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Document and Entity Information - shares	9 Months Ended
Document and Entity Information - shares	Sep. 30, 2016	Nov. 07, 2016
Document and Entity Information
Entity Registrant Name	Voyager Therapeutics, Inc.
Entity Central Index Key	0001640266
Document Type	10-Q
Document Period End Date	Sep. 30, 2016
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Non-accelerated Filer
Entity Common Stock, Shares Outstanding		26,720,082
Document Fiscal Year Focus	2016
Document Fiscal Period Focus	Q3

Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Assets, Current
Cash and cash equivalents, fair value	$ 63,507	$ 31,309
Marketable securities	127,646	163,028
Prepaid Expense and Other Assets, Current	1,868	1,557
Total Current Assets	193,021	195,894
Property, Plant and Equipment, Net	4,253	3,234
Deposits and other non-current assets	2,294	321
Marketable securities	2,416	30,008
Total Assets	201,984	229,457
Liabilities, Current
Accounts Payable	787	612
Accrued expenses	6,304	3,430
Deferred rent, current portion		300
Deferred revenue, current portion	12,296	19,589
Total current liabilities	19,387	23,931
Deferred rent, net of current portion	1,988	1,015
Deferred revenue, net of current portion	31,456	35,393
Other non-current liabilities	29	44
Total Liabilities	52,860	60,383
Stockholders' Equity Attributable to Parent
Common stock, $0.001 par value: 120,000,000 shares authorized at September 30, 2016 and December 31, 2015; 25,419,245 and 24,930,979 shares issued and outstanding at September 30, 2016 and December 31, 2015, respectively	25	25
Additional Paid in Capital	223,811	219,122
Accumulated other comprehensive gain	630	(251)
Accumulated deficit	(75,342)	(49,822)
Total stockholders’ deficit	149,124	169,074
Total liabilities, redeemable convertible preferred stock and stockholders’ deficit	$ 201,984	$ 229,457

Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
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	25,419,245	24,930,979
Common Stock, Shares, Outstanding	25,419,245	24,930,979

Statement of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Income Statement [Abstract]
Collaboration revenue	$ 3,308	$ 4,937	$ 11,858	$ 12,397
Operating Expenses [Abstract]
Research and development	10,309	6,481	29,526	18,459
General and administrative	3,370	2,475	9,789	6,752
Total operating expenses	13,679	8,956	39,315	25,211
Operating loss	(10,371)	(4,019)	(27,457)	(12,814)
Other expense, net
Interest income	1,171	102	2,069	175
Other expense, net	99		435	9,750
Total other income (expense)	1,072	102	1,634	(9,575)
Loss before income taxes	(9,299)	(3,917)	(25,823)	(22,389)
Income tax benefit	303		303
Net loss	(8,996)	(3,917)	(25,520)	(22,389)
Other comprehensive loss
Net unrealized gain on available-for-sale-securities, net of tax expense of $570 for the three and nine months ended September 30, 2016	570	58	881	38
Total other comprehensive gain	570	58	881	38
Comprehensive loss	(8,426)	(3,859)	(24,639)	(22,351)
Reconciliation of net loss to net loss attributable to common stockholder:
Accretion of redeemable convertible preferred stock to redemption value		(2,594)		(6,045)
Accrued dividends on series A preferred stock		(403)		(1,039)
Net loss attributable to common stockholders	$ (8,996)	$ (6,914)	$ (25,520)	$ (29,473)
Net loss per share attributable to common stock, basic and diluted	$ (0.35)	$ (5.25)	$ (1.01)	$ (25.36)
Weighted-average common shares outstanding, basic and diluted	25,374,381	1,317,150	25,227,058	1,161,982

Statement of Cash Flows - USD ($) $ in Thousands	9 Months Ended
Statement of Cash Flows - USD ($) $ in Thousands	Sep. 30, 2016	Sep. 30, 2015
Cash flow from operating activities
Net loss	$ (25,520)	$ (22,389)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense	4,528	2,061
Depreciation	448	436
Amortization of premiums and discounts on marketable securities	571	261
Change in fair value of preferred stock tranche liability		9,750
In-kind research and development expenses	989	2,190
Other non-cash items	(409)	(205)
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	(311)	243
Other non-current assets	57	14
Deferred revenue	(12,219)	57,604
Accounts payable	175	(1,013)
Accrued expenses	2,301	1,952
Other non-current liabilities		(186)
Lease incentive benefit		138
Net cash provided by (used in) operating activities	(29,390)	50,856
Cash flow from investing activities
Purchases of property and equipment	(1,160)	(909)
Change in restricted cash	(471)
Purchases of marketable securities	(66,627)	(100,283)
Proceeds from maturities of marketable securities	129,700	6,000
Net cash used in investing activities	61,442	(95,192)
Cash flow from financing activities
Proceeds from the issuance of redeemable convertible preferred stock net of discount and issuance costs		104,779
Deferred initial public offering costs		(954)
Proceeds from the exercise of stock options and issuance of restricted stock	146	9
Net cash provided by financing activities	146	103,834
Net increase in cash and cash equivalents	32,198	59,498
Cash and cash equivalents, beginning of period	31,309	7,035
Cash and cash equivalents, end of period	$ 63,507	66,533
Supplemental Disclosure of Cash and non-cash Activities
Accretion of redeemable convertible preferred stock to redemption value		6,045
Deferred initial public offering costs included in accrued expenses		$ 348

Summary of significant accounting policies	9 Months Ended
Summary of significant accounting policies	Sep. 30, 2016
Summary of significant accounting policies
Summary of significant accounting policies	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, 2015 as filed with the Securities and Exchange Commission (“SEC”). 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”). The accompanying condensed consolidated financial statements include those of the Company and its wholly owned subsidiary, Voyager Securities Corporation, after elimination of all intercompany accounts and transactions. In November 2015, the Company completed the sale of 5,750,000 shares of its common stock in its initial public offering (the “IPO”), at a price to the public of $14.00 per share, resulting in net proceeds to the Company of $72.9 million after deducting underwriting discounts, commissions, and offering expenses paid by the Company. On October 29, 2015, in preparation for the Company's IPO, the Company's Board of Directors and stockholders approved a 1-for-4.25 reverse split of the Company's common stock, which became effective on October 29, 2015. All share and per share amounts in the condensed consolidated financial statements and notes thereto have been retroactively adjusted for all periods presented to give effect to this reverse split, including reclassifying an amount equal to the reduction in par value of common stock to additional paid-in capital. In connection with the closing of the IPO, all of the Company’s outstanding redeemable convertible preferred stock automatically converted into shares of common stock as of November 16, 2015, resulting in the issuance by the Company of an additional 17,647,054 shares of common stock. The significant increase in shares outstanding in November 2015 is expected to impact the year-over-year comparability of the Company’s net loss per share calculation. These condensed consolidated financial statements should be read in conjunction with the Company's audited consolidated financial statements included in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 as filed with the SEC. Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the 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, valuation of the tranche rights, stock‑based compensation expense, income taxes, and prior to the closing of the IPO, the fair value of common stock. 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. Recent Accounting Pronouncements In May 2014, the FASB issued ASU No. 2014‑09, Revenue From Contracts With Customers. ASU 2014‑09 amends ASC 605, Revenue Recognition, by outlining a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers. The adoption of this ASU has been subsequently amended by ASU 2015-14, Revenue from Contracts with Customers (Topic 606): Deferral of the Effective Date; ASU 2016-10, Revenue from Contracts with Customers (Topic 606): Identifying Performance Obligations and Licensing; and ASU 2016-12, Revenue from Contracts with Customers (Topic 606): Narrow-Scope Improvements and Practical Expedients. The new standard provides a five step framework whereby revenue is recognized when promised goods or services are transferred to a customer at an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The standard is effective for interim and annual periods beginning after December 15, 2017, with early adoption one year prior to the effectice date allowed, and allows for adoption using a full retrospective method, or a modified retrospective method. The Company has not yet determined which adoption method it will utilize or the effect that the adoption of this guidance will have on its consolidated financial statements. In August 2014, the FASB issued ASU No. 2014‑15, Presentations of Financial Statements, Going Concern, which requires management to assess an entity’s ability to continue as a going concern every reporting period, and provide certain disclosures if management has substantial doubt about the entity’s ability to operate as a going concern, or an express statement if not, by incorporating and expanding upon certain principles that are currently in U.S. auditing standards. This guidance is effective for the annual period ending after December 15, 2016, and for annual periods and interim periods thereafter. The adoption of this accounting standard may affect the Company’s financial statement disclosures in future periods. The Company has evaluated the impact of this ASU if it had been applied to these financial statements and determined that they would have concluded that there is not substantial doubt about the Company’s ability to continue as a going concern. In February 2016, the FASB issued ASU 2016-02, Leases, which requires a lessee to recognize assets and liabilities on the balance sheet for operating leases and changes many key definitions, including the definition of a lease. The new standard includes a short-term lease exception for leases with a term of 12 months or less, as part of which a lessee can make an accounting policy election not to recognize lease assets and lease liabilities. Lessees will continue to differentiate between finance leases (previously referred to as capital leases) and operating leases using classification criteria that are substantially similar to the previous guidance. The new standard will be effective beginning January 1, 2019, and early adoption is permitted for public entities. The Company is currently evaluating the potential impact this ASU may have on its financial position. In March 2016, the FASB issued ASU No. 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting, which aims to simplify several aspects of the accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, classification of certain items on the statement of cash flows and accounting for forfeitures. The ASU is effective for public entities for fiscal years beginning after December 15, 2016, with early adoption permitted. The Company has not yet completed its assessment of the impact of the new standard on its consolidated financial statements.

