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Document and Entity Information - shares	3 Months Ended
Document and Entity Information - shares	Mar. 31, 2017	Apr. 21, 2017
Document and Entity Information [Abstract]
Entity Registrant Name	VERTEX PHARMACEUTICALS INC / MA
Entity Central Index Key	0000875320
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Document Type	10-Q
Document Period End Date	Mar. 31, 2017
Document Fiscal Year Focus	2017
Document Fiscal Period Focus	Q1
Amendment Flag	false
Entity Common Stock, Shares Outstanding (in shares)		249,068,782

Condensed Consolidated Statements of Operations (unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Revenues:
Product revenues, net	$ 480,622	$ 394,410
Royalty revenues	1,551	3,596
Collaborative revenues	232,545	74
Total revenues	714,718	398,080
Costs and expenses:
Cost of product revenues	46,242	49,789
Royalty expenses	746	860
Research and development expenses	273,563	255,860
Sales, general and administrative expenses	113,326	105,214
Restructuring expenses, net	9,999	687
Total costs and expenses	443,876	412,410
Income (loss) from operations	270,842	(14,330)
Interest expense, net	(16,765)	(20,698)
Other (expenses) income, net	(544)	4,411
Income (loss) before provision for income taxes	253,533	(30,617)
Provision for income taxes	3,985	5,485
Net income (loss)	249,548	(36,102)
Income attributable to noncontrolling interest	(1,792)	(5,529)
Net income (loss) attributable to Vertex	$ 247,756	$ (41,631)
Net income (loss):
Basic (in dollars per share)	$ 1.01	$ (0.17)
Diluted (in dollars per share)	$ 0.99	$ (0.17)
Shares used in per share calculations:
Basic (in shares)	246,024	243,831
Diluted (in shares)	248,700	243,831

Condensed Consolidated Statements of Comprehensive Income (Loss) (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Net income (loss)	$ 249,548	$ (36,102)
Changes in other comprehensive income (loss):
Unrealized holding gains on marketable securities, net of tax	3,534	229
Unrealized (losses) on foreign currency forward contracts, net of tax	(6,681)	(5,212)
Foreign currency translation adjustment	(2,001)	(1,740)
Total changes in other comprehensive income (loss)	(5,148)	(6,723)
Comprehensive income (loss)	244,400	(42,825)
Comprehensive income attributable to noncontrolling interest	(1,792)	(5,529)
Comprehensive income (loss) attributable to Vertex	$ 242,608	$ (48,354)

Condensed Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Current assets:
Cash and cash equivalents	$ 1,003,679	$ 1,183,945
Marketable securities, available for sale	405,103	250,612
Restricted cash and cash equivalents (VIE)	44,564	47,762
Accounts receivable, net	207,955	201,083
Inventories	82,020	77,604
Prepaid expenses and other current assets	128,493	70,534
Total current assets	1,871,814	1,831,540
Property and equipment, net	708,395	698,362
Intangible assets	284,340	284,340
Goodwill	50,384	50,384
Cost method investments	20,276	20,276
Other assets	11,494	11,885
Total assets	2,946,703	2,896,787
Current liabilities:
Accounts payable	63,145	61,451
Accrued expenses	277,962	315,249
Deferred revenues, current portion	6,057	6,005
Accrued restructuring expenses, current portion	7,634	6,047
Capital lease obligations, current portion	19,270	19,426
Customer deposits	104,774	73,416
Credit facility	0	300,000
Other liabilities, current portion	10,954	10,943
Total current liabilities	489,796	792,537
Deferred revenues, excluding current portion	5,742	6,632
Accrued restructuring expenses, excluding current portion	613	1,907
Capital lease obligations, excluding current portion	30,355	34,976
Deferred tax liability	135,402	134,063
Construction financing lease obligation, excluding current portion	498,775	486,359
Advance from collaborator	74,760	73,423
Other liabilities, excluding current portion	28,467	28,699
Total liabilities	1,263,910	1,558,596
Commitments and contingencies
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding	0	0
Common stock, $0.01 par value; 500,000,000 shares authorized; 248,890,834 and 248,300,517 shares issued and outstanding at March 31, 2017 and December 31, 2016, respectively	2,459	2,450
Additional paid-in capital	6,616,975	6,506,795
Accumulated other comprehensive income	16,025	21,173
Accumulated deficit	(5,135,451)	(5,373,836)
Total Vertex shareholders’ equity	1,500,008	1,156,582
Noncontrolling interest	182,785	181,609
Total shareholders’ equity	1,682,793	1,338,191
Total liabilities and shareholders’ equity	$ 2,946,703	$ 2,896,787

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Mar. 31, 2017	Dec. 31, 2016
Statement of Financial Position [Abstract]
Preferred stock, par value (usd per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	1,000,000	1,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (usd per share)	$ 0.01	$ 0.01
Common stock, shares authorized	500,000,000	500,000,000
Common stock, shares issued	248,890,834	248,300,517
Common stock, shares outstanding	248,890,834	248,300,517

Condensed Consolidated Statements of Shareholders' Equity and Noncontrolling Interest (unaudited) - USD ($) shares in Thousands, $ in Thousands	Total	Total Vertex Shareholders’ Equity	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive (Loss) Income	Accumulated Deficit	Noncontrolling Interest
Balance (shares) at Dec. 31, 2015			246,307
Beginning Balance at Dec. 31, 2015	$ 1,093,628	$ 939,967	$ 2,427	$ 6,197,500	$ 1,824	$ (5,261,784)	$ 153,661
Increase (Decrease) in Stockholders' Equity
Other comprehensive loss, net of tax	(6,723)	(6,723)			(6,723)
Net income (loss)	(36,102)	(41,631)				(41,631)	5,529
Issuance of common stock under benefit plans (shares)			980
Issuance of common stock under benefit plans	9,149	9,149	$ 2	9,147			0
Stock-based compensation expense	56,246	56,317		56,317			(71)
Balance (shares) at Mar. 31, 2016			247,287
Ending Balance at Mar. 31, 2016	1,116,198	957,079	$ 2,429	6,262,964	(4,899)	(5,303,415)	159,119
Increase (Decrease) in Stockholders' Equity
Cumulative effect adjustment for adoption of new accounting guidance \| Accounting Standards Update 2016-09, Forfeiture Rate Component				9,371		(9,371)
Balance (shares) at Dec. 31, 2016			248,301
Beginning Balance at Dec. 31, 2016	1,338,191	1,156,582	$ 2,450	6,506,795	21,173	(5,373,836)	181,609
Increase (Decrease) in Stockholders' Equity
Other comprehensive loss, net of tax	(5,148)	(5,148)			(5,148)
Net income (loss)	249,548	247,756				247,756	1,792
Issuance of common stock under benefit plans (shares)			590
Issuance of common stock under benefit plans	31,028	31,028	$ 9	31,019			0
Stock-based compensation expense	69,790	69,790		69,790			0
Other	(616)						(616)
Balance (shares) at Mar. 31, 2017			248,891
Ending Balance at Mar. 31, 2017	$ 1,682,793	$ 1,500,008	$ 2,459	$ 6,616,975	$ 16,025	$ (5,135,451)	$ 182,785

Condensed Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Cash flows from operating activities:
Net income (loss)	$ 249,548	$ (36,102)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Stock-based compensation expense	68,982	55,472
Depreciation and amortization expense	14,850	16,415
Deferred income taxes	1,212	2,060
Impairment of property and equipment	1,946	0
Other non-cash items, net	(5,152)	(3,835)
Changes in operating assets and liabilities:
Accounts receivable, net	(5,118)	(2,512)
Inventories	(3,650)	(4,771)
Prepaid expenses and other assets	(47,178)	(7,325)
Accounts payable	717	(343)
Accrued expenses and other liabilities	(9,931)	(29,922)
Accrued restructuring expense	305	(1,459)
Deferred revenues	(839)	(2,815)
Net cash provided by (used in) operating activities	265,692	(15,137)
Cash flows from investing activities:
Purchases of marketable securities	(248,273)	(224,624)
Maturities of marketable securities	98,393	131,173
Expenditures for property and equipment	(11,159)	(11,974)
Decrease in restricted cash and cash equivalents (VIE)	3,198	2,637
(Increase) decrease in other assets	60	80
Net cash used in investing activities	(157,781)	(102,708)
Cash flows from financing activities:
Issuances of common stock under benefit plans	11,249	8,846
Payments on revolving credit facility	(300,000)	0
Advance from collaborator	5,000	0
Payments on capital lease obligations	(4,703)	(4,041)
Payments on construction financing lease obligation	(117)	(103)
Repayments of advanced funding	(994)	0
Net cash (used in) provided by financing activities	(289,565)	4,702
Effect of changes in exchange rates on cash	1,388	2,620
Net decrease in cash and cash equivalents	(180,266)	(110,523)
Cash and cash equivalents—beginning of period	1,183,945	714,768
Cash and cash equivalents—end of period	1,003,679	604,245
Supplemental disclosure of cash flow information:
Cash paid for interest	17,527	20,603
Cash paid for income taxes	1,164	581
Capitalization of costs related to construction financing lease obligation	12,549	0
Issuances of common stock from employee benefit plans receivable	$ 19,847	$ 593

Basis of Presentation and Accounting Policies	3 Months Ended
Basis of Presentation and Accounting Policies	Mar. 31, 2017
Accounting Policies [Abstract]
Basis of Presentation and Accounting Policies	Basis of Presentation and Accounting Policies Basis of Presentation The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated (“Vertex” or the “Company”) in accordance with accounting principles generally accepted in the United States of America (“GAAP”). The condensed consolidated financial statements reflect the operations of (i) the Company, (ii) its wholly-owned subsidiaries and (iii) consolidated variable interest entities (VIEs). All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended March 31, 2017 and 2016. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, 2016, which are contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016 that was filed with the Securities and Exchange Commission (the “SEC”) on February 23, 2017 (the “2016 Annual Report on Form 10-K”). Use of Estimates and Summary of Significant Accounting Policies The preparation of condensed consolidated financial statements in accordance with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with the calculation of revenues, inventories, research and development expenses, stock-based compensation expense, restructuring expense, the fair value of intangible assets, goodwill, contingent consideration, noncontrolling interest, the consolidation of VIEs, leases, the fair value of cash flow hedges and the provision for or benefit from income taxes. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known. The Company’s significant accounting policies are described in Note A, “Nature of Business and Accounting Policies,” in the 2016 Annual Report on Form 10-K. Recent Accounting Pronouncements In 2014, the Financial Accounting Standards Board (“FASB”) issued new guidance applicable to revenue recognition that will be effective January 1, 2018. Early adoption was permitted for the year-ending December 31, 2017. The new guidance applies a more principles based approach to recognizing revenue. Under the new guidance, revenue is recognized when a customer obtains control of promised goods or services and is recognized in an amount that reflects the consideration that an entity expects to receive in exchange for those goods or services. In addition, the standard requires disclosure of the nature, amount, timing, and uncertainty of revenue and cash flows arising from contracts with customers. The new guidance must be adopted using either a modified retrospective approach or a full retrospective approach for all periods presented. Under the modified retrospective method, the cumulative effect of applying the standard would be recognized at the date of initial application within retained earnings. Under the full retrospective approach, the standard would be applied to each prior reporting period presented. Upon adoption, the Company will use the modified retrospective method. The Company is in the process of evaluating the new guidance and determining whether the expected effect is material to its condensed consolidated financial statements. The Company has formed a project team to review its portfolio of existing customer contracts and current accounting policies to identify and assess the potential differences that would result from applying the requirements of the new standard. The Company is also in the process of implementing appropriate changes to its controls to support revenue recognition and disclosure under the new standard. The new guidance could impact the Company’s accounting for product shipments to certain countries through early access programs, including the French early access programs, whereby the associated product has received regulatory approval but the reimbursement rate has not been finalized. In 2015, the FASB issued amended guidance applicable to inventory. The amended guidance simplifies the subsequent measurement of inventory by requiring inventory to be measured at the lower of cost and net realizable value. The amended guidance became effective for the Company during the first quarter of 2017. Adoption of the amended guidance did not have a significant effect on its condensed consolidated financial statements. In 2016, the FASB issued amended guidance applicable to share-based compensation to employees that simplifies the accounting for employee share-based payment transactions, including the accounting for income taxes, forfeitures, and statutory tax withholding requirements, as well as classification in the statement of cash flows. The amended guidance became effective for the Company during the first quarter of 2017. The amended guidance eliminates the requirement that excess tax benefits be realized as a reduction in current taxes payable before the associated tax benefit can be recognized as an increase in additional paid-in capital. This created approximately $410.8 million of deferred tax asset (“DTA”) relating to federal and state net operating losses (“NOLs”) that are fully reserved by an equal increase in valuation allowance. The Company recorded DTAs of approximately $404.7 million relating to Federal NOLs and approximately $6.1 million relating to State NOLs, both of which are offset by a full valuation allowance. Upon adoption, the Company also elected to change its accounting policy to account for forfeitures as they occur. The change was applied on a modified retrospective basis with a cumulative effect adjustment to accumulated deficit of $9.4 million, which increased the accumulated deficit as of January 1, 2017. This change also resulted in an increase to DTA by $3.4 million, which is offset by a full valuation allowance. As a result, there was no cumulative-effect adjustment to accumulated deficit. The provisions related to the recognition of excess tax benefits in the income statement and classification in the statement of cash flows were adopted prospectively, and as such, the prior periods were not retrospectively adjusted. In January 2016, the FASB issued amended guidance related to the recording of financial assets and financial liabilities. Under the amended guidance, equity investments (except those accounted for under the equity method of accounting or those that result in consolidation of the investee) are to be measured at fair value with changes in fair value recognized in net income. However, an entity has the option to either measure equity investments without readily determinable fair values at fair value or at cost adjusted for changes in observable prices minus impairment. Changes in measurement under either alternative will be recognized in net income. The amended guidance is effective for the year-ending December 31, 2018. Early adoption is permitted. The Company expects the implementation of this standard to have an impact on its consolidated financial statements and related disclosures, as the Company held publicly traded equity investments at March 31, 2017 as well as equity investments accounted for under the cost method. A cumulative-effect adjustment to the balance sheet will be recorded as of the beginning of the fiscal year of adoption. The implementation of this amended guidance is expected to increase volatility in net income as the volatility currently recorded in other comprehensive income related to changes in the fair market value of available-for-sale equity investments will be reflected in net income after adoption. In January 2017, the FASB issued amended guidance related to business combinations. The amended guidance clarifies the definition of a business with the objective of adding guidance to assist entities with evaluating whether transactions should be accounted for as acquisitions (or disposals) of assets or businesses. The new accounting guidance is effective for annual periods beginning after December 15, 2017, including interim periods within those periods. Early adoption is permitted. The Company early adopted this new guidance as of January 1, 2017 and will apply this new guidance to future acquisitions. In January 2017, the FASB issued amended guidance related the subsequent measurement of goodwill. The amended guidance eliminates a step from the goodwill impairment test. Under the amended guidance, an entity should perform its annual, or interim, goodwill impairment test by comparing the fair value of a reporting unit with its carrying amount. An entity should recognize an impairment charge for the amount by which the carrying amount exceeds the reporting unit’s fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. The amended guidance is effective for the year-ending December 31, 2020. Early adoption is permitted. The Company does not expect a significant effect on its condensed consolidated financial statements upon adoption of this new guidance. For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2016 Annual Report on Form 10-K.

