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Document and Entity Information - shares	6 Months Ended
Document and Entity Information - shares	Jun. 30, 2017	Aug. 04, 2017
Document and Entity Information
Entity Registrant Name	Voyager Therapeutics, Inc.
Entity Central Index Key	0001640266
Document Type	10-Q
Document Period End Date	Jun. 30, 2017
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		26,903,694
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q2

Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Assets, Current
Cash and cash equivalents, fair value	$ 66,300	$ 36,641
Marketable securities	75,023	137,777
Prepaid Expense and Other Assets, Current	3,403	4,368
Total Current Assets	144,726	178,786
Property, Plant and Equipment, Net	10,674	7,893
Deposits and other non-current assets	1,534	1,527
Marketable securities	1,480	1,360
Total Assets	158,414	189,566
Liabilities, Current
Accounts Payable	307	550
Accrued expenses	7,314	6,488
Deferred revenue, current portion	4,215	6,764
Total current liabilities	11,836	13,802
Deferred rent, net of current portion	5,430	4,999
Deferred revenue, net of current portion	34,838	34,818
Other non-current liabilities	1,019	25
Total Liabilities	53,123	53,644
Stockholders' Equity Attributable to Parent
Common stock, $0.001 par value: 120,000,000 shares authorized at June 30, 2017 and December 31, 2016; 26,002,873 and 25,597,912 shares issued and outstanding at June 30, 2017 and December 31, 2016, respectively	26	26
Additional Paid in Capital	230,773	225,963
Accumulated other comprehensive gain	30	(52)
Accumulated deficit	(125,538)	(90,015)
Total stockholders’ deficit	105,291	135,922
Total liabilities, redeemable convertible preferred stock and stockholders’ deficit	$ 158,414	$ 189,566

Statement of Operations and Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Income Statement [Abstract]
Collaboration revenue	$ 1,177	$ 3,720	$ 2,642	$ 8,550
Operating Expenses [Abstract]
Research and development	15,300	10,484	29,372	19,216
General and administrative	4,516	2,854	9,430	6,419
Total operating expenses	19,816	13,338	38,802	25,635
Operating loss	(18,639)	(9,618)	(36,160)	(17,085)
Other expense, net
Interest income	255	433	508	898
Other expense, net	(297)	(150)	98	(336)
Total other income (expense)	(42)	283	606	562
Loss before income taxes	(18,681)	(9,335)	(35,554)	(16,523)
Income tax benefit	(195)		31
Net loss	(18,876)	(9,335)	(35,523)	(16,523)
Other comprehensive loss
Unrealized gain (loss) on available-for-sale-securities, net of income tax provision of $(191) and $53 for the three and six months ended June 30, 2017, respectively	(295)	30	82	311
Total other comprehensive gain	(295)	30	82	311
Comprehensive loss	$ (19,171)	$ (9,305)	$ (35,441)	$ (16,212)
Reconciliation of net loss to net loss attributable to common stockholder:
Net loss per share attributable to common stock, basic and diluted	$ (0.73)	$ (0.37)	$ (1.37)	$ (0.66)
Weighted-average common shares outstanding, basic and diluted	25,946,333	25,228,405	25,869,390	25,152,587

Statement of Cash Flows - USD ($) $ in Thousands	6 Months Ended
Statement of Cash Flows - USD ($) $ in Thousands	Jun. 30, 2017	Jun. 30, 2016
Cash flow from operating activities
Net loss	$ (35,523)	$ (16,523)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense	3,704	2,739
Depreciation	726	288
Amortization of premiums and discounts on marketable securities	169	427
In-kind research and development expenses	113	752
Other non-cash items	(144)	75
Changes in operating assets and liabilities:
Prepaid expenses and other current assets	965	73
Other non-current assets		57
Deferred revenue	(2,642)	(8,550)
Accounts payable	(243)	(158)
Accrued expenses	731	1,619
Other non-current liabilities	1,000
Lease incentive benefit	515
Net cash provided by (used in) operating activities	(30,629)	(19,201)
Cash flow from investing activities
Purchases of property and equipment	(3,412)	(657)
Change in restricted cash		(471)
Purchases of marketable securities		(12,041)
Proceeds from maturities of marketable securities	62,600	68,000
Net cash used in investing activities	59,188	54,831
Cash flow from financing activities
Proceeds from the exercise of stock options and issuance of restricted stock	1,100	93
Net cash provided by financing activities	1,100	93
Net increase in cash and cash equivalents	29,659	35,723
Cash and cash equivalents, beginning of period	36,641	31,309
Cash and cash equivalents, end of period	66,300	$ 67,032
Supplemental Disclosure of Cash and non-cash Activities
Capital Expenditures Incurred but Not yet Paid	$ 95