Fair Value Measurements

9 Months Ended

Sep. 30, 2016

Fair Value Measurements

Fair value of financial measurements

3. Fair Value Measurements

Assets and liabilities measured at fair value on a recurring basis as of September 30, 2016 and December 31, 2015 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, 2016	(in thousands)
Money market funds included in cash and cash equivalents	$	63,008	$	63,008	$	—	$	—
Marketable securities:
U.S. Treasury notes		112,486		112,486		—		—
U.S. Government agency securities		15,160		—		15,160		—
Equity securities		2,416		2,416		—		—
Total marketable securities	$	130,062	$	114,902	$	15,160	$	—
Warrants to purchase equity securities		1,559		—		1,559		—
Total	$	194,629	$	177,910	$	16,719	$	—
December 31, 2015
Money market funds included in cash and cash equivalents	$	29,601	$	29,601	$	—	$	—
Marketable securities:
U.S. Treasury notes		157,981		157,981		—		—
U.S. Government agency securities		35,055		—		35,055		—
Total marketable securities		193,036		157,981		35,055		—
Total	$	222,637	$	187,582	$	35,055	$	—

The Company measures the fair value of money market funds, U.S. Treasuries and equity securities based on quoted prices in active markets for identical securities. The Level 2 debt securities include U.S. Government agency securities that are valued either based on recent trades of securities in inactive markets or based on quoted market prices of similar instruments and other significant inputs derived from or corroborated by observable market data. 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 assuptions, 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 on the acquisition date, September 2, 2016, and as of September 30, 2016 are as follows:


	As of September 2,		As of September 30,
	2016		2016
Risk-free interest rate	1.2	%	1.1	%
Expected dividend yield	—	%	—	%
Expected term (in years)	5.0		4.9
Expected volatility	92.3	%	92.3	%

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 issues 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

Cash, Cash Equivalents, and Available for Sale Marketable Investments

9 Months Ended

Sep. 30, 2016

Cash and Cash Equivalents [Abstract]

Cash, Cash Equivalents, and Available for Sale Marketable Investments

4. Cash, Cash Equivalents, and Available for Sale Marketable Securities

Cash equivalents include all highly liquid investments maturing within 90 days from the date of purchase. Investments consist of securities with original maturities greater than 90 days when purchased. The Company classifies these investments as available-for-sale and records them at fair value in the accompanying condensed consolidated balance sheets. Unrealized gains or losses are included in accumulated other comprehensive income (loss). Premiums or discounts from par value are amortized to investment income over the life of the underlying investment.

The Company classifies marketable debt securities with a remaining maturity when purchased of greater than three months as available‑for‑sale. Marketable debt securities with a remaining maturity date greater than one year and marketable equity securities are classified as non‑current where the Company has the intent and ability to hold these securities for at least the next 12 months. Available‑for‑sale debt securities are maintained by an investment manager and consist of U.S. Treasury securities and U.S. Government agency securities. During the third quarter in 2016, the Company invested in a supplier and received common stock and warrants to purchase common stock in that entity. The common stock is included in non-current marketable securities and the warrants are included in non-current assets.

All available‑for‑sale securities are carried at fair value with the unrealized gains and losses included in other comprehensive income (loss) as a component of stockholders’ equity until realized. Any premium or discount arising at purchase is amortized and/or accreted to interest income and/or expense. Realized gains and losses are determined using the specific identification method and are included in other income (expense). If any adjustment to fair value reflects a decline in value of the investment, the Company considers all available evidence to evaluate the extent to which the decline is “other‑than‑temporary” and, if so, recognizes the unrealized loss through a charge to the Company’s statement of operations and comprehensive loss. No other temporary losses have been recognized.

Cash, cash equivalents, and marketable securities included the following at September 30, 2016 and December 31, 2015:


	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value
	(in thousands)
As of September 30, 2016
Money market funds included in cash and cash equivalents	$	63,008	$	—	$	—	$	63,008
Total money market funds included in cash and cash equivalents	$	63,008	$	—	$	—	$	63,008
Marketable securities:
U.S. Treasury notes		112,489		—		3		112,486
U.S. Government agency bonds		15,153		7		—		15,160
Total debt securities	$	127,642	$	7	$	3	$	127,646
Equity securities		1,220		1,196		—		2,416
Total marketable securities	$	128,862	$	1,203	$	3	$	130,062
Total money market funds and marketable securities	$	191,870	$	1,203	$	3	$	193,070
As of December 31, 2015
Money market funds included in cash and cash equivalents	$	29,601	$	—	$	—	$	29,601
Total money market funds included in cash and cash equivalents	$	29,601	$	—	$	—	$	29,601
Marketable securities:
U.S. Treasury notes		158,166		—		185		157,981
U.S. Government agency bonds		35,121		—		66		35,055
Total marketable securities	$	193,287	$	—	$	251	$	193,036
Total money market funds and marketable securities	$	222,888	$	—	$	251	$	222,637

The estimated fair value of the Company’s debt securities balance at September 30, 2016, by contractual maturity, is as follows:


Due in one year or less		$	127,646

- Definition

The entire disclosure for cash and cash equivalent footnotes, which may include the types of deposits and money market instruments, applicable carrying amounts, restricted amounts and compensating balance arrangements. Cash and equivalents include: (1) currency on hand (2) demand deposits with banks or financial institutions (3) other kinds of accounts that have the general characteristics of demand deposits (4) short-term, highly liquid investments that are both readily convertible to known amounts of cash and so near their maturity that they present insignificant risk of changes in value because of changes in interest rates. Generally, only investments maturing within three months from the date of acquisition qualify.

+ References + Details

Commitments and contingencies

9 Months Ended

Sep. 30, 2016

Commitments and Contingencies

Commitments and contingencies

6. Commitments and Contingencies

Operating Leases

During March 2014, the Company entered into an agreement to lease its facility under a non‑cancelable operating lease that expires on December 15, 2019. The lease contains escalating rent clauses which require higher rent payments in future years. The Company expenses rent on a straight‑line basis over the term of the lease, including any rent‑free periods.

The Company received a leasehold improvement incentive from the landlord totaling $1.3 million. The Company recorded these incentives as a component of deferred rent and will amortize these incentives as a reduction of rent expense over the life of the lease. These leasehold improvements have been recorded as fixed assets.

In January 2016, the Company executed an amendment to extend the lease to December 2024 to coincide with an agreement to lease an additional facility of approximately 26,000 square feet in Cambridge, Massachusetts. The leases include two renewal options, each for five year terms, and at fair market value upon exercise. The Company will expense rent on a straight‑line basis over the term of the new lease, including any rent‑free periods once the landlord delivery date has commenced, and the Company gains access to the facility. The Company received delivery of the property in September 2016 and the new space is projected to be ready for occupancy in early 2017.

The Company is entitled to receive a leasehold improvement incentive for the new lease from the landlord totaling $3.5 million. The Company will record these incentives as a component of deferred rent and will amortize these incentives as a reduction of rent expense over the life of the lease.

The following table summarizes our significant contractual obligations as of payment due date by period at September 30, 2016:


	Total Minimum
	Lease Payments
	(in thousands)
2016		298
2017		3,211
2018		3,290
2019		3,382
2020		3,762
2021+		16,140
	$	30,083

Significant Agreements

Genzyme Collaboration Agreement

Summary of Agreement

In February 2015, the Company entered into an agreement with Genzyme (“Collaboration Agreement”), which included a non‑refundable upfront payment of $65.0 million. In addition, contemporaneous with entering into the Collaboration Agreement, Genzyme entered into a Series B Stock Purchase Agreement, under which Genzyme purchased 10,000,000 shares of 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 Collaboration Agreement.

Under the Collaboration Agreement, the Company granted 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‑AADC01 (“Parkinson’s Program”), VY‑FXN01 (“Friedreich’s Ataxia Program”), a future program to be designated by Genzyme (“Future Program”) and VY‑HTT01 (“Huntington’s Program”) with an incremental option to co‑commercialize VY‑HTT01 in the United States and (ii) worldwide rights to VY‑SMN101 (“Spinal Muscular Atrophy Program”). 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.

Prior to any option exercise by Genzyme, the Company will collaborate with Genzyme in the development of products under each Split Territory Program and VY‑SMN101 pursuant to a written development plan and under the guidance of an Alliance Joint Steering Committee (“AJSC”), comprised of an equal number of employees from the Company and Genzyme.