Product Revenues, Net

3 Months Ended

Mar. 31, 2017

Product Revenues [Abstract]

Product Revenues, Net

The Company sells its products principally to a limited number of specialty pharmacy providers and selected regional wholesalers in North America as well as government-owned and supported customers in international markets (collectively, its “Customers”). The Company’s Customers in North America subsequently resell the products to patients and health care providers. The Company recognizes net revenues from product sales upon delivery to the Customer as long as (i) there is persuasive evidence that an arrangement exists between the Company and the Customer, (ii) collectibility is reasonably assured and (iii) the price is fixed or determinable.

In order to conclude that the price is fixed or determinable, the Company must be able to (i) calculate its gross product revenues from sales to Customers and (ii) reasonably estimate its net product revenues upon delivery to its Customers’ locations. The Company calculates gross product revenues based on the price that the Company charges its Customers. The Company estimates its net product revenues by deducting from its gross product revenues (a) trade allowances, such as invoice discounts for prompt payment and Customer fees, (b) estimated government and private payor rebates, chargebacks and discounts, (c) estimated reserves for expected product returns and (d) estimated costs of co-pay assistance programs for patients, as well as other incentives for certain indirect customers.

The Company makes significant estimates and judgments that materially affect the Company’s recognition of net product revenues. In certain instances, the Company may be unable to reasonably conclude that the price is fixed or determinable at the time of delivery, in which case it defers the recognition of revenues. Once the Company is able to determine that the price is fixed or determinable, it recognizes the revenues associated with the units in which revenue recognition was deferred. ORKAMBI net product revenues do not include any revenues from product sales in France. The Company began distributing ORKAMBI through early access programs in the fourth quarter of 2015. The Company’s condensed consolidated balance sheet includes $104.8 million collected as of March 31, 2017 in France related to ORKAMBI that is classified as customer deposits. The Company expects that revenues from these early access programs will be recognized in the period that a formal reimbursement agreement in France is reached based on the terms of such agreement.

The following table summarizes activity in each of the product revenue allowance and reserve categories for the three months ended March 31, 2017:



	Trade Allowances			Rebates, Chargebacks and Discounts			Product Returns			Other Incentives			Total
	(in thousands)
Balance at December 31, 2016	$	2,568		$	81,927		$	3,492		$	1,214		$	89,201
Provision related to current period sales	5,638			28,567			370			6,093			40,668
Adjustments related to prior period sales	(169		)	(2,344		)	(48		)	(56		)	(2,617		)
Credits/payments made	(5,654		)	(27,916		)	(170		)	(4,428		)	(38,168		)
Balance at March 31, 2017	$	2,383		$	80,234		$	3,644		$	2,823		$	89,084

Collaborative Arrangements and Pending Acquisition

3 Months Ended

Mar. 31, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaborative Arrangements and Pending Acquisition

Cystic Fibrosis Foundation Therapeutics Incorporated

The Company has a research, development and commercialization agreement with Cystic Fibrosis Foundation Therapeutics Incorporated (“CFFT”) that was originally entered into in May 2004, and was most recently amended on October 13, 2016 (the “2016 Amendment”). Pursuant to the agreement, as amended, the Company has agreed to pay royalties ranging from low single digits to mid-single digits on potential sales of certain compounds first synthesized and/or tested between March 1, 2014 and August 31, 2016 and tiered royalties ranging from single digits to sub-teens on any approved drugs first synthesized and/or tested during a research term on or before February 28, 2014, including KALYDECO (ivacaftor), ORKAMBI (lumacaftor in combination with ivacaftor), lumacaftor and tezacaftor. For combination products, such as ORKAMBI, sales will be allocated equally to each of the active pharmaceutical ingredients in the combination product.

In the first quarter of 2016, CFFT earned a commercial milestone payment of $13.9 million from the Company upon achievement of certain sales levels of lumacaftor. There are no additional commercial milestone payments payable by the Company to CFFT pursuant to the agreement. Pursuant to the 2016 Amendment, the CFFT provided the Company an upfront program award of $75.0 million and agreed to provide development funding to the Company of up to $6.0 million annually. The program award plus any future development funding represent a form of financing pursuant to Accounting Standards Codification (ASC) 730, Research and Development, and thus the amounts are recorded as a liability on the condensed consolidated balance sheet, primarily reflected in Advance from collaborator. The liability is reduced over the estimated royalty term of the agreement. Reductions in the liability are reflected as an offset to cost of product revenues and as interest expense.

The Company began marketing KALYDECO in the United States and certain countries in the European Union in 2012 and began marketing ORKAMBI in the United States in 2015. The Company received approval for ORKAMBI In the European Union in 2015 and in Canada and Australia in 2016. The Company has royalty obligations to CFFT for ivacaftor, lumacaftor and tezacaftor until the expiration of patents covering those compounds. The Company has patents in the United States and European Union covering the composition-of-matter of ivacaftor that expire in 2027 and 2025, respectively, subject to potential patent extensions. The Company has patents in the United States and European Union covering the composition-of-matter of lumacaftor that expire in 2030 and 2026, respectively, subject to potential extension. The Company has patents in the United States and European Union covering the composition-of-matter of tezacaftor that expire in 2027 and 2028, respectively, subject to potential extension.

CRISPR Therapeutics AG

In October 2015, the Company entered into a strategic collaboration, option and license agreement (the “CRISPR Agreement”) with CRISPR Therapeutics AG and its affiliates (“CRISPR”) to collaborate on the discovery and development of potential new treatments aimed at the underlying genetic causes of human diseases using CRISPR-Cas9 gene editing technology. The Company has the exclusive right to license up to six CRISPR-Cas9-based targets. In connection with the CRISPR Agreement, the Company made an upfront payment to CRISPR of $75.0 million and a $30.0 million investment in CRISPR pursuant to a convertible loan agreement that converted into preferred stock in January 2016. The Company expensed $75.0 million to research and development, and the $30.0 million investment was recorded at cost and is classified as a long-term asset on the Company’s condensed consolidated balance sheets. In the second quarter of 2016, the Company made an additional preferred stock investment in CRISPR of approximately $3.1 million. In connection with CRISPR’s initial public offering in October 2016, the Company purchased $10 million of common shares at public offering price and the Company’s preferred stock investments in CRISPR converted into common shares. As of March 31, 2017, the Company recorded the CRISPR common shares it holds at fair value and included the fair value of the common shares in its marketable securities and the unrecognized gain related to these common shares in accumulated other comprehensive income (loss) on the condensed consolidated balance sheet.

The Company will fund all of the discovery activities conducted pursuant to the CRISPR Agreement. For potential hemoglobinapathy treatments, including treatments for sickle cell disease, the Company and CRISPR will share equally all research and development costs and worldwide revenues. For other targets that the Company elects to license, the Company would lead all development and global commercialization activities. For each of up to six targets that the Company elects to license, other than hemoglobinapathy targets, CRISPR has the potential to receive up to $420.0 million in development, regulatory and commercial milestones and royalties on net product sales.

The Company may terminate the CRISPR Agreement upon 90 days’ notice to CRISPR prior to any product receiving marketing approval or upon 270 days’ notice after a product has received marketing approval. The CRISPR Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the CRISPR Agreement will continue in effect until the expiration of the Company’s payment obligations under the CRISPR Agreement.

Merck KGaA

On January 10, 2017, the Company entered into a strategic collaboration and license agreement (the “Merck KGaA Agreement”) with Merck KGaA, Darmstadt, Germany (“Merck KGaA”). Pursuant to the Merck KGaA Agreement, the Company granted Merck KGaA an exclusive worldwide license to research, develop and commercialize four oncology research and development programs. Under the Merck KGaA Agreement, the Company granted Merck KGaA exclusive, worldwide rights to two clinical-stage programs targeting DNA damage repair: its ataxia telangiectasia and Rad3-related protein inhibitor program, including VX-970 and VX-803, and its DNA-dependent protein kinase inhibitor program, including VX-984. In addition, the Company granted Merck KGaA exclusive, worldwide rights to two pre-clinical programs.

The Merck KGaA Agreement provided for an up-front payment from Merck KGaA to the Company of $230.0 million. During the first quarter of 2017, the Company received $193.6 million of the up-front payment and the remaining $36.4 million was remitted to the German tax authorities. Pursuant to a tax treaty between the United States and Germany, the Company filed a refund application for the tax withholding and expects to receive the refund in approximately six months. The income tax receivable is included in Prepaid expenses and other current assets at March 31, 2017. In addition to the up-front payment, the Company will receive tiered royalties on potential sales of licensed products, calculated as a percentage of net sales, that range from (i) mid-single digits to mid-twenties for clinical-stage programs and (ii) mid-single digits to high single digits for the pre-clinical research programs. Merck KGaA has assumed full responsibility for development and commercialization costs for all programs.

The Company evaluated the deliverables, primarily consisting of a license to the four programs and the obligation to complete certain fully-reimbursable research and development and transition activities as directed by Merck KGaA, pursuant to the Merck KGaA Agreement, under the multiple element arrangement accounting guidance. The Company concluded that the license has stand-alone value from the research and development and transition activities based on the resources and know-how possessed by Merck KGaA, and thus concluded that there are two units of accounting in the arrangement. The Company determined the relative selling price of the units of accounting based on the Company’s best estimate of selling price. The Company utilized key assumptions to determine the best estimate of selling price for the license, which included future potential net sales of licensed products, development timelines, reimbursement rates for personnel costs, discount rates, and estimated third-party development costs. The Company utilized a discounted cash flow model to determine its best estimate of selling price for the license and determined the best estimate of selling price for the research and development and transition activities based on what it would sell the services for separately. Based on this analysis, the Company recognized approximately $231.7 million in collaborative revenues related to the up-front payment upon delivery of the license and to the research and development and transition activities provided during the quarter. The Company recorded the reimbursement for the research and development and transition activities as revenue in the Company’s consolidated statements of operations primarily due to the fact that the Company is the primary obligor in the arrangement. The Company expects to provide research and development and transition activities through the end of the fiscal year and will recognize the revenues and associated expenses as the services are provided.

Merck KGaA may terminate the Merck KGaA Agreement or any individual program by providing 90 days’ notice, or, in the case of termination of a program with a product that has received marketing approval, 180 days’ notice. The Merck KGaA Agreement also may be terminated by either party for a material breach by the other party, subject to notice and cure provisions. Unless earlier terminated, the Merck KGaA Agreement will continue in effect until the date on which the royalty term and all payment obligations with respect to all products in all countries have expired.

Variable Interest Entities

The Company has entered into several agreements pursuant to which it has licensed rights to certain drug candidates from third-party collaborators, which has resulted in the consolidation of the third parties’ financial statements into the Company’s condensed consolidated financial statements as VIEs. In order to account for the fair value of the contingent payments, which consist of milestone, royalty and option payments, related to these collaborations under GAAP, the Company uses present-value models based on assumptions regarding the probability of achieving the relevant milestones, estimates regarding the timing of achieving the milestones, estimates of future product sales and the appropriate discount rates. The Company bases its estimate of the probability of achieving the relevant milestones on industry data for similar assets and its own experience. The discount rates used in the valuation model represent a measure of credit risk and market risk associated with settling the liabilities. Significant judgment is used in determining the appropriateness of these assumptions at each reporting period. Changes in these assumptions could have a material effect on the fair value of the contingent payments. The following collaborations are reflected in the Company’s financial statements as consolidated VIEs:

Parion Sciences, Inc.

In June 2015, the Company entered into a strategic collaboration and license agreement (the “Parion Agreement”) with Parion Sciences, Inc. (“Parion”). Pursuant to the agreement, the Company is collaborating with Parion to develop investigational epithelial sodium channel (“ENaC”) inhibitors, including VX-371 (formerly P-1037) and VX-551 (formerly P-1055), for the potential treatment of CF, and all other pulmonary diseases. The Company is leading development activities for VX-371 and VX-551 and is responsible for all costs, subject to certain exceptions, related to development and commercialization of the compounds.

Pursuant to the Parion Agreement, the Company has worldwide development and commercial rights to Parion’s lead investigational ENaC inhibitors, VX-371 and VX-551, for the potential treatment of CF and all other pulmonary diseases and has the option to select additional compounds discovered in Parion’s research program. Parion received an $80.0 million up-front payment and has the potential to receive up to an additional (i) $490.0 million in development and regulatory milestone payments for development of ENaC inhibitors in CF, including $360.0 million related to global filing and approval milestones, (ii) $370.0 million in development and regulatory milestones for VX-371 and VX-551 in non-CF pulmonary indications and (iii) $230.0 million in development and regulatory milestones should the Company elect to develop an additional ENaC inhibitor from Parion’s research program. The Company has agreed to pay Parion tiered royalties that range from the low double digits to mid-teens as a percentage of potential sales of licensed products.

The Company may terminate the Parion Agreement upon 90 days’ notice to Parion prior to any licensed product receiving marketing approval or upon 180 days’ notice after a licensed product has received marketing approval. If the Company experiences a change of control prior to the initiation of the first Phase 3 clinical trial for a licensed product, Parion may terminate the Parion Agreement upon 30 days’ notice, subject to the Company’s right to receive specified royalties on any subsequent commercialization of licensed products. The Parion Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the Parion Agreement will continue in effect until the expiration of the Company’s royalty obligations, which expire on a country-by-country basis on the later of (i) the date the last-to-expire patent covering a licensed product expires or (ii) ten years after the first commercial sale in the country.

The Company determined that it has a variable interest in Parion via the Parion Agreement, and that the variable interest represents a variable interest in Parion as a whole since the fair value of the ENaC inhibitors represents more than half of the total fair value of Parion’s assets. The Company also concluded that it is the primary beneficiary as it has the power to direct the activities that most significantly affect the economic performance of Parion and it has the obligation to absorb losses and right to receive benefits that potentially could be significant to Parion. Accordingly, the Company consolidated Parion's financial statements beginning on June 4, 2015. However, the Company's interests in Parion are limited to those accorded to the Company in the Parion Agreement.