Summary of significant accounting policies	6 Months Ended
Summary of significant accounting policies	Jun. 30, 2017
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, 2016 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”). Principles of Consolidation The unaudited interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries as disclosed in Note 2, Summary of Significant Accounting Policies, within the “Notes to Consolidated Financial Statements” accompanying its Annual Report on Form 10-K for the fiscal year ended December 31, 2016. Intercompany accounts and transactions have been eliminated. 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, stock‑based compensation expense, income taxes, and 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 (Topic 606) (“ASU 2014-09”). Subsequently, the FASB also issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606), which adjusted the effective date of ASU 2014-09; ASU No. 2016-08, Revenue from Contracts with Customers (Topic 606): Principal versus Agent Considerations (Reporting Revenue Gross versus Net), which amends the principal-versus-agent implementation guidance and illustrations in ASU 2014-09; ASU No. 2016-10, Revenue from Contracts with Customers (Topic 606): Identifying Performance Obligations and Licensing, which clarifies identifying performance obligation and licensing implementation guidance and illustrations in ASU 2014-09; and ASU No. 2016-12, Revenue from Contracts with Customers (Topic 606): Narrow-Scope Improvements and Practical Expedients, which addresses implementation issues and is intended to reduce the cost and complexity of applying the new revenue standard in ASU 2014-09 (collectively, the “Revenue ASUs”). The Revenue ASUs provide an accounting standard for a single comprehensive model for use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance. The accounting standard is effective for interim and annual periods beginning after December 15, 2017, with an option to early adopt for interim and annual periods beginning after December 15, 2016. The guidance permits two methods of adoption: retrospectively to each prior reporting period presented (the full retrospective method), or retrospectively with the cumulative effect of initially applying the guidance recognized at the date of initial application (the modified retrospective method). The Company will adopt the Revenue ASUs effective January 1, 2018 and expects to utilize the modified retrospective methodology. As of June 30, 2017, revenue is generated exclusively from the Company’s collaboration arrangement with Sanofi-Genzyme. The Company is currently evaluating the potential impact that ASU 2014-09 may have on its financial position and results of operations as it relates to this single arrangement. The adoption of the Revenue ASUs is expected to have a significant impact on the Company’s notes to consolidated financial statements and its internal controls over financial reporting. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”), which simplifies several aspects of the accounting for employee share-based payment transactions, including income tax consequences, classification of awards as either equity or liabilities, and classification in the statement of cash flows. ASU 2016-09 is effective for annual reporting periods beginning after December 15, 2016, including interim periods within those annual reporting periods. The new standard was effective for the Company on January 1, 2017. Adoption of ASU 2016-09 did not have a material impact on the Company’s consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (“ASC 842”), which sets out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e., lessees and lessors). The standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight-line basis over the term of the lease. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for similarly to existing guidance for operating leases today. ASC 842 supersedes the previous leases standard, ASC 840 Leases. The standard will be effective on January 1, 2019, with early adoption permitted. The Company is in the process of evaluating the impact that this new guidance will have on its consolidated financial statements. In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments (“Topic 230”). The new standard clarifies certain aspects of the statement of cash flows, including the classification of contingent consideration payments made after a business combination and several other clarifications not currently applicable to the Company. The new standard also clarifies that an entity should determine each separately identifiable source or use within the cash receipts and cash payments on the basis of the nature of the underlying cash flows. In situations in which cash receipts and payments have aspects of more than one class of cash flows and cannot be separated by source or use, the appropriate classification should depend on the activity that is likely to be the predominant source or use of cash flows for the item. The new standard will be effective for the Company on January 1, 2018. The adoption of this standard is not expected to have a material impact on the Company’s condensed consolidated statements of cash flows upon adoption. In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows: Restricted Cash (“ASU 2016-18”). The amendments in this update require that amounts generally described as restricted cash and restricted cash equivalents be included within cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. ASU 2016-18 will be effective January 1, 2018, with early adoption permitted. As of June 30, 2017, the Company has not elected to early adopt this guidance, but expects the adoption to have an impact on its consolidated statement of cash flows as, upon adoption, it will include the Company’s restricted cash balance in the cash and cash equivalents reconciliation of operating, investing and financing activities.

Fair Value Measurements

6 Months Ended

Jun. 30, 2017

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 June 30, 2017 and December 31, 2016 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)
June 30, 2017	(in thousands)
Money market funds included in cash and cash equivalents	$	65,740	$	65,740	$	—	$	—
Marketable securities:
U.S. Treasury notes		75,023		75,023		—		—
Equity securities		1,480		1,480		—		—
Total marketable securities	$	76,503	$	76,503	$	—	$	—
Warrants to purchase equity securities		799		—		799		—
Total	$	143,042	$	142,243	$	799	$	—
December 31, 2016
Money market funds included in cash and cash equivalents	$	36,003	$	36,003	$	—	$	—
Marketable securities:
U.S. Treasury notes		130,173		130,173		—		—
U.S. Government agency securities		7,604		—		7,604		—
Equity securities		1,360		1,360		—		—
Total marketable securities	$	139,137	$	131,533	$	7,604	$	—
Warrants to purchase equity securities		792		—		792		—
Total	$	175,932	$	167,536	$	8,396	$	—

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 assumptions, including (a) the expected stock price volatility, (b) the calculation of expected term of the awards, (c) the risk-free interest rate, and (d) expected dividends. The assumptions utilized to value the warrants to purchase equity securities as of June 30, 2017 and December 31, 2016 are as follows:


	As of June 30,		As of December 31,
	2017		2016
Risk-free interest rate	1.7	%	1.8	%
Expected dividend yield	—	%	—	%
Expected term (in years)	4.2		4.7
Expected volatility	92.9	%	97.5	%

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

- Definition

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

+ References + Details

Cash, Cash Equivalents, and Available for Sale Marketable Investments

6 Months Ended

Jun. 30, 2017

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 June 30, 2017 and December 31, 2016:


	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value
	(in thousands)
As of June 30, 2017
Money market funds included in cash and cash equivalents	$	65,740	$	—	$	—	$	65,740
Marketable securities:
U.S. Treasury notes		75,071		—		48		75,023
Equity securities		1,220		260		—		1,480
Total marketable securities	$	76,291	$	260	$	48	$	76,503
Total money market funds and marketable securities	$	142,031	$	260	$	48	$	142,243
As of December 31, 2016
Money market funds included in cash and cash equivalents	$	36,003	$	—	$	—	$	36,003
Marketable securities:
U.S. Treasury notes		130,237		2		66		130,173
U.S. Government agency bonds		7,604		—		—		7,604
Total debt securities	$	137,841	$	2	$	66	$	137,777
Equity securities		1,220		140		—		1,360
Total marketable securities	$	139,061	$	142	$	66	$	139,137
Total money market funds and marketable securities	$	175,064	$	142	$	66	$	175,140

The estimated fair value of the Company’s debt securities balance at June 30, 2017, by contractual maturity, is as follows:


Due in one year or less		$	75,023

Commitments and contingencies

6 Months Ended

Jun. 30, 2017

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 located at 75 Sidney Street under a non-cancelable operating lease that would expire 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.

In January 2016, the Company executed an amendment to extend the 75 Sidney Street lease and executed an agreement to lease the 64 Sidney Street facility until December 31, 2024. The additional facility includes laboratory and office space, and was ready for occupancy in early 2017. The table below includes estimated payments related to the amended 75 Sidney Street lease and the new lease for 64 Sidney Street through December 2024.

The Company received leasehold improvement incentives from the landlord totaling $1.3 million and $3.5 million for 75 Sidney Street and 64 Sidney Street, respectively. The Company recorded these incentives as a component of deferred rent and will amortize these incentives as a reduction of rent expense over the life of the lease. The leasehold improvements have been recorded as fixed assets.

The following table summarizes the Company’s significant contractual obligations as of payment due date by period at June 30, 2017:


	Total Minimum
	Lease Payments
	(in thousands)
2017	$	1,610
2018		3,290
2019		3,382
2020		3,762
2021		3,868
2022+		12,273
	$	28,185

Significant Agreements

Sanofi-Genzyme Collaboration Agreement

Summary of Agreement

In February 2015, the Company entered into an agreement with Sanofi-Genzyme (“Collaboration Agreement”), which included a non‑refundable upfront payment of $65.0 million. In addition, contemporaneous with entering into the Collaboration Agreement, Sanofi-Genzyme entered into a Series B Stock Purchase Agreement, under which Sanofi-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 Sanofi-Genzyme an exclusive option to license, develop and commercialize (i) ex‑U.S. rights to the following programs, which are referred to as Split Territory Programs; VY‑AADC01 (“Parkinson’s Program”), VY‑FXN01 (“Friedreich’s Ataxia Program”), a future program to be designated by Sanofi-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”). Sanofi-Genzyme’s option for the Split Territory Programs and the Spinal Muscular Atrophy Program is triggered following the completion of the first proof‑of‑principle human clinical study (“POP Study”), on a program-by-program basis.