The Company is required to use commercially reasonable efforts to develop products under each Split Territory Program and the Spinal Muscular Atrophy Program through the completion of the applicable POP Study. During the development of these joint programs, the activities are guided by a Development Advisory Committee (“DAC”). The DAC may elect to utilize certain Genzyme technology relating to the Parkinson’s Program, the Huntington’s Program, or generally with the manufacture of Split Territory Program products.

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

Other than the Parkinson’s Program (for which a POP Study has already been commenced), if the Company does not initiate a POP Study for a given Split Territory Program by December 31, 2026 (or for the Future Program by the tenth anniversary of the date the Future Program is nominated by Genzyme), and Genzyme has not terminated the Collaboration Agreement with respect to the collaboration program, then Genzyme shall be entitled, as its sole and exclusive remedy, to a credit of $10.0 million for each such program against other milestone or royalty payments payable by Genzyme under the Collaboration Agreement. However, if the POP Study is not initiated due to a regulatory delay or a force majeure event, such time period shall be extended for so long as such delay continues.

With the exception of the Parkinson’s Program, Genzyme is required to pay an option exercise payment of $20.0 million or $30.0 million for each Split Territory Program, as well as the Spinal Muscular Atrophy Program.

Upon Genzyme’s exercise of its option to license a given product in a Split Territory Program (“Split Territory Licensed Product”), the Company will have sole responsibility for the development of such Split Territory Licensed Product in the United States and Genzyme shall have sole responsibility for development of such Split Territory Licensed Product in the rest of the world. The Company and Genzyme will have shared responsibility for execution of ongoing development of such Split Territory Licensed Product that is not specific to either territory, including costs associated therewith. The Company is responsible for all commercialization activities relating to Split Territory Licensed Products in the United States, including all of the associated costs. Genzyme is responsible for all commercialization activities relating to the Split Territory Licensed Products in the rest of the world, including all of the associated costs. If Genzyme exercised its co‑commercialization rights for the Huntingtons’ Program product (“Huntington’s Licensed Product”), Genzyme will be the lead party responsible for all commercialization activities related to such product in the United States.

Upon exercise of the option, Genzyme shall have the sole right to develop the licensed product from the Spinal Muscular Atrophy Program (the “Spinal Muscular Atrophy Licensed Product”) worldwide. Genzyme shall be responsible for all of the development costs that occur after the option exercise date for the Spinal Muscular Atrophy Program. Genzyme is also responsible for commercialization activities relating to the Spinal Muscular Atrophy Licensed Product worldwide.

Genzyme is required to pay the Company for specified regulatory and commercial milestones, if achieved, up to $645 million across all programs. The regulatory approval milestones are payable upon either regulatory approval in the United States or regulatory and reimbursement approval in the European Union and range from $40.0 million to $50.0 million per milestone, with an aggregate total of $265 million. The commercial milestones are payable upon achievement of specified annual net sales in each program and range from $50.0 million to $100 million per milestone, with an aggregate total of $380 million.

In addition, to the extent any Split Territory Licensed Products or the Spinal Muscular Atrophy Licensed Product are commercialized, the Company is entitled to tiered royalty payments ranging from the mid‑single digits to mid‑teens based on a percentage of net sales by Genzyme. Genzyme is entitled to receive tiered royalty payments related to sales of Split Territory Licensed Product ranging from the low‑single digits to mid‑single digits based on a percentage of net sales by the Company depending on whether the Company uses Genzyme technology in the Split Territory Licensed Product. If Genzyme elects to co‑commercialize VY‑HTT01 in the United States, the Company and Genzyme will share in any profits or losses from VY‑HTT01 product sales.

The Collaboration Agreement will continue in effect until the later of (i) the expiration of the last to expire of the option rights and (ii) the expiration of all payment obligations unless sooner terminated by the Company or Genzyme. The Company and Genzyme have customary termination rights including the right to terminate for an uncured material breach of the agreement committed by the other party and Genzyme has the right to terminate for convenience.

Accounting Analysis

The Collaboration Agreement includes the following deliverables: (i) research and development services for each of the Split Territory License Programs and the Spinal Muscular Atrophy Program, (ii) participation in the AJSC, (iii) participation in the DAC and (iv) the option to obtain a development and commercial license in the Parkinson’s Program and related deliverables. The Company has determined that the option to obtain a development and commercial license in the Parkinson’s Program is not a substantive option for accounting purposes, primarily because there is no additional option exercise payment payable by Genzyme at the time the option is exercised. Therefore, the option to obtain a license and other obligations of the Company that are contingent upon exercise of the option are considered deliverables at the inception of the arrangement. The options in the other Split Territory Programs and the Spinal Muscular Atrophy Program are considered substantive as there is substantial option exercise payments payable by Genzyme upon exercise. In addition, as a result of the uncertainties related to the discovery, research, development and commercialization activities, the Company is at risk with regard to whether Genzyme will exercise the options. Moreover, the substantive options are not priced at a significant incremental discount. Accordingly, the substantive options are not considered deliverables at the inception of the arrangement and the associated option exercise payments are not included in allocable arrangement consideration. The Company has also determined that any obligations which are contingent upon the exercise of a substantive option are not considered deliverables at the outset of the arrangement, as these deliverables are contingent upon the exercise of the options. In addition, any option exercise payments associated with the substantive options are not included in the allocable arrangement consideration.

The Company has concluded that each of the deliverables identified at the inception of the arrangement has standalone value from the other undelivered elements. Additionally, the Collaboration Agreement does not include return rights related to the initial collaboration term. Accordingly, each deliverable qualifies as a separate unit of accounting.

The Company has identified $79.3 million of allocable arrangement consideration consisting of the $65 million upfront fee, the $5.0 million premium paid in excess of fair value of the Series B Preferred Stock and $9.3 million of Genzyme “in‑kind” and other funding.

The Company has allocated the allocable arrangement consideration based on the relative selling price of each unit of accounting. For all units of accounting, the Company determined the selling price using the best estimate of selling price (“BESP”). The Company determined the BESP for the service related deliverable for the research and development activities based on internal estimates of the costs to perform the services, including expected internal expenses and expenses with third parties for services and supplies, marked up to include a reasonable profit margin and adjusted for the scope of the potential license. Significant inputs used to determine the total expense of the research and development activities include, the length of time required and the number and costs of various studies that will be performed to complete the applicable POP Study. The BESP for the AJSC and DAC have been estimated based on the costs incurred to participate in the committees, marked up to include a reasonable profit margin. The BESP for the license option was determined based on the estimated value of the license and related deliverables adjusted for the estimated probability that the option would be exercised by Genzyme.

Based on the relative selling price allocation, the allocable arrangement consideration was allocated as follows:


Unit of Accounting	Amount
	(in thousands)
Research and Development Services for:
Huntington’s Program	$	15,662
Parkinson’s Program		6,648
Friedreich’s Ataxia Program		16,315
Spinal Muscular Atrophy Program		32,050
Future Program		2,464
Committee Obligations:
AJSC		147
DAC		227
License Option and related deliverables		5,743
Total	$	79,256

The Company recognizes the amounts associated with research and development services on a straight line basis over the estimated period of service as there is no discernable pattern or objective measure of performance for the services. Similarly, the Company recognizes the amount associated with the committee obligations on a straight line basis over the period of service consistent with the expected pattern of performance. The amounts allocated to the license option will be deferred until the option is exercised. The revenue recognition upon option exercise will be determined based on whether the license has standalone value from the remaining deliverables at the time of exercise.

During the second quarter of 2016, the Company reassessed the estimated period of performance for each of its units of accounting and, based on then current facts and circumstances, determined that the estimated period would be extended for two units of accounting. This adjustment was made on a prospective basis and resulted in a decrease in revenues recognized by $1.2 million per quarter due to this adjustment. During the third quarter of 2016, the Company reassessed and reduced the estimates related to the amount of “in-kind” services that are expected to be provided by Genzyme. This adjustment was made on a prospective basis and resulted in a decrease in revenues recognized by $0.5 million during the three months ended September 30, 2016.

The Company has evaluated all of the milestones that may be received in connection with each Split Territory Licensed Product and the Spinal Muscular Atrophy Licensed Product. In evaluating if a milestone is substantive, the Company assesses whether: (i) the consideration is commensurate with either the Company’s performance to achieve the milestone or the enhancement of the value of the delivered item(s) as a result of a specific outcome resulting from the Company performance to achieve the milestone, (ii) the consideration relates solely to past performance and (iii) the consideration is reasonable relative to all of the deliverables and payment terms within the arrangement. All regulatory milestones are considered substantive on the basis of the contingent nature of the milestone, specifically reviewing factors such as the scientific, clinical, regulatory, and other risks that must be overcome to achieve the milestone as well as the level of effort and investment required. Accordingly, such amounts will be recognized as revenue in full in the period in which the associated milestone is achieved, assuming all other revenue recognition criteria are met. All commercial milestones will be accounted for in the same manner as royalties and recorded as revenue upon achievement of the milestone, assuming all other revenue recognition criteria are met.