While there was a transfer of $80.0 million to Parion, the cash remained within the Company’s condensed consolidated financial statements since Parion is part of the consolidated entity. The cash received, net of any cash spend by Parion, is classified as restricted cash and cash equivalents (VIE) within the condensed consolidated balance sheet as it is attributed to the noncontrolling interest holders of Parion. When determining the valuation of goodwill, the fair value of consideration for the license is zero since there was no consideration transferred outside the condensed consolidated financial statements. The Company recorded $255.3 million of intangible assets on the Company’s condensed consolidated balance sheet for Parion’s in-process research and development assets. These in-process research and development assets relate to Parion’s pulmonary ENaC platform, including the intellectual property related to VX-371 and VX-551, that are licensed by Parion to the Company. The Company also recorded the fair value of the net assets attributable to noncontrolling interest of $164.3 million, deferred tax liability of $91.0 million resulting from a basis difference in the intangible assets and certain other net liabilities held by Parion of $10.5 million. The difference between the fair values of the consideration and noncontrolling interest and the fair value of Parion’s net assets was recorded as goodwill.

BioAxone Biosciences, Inc.

In October 2014, the Company entered into a license and collaboration agreement (the “BioAxone Agreement”) with BioAxone Biosciences, Inc. (“BioAxone”), which resulted in the consolidation of BioAxone as a VIE beginning on October 1, 2014. The Company paid BioAxone initial payments of $10.0 million in the fourth quarter of 2014.

BioAxone has the potential to receive up to $90.0 million in milestones and fees, including development, regulatory and milestone payments and a license continuation fee. In addition, BioAxone would receive royalties and commercial milestones on future net product sales of VX-210, if any. The Company recorded an in-process research and development intangible asset of $29.0 million for VX-210 and a corresponding deferred tax liability of $11.3 million attributable to BioAxone. The Company holds an option to purchase BioAxone at a predetermined price. The option expires on the earliest of (a) the day the FDA accepts the Biologics License Application submission for VX-210, (b) the day the Company elects to continue the license instead of exercising the option to purchase BioAxone and (c) March 15, 2018, subject to the Company’s option to extend this date by one year.

Aggregate VIE Financial Information

An aggregate summary of net income attributable to noncontrolling interest related to the Company’s VIEs for the three months ended March 31, 2017 and 2016 is as follows:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Loss attributable to noncontrolling interest before provision for income taxes	$	1,547		$	839
Provision for income taxes	391			3,062
Increase in fair value of contingent payments	(3,730		)	(9,430		)
Net income attributable to noncontrolling interest	$	(1,792	)	$	(5,529	)

The increase in the noncontrolling interest holders’ claim to net assets with respect to the fair value of the contingent payments in the three months ended March 31, 2017 was primarily due to changes in market interest rates and the time value of money. During the three months ended March 31, 2017 and 2016, the increase in the fair value of the contingent payments related to the Company’s VIEs was as follows:



	Three Months Ended March 31,
	2017		2016
	(in thousands)
Parion	$	2,830	$	9,000
BioAxone	900		430

As of March 31, 2017, the fair value of the contingent payments related to the Parion Agreement and the BioAxone Agreement was $241.6 million and $18.9 million, respectively. As of December 31, 2016, the fair value of the contingent milestone and royalty payments related to the Parion collaboration and the BioAxone collaboration was $238.8 million and $18.0 million, respectively.

The following table summarizes items related to the Company’s VIEs included in the Company’s condensed consolidated balance sheets as of the dates set forth in the table:



	March 31, 2017		December 31, 2016
	(in thousands)
Restricted cash and cash equivalents (VIE)	$	44,564	$	47,762
Prepaid expenses and other current assets	5,957		6,812
Intangible assets	284,340		284,340
Goodwill	19,391		19,391
Other assets	687		399
Accounts payable	1,080		415
Taxes payable	1,159		1,330
Other current liabilities	1,998		2,137
Deferred tax liability, net	133,058		131,446
Other liabilities	300		300
Noncontrolling interest	182,785		181,609

The Company has recorded the VIEs’ cash and cash equivalents as restricted cash and cash equivalents (VIE) because (i) the Company does not have any interest in or control over the VIEs’ cash and cash equivalents and (ii) the Company’s agreements with each VIE do not provide for the VIEs’ cash and cash equivalents to be used for the development of the assets that the Company licensed from the applicable VIE. Assets recorded as a result of consolidating the Company’s VIEs’ financial condition into the Company’s balance sheet do not represent additional assets that could be used to satisfy claims against the Company’s general assets.

Other Collaborations

The Company has entered into various agreements pursuant to which it collaborates with third parties, including inlicensing and outlicensing arrangements. Although the Company does not consider any of these arrangements to be material, the most notable of these arrangements are described below.

Moderna Therapeutics, Inc.

In July 2016, the Company entered into a strategic collaboration and licensing agreement (the “Moderna Agreement”) with Moderna Therapeutics, Inc. (“Moderna”) pursuant to which the parties are seeking to identify and develop messenger Ribonucleic Acid (“mRNA”) Therapeutics for the treatment of CF. In connection with the Moderna Agreement in the third quarter of 2016, the Company made an upfront payment to Moderna of $20.0 million and a $20.0 million cost-method investment in Moderna pursuant to a convertible promissory note that converted into preferred stock in August 2016. Moderna has the potential to receive future development and regulatory milestones of up to $275.0 million, including $220.0 million in approval and reimbursement milestones, as well as tiered royalty payments on future sales.

Under the terms of the Moderna Agreement, Moderna will lead discovery efforts and the Company will lead all preclinical, development and commercialization activities associated with the advancement of mRNA Therapeutics that result from this collaboration and will fund all expenses related to the collaboration.

The Company may terminate the Moderna Agreement by providing advanced notice to Moderna, with the required length of notice dependent on whether any product developed under the Moderna Agreement has received marketing approval. The Moderna Agreement also may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, the Moderna Agreement will continue in effect until the expiration of the Company’s payment obligations under the Moderna Agreement.

Janssen Pharmaceuticals, Inc.

In June 2014, the Company entered into an agreement (the “Janssen Influenza Agreement”) with Janssen Pharmaceuticals, Inc. (“Janssen Inc.”), which was amended in October 2014 to clarify certain roles and responsibilities of the parties.

Pursuant to the Janssen Influenza Agreement, Janssen Inc. has an exclusive worldwide license to develop and commercialize certain drug candidates for the treatment of influenza, including VX-787. The Company received non-refundable payments of $35.0 million from Janssen Inc. in 2014, which were recorded as collaborative revenue. The Company has the potential to receive development, regulatory and commercial milestone payments as well as royalties on future product sales, if any. Janssen Inc. may terminate the Janssen Influenza Agreement, subject to certain exceptions, upon six months’ notice.

Janssen Inc. is responsible for costs related to the development and commercialization of the compounds. During the three months ended March 31, 2017 and 2016, the Company recorded reimbursement for these development activities of $0.9 million and $3.5 million, respectively. The reimbursements are recorded as a reduction to development expense in the Company’s condensed consolidated statements of operations primarily due to the fact that Janssen Inc. directs the activities and selects the suppliers associated with these activities.

Pending Acquisition

Concert Pharmaceuticals

On March 6, 2017, the Company entered into an asset purchase agreement (the “Concert Agreement”) with Concert Pharmaceuticals (“Concert”). Pursuant to the Concert Agreement, the Company will acquire certain assets including CTP-656 from Concert. CTP-656 is an investigational CFTR potentiator that has the potential to be used as part of future once-daily combination regimens of CFTR modulators that treat the underlying cause of CF. As part of the Concert Agreement, Vertex will pay Concert $160 million in cash for all worldwide development and commercialization rights to CTP-656. If CTP-656 is approved as part of a combination regimen to treat CF, Concert could receive up to an additional $90 million in milestones based on regulatory approval in the U.S. and reimbursement in the UK, Germany or France. The Concert Agreement is subject to approval by Concert's shareholders and clearance under the Hart-Scott-Rodino Antitrust Improvements Act. The waiting period had not expired as of March 31, 2017; therefore, there was no accounting impact relating to this agreement during the three months ended March 31, 2017. The Company is in the process of evaluating the expected accounting effect of the pending transaction on its consolidated financial statements.

Earnings Per Share

3 Months Ended

Mar. 31, 2017

Earnings Per Share [Abstract]

Earnings Per Share

Basic net loss per share attributable to Vertex common shareholders is based upon the weighted-average number of common shares outstanding during the period, excluding restricted stock and restricted stock units that have been issued but are not yet vested. Diluted net loss per share attributable to Vertex common shareholders is based upon the weighted-average number of common shares outstanding during the period plus additional weighted-average common equivalent shares outstanding during the period when the effect is dilutive.

The following table sets forth the computation of basic and diluted net income (loss) per share for the periods ended:



	Three Months Ended March 31,
	2017			2016
	(in thousands, except per share amounts)
Basic net income (loss) attributable to Vertex per common share calculation:
Net income (loss) attributable to Vertex common shareholders	$	247,756		$	(41,631	)
Less: Undistributed earnings allocated to participating securities	(406		)	—
Net income (loss) attributable to Vertex common shareholders—basic	$	247,350		$	(41,631	)

Basic weighted-average common shares outstanding	246,024			243,831
Basic net income (loss) attributable to Vertex per common share	$	1.01		$	(0.17	)

Diluted net income (loss) attributable to Vertex per common share calculation:
Net income (loss) attributable to Vertex common shareholders	$	247,756		$	(41,631	)
Less: Undistributed earnings allocated to participating securities	(401		)	—
Net income (loss) attributable to Vertex common shareholders—diluted	$	247,355		$	(41,631	)

Weighted-average shares used to compute basic net income (loss) per common share	246,024			243,831
Effect of potentially dilutive securities:
Stock options	2,037			—
Restricted stock and restricted stock units	627			—
Other	12			—
Weighted-average shares used to compute diluted net income (loss) per common share	248,700			243,831
Diluted net income (loss) attributable to Vertex per common share	$	0.99		$	(0.17	)

The Company did not include the securities in the following table in the computation of the net income (loss) per share attributable to Vertex common shareholders calculations because the effect would have been anti-dilutive during each period:



	Three Months Ended March 31,
	2017	2016
	(in thousands)
Stock options	8,303	12,619
Unvested restricted stock and restricted stock units	807	3,565

Fair Value Measurements

3 Months Ended

Mar. 31, 2017

Fair Value Disclosures [Abstract]

Fair Value Measurements

The fair value of the Company’s financial assets and liabilities reflects the Company’s estimate of amounts that it would have received in connection with the sale of the assets or paid in connection with the transfer of the liabilities in an orderly transaction between market participants at the measurement date. In connection with measuring the fair value of its assets and liabilities, the Company seeks to maximize the use of observable inputs (market data obtained from sources independent from the Company) and to minimize the use of unobservable inputs (the Company’s assumptions about how market participants would price assets and liabilities). The following fair value hierarchy is used to classify assets and liabilities based on the observable inputs and unobservable inputs used in order to value the assets and liabilities:



Level 1:	Quoted prices in active markets for identical assets or liabilities. An active market for an asset or liability is a market in which transactions for the asset or liability occur with sufficient frequency and volume to provide pricing information on an ongoing basis.
Level 2:	Observable inputs other than Level 1 inputs. Examples of Level 2 inputs include quoted prices in active markets for similar assets or liabilities and quoted prices for identical assets or liabilities in markets that are not active.
Level 3:	Unobservable inputs based on the Company’s assessment of the assumptions that market participants would use in pricing the asset or liability.

The Company’s investment strategy is focused on capital preservation. The Company invests in instruments that meet the credit quality standards outlined in the Company’s investment policy. This policy also limits the amount of credit exposure to any one issue or type of instrument. As of March 31, 2017, the Company’s investments were primarily in money market funds, corporate equity securities, corporate debt securities and commercial paper.

As of March 31, 2017, all of the Company’s financial assets that were subject to fair value measurements were valued using observable inputs. The Company’s financial assets valued based on Level 1 inputs consisted of money market funds, corporate debt securities, commercial paper and corporate equity securities. The Company’s financial assets valued based on Level 2 inputs consisted of corporate debt securities and commercial paper, which consisted of investments in highly-rated investment-grade corporations.

The following table sets forth the Company’s financial assets (excluding VIE cash and cash equivalents) and liabilities subject to fair value measurements:



	Fair Value Measurements as of March 31, 2017
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset position):
Cash equivalents:
Money market funds	$	313,629		$	313,629	$	—		$	—
Corporate debt securities	11,027			11,027		—			—
Commercial paper	6,834			6,834		—			—
Marketable securities:
Corporate equity securities	69,372			69,372		—			—
Corporate debt securities	203,181			—		203,181			—
Commercial paper	132,550			—		132,550			—
Prepaid and other current assets:
Foreign currency forward contracts	8,318			—		8,318			—
Other assets:
Foreign currency forward contracts	249			—		249			—
Total financial assets	$	745,160		$	400,862	$	344,298		$	—
Financial instruments carried at fair value (liability position):
Other liabilities, current portion:
Foreign currency forward contracts	$	(613	)	$	—	$	(613	)	$	—
Other liabilities, excluding current portion:
Foreign currency forward contracts	(86		)	—		(86		)	—
Total financial liabilities	$	(699	)	$	—	$	(699	)	$	—



	Fair Value Measurements as of December 31, 2016
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset position):
Cash equivalents:
Money market funds	$	280,560		$	280,560	$	—		$	—
Marketable securities:
Government-sponsored enterprise securities	15,508			15,508		—			—
Corporate equity securities	64,560			64,560		—			—
Commercial paper	59,404			—		59,404			—
Corporate debt securities	111,140			—		111,140			—
Prepaid and other current assets:
Foreign currency forward contracts	14,407			—		14,407			—
Other assets:
Foreign currency forward contracts	1,186			$	—	1,186			$	—
Total financial assets	$	546,765		$	360,628	$	186,137		$	—
Financial instruments carried at fair value (liability position):
Other liabilities, current portion:
Foreign currency forward contracts	$	(144	)	$	—	$	(144	)	$	—
Total financial liabilities	$	(144	)	$	—	$	(144	)	$	—

The Company’s VIEs invested in cash equivalents consisting of money market funds of $44.1 million as of March 31, 2017, which are valued based on Level 1 inputs. These cash equivalents are not included in the table above. The Company’s noncontrolling interest related to VIEs includes the fair value of the contingent payments, which consist of milestone, royalty and option payments, which are valued based on Level 3 inputs. Please refer to Note C, “Collaborative Arrangements,” for further information.