Prior to any option exercise by Sanofi-Genzyme, the Company will collaborate with Sanofi-Genzyme in the development of products under each Split Territory Program and the Spinal Muscular Atrophy Program 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 Sanofi-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 Sanofi-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 Sanofi-Genzyme except that, at the Company’s request and upon mutual agreement, Sanofi-Genzyme will provide “in‑kind” services valued at up to $5.0 million.

Other than the Parkinson’s Program (for which a POP Study has already 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 Sanofi-Genzyme), and Sanofi-Genzyme has not terminated the Collaboration Agreement with respect to the collaboration program, then Sanofi-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 Sanofi-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, Sanofi-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 Sanofi-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 Sanofi-Genzyme shall have sole responsibility for development of such Split Territory Licensed Product in the rest of the world. The Company and Sanofi-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. Sanofi-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 Sanofi-Genzyme exercises its co‑commercialization rights for the Huntingtons’ Program product (“Huntington’s Licensed Product”), Sanofi-Genzyme will be the lead party responsible for all commercialization activities related to such product in the United States.

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

Sanofi-Genzyme is required to pay the Company for specified regulatory and commercial milestones, if achieved, up to $645.0 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 $265.0 million. The commercial milestones are payable upon achievement of specified annual net sales in each program and range from $50.0 million to $100.0 million per milestone, with an aggregate total of $380.0 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 Sanofi-Genzyme. Sanofi-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 Sanofi-Genzyme technology in the Split Territory Licensed Product. If Sanofi-Genzyme elects to co‑commercialize the Huntington’s Licensed Product in the United States, the Company and Sanofi-Genzyme will share in any profits or losses from sales of such product.

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 Sanofi-Genzyme. The Company and Sanofi-Genzyme have customary termination rights including the right to terminate for an uncured material breach of the agreement committed by the other party and Sanofi-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 Sanofi-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 are substantial option exercise payments payable by Sanofi-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 Sanofi-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 $65.0 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 Sanofi-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 Sanofi-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 2016, the Company reassessed the estimated period of performance for each of the units of accounting and determined that the estimated period would be extended for two units of accounting. Additionally, the Company and Sanofi-Genzyme agreed to deprioritize the development of the Spinal Muscular Atrophy Licensed Product and reduce the estimates related to the amount of “in-kind” services that would be provided by Sanofi-Genzyme. These adjustments were made on a prospective basis and resulted in decreases in revenue recognized by $2.4 million per quarter.

During the first quarter of 2017, 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 revenue recognized by $0.4 million per quarter. During the second quarter of 2017, 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 three units of accounting. This adjustment was made on a prospective basis and will result in a decrease in revenue recognized by $0.1 million per quarter.

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 six months ended June 30, 2017, the Company recognized $1.2 million and $2.6 million, respectively, of revenue associated with its collaboration with Sanofi-Genzyme related to research and development services performed during the periods. As of June 30, 2017, there is $39.1 million of deferred revenue related to the Collaboration Agreement, which is classified as either current or noncurrent in the accompanying consolidated balance sheet based on the period the services are expected to be delivered.

Costs incurred relating to the programs that Sanofi-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. These costs are included in research and development expenses in the Company’s statement of operations during the three and six months ended June 30, 2017. The Company estimates that the majority of research and development expense during the period relate to programs for which Sanofi-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.

During the three months ended March 31, 2017, the Company terminated the License Agreement with MRIC and all prior and future commitments and obligations under such agreement became null and void. The Company continues to hold the common stock and warrants to purchase additional shares of common stock as an available-for-sale security and non-current asset, respectively.

Other Agreements

During September 2016, the Company entered into a research and development funding arrangement with a non-profit organization that provides up to $4.0 million in funding upon the achievement of clinical and development milestones. The agreement provides that the Company repay amounts received under certain circumstances including termination of the agreement, and to pay an amount up to 2.6 times the funding received upon successful development and commercialization of any products developed. During the three months ended March 31, 2017, the Company earned a milestone payment of $1.0 million. No milestone payments were earned in the three months ended June 30, 2017. The Company has evaluated the arrangement and has concluded that it represents a research and development financing arrangement as it is probable that the Company will repay amounts received under the arrangement. As a result, the $1.0 million earned to date is recorded as a long-term liability in the accompanying balance sheet.

Litigation

The Company is not a party to any litigation and does not have contingency reserves established for any litigation liabilities as of June 30, 2017 or December 31, 2016.

Stock-based compensation

6 Months Ended

Jun. 30, 2017

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 and 2017, an additional 1,069,971 and 1,070,635 shares, respectively, were added to the Company’s 2015 Stock Option Plan for future issuance. As of June 30, 2017, there were 1,851,345 shares of common stock available for future award grants under the 2015 Stock Option Plan. During the three and six months ended June 30, 2017, the Company issued a total of 211,700 and 1,255,500 stock options, respectively, to employees and directors under the 2015 Stock Option Plan. There were no new stock options issued to non-employees under the 2015 Stock Option Plan during the three and six months ended June 30, 2017.

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

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 2016, management determined that the achievement of the performance milestone for one of the three performance‑based awards had become probable and began recognizing stock-based compensation accordingly. The Company recorded a reduction of $0.3 million in stock-based compensation expense related to this award during the three months ended June 30, 2017. The Company recorded $0.9 million in stock-based compensation expense related to this award during the six months ended June 30, 2017. No stock‑based compensation expense was recorded for the remaining two founders’ awards with performance-based vesting as of June 30, 2017 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 employees 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 deductions 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 and 2017, 267,492 and 267,658 shares of common stock, respectively, 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				Six Months Ended
	June 30,				June 30,
	2017		2016		2017		2016
	(in thousands)
Research and development	$	617	$	931	$	1,875	$	2,048
General and administrative		921		387		1,829		691
Total stock compensation expense	$	1,538	$	1,318	$	3,704	$	2,739

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, 2016	1,167,984	$	0.76
Issued	—		—
Vested	(277,955)	$	0.79
Repurchased	(26,594)	$	0.51
Unvested restricted common stock as of June 30, 2017	863,435	$	0.73

The expense related to awards granted to employees and non-employees was $0.1 million and $29.0 thousand, respectively, for the three months ended June 30, 2017, and $0.2 million and $0.7 million for the six months ended June 30, 2017, respectively. The expense related to awards granted to employees and non-employees was $0.1 million and $0.5 million, respectively, for the three months ended June 30, 2016, and $0.3 million and $1.2 million for the six months ended June 30, 2016, respectively.

