs and expenses during the Research Period. During a specified portion of the Research Period, AbbVie had the right to exercise one or more of its exclusive development options (each, a “Development Option”) to select up to a total of three Research Compounds (the “Selected Research Compounds”) and their corresponding Product Candidates (the “Selected Product Candidates”) to proceed to the Development Period.

Upon AbbVie’s exercise of a Development Option, AbbVie agreed to pay the Company $80.0 million for the first Selected Research Compound and $30.0 million each for up to two additional Selected Research Compounds. During the Development Period, the Company was obligated to use diligent efforts to conduct development activities, including IND application-enabling and Phase 1 clinical trial activities, for the Selected Research Compounds and corresponding Selected Product Candidates. The Company was solely responsible for the costs and expenses during the Development Period. During a specified portion of the Development Period (the “License Option Period”), AbbVie had the right to exercise its License Option to further develop and commercialize all of the Research Compounds (the “Licensed Compounds”), and corresponding product candidates (the “Licensed Products”). Upon AbbVie’s exercise of its License Option, AbbVie agreed to provide a one-time payment of $75.0 million to the Company, and the Company agreed to grant to AbbVie an exclusive, worldwide license, with the right to sublicense, under certain of the Company’s intellectual property rights to develop and commercialize the Licensed Compounds and the Licensed Products for all human diagnostic, prophylactic and therapeutic uses. In addition, after AbbVie’s exercise of the License Option, the Company had certain obligations to complete any remaining research and development activities that had not been completed for any Research Compounds and Product Candidates.

The Company’s research and development activities were to be conducted pursuant to the plans agreed to by the parties and overseen by a joint governance committee (“JGC”) as detailed in the AbbVie Tau Collaboration Agreement. Any material amendment to the research or development plans were required to be mutually agreed to by the Company and AbbVie, which could be through the JGC.

Under the AbbVie Tau Collaboration Agreement, AbbVie agreed to use commercially reasonable efforts to develop and commercialize at least one Licensed Product in each of the United States, Japan, the United Kingdom, Germany, France, Italy, and Spain. After exercise of the License Option, AbbVie was to be solely responsible for all development and commercialization activities relating to Licensed Compounds and Licensed Products at its sole cost and expense, subject to the agreed-upon research and development plans. The Company had the option to elect to share in AbbVie’s development costs relating to a Licensed Product on an indication-by-indication basis in exchange for a specified increase in royalties (a “Cost-Sharing Option”). If the Company exercised a Cost-Sharing Option, the Company would either reimburse AbbVie for AbbVie’s applicable development costs or, in the case of certain budget overruns, AbbVie would instead deduct applicable development costs, up to a specified cap, from milestone and royalty payments owed by AbbVie to the Company.

Under the AbbVie Tau Collaboration Agreement, the Company was eligible to receive specified development and first-sale milestone payments for each Licensed Compound of up to an aggregate of $550.0 million in the case of an Alzheimer’s disease indication, up to $230.0 million in the case of the first indication other than Alzheimer’s disease and up to $115.0 million for a subsequent non-Alzheimer’s disease indication. Additionally, the Company was eligible to receive tiered, escalating royalties, in a range from a high-single digit to a mid-to-high teen (or, if the Company had exercised its Cost-Sharing Option, low-twenties) percentage of aggregate net sales of Licensed Products on a Licensed Compound by Licensed Compound basis, subject to potential reductions in certain circumstances. For each Licensed Product, AbbVie also had the right to decrease or eliminate its royalty payments on such Licensed Product in exchange for a one-time payment by AbbVie at a fair market value to be negotiated by the parties or determined pursuant to dispute resolution procedures specified in the AbbVie Tau Collaboration Agreement.

Termination

On August 3, 2020 (the “AbbVie Collaboration Termination Date”), the termination of the AbbVie Tau Collaboration Agreement in its entirety became effective, in accordance with its terms and conditions, subject to surviving rights and obligations thereunder. In connection with such termination, the Company was obligated to undertake certain transition activities, including transferring to AbbVie data and reports generated under the collaboration as well as any regulatory filing relating to certain compounds and product candidates investigated in the collaboration. All such activities were completed on or prior to September 30, 2020. As a result of the termination, the Company has been relieved of future research and development obligations under the collaboration. Exclusivity provisions restricting either party or any of its respective affiliates from directly or indirectly exploiting any vectorized antibody compound targeting a tau protein and restricting the Company, alone or jointly with any third party, from

directly or indirectly exploiting specified antibodies targeting a tau protein have also terminated. Each party retains a royalty-free, exclusive license to the other’s interest in certain intellectual property rights developed by or on behalf of either party under the collaboration (the “Joint IP”) to exploit antibodies it contributed to the collaboration as well as a royalty-free, non-exclusive license to the Joint IP for any other purpose. Further, AbbVie has granted the Company, effective as of the AbbVie Collaboration Termination Date, a worldwide, royalty-free, transferable, sublicensable (though multiple tiers), exclusive license to AbbVie’s interest in Joint IP to exploit research compounds or product candidates that were investigated under the collaboration and do not encode antibodies contributed by AbbVie or include active pharmaceutical ingredients owned by AbbVie or its affiliates, for all human diagnostic, prophylactic and therapeutic uses. The Company is not obligated to repay the upfront payment it received from AbbVie in connection with entering into the AbbVie Tau Collaboration Agreement but is no longer eligible to receive option payments, milestone payments or royalties thereunder.

Accounting Analysis

The Company assessed the promised goods and services under the AbbVie Tau Collaboration Agreement, in accordance with ASC 606, Revenue from Contracts with Customers (“ASC 606”) and determined that the AbbVie Tau Collaboration Agreement included the following performance obligations: (i) research services during the Research Period (through the delivery of the final research report) including the identification of the Research Antibodies, conduct of research activities and provision of information to AbbVie to allow AbbVie to determine whether to exercise up to three development options to be rendered (collectively, the “Research Services”), and (ii) a material right associated with the Development Option on the first Research Compound and associated Product Candidates (“First Development Option Material Right”). The first Development Option provided AbbVie with (i) additional development services on a selected Research Compound and (ii) the ability to exercise the License Option. The Company concluded the option provided a material right as the consideration paid by AbbVie upon exercise of the first Development Option would have been less than the amount that the Company would otherwise have expected to receive outside the context of the contract.

The Company concluded that the First Development Option Material Right was a separate performance obligation under ASC 606 as AbbVie would have been provided additional services and a License Option for additional consideration that represented a significant discount from amounts that would otherwise be offered outside the context of the contract. The First Development Option Material Right was distinct from the other performance obligations in the arrangement as it was an option in the contract that was not required for AbbVie to obtain the benefit of the other promised goods or services in the arrangement. The First Development Option Material Right did not include the underlying goods or services that were delivered upon exercise of the option, but rather represented the value to the customer of having the right to obtain development services and the right to the License Option at an advantageous price.

The Company received a nonrefundable, upfront payment of $69.0 million as consideration under the AbbVie Tau Collaboration Agreement, which represented the transaction price at inception. Additional consideration to be paid to the Company upon the exercise of the Development and License Options by AbbVie or upon reaching certain milestones was excluded from the transaction price as they relate to option fees and milestones that could only be achieved subsequent to the option exercise or were outside of the initial contract term.

The Company allocated the transaction price to the separate performance obligations based on their relative standalone selling price. The Company determined the standalone selling price at contract inception based on each obligation’s estimated standalone selling price (“ESP”). The Company determined the ESP for the research services obligation based on internal estimates of the costs to perform the services, including expected internal expenses and expenses with third parties for services and supplies, inclusive of a reasonable profit margin. Significant inputs used to determine the total expense of the research services include the length of time required, the internal hours expected to be incurred on the services and the number and costs of various studies that would be performed to complete the Research Plan. The ESP for the First Development Option Material Right was determined based on the fees AbbVie would pay to exercise the Development and License Options, the estimated costs to perform the development services, inclusive of a reasonable profit margin, the estimated value of the License Option using comparable transactions, and the probability that the Development and License Options would be exercised by AbbVie.

Based on the relative standalone selling price, the allocation of the transaction price to the separate performance obligations was as follows:


Performance Obligation	Amount
	(in thousands)
Research Services	$	34,482
First Development Option Material Right		34,518
Total	$	69,000

The Company recognized the amounts associated with Research Services on a proportional performance basis over the period of service using input-based measurements of total cost of research incurred to estimate proportion performed and remeasured its progress towards completion at the end of each reporting period. The amount allocated to the First Development Option Material Right was recorded as deferred revenue and was expected to be recognized either over the period in which goods and services underlying the option are transferred or upon expiry of the option.

During the three and nine months ended September 30, 2020, the Company recognized $0.9 million and $4.5 million, respectively, of revenue related to the Research Services associated with the AbbVie Tau Collaboration Agreement performed prior to the AbbVie Collaboration Termination Date. During the three and nine months ended September 30, 2020, the Company recognized additional revenue of $46.3 million, related to the remaining amounts included in deferred revenue at the AbbVie Collaboration Termination Date, given that the Company does not have any performance obligations under the AbbVie Tau Collaboration Agreement subsequent to September 30, 2020. During the three and nine months ended September 30, 2019 the Company recognized $3.2 million and $8.1 million, respectively, of revenue related to Research Services associated with the AbbVie Tau Collaboration Agreement. As of September 30, 2020, there was no remaining deferred revenue related to the AbbVie Tau Collaboration Agreement.

Costs incurred relating to the AbbVie Tau Collaboration Agreement consisted of internal and external research and development costs, which primarily include: salaries and benefits, lab supplies, and preclinical research studies. All of these costs are included in research and development expenses in the Company’s condensed consolidated statement of operations during the three and nine months ended September 30, 2020.