- Definition

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

+ References + Details

Marketable Securities

3 Months Ended

Mar. 31, 2017

Cash and Cash Equivalents [Abstract]

Marketable Securities

A summary of the Company’s cash, cash equivalents and marketable securities is shown below:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
As of March 31, 2017
Cash and cash equivalents:
Cash and money market funds	$	985,818	$	—	$	—		$	985,818
Commercial paper	6,834		—		—			6,834
Corporate debt securities	11,027		—		—			11,027
Total cash and cash equivalents	$	1,003,679	$	—	$	—		$	1,003,679
Marketable securities:
Corporate equity securities	43,213		26,159		—			69,372
Commercial paper (matures within 1 year)	132,640		1		(91		)	132,550
Corporate debt securities (matures within 1 year)	180,465		3		(143		)	180,325
Corporate debt securities (matures after 1 year)	$	22,882	$	—	$	(26	)	$	22,856
Total marketable securities	$	379,200	$	26,163	$	(260	)	$	405,103
Total cash, cash equivalents and marketable securities	$	1,382,879	$	26,163	$	(260	)	$	1,408,782

As of December 31, 2016
Cash and cash equivalents:
Cash and money market funds	$	1,183,945	$	—	$	—		$	1,183,945
Total cash and cash equivalents	$	1,183,945	$	—	$	—		$	1,183,945
Marketable securities:
Government-sponsored enterprise securities (matures within 1 year)	$	15,506	$	2	$	—		$	15,508
Corporate equity securities	43,213		21,347		—			64,560
Commercial paper (matures within 1 year)	59,331		73		—			59,404
Corporate debt securities (matures within 1 year)	111,225		—		(85		)	111,140
Total marketable securities	$	229,275	$	21,422	$	(85	)	$	250,612
Total cash, cash equivalents and marketable securities	$	1,413,220	$	21,422	$	(85	)	$	1,434,557

The Company has a limited number of marketable securities in insignificant loss positions as of March 31, 2017, which the Company does not intend to sell and has concluded it will not be required to sell before recovery of the amortized costs for the investment at maturity. There were no charges recorded for other-than-temporary declines in fair value of marketable securities nor gross realized gains or losses recognized in the three months ended March 31, 2017 and 2016.

Accumulated Other Comprehensive Income (Loss)

3 Months Ended

Mar. 31, 2017

Equity [Abstract]

Accumulated Other Comprehensive Income (Loss)

Accumulated Other Comprehensive Income (loss)

A summary of the Company’s changes in accumulated other comprehensive income (loss) by component is shown below:



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities, net of tax		Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax			Total
	(in thousands)
Balance at December 31, 2016	$	(7,862	)	$	17,521	$	11,514		$	21,173
Other comprehensive (loss) income before reclassifications	(2,001		)	3,534		(2,802		)	(1,269		)
Amounts reclassified from accumulated other comprehensive loss	—			—		(3,879		)	(3,879		)
Net current period other comprehensive (loss) income	$	(2,001	)	$	3,534	$	(6,681	)	$	(5,148	)
Balance at March 31, 2017	$	(9,863	)	$	21,055	$	4,833		$	16,025



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities		Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax			Total
	(in thousands)
Balance at December 31, 2015	$	(2,080	)	$	126	$	3,778		$	1,824
Other comprehensive (loss) income before reclassifications	(1,740		)	229		(3,827		)	(5,338		)
Amounts reclassified from accumulated other comprehensive loss	—			—		(1,385		)	(1,385		)
Net current period other comprehensive (loss) income	$	(1,740	)	$	229	$	(5,212	)	$	(6,723	)
Balance at March 31, 2016	$	(3,820	)	$	355	$	(1,434	)	$	(4,899	)

- Definition

The entire disclosure for comprehensive income, which includes, but is not limited to, 1) the amount of income tax expense or benefit allocated to each component of other comprehensive income, including reclassification adjustments, 2) the reclassification adjustments for each classification of other comprehensive income and 3) the ending accumulated balances for each component of comprehensive income.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e689-108580

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 1A
-URI http://asc.fasb.org/extlink&oid=66004124&loc=SL7669619-108580

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 12
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e640-108580

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 17
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e716-108580

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 16
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e709-108580

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.3-04)
-URI http://asc.fasb.org/extlink&oid=27012166&loc=d3e187085-122770

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 11
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e637-108580

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 14
-URI http://asc.fasb.org/extlink&oid=66004124&loc=d3e681-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Reclassification Adjustments
-URI http://asc.fasb.org/extlink&oid=6522872

+ Details

Hedging

3 Months Ended

Mar. 31, 2017

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Hedging

The Company maintains a hedging program intended to mitigate the effect of changes in foreign exchange rates for a portion of the Company’s forecasted product revenues denominated in certain foreign currencies. The program includes foreign currency forward contracts that are designated as cash flow hedges under GAAP having contractual durations from one to eighteen months.

The Company formally documents the relationship between foreign currency forward contracts (hedging instruments) and forecasted product revenues (hedged items), as well as the Company’s risk management objective and strategy for undertaking various hedging activities, which includes matching all foreign currency forward contracts that are designated as cash flow hedges to forecasted transactions. The Company also formally assesses, both at the hedge’s inception and on an ongoing basis, whether the foreign currency forward contracts are highly effective in offsetting changes in cash flows of hedged items on a prospective and retrospective basis. If the Company determines that a (i) foreign currency forward contract is not highly effective as a cash flow hedge, (ii) foreign currency forward contract has ceased to be a highly effective hedge or (iii) forecasted transaction is no longer probable of occurring, the Company would discontinue hedge accounting treatment prospectively. The Company measures effectiveness based on the change in fair value of the forward contracts and the fair value of the hypothetical foreign currency forward contracts with terms that match the critical terms of the risk being hedged. As of March 31, 2017, all hedges were determined to be highly effective and the Company had not recorded any ineffectiveness related to the hedging program.

The following table summarizes the notional amount of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges:



	As of March 31, 2017		As of December 31, 2016
Foreign Currency	(in thousands)
Euro	$	187,375	$	164,368
British pound sterling	66,133		65,237
Australian dollar	28,645		23,776
Total foreign currency forward contracts	$	282,153	$	253,381

The following table summarizes the fair value of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges under GAAP included on the Company’s condensed consolidated balance sheets:



As of March 31, 2017
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	8,318	Other liabilities, current portion	$	(613	)
Other assets	249		Other liabilities, excluding current portion	(86		)
Total assets	$	8,567	Total liabilities	$	(699	)



As of December 31, 2016
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	14,407	Other liabilities, current portion	$	(144	)
Other assets	1,186		Other liabilities, excluding current portion	—
Total assets	$	15,593	Total liabilities	$	(144	)

The following table summarizes the potential effect of offsetting derivatives by type of financial instrument on the Company’s condensed consolidated balance sheets:



	As of March 31, 2017
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	8,567		$	—	$	8,567		$	(699	)	$	7,868
Total liabilities	$	(699	)	$	—	$	(699	)	$	699		$	—



	As of December 31, 2016
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	15,593		$	—	$	15,593		$	(144	)	$	15,449
Total liabilities	$	(144	)	$	—	$	(144	)	$	144		$	—

- Definition

The entire disclosure for derivative instruments and hedging activities including, but not limited to, risk management strategies, non-hedging derivative instruments, assets, liabilities, revenue and expenses, and methodologies and assumptions used in determining the amounts.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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+ Details

Inventories

3 Months Ended

Mar. 31, 2017

Inventory Disclosure [Abstract]

Inventories

Inventories consisted of the following:



	As of March 31, 2017		As of December 31, 2016
	(in thousands)
Raw materials	$	9,172	$	6,348
Work-in-process	60,921		56,672
Finished goods	11,927		14,584
Total	$	82,020	$	77,604

Based on its evaluation of, among other factors, information regarding tezacaftor's safety and efficacy, the Company has begun capitalizing insignificant inventory costs for tezacaftor manufactured in preparation for its potential product launch. In periods prior, the Company expensed costs associated with tezacaftor’s raw materials and work-in-process as a development expense. The Company is planning to submit a New Drug Application to the United States Food and Drug Administration and a Marketing Authorization Application to the European Medicines Agency for tezacaftor in combination with ivacaftor during the third quarter of 2017. The Company plans to continue to monitor the status of the tezacaftor regulatory process and the other factors used to determine whether or not to capitalize the tezacaftor inventory and, if there are significant negative developments regarding tezacaftor, the Company could be required to impair previously capitalized costs.

Intangible Assets and Goodwill	3 Months Ended
Intangible Assets and Goodwill	Mar. 31, 2017
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible Assets and Goodwill	Intangible Assets and Goodwill Intangible Assets As of March 31, 2017 and December 31, 2016, in-process research and development intangible assets of $284.3 million were recorded on the Company’s condensed consolidated balance sheet. In 2015, the Company recorded an in-process research development intangible asset of $255.3 million related to Parion’s pulmonary ENaC platform, including the intellectual property related to VX-371 and VX-551, that are licensed by Parion to the Company. In 2014, the Company recorded an in-process research development intangible asset of $29.0 million related to VX-210 that is licensed by BioAxone to the Company. Goodwill As of March 31, 2017 and December 31, 2016, goodwill of $50.4 million was recorded on the Company’s condensed consolidated balance sheet.

- Definition

The entire disclosure for the aggregate amount of goodwill and a description of intangible assets, which may include (a) for amortizable intangible assets (also referred to as finite-lived intangible assets), the carrying amount, the amount of any significant residual value, and the weighted-average amortization period, (b) for intangible assets not subject to amortization (also referred to as indefinite-lived intangible assets), the carrying amount, and (c) the amount of research and development assets acquired and written off in the period, including the line item in the income statement in which the amounts written off are aggregated, if not readily apparent from the income statement. Also discloses (a) for amortizable intangibles assets in total and by major class, the gross carrying amount and accumulated amortization, the total amortization expense for the period, and the estimated aggregate amortization expense for each of the five succeeding fiscal years, (b) for intangible assets not subject to amortization the carrying amount in total and by major class, and (c) for goodwill, in total and for each reportable segment, the changes in the carrying amount of goodwill during the period (including the aggregate amount of goodwill acquired, the aggregate amount of impairment losses recognized, and the amount of goodwill included in the gain (loss) on disposal of a reporting unit). If any part of goodwill has not been allocated to a reportable segment, discloses the unallocated amount and the reasons for not allocating. For each impairment loss recognized related to an intangible asset (excluding goodwill), discloses: (a) a description of the impaired intangible asset and the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method for determining fair value, (c) the caption in the income statement or the statement of activities in which the impairment loss is aggregated, and (d) the segment in which the impaired intangible asset is reported. For each goodwill impairment loss recognized, discloses: (a) a description of the facts and circumstances leading to the impairment, (b) the amount of the impairment loss and the method of determining the fair value of the associated reporting unit, and (c) if a recognized impairment loss is an estimate not finalized and the reasons why the estimate is not final. May also disclose the nature and amount of any significant adjustments made to a previous estimate of an impairment loss.

+ References + Details

Long-term Obligations	3 Months Ended
Long-term Obligations	Mar. 31, 2017
Long-term Debt and Capital Lease Obligations [Abstract]
Long-term Obligations	Long-term Obligations Fan Pier Leases In 2011, the Company entered into two lease agreements, pursuant to which the Company leases approximately 1.1 million square feet of office and laboratory space in two buildings (the “Buildings”) at Fan Pier in Boston, Massachusetts (the “Fan Pier Leases”). The Company commenced lease payments in December 2013, and will make lease payments pursuant to the Fan Pier Leases through December 2028. The Company has an option to extend the term of the Fan Pier Leases for an additional ten years. Because the Company was involved in the construction project, the Company was deemed for accounting purposes to be the owner of the Buildings during the construction period and recorded project construction costs incurred by the landlord. Upon completion of the Buildings, the Company evaluated the Fan Pier Leases and determined that the Fan Pier Leases did not meet the criteria for “sale-leaseback” treatment. Accordingly, the Company began depreciating the asset and incurring interest expense related to the financing obligation in 2013. The Company bifurcates its lease payments pursuant to the Fan Pier Leases into (i) a portion that is allocated to the Buildings and (ii) a portion that is allocated to the land on which the Buildings were constructed. The portion of the lease obligations allocated to the land is treated as an operating lease that commenced in 2011. Property and equipment, net, included $485.7 million and $489.0 million as of March 31, 2017 and December 31, 2016, respectively, related to construction costs for the Buildings. The carrying value of the Company’s lease agreement liability for the Buildings was $472.5 million and $472.6 million as of March 31, 2017 and December 31, 2016, respectively. San Diego Lease On December 2, 2015, the Company entered into a lease agreement for 3215 Merryfield Row, San Diego, California with ARE-SD Region No. 23, LLC. Pursuant to this agreement, the Company agreed to lease approximately 170,000 square feet of office and laboratory space in a building to be built in San Diego, California. The lease will commence upon completion of the building, scheduled for the first half of 2018, and will extend for 16 years from the commencement date. Pursuant to the lease agreement, during the initial 16-year term, the Company will pay an average of approximately $10.2 million per year in aggregate rent, exclusive of operating expenses. The Company has the option to extend the lease term for up to two additional five-year terms. Because the Company is involved in the construction project, the Company is deemed for accounting purposes to be the owner of the San Diego building during the construction period and recorded project construction costs incurred by the landlord. The Company bifurcates its lease payments pursuant to the San Diego Lease into (i) a portion that is allocated to the San Diego building and (ii) a portion that is allocated to the land on which the San Diego building was constructed. Although the Company will not begin making lease payments pursuant to the San Diego Lease until the commencement date, the portion of the lease obligation allocated to the land is treated for accounting purposes as an operating lease that commenced in the fourth quarter of 2016. Upon completion of the San Diego building, the Company will evaluate the San Diego Lease and determine if the San Diego Lease meets the criteria for “sale-leaseback” treatment. If the San Diego Lease meets the “sale-leaseback” criteria, the Company will remove the asset and the related liability from its consolidated balance sheet and treat the San Diego Lease as either an operating or a capital lease based on the Company’s assessment of the accounting guidance. The Company expects that upon completion of construction of the San Diego building the San Diego Lease will not meet the “sale-leaseback” criteria. If the San Diego Lease does not meet “sale-leaseback” criteria, the Company will treat the San Diego Lease as a financing obligation and will depreciate the asset over its estimated useful life. The Company has capitalized $28.9 million and $15.0 million as of March 31, 2017 and December 31, 2016, respectively. Revolving Credit Facility In October 2016, the Company entered into a Credit Agreement (the “Credit Agreement”) with Bank of America, N.A., as administrative agent and the lenders referred to therein. The Credit Agreement provides for a $500.0 million revolving facility, $300.0 million of which was drawn at closing (the “Loans”). The Credit Agreement also provides that, subject to satisfaction of certain conditions, the Company may request that the borrowing capacity under the Credit Agreement be increased by an additional $300.0 million. The Credit Agreement matures on October 13, 2021. The proceeds of the borrowing under the Credit Agreement were used primarily to repay the Company’s then outstanding indebtedness under the Macquarie Loan. The Loans will bear interest, at the Company’s option, at either a base rate or a Eurodollar rate, in each case plus an applicable margin. Under the Credit Agreement, the applicable margins on base rate loans range from 0.75% to 1.50% and the applicable margins on Eurodollar loans range from 1.75% to 2.50%, in each case based on the Company’s consolidated leverage ratio (the ratio of the Company’s total consolidated debt to the Company’s trailing twelve-month EBITDA). The Loans are guaranteed by certain of the Company’s domestic subsidiaries and secured by substantially all of the Company’s assets and the assets of the Company’s domestic subsidiaries (excluding intellectual property, owned and leased real property and certain other excluded property) and by the equity interests of the Company’s subsidiaries, subject to certain exceptions. Under the terms of the Credit Agreement, the Company must maintain, subject to certain limited exceptions, a consolidated leverage ratio of 3.00 to 1.00 and consolidated EBITDA of at least $200.0 million, in each case to be measured on a quarterly basis. The Credit Agreement contains customary representations and warranties and usual and customary affirmative and negative covenants. The Credit Agreement also contains customary events of default. In the case of a continuing event of default, the administrative agent would be entitled to exercise various remedies, including the acceleration of amounts due under outstanding loans. In February 2017, the Company repaid all $300.0 million outstanding under the Credit Agreement. Term Loan In July 2014, the Company entered into a credit agreement with the lenders party thereto, and Macquarie US Trading LLC (“Macquarie”), as administrative agent. The credit agreement provided for a $300.0 million senior secured term loan (“Macquarie Loan”). On October 13, 2016, the Company terminated and repaid all outstanding obligations under the Macquarie Loan. The Macquarie Loan initially bore interest at a rate of 7.2% per annum, which was reduced to 6.2% per annum based on the FDA’s approval of ORKAMBI. The Term Loan bore interest at a rate of LIBOR plus 5.0% per annum during the third year of the term. The Company incurred $5.3 million in fees paid to Macquarie that were recorded as a discount on the Macquarie Loan and were recorded as interest expense using the effective interest method over the term of the loan in the Company’s condensed consolidated statements of operations.