During the three and nine months ended September 30, 2016, the Company recognized $3,308,000 and $11,858,000, respectively of revenue associated with its collaboration with Genzyme related to research and development services performed during the periods. As of September 30, 2016, there is $43,752,000 of deferred revenue related to the Collaboration Agreement, which is classified as either current or noncurrent in the accompanying balance sheet based on the period the services are expected to be delivered.

Costs incurred relating to the programs that Genzyme has the option to license under the Collaboration Agreement consist of internal and external research and development costs, which primarily include: salaries and benefits, lab supplies and preclinical research studies. The Company does not separately track or segregate the amount of costs incurred under the Collaboration Agreement. All of these costs are included in research and development expenses in the Company’s statement of operations during the three and nine months ended September 30, 2016. The Company estimates that the majority of research and development expense during the period relate to programs for which Genzyme has an option right.

MRI Interventions License and Securities Purchase Agreements

In September 2016, the Company entered into Securities Purchase and License agreements with MRI Interventions, Inc. (“MRIC”). MRIC is the primary supplier of the ClearPoint System, which is being used by the Company in ongoing development and clinical trials. Under the Securities Purchase Agreement, the Company paid $2.0 million for shares of MRIC common stock and a warrant to purchase additional shares of MRIC common stock. The License Agreement provides for certain rights to MRIC technology, and for MRIC to transfer the rights and know-how to manufacture the ClearPoint System, in order to enable the Company to utilize an alternative supplier for the ClearPoint System for use in the Company’s development and clinical trials. Upon completion of the transfer of the manufacturing and know how, the Company may be obligated to purchase an additional $1.0 million of MRIC common stock at the then fair market value. In addition, the Company has purchased approximately $0.3 million of supplies for use in the ongoing development and clinical trials and have agreed to negotiate a Development and Supply agreement in the future.

Accounting Analysis

The Company has accounted for its interest in MRIC common stock under ASC 320 “Investments - Debt and Equity Securities” since the Company does not have the ability to control or exercise significant influence over the operations of MRIC. As the MRIC common stock is actively traded, the Company has accounted for the investment in MRIC common stock as an available-for-sale marketable security. The $2.0 million payment was allocated to the common stock and warrant, based on relative fair value. The investment in MRIC common stock was initially recorded at $1.2 million and the warrant was recorded at $0.8 million.

The shares of MRIC common stock are classified as non-current available-for-sale marketable securities and the warrants are classified as other assets in the accompanying balance sheet. Remeasurement gains related to the marketable securities are recorded as a component of other comprehensive income and gains related to the warrant are recorded as a component of other expenses in the consolidated statement of operations.

The Company concluded that the fair value of the potential obligation to purchase an additional $1.0 million of common stock was insignificant as the share acquisition price will be based on the market price of the MRIC common stock upon completion of the transfer of manufacturing and know how.

Litigation

The Company is not a party to any litigation and does not have contingency reserves established for any litigation liabilities as of September 30, 2016 or December 31, 2015.

Stock-based compensation

9 Months Ended

Sep. 30, 2016

Stock based compensation

Disclosure of Compensation Related Costs, Share-based Payments [Text Block]

8. Stock‑Based Compensation

2015 Stock Option Plan

In October 2015, the Company’s board of directors and stockholders approved the 2015 Stock Option and Incentive Plan, or 2015 Stock Option Plan, which became effective upon the completion of the IPO. The 2015 Stock Option Plan provides the Company with the flexibility to use various equity-based incentive and other awards as compensation tools to motivate its workforce. These tools include stock options, stock appreciation rights, restricted stock, restricted stock units, unrestricted stock, performance share awards and cash-based awards. The 2015 Stock Option Plan replaced the Voyager Therapeutics, Inc. 2014 Stock Option and Grant Plan, or the 2014 Plan. Any options or awards outstanding under the 2014 Plan remained outstanding and effective. The number of shares initially reserved for issuance under the 2015 Stock Option Plan is the sum of (i) 1,311,812 shares of common stock and (ii) the number of shares under the 2014 Plan that are not needed to fulfill the Company’s obligations for awards issued under the 2014 Plan as a result of forfeiture, expiration, cancellation, termination or net issuances of awards thereunder. The number of shares of common stock that may be issued under the 2015 Stock Option Plan is also subject to increase on the first day of each fiscal year by up to 4% of the Company’s issued and outstanding shares of common stock on the immediately preceding December 31.

Effective January 1, 2016, an additional 1,069,971 shares were added to the Company’s 2015 Stock Option Plan for future issuance. As of September 30, 2016, there were 1,879,606 shares of common stock available for future award grants under the 2015 Stock Option Plan. During the three and nine months ended September 30, 2016, the Company issued a total of 84,600 and 888,110 stock options, respectively, to employees and directors under the 2015 Stock Option Plan. During the three and nine months ended September 30, 2016, the Company issued a total of 6,000 and 8,500 stock options, respectively, to non-employees under the 2015 Stock Option Plan.

2014 Stock Option and Grant Plan

In January 2014 the Company adopted the 2014 Plan, under which it may grant incentive stock options, non‑qualified stock options, restricted stock awards, unrestricted stock awards, or restricted stock units to purchase up to 823,529 shares of Common Stock to employees, officers, directors and consultants of the Company.

In April 2014 the Company amended the 2014 Plan to allow for the issuance of up to 1,411,764 shares of common stock. In August 2014, April 2015, August 2015, and October 2015, the Company further amended the 2014 Plan to allow for the issuance of up to 2,000,000, 2,047,058, 2,669,411, and 2,998,823 shares of Common Stock, respectively. During 2014 the Company issued only restricted stock awards under the 2014 Plan and during 2015 the Company only granted stock options.

The terms of stock awards agreements, including vesting requirements, are determined by the Board of Directors and are subject to the provisions of the 2014 Plan.

Founder Awards

In January 2014 the Company issued 1,188,233 shares of restricted stock to its Founders at an original issuance price of $0.0425 per share. Of the total restricted shares awarded to the Founders, 835,292 shares generally vest over one to four years, based on each Founder’s continued service to the Company in varying capacity as a Scientific Advisory Board member, consultant, director, officer or employee, as set forth in each grantee’s individual restricted stock purchase agreement. The remaining 352,941 of the shares issued will begin vesting upon the achievement of certain performance objectives as well as continued service to the Company, as set forth in the agreements.

These performance conditions are tied to certain milestone events specific to the Company’s corporate goals, including but not limited to preclinical and clinical development milestones related to the Company’s product candidates. Stock‑based compensation expense associated with these performance‑based awards is recognized when the achievement of the performance condition is considered probable, using management’s best estimates. During the nine months ended September 30, 2016, management determined that the achievement of the performance milestone for one of the three performance‑based awards had become probable. Accordingly, stock-based compensation expense in the amount of $151,000 and $960,000 was recorded related to this award during the three and nine months ended September 30, 2016, respectively. No stock‑based compensation expense was recorded for the remaining two Founders’ awards with performance-based vesting as of September 30, 2016 as the performance-based milestones related to these awards were not probable.

2015 Employee Stock Purchase Plan

In October 2015, the Company’s board of directors and stockholders approved the 2015 Employee Stock Purchase Plan, or the 2015 ESPP. Under the 2015 ESPP, all full-time employees of the Company are eligible to purchase common stock of the Company twice per year, at the end of each six-month payment period. During each payment period, eligible cmployees who so elect, may authorize payroll deductions in an amount of 1% to 10% (whole percentages only) of the employee’s base pay for each payroll period. At the end of each payment period, the accumulated deducations are used to purchase shares of common stock from the Company at a discount. A total of 262,362 shares of common stock were initially authorized for issuance under this plan. The 2015 ESPP became effective upon the completion of the IPO. Effective January 1, 2016, 267,492 shares of common stock were added to the 2015 ESPP.

Stock‑Based Compensation Expense

Total compensation cost recognized for all stock‑based compensation awards in the statements of operations and comprehensive loss is as follows:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2016		2015		2016		2015
	(in thousands)
Research and development	$	1,378	$	627	$	3,426	$	1,486
General and administrative		411		230		1,103		575
Total stock-compensation expense	$	1,789	$	857	$	4,529	$	2,061

Restricted Stock

A summary of the status of and changes in unvested restricted stock unit activity under the Company’s equity award plan was as follows:


		Weighted
		Average
		Grant Date
		Fair Value
	Shares	Per Share
Unvested restricted common stock as of December 31, 2015	1,818,261	$	0.76
Issued	—		—
Vested	(468,648)	$	0.77
Repurchased	(48,776)		—
Unvested restricted common stock as of September 30, 2016	1,300,837	$	0.74

The expense related to awards granted to employees and non-employees was $128,000 and $691,000, respectively, for the three months ended September 30, 2016, and $393,000 and $1,871,000 for the nine months ended September 30, 2016, respectively. The expense related to awards granted to employees and non-employees was $134,000 and $457,000, respectively, for the three months ended September 30, 2015, and $325,000 and $1,119,000 for the nine months ended September 30, 2015.