AbbVie Alpha Synuclein Collaboration Agreement

Summary of Agreement

In February 2019, the Company entered into an exclusive collaboration and option agreement (“the AbbVie Alpha-Synuclein Collaboration Agreement”) with AbbVie, for the research, development and commercialization of AAV and other virus-based gene therapy products directed against pathological species of alpha-synuclein for the potential treatment of Parkinson’s disease and other diseases characterized by the abnormal accumulation of misfolded alpha-synuclein protein (“synucleinopathies”). Under the AbbVie Alpha-Synuclein Collaboration Agreement, the Company and AbbVie agreed to collaborate on the research and development of specified vectorized antibody compounds comprised of an AAV or other viral capsid and a virus vector genome that encodes one or more antibodies that target and bind to the alpha-synuclein protein. The collaboration was comprised of a research period (the “ASN Research Period”), an optional development period (the “ASN Development Period”), and an exclusive license option (the “ASN License Option”). The AbbVie Alpha-Synuclein Collaboration Agreement included a non-refundable upfront payment to the Company of $65.0 million for services during the ASN Research Period.

During the ASN Research Period, the Company was obligated to conduct research activities directed to constructing one or more virus vectors that encode antibodies designated by AbbVie (the “AbbVie Designated Antibodies”) which initially were to be antibodies provided by AbbVie. The Company was obligated to use diligent efforts to conduct research activities to create research compounds (“ASN Research Compounds”) and to develop product candidates containing or comprised of the ASN Research Compounds (“ASN Product Candidates”). The Company was solely responsible for the costs and expenses during the ASN Research Period. During a specified portion of the ASN Research Period, AbbVie had the right to exercise one or more of its exclusive development options to select

up to a total of four ASN Research Compounds and their corresponding ASN Product Candidates to proceed to the ASN Development Period.

Upon AbbVie’s exercise of an option to proceed to the ASN Development Period (an “ASN Development Option”), AbbVie agreed to pay the Company $80.0 million for the first ASN Research Compound and $30.0 million each for up to three additional ASN Research Compounds. During the ASN Development Period, the Company was obligated to use diligent efforts to conduct development activities, including IND application-enabling and Phase 1 clinical trial activities, for each selected ASN Research Compound and corresponding selected ASN Product Candidates. The Company was solely responsible for the costs and expenses during the ASN Development Period. During a specified portion of the ASN Development Period, AbbVie had the right to exercise its ASN License Option to further develop and commercialize all of the ASN Research Compounds and corresponding ASN Product Candidates. Upon AbbVie’s exercise of its ASN License Option, the Company agreed to grant to AbbVie an exclusive, worldwide license, with the right to sublicense, under certain of the Company’s intellectual property rights to develop and commercialize the licensed compounds and the licensed products for all human diagnostic, prophylactic and therapeutic uses. In addition, after AbbVie’s exercise of the ASN License Option, the Company had certain obligations to complete any remaining research and development activities that were not completed for any ASN Research Compounds and ASN Product Candidates.

The Company’s research and development activities were to be conducted pursuant to the plans agreed to by the parties and overseen by a joint governance committee (or “ASN JGC”) as detailed in the AbbVie Alpha-Synuclein Collaboration Agreement. Any material amendment to the research or development plans, however, were required to be mutually agreed to by the parties, which could be through the ASN JGC.

Under the AbbVie Alpha-Synuclein Collaboration Agreement, AbbVie agreed to use commercially reasonable efforts to develop and commercialize at least one licensed product in each of the United States, Japan, the United Kingdom, Germany, France, Italy and Spain. After exercise of the ASN License Option, AbbVie was solely responsible for all development and commercialization activities relating to licensed compounds and licensed products at its sole cost and expense, subject to the Company’s obligation to complete any remaining research and development activities set forth in the agreed-upon research and development plans.

Under the terms of the AbbVie Alpha-Synuclein Collaboration Agreement, the Company was eligible to receive (i) specified development and first-sale milestone payments for each licensed compound of up to an aggregate of $450.0 million in the case of a Parkinson’s disease indication and up to $185.0 million in the case of the first indication other than Parkinson’s disease and $92.5 million for a subsequent non-Parkinson’s disease indication; (ii) specified commercial milestone payments based on net sales for all licensed products and all indications up to an aggregate of $500.0 million; and (iii) tiered, escalating royalties, in the mid-single digit percentage range for aggregate net sales of licensed products on a licensed compound by licensed compound basis, subject to potential reductions in certain circumstances.

Termination

On August 3, 2020 (the “AbbVie Collaboration Termination Date”), the termination of the AbbVie Alpha-Synuclein Collaboration Agreement in its entirety became effective, in accordance with its terms and conditions, subject to surviving rights and obligations thereunder. In connection with such termination, the Company was obligated to undertake certain transition activities including transferring to AbbVie data and reports generated under the collaboration as well as any regulatory filings relating to compounds and product candidates investigated in the collaboration. All such activities were completed on or prior to September 30, 2020. As a result of the termination, the Company has been relieved of future research and development obligations under the collaboration. Exclusivity provisions restricting either party or any of its respective affiliates from directly or indirectly exploiting any vectorized antibody compound targeting an alpha-synuclein protein and restricting the Company, alone or jointly with any third party, from directly or indirectly exploiting specified antibodies have also terminated. AbbVie retains a royalty-free, exclusive license to the Company’s interest in the Joint IP to exploit antibodies AbbVie contributed to the collaboration. The Company otherwise retains a royalty-free, non-exclusive license to AbbVie’s interest in the Joint IP. The Company is not obligated to repay the

upfront payment it received from AbbVie in connection with entering into the AbbVie Alpha-Synuclein Collaboration Agreement but is no longer eligible to receive option payments, milestone payments, or royalties thereunder.

Accounting Analysis

The Company assessed the promised goods and services under the AbbVie Alpha-Synuclein Collaboration Agreement, in accordance with ASC 606, and determined that the AbbVie Alpha-Synuclein Collaboration Agreement included the following performance obligations: (i) research services during the ASN Research Period (through the delivery of the final research report) including the conduct of research activities and provision of information to AbbVie to allow AbbVie to determine whether to exercise up to four ASN Development Options (collectively, the “ASN Research Services”), and (ii) a material right associated with the first ASN Development Option on the first ASN Research Compound and associated ASN Product Candidates (“ASN First Development Option Material Right”). The exercise of the first ASN Development Option provided AbbVie with (i) additional development services on a selected ASN Research Compound and (ii) the ability to exercise the ASN License Option. The Company has concluded the option provided a material right as the consideration paid by AbbVie upon exercise of the first ASN Development Option would have been less than the amount that the Company would otherwise have expected to receive outside the context of the contract.

The Company concluded that the ASN First Development Option Material Right was a separate performance obligation under ASC 606 as AbbVie was provided additional services and an ASN License Option for additional consideration that represented a significant discount from amounts that would otherwise be offered outside the context of the contract. The ASN First Development Option Material Right was distinct from the other performance obligations in the arrangement as it was an option in the contract that was not required for AbbVie to obtain the benefit of the other promised goods or services in the arrangement. The ASN First Development Option Material Right does not include the underlying goods or services that were delivered upon exercise of the option, but rather represented the value to the customer of having the right to obtain development services and the right to the ASN License Option at an advantageous price.

The Company received a nonrefundable, upfront payment of $65.0 million as consideration under the AbbVie Alpha-Synuclein Collaboration Agreement, which represented the transaction price at inception. Additional consideration to be paid to the Company upon the exercise of the ASN Development and ASN License Options by AbbVie or upon reaching certain milestones were excluded from the transaction price as they related to option fees and milestones that could only be achieved subsequent to the option exercise or are outside of the initial contract term.

The Company allocated the transaction price to the separate performance obligations based on their relative standalone selling price. The Company determined the standalone selling price at contract inception based on each obligation’s ESP. The Company determined the ESP for the research services obligation based on internal estimates of the costs to perform the services, including expected internal expenses and expenses with third parties for services and supplies, inclusive of a reasonable profit margin. Significant inputs used to determine the total expense of the research services include the length of time required, the internal hours expected to be incurred on the services and the number and costs of various studies that would have been performed to complete the agreed upon ASN research plan. The ESP for the ASN First Development Option Material Right was determined based on the fees AbbVie would pay to exercise the ASN Development and ASN License Options, the estimated costs to perform the development services, inclusive of a reasonable profit margin, the estimated value of the ASN License Option using comparable transactions, and the probability that the ASN Development and License Options would be exercised by AbbVie.

Based on the relative standalone selling price, the allocation of the transaction price to the separate performance obligations was as follows:


Performance Obligation	Amount
	(in thousands)
ASN Research Services	$	23,768
ASN First Development Option Material Right		41,232
Total	$	65,000

The Company recognized the amounts associated with the ASN Research Services on a proportional performance basis over the period of service using input-based measurements of total cost of research incurred to estimate proportion performed and remeasured its progress towards completion at the end of each reporting period. The amount allocated to the ASN First Development Option Material Right was recorded as deferred revenue and was expected to be recognized either over the period in which goods and services underlying the option are transferred or upon expiry of the option.

During the three and nine months ended September 30, 2020, the Company recognized $0.5 million and $4.8 million, respectively, of revenue related to ASN Research Services associated with the AbbVie Alpha-Synuclein Collaboration Agreement performed prior to the AbbVie Collaboration Termination Date, given that the Company does not have any performance obligations under the AbbVie Tau Collaboration Agreement subsequent to September 30, 2020. During the three and nine months ended September 30, 2020, the Company recognized additional revenue of $58.9 million, related to the remaining amounts included in deferred revenue at the AbbVie Collaboration Termination Date. During the three and nine months ended September 30, 2019, the Company recognized $0.2 million and $0.7 million, respectively, of revenue related to ASN Research Services associated with the AbbVie Alpha-Synuclein Collaboration Agreement. As of September 30, 2020, there was no remaining deferred revenue related to the AbbVie Alpha-Synuclein Collaboration Agreement.

Costs incurred relating to the AbbVie Alpha-Synuclein Collaboration Agreement consist of internal and external research and development costs, which primarily include salaries and benefits, lab supplies, and preclinical research studies. All of these costs are included in research and development expenses in the Company’s condensed consolidated statement of operations during the three and nine months ended September 30, 2020.