As of June 30, 2017, the Company had unrecognized stock-based compensation expense related to its unvested restricted stock unit awards of $4.7 million, which is expected to be recognized over the remaining average vesting period of 0.9 years.

Stock Options

The following is a summary of stock option activity for the six months ended June 30, 2017:


		Weighted		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value
	Shares	Price		(in years)	(in thousands)
Outstanding at December 31, 2016	1,871,237	$	10.21
Granted	1,255,500	$	11.51
Exercised	(97,740)	$	8.43
Cancelled or forfeited	(184,442)	$	10.08
Outstanding at June 30, 2017	2,844,555	$	10.85	8.9	$	622
Exercisable at June 30, 2017	717,686	$	10.13	8.3	$	320
Vested and expected to vest at June 30, 2017	2,844,555	$	10.85	8.9	$	622

Using the Black‑Scholes option pricing model, the weighted average fair value of options granted to employees and directors during the three and six months ended June 30, 2017 was $6.26 and $7.55 per share, respectively. The expense related to awards granted to employees and directors was $1.3 million and $2.5 million for the three and six months ended June 30, 2017, respectively. The weighted average fair value of options granted to employees and directors during the three and six months ended June 30, 2016 was $8.27 and $7.48 per share, respectively. The expense related to awards granted to employees and directors was $0.7 million and $1.2 million for the three and six months ended June 30, 2016, 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				Six Months Ended
	June 30,				June 30,
	2017		2016		2017		2016
Risk-free interest rate	1.9	%	1.3	%	2.0	%	1.5	%
Expected dividend yield	—	%	—	%	—	%	—	%
Expected term (in years)	6.0		6.0		6.0		6.0
Expected volatility	75.9	%	73.5	%	74.0	%	73.1	%

There were no new options granted to non‑employees during the three and six months ended June 30, 2017. 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 $0.1 million and $0.3 million for the three and six months ended June 30, 2017, respectively. The weighted average grant date fair value of options granted to non-employees during the six months ended June 30, 2016 was $7.10 per share. The expense related to awards granted to non-employees was $42.0 thousand and $0.1 million the three and six months ended June 30, 2016, 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 June 30,
	2017		2016
Risk-free interest rate	2.0	%	1.5	%
Expected dividend yield	—	%	—	%
Expected term (in years)	8.5		10.0
Expected volatility	78.4	%	84.1	%

As of June 30, 2017, the Company had unrecognized stock-based compensation expense related to its unvested stock options of $14.5 million which is expected to be recognized over the remaining weighted average vesting period of 2.9 years.

For the three and six months ended June 30, 2017 and 2016, expected volatility was estimated using the historical volatility of the common stock of a peer group of publicly-traded companies that are similarly situated 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.

Summary of significant accounting policies (Policies)	6 Months Ended
Summary of significant accounting policies (Policies)	Jun. 30, 2017
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, 2016 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”).
Principles of consolidation	Principles of Consolidation The unaudited interim consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries as disclosed in Note 2, Summary of Significant Accounting Policies, within the “Notes to Consolidated Financial Statements” accompanying its Annual Report on Form 10-K for the fiscal year ended December 31, 2016. Intercompany accounts and transactions have been eliminated.
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, stock‑based compensation expense, income taxes, and 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 (Topic 606) (“ASU 2014-09”). Subsequently, the FASB also issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606), which adjusted the effective date of ASU 2014-09; ASU No. 2016-08, Revenue from Contracts with Customers (Topic 606): Principal versus Agent Considerations (Reporting Revenue Gross versus Net), which amends the principal-versus-agent implementation guidance and illustrations in ASU 2014-09; ASU No. 2016-10, Revenue from Contracts with Customers (Topic 606): Identifying Performance Obligations and Licensing, which clarifies identifying performance obligation and licensing implementation guidance and illustrations in ASU 2014-09; and ASU No. 2016-12, Revenue from Contracts with Customers (Topic 606): Narrow-Scope Improvements and Practical Expedients, which addresses implementation issues and is intended to reduce the cost and complexity of applying the new revenue standard in ASU 2014-09 (collectively, the “Revenue ASUs”). The Revenue ASUs provide an accounting standard for a single comprehensive model for use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance. The accounting standard is effective for interim and annual periods beginning after December 15, 2017, with an option to early adopt for interim and annual periods beginning after December 15, 2016. The guidance permits two methods of adoption: retrospectively to each prior reporting period presented (the full retrospective method), or retrospectively with the cumulative effect of initially applying the guidance recognized at the date of initial application (the modified retrospective method). The Company will adopt the Revenue ASUs effective January 1, 2018 and expects to utilize the modified retrospective methodology. As of June 30, 2017, revenue is generated exclusively from the Company’s collaboration arrangement with Sanofi-Genzyme. The Company is currently evaluating the potential impact that ASU 2014-09 may have on its financial position and results of operations as it relates to this single arrangement. The adoption of the Revenue ASUs is expected to have a significant impact on the Company’s notes to consolidated financial statements and its internal controls over financial reporting. In March 2016, the FASB issued ASU No. 2016-09, Compensation – Stock Compensation (Topic 718): Improvements to Employee Share-Based Payment Accounting (“ASU 2016-09”), which simplifies several aspects of the accounting for employee share-based payment transactions, including income tax consequences, classification of awards as either equity or liabilities, and classification in the statement of cash flows. ASU 2016-09 is effective for annual reporting periods beginning after December 15, 2016, including interim periods within those annual reporting periods. The new standard was effective for the Company on January 1, 2017. Adoption of ASU 2016-09 did not have a material impact on the Company’s consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (“ASC 842”), which sets out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e., lessees and lessors). The standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight-line basis over the term of the lease. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for similarly to existing guidance for operating leases today. ASC 842 supersedes the previous leases standard, ASC 840 Leases. The standard will be effective on January 1, 2019, with early adoption permitted. The Company is in the process of evaluating the impact that this new guidance will have on its consolidated financial statements. In August 2016, the FASB issued ASU 2016-15, Statement of Cash Flows: Classification of Certain Cash Receipts and Cash Payments (“Topic 230”). The new standard clarifies certain aspects of the statement of cash flows, including the classification of contingent consideration payments made after a business combination and several other clarifications not currently applicable to the Company. The new standard also clarifies that an entity should determine each separately identifiable source or use within the cash receipts and cash payments on the basis of the nature of the underlying cash flows. In situations in which cash receipts and payments have aspects of more than one class of cash flows and cannot be separated by source or use, the appropriate classification should depend on the activity that is likely to be the predominant source or use of cash flows for the item. The new standard will be effective for the Company on January 1, 2018. The adoption of this standard is not expected to have a material impact on the Company’s condensed consolidated statements of cash flows upon adoption. In November 2016, the FASB issued ASU 2016-18, Statement of Cash Flows: Restricted Cash (“ASU 2016-18”). The amendments in this update require that amounts generally described as restricted cash and restricted cash equivalents be included within cash and cash equivalents when reconciling the beginning-of-period and end-of-period total amounts shown on the statement of cash flows. ASU 2016-18 will be effective January 1, 2018, with early adoption permitted. As of June 30, 2017, the Company has not elected to early adopt this guidance, but expects the adoption to have an impact on its consolidated statement of cash flows as, upon adoption, it will include the Company’s restricted cash balance in the cash and cash equivalents reconciliation of operating, investing and financing activities