As of September 30, 2016, the Company had unrecognized stock-based compensation expense related to its unvested restricted stock awards of $11,808,000, which is expected to be recognized over the remaining average vesting period of 1.6 years.

Stock Options

The following is a summary of stock option activity for the nine months ended September 30, 2016:


		Weighted		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value
	Shares	Price		(in years)	(in thousands)
Outstanding at December 31, 2015	1,022,617	$	8.35
Granted	896,610	$	11.83
Exercised	(19,618)	$	7.50
Cancelled or forfeited	(36,990)	$	10.07
Outstanding at September 30, 2016	1,862,619	$	10.01	9.1	$	4,353
Exercisable at September 30, 2016	388,345	$	8.65	8.7	$	1,311
Vested and expected to vest at September 30, 2016	1,862,619	$	10.01	9.1	$	4,353

Using the Black‑Scholes option pricing model, the weighted average fair value of options granted to employees and directors during the three and nine months ended September 30, 2016 was $8.98 and $7.62 per share, respectively. The expense related to awards granted to employees and directors was $914,000 and $2,155,000 for the three and nine months ended September 30, 2016, respectively. The weighted average fair value of options granted to employees and directors during the three and nine months ended September 30, 2015 was $5.66 and $5.39 per share, respectively. The expense related to awards granted to employees and directors was $215,000 and $352,000 for the three and nine months ended September 30, 2015, respectively.

The fair value of each option issued to employees and directors was estimated at the date of grant using the Black‑Scholes option pricing model with the following weighted‑average assumptions:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2016		2015		2016		2015
Risk-free interest rate	1.2	%	1.7	%	1.5	%	1.6	%
Expected dividend yield	—	%	—	%	—	%	—	%
Expected term (in years)	6.0		6.0		6.0		6.0
Expected volatility	73.2	%	78.4	%	73.1	%	78.6	%

Using the Black‑Scholes option pricing model, the weighted average grant date fair value of options granted to non‑employees during the nine months ended September 30, 2016 was $9.21 per share. Unvested options granted to non‑employees are revalued at each measurement period until fully vested. The expense related to awards granted to non‑employees was $56,000 and $110,000 for the three and nine months ended September 30, 2016, respectively. The weighted average grant date fair value of options granted to non-employees during the nine months ended September 30, 2015 was $6.23 per share. The expense related to awards granted to non-employees was $49,000 and $263,000 for the three and nine months ended September 30, 2015, respectively.

The fair value of each option issued to non‑employees was estimated at each vesting and reporting date using the Black‑Scholes option pricing model. The reporting date fair value was determined using the following weighted‑average assumptions:


	As of September 30,
	2016		2015
Risk-free interest rate	1.9	%	2.2	%
Expected dividend yield	—	%	—	%
Expected term (in years)	8.9		10.0
Expected volatility	84.0	%	82.6	%

As of September 30, 2016, the Company had unrecognized stock-based compensation expense related to its unvested stock options of $9,413,000 which is expected to be recognized over the remaining weighted average vesting period of 2.9 years.

For the three and nine months ended September 30, 2016 and September 30, 2015, expected volatility was estimated using the historical volatility of the common stock of a peer group of publicly-traded companies that are similarly situatied to the Company. The Company will continue to apply this process until a sufficient amount of historical information regarding the volatility of its own stock price becomes available.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

+ References + Details

Summary of significant accounting policies (Policies)	9 Months Ended
Summary of significant accounting policies (Policies)	Sep. 30, 2016
Summary of significant accounting policies
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, 2015 as filed with the Securities and Exchange Commission (“SEC”). 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”). The accompanying condensed consolidated financial statements include those of the Company and its wholly owned subsidiary, Voyager Securities Corporation, after elimination of all intercompany accounts and transactions.
Use of estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the 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, valuation of the tranche rights, stock‑based compensation expense, income taxes, and prior to the closing of the IPO, the fair value of common stock. 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.
Recent accounting pronouncements	Recent Accounting Pronouncements In May 2014, the FASB issued ASU No. 2014‑09, Revenue From Contracts With Customers. ASU 2014‑09 amends ASC 605, Revenue Recognition, by outlining a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers. The adoption of this ASU has been subsequently amended by ASU 2015-14, Revenue from Contracts with Customers (Topic 606): Deferral of the Effective Date; ASU 2016-10, Revenue from Contracts with Customers (Topic 606): Identifying Performance Obligations and Licensing; and ASU 2016-12, Revenue from Contracts with Customers (Topic 606): Narrow-Scope Improvements and Practical Expedients. The new standard provides a five step framework whereby revenue is recognized when promised goods or services are transferred to a customer at an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. The standard is effective for interim and annual periods beginning after December 15, 2017, with early adoption one year prior to the effectice date allowed, and allows for adoption using a full retrospective method, or a modified retrospective method. The Company has not yet determined which adoption method it will utilize or the effect that the adoption of this guidance will have on its consolidated financial statements. In August 2014, the FASB issued ASU No. 2014‑15, Presentations of Financial Statements, Going Concern, which requires management to assess an entity’s ability to continue as a going concern every reporting period, and provide certain disclosures if management has substantial doubt about the entity’s ability to operate as a going concern, or an express statement if not, by incorporating and expanding upon certain principles that are currently in U.S. auditing standards. This guidance is effective for the annual period ending after December 15, 2016, and for annual periods and interim periods thereafter. The adoption of this accounting standard may affect the Company’s financial statement disclosures in future periods. The Company has evaluated the impact of this ASU if it had been applied to these financial statements and determined that they would have concluded that there is not substantial doubt about the Company’s ability to continue as a going concern. In February 2016, the FASB issued ASU 2016-02, Leases, which requires a lessee to recognize assets and liabilities on the balance sheet for operating leases and changes many key definitions, including the definition of a lease. The new standard includes a short-term lease exception for leases with a term of 12 months or less, as part of which a lessee can make an accounting policy election not to recognize lease assets and lease liabilities. Lessees will continue to differentiate between finance leases (previously referred to as capital leases) and operating leases using classification criteria that are substantially similar to the previous guidance. The new standard will be effective beginning January 1, 2019, and early adoption is permitted for public entities. The Company is currently evaluating the potential impact this ASU may have on its financial position. In March 2016, the FASB issued ASU No. 2016-09, Compensation - Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting, which aims to simplify several aspects of the accounting for share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, classification of certain items on the statement of cash flows and accounting for forfeitures. The ASU is effective for public entities for fiscal years beginning after December 15, 2016, with early adoption permitted. The Company has not yet completed its assessment of the impact of the new standard on its consolidated financial statements.

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2016

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, 2016 and December 31, 2015 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, 2016	(in thousands)
Money market funds included in cash and cash equivalents	$	63,008	$	63,008	$	—	$	—
Marketable securities:
U.S. Treasury notes		112,486		112,486		—		—
U.S. Government agency securities		15,160		—		15,160		—
Equity securities		2,416		2,416		—		—
Total marketable securities	$	130,062	$	114,902	$	15,160	$	—
Warrants to purchase equity securities		1,559		—		1,559		—
Total	$	194,629	$	177,910	$	16,719	$	—
December 31, 2015
Money market funds included in cash and cash equivalents	$	29,601	$	29,601	$	—	$	—
Marketable securities:
U.S. Treasury notes		157,981		157,981		—		—
U.S. Government agency securities		35,055		—		35,055		—
Total marketable securities		193,036		157,981		35,055		—
Total	$	222,637	$	187,582	$	35,055	$	—

Assumptions

The assumptions utilized to value the warrants to purchase equity securities on the acquisition date, September 2, 2016, and as of September 30, 2016 are as follows:


	As of September 2,		As of September 30,
	2016		2016
Risk-free interest rate	1.2	%	1.1	%
Expected dividend yield	—	%	—	%
Expected term (in years)	5.0		4.9
Expected volatility	92.3	%	92.3	%

Cash, Cash Equivalents, and Available for Sale Marketable Investments (Tables)

9 Months Ended

Sep. 30, 2016

Cash and Cash Equivalents [Abstract]

Cash, cash equivalents and investments, available for sale

Cash, cash equivalents, and marketable securities included the following at September 30, 2016 and December 31, 2015:


	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value
	(in thousands)
As of September 30, 2016
Money market funds included in cash and cash equivalents	$	63,008	$	—	$	—	$	63,008
Total money market funds included in cash and cash equivalents	$	63,008	$	—	$	—	$	63,008
Marketable securities:
U.S. Treasury notes		112,489		—		3		112,486
U.S. Government agency bonds		15,153		7		—		15,160
Total debt securities	$	127,642	$	7	$	3	$	127,646
Equity securities		1,220		1,196		—		2,416
Total marketable securities	$	128,862	$	1,203	$	3	$	130,062
Total money market funds and marketable securities	$	191,870	$	1,203	$	3	$	193,070
As of December 31, 2015
Money market funds included in cash and cash equivalents	$	29,601	$	—	$	—	$	29,601
Total money market funds included in cash and cash equivalents	$	29,601	$	—	$	—	$	29,601
Marketable securities:
U.S. Treasury notes		158,166		—		185		157,981
U.S. Government agency bonds		35,121		—		66		35,055
Total marketable securities	$	193,287	$	—	$	251	$	193,036
Total money market funds and marketable securities	$	222,888	$	—	$	251	$	222,637