Neurocrine Collaboration Agreement

Summary of Agreement

In March 2019, the Company entered into the Neurocrine Collaboration Agreement for the research, development and commercialization of certain of its AAV gene therapy products. Under the Neurocrine Collaboration Agreement, the Company has agreed to collaborate on the conduct of four collaboration programs (the “Neurocrine Programs”) which include: (i) the VY-AADC Program, (ii) the FA Program (collectively with the VY-AADC Program, the “Existing Programs”), and (iii) two programs to be determined by the Company and Neurocrine at a later date (the “Discovery Programs”).

In June 2019, in conjunction with the termination of the Sanofi Genzyme Collaboration Agreement, the Company gained ex-U.S. rights to the FA Program. The Company’s ex-U.S. rights to the FA Program were subsequently transferred to Neurocrine under the terms of the Neurocrine Collaboration Agreement. To facilitate the transfer of the ex-U.S. rights to the FA Program to Neurocrine, the Company and Neurocrine executed an amendment to the Neurocrine Collaboration Agreement (the “June 2019 Modification”), and Neurocrine paid $5.0 million to the Company. There were no other changes in pricing or scope of the obligations required to be performed under the Neurocrine Collaboration Agreement.

Under the terms of the Neurocrine Collaboration Agreement, the Company has agreed to collaborate with Neurocrine on, and to grant, exclusive, royalty-bearing, non-transferable, sublicensable licenses to certain of its intellectual property rights, for all human and veterinary diagnostic, prophylactic, and therapeutic uses, for the research,

development, and commercialization of gene therapy products (the “Collaboration Products”) on a worldwide basis under (i) the VY-AADC Program; (ii) the FA Program; and (iii) each Discovery Program.

Pursuant to development plans to be agreed by the parties, which will be overseen by a joint steering committee (“JSC”), the Company has operational responsibility, subject to certain exceptions, for the conduct of each Neurocrine Program prior to the occurrence of a specified event for such Neurocrine Program (a “Transition Event”), as described below, and is required to use commercially reasonable efforts to develop the corresponding Collaboration Products. Neurocrine has agreed to be responsible for all costs incurred by the Company in conducting these activities for each Neurocrine Program, in accordance with an agreed budget for each Neurocrine Program. If the Company breaches its development responsibilities or in certain circumstances upon a change in control, Neurocrine has the right but not the obligation to assume the activities under such Neurocrine Program.

Upon the occurrence of a Transition Event, Neurocrine has agreed to assume responsibility for development, manufacturing and commercialization activities for such Neurocrine Program from the Company and to pay milestones and royalties on future net sales as described further below. The Transition Events are (i) with respect to the VY-AADC Program, the Company’s receipt of topline data for the RESTORE-1 Phase 2 clinical trial for VY-AADC (NBIb-1817); (ii) with respect to the FA Program, the Company’s receipt of topline data for the initial Phase 1 clinical trial for a FA Program product candidate; and (iii) with respect to each Discovery Program, the preparation by the Company and the approval by Neurocrine of an IND application to be filed with the Food and Drug Administration (the “FDA”) by Neurocrine for the first development candidate in such Discovery Program. For each Existing Program, the Company has the option (the “Co-Co Option”) to co-develop and co-commercialize such Neurocrine Program upon the occurrence of a specified event (a “Co-Co Trigger Event”). Should the Company elect to exercise its Co-Co Option, the Company has agreed to enter into a cost- and profit-sharing arrangement with Neurocrine (a “Co-Co Agreement”), whereby it has agreed to jointly develop and commercialize Collaboration Products for such Neurocrine Existing Program (“Co-Co Products”) and share in its costs, profits and losses, and the Company agrees to forfeit certain milestones and royalties on net sales in the United States during the effective period of the applicable Co-Co Agreement. The Co-Co Trigger Events are (i) with respect to the VY-AADC Program, the Company’s receipt of topline data for the ongoing RESTORE-1 Phase 2 clinical trial for VY-AADC (NBIb-1817) and (ii) with respect to the FA Program, the receipt of topline data for the initial Phase 1 clinical trial for a FA Program product candidate.

Subject to exceptions specified in the Neurocrine Collaboration Agreement, profits and losses under the Company’s Co-Co Option are agreed to be allocated (i) 50% to Neurocrine and 50% to the Company for a Collaboration Product from the VY-AADC Program and (ii) 60% to Neurocrine and 40% to the Company for a Collaboration Product from the FA Program; provided, however, that Neurocrine may elect, within a specified period following the acceptance for filing of a biologics license application from the FDA, to pay a $35.0 million rate-shifting fee to the Company to change the allocation for the VY-AADC Program to 55% to Neurocrine and 45% to the Company. The parties have agreed that each Co-Co Agreement will provide the Company the right to terminate for any reason upon prior written notice to Neurocrine and Neurocrine the right to terminate in certain circumstances upon change of control.

The Company’s research and development activities under the Neurocrine Collaboration Agreement are to be conducted pursuant to plans agreed to by the parties, on a program-by-program basis, and overseen by the JSC, as detailed in the Neurocrine Collaboration Agreement.

The parties have committed to agree on a list of up to eight target genes (the “Targets”) from which Neurocrine has the right to nominate Targets for the two Discovery Programs. The Targets nominated for the Discovery Programs must be approved by a consensus of the JSC or the executive officers.

The Neurocrine Collaboration Agreement provides for an upfront non-refundable payment of $115.0 million, as well as for aggregate development and regulatory milestone payments from Neurocrine to the Company for Collaboration Products under (i) the VY-AADC Program of up to $170.0 million; (ii) the FA Program of up to $195.0 million, and (iii) each of the two Discovery Programs of up to $130.0 million per Discovery Program. The Company may be entitled to receive aggregate commercial milestone payments for each Collaboration Product of up to $275.0 million, subject to an aggregate cap on commercial milestone payments across all Neurocrine Programs of $1.1 billion. Furthermore, in connection with the Neurocrine Collaboration Agreement, Neurocrine has purchased 4,179,728 shares of the Company’s common stock at a price of $11.9625 per share, for an aggregate purchase price of $50.0 million.

Neurocrine has also agreed to pay the Company royalties, based on future net sales of the Collaboration Products. Such royalty percentages, for net sales in and outside the United States, as applicable, range (i) for the VY-AADC Program, from the mid-teens to low thirties and the low-teens to low twenties, respectively; (ii) for the FA Program, from the low-teens to high-teens and high-single digits to mid-teens, respectively; and (iii) for each Discovery Program, from the high-single digits to mid-teens and mid-single digits to low-teens, respectively. On a country-by-country and program-by-program basis, royalty payments would commence on the first commercial sale of a Collaboration Product and terminate on the later of (a) the expiration of the last patent covering the Collaboration Product or its method of use in such country, (b) ten years from the first commercial sale of the Collaboration Product in such country and (c) the expiration of regulatory exclusivity in such country, or the Royalty Term. Royalty payments may be reduced by up to 50% in specified circumstances, including expiration of patents rights related to a Collaboration Product, approval of biosimilar products in a given country or required payment of licensing fees to third parties related to the development and commercialization of any Collaboration Product. Additionally, the licenses granted to Neurocrine shall automatically convert to fully paid-up, non-royalty bearing, perpetual, irrevocable, exclusive licenses on a country-by-country and product-by-product basis upon the expiration of the Royalty Term applicable to such Collaboration Product in such country.

Under the terms of the Neurocrine Collaboration Agreement and subject to specified exceptions therein, each party owns the entire right, title and interest in and to all intellectual property rights made solely by its employees or agents in the course of the collaboration. The parties jointly own all rights, title and interest in and to all intellectual property rights made or invented jointly by employees or agents of both parties.

During the term of the Neurocrine Collaboration Agreement, neither party nor any of its respective affiliates is permitted to directly or indirectly exploit any AAV-based gene therapy products directed to a Target to which a Collaboration Product is directed, subject to specified exceptions including the parties’ conduct of basic research activities.

Unless earlier terminated, the Neurocrine Collaboration Agreement expires on the later of (i) the expiration of the last to expire royalty term with respect to a Collaboration Product in all countries in the relevant territory or (ii) the expiration or termination of all Co-Co Agreements. Neurocrine may terminate the Neurocrine Collaboration Agreement in its entirety or on a program-by-program or country-by-country basis by providing at least (x) 180-day advance notice if such notice is provided prior to the first commercial sale of the Collaboration Product to which the termination applies or (y) one-year advance notice if such notice is provided after the first commercial sale of the Collaboration Product to which the termination applies. The Company may terminate the Neurocrine Collaboration Agreement, subject to specified conditions, if Neurocrine challenges the validity or enforceability of certain of the Company’s intellectual property rights. Subject to a cure period, either party may terminate the Neurocrine Collaboration Agreement in the event of a material breach by the other party in whole or in part, subject to specified conditions.

Upon termination in certain cases, Neurocrine has agreed to grant to the Company licenses to certain Neurocrine intellectual property, subject to a negotiation between the parties to establish royalty rates for use of such intellectual property. In the event of a breach by the Company with respect to a Neurocrine Program, if such termination were to occur after a Transition Event, then (i) if a Co-Co Agreement is in effect with respect to such program, Neurocrine can terminate the Co-Co Agreement for such program and the Company would no longer have co-development and co-commercialization rights with respect to the Collaboration Product and (ii) subject to any license agreements, Neurocrine would no longer have any obligations with respect to any Collaboration Products resulting from such program.

Accounting Analysis

At inception, the Neurocrine Collaboration Agreement included the following performance obligations: (i) research and development services for each Existing Program combined with a development and commercialization license for each such program and (ii) research and development services for each Discovery Program combined with a development and commercialization license for each program. The research services and license on a program by program basis are not distinct as Neurocrine cannot benefit from such license on its own or from other resources commonly available

in the industry, without the corresponding research services due to the unique and specialized expertise of the Company that is not readily available in the marketplace.