Fair Value Measurements (Tables)

6 Months Ended

Jun. 30, 2017

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 June 30, 2017 and December 31, 2016 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)
June 30, 2017	(in thousands)
Money market funds included in cash and cash equivalents	$	65,740	$	65,740	$	—	$	—
Marketable securities:
U.S. Treasury notes		75,023		75,023		—		—
Equity securities		1,480		1,480		—		—
Total marketable securities	$	76,503	$	76,503	$	—	$	—
Warrants to purchase equity securities		799		—		799		—
Total	$	143,042	$	142,243	$	799	$	—
December 31, 2016
Money market funds included in cash and cash equivalents	$	36,003	$	36,003	$	—	$	—
Marketable securities:
U.S. Treasury notes		130,173		130,173		—		—
U.S. Government agency securities		7,604		—		7,604		—
Equity securities		1,360		1,360		—		—
Total marketable securities	$	139,137	$	131,533	$	7,604	$	—
Warrants to purchase equity securities		792		—		792		—
Total	$	175,932	$	167,536	$	8,396	$	—

Assets and liabilities measured at fair value using Level 3 significant unobservable inputs

The assumptions utilized to value the warrants to purchase equity securities as of June 30, 2017 and December 31, 2016 are as follows:


	As of June 30,		As of December 31,
	2017		2016
Risk-free interest rate	1.7	%	1.8	%
Expected dividend yield	—	%	—	%
Expected term (in years)	4.2		4.7
Expected volatility	92.9	%	97.5	%

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

6 Months Ended

Jun. 30, 2017

Cash and Cash Equivalents [Abstract]

Cash, cash equivalents and investments, available for sale

Cash, cash equivalents, and marketable securities included the following at June 30, 2017 and December 31, 2016:


	Amortized		Unrealized		Unrealized		Fair
	Cost		Gains		Losses		Value
	(in thousands)
As of June 30, 2017
Money market funds included in cash and cash equivalents	$	65,740	$	—	$	—	$	65,740
Marketable securities:
U.S. Treasury notes		75,071		—		48		75,023
Equity securities		1,220		260		—		1,480
Total marketable securities	$	76,291	$	260	$	48	$	76,503
Total money market funds and marketable securities	$	142,031	$	260	$	48	$	142,243
As of December 31, 2016
Money market funds included in cash and cash equivalents	$	36,003	$	—	$	—	$	36,003
Marketable securities:
U.S. Treasury notes		130,237		2		66		130,173
U.S. Government agency bonds		7,604		—		—		7,604
Total debt securities	$	137,841	$	2	$	66	$	137,777
Equity securities		1,220		140		—		1,360
Total marketable securities	$	139,061	$	142	$	66	$	139,137
Total money market funds and marketable securities	$	175,064	$	142	$	66	$	175,140

Estimated fair value of the Company’s marketable securities balance

The estimated fair value of the Company’s debt securities balance at June 30, 2017, by contractual maturity, is as follows:


Due in one year or less		$	75,023

Commitments and contingencies (Tables)

6 Months Ended

Jun. 30, 2017

Commitments and Contingencies

Summary of contractual obligations as of payment due date

The following table summarizes the Company’s significant contractual obligations as of payment due date by period at June 30, 2017:


	Total Minimum
	Lease Payments
	(in thousands)
2017	$	1,610
2018		3,290
2019		3,382
2020		3,762
2021		3,868
2022+		12,273
	$	28,185

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)

6 Months Ended

Jun. 30, 2017

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				Six Months Ended
	June 30,				June 30,
	2017		2016		2017		2016
	(in thousands)
Research and development	$	617	$	931	$	1,875	$	2,048
General and administrative		921		387		1,829		691
Total stock compensation expense	$	1,538	$	1,318	$	3,704	$	2,739

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, 2016	1,167,984	$	0.76
Issued	—		—
Vested	(277,955)	$	0.79
Repurchased	(26,594)	$	0.51
Unvested restricted common stock as of June 30, 2017	863,435	$	0.73

Summary of status and changes in stock options

The following is a summary of stock option activity for the six months ended June 30, 2017:


		Weighted		Remaining	Aggregate
		Average		Contractual	Intrinsic
		Exercise		Life	Value
	Shares	Price		(in years)	(in thousands)
Outstanding at December 31, 2016	1,871,237	$	10.21
Granted	1,255,500	$	11.51
Exercised	(97,740)	$	8.43
Cancelled or forfeited	(184,442)	$	10.08
Outstanding at June 30, 2017	2,844,555	$	10.85	8.9	$	622
Exercisable at June 30, 2017	717,686	$	10.13	8.3	$	320
Vested and expected to vest at June 30, 2017	2,844,555	$	10.85	8.9	$	622

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				Six Months Ended
	June 30,				June 30,
	2017		2016		2017		2016
Risk-free interest rate	1.9	%	1.3	%	2.0	%	1.5	%
Expected dividend yield	—	%	—	%	—	%	—	%
Expected term (in years)	6.0		6.0		6.0		6.0
Expected volatility	75.9	%	73.5	%	74.0	%	73.1	%

Non-employees stock options

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

Assumptions


	As of June 30,
	2017		2016
Risk-free interest rate	2.0	%	1.5	%
Expected dividend yield	—	%	—	%
Expected term (in years)	8.5		10.0
Expected volatility	78.4	%	84.1	%