Estimated fair value of the Company’s marketable securities balance

The estimated fair value of the Company’s debt securities balance at September 30, 2016, by contractual maturity, is as follows:


Due in one year or less		$	127,646

Commitments and contingencies (Tables)

9 Months Ended

Sep. 30, 2016

Commitments and Contingencies

Summary of contractual obligations as of payment due date

The following table summarizes our significant contractual obligations as of payment due date by period at September 30, 2016:


	Total Minimum
	Lease Payments
	(in thousands)
2016		298
2017		3,211
2018		3,290
2019		3,382
2020		3,762
2021+		16,140
	$	30,083

Allocable arrangement consideration allocation


Unit of Accounting	Amount
	(in thousands)
Research and Development Services for:
Huntington’s Program	$	15,662
Parkinson’s Program		6,648
Friedreich’s Ataxia Program		16,315
Spinal Muscular Atrophy Program		32,050
Future Program		2,464
Committee Obligations:
AJSC		147
DAC		227
License Option and related deliverables		5,743
Total	$	79,256

Stock based compensation (Tables)

9 Months Ended

Sep. 30, 2016

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Compensation cost recognized for all stock-based compensation awards

Total compensation cost recognized for all stock‑based compensation awards in the statements of operations and comprehensive loss is as follows:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2016		2015		2016		2015
	(in thousands)
Research and development	$	1,378	$	627	$	3,426	$	1,486
General and administrative		411		230		1,103		575
Total stock-compensation expense	$	1,789	$	857	$	4,529	$	2,061

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 plan was as follows:


		Weighted
		Average
		Grant Date
		Fair Value
	Shares	Per Share
Unvested restricted common stock as of December 31, 2015	1,818,261	$	0.76
Issued	—		—
Vested	(468,648)	$	0.77
Repurchased	(48,776)		—
Unvested restricted common stock as of September 30, 2016	1,300,837	$	0.74

Summary of status and changes in stock options

The following is a summary of stock option activity for the nine months ended September 30, 2016:


		Weighted		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value
	Shares	Price		(in years)	(in thousands)
Outstanding at December 31, 2015	1,022,617	$	8.35
Granted	896,610	$	11.83
Exercised	(19,618)	$	7.50
Cancelled or forfeited	(36,990)	$	10.07
Outstanding at September 30, 2016	1,862,619	$	10.01	9.1	$	4,353
Exercisable at September 30, 2016	388,345	$	8.65	8.7	$	1,311
Vested and expected to vest at September 30, 2016	1,862,619	$	10.01	9.1	$	4,353

Assumptions

The assumptions utilized to value the warrants to purchase equity securities on the acquisition date, September 2, 2016, and as of September 30, 2016 are as follows:


	As of September 2,		As of September 30,
	2016		2016
Risk-free interest rate	1.2	%	1.1	%
Expected dividend yield	—	%	—	%
Expected term (in years)	5.0		4.9
Expected volatility	92.3	%	92.3	%

Employees and directors stock options

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Assumptions

The fair value of each option issued to employees and directors was estimated at the date of grant using the Black‑Scholes option pricing model with the following weighted‑average assumptions:


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2016		2015		2016		2015
Risk-free interest rate	1.2	%	1.7	%	1.5	%	1.6	%
Expected dividend yield	—	%	—	%	—	%	—	%
Expected term (in years)	6.0		6.0		6.0		6.0
Expected volatility	73.2	%	78.4	%	73.1	%	78.6	%

Non-employees stock options

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Assumptions


	As of September 30,
	2016		2015
Risk-free interest rate	1.9	%	2.2	%
Expected dividend yield	—	%	—	%
Expected term (in years)	8.9		10.0
Expected volatility	84.0	%	82.6	%

Fair Value Measurements - Assets measured on a recurring basis - (Details) - USD ($) $ in Thousands		9 Months Ended
	Sep. 02, 2016	Sep. 30, 2016	Dec. 31, 2015
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		$ 130,062	$ 193,036
Warrants to purchase equity securities		1,559
Total assets measured at fair value		194,629	222,637
Fair value assumptions
Risk-free interest rate	1.20%
Expected term (in years)	5 years
Expected volatility	92.30%
Level 1
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		114,902	157,981
Total assets measured at fair value		177,910	187,582
Level 2
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		15,160	35,055
Warrants to purchase equity securities		1,559
Total assets measured at fair value		16,719	35,055
U.S. Treasury notes
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		112,486	157,981
U.S. Treasury notes \| Level 1
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		112,486	157,981
U. S. Government agency bonds
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		15,160	35,055
U. S. Government agency bonds \| Level 2
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		15,160	35,055
Equity securities
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		2,416
Equity securities \| Level 1
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		$ 2,416
Warrants
Fair value assumptions
Risk-free interest rate		1.10%
Expected term (in years)		4 years 10 months 24 days
Expected volatility		92.30%
Money market funds
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents		$ 63,008	29,601
Money market funds \| Level 1
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents		$ 63,008	$ 29,601

Cash, Cash Equivalents, and Available for Sale Marketable Investments (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015	Sep. 30, 2015	Dec. 31, 2014
Amortized Cost Basis [Abstract]
Cash and Cash Equivalents, at Carrying Value	$ 63,507	$ 31,309	$ 66,533	$ 7,035
Total marketable securities, amortized cost	128,862	193,287
Total money market funds and marketable securities	191,870	222,888
Fair Value Disclosure [Abstract]
Cash and cash equivalents, fair value	63,507	31,309	$ 66,533	$ 7,035
Marketable securities, fair value	130,062	193,036
Total money market funds and marketable securities	193,070	222,637
Amortized Cost Abstract
Unrealized gains	1,203
Total money market funds and marketable securities	1,203
Unrealized losses	3	251
Total money market funds and marketable securities	3	251
Available-for-sale Securities, Debt Maturities, Single Maturity Date, Amortized Cost Basis, Rolling Maturity [Abstract]
Due in one year or less	127,646
Money market funds
Amortized Cost Basis [Abstract]
Cash and Cash Equivalents, at Carrying Value	63,008	29,601
Fair Value Disclosure [Abstract]
Cash and cash equivalents, fair value	63,008	29,601
Debt Securities [Member]
Amortized Cost Basis [Abstract]
Marketable debt securities, amortized cost	127,642
Fair Value Disclosure [Abstract]
Marketable debt securities, fair value	127,646
Amortized Cost Abstract
Available-for-sale Debt Securities, Accumulated Gross Unrealized Gain, before Tax	7
Available-for-sale Debt Securities, Accumulated Gross Unrealized Loss, before Tax	3
U.S. Treasury notes
Amortized Cost Basis [Abstract]
Marketable debt securities, amortized cost	112,489	158,166
Fair Value Disclosure [Abstract]
Marketable debt securities, fair value	112,486	157,981
Amortized Cost Abstract
Available-for-sale Debt Securities, Accumulated Gross Unrealized Loss, before Tax	3	185
U. S. Government agency bonds
Amortized Cost Basis [Abstract]
Marketable debt securities, amortized cost	15,153	35,121
Fair Value Disclosure [Abstract]
Marketable debt securities, fair value	15,160	35,055
Amortized Cost Abstract
Available-for-sale Debt Securities, Accumulated Gross Unrealized Gain, before Tax	7
Available-for-sale Debt Securities, Accumulated Gross Unrealized Loss, before Tax		$ 66
Equity securities
Amortized Cost Basis [Abstract]
Marketable equity securities, amortized cost	1,220
Fair Value Disclosure [Abstract]
Marketable equity securities, fair value	2,416
Amortized Cost Abstract
Available-for-sale Equity Securities, Accumulated Gross Unrealized Gain, before Tax	$ 1,196

Accrued expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Accrued expenses
Research and development costs	$ 2,552	$ 1,329
Employee compensation costs	1,953	1,338
Professional services	887	350
Patent costs	856	178
Other	56	235
Total	$ 6,304	$ 3,430

Commitments and contingencies - Operating Leases - (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Mar. 31, 2014
Commitments and Contingencies
Leasehold incentive received from landlord		$ 1,300
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2016	$ 298
2017	3,211
2018	3,290
2019	3,382
2020	3,762
2121 +	16,140
Total minimum lease payments	$ 30,083