The Company has identified $92.4 million of fixed transaction price consisting of the $115.0 million upfront fee and $5.0 million payment from the June 2019 Modification, offset by a discount of $27.6 million related to the $50.0 million equity investment of 4,179,728 shares when measured at fair value on the date of issuance. The Company is also entitled to reimbursement of costs incurred by the Company prior to the Transition Events associated with each Neurocrine Program. These amounts are determinable based on program plans and budgets, and the Company has a contractual right to the payment of costs incurred under the agreed upon program plans. The Company has utilized the most likely amount approach and estimated the expected cost reimbursement to be $431.1 million at inception. The Company has concluded that these amounts do not require a constraint and are included in the transaction price at inception. The Company considers this estimate at each reporting date and updates the estimate based on information available. During the second quarter of 2020, the Company has further revised the estimate of the expected reimbursement to $340.4 million based on current expectations. Additional consideration to be paid to the Company upon reaching certain milestones are excluded from the transaction price at inception due to the uncertainty of achieving the development and regulatory milestones.

The Company has allocated the fixed transaction price to the separate performance obligations based on the relative standalone selling price of each performance obligation or in the case of certain variable consideration to one or more performance obligations. The estimated standalone selling prices for performance obligations, that include a license and research services, were developed using the estimated selling price of the license, using comparable and market data, and an estimate of the overall effort to perform the research services along with a reasonable profit for research services.

The Company has concluded that the variable consideration related to the cost reimbursement of each program will be allocated to each respective program as the cost reimbursement relates specifically to the respective program services being performed under the Neurocrine Collaboration. The reimbursement of research services is considered to be at a market rate and the allocation of the fixed consideration to all of the performance obligations depicts the estimated amounts in which it would expect to receive for these obligations, absent the variable consideration related to the research reimbursement. The total variable consideration allocated to each program related to the expected cost reimbursement was as follows as of September 30, 2020:


Performance Obligation	Amount
	(in thousands)
Variable Consideration
VY-AADC Program	$	83,983
FA Program		113,033
Discovery Program 1		72,164
Discovery Program 2		71,262
Total	$	340,442

Based on the relative standalone selling price allocation, the allocation of the transaction price, exclusive of the variable consideration allocated to the individual performance obligations, to the separate performance obligations was as follows:


Performance Obligation	Amount
	(in thousands)
Fixed Consideration
VY-AADC Program	$	80,373
FA Program		6,005
Discovery Program 1		3,002
Discovery Program 2		3,002
Total	$	92,382

The Company recognizes the transaction price associated with each performance obligation on a proportional performance basis over the period of service using input-based measurements such as costs incurred to date, to estimate proportion performed, and remeasures its progress towards completion at the end of each reporting period.

During the three and nine months ended September 30, 2020, the Company recognized $11.2 million and $50.1 million of revenue, respectively, associated with its collaboration with Neurocrine related to research and development services performed during the period and the corresponding cost reimbursement receivable. During the three and nine months ended September 30, 2019, the Company recognized $16.8 million and $31.1 million of revenue, respectively, associated with its collaboration with Neurocrine related to research and development services performed during the period and the corresponding cost reimbursement receivable.

The following table presents changes in the balances of the Company’s related party collaboration receivables and contract liabilities during the nine months ended September 30, 2020:


	Balance at						Balance at
	December 31, 2019		Additions		Deductions		September 30, 2020

		(in thousands)
Related party collaboration receivable	$	18,496	$	29,152	$	(34,959)	$	12,689

Contract liabilities:
Deferred revenue	$	70,040	$		$	(24,369)	$	45,671

The change in the receivables balance for the nine months ended September 30, 2020 is primarily driven by amounts owed to the Company for research and development services provided, offset by amounts collected from Neurocrine during the period.

As of September 30, 2020, there was $45.7 million of deferred revenue related to the Neurocrine Collaboration Agreement, which is classified as either current or non-current in the accompanying condensed consolidated balance sheet based on the period the services are expected to be delivered. Additionally, as of September 30, 2020, there was $12.7 million of related party collaboration receivables related to reimbursable costs expected to be received from Neurocrine for research and development services performed.

Costs incurred relating to the Collaboration Programs consist of internal and external research and development costs, which primarily include: salaries and benefits, lab supplies, preclinical research studies, clinical studies, consulting services, and commercial development. These costs are included in research and development expenses in the Company’s condensed consolidated statement of operations during the three and nine months ended September 30, 2020.

The Company incurred approximately $0.8 million of costs to obtain the Neurocrine Collaboration Agreement which were payable only upon the close of the deal and therefore considered incremental costs of obtaining a contract with a customer and capitalized. The costs are recorded in prepaid expenses and other non-current assets and are being amortized over the period in which the research services will be provided.

Other Agreements

The Company has entered into various agreements with contract research organizations and institutions to license intellectual property. In consideration for the rights licensed under such agreements, the Company generally made upfront payments, which were recorded as research and development expense as the acquired technologies were considered in-process research and development. The license agreements obligate the Company to make additional payments that are contingent upon specific clinical trial and regulatory approval milestones being achieved as well as royalties on future product sales. The agreements to license intellectual property include potential milestone payments that are dependent upon the development of products licensed under the agreements and contingent upon the achievement of clinical trial or regulatory approval milestones. To date, the Company reached a milestone related to first

patient dosing on the RESTORE-1 Phase 2 clinical trial which resulted in a $0.1 million milestone payment to one of its licensors. The Company can generally terminate the license agreements upon 30 to 90 days’ prior written notice.

Additionally, certain license agreements require the Company to reimburse the licensor for certain past and ongoing patent related expenses.

During the year ended December 31, 2016, the Company entered into a research and development funding arrangement with a non-profit organization that provides up to $4.0 million in funding to the Company upon the achievement of clinical and development milestones. The agreement provides that the Company repay amounts received under certain circumstances including termination of the agreement, and to pay an amount up to 2.6 times the funding received upon successful development and commercialization of any products developed. During the year ended December 31, 2017, the Company earned a milestone payment of $1.0 million. The Company has evaluated the arrangement and has concluded that it represents a research and development financing arrangement as it is probable that the Company will repay amounts received under the arrangement. As a result, the $1.0 million earned to date is recorded as a non-current liability in the condensed consolidated balance sheet.

Litigation

The Company is not a party to any material legal matters or claims and did not have contingency reserves established for any litigation liabilities as of September 30, 2020 or December 31, 2019.

Commitments and contingencies - Neurocrine Collaboration Agreement - (Details) $ / shares in Units, $ in Thousands	3 Months Ended				6 Months Ended	9 Months Ended
	Sep. 30, 2020 USD ($)	Jun. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Mar. 31, 2019 USD ($) item $ / shares shares	Jun. 30, 2019 USD ($) shares	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)
Allocation of Transaction Price
Revenue recognized						$ 24,369
Deferred revenue	$ 45,671					45,671		$ 70,040
Related party collaboration receivable	12,689					12,689		$ 18,496
Neurocrine \| FA Program
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Percentage of profit or loss under co-co option after paying rate-shifting fee				60.00%
Neurocrine Collaboration Agreement \| VY-AADC
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Percentage of profit or loss under co-co option				50.00%
Percentage of profit or loss under co-co option after paying rate-shifting fee				45.00%
Neurocrine Collaboration Agreement \| FA Program
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Percentage of profit or loss under co-co option after paying rate-shifting fee				40.00%
Neurocrine Collaboration Agreement \| Neurocrine
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Number of collaboration programs \| item				4
Number of discovery programs \| item				2
Programs added later \| item				2
Number of targets \| item				8
Upfront payment				$ 115,000	$ 115,000
Purchase of common stock, shares \| shares				4,179,728	4,179,728
Purchase of common stock				$ 50,000	$ 50,000
Price per share \| $ / shares				$ 11.9625
Estimated cost reimbursement		$ 340,400			431,100
Termination period				10 years
Period of advance notice for termination prior to first commercial sale				180 days
Period of advance notice for termination after first commercial sale				1 year
Payment from June 2019 Modification					5,000
Discount related to equity investment					27,600
Allocation of Transaction Price
Allocation of variable consideration	340,442					340,442
Allocation of fixed consideration	92,382				92,400	92,382
Revenue recognized	11,200		$ 16,800			50,100	$ 31,100
Deferred revenue	45,700					45,700
Reimbursement costs expected to be received	12,700					12,700
Costs to obtain collaboration agreement	800					800
Consideration received					$ 5,000
Neurocrine Collaboration Agreement \| Neurocrine \| Maximum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Percentage of reduction in royalty payments				50.00%
Neurocrine Collaboration Agreement \| Neurocrine \| VY-AADC
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Percentage of profit or loss under co-co option				50.00%
Rate-shifting fee				$ 35,000
Percentage of profit or loss under co-co option after paying rate-shifting fee				55.00%
Allocation of Transaction Price
Allocation of variable consideration	83,983					83,983
Allocation of fixed consideration	80,373					80,373
Neurocrine Collaboration Agreement \| Neurocrine \| FA Program
Allocation of Transaction Price
Allocation of variable consideration	113,033					113,033
Allocation of fixed consideration	6,005					6,005
Neurocrine Collaboration Agreement \| Neurocrine \| Discovery program 1
Allocation of Transaction Price
Allocation of variable consideration	72,164					72,164
Allocation of fixed consideration	3,002					3,002
Neurocrine Collaboration Agreement \| Neurocrine \| Discovery program 2
Allocation of Transaction Price
Allocation of variable consideration	71,262					71,262
Allocation of fixed consideration	$ 3,002					$ 3,002
Neurocrine Collaboration Agreement \| Neurocrine \| Development and regulatory milestones \| VY-AADC
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner				$ 170,000
Neurocrine Collaboration Agreement \| Neurocrine \| Development and regulatory milestones \| FA Program
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner				195,000
Neurocrine Collaboration Agreement \| Neurocrine \| Development and regulatory milestones \| Discovery program 1
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner				130,000
Neurocrine Collaboration Agreement \| Neurocrine \| Commercial Milestone
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner				275,000
Aggregate maximum milestone payments to be received from collaborative partner				$ 1,100,000