Fair Value Measurements - Assets measured on a recurring basis - (Details) - USD ($) $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2017	Dec. 31, 2016
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	$ 65,740	$ 36,003
Investments, Fair Value Disclosure	76,503	139,137
Warrants to purchase equity securities	799	792
Total assets measured at fair value	$ 143,042	175,932
Fair value assumptions
Risk-free interest rate	1.70%
Expected dividend yield	0.00%
Expected term (in years)	4 years 2 months 12 days
Expected volatility	92.90%
Level 1
Assets, Fair Value Disclosure [Abstract]
Cash and cash equivalents	$ 65,740	36,003
Investments, Fair Value Disclosure	76,503	131,533
Total assets measured at fair value	142,243	167,536
Level 2
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure		7,604
Warrants to purchase equity securities	799	792
Total assets measured at fair value	799	8,396
U.S. Treasury notes
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure	75,023	130,173
U.S. Treasury notes \| Level 1
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure	75,023	130,173
U. S. Government agency bonds
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure	7,604
U. S. Government agency bonds \| Level 2
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure	7,604
Equity Securities
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure	1,480	1,360
Equity Securities \| Level 1
Assets, Fair Value Disclosure [Abstract]
Investments, Fair Value Disclosure	$ 1,480	$ 1,360
Warrants
Fair value assumptions
Risk-free interest rate		1.80%
Expected dividend yield		0.00%
Expected term (in years)		4 years 8 months 12 days
Expected volatility		97.50%

Cash, Cash Equivalents, and Available for Sale Marketable Investments (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016	Jun. 30, 2016	Dec. 31, 2015
Amortized Cost Basis [Abstract]
Cash and Cash Equivalents, at Carrying Value	$ 66,300	$ 36,641	$ 67,032	$ 31,309
Total marketable securities, amortized cost	76,291	139,061
Total money market funds and marketable securities	142,031	175,064
Fair Value Disclosure [Abstract]
Cash and cash equivalents, fair value	66,300	36,641	$ 67,032	$ 31,309
Total marketable securities	76,503	139,137
Total money market funds and marketable securities	142,243	175,140
Unrealized Gain Loss [Abstract]
Unrealized gains	260	142
Total money market funds and marketable securities	260	142
Available-for-sale Securities, Accumulated Gross Unrealized Loss, before Tax	48	66
Total money market funds and marketable securities	48	66
Available-for-sale Securities, Debt Maturities, Single Maturity Date, Amortized Cost Basis, Rolling Maturity [Abstract]
Due in one year or less	75,023
Money market funds
Amortized Cost Basis [Abstract]
Cash and Cash Equivalents, at Carrying Value	65,740	36,003
Fair Value Disclosure [Abstract]
Cash and cash equivalents, fair value	65,740	36,003
Debt Securities [Member]
Amortized Cost Basis [Abstract]
Marketable debt securities, amortized cost		137,841
Fair Value Disclosure [Abstract]
Marketable debt securities, fair value		137,777
Unrealized Gain Loss [Abstract]
Available-for-sale Debt Securities, Accumulated Gross Unrealized Gain, before Tax		2
Available-for-sale Debt Securities, Accumulated Gross Unrealized Loss, before Tax		66
U.S. Treasury notes
Amortized Cost Basis [Abstract]
Marketable debt securities, amortized cost	75,071	130,237
Fair Value Disclosure [Abstract]
Marketable debt securities, fair value	75,023	130,173
Unrealized Gain Loss [Abstract]
Available-for-sale Debt Securities, Accumulated Gross Unrealized Gain, before Tax		2
Available-for-sale Debt Securities, Accumulated Gross Unrealized Loss, before Tax	48	66
U. S. Government agency bonds
Amortized Cost Basis [Abstract]
Marketable debt securities, amortized cost		7,604
Fair Value Disclosure [Abstract]
Marketable debt securities, fair value		7,604
Equity Securities
Amortized Cost Basis [Abstract]
Marketable equity securities, amortized cost	1,220	1,220
Fair Value Disclosure [Abstract]
Marketable equity securities, fair value	1,480	1,360
Unrealized Gain Loss [Abstract]
Available-for-sale Equity Securities, Accumulated Gross Unrealized Gain, before Tax	$ 260	$ 140

Commitments and contingencies - Operating Leases - (Details) $ in Thousands	Jun. 30, 2017 USD ($)
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]
2017	$ 1,610
2018	3,290
2019	3,382
2020	3,762
2021	3,868
2022 +	12,273
Total minimum lease payments	28,185
75 Sidney Street
Leasehold incentive received from landlord	1,300
64 Sidney Street
Leasehold incentive received from landlord	$ 3,500

Commitments and contingencies - Significant Agreements - (Details) - Collaborative Arrangement $ in Thousands	1 Months Ended
	Feb. 28, 2015 USD ($) shares
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Non-refundable upfront payment received	$ 65,000
Premium over fair value on temporary equity issued	5,000
Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Non-refundable upfront payment received	65,000
Temporary equity issued	10,000
Amount of reduction in milestone or royalty payments to be made by collaborative partner for each program specified	10,000
Per Milestone, maximum milestone payments to be received from collaborative partner	645,000
Regulatory approval milestone \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner	265,000
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	40,000
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	50,000
Commerical milestone \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Aggregate maximum milestone payments to be received from collaborative partner	380,000
Commerical milestone \| Minimum \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner	50,000
Commerical milestone \| Maximum \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Per Milestone, maximum milestone payments to be received from collaborative partner	100,000
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	5,000
Option exercise payment required from collaborative partner for each program specified	30,000
Split Territory Program \| Genzyme
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Option exercise payment required from collaborative partner for each program specified	20,000
Redeemable Convertible Preferred Stock Series B
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Fair value of temporary equity issued	$ 25,000
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	$ 30,000
Premium over fair value on temporary equity issued	$ 5,000

Commitments and contingencies - Accounting Analysis - (Details) - USD ($) $ in Thousands	1 Months Ended		3 Months Ended			6 Months Ended		12 Months Ended
	Sep. 30, 2016	Feb. 28, 2015	Jun. 30, 2017	Mar. 31, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016	Dec. 31, 2016
Allocable arrangement consideration allocation
Committee Obligations: Alliance Joint Steering Committee ("AJSC")		$ 147
Committee Obligations: Development Advisory Committee ("DAC")		227
License Option and related deliverables		5,743
Total allocable arrangement consideration allocations.		79,256
Income Statement Related Disclosures [Abstract]
Collaboration revenue			$ 1,177		$ 3,720	$ 2,642	$ 8,550
Revenue adjustment on account of change in estimated period of performance			100	$ 400
Huntington's Program
Allocable arrangement consideration allocation
Research and development services		15,662
Parkinson's Program
Allocable arrangement consideration allocation
Research and development services		6,648
Friedreich's Ataxia Program
Allocable arrangement consideration allocation
Research and development services		16,315
Spinal Muscular Atrophy Program
Allocable arrangement consideration allocation
Research and development services		32,050
Future Program
Allocable arrangement consideration allocation
Research and development services		2,464
Collaborative Arrangement
Allocable arrangement consideration
Collaborative Arrangement Nonredeemable Up Front Fee Received		65,000
Additional consideration, premium over fair value on temporary equity issued		5,000
Genzyme
Income Statement Related Disclosures [Abstract]
Revenue adjustment on account of change in estimated period of performance								$ 2,400
Genzyme \| Collaborative Arrangement
Allocable arrangement consideration
Collaborative Arrangement Nonredeemable Up Front Fee Received		65,000
In-kind services and other funding to be provided by collaborative partner		9,300
Total allocable arrangement consideration		79,300
Income Statement Related Disclosures [Abstract]
Collaboration revenue			$ 1,200			$ 2,600
MRIC
Income Statement Related Disclosures [Abstract]
Payments for shares	$ 2,000
Redeemable Convertible Preferred Stock Series B \| Genzyme \| Collaborative Arrangement
Allocable arrangement consideration
Additional consideration, premium over fair value on temporary equity issued		$ 5,000