Commitments and contingencies - Significant Agreements - (Details) - Collaborative Arrangement $ in Millions	1 Months Ended
	Feb. 28, 2015 USD ($) shares
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Non-refundable upfront payment received	$ 65.0
Premium over fair value on temporary equity issued	5.0
Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Non-refundable upfront payment received	65.0
Amount of reduction in milestone or royalty payments to be made by collaborative partner for each program specified	10.0
Per Milestone, maximum milestone payments to be received from collaborative partner	645.0
Regulatory approval milestone \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner	265.0
Regulatory approval milestone \| Minimum \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner	40.0
Regulatory approval milestone \| Maximum \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner	50.0
Commerical milestone \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner	380.0
Commerical milestone \| Minimum \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner	50.0
Commerical milestone \| Maximum \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner	100.0
Spinal Muscular Atrophy Program \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum potential in-kind services to be provided by collaborative partner	5.0
Option exercise payment required from collaborative partner for each program specified	30.0
Split Territory Program \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Option exercise payment required from collaborative partner for each program specified	20.0
Redeemable Convertible Preferred Stock Series B
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Fair value of temporary equity issued	$ 25.0
Redeemable Convertible Preferred Stock Series B \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Temporary equity issued (in shares) \| shares	10,000,000
Temporary equity issued	$ 30.0
Premium over fair value on temporary equity issued	$ 5.0

Commitments and contingencies - Accounting Analysis - (Details) - USD ($)	1 Months Ended	3 Months Ended		9 Months Ended
	Feb. 28, 2015	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Allocable arrangement consideration allocation
Committee Obligations: Alliance Joint Steering Committee ("AJSC")	$ 147,000
Committee Obligations: Development Advisory Committee ("DAC")	227,000
License Option and related deliverables	5,743,000
Total allocable arrangement consideration allocations.	79,256,000
Income Statement Related Disclosures [Abstract]
Collaboration revenue		$ 3,308,000	$ 4,937,000	$ 11,858,000	$ 12,397,000
Revenue adjustment on account of change in estimated period of performance		500,000
Huntington's Program
Allocable arrangement consideration allocation
Research and development services	15,662,000
Parkinson's Program
Allocable arrangement consideration allocation
Research and development services	6,648,000
Friedreich's Ataxia Program
Allocable arrangement consideration allocation
Research and development services	16,315,000
Spinal Muscular Atrophy Program
Allocable arrangement consideration allocation
Research and development services	32,050,000
Future Program
Allocable arrangement consideration allocation
Research and development services	2,464,000
Collaborative Arrangement
Allocable arrangement consideration
Collaborative Arrangement Nonredeemable Up Front Fee Received	65,000,000
Additional consideration, premium over fair value on temporary equity issued	5,000,000
Genzyme \| Collaborative Arrangement
Allocable arrangement consideration
Collaborative Arrangement Nonredeemable Up Front Fee Received	65,000,000
In-kind services and other funding to be provided by collaborative partner	9,300,000
Total allocable arrangement consideration	79,300,000
Income Statement Related Disclosures [Abstract]
Collaboration revenue		3,308,000		11,858,000
Deferred Revenue		$ 43,752,000		$ 43,752,000
Redeemable Convertible Preferred Stock Series B \| Genzyme \| Collaborative Arrangement
Allocable arrangement consideration
Additional consideration, premium over fair value on temporary equity issued	$ 5,000,000

Stock based compensation - 2014 Stock Option and Grant Plan - (Details)		1 Months Ended	3 Months Ended		9 Months Ended
	Jan. 01, 2016 shares	Jan. 31, 2014 $ / shares shares	Sep. 30, 2016 USD ($) shares	Sep. 30, 2015 USD ($)	Sep. 30, 2016 USD ($) shares	Sep. 30, 2015 USD ($)	Oct. 31, 2015 shares	Aug. 31, 2015 shares	Apr. 30, 2015 shares	Aug. 31, 2014 shares	Apr. 30, 2014 shares
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $			$ 1,789,000	$ 857,000	$ 4,529,000	$ 2,061,000
Stock options granted (in shares)					896,610
2014 Stock Option and Grant Plan (2014 Plan)
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Number of shares authorized for stock-based compensation plan (in shares)		823,529					2,998,823	2,669,411	2,047,058	2,000,000	1,411,764
2015 Employee Stock Purchase Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future issuance (in shares)			267,492		267,492		262,362
2015 Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future issuance (in shares)			1,879,606		1,879,606		1,311,812
Percentage limit of issued and outstanding shares upto which additional shares may be issued					4.00
Additional shares added to stock option plan	1,069,971
Unvested restricted stock awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized stock-based compensation expense \| $			$ 11,808,000		$ 11,808,000
Employees restricted stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $			128,000		393,000	134,000
Non-employee consultants restricted stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $					1,871,000	457,000
Performance based milestone awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $			151,000		960,000
Founders restricted stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $					0
Restricted stock granted (in shares)		1,188,233
Restricted stock granted, original issued price (in dollars per share) \| $ / shares		$ 0.0425
Founders restricted stock \| Vesting period, tranche one
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stock granted (in shares)		835,292
Founders restricted stock \| Vesting period, tranche two
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Restricted stock granted (in shares)		352,941
Founders restricted stock \| Minimum \| Vesting period, tranche one
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period		1 year
Founders restricted stock \| Maximum \| Vesting period, tranche one
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Vesting period		4 years
Employees and directors stock options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $			$ 914,000		$ 2,155,000	215,000
Employees and directors stock options \| 2015 Stock Option and Incentive Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options granted (in shares)			84,600
Employees and directors stock options \| 2015 Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock options granted (in shares)					888,110
Non-employees stock options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $			$ 56,000	$ 49,000	$ 110,000	$ 263,000

Stock based compensation - Restricted Stock - (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Shares
Balance, beginning (in shares)			1,818,261
Vested (in shares)			(468,648)
Repurchased (in shares)			(48,776)
Balance, ending (in shares)	1,300,837		1,300,837
Weighted Average Grant Date Fair Value Per Share
Balance, beginning (in dollars per share)			$ 0.76
Vested (in dollars per share)			0.77
Balance, ending (in dollars per share)	$ 0.74		$ 0.74
Restricted stock disclosures
Stock-based compensation	$ 1,789,000	$ 857,000	$ 4,529,000	$ 2,061,000
Unvested restricted stock awards
Restricted stock disclosures
Unrecognized stock-based compensation expense	11,808,000		$ 11,808,000
Remaining weighted-average remaining vesting period			1 year 7 months 6 days
Employees restricted stock
Restricted stock disclosures
Stock-based compensation	$ 128,000		$ 393,000	134,000
Non-employee consultants restricted stock
Restricted stock disclosures
Stock-based compensation			$ 1,871,000	$ 457,000

Stock based compensation - Stock Options - (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Outstanding, beginning balance (in shares)			1,022,617
Granted (in shares)			896,610
Exercised (in shares)			(19,618)
Cancelled or forfeited (in shares)			(36,990)
Outstanding, ending balance (in shares)	1,862,619		1,862,619
Exerciseable (in shares)	388,345		388,345
Vested and expected to vest (in shares)	1,862,619		1,862,619
Weighted Average Exercise Price
Oustanding (in dollars per share)			$ 8.35
Granted (in dollars per share)			11.83
Exercised (in dollars per share)			7.50
Cancelled or forfeited (in dollars per share)			10.07
Oustanding (in dollars per share)	$ 10.01		10.01
Exercisable (in dollars per share)	8.65		8.65
Vested and expected to vest (in dollars per share)	$ 10.01		$ 10.01
Remaining Contractual Life
Outstanding			9 years 1 month 6 days
Exerciseable			8 years 8 months 12 days
Vested and expected to vest			9 years 1 month 6 days
Aggregate Intrinsic Value
Oustanding	$ 4,353,000		$ 4,353,000
Exerciseable	1,311,000		1,311,000
Vested and expected to vest	4,353,000		4,353,000
Options disclosures
Stock-based compensation	$ 1,789,000	$ 857,000	$ 4,529,000	$ 2,061,000
Employees and directors stock options
Options disclosures
Weighted average fair value of grants (in dollars per share)	$ 8.98		$ 7.62
Stock-based compensation	$ 914,000		$ 2,155,000	$ 215,000
Non-employees stock options
Options disclosures
Weighted average fair value of grants (in dollars per share)			$ 9.21	$ 6.23
Stock-based compensation	$ 56,000	$ 49,000	$ 110,000	$ 263,000

Stock based compensation - Black-Scholes options pricing model - (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Options disclosures
Stock-based compensation	$ 1,789,000	$ 857,000	$ 4,529,000	$ 2,061,000
Stock options granted (in shares)			896,610
Employees and directors stock options
Fair value assumptions
Risk-free interest rate	1.20%	1.70%	1.50%	1.60%
Expected term	6 years	6 years	6 years	6 years
Expected volatility	73.20%	78.40%	73.10%	78.60%
Options disclosures
Weighted average fair value of grants (in dollars per share)	$ 8.98		$ 7.62
Stock-based compensation	$ 914,000		$ 2,155,000	$ 215,000
Non-employees stock options
Options disclosures
Weighted average fair value of grants (in dollars per share)			$ 9.21	$ 6.23
Stock-based compensation	56,000	$ 49,000	$ 110,000	$ 263,000
Unvested stock options
Options disclosures
Unrecognized stock-based compensation expense	$ 9,413,000		$ 9,413,000
Remaining weighted-average remaining vesting period			2 years 10 months 24 days