Stock-based Compensation Expense

3 Months Ended

Mar. 31, 2017

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

Stock-based Compensation Expense

During the three months ended March 31, 2017 and 2016, the Company recognized the following stock-based compensation expense:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Stock-based compensation expense by type of award:
Stock options	$	26,981		$	26,260
Restricted stock and restricted stock units	40,745			27,533
ESPP share issuances	2,064			2,524
Less stock-based compensation expense capitalized to inventories	(808		)	(845		)
Total stock-based compensation included in costs and expenses	$	68,982		$	55,472

Stock-based compensation expense by line item:
Research and development expenses	$	44,837		$	34,448
Sales, general and administrative expenses	24,145			21,024
Total stock-based compensation included in costs and expenses	$	68,982		$	55,472

The following table sets forth the Company’s unrecognized stock-based compensation expense by type of award and the weighted-average period over which that expense is expected to be recognized:



	As of March 31, 2017
	Unrecognized Expense		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Stock options	$	200,906	2.65
Restricted stock and restricted stock units	$	291,088	2.57
ESPP share issuances	$	2,016	0.43

The following table summarizes information about stock options outstanding and exercisable at March 31, 2017:



	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$18.93–$20.00	134	0.85	$	18.93	134	$	18.93
$20.01–$40.00	1,576	2.95	$	33.77	1,576	$	33.77
$40.01–$60.00	1,678	5.34	$	48.36	1,678	$	48.36
$60.01–$80.00	1,279	6.88	$	75.86	924	$	75.61
$80.01–$100.00	5,932	8.65	$	89.51	1,757	$	89.81
$100.01–$120.00	1,572	7.79	$	109.33	799	$	109.30
$120.01–$134.69	1,427	8.22	$	130.53	668	$	130.27
Total	13,598	7.19	$	82.60	7,536	$	71.52

- Definition

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

+ References + Details

Other Arrangements	3 Months Ended
Other Arrangements	Mar. 31, 2017
Other Income and Expenses [Abstract]
Other Arrangements	Other Arrangements Sale of HIV Protease Inhibitor Royalty Stream In 2008, the Company sold to a third party its rights to receive royalty payments from GlaxoSmithKline plc, net of royalty amounts to be earned by and due to a third party, for a one-time cash payment of $160.0 million. These royalty payments relate to net sales of HIV protease inhibitors, which had been developed pursuant to a collaboration agreement between the Company and GlaxoSmithKline plc. As of March 31, 2017, the Company had $11.8 million in deferred revenues related to the one-time cash payment, which it is recognizing over the life of the collaboration agreement with GlaxoSmithKline plc based on the units-of-revenue method. In addition, the Company continues to recognize royalty revenues equal to the amount of the third-party subroyalty and an offsetting royalty expense for the third-party subroyalty payment.

Income Taxes	3 Months Ended
Income Taxes	Mar. 31, 2017
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company is subject to United States federal, state, and foreign income taxes. For the three months ended March 31, 2017, the Company recorded a provision for income taxes of $4.0 million. The provision for income taxes recorded in the three months ended March 31, 2017 included a provision of $0.4 million related to the Company’s VIEs’ income tax provision. The Company has no liability for taxes payable by the Company’s VIEs and the income tax provision and related liability have been allocated to noncontrolling interest (VIE). For the three months ended March 31, 2016, the Company recorded a provision for income taxes of $5.5 million. The provision for income taxes recorded in the three months ended March 31, 2016 included a benefit of $3.1 million related to the Company’s VIEs’ income tax provision. As of March 31, 2017 and December 31, 2016, the Company did not have unrecognized tax benefits. The Company recognizes interest and penalties related to income taxes as a component of income tax expense. As of March 31, 2017, no interest and penalties have been accrued. The Company does not expect that its unrecognized tax benefits will materially increase within the next twelve months. The Company did not recognize any material interest or penalties related to uncertain tax positions as of March 31, 2017 and December 31, 2016. The Company continues to maintain a valuation allowance against certain deferred tax assets where it is more likely than not that the deferred tax asset will not be realized because of its extended history of annual losses. As described in Footnote A, the Company adopted Accounting Standards Update (ASU) 2016-09, during the three month period ended March 31, 2017. The ASU eliminates additional paid in capital (“APIC”) pools and requires excess tax benefits and tax deficiencies to be recorded in the consolidated statement of operations when the awards vest or are settled. Amendments related to accounting for excess tax benefits have been adopted prospectively resulting in a tax benefit of $0.4 million for the three months ended March 31, 2017. In connection with the adoption of this new standard, the Company recorded a cumulative-effect adjustment of $410.8 million as of January 1, 2017 to accumulated deficit and deferred tax assets, with an equal offsetting adjustment to the valuation allowance. In addition, the Company has recorded $9.4 million related to the impact from adoption of the provisions related to forfeiture rates to accumulated deficit. This change also increased the deferred tax assets by $3.4 million that is offset by an increase to the valuation allowance in the same amount. The Company files United States federal income tax returns and income tax returns in various state, local and foreign jurisdictions. The Company is no longer subject to any tax assessment from an income tax examination in the United States or any other major taxing jurisdiction for years before 2011, except where the Company has net operating losses or tax credit carryforwards that originate before 2011. The Company currently is under examination by Canada Revenue Agency for the years ending December 31, 2011 through December 31, 2013. No adjustments have been reported. At March 31, 2017, foreign earnings, which were not significant, have been retained indefinitely by foreign subsidiary companies for reinvestment; therefore, no provision has been made for income taxes that would be payable upon the distribution of such earnings, and it would not be practicable to determine the amount of the related unrecognized deferred income tax liability. Upon repatriation of those earnings, in the form of dividends or otherwise, the Company would be subject to United States federal income taxes (subject to an adjustment for foreign tax credits) and withholding taxes payable to the various foreign countries.

Restructuring Liabilities

3 Months Ended

Mar. 31, 2017

Restructuring and Related Activities [Abstract]

Restructuring Liabilities

Research and Development Restructuring

In February 2017, the Company decided to consolidate its research activities into its Boston, Milton Park and San Diego locations and to close the research site in Canada. As a result, the Company is in the process of closing one of its research sites. In connection with this decision, approximately 70 positions were affected. The Company estimates that it will incur aggregate restructuring charges of approximately $11.3 million to $13.0 million, including $6.8 million for employee salary, severance and benefit costs, $2.0 million in assets associated with the restructuring that have become impaired and $2.5 million to $4.2 million for other costs primarily related to the Company’s exit from the facility.

The restructuring charge and other activities recorded during the the three months ended March 31, 2017 and the related liability balance as of March 31, 2017 were as follows:



	Three Months Ended March 31,
	2017
	(in thousands)
Liability, beginning of the period	$	—
Restructuring expense	9,218
Cash payments	(3,258		)
Asset impairments and other non-cash expense	(2,233		)
Liability, end of the period	$	3,727

2003 Kendall Restructuring

In 2003, the Company adopted a plan to restructure its operations to coincide with its increasing internal emphasis on advancing drug candidates through clinical development to commercialization. The restructuring liability relates to specialized laboratory and office space that is leased to the Company pursuant to a 15-year lease that terminates in 2018. The Company has not used more than 50% of this space since it adopted the plan to restructure its operations in 2003. This unused laboratory and office space currently is subleased to third parties.

The activities related to the restructuring liability for the three months ended March 31, 2017 and 2016 were as follows:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Liability, beginning of the period	$	4,328		$	7,944
Restructuring expense	485			203
Cash payments	(5,264		)	(3,931		)
Cash received from subleases	2,976			3,008
Liability, end of the period	$	2,525		$	7,224

Fan Pier Move Restructuring

In connection with the relocation of its Massachusetts operations to Fan Pier in Boston, Massachusetts, which commenced in 2013, the Company is incurring restructuring charges related to its remaining lease obligations at its facilities in Cambridge, Massachusetts. The majority of these restructuring charges were recorded in the third quarter of 2014 upon decommissioning three facilities in Cambridge. During the first quarter of 2015, the Company terminated two of these lease agreements resulting in a credit to restructuring expense equal to the difference between the Company’s estimated future cash flows related to its lease obligations for these facilities and the termination payment paid to the Company’s landlord on the effective date of the termination. The third major facility included in this restructuring activity is 120,000 square feet of the Kendall Square Facility that the Company continued to use for its operations following its 2003 Kendall Restructuring. The rentable square footage in this portion of the Kendall Square Facility was subleased to a third party in February 2015. The Company will continue to incur charges through April 2018 related to the difference between the Company’s estimated future cash flows related to this portion of the Kendall Square Facility, which include an estimate for sublease income to be received from the Company’s sublessee and its actual cash flows. The Company discounted the estimated cash flows related to this restructuring activity at a discount rate of 9%.

The activities related to the restructuring liability for the three months ended March 31, 2017 and 2016 were as follows:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Liability, beginning of the period	$	3,626		$	5,964
Restructuring expense	296			233
Cash payments	(4,405		)	(3,156		)
Cash received from subleases	2,478			2,408
Liability, end of the period	$	1,995		$	5,449

Other Restructuring Activities

The Company has engaged in several other restructuring activities that are unrelated to its 2003 Kendall Restructuring and Fan Pier Move Restructuring. The most significant activity commenced in October 2013 when the Company adopted a restructuring plan that included (i) a workforce reduction primarily related to the commercial support of INCIVEK following the continued and rapid decline in the number of patients being treated with INCIVEK as new medicines for the treatment of HCV infection neared approval and (ii) the write-off of certain assets. This action resulted from the Company’s decision to focus its investment on future opportunities in CF and other research and development programs.

The remaining restructuring activities were completed in 2016. As such, there was no outstanding liability as of March 31, 2017. The activities related to the Company’s other restructuring liabilities for the three months ended March 31, 2016 were as follows:



	Three Months Ended March 31,
	2016
	(in thousands)
Liability, beginning of the period	$	1,450
Restructuring expense	251
Cash payments	(439		)
Liability, end of the period	$	1,262

Commitments and Contingencies	3 Months Ended
Commitments and Contingencies	Mar. 31, 2017
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Guaranties and Indemnifications As permitted under Massachusetts law, the Company’s Articles of Organization and By-laws provide that the Company will indemnify certain of its officers and directors for certain claims asserted against them in connection with their service as an officer or director. The maximum potential amount of future payments that the Company could be required to make under these indemnification provisions is unlimited. However, the Company has purchased directors’ and officers’ liability insurance policies that could reduce its monetary exposure and enable it to recover a portion of any future amounts paid. No indemnification claims currently are outstanding, and the Company believes the estimated fair value of these indemnification arrangements is minimal. The Company customarily agrees in the ordinary course of its business to indemnification provisions in agreements with clinical trial investigators and sites in its drug development programs, sponsored research agreements with academic and not-for-profit institutions, various comparable agreements involving parties performing services for the Company and its real estate leases. The Company also customarily agrees to certain indemnification provisions in its drug discovery, development and commercialization collaboration agreements. With respect to the Company’s clinical trials and sponsored research agreements, these indemnification provisions typically apply to any claim asserted against the investigator or the investigator’s institution relating to personal injury or property damage, violations of law or certain breaches of the Company’s contractual obligations arising out of the research or clinical testing of the Company’s compounds or drug candidates. With respect to lease agreements, the indemnification provisions typically apply to claims asserted against the landlord relating to personal injury or property damage caused by the Company, to violations of law by the Company or to certain breaches of the Company’s contractual obligations. The indemnification provisions appearing in the Company’s collaboration agreements are similar to those for the other agreements discussed above, but in addition provide some limited indemnification for its collaborator in the event of third-party claims alleging infringement of intellectual property rights. In each of the cases above, the indemnification obligation generally survives the termination of the agreement for some extended period, although the Company believes the obligation typically has the most relevance during the contract term and for a short period of time thereafter. The maximum potential amount of future payments that the Company could be required to make under these provisions is generally unlimited. The Company has purchased insurance policies covering personal injury, property damage and general liability that reduce its exposure for indemnification and would enable it in many cases to recover all or a portion of any future amounts paid. The Company has never paid any material amounts to defend lawsuits or settle claims related to these indemnification provisions. Accordingly, the Company believes the estimated fair value of these indemnification arrangements is minimal. Other Contingencies The Company has certain contingent liabilities that arise in the ordinary course of its business activities. The Company accrues a reserve for contingent liabilities when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. There were no material contingent liabilities accrued as of March 31, 2017 or December 31, 2016.