Commitments and contingencies - Significant Agreements - (Details) - Collaborative Arrangement - Sanofi Genzyme $ in Millions	1 Months Ended
	Feb. 28, 2015 USD ($) shares
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Non-refundable upfront payment received	$ 65.0
Premium over fair value on temporary equity issued	$ 5.0
Redeemable Convertible Preferred Stock Series B
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Temporary equity issued (in shares) \| shares	10,000,000
Temporary equity issued	$ 30.0
Fair value of temporary equity issued	25.0
Maximum potential in-kind services to be provided by collaborative partner	$ 5.0

Commitments and contingencies - Other Agreements - (Details) $ in Millions	9 Months Ended	12 Months Ended
	Sep. 30, 2020 USD ($)	Dec. 31, 2016 USD ($) multiple	Dec. 31, 2017 USD ($)
Various contract research organizations and institutions
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Milestone payable upon achievement	$ 0.1
Various contract research organizations and institutions \| Minimum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Number of days written notice required by reporting entity to terminate agreement	30 days
Various contract research organizations and institutions \| Maximum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Number of days written notice required by reporting entity to terminate agreement	90 days
Non-profit organization agreement
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Maximum funding		$ 4.0
Funding multiple \| multiple		2.6
Milestone payment liability			$ 1.0

Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2020	Nov. 04, 2020
Document and Entity Information
Document Type	10-Q
Document Quarterly Report	true
Document Transition Report	false
Document Period End Date	Sep. 30, 2020
Entity File Number	001-37625
Entity Registrant Name	Voyager Therapeutics, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	46-3003182
Entity Address, Address Line One	75 Sidney Street
Entity Address, City or Town	Cambridge
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02139
City Area Code	857
Local Phone Number	259-5340
Title of 12(b) Security	Common Stock, $0.001 par value
Trading Symbol	VYGR
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	true
Entity Ex Transition Period	true
Entity Shell Company	false
Entity Central Index Key	0001640266
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2020
Document Fiscal Period Focus	Q3
Entity Common Stock, Shares Outstanding		37,465,777

Accrued expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Accrued expenses
Research and development costs	$ 9,353	$ 13,248
Employee compensation costs	6,649	5,733
Accrued goods and services	4,608	1,386
Professional services	976	897
Other	79	252
Total	$ 21,665	$ 21,516

Cash, cash equivalents, restricted cash, and available-for-sale marketable securities (Tables)

9 Months Ended

Sep. 30, 2020

Cash, cash equivalents, restricted cash, and available-for-sale marketable securities

Schedule of money market funds and marketable securities

Cash, cash equivalents, and marketable securities included the following September 30, 2020 and December 31, 2019:


	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value

	(in thousands)
As of September 30, 2020
Money market funds included in cash and cash equivalents	$	145,390	$	—	$	—	$	145,390
Marketable securities:
U.S. Treasury notes		52,503		68		—		52,571
Equity securities		1,220		964		—		2,184
Total marketable securities	$	53,723	$	1,032	$	—	$	54,755
Total money market funds and marketable securities	$	199,113	$	1,032	$	—	$	200,145
As of December 31, 2019
Money market funds included in cash and cash equivalents	$	78,303	$	—	$	—	$	78,303
Marketable securities:
U.S. Treasury notes		195,467		52		28		195,491
Equity securities		1,220		700		—		1,920
Total marketable securities	$	196,687	$	752	$	28	$	197,411
Total money market funds and marketable securities	$	274,990	$	752	$	28	$	275,714

Reconciliation of cash, cash equivalents, and restricted cash


	As of September 30,		As of December 31,
	2020		2019

	(in thousands)
Cash and cash equivalents	$	147,447	$	86,042
Restricted cash included in deposits and other non-current assets		1,779		735
Total cash, cash equivalents, and restricted cash	$	149,226	$	86,777

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2020	Dec. 31, 2019
Condensed Consolidated Balance Sheets
Preferred Stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred Stock, Shares Authorized	5,000,000	5,000,000
Preferred Stock, Shares Issued	0	0
Preferred Stock, Shares Outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common Stock, Shares Authorized	120,000,000	120,000,000
Common Stock, Shares, Issued	37,262,703	36,865,116
Common Stock, Shares, Outstanding	37,262,703	36,865,116

Nature of business

9 Months Ended

Sep. 30, 2020

Nature of business

Nature of business

VOYAGER THERAPEUTICS INC.

NOTES TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

1. Nature of business

Voyager Therapeutics, Inc. (the “Company”) is a clinical-stage gene therapy company focused on developing life-changing treatments for patients suffering from severe neurological diseases. The Company is focused on neurological diseases where it believes an adeno-associated virus (“AAV”) gene therapy approach that either increases or decreases the production of a specific protein can slow or reduce the symptoms experienced by patients, and therefore have a clinically meaningful impact. The Company has built a gene therapy platform that it believes positions itself to be a leading company at the intersection of AAV gene therapy and severe neurological disease. The Company’s gene therapy platform enables it to engineer, optimize, manufacture and deliver its AAV-based gene therapies that have the potential to provide durable efficacy following a single administration.

Additionally, the Company is working to identify novel AAV capsids, which are the outer viral protein shells that enclose the genetic material of the virus payload. The Company’s team of experts in the fields of AAV gene therapy and neuroscience first identifies and selects severe neurological diseases that are well-suited for treatment using AAV gene therapy. The Company then engineers and optimizes AAV vectors for delivery of the virus payload to the targeted tissue or cells. The Company’s manufacturing process employs an established system that it believes will enable production of high quality AAV vectors at commercial scale. In addition to the Company’s capsid optimization efforts, it leverages novel delivery paradigms, established routes of administration, and advances in dosing techniques to optimize delivery of its AAV gene therapies to target tissues, regions and cell types that are critical to the disease of interest. The Company believes it can achieve this directly, with targeted infusions to discrete regions of the brain, the spinal cord, or systemically, in conjunction with its novel capsids.

The Company’s business strategy focuses on discovering, developing, manufacturing and commercializing its gene therapy programs. As part of this strategy, the Company has developed core competencies specific to AAV gene therapy development and manufacturing and is beginning to build its commercial infrastructure. This business strategy also includes business development activities that may include in-licensing activities or partnering certain programs in certain geographies with collaborators, as the Company has demonstrated through its ongoing collaboration with Neurocrine Biosciences, Inc. (the “Neurocrine Collaboration. The Company is devoting substantially all of its efforts to product research and development, market development, and raising capital. The Company is subject to risks common to companies in the biotechnology and gene therapy industries, including but not limited to, the need to obtain sufficient capital to continue to fund its operations, risks of failure of preclinical studies and clinical trials, the need to obtain marketing approval for its product candidates, the need to successfully commercialize and gain market acceptance of its product candidates, dependence on key personnel, protection of proprietary information and technology, protection against data breaches and other cybersecurity threats, compliance with government regulations, development by competitors of technological innovations, and ability to transition from pilot-scale manufacturing to large-scale production of products.

The Company has incurred annual net operating losses every year prior to 2020. As of September 30, 2020, the Company had an accumulated deficit of $260.0 million. The Company has not generated any product revenue and has financed its operations primarily through public offerings and private placements of its equity securities and funding from its prior collaborations with Sanofi Genzyme Corporation (“Sanofi Genzyme”) and AbbVie Biotechnology Ltd and AbbVie Ireland Unlimited Company (collectively, “AbbVie”) and its ongoing collaboration with Neurocrine Biosciences, Inc. (“Neurocrine”)

Through September 30, 2020, the Company has raised approximately $640.0 million of proceeds from sales of convertible preferred stock and common stock, including its initial public offering and follow-on public offering, and proceeds from collaboration agreements. As of September 30, 2020, the Company had cash, cash equivalents, and marketable debt securities of $200.0 million. Based upon its current operating plan, the Company expects that its existing cash, cash equivalents, and marketable debt securities, as well as ongoing reimbursement amounts expected from development costs related to its collaboration and license agreement with Neurocrine, or the Neurocrine

Collaboration Agreement, will enable the Company to meet its planned operating expenses and capital expenditure requirements into mid-2022.

There can be no assurance that the Company will be able to obtain additional debt or equity financing or generate product revenue or revenue from collaboration partners on terms acceptable to the Company, on a timely basis or at all. The failure of the Company to obtain sufficient funds on acceptable terms when needed could have a material adverse effect on the Company’s business, results of operations, and financial condition.

Commitments and contingencies - AbbVie Alpha Synuclein Collaboration Agreement - (Details) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Feb. 28, 2019 USD ($) item	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($) item	Sep. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Deferred revenue		$ 45,671		$ 45,671		$ 70,040
Revenue recognized				$ 24,369
AbbVie Alpha Synuclein Collaboration Agreement \| AbbVie
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Number of antibodies encoded by virus \| item	1
Number of research antibodies \| item	1
Non-refundable upfront payment received	$ 65,000
First Research Compound payment	80,000
Three additional research compounds payment to be received for each	$ 30,000
Number of additional research compounds \| item	3
Milestone payments to be received for licensed compound in case Parkinson's disease indication	$ 450,000
Milestone payments to be received for licensed compound in case first indication other than Parkinson's disease	185,000
Milestone payments to be received for licensed compound for subsequent non-Parkinson's disease indication	92,500
Number of development options \| item				4
Deferred revenue		0		$ 0
Revenue recognized		58,900		58,900
Allocation of Transaction Price
Allocation of Transaction Price	$ 65,000
AbbVie Alpha Synuclein Collaboration Agreement \| AbbVie \| Minimum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Antibodies to include in Research Period \| item	1
The number of Licensed Products \| item	1
AbbVie Alpha Synuclein Collaboration Agreement \| AbbVie \| Maximum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Antibodies to include in Research Period \| item	4
AbbVie Alpha Synuclein Collaboration Agreement \| AbbVie \| Research Services
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Revenue recognized		$ 500	$ 200	$ 4,800	$ 700
Allocation of Transaction Price
Allocation of Transaction Price	$ 23,768
AbbVie Alpha Synuclein Collaboration Agreement \| AbbVie \| First Development Option Material Right
Allocation of Transaction Price
Allocation of Transaction Price	41,232
AbbVie Alpha Synuclein Collaboration Agreement \| Commercial Milestone \| AbbVie
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Specified commercial milestone payments	$ 500,000