Nature of business	9 Months Ended
Nature of business	Sep. 30, 2016
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 diseases of the central nervous system (the “CNS”). The Company focuses on CNS diseases where it believes that an adeno‑associated virus (“AAV”) gene therapy approach can have a clinically meaningful impact by either increasing or decreasing the production of a specific protein. The Company has created a product engine that 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 directly to the CNS. The Company’s product engine has rapidly generated six programs for CNS indications, including advanced Parkinson’s disease, a form of monogenic amyotrophic lateral sclerosis, Friedreich’s ataxia, Huntington’s disease, frontotemporal dementia / Alzheimer’s disease, and severe, chronic pain. The Company’s most advanced clinical candidate, VY‑AADC01, is being evaluated for the treatment of advanced Parkinson’s disease in an open‑label, Phase 1b clinical trial with the goal of generating human proof‑of‑concept data in early December 2016. The Company is subject to risks common to companies in the biotechnology and gene therapy industry, including but not limited to, risks of failure of pre‑clinical studies and clinical trials, the need to obtain adequate additional funding, the need to obtain marketing approval for its drug product candidates, the need to successfully commercialize and gain market acceptance of its drug product candidates, dependence on key personnel, protection of proprietary technology, compliance with government regulations, development by competitors of technological innovations, ability to transition from pilot‑scale manufacturing to large‑scale production of products, and reliance on external sources for financing. If the Company does not successfully commercialize any of its products, it will be unable to generate product revenue or achieve profitability. In February 2015, the Company entered into an agreement with Genzyme (“Collaboration Agreement”), which included a non-refundable upfront payment of $65.0 million. In addition, contemporaneous with entering into the Collaboration Agreement, Genzyme entered into a Series B Stock Purchase Agreement, under which Genzyme purchased 10,000,000 shares of Series B Preferred Stock for $30.0 million. Through September 30, 2016, the Company had raised approximately $278.0 million of proceeds from sales of convertible preferred stock and common stock, including its initial public offering, and proceeds from the Collaboration Agreement. The Company believes that its cash, cash equivalents, and marketable debt securities of $191.2 million as of September 30, 2016 is sufficient to fund its current operating plan into 2019. There can be no assurance, however, that the current operating plan will be achieved in the timeframe anticipated by the Company, or that its cash resources will fund the Company’s operating plan for the period anticipated by the Company, or if the Company needs additional funding that such funding will be available on terms acceptable to the Company, or at all.

Redeemable Convertible Preferred Stock	9 Months Ended
Redeemable Convertible Preferred Stock	Sep. 30, 2016
Redeemable Convertible Preferred Stock Disclosure [Abstract]
Redeemable Convertible Preferred Stock [Text Block]	7. Redeemable Convertible Preferred Stock In November 2015, upon the closing of the Company’s IPO, all issued and outstanding redeemable convertible preferred stock was automatically converted into 17,647,054 shares of common stock. The Company has authorized preferred stock amounting to 5,000,000 shares as of September 30, 2016 and December 31, 2015. The authorized preferred stock was classified under stockholders’ equity at September 30, 2016 and December 31, 2015.

Income taxes	9 Months Ended
Income taxes	Sep. 30, 2016
Income taxes
Income taxes	9. Income taxes Deferred tax assets and deferred tax liabilities are recognized based on temporary differences between the financial reporting and tax basis of assets and liabilities using statutory rates. A valuation allowance is recorded against deferred tax assets if it is more likely than not that some or all of the deferred tax assets will not be realized. Due to the uncertainty surrounding the realization of the favorable tax attributes in future tax returns, the Company has recorded a full valuation allowance against the Company’s otherwise recognizable net deferred tax assets. For the three and nine months ended September 30, 2016, the Company recognized an income tax benefit of $0.3 million, and tax expense in other comprehensive loss of $0.6 million related to the unrealized gain on available-for-sale securities. As of September 30, 2016, the Company recorded an accrued income tax provision of $0.3 million related to this tax benefit included within accrued expenses and other current liabilities in the condensed consolidated balance sheet, which is expected to be generated from continuing operations.

Related party transactions	9 Months Ended
Related party transactions	Sep. 30, 2016
Related party transactions
Related party transactions	11. Related‑Party Transactions During the three and nine months ended September 30, 2016 and September 30, 2015, the Company received consulting and management services from one of its investors. The total amount of consulting and management services provided by this investor was approximately $19,000 and $35,000 during the three and nine months ended September 30, 2016, respectively. The total amount of services provided by this investor was approximately $6,000 and $115,000 during the three and nine months ended September 30, 2015, respectively. As of September 30, 2016, the Company had a balance of $19,000 in accounts payable related to consulting and management service fees charged by this investor. During the three and nine months ended September 30, 2016, the Company recognized $3,308,000 and $11,858,000, respectively, of revenue associated with the Collaboration Agreement related to research and development services provided during this period. During the three and nine months ended September 30, 2015, the Company recognized $4,937,000 and $12,397,000, respectively, of revenue associated with the Collaboration Agreement related to research and development services provided during the period. The Company also recognized $236,000 and $989,000 of expense during the three and nine months ended September 30, 2016, respectively, related to in‑kind services provided by Genzyme associated with the Collaboration Agreement. The Company recognized $125,000 and $2,190,000 of expense during the three and nine months ended September 30, 2015, respectively, related to in-kind services provided by Genzyme under the Collaboration Agreement.

Summary of significant accounting policies - Basis of Presentation - (Details) $ / shares in Units, $ in Millions		1 Months Ended
	Nov. 16, 2015 shares	Nov. 30, 2015 USD ($) $ / shares shares	Sep. 30, 2016 shares	Dec. 31, 2015 shares
Common stock sales			25,419,245	24,930,979
IPO
Common stock sales		5,750,000
Price per share \| $ / shares		$ 14.00
Net proceeds \| $		$ 72.9
Reverse split ratio		0.24
Common Stock
Shares issued upon conversion of redeemable convertible preferred stock	17,647,054	17,647,054

Nature of business (Details) - USD ($) $ in Millions	1 Months Ended	9 Months Ended
Nature of business (Details) - USD ($) $ in Millions	Feb. 28, 2015	Sep. 30, 2016
Net proceeds		$ 278.0
Cash, cash equivalent, and available-for-sale securities		$ 191.2
Collaborative Arrangement
Collaborative Arrangement Nonredeemable Up Front Fee Received	$ 65.0
Genzyme \| Collaborative Arrangement
Collaborative Arrangement Nonredeemable Up Front Fee Received	$ 65.0
Genzyme \| Redeemable Convertible Preferred Stock Series B \| Collaborative Arrangement
Temporary Equity Stock Issued During Period Shares New Issues Upon Exchange Of Convertible Debt	10,000,000
Temporary equity issued	$ 30.0

Commitments and contingencies - Other Agreements - (Details) - USD ($)	Sep. 30, 2016	Dec. 31, 2015
Loss Contingency [Abstract]
Contingency reserves for litigation liabilities	$ 0	$ 0

Redeemable Convertible Preferred Stock - Series A Preferred Stock- Series A Preferred Stock- (Details) - shares		1 Months Ended
	Nov. 16, 2015	Nov. 30, 2015	Sep. 30, 2016	Dec. 31, 2015
Temporary Equity [Line Items]
Preferred Stock, Shares Authorized			5,000,000	5,000,000
Common Stock
Temporary Equity [Line Items]
Shares issued upon conversion of redeemable convertible preferred stock	17,647,054	17,647,054

Income taxes (Details) $ in Thousands	3 Months Ended	9 Months Ended
Income taxes (Details) $ in Thousands	Sep. 30, 2016 USD ($)	Sep. 30, 2016 USD ($)
Tax expense recognized in OCI	$ 570	$ 570
Income Tax Expense (Benefit)	(303)	(303)
Accrued expenses and other current liabilities
Accrued income tax provision	$ 300	$ 300

Net loss per share (Details) - shares	9 Months Ended
Net loss per share (Details) - shares	Sep. 30, 2016	Sep. 30, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share (in common stock equivalent shares)	3,163,456	20,512,443
Redeemable convertible preferred stock
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share (in common stock equivalent shares)		17,647,054
Unvested restricted stock awards
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share (in common stock equivalent shares)	1,300,837	2,013,140
Outstanding stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share (in common stock equivalent shares)	1,862,619	852,249

Related party transactions (Details) - USD ($)	3 Months Ended		9 Months Ended
Related party transactions (Details) - USD ($)	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Investor
Related Party Transaction [Line Items]
Accounts payable to related party	$ 19,000		$ 19,000
Investor \| Consulting and management services
Related Party Transaction [Line Items]
Total amount of services received	19,000	$ 6,000	35,000	$ 115,000
Genzyme \| Collaboration arrangement
Related Party Transaction [Line Items]
Revenue recognized	3,308,000	4,937,000	11,858,000	12,397,000
Expense recognized	$ 236,000	$ 125,000	$ 989,000	$ 2,190,000