Basis of Presentation and Accounting Policies (Policies)	3 Months Ended
	Mar. 31, 2017
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying condensed consolidated financial statements are unaudited and have been prepared by Vertex Pharmaceuticals Incorporated (“Vertex” or the “Company”) in accordance with accounting principles generally accepted in the United States of America (“GAAP”). The condensed consolidated financial statements reflect the operations of (i) the Company, (ii) its wholly-owned subsidiaries and (iii) consolidated variable interest entities (VIEs). All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. These interim financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for a fair presentation of the financial position and results of operations for the interim periods ended March 31, 2017 and 2016. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for the full fiscal year. These interim financial statements should be read in conjunction with the audited financial statements for the year ended December 31, 2016, which are contained in the Company’s Annual Report on Form 10-K for the year ended December 31, 2016 that was filed with the Securities and Exchange Commission (the “SEC”) on February 23, 2017 (the “2016 Annual Report on Form 10-K”).
Use of Estimates and Summary of Significant Accounting Policies	Use of Estimates and Summary of Significant Accounting Policies The preparation of condensed consolidated financial statements in accordance with GAAP requires management to make certain estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, and the amounts of revenues and expenses during the reported periods. Significant estimates in these condensed consolidated financial statements have been made in connection with the calculation of revenues, inventories, research and development expenses, stock-based compensation expense, restructuring expense, the fair value of intangible assets, goodwill, contingent consideration, noncontrolling interest, the consolidation of VIEs, leases, the fair value of cash flow hedges and the provision for or benefit from income taxes. The Company bases its estimates on historical experience and various other assumptions, including in certain circumstances future projections that management believes to be reasonable under the circumstances. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.
Recent Accounting Pronouncements	Recent Accounting Pronouncements In 2014, the Financial Accounting Standards Board (“FASB”) issued new guidance applicable to revenue recognition that will be effective January 1, 2018. Early adoption was permitted for the year-ending December 31, 2017. The new guidance applies a more principles based approach to recognizing revenue. Under the new guidance, revenue is recognized when a customer obtains control of promised goods or services and is recognized in an amount that reflects the consideration that an entity expects to receive in exchange for those goods or services. In addition, the standard requires disclosure of the nature, amount, timing, and uncertainty of revenue and cash flows arising from contracts with customers. The new guidance must be adopted using either a modified retrospective approach or a full retrospective approach for all periods presented. Under the modified retrospective method, the cumulative effect of applying the standard would be recognized at the date of initial application within retained earnings. Under the full retrospective approach, the standard would be applied to each prior reporting period presented. Upon adoption, the Company will use the modified retrospective method. The Company is in the process of evaluating the new guidance and determining whether the expected effect is material to its condensed consolidated financial statements. The Company has formed a project team to review its portfolio of existing customer contracts and current accounting policies to identify and assess the potential differences that would result from applying the requirements of the new standard. The Company is also in the process of implementing appropriate changes to its controls to support revenue recognition and disclosure under the new standard. The new guidance could impact the Company’s accounting for product shipments to certain countries through early access programs, including the French early access programs, whereby the associated product has received regulatory approval but the reimbursement rate has not been finalized. In 2015, the FASB issued amended guidance applicable to inventory. The amended guidance simplifies the subsequent measurement of inventory by requiring inventory to be measured at the lower of cost and net realizable value. The amended guidance became effective for the Company during the first quarter of 2017. Adoption of the amended guidance did not have a significant effect on its condensed consolidated financial statements. In 2016, the FASB issued amended guidance applicable to share-based compensation to employees that simplifies the accounting for employee share-based payment transactions, including the accounting for income taxes, forfeitures, and statutory tax withholding requirements, as well as classification in the statement of cash flows. The amended guidance became effective for the Company during the first quarter of 2017. The amended guidance eliminates the requirement that excess tax benefits be realized as a reduction in current taxes payable before the associated tax benefit can be recognized as an increase in additional paid-in capital. This created approximately $410.8 million of deferred tax asset (“DTA”) relating to federal and state net operating losses (“NOLs”) that are fully reserved by an equal increase in valuation allowance. The Company recorded DTAs of approximately $404.7 million relating to Federal NOLs and approximately $6.1 million relating to State NOLs, both of which are offset by a full valuation allowance. Upon adoption, the Company also elected to change its accounting policy to account for forfeitures as they occur. The change was applied on a modified retrospective basis with a cumulative effect adjustment to accumulated deficit of $9.4 million, which increased the accumulated deficit as of January 1, 2017. This change also resulted in an increase to DTA by $3.4 million, which is offset by a full valuation allowance. As a result, there was no cumulative-effect adjustment to accumulated deficit. The provisions related to the recognition of excess tax benefits in the income statement and classification in the statement of cash flows were adopted prospectively, and as such, the prior periods were not retrospectively adjusted. In January 2016, the FASB issued amended guidance related to the recording of financial assets and financial liabilities. Under the amended guidance, equity investments (except those accounted for under the equity method of accounting or those that result in consolidation of the investee) are to be measured at fair value with changes in fair value recognized in net income. However, an entity has the option to either measure equity investments without readily determinable fair values at fair value or at cost adjusted for changes in observable prices minus impairment. Changes in measurement under either alternative will be recognized in net income. The amended guidance is effective for the year-ending December 31, 2018. Early adoption is permitted. The Company expects the implementation of this standard to have an impact on its consolidated financial statements and related disclosures, as the Company held publicly traded equity investments at March 31, 2017 as well as equity investments accounted for under the cost method. A cumulative-effect adjustment to the balance sheet will be recorded as of the beginning of the fiscal year of adoption. The implementation of this amended guidance is expected to increase volatility in net income as the volatility currently recorded in other comprehensive income related to changes in the fair market value of available-for-sale equity investments will be reflected in net income after adoption. In January 2017, the FASB issued amended guidance related to business combinations. The amended guidance clarifies the definition of a business with the objective of adding guidance to assist entities with evaluating whether transactions should be accounted for as acquisitions (or disposals) of assets or businesses. The new accounting guidance is effective for annual periods beginning after December 15, 2017, including interim periods within those periods. Early adoption is permitted. The Company early adopted this new guidance as of January 1, 2017 and will apply this new guidance to future acquisitions. In January 2017, the FASB issued amended guidance related the subsequent measurement of goodwill. The amended guidance eliminates a step from the goodwill impairment test. Under the amended guidance, an entity should perform its annual, or interim, goodwill impairment test by comparing the fair value of a reporting unit with its carrying amount. An entity should recognize an impairment charge for the amount by which the carrying amount exceeds the reporting unit’s fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. The amended guidance is effective for the year-ending December 31, 2020. Early adoption is permitted. The Company does not expect a significant effect on its condensed consolidated financial statements upon adoption of this new guidance. For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2016 Annual Report on Form 10-K.

Product Revenues, Net (Tables)

3 Months Ended

Mar. 31, 2017

Product Revenues [Abstract]

Schedule of product revenue allowances and reserve categories

The following table summarizes activity in each of the product revenue allowance and reserve categories for the three months ended March 31, 2017:



	Trade Allowances			Rebates, Chargebacks and Discounts			Product Returns			Other Incentives			Total
	(in thousands)
Balance at December 31, 2016	$	2,568		$	81,927		$	3,492		$	1,214		$	89,201
Provision related to current period sales	5,638			28,567			370			6,093			40,668
Adjustments related to prior period sales	(169		)	(2,344		)	(48		)	(56		)	(2,617		)
Credits/payments made	(5,654		)	(27,916		)	(170		)	(4,428		)	(38,168		)
Balance at March 31, 2017	$	2,383		$	80,234		$	3,644		$	2,823		$	89,084

Collaborative Arrangements and Pending Acquisition (Tables)

3 Months Ended

Mar. 31, 2017

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedule of Collaborative Arrangement Activity Net Loss Attributable to Noncontrolling Interest

An aggregate summary of net income attributable to noncontrolling interest related to the Company’s VIEs for the three months ended March 31, 2017 and 2016 is as follows:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Loss attributable to noncontrolling interest before provision for income taxes	$	1,547		$	839
Provision for income taxes	391			3,062
Increase in fair value of contingent payments	(3,730		)	(9,430		)
Net income attributable to noncontrolling interest	$	(1,792	)	$	(5,529	)

Changes In Fair Value Of Contingent Consideration

During the three months ended March 31, 2017 and 2016, the increase in the fair value of the contingent payments related to the Company’s VIEs was as follows:



	Three Months Ended March 31,
	2017		2016
	(in thousands)
Parion	$	2,830	$	9,000
BioAxone	900		430

Schedule Of Collaborative Arrangement Summary Of Items Related To Variable Interest Entities

The following table summarizes items related to the Company’s VIEs included in the Company’s condensed consolidated balance sheets as of the dates set forth in the table:



	March 31, 2017		December 31, 2016
	(in thousands)
Restricted cash and cash equivalents (VIE)	$	44,564	$	47,762
Prepaid expenses and other current assets	5,957		6,812
Intangible assets	284,340		284,340
Goodwill	19,391		19,391
Other assets	687		399
Accounts payable	1,080		415
Taxes payable	1,159		1,330
Other current liabilities	1,998		2,137
Deferred tax liability, net	133,058		131,446
Other liabilities	300		300
Noncontrolling interest	182,785		181,609

Earnings Per Share (Tables)

3 Months Ended

Mar. 31, 2017

Earnings Per Share [Abstract]

Schedule of Computation of Basic and Diluted Net Income (Loss) Per Share

The following table sets forth the computation of basic and diluted net income (loss) per share for the periods ended:



	Three Months Ended March 31,
	2017			2016
	(in thousands, except per share amounts)
Basic net income (loss) attributable to Vertex per common share calculation:
Net income (loss) attributable to Vertex common shareholders	$	247,756		$	(41,631	)
Less: Undistributed earnings allocated to participating securities	(406		)	—
Net income (loss) attributable to Vertex common shareholders—basic	$	247,350		$	(41,631	)

Basic weighted-average common shares outstanding	246,024			243,831
Basic net income (loss) attributable to Vertex per common share	$	1.01		$	(0.17	)

Diluted net income (loss) attributable to Vertex per common share calculation:
Net income (loss) attributable to Vertex common shareholders	$	247,756		$	(41,631	)
Less: Undistributed earnings allocated to participating securities	(401		)	—
Net income (loss) attributable to Vertex common shareholders—diluted	$	247,355		$	(41,631	)

Weighted-average shares used to compute basic net income (loss) per common share	246,024			243,831
Effect of potentially dilutive securities:
Stock options	2,037			—
Restricted stock and restricted stock units	627			—
Other	12			—
Weighted-average shares used to compute diluted net income (loss) per common share	248,700			243,831
Diluted net income (loss) attributable to Vertex per common share	$	0.99		$	(0.17	)

Potential gross common equivalent shares



	Three Months Ended March 31,
	2017	2016
	(in thousands)
Stock options	8,303	12,619
Unvested restricted stock and restricted stock units	807	3,565

Fair Value Measurements (Tables)

3 Months Ended

Mar. 31, 2017

Fair Value Disclosures [Abstract]

Financial assets subject to fair value measurements (excluding restricted cash and cash equivalents (Alios))

The following table sets forth the Company’s financial assets (excluding VIE cash and cash equivalents) and liabilities subject to fair value measurements:



	Fair Value Measurements as of March 31, 2017
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset position):
Cash equivalents:
Money market funds	$	313,629		$	313,629	$	—		$	—
Corporate debt securities	11,027			11,027		—			—
Commercial paper	6,834			6,834		—			—
Marketable securities:
Corporate equity securities	69,372			69,372		—			—
Corporate debt securities	203,181			—		203,181			—
Commercial paper	132,550			—		132,550			—
Prepaid and other current assets:
Foreign currency forward contracts	8,318			—		8,318			—
Other assets:
Foreign currency forward contracts	249			—		249			—
Total financial assets	$	745,160		$	400,862	$	344,298		$	—
Financial instruments carried at fair value (liability position):
Other liabilities, current portion:
Foreign currency forward contracts	$	(613	)	$	—	$	(613	)	$	—
Other liabilities, excluding current portion:
Foreign currency forward contracts	(86		)	—		(86		)	—
Total financial liabilities	$	(699	)	$	—	$	(699	)	$	—



	Fair Value Measurements as of December 31, 2016
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset position):
Cash equivalents:
Money market funds	$	280,560		$	280,560	$	—		$	—
Marketable securities:
Government-sponsored enterprise securities	15,508			15,508		—			—
Corporate equity securities	64,560			64,560		—			—
Commercial paper	59,404			—		59,404			—
Corporate debt securities	111,140			—		111,140			—
Prepaid and other current assets:
Foreign currency forward contracts	14,407			—		14,407			—
Other assets:
Foreign currency forward contracts	1,186			$	—	1,186			$	—
Total financial assets	$	546,765		$	360,628	$	186,137		$	—
Financial instruments carried at fair value (liability position):
Other liabilities, current portion:
Foreign currency forward contracts	$	(144	)	$	—	$	(144	)	$	—
Total financial liabilities	$	(144	)	$	—	$	(144	)	$	—

Marketable Securities (Tables)

3 Months Ended

Mar. 31, 2017

Cash and Cash Equivalents [Abstract]

Summary of cash, cash equivalents and marketable securities

A summary of the Company’s cash, cash equivalents and marketable securities is shown below:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
As of March 31, 2017
Cash and cash equivalents:
Cash and money market funds	$	985,818	$	—	$	—		$	985,818
Commercial paper	6,834		—		—			6,834
Corporate debt securities	11,027		—		—			11,027
Total cash and cash equivalents	$	1,003,679	$	—	$	—		$	1,003,679
Marketable securities:
Corporate equity securities	43,213		26,159		—			69,372
Commercial paper (matures within 1 year)	132,640		1		(91		)	132,550
Corporate debt securities (matures within 1 year)	180,465		3		(143		)	180,325
Corporate debt securities (matures after 1 year)	$	22,882	$	—	$	(26	)	$	22,856
Total marketable securities	$	379,200	$	26,163	$	(260	)	$	405,103
Total cash, cash equivalents and marketable securities	$	1,382,879	$	26,163	$	(260	)	$	1,408,782

As of December 31, 2016
Cash and cash equivalents:
Cash and money market funds	$	1,183,945	$	—	$	—		$	1,183,945
Total cash and cash equivalents	$	1,183,945	$	—	$	—		$	1,183,945
Marketable securities:
Government-sponsored enterprise securities (matures within 1 year)	$	15,506	$	2	$	—		$	15,508
Corporate equity securities	43,213		21,347		—			64,560
Commercial paper (matures within 1 year)	59,331		73		—			59,404
Corporate debt securities (matures within 1 year)	111,225		—		(85		)	111,140
Total marketable securities	$	229,275	$	21,422	$	(85	)	$	250,612
Total cash, cash equivalents and marketable securities	$	1,413,220	$	21,422	$	(85	)	$	1,434,557

Accumulated Other Comprehensive Income (Loss) (Tables)

3 Months Ended

Mar. 31, 2017

Equity [Abstract]

Accumulated Other Comprehensive Income (Loss)

A summary of the Company’s changes in accumulated other comprehensive income (loss) by component is shown below:



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities, net of tax		Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax			Total
	(in thousands)
Balance at December 31, 2016	$	(7,862	)	$	17,521	$	11,514		$	21,173
Other comprehensive (loss) income before reclassifications	(2,001		)	3,534		(2,802		)	(1,269		)
Amounts reclassified from accumulated other comprehensive loss	—			—		(3,879		)	(3,879		)
Net current period other comprehensive (loss) income	$	(2,001	)	$	3,534	$	(6,681	)	$	(5,148	)
Balance at March 31, 2017	$	(9,863	)	$	21,055	$	4,833		$	16,025



	Foreign Currency Translation Adjustment			Unrealized Holding Gains on Marketable Securities		Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax			Total
	(in thousands)
Balance at December 31, 2015	$	(2,080	)	$	126	$	3,778		$	1,824
Other comprehensive (loss) income before reclassifications	(1,740		)	229		(3,827		)	(5,338		)
Amounts reclassified from accumulated other comprehensive loss	—			—		(1,385		)	(1,385		)
Net current period other comprehensive (loss) income	$	(1,740	)	$	229	$	(5,212	)	$	(6,723	)
Balance at March 31, 2016	$	(3,820	)	$	355	$	(1,434	)	$	(4,899	)

Hedging (Tables)

3 Months Ended

Mar. 31, 2017

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Schedule of Cash Flow Hedging Instruments

The following table summarizes the notional amount of the Company’s outstanding foreign currency forward contracts designated as cash flow hedges:



	As of March 31, 2017		As of December 31, 2016
Foreign Currency	(in thousands)
Euro	$	187,375	$	164,368
British pound sterling	66,133		65,237
Australian dollar	28,645		23,776
Total foreign currency forward contracts	$	282,153	$	253,381

Schedule of Foreign Exchange Contracts



As of March 31, 2017
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	8,318	Other liabilities, current portion	$	(613	)
Other assets	249		Other liabilities, excluding current portion	(86		)
Total assets	$	8,567	Total liabilities	$	(699	)



As of December 31, 2016
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid and other current assets	$	14,407	Other liabilities, current portion	$	(144	)
Other assets	1,186		Other liabilities, excluding current portion	—
Total assets	$	15,593	Total liabilities	$	(144	)

Derivatives Offsetting

The following table summarizes the potential effect of offsetting derivatives by type of financial instrument on the Company’s condensed consolidated balance sheets:



	As of March 31, 2017
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	8,567		$	—	$	8,567		$	(699	)	$	7,868
Total liabilities	$	(699	)	$	—	$	(699	)	$	699		$	—



	As of December 31, 2016
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	15,593		$	—	$	15,593		$	(144	)	$	15,449
Total liabilities	$	(144	)	$	—	$	(144	)	$	144		$	—

Inventories (Tables)

3 Months Ended

Mar. 31, 2017

Inventory Disclosure [Abstract]

Schedule of Inventories by Type

Inventories consisted of the following:



	As of March 31, 2017		As of December 31, 2016
	(in thousands)
Raw materials	$	9,172	$	6,348
Work-in-process	60,921		56,672
Finished goods	11,927		14,584
Total	$	82,020	$	77,604

Stock-based Compensation Expense (Tables)

3 Months Ended

Mar. 31, 2017

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

Stock-based compensation expense by line item

During the three months ended March 31, 2017 and 2016, the Company recognized the following stock-based compensation expense:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Stock-based compensation expense by type of award:
Stock options	$	26,981		$	26,260
Restricted stock and restricted stock units	40,745			27,533
ESPP share issuances	2,064			2,524
Less stock-based compensation expense capitalized to inventories	(808		)	(845		)
Total stock-based compensation included in costs and expenses	$	68,982		$	55,472

Stock-based compensation expense by line item:
Research and development expenses	$	44,837		$	34,448
Sales, general and administrative expenses	24,145			21,024
Total stock-based compensation included in costs and expenses	$	68,982		$	55,472

Unrecognized stock-based compensation expense, net of estimated forfeitures

The following table sets forth the Company’s unrecognized stock-based compensation expense by type of award and the weighted-average period over which that expense is expected to be recognized:



	As of March 31, 2017
	Unrecognized Expense		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Stock options	$	200,906	2.65
Restricted stock and restricted stock units	$	291,088	2.57
ESPP share issuances	$	2,016	0.43

Stock options outstanding and exercisable

The following table summarizes information about stock options outstanding and exercisable at March 31, 2017:



	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$18.93–$20.00	134	0.85	$	18.93	134	$	18.93
$20.01–$40.00	1,576	2.95	$	33.77	1,576	$	33.77
$40.01–$60.00	1,678	5.34	$	48.36	1,678	$	48.36
$60.01–$80.00	1,279	6.88	$	75.86	924	$	75.61
$80.01–$100.00	5,932	8.65	$	89.51	1,757	$	89.81
$100.01–$120.00	1,572	7.79	$	109.33	799	$	109.30
$120.01–$134.69	1,427	8.22	$	130.53	668	$	130.27
Total	13,598	7.19	$	82.60	7,536	$	71.52

Restructuring Liabilities (Tables)

3 Months Ended

Mar. 31, 2017

Research and Development Restructuring

Restructuring Cost and Reserve [Line Items]

The restructuring charge and other activities recorded during the the three months ended March 31, 2017 and the related liability balance as of March 31, 2017 were as follows:



	Three Months Ended March 31,
	2017
	(in thousands)
Liability, beginning of the period	$	—
Restructuring expense	9,218
Cash payments	(3,258		)
Asset impairments and other non-cash expense	(2,233		)
Liability, end of the period	$	3,727

Kendall Restructuring

Restructuring Cost and Reserve [Line Items]

The activities related to the restructuring liability for the three months ended March 31, 2017 and 2016 were as follows:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Liability, beginning of the period	$	4,328		$	7,944
Restructuring expense	485			203
Cash payments	(5,264		)	(3,931		)
Cash received from subleases	2,976			3,008
Liability, end of the period	$	2,525		$	7,224

Fan Pier Move Restructuring

Restructuring Cost and Reserve [Line Items]

The activities related to the restructuring liability for the three months ended March 31, 2017 and 2016 were as follows:



	Three Months Ended March 31,
	2017			2016
	(in thousands)
Liability, beginning of the period	$	3,626		$	5,964
Restructuring expense	296			233
Cash payments	(4,405		)	(3,156		)
Cash received from subleases	2,478			2,408
Liability, end of the period	$	1,995		$	5,449

Other Restructuring

Restructuring Cost and Reserve [Line Items]

The activities related to the Company’s other restructuring liabilities for the three months ended March 31, 2016 were as follows:



	Three Months Ended March 31,
	2016
	(in thousands)
Liability, beginning of the period	$	1,450
Restructuring expense	251
Cash payments	(439		)
Liability, end of the period	$	1,262

Basis of Presentation and Accounting Policies (Details)	3 Months Ended
Basis of Presentation and Accounting Policies (Details)	Mar. 31, 2017 USD ($) segment	Dec. 31, 2016 USD ($)
Accounting Policies [Abstract]
Number of operating segments \| segment	1
Accounting Standards Update 2016-09, Forfeiture Rate Component \| Accumulated Deficit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of new accounting principle in period of adoption		$ 9,371,000
Accounting Standards Update 2016-09, Forfeiture Rate Component \| Additional Paid-in Capital
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of new accounting principle in period of adoption		(9,371,000)
Accounting Standards Update 2016-09, Excess Tax Benefit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Deferred income tax assets, net		3,400,000
Operating loss carryforwards	$ 410,800,000
Accounting Standards Update 2016-09 \| Accumulated Deficit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect of new accounting principle in period of adoption		$ 0
Domestic Tax Authority \| Accounting Standards Update 2016-09, Excess Tax Benefit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Operating loss carryforwards	404,700,000
State and Local Jurisdiction \| Accounting Standards Update 2016-09, Excess Tax Benefit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Operating loss carryforwards	$ 6,100,000

Product Revenues, Net (Details) - USD ($) $ in Thousands	3 Months Ended
Product Revenues, Net (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Valuation and Qualifying Accounts Disclosure [Line Items]
Customer deposits	$ 104,774	$ 73,416
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2016	89,201
Provision related to current period sales	40,668
Adjustments related to prior period sales	(2,617)
Credits/payments made	(38,168)
Balance at March 31, 2017	89,084
Trade Allowances
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2016	2,568
Provision related to current period sales	5,638
Adjustments related to prior period sales	(169)
Credits/payments made	(5,654)
Balance at March 31, 2017	2,383
Rebates, Chargebacks and Discounts
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2016	81,927
Provision related to current period sales	28,567
Adjustments related to prior period sales	(2,344)
Credits/payments made	(27,916)
Balance at March 31, 2017	80,234
Product Returns
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2016	3,492
Provision related to current period sales	370
Adjustments related to prior period sales	(48)
Credits/payments made	(170)
Balance at March 31, 2017	3,644
Other Incentives
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2016	1,214
Provision related to current period sales	6,093
Adjustments related to prior period sales	(56)
Credits/payments made	(4,428)
Balance at March 31, 2017	2,823
Cystic Fibrosis Foundation Therapeutics Incorporated
Valuation and Qualifying Accounts Disclosure [Line Items]
Customer deposits	$ 104,800

Collaborative Arrangements and Pending Acquisition - Cystic Fibrosis Foundation Therapeutics Incorporated (Details) - USD ($)		3 Months Ended
	Oct. 13, 2016	Mar. 31, 2017	Mar. 31, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenues		$ 232,545,000	$ 74,000
Cystic Fibrosis Foundation Therapeutics Incorporated
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone Payments			$ 13,900,000
Collaborative funding	$ 75,000,000.0
Additional Milestone Payments		$ 0
Additional Collaborative Funding	$ 6,000,000.0

Collaborative Arrangements and Pending Acquisition - CRISPR Therapeutics AG (Details) - CRISPR Therapeutics	1 Months Ended		3 Months Ended
	Oct. 31, 2016 USD ($)	Oct. 31, 2015 USD ($) target	Jun. 30, 2016 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Right to license, number of targets (up to) \| target		6
Up-front payment		$ 75,000,000
Investment in collaborative partner, pursuant to convertible loan agreement	$ 10,000,000	30,000,000	$ 3,100,000
Collaborative funding		75,000,000
Collaborative arrangement development and regulatory potential milestone payments maximum		$ 420,000,000
Prior to marketing approval, time period of notice required to terminate (in days)		90 days
Subsequent to marketing approval, time period of notice required to terminate (in days)		270 days

Collaborative Arrangements and Pending Acquisition - Merck KGaA (Details)		3 Months Ended
	Jan. 10, 2017 USD ($) pre-clinical_stage_program clinical-stage_program development_program	Mar. 31, 2017 USD ($)	Mar. 31, 2016 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenues		$ 232,545,000	$ 74,000
Collaborative revenues, related to upfront payment upon delivery of license and to research and development transition activities		231,700,000
Merck KGaA
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Right to license, number of development programs \| development_program	4
Right to license, number of clinical stage programs \| clinical-stage_program	2
Number of pre-clinical stage programs \| pre-clinical_stage_program	2
Up-front payment	$ 230,000,000.0
Collaborative revenues		193,600,000
Time period of notice required to terminate	90 days
Time period of notice required to terminate after a product has received marketing approval	180 days
German Tax Authority \| Merck KGaA
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenues, tax withholding		$ 36,400,000

Collaborative Arrangements and Pending Acquisition - Parion Sciences, Inc. (Details) - USD ($)		1 Months Ended
	Jun. 04, 2015	Jun. 30, 2015	Mar. 31, 2017	Dec. 31, 2016
Business Combination, Consideration Transferred [Abstract]
Intangible assets			$ 284,340,000	$ 284,340,000
Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Up-front payment	$ 80,000,000	$ 80,000,000
Prior to marketing approval, time period of notice required to terminate (in days)		90 days
Subsequent to marketing approval, time period of notice required to terminate (in days)		180 days
Change of control prior to clinical trial, time period of notice required to terminate (in days)		30 days
Term of agreement following first commercial sale (in years)		10 years
Business Combination, Consideration Transferred [Abstract]
Intangible assets		$ 255,300,000
Noncontrolling interest, fair value	164,300,000
Deferred tax liabilities, net	91,000,000
Other Liabilities Assets Net	$ 10,500,000
ENaC Inhibitors in CF \| Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum		490,000,000
Collaborative arrangement regulatory potential milestone payments maximum, global filling and approval		360,000,000
Enac Inhibitors in Non Cf \| Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum		370,000,000
Additional Enac Inhibitors \| Parion Sciences, Inc
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum		$ 230,000,000

Collaborative Arrangements and Pending Acquisition - BioAxone Biosciences, Inc. (Details) - BioAxone Biosciences Inc - USD ($)	1 Months Ended	3 Months Ended
	Oct. 31, 2014	Dec. 31, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Up-front payment		$ 10,000,000
Maximum license fees and milestone payments	$ 90,000,000.0
In-process research and development intangible asset	29,000,000
Deferred tax liability attributable to BioAxone	$ 11,300,000
Purchase option, term of extension of expiration date (in years)	1 year

Collaborative Arrangements and Pending Acquisition - Aggregate VIE Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2016	Dec. 31, 2015	Jun. 30, 2015	Dec. 31, 2014
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Provision for income taxes	$ (3,985)	$ (5,485)
Net income attributable to noncontrolling interest	(1,792)	(5,529)
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Restricted cash and cash equivalents (VIE)	44,564		$ 47,762
Prepaid expenses and other current assets	128,493		70,534
Intangible assets	284,340		284,340
Goodwill	50,384		50,384
Other assets	11,494		11,885
Accounts payable	63,145		61,451
Other current liabilities	277,962		315,249
Deferred tax liability, net	135,402		134,063
Other liabilities	28,467		28,699
Noncontrolling interest	182,785		181,609
BioAxone Biosciences Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Contingent consideration, liability	18,900		18,000
Parion Sciences, Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Provision for income taxes	(400)	(3,100)
Contingent consideration, liability	241,600		238,800
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Intangible assets					$ 255,300
Variable Interest Entity, Primary Beneficiary
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Loss attributable to noncontrolling interest before provision for income taxes	1,547	839
Provision for income taxes	391	3,062
(Increase) decrease in fair value of contingent milestone and royalty payments	(3,730)	(9,430)
Net income attributable to noncontrolling interest	(1,792)	(5,529)
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Restricted cash and cash equivalents (VIE)	44,564		47,762
Prepaid expenses and other current assets	5,957		6,812
Intangible assets	284,340		284,340
Goodwill	19,391		19,391
Other assets	687		399
Accounts payable	1,080		415
Taxes payable	1,159		1,330
Other current liabilities	1,998		2,137
Deferred tax liability, net	133,058		131,446
Other liabilities	300		300
Noncontrolling interest	182,785		$ 181,609
Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
(Increase) decrease in fair value of contingent milestone and royalty payments	(900)	(430)
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Intangible assets						$ 29,000
Variable Interest Entity, Primary Beneficiary \| Parion Sciences, Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
(Increase) decrease in fair value of contingent milestone and royalty payments	$ (2,830)	$ (9,000)
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Intangible assets				$ 255,300