Stock based compensation (Tables)

9 Months Ended

Sep. 30, 2020

Stock based compensation

Compensation cost recognized for all stock-based compensation awards

Total compensation cost recognized for all stock-based compensation awards in the condensed consolidated statements of operations and comprehensive income (loss) is as follows:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2020		2019		2020		2019

	(in thousands)
Research and development	$	1,524	$	1,304	$	4,973	$	5,975
General and administrative		2,008		2,045		6,459		6,145
Total stock-based compensation expense	$	3,532	$	3,349	$	11,432	$	12,120

Summary of stock-based compensation expense by classification


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2020		2019		2020		2019

	(in thousands)
Stock options	$	2,696	$	3,008	$	8,834	$	10,312
Restricted stock awards and units		740		259		2,345		1,609
Employee stock purchase plan awards		96		82		252		199
Total stock-based compensation expense	$	3,532	$	3,349		11,432		12,120

Summary of status and changes in unvested restricted stock

A summary of the status of and changes in unvested restricted stock unit activity under the Company’s equity award plans for the nine months ended September 30, 2020 was as follows:


		Weighted
		Average
		Grant Date
		Fair Value
	Units	Per Unit
Unvested restricted stock units as of December 31, 2019	455,404		12.16
Granted	455,284	$	12.83
Vested	(138,305)		11.77
Forfeited	(128,376)	$	11.14
Unvested restricted stock units as of September 30, 2020	644,007	$	12.92

Summary of status and changes in stock options

The following is a summary of stock option activity for the nine months ended September 30, 2020:


		Weighted		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value
	Shares	Price		(in years)	(in thousands)
Outstanding at December 31, 2019	5,317,326	$	15.98
Granted	1,388,135	$	12.07
Exercised	(214,287)	$	10.24
Cancelled or forfeited	(837,339)	$	16.99
Outstanding at September 30, 2020	5,653,835	$	15.09	7.6	$	2,078
Exercisable at September 30, 2020	2,997,805	$	15.50	6.5	$	1,312

Other liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Other current liabilities
Lease liability	$ 3,539	$ 3,193
Total other current liabilities	3,539	3,193
Other non-current liabilities
Lease liability	28,259	30,975
Other	1,001	1,001
Total other non-current liabilities	$ 29,260	$ 31,976

Related party transactions

9 Months Ended

Sep. 30, 2020

Related party transactions

Related party transactions

11. Related-party transactions

During the three and nine months ended September 30, 2020, the Company received board and scientific advisory services from two of its prior executives, Steven M. Paul, M.D., the Company’s former President and Chief Executive Officer, and Dinah Sah, Ph.D., the Company’s former Chief Scientific Officer. The total amount of fees paid to Dr. Paul for services provided during each of the three and nine months ended September 30, 2020 and 2019 was $50 thousand and $0.2 million, respectively. The total amount of fees paid to Dr. Sah for services provided during the three and nine months ended September 30, 2020 was $0.2 million and $0.3 million, respectively.

Under the collaboration agreement, the Company and Neurocrine have agreed to conduct research, development and commercialization of certain of the Company’s AAV gene therapy products (Note 8). Amounts due from Neurocrine are reflected as related party collaboration receivables. As of September 30, 2020, the Company had approximately $12.7 million in related party collaboration receivable associated with Neurocrine.

Net income (loss) per share (Tables)

9 Months Ended

Sep. 30, 2020

Net income (loss) per share

Outstanding potentially dilutive securities excluded in the calculation of diluted net loss per share

The following table sets forth the outstanding potentially dilutive securities that have been excluded in the calculation of diluted net loss per share because to include them would be anti-dilutive:


	As of September 30,
	2020	2019
Unvested restricted common stock awards	117,647	235,294
Unvested restricted common stock units	—	421,182
Outstanding stock options	4,013,244	5,235,548
Total	4,130,891	5,892,024

Schedule of weighted average number of shares, basic and diluted


	Three Months Ended September 30,				Nine Months Ended September 30,
	2020		2019		2020		2019

	(in thousands, except share data)
Numerator:
Net income (loss)	$	85,611	$	(15,006)	$	52,667	$	(31,023)
Denominator for basic net income (loss) per share:
Weighted average shares outstanding-basic		37,242,504		36,742,993		37,079,242		35,581,408
Denominator for diluted net income (loss) per share:
Weighted average shares outstanding		37,242,504		36,742,993		37,079,242		35,581,408
Common stock options and restricted stock units		429,824		—		420,913		—
Weighted average shares outstanding-diluted		37,672,328		36,742,993		37,500,155		35,581,408

Net income (loss) per share

9 Months Ended

Sep. 30, 2020

Net income (loss) per share

Net income (loss) per share

10. Net income (loss) per share

The following table sets forth the outstanding potentially dilutive securities that have been excluded in the calculation of diluted net loss per share because to include them would be anti-dilutive:


	As of September 30,
	2020	2019
Unvested restricted common stock awards	117,647	235,294
Unvested restricted common stock units	—	421,182
Outstanding stock options	4,013,244	5,235,548
Total	4,130,891	5,892,024

Basic net income (loss) and diluted weighted-average shares outstanding are as follows for the three and nine months ended September 30, 2020 and 2019.


	Three Months Ended September 30,				Nine Months Ended September 30,
	2020		2019		2020		2019

	(in thousands, except share data)
Numerator:
Net income (loss)	$	85,611	$	(15,006)	$	52,667	$	(31,023)
Denominator for basic net income (loss) per share:
Weighted average shares outstanding-basic		37,242,504		36,742,993		37,079,242		35,581,408
Denominator for diluted net income (loss) per share:
Weighted average shares outstanding		37,242,504		36,742,993		37,079,242		35,581,408
Common stock options and restricted stock units		429,824		—		420,913		—
Weighted average shares outstanding-diluted		37,672,328		36,742,993		37,500,155		35,581,408

Basic net income (loss) per share for the nine months ended September 30, 2019, is the same as diluted net income (loss) per share as shown on the Company’s condensed consolidated statement of operations.

Lease obligation (Tables)

9 Months Ended

Sep. 30, 2020

Lease obligation

Summary of significant contractual obligations under operating leases


	Total Minimum
	Lease Payments
	(in thousands)
2020 (remainder of year)		1,490
2021		6,139
2022		6,323
2023		6,512
2024		6,708
2025+		14,189
Total future minimum lease payments	$	41,360
Less: imputed interest		(9,562)
Total lease liability	$	31,798
Reported as:
Other current liabilities	$	3,539
Other non-current liabilities		28,259
Total lease liability	$	31,798

Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Condensed Consolidated Statements of Operations and Comprehensive Income (Loss)
Collaboration revenue	$ 117,843	$ 20,433	$ 164,591	$ 71,717
Operating expenses:
Research and development	25,039	29,777	86,757	83,184
General and administrative	8,277	8,463	26,721	26,444
Total operating expenses	33,316	38,240	113,478	109,628
Operating income (loss)	84,527	(17,807)	51,113	(37,911)
Other income:
Interest income	254	1,823	1,578	5,065
Other income (expense), net	830	978	(24)	1,823
Total other income	1,084	2,801	1,554	6,888
Net income (loss)	85,611	(15,006)	52,667	(31,023)
Other comprehensive income (loss)
Net unrealized (loss) gain on available-for-sale-securities	(205)	(116)	44	118
Total other comprehensive (loss) income	(205)	(116)	44	118
Comprehensive income (loss)	$ 85,406	$ (15,122)	$ 52,711	$ (30,905)
Net income (loss) per share, basic	$ 2.30	$ (0.41)	$ 1.42	$ (0.87)
Net income (loss) per share, diluted	$ 2.27	$ (0.41)	$ 1.40	$ (0.87)
Weighted-average common shares outstanding, basic	37,242,504	36,742,993	37,079,242	35,581,408
Weighted-average common shares outstanding, diluted	37,672,328	36,742,993	37,500,155	35,581,408

Fair value measurements (Tables)

9 Months Ended

Sep. 30, 2020

Fair value measurements

Assets and liabilities measured at fair value on a recurring basis

Assets and liabilities measured at fair value on a recurring basis as of September 30, 2020 and December 31, 2019 are as follows:


			Quoted Prices		Significant
			in Active		Other		Significant
			Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
Assets	Total		(Level 1)		(Level 2)		(Level 3)

September 30, 2020	(in thousands)
Money market funds included in cash and cash equivalents	$	145,390	$	145,390	$	—	$	—
Marketable securities:
U.S. Treasury notes		52,571		52,571		—		—
Equity securities		2,184		2,184		—		—
Total marketable securities	$	54,755	$	54,755	$	—	$	—
Warrants to purchase equity securities		266		—		266		—
Total	$	200,411	$	200,145	$	266	$	—
December 31, 2019
Money market funds included in cash and cash equivalents	$	78,303	$	78,303	$	—	$	—
Marketable securities:
U.S. Treasury notes		195,491		195,491		—		—
Equity securities		1,920		1,920		—		—
Total marketable securities	$	197,411	$	197,411	$	—	$	—
Warrants to purchase equity securities		554		—		554		—
Total	$	276,268	$	275,714	$	554	$	—

Schedule of fair value assumptions

The assumptions utilized to value the warrants to purchase equity securities as of September 30, 2020 and December 31, 2019 are as follows:


	As of September 30,		As of December 31,
	2020		2019
Risk-free interest rate	0.1	%	1.6	%
Expected dividend yield	—	%	—	%
Expected term (in years)	0.9		1.7
Expected volatility	82.5	%	71.6	%