Stock based compensation - 2014 Stock Option and Grant Plan - (Details)			1 Months Ended		3 Months Ended		6 Months Ended
	Jan. 01, 2017 shares	Jan. 01, 2016 shares	Oct. 31, 2015 shares	Jan. 31, 2014 $ / shares shares	Jun. 30, 2017 USD ($) shares	Jun. 30, 2016 USD ($)	Jun. 30, 2017 USD ($) shares	Jun. 30, 2016 USD ($)	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 \| $					$ 1,538,000	$ 1,318,000	$ 3,704,000	$ 2,739,000
Stock options granted (in shares)							1,255,500
Share-based Compensation Arrangement by Share-based Payment Award, Shares Issued in Period					0		0
New stock options issued					0		0
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)			2,998,823	823,529					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)	267,658		262,362		267,492		267,492
2015 Employee Stock Purchase Plan \| Minimum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Payroll deduction percentage			1.00
2015 Employee Stock Purchase Plan \| Maximum
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Payroll deduction percentage			10.00
2015 Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares available for future issuance (in shares)			1,311,812		1,851,345		1,851,345
Percentage limit of issued and outstanding shares upto which additional shares may be issued							4.00
Additional shares added to stock option plan	1,070,635	1,069,971
Founder Awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $					$ 300,000
Unvested restricted stock awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Unrecognized stock-based compensation expense \| $					4,700,000		$ 4,700,000
Employees restricted stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $					100,000	100,000	200,000	300,000
Non-employee consultants restricted stock
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $					29.0	500,000	700,000	1,200,000
Performance based milestone awards
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $							900,000
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 \| $					$ 1,300,000	700,000	$ 2,500,000	1,200,000
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)					211,700
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)							1,255,500
Non-employees stock options
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Stock-based compensation \| $					$ 100,000	$ 42,000	$ 300,000	$ 100,000
Stock options granted (in shares)					0		0

Stock based compensation - Restricted Stock - (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Shares
Balance, beginning (in shares)			1,167,984
Vested (in shares)			(277,955)
Repurchased (in shares)			(26,594)
Balance, ending (in shares)	863,435		863,435
Weighted Average Grant Date Fair Value Per Share
Balance, beginning (in dollars per share)			$ 0.76
Vested (in dollars per share)			0.79
Repurchased (in dollars per share)			0.51
Balance, ending (in dollars per share)	$ 0.73		$ 0.73
Restricted stock disclosures
Stock-based compensation	$ 1,538,000	$ 1,318,000	$ 3,704,000	$ 2,739,000
Unvested restricted stock awards
Restricted stock disclosures
Unrecognized stock-based compensation expense	4,700,000		$ 4,700,000
Remaining weighted-average remaining vesting period			10 months 24 days
Employees restricted stock
Restricted stock disclosures
Stock-based compensation	100,000	100,000	$ 200,000	300,000
Non-employee consultants restricted stock
Restricted stock disclosures
Stock-based compensation	$ 29.0	$ 500,000	$ 700,000	$ 1,200,000

Stock based compensation - Stock Options - (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Outstanding, beginning balance (in shares)			1,871,237
Granted (in shares)			1,255,500
Exercised (in shares)			(97,740)
Cancelled or forfeited (in shares)			(184,442)
Outstanding, ending balance (in shares)	2,844,555		2,844,555
Exercisable (in shares)	717,686		717,686
Vested and expected to vest (in shares)	2,844,555		2,844,555
Weighted Average Exercise Price
Outstanding (in dollars per share)			$ 10.21
Granted (in dollars per share)			11.51
Exercised (in dollars per share)			8.43
Cancelled or forfeited (in dollars per share)			10.08
Outstanding (in dollars per share)	$ 10.85		10.85
Exercisable (in dollars per share)	10.13		10.13
Vested and expected to vest (in dollars per share)	$ 10.85		$ 10.85
Remaining Contractual Life
Outstanding			8 years 10 months 24 days
Exerciseable			8 years 3 months 18 days
Vested and expected to vest			8 years 10 months 24 days
Aggregate Intrinsic Value
Oustanding	$ 622		$ 622
Exerciseable	320		320
Vested and expected to vest	622		622
Options disclosures
Stock-based compensation	$ 1,538	$ 1,318	$ 3,704	$ 2,739
Employees and directors stock options
Options disclosures
Weighted average fair value of grants (in dollars per share)	$ 6.26	$ 8.27	$ 7.55	$ 7.48
Stock-based compensation	$ 1,300	$ 700	$ 2,500	$ 1,200
Non-employees stock options
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]
Granted (in shares)	0		0
Options disclosures
Weighted average fair value of grants (in dollars per share)				$ 7.10
Stock-based compensation	$ 100	$ 42	$ 300	$ 100

Stock based compensation - Black-Scholes options pricing model - (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Options disclosures
Stock-based compensation	$ 1,538	$ 1,318	$ 3,704	$ 2,739
Stock options granted (in shares)			1,255,500
Employees and directors stock options
Fair value assumptions
Risk-free interest rate	1.90%	1.30%	2.00%	1.50%
Expected term	6 years	6 years	6 years	6 years
Expected volatility	75.90%	73.50%	74.00%	73.10%
Options disclosures
Weighted average fair value of grants (in dollars per share)	$ 6.26	$ 8.27	$ 7.55	$ 7.48
Stock-based compensation	$ 1,300	$ 700	$ 2,500	$ 1,200
Non-employees stock options
Fair value assumptions
Risk-free interest rate			2.00%	1.50%
Expected term			8 years 6 months	10 years
Expected volatility			78.40%	84.10%
Options disclosures
Weighted average fair value of grants (in dollars per share)				$ 7.10
Stock-based compensation	$ 100	$ 42	$ 300	$ 100
Stock options granted (in shares)	0		0
Unvested stock options
Options disclosures
Unrecognized stock-based compensation expense	$ 14,500		$ 14,500
Remaining weighted-average remaining vesting period			2 years 10 months 24 days

Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2017	Dec. 31, 2016
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	26,002,873	25,597,912
Common Stock, Shares, Outstanding	26,002,873	25,597,912

Nature of business	6 Months Ended
Nature of business	Jun. 30, 2017
Nature of business
Nature of business	VOYAGER THERAPEUTICS INC. NOTES TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS 1. Nature of business Voyager Therapeutics, Inc. (“the Company”) is a clinical stage gene therapy company focused on developing life changing treatments for patients suffering from severe neurological diseases. The Company focuses on neurological 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. The Company’s pipeline consists of six programs including advanced Parkinson's disease; a monogenic form of amyotrophic lateral sclerosis; Huntington's disease; Friedreich's ataxia; frontotemporal dementia / Alzheimer’s disease; and severe, chronic pain. The Company is devoting substantially all of its efforts to product research and development, activities related to its product engine, and raising capital. 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 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 and ability to transition from pilot scale manufacturing to large scale production of products. In February 2015, the Company entered into an agreement with Sanofi-Genzyme (“Collaboration Agreement”), which included a non-refundable upfront payment of $65.0 million. In addition, contemporaneous with entering into the Collaboration Agreement, Sanofi-Genzyme entered into a Series B Stock Purchase Agreement, under which Sanofi-Genzyme purchased 10,000,000 shares of Series B Preferred Stock for $30.0 million. Through June 30, 2017, 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 $141.3 million as of June 30, 2017 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	6 Months Ended
Redeemable Convertible Preferred Stock	Jun. 30, 2017
Redeemable Convertible Preferred Stock Disclosure [Abstract]
Redeemable Convertible Preferred Stock [Text Block]	7. Redeemable Convertible Preferred Stock The Company has authorized preferred stock amounting to 5,000,000 shares as of June 30, 2017 and December 31, 2016. The authorized preferred stock was classified under stockholders’ equity at June 30, 2017 and December 31, 2016.

Income taxes	6 Months Ended
Income taxes	Jun. 30, 2017
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 six months ended June 30, 2017, the Company recognized a tax expense in other comprehensive income of $0.1 million related to the unrealized gain on available-for-sale securities.

Related party transactions	6 Months Ended
Related party transactions	Jun. 30, 2017
Related party transactions
Related party transactions	11. Related‑Party Transactions During the three and six months ended June 30, 2017 and 2016, 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 $7.8 thousand and $16.9 thousand during the three and six months ended June 30, 2017, respectively. The total amount of services provided by this investor was approximately $16.0 thousand and $19.0 thousand during the three and six months ended June 30, 2016, respectively. As of June 30, 2017, the Company had a liability of $18.9 thousand related to consulting and management service fees charged by this investor. During the three and six months ended June 30, 2017, the Company recognized $1.2 million and $2.6 million, respectively, of revenue associated with the Collaboration Agreement related to research and development services provided during this period. During the three and six months ended June 30, 2016, the Company recognized $3.7 million and $8.6 million, respectively, of revenue associated with the Collaboration Agreement related to research and development services provided during the period. The Company also recognized $68.4 thousand and $0.1 million of expense during the three and six months ended June 30, 2017, respectively, related to “in‑kind” services provided by Sanofi-Genzyme associated with the Collaboration Agreement. The Company recognized $0.3 million and $0.8 million of expense during the three and six months ended June 30, 2016, respectively, related to “in-kind” services provided by Sanofi-Genzyme under the Collaboration Agreement.

Nature of business (Details) $ in Thousands	1 Months Ended	6 Months Ended
Nature of business (Details) $ in Thousands	Feb. 28, 2015 USD ($) shares	Jun. 30, 2017 USD ($) Program
Number of programs included in pipeline \| Program		6
Net proceeds		$ 278,000
Cash, cash equivalent, and available-for-sale securities		$ 141,300
Collaborative Arrangement
Collaborative Arrangement Nonredeemable Up Front Fee Received	$ 65,000
Genzyme \| Collaborative Arrangement
Collaborative Arrangement Nonredeemable Up Front Fee Received	65,000
Temporary equity issued	10,000
Net proceeds	$ 30,000
Genzyme \| Redeemable Convertible Preferred Stock Series B \| Collaborative Arrangement
Issuance of stock (in shares) \| shares	10,000,000
Temporary equity issued	$ 30,000

Accrued expenses (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Dec. 31, 2016
Accrued expenses
Research and development costs	$ 3,756	$ 2,384
Employee compensation costs	1,912	2,399
Professional services	898	698
Accrued goods and services	552	842
Other	116	76
Patent costs	80	89
Total	$ 7,314	$ 6,488

Commitments and contingencies - Other Agreements - (Details)	Jun. 30, 2017 USD ($)	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Sep. 30, 2016 USD ($)
Commitments and Contingencies
Maximum funding				$ 4,000,000
Funding multiple				2.6
Milestone payment liability	$ 0	$ 1,000,000
Loss Contingency [Abstract]
Contingency reserves for litigation liabilities	$ 0		$ 0

Redeemable Convertible Preferred Stock - Series A Preferred Stock- Series A Preferred Stock- (Details) - shares	Jun. 30, 2017	Dec. 31, 2016
Temporary Equity Disclosure [Abstract]
Preferred Stock, Shares Authorized	5,000,000	5,000,000

Income taxes (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
Income taxes (Details) - USD ($) $ in Thousands	Jun. 30, 2017	Jun. 30, 2017
Income taxes
Tax expense recognized in OCI	$ (191)	$ 53

Net loss per share (Details) - shares	6 Months Ended
Net loss per share (Details) - shares	Jun. 30, 2017	Jun. 30, 2016
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)	3,707,990	3,234,303
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)	863,435	1,450,352
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)	2,844,555	1,783,951

Related party transactions (Details) - USD ($)	3 Months Ended		6 Months Ended
Related party transactions (Details) - USD ($)	Jun. 30, 2017	Jun. 30, 2016	Jun. 30, 2017	Jun. 30, 2016
Investor
Related Party Transaction [Line Items]
Accounts payable to related party	$ 18,900		$ 18,900
Investor \| Consulting and management services
Related Party Transaction [Line Items]
Total amount of services received	7,800	$ 16.0	16,900	$ 19.0
Genzyme \| Collaboration arrangement
Related Party Transaction [Line Items]
Revenue recognized	1,200,000	3,700,000	2,600,000	8,600,000
Expense recognized	$ 68,400	$ 300,000	$ 100,000	$ 800,000