Collaborative Arrangements and Pending Acquisition - Moderna Therapeutics, Inc. (Details) - Moderna Therapeutics, Inc. $ in Millions	1 Months Ended
	Jul. 31, 2016 USD ($)
Schedule of Collaborative Arrangement Agreements [Line Items]
Collaborative arrangement development and regulatory potential milestone payments maximum	$ 275.0
Collaborative Arrangement Approval and Reimbursement Milestones	220.0
Collaborative Arrangement, Investment in Collaborative Partner, Amount	20.0
Collaborative Arrangement Up-front License Fee	$ 20.0

Collaborative Arrangements and Pending Acquisition - Janssen Pharmaceuticals, Inc. (Details) - Janssen - USD ($) $ in Millions	3 Months Ended		12 Months Ended
	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Up-front payment			$ 35.0
Time period of notice required to terminate	6 months
Reimbursement for development and commercialization of compounds	$ 0.9	$ 3.5

Collaborative Arrangements and Pending Acquisition - Concert Pharmaceuticals (Details) - Concert Pharmaceuticals $ in Millions	Mar. 06, 2017 USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement, development and commercialization rights potential maximum milestone payments	$ 160
Collaborative arrangement, additional maximum milestone payments based on regulatory approval	$ 90

Earnings Per Share - Schedule of Earnings Per Share Computation Statement (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Basic net income (loss) attributable to Vertex per common share calculation:
Net income (loss) attributable to Vertex common shareholders	$ 247,756	$ (41,631)
Less: Undistributed earnings allocated to participating securities	(406)	0
Net income (loss) attributable to Vertex common shareholders—basic	$ 247,350	$ (41,631)
Basic weighted-average common shares outstanding	246,024	243,831
Basic net income (loss) attributable to Vertex per common share	$ 1.01	$ (0.17)
Diluted net income (loss) attributable to Vertex per common share calculation:
Less: Undistributed earnings allocated to participating securities	$ (401)	$ 0
Net income (loss) attributable to Vertex common shareholders—diluted	$ 247,355	$ (41,631)
Effect of potentially dilutive securities:
Other	12	0
Weighted-average shares used to compute diluted net income (loss) per common share	248,700	243,831
Diluted net income (loss) attributable to Vertex per common share	$ 0.99	$ (0.17)
Stock options
Effect of potentially dilutive securities:
Share-based payment arrangements	2,037	0
Restricted stock and restricted stock units
Effect of potentially dilutive securities:
Share-based payment arrangements	627	0

Earnings Per Share (Details) - shares shares in Thousands	3 Months Ended
Earnings Per Share (Details) - shares shares in Thousands	Mar. 31, 2017	Mar. 31, 2016
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	8,303	12,619
Unvested restricted stock and restricted stock units
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	807	3,565

Fair Value Measurements (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Recurring basis
Financial instruments carried at fair value (asset position):
Total financial assets	$ 745,160	$ 546,765
Financial instruments carried at fair value (liability position):
Total financial liabilities	(699)	(144)
Recurring basis \| Money market funds
Financial instruments carried at fair value (asset position):
Cash equivalents	313,629	280,560
Recurring basis \| Government-sponsored enterprise securities
Financial instruments carried at fair value (asset position):
Marketable securities		15,508
Recurring basis \| Corporate equity securities
Financial instruments carried at fair value (asset position):
Marketable securities	69,372	64,560
Recurring basis \| Corporate debt securities
Financial instruments carried at fair value (asset position):
Cash equivalents	11,027
Marketable securities	203,181	111,140
Recurring basis \| Commercial paper
Financial instruments carried at fair value (asset position):
Cash equivalents	6,834
Marketable securities	132,550	59,404
Recurring basis \| Level 1
Financial instruments carried at fair value (asset position):
Total financial assets	400,862	360,628
Financial instruments carried at fair value (liability position):
Total financial liabilities	0	0
Recurring basis \| Level 1 \| Money market funds
Financial instruments carried at fair value (asset position):
Cash equivalents	313,629	280,560
Recurring basis \| Level 1 \| Government-sponsored enterprise securities
Financial instruments carried at fair value (asset position):
Marketable securities		15,508
Recurring basis \| Level 1 \| Corporate equity securities
Financial instruments carried at fair value (asset position):
Marketable securities	69,372	64,560
Recurring basis \| Level 1 \| Corporate debt securities
Financial instruments carried at fair value (asset position):
Cash equivalents	11,027
Marketable securities	0	0
Recurring basis \| Level 1 \| Commercial paper
Financial instruments carried at fair value (asset position):
Cash equivalents	6,834
Marketable securities	0	0
Recurring basis \| Level 2
Financial instruments carried at fair value (asset position):
Total financial assets	344,298	186,137
Financial instruments carried at fair value (liability position):
Total financial liabilities	(699)	(144)
Recurring basis \| Level 2 \| Money market funds
Financial instruments carried at fair value (asset position):
Cash equivalents	0	0
Recurring basis \| Level 2 \| Government-sponsored enterprise securities
Financial instruments carried at fair value (asset position):
Marketable securities		0
Recurring basis \| Level 2 \| Corporate equity securities
Financial instruments carried at fair value (asset position):
Marketable securities	0	0
Recurring basis \| Level 2 \| Corporate debt securities
Financial instruments carried at fair value (asset position):
Cash equivalents	0
Marketable securities	203,181	111,140
Recurring basis \| Level 2 \| Commercial paper
Financial instruments carried at fair value (asset position):
Cash equivalents	0
Marketable securities	132,550	59,404
Recurring basis \| Level 3
Financial instruments carried at fair value (asset position):
Total financial assets	0	0
Financial instruments carried at fair value (liability position):
Total financial liabilities	0	0
Recurring basis \| Level 3 \| Money market funds
Financial instruments carried at fair value (asset position):
Cash equivalents	0	0
Recurring basis \| Level 3 \| Government-sponsored enterprise securities
Financial instruments carried at fair value (asset position):
Marketable securities		0
Recurring basis \| Level 3 \| Corporate equity securities
Financial instruments carried at fair value (asset position):
Marketable securities	0	0
Recurring basis \| Level 3 \| Corporate debt securities
Financial instruments carried at fair value (asset position):
Cash equivalents	0
Marketable securities	0	0
Recurring basis \| Level 3 \| Commercial paper
Financial instruments carried at fair value (asset position):
Cash equivalents	0
Marketable securities	0	0
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	8,318	14,407
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	0	0
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	8,318	14,407
Prepaid and other current assets \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	0	0
Other Assets \| Foreign currency forward contracts \| Recurring basis
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	249	1,186
Other Assets \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	0	0
Other Assets \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	249	1,186
Other Assets \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset position):
Foreign currency forward contracts	0	0
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis
Financial instruments carried at fair value (liability position):
Derivative liability current	(613)	(144)
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial instruments carried at fair value (liability position):
Derivative liability current	0	0
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial instruments carried at fair value (liability position):
Derivative liability current	(613)	(144)
Other liabilities, current portion \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial instruments carried at fair value (liability position):
Derivative liability current	0	$ 0
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis
Financial instruments carried at fair value (liability position):
Derivative liability, noncurrent	(86)
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis \| Level 1
Financial instruments carried at fair value (liability position):
Derivative liability, noncurrent	0
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis \| Level 2
Financial instruments carried at fair value (liability position):
Derivative liability, noncurrent	(86)
Other liabilities, excluding current portion \| Foreign currency forward contracts \| Recurring basis \| Level 3
Financial instruments carried at fair value (liability position):
Derivative liability, noncurrent	0
Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc \| Level 1
Financial instruments carried at fair value (liability position):
Cash and cash equivalents	$ 44,100

Marketable Securities (Details) - USD ($)	3 Months Ended
Marketable Securities (Details) - USD ($)	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2016
Summary of cash, cash equivalents and marketable securities
Amortized Cost	$ 1,382,879,000		$ 1,413,220,000
Gross Unrealized Gains	26,163,000		21,422,000
Gross Unrealized Losses	(260,000)		(85,000)
Fair Value	1,408,782,000		1,434,557,000
Other than temporary impairment losses, investments	0	$ 0
Gross realized gains (losses)	0	$ 0
Total cash and cash equivalents
Summary of cash, cash equivalents and marketable securities
Amortized Cost	1,003,679,000		1,183,945,000
Gross Unrealized Gains	0		0
Gross Unrealized Losses	0		0
Fair Value	1,003,679,000		1,183,945,000
Cash and money market funds
Summary of cash, cash equivalents and marketable securities
Amortized Cost	985,818,000		1,183,945,000
Gross Unrealized Gains	0		0
Gross Unrealized Losses	0		0
Fair Value	985,818,000		1,183,945,000
Commercial paper
Summary of cash, cash equivalents and marketable securities
Amortized Cost	6,834,000
Gross Unrealized Gains	0
Gross Unrealized Losses	0
Fair Value	6,834,000
Corporate debt securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	11,027,000
Gross Unrealized Gains	0
Gross Unrealized Losses	0
Fair Value	11,027,000
Total marketable securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	379,200,000		229,275,000
Gross Unrealized Gains	26,163,000		21,422,000
Gross Unrealized Losses	(260,000)		(85,000)
Fair Value	405,103,000		250,612,000
Government-sponsored enterprise securities (matures within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost			15,506,000
Gross Unrealized Gains			2,000
Gross Unrealized Losses			0
Fair Value			15,508,000
Corporate equity securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	43,213,000		43,213,000
Gross Unrealized Gains	26,159,000		21,347,000
Gross Unrealized Losses	0		0
Fair Value	69,372,000		64,560,000
Commercial paper (matures within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	132,640,000		59,331,000
Gross Unrealized Gains	1,000		73,000
Gross Unrealized Losses	(91,000)		0
Fair Value	132,550,000		59,404,000
Corporate debt securities (matures within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	180,465,000		111,225,000
Gross Unrealized Gains	3,000		0
Gross Unrealized Losses	(143,000)		(85,000)
Fair Value	180,325,000		$ 111,140,000
Corporate Debt Securities, (matures after 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	22,882,000
Gross Unrealized Gains	0
Gross Unrealized Losses	(26,000)
Fair Value	$ 22,856,000

Accumulated Other Comprehensive Income (Loss) (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	$ 1,338,191	$ 1,093,628
Total changes in other comprehensive income (loss)	(5,148)	(6,723)
Ending Balance	1,682,793	1,116,198
Foreign Currency Translation Adjustment
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	(7,862)	(2,080)
Other comprehensive (loss) income before reclassifications	(2,001)	(1,740)
Amounts reclassified from accumulated other comprehensive loss	0	0
Total changes in other comprehensive income (loss)	(2,001)	(1,740)
Ending Balance	(9,863)	(3,820)
Unrealized Holding Gains on Marketable Securities, net of tax
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	17,521	126
Other comprehensive (loss) income before reclassifications	3,534	229
Amounts reclassified from accumulated other comprehensive loss	0	0
Total changes in other comprehensive income (loss)	3,534	229
Ending Balance	21,055	355
Unrealized Gains (Losses) on Foreign Currency Forward Contracts, net of tax
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	11,514	3,778
Other comprehensive (loss) income before reclassifications	(2,802)	(3,827)
Amounts reclassified from accumulated other comprehensive loss	(3,879)	(1,385)
Total changes in other comprehensive income (loss)	(6,681)	(5,212)
Ending Balance	4,833	(1,434)
AOCI Attributable to Parent
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	21,173	1,824
Other comprehensive (loss) income before reclassifications	(1,269)	(5,338)
Amounts reclassified from accumulated other comprehensive loss	(3,879)	(1,385)
Total changes in other comprehensive income (loss)	(5,148)	(6,723)
Ending Balance	$ 16,025	$ (4,899)

Hedging (Details) - USD ($) $ in Thousands	3 Months Ended
Hedging (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Derivative [Line Items]
Amount of Ineffectiveness on Net Investment Hedges	$ 0
Foreign Currency Forward Contract
Offsetting Derivative Assets [Abstract]
Gross Amounts Recognized	8,567	$ 15,593
Gross Amounts Offset	0	0
Gross Amounts Presented	8,567	15,593
Gross Amounts Not Offset	(699)	(144)
Legal Offset	7,868	15,449
Offsetting Derivative Liabilities [Abstract]
Gross Amounts Recognized	(699)	(144)
Gross Amounts Offset	0	0
Gross Amounts Presented	(699)	(144)
Gross Amounts Not Offset	699	144
Legal Offset	0	0
Prepaid and other current assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	8,318	14,407
Other assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	249	1,186
Other liabilities, current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(613)	(144)
Other liabilities, excluding current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(86)	0
Designated as hedging instrument \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	282,153	253,381
Designated as hedging instrument \| Euro \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	187,375	164,368
Designated as hedging instrument \| British pound sterling \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	66,133	65,237
Designated as hedging instrument \| Australian dollar \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 28,645	$ 23,776
Minimum \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Derivative term	1 month
Maximum \| Foreign Currency Forward Contract \| Cash Flow Hedging
Derivative [Line Items]
Derivative term	18 months

Inventories - Schedule of Inventories (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Raw materials	$ 9,172	$ 6,348
Work-in-process	60,921	56,672
Finished goods	11,927	14,584
Total Inventories	$ 82,020	$ 77,604

Intangible Assets and Goodwill (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016	Dec. 31, 2015	Jun. 30, 2015	Dec. 31, 2014	Oct. 31, 2014
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets	$ 284,340	$ 284,340
Goodwill	50,384	50,384
Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets				$ 255,300
BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
In-process research and development intangible asset						$ 29,000
Variable Interest Entity, Primary Beneficiary
Indefinite-Lived Intangible Assets [Line Items]
In-process research and development intangible asset	284,300	284,300
Intangible assets	284,340	284,340
Goodwill	$ 19,391	$ 19,391
Variable Interest Entity, Primary Beneficiary \| Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets			$ 255,300
Variable Interest Entity, Primary Beneficiary \| BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
Intangible assets					$ 29,000

Long-term Obligations - Fan Pier Leases (Details) $ in Thousands, ft² in Millions	12 Months Ended
	Dec. 31, 2011 ft² lease building	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)
Property, Plant and Equipment [Line Items]
Property and equipment, net		$ 708,395	$ 698,362
Fan Pier Leases
Property, Plant and Equipment [Line Items]
Number of leases \| lease	2
Area of real estate property (in square feet) \| ft²	1.1
Number of buildings under lease agreement \| building	2
Optional term of lease agreement (in years)	10 years
Fan Pier Leases \| Buildings
Property, Plant