Fair value measurements - Assets measured on a recurring basis - (Details) $ in Thousands	Sep. 30, 2020 USD ($) item	Dec. 31, 2019 USD ($) item
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	$ 147,447	$ 86,042
Measurement Input, Risk-Free Interest Rate
Fair value assumptions
Warrants, measurement input \| item	0.001	0.016
Measurement Input, Expected Term
Fair value assumptions
Warrants, measurement input \| item	0.9	1.7
Measurement Input, Expected Volatility
Fair value assumptions
Warrants, measurement input \| item	0.825	0.716
Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Marketable securities	$ 54,755	$ 197,411
Total assets measured at fair value	200,411	276,268
Level 1 \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Marketable securities	54,755	197,411
Total assets measured at fair value	200,145	275,714
Level 2 \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Total assets measured at fair value	266	554
U.S. Treasury notes \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Marketable securities	52,571	195,491
U.S. Treasury notes \| Level 1 \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Marketable securities	52,571	195,491
Equity securities \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Marketable securities	2,184	1,920
Equity securities \| Level 1 \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Marketable securities	2,184	1,920
Warrants \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Warrants to purchase equity securities	266	554
Warrants \| Level 2 \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Warrants to purchase equity securities	266	554
Money market funds
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	145,390	78,303
Money market funds \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	145,390	78,303
Money market funds \| Level 1 \| Fair Value, Measurements, Recurring
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	$ 145,390	$ 78,303

Fair value measurements

9 Months Ended

Sep. 30, 2020

Fair value measurements

Fair value measurements

3. Fair value measurements

Assets and liabilities measured at fair value on a recurring basis as of September 30, 2020 and December 31, 2019 are as follows:


			Quoted Prices		Significant
			in Active		Other		Significant
			Markets for		Observable		Unobservable
			Identical Assets		Inputs		Inputs
Assets	Total		(Level 1)		(Level 2)		(Level 3)

September 30, 2020	(in thousands)
Money market funds included in cash and cash equivalents	$	145,390	$	145,390	$	—	$	—
Marketable securities:
U.S. Treasury notes		52,571		52,571		—		—
Equity securities		2,184		2,184		—		—
Total marketable securities	$	54,755	$	54,755	$	—	$	—
Warrants to purchase equity securities		266		—		266		—
Total	$	200,411	$	200,145	$	266	$	—
December 31, 2019
Money market funds included in cash and cash equivalents	$	78,303	$	78,303	$	—	$	—
Marketable securities:
U.S. Treasury notes		195,491		195,491		—		—
Equity securities		1,920		1,920		—		—
Total marketable securities	$	197,411	$	197,411	$	—	$	—
Warrants to purchase equity securities		554		—		554		—
Total	$	276,268	$	275,714	$	554	$	—

The Company measures the fair value of money market funds, U.S. Treasury notes and equity securities based on quoted prices in active markets for identical securities. The Level 2 equity securities include warrants used to purchase equity securities that are valued using the Black-Scholes model. The Black-Scholes option pricing model

requires inputs based on certain subjective assumptions, including (a) the expected stock price volatility, (b) the calculation of expected term of the awards, (c) the risk-free interest rate, and (d) expected dividends. The assumptions utilized to value the warrants to purchase equity securities as of September 30, 2020 and December 31, 2019 are as follows:


	As of September 30,		As of December 31,
	2020		2019
Risk-free interest rate	0.1	%	1.6	%
Expected dividend yield	—	%	—	%
Expected term (in years)	0.9		1.7
Expected volatility	82.5	%	71.6	%

The expected volatility is based on the historic volatility for the equity securities underlying the warrants and is calculated based on a period of time commensurate with the expected term assumption. The expected term is based on the remaining contractual life of the warrants on each measurement date. The risk-free interest rate is based on a treasury instrument whose term is consistent with the expected term of the warrants. The expected dividend yield is assumed to be zero as the entity that issued the warrants has never paid and has not indicated any intention to pay dividends.

- 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

Accrued expenses

9 Months Ended

Sep. 30, 2020

Accrued expenses

Accrued expenses

5. Accrued expenses

Accrued expenses as of September 30, 2020 and December 31, 2019 consist of the following:


	As of September 30,		As of December 31,
	2020		2019

	(in thousands)
Research and development costs	$	9,353	$	13,248
Employee compensation costs		6,649		5,733
Accrued goods and services		4,608		1,386
Professional services		976		897
Other		79		252
Total	$	21,665	$	21,516

Stock based compensation - Unrecognized expense and weighted-average period (Details) - Outstanding stock options $ in Millions	9 Months Ended
	Sep. 30, 2020 USD ($)
Options disclosures
Unrecognized stock-based compensation expense	$ 23.4
Remaining weighted-average remaining vesting period	2 years 7 months 6 days

Cash, cash equivalents, restricted cash and available-for-sale marketable securities (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Dec. 31, 2019
Amortized Cost
Cash and cash equivalents	$ 147,447	$ 86,042
Marketable securities, amortized cost	53,723	196,687
Total money market funds and marketable securities	199,113	274,990
Fair Value
Marketable securities, fair value	54,755	197,411
Total money market funds and marketable securities	200,145	275,714
Unrealized Gains and Losses
Marketable securities, unrealized gains	1,032	752
Total money market funds and marketable securities	$ 1,032	752
Marketable securities, unrealized losses		28
Total money market funds and marketable securities		28
Maximum
Unrealized Gains and Losses
Debt securities, contractual maturity period	1 year
Money market funds
Amortized Cost
Cash and cash equivalents	$ 145,390	78,303
U.S. Treasury notes
Amortized Cost
Marketable securities, amortized cost	52,503	195,467
Fair Value
Marketable securities, fair value	52,571	195,491
Unrealized Gains and Losses
Marketable securities, unrealized gains	68	52
Marketable securities, unrealized losses		28
Equity securities
Amortized Cost
Marketable securities, amortized cost	1,220	1,220
Fair Value
Marketable securities, fair value	2,184	1,920
Unrealized Gains and Losses
Marketable securities, unrealized gains	$ 964	$ 700

Nature of business (Details) - USD ($) $ in Thousands	9 Months Ended
Nature of business (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019
Nature of business
Accumulated deficit	$ (259,981)	$ (312,648)
Proceeds raised	640,000
Cash, cash equivalents, and marketable debt securities	$ 200,000

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019
Cash flow from operating activities
Net income (loss)	$ 52,667	$ (31,023)
Adjustments to reconcile net loss to net cash provided by operating activities:
Stock-based compensation expense	11,432	12,120
Depreciation	2,830	2,007
Amortization of premiums and discounts on marketable securities	(57)	(2,927)
In-kind research and development expenses		616
Other non-cash items	24	(1,810)
Changes in operating assets and liabilities:
Related party collaboration receivable	5,807	(14,033)
Prepaid expenses and other current assets	1,379	52
Operating lease, right-of-use asset	2,341	2,092
Other non-current assets	207	(413)
Accounts payable	(684)	2,988
Accrued expenses	(3,440)	6,244
Operating lease liabilities	(2,370)	(1,860)
Lease incentive benefit	3,947
Deferred revenue	(148,822)	97,973
Net cash (used in) provided by operating activities	(74,739)	72,026
Cash flow from investing activities
Purchases of property and equipment	(8,541)	(4,342)
Proceeds from sale of equipment	31	171
Purchases of marketable securities	(24,979)	(409,068)
Proceeds from maturities of marketable securities	168,000	296,300
Net cash provided by (used in) investing activities	134,511	(116,939)
Cash flow from financing activities
Proceeds from the exercise of stock options	2,195	2,606
Proceeds from the issuance of common stock in connection with the Neurocrine Collaboration Agreement, net		77,617
Proceeds from the purchase of common stock under ESPP	482	471
Net cash provided by financing activities	2,677	80,694
Net increase in cash and cash equivalents	62,449	35,781
Cash, cash equivalents, and restricted cash beginning of period	86,777
Cash, cash equivalents, and restricted cash end of period	149,226	83,375
Supplemental disclosure of cash and non-cash activities
Capital expenditures incurred but not yet paid	$ 454	$ 357

Commitments and contingencies - Collaboration receivables and contract liabilities - (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2020 USD ($)
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Related party collaboration receivable, beginning balance	$ 18,496
Additions	29,152
Deductions	(34,959)
Related party collaboration receivable, ending balance	12,689
Deferred revenue, beginning balance	70,040
Deductions	(24,369)
Deferred revenue, ending balance	$ 45,671

Lease obligation (Details) $ in Thousands	3 Months Ended		9 Months Ended
Lease obligation (Details) $ in Thousands	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Mar. 31, 2020 USD ($)	Dec. 31, 2019 USD ($)
Lease expense	$ 1,600	$ 1,100	$ 5,000	$ 4,100
Restricted cash included in deposits and other noncurrent assets	$ 1,779		$ 1,779			$ 735
Weighted average remaining lease term	6 years 2 months 12 days		6 years 2 months 12 days
Weighted average incremental borrowing rate	8.5		8.5
Total minimum lease payments
2020 (remainder of year)	$ 1,490		$ 1,490
2021	6,139		6,139
2022	6,323		6,323
2023	6,512		6,512
2024	6,708		6,708
2025+	14,189		14,189
Total future minimum lease payments	41,360		41,360
Less: imputed interest	(9,562)		(9,562)
Total lease liability	31,798		31,798
Current lease liabilities	$ 3,539		$ 3,539			3,193
Operating Lease, Liability, Current, Statement of Financial Position [Extensible List]	us-gaap:OtherCurrentLiabilitiesMember		us-gaap:OtherCurrentLiabilitiesMember
Non-current lease liabilities	$ 28,259		$ 28,259			$ 30,975
Operating Lease, Liability, Noncurrent, Statement of Financial Position [Extensible List]	us-gaap:OtherNoncurrentLiabilitiesMember		us-gaap:OtherNoncurrentLiabilitiesMember
75 Sidney Street
Leasehold improvements	$ 1,300		$ 1,300
64 Sidney Street
Leasehold improvements	3,500		3,500
75 Hayden Avenue
Lease term					10 years
Leasehold improvements	3,900		3,900
Entitled leasehold improvements	$ 5,600		$ 5,600
Total minimum lease payments
Total lease liability					$ 25,600

Stock based compensation - Compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 3,532	$ 3,349	$ 11,432	$ 12,120
Outstanding stock options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	2,696	3,008	8,834	10,312
Restricted stock units
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	740	259	2,345	1,609
Employee stock purchase plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	96	82	252	199
Research and development
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	1,524	1,304	4,973	5,975
General and administrative
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation	$ 2,008	$ 2,045	$ 6,459	$ 6,145

Commitments and contingencies - Accounting Analysis - (Details) $ in Thousands		1 Months Ended		3 Months Ended		9 Months Ended
	Jun. 14, 2019 USD ($)	Feb. 28, 2018 USD ($) item	Feb. 28, 2015 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($) item	Sep. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)
Income Statement Related Disclosures [Abstract]
Revenue recognized						$ 24,369
Deferred revenue				$ 45,671		45,671		$ 70,040
Sanofi Genzyme \| Collaborative Arrangement
Allocable arrangement consideration
Non-refundable upfront payment received			$ 65,000
Additional consideration, premium over fair value on temporary equity issued			$ 5,000
Income Statement Related Disclosures [Abstract]
Revenue recognized				0	$ 200	0	$ 31,800
Deferred revenue	$ 48,700			0		0
Milestone payable upon achievement	10,000
Total payable amount	20,000
Sanofi Genzyme \| Termination Agreement
Allocable arrangement consideration
Non-refundable upfront payment received	1,000
Income Statement Related Disclosures [Abstract]
Revenue recognized	28,700
Up-front fee paid on date of termination	$ 10,000
AbbVie \| AbbVie Tau Collaboration Agreement
Allocable arrangement consideration
Non-refundable upfront payment received		$ 69,000
Income Statement Related Disclosures [Abstract]
Revenue recognized				46,300		46,300
Deferred revenue				0		$ 0
Number of development options \| item		3				3
AbbVie \| AbbVie Tau Collaboration Agreement \| Research Services
Income Statement Related Disclosures [Abstract]
Revenue recognized				$ 900	$ 3,200	$ 4,500	$ 8,100

Cash, cash equivalents, restricted cash, and available-for-sale marketable securities

9 Months Ended

Sep. 30, 2020

Cash, cash equivalents, restricted cash, and available-for-sale marketable securities

Cash, cash equivalents, restricted cash, and available-for-sale marketable securities

4. Cash, cash equivalents, restricted cash, and available-for-sale marketable securities

Cash, cash equivalents, and marketable securities included the following September 30, 2020 and December 31, 2019:


	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value

	(in thousands)
As of September 30, 2020
Money market funds included in cash and cash equivalents	$	145,390	$	—	$	—	$	145,390
Marketable securities:
U.S. Treasury notes		52,503		68		—		52,571
Equity securities		1,220		964		—		2,184
Total marketable securities	$	53,723	$	1,032	$	—	$	54,755
Total money market funds and marketable securities	$	199,113	$	1,032	$	—	$	200,145
As of December 31, 2019
Money market funds included in cash and cash equivalents	$	78,303	$	—	$	—	$	78,303
Marketable securities:
U.S. Treasury notes		195,467		52		28		195,491
Equity securities		1,220		700		—		1,920
Total marketable securities	$	196,687	$	752	$	28	$	197,411
Total money market funds and marketable securities	$	274,990	$	752	$	28	$	275,714

All of the Company’s marketable debt securities as of September 30, 2020, have a contractual maturity of one year or less.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash within the condensed consolidated balance sheets that sum to the total of the same such amounts shown in the condensed consolidated statements of cash flows:


	As of September 30,		As of December 31,
	2020		2019

	(in thousands)
Cash and cash equivalents	$	147,447	$	86,042
Restricted cash included in deposits and other non-current assets		1,779		735
Total cash, cash equivalents, and restricted cash	$	149,226	$	86,777

Commitments and contingencies - AbbVie Tau Collaboration Agreement - (Details) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Feb. 28, 2018 USD ($) item	Sep. 30, 2020 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2020 USD ($) item	Sep. 30, 2019 USD ($)	Dec. 31, 2019 USD ($)
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Deferred revenue		$ 45,671		$ 45,671		$ 70,040
Revenue recognized				$ 24,369
AbbVie Tau Collaboration Agreement \| AbbVie
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Non-refundable upfront payment received	$ 69,000
First Research Compound payment	80,000
Two additional research compounds payment to be received for each	$ 30,000
Number of additional research compounds \| item	2
One-time payment upon exercise of license option	$ 75,000
Milestone payments to be received for licensed compound in case Alzheimer disease indication	550,000
Milestone payments to be received for licensed compound in case first indication other than Alzheimer disease	230,000
Milestone payments to be received for licensed compound for subsequent non-Alzheimer disease indication	$ 115,000
Number of development options \| item	3			3
Number of research antibodies \| item	1
Deferred revenue		0		$ 0
Revenue recognized		46,300		46,300
Allocation of Transaction Price
Allocation of Transaction Price		69,000		69,000
AbbVie Tau Collaboration Agreement \| AbbVie \| Minimum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Antibodies to include in Research Period \| item	2
The number of Licensed Products \| item	1
AbbVie Tau Collaboration Agreement \| AbbVie \| Maximum
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Number of antibodies encoded by virus \| item	5
Antibodies to include in Research Period \| item	3
AbbVie Tau Collaboration Agreement \| AbbVie \| Research Services
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Revenue recognized		900	$ 3,200	4,500	$ 8,100
Allocation of Transaction Price
Allocation of Transaction Price		34,482		34,482
AbbVie Tau Collaboration Agreement \| AbbVie \| First Development Option Material Right
Allocation of Transaction Price
Allocation of Transaction Price		$ 34,518		$ 34,518

Cash, cash equivalents, restricted cash and available-for-sale marketable securities - Reconciliation of cash, cash equivalents, and restricted cash (Details) - USD ($) $ in Thousands	Sep. 30, 2020	Dec. 31, 2019	Sep. 30, 2019	Dec. 31, 2017
Cash, cash equivalents, restricted cash, and available-for-sale marketable securities
Cash and cash equivalents	$ 147,447	$ 86,042
Restricted cash included in deposits and other noncurrent assets	1,779	735
Total cash, cash equivalents, and restricted cash	$ 149,226	$ 86,777	$ 83,375	$ 47,594

Lease obligation

9 Months Ended

Sep. 30, 2020

Lease obligation

Lease obligation

6. Lease obligation

Operating Leases

As of September 30, 2020, the Company has leases for office and lab space at 75 and 64 Sidney Street in Cambridge, Massachusetts through November 30, 2026.

In March 2020, the Company entered into an agreement to lease an additional facility at 75 Hayden Avenue in Lexington, Massachusetts through October 29, 2030. The facility includes laboratory and office space. The Company currently expects the facility to be ready for occupancy in late 2020. As of September 30, 2020, the Company did not have control of the space and therefore, did not record a right-of-use asset and corresponding lease liability. The expected contractual obligation under this lease is approximately $25.6 million, to be paid over the ten-year term of the lease. These payments are not included in the detailed table below.

The Company has received leasehold improvement incentives from the landlord totaling $1.3 million and $3.5 million for 75 Sidney Street and 64 Sidney Street, respectively. The Company recorded these incentives as a component of its right-of-use asset and is amortizing these incentives as a reduction of rent expense over the life of the leases. The leasehold improvements have been capitalized as fixed assets. The Company is also entitled to receive approximately $5.6 million of leasehold improvements for the space at 75 Hayden Avenue. Upon gaining control of the space, the Company will record these amounts as a component of the right-of-use asset and will amortize them as a reduction of rent expense over the life of the lease. To date, the Company has received $3.9 million of leasehold improvements for 75 Hayden Avenue. These amounts are included in accrued expenses as of September 30, 2020.

The Company’s lease agreements require the Company to maintain a cash deposit or irrevocable letter of credit in the aggregate amount of $1.8 million payable to its landlords as security for the performance of its obligations under the leases. These amounts are recorded as restricted cash and included in deposits and other non-current assets in the accompanying condensed consolidated balance sheets.

The following table summarizes the Company’s significant contractual obligations under operating leases as of payment due date by period as of September 30, 2020:


	Total Minimum
	Lease Payments
	(in thousands)
2020 (remainder of year)		1,490
2021		6,139
2022		6,323
2023		6,512
2024		6,708
2025+		14,189
Total future minimum lease payments	$	41,360
Less: imputed interest		(9,562)
Total lease liability	$	31,798
Reported as:
Other current liabilities	$	3,539
Other non-current liabilities		28,259
Total lease liability	$	31,798

During the three and nine months ended September 30, 2020, the Company incurred lease expense of $1.6 million and $5.0 million, respectively, for operating leases. During the three and nine months ended September 30, 2019, the Company incurred lease expense of $1.1 million and $4.1 million, respectively, for operating leases. As of September 30, 2020, the weighted average remaining lease term was 6.2 years and the weighted average incremental borrowing rate used to determine the operating lease liability was 8.5%.

Stock based compensation - Restricted Stock - (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2020	Sep. 30, 2019	Sep. 30, 2020	Sep. 30, 2019
Restricted stock disclosures
Stock-based compensation	$ 3,532	$ 3,349	$ 11,432	$ 12,120
Restricted stock units
Shares
Balance, beginning (in shares)			455,404
Granted (in shares)			455,284
Vested (in shares)			(138,305)
Forfeited (in shares)			(128,376)
Balance, ending (in shares)	644,007		644,007
Weighted Average Grant Date Fair Value Per Share
Balance, beginning (in dollars per share)			$ 12.16
Granted (in dollars per share)			12.83
Vested (in dollars per share)			11.77
Forfeited (in dollars per share)			11.14
Balance, ending (in dollars per share)	$ 12.92		$ 12.92
Restricted stock disclosures
Vesting period	3 years		3 years
Stock-based compensation	$ 740	$ 259	$ 2,345	$ 1,609
Unrecognized stock-based compensation expense	$ 6,300		$ 6,300
Remaining weighted-average remaining vesting period			2 years
Share-based Payment Arrangement, Employee \| Restricted stock units
Weighted Average Grant Date Fair Value Per Share
Granted (in dollars per share)	$ 13.34	$ 25.40	$ 12.83	$ 11.65
Restricted stock disclosures
Stock-based compensation	$ 600	$ 300	$ 2,100	$ 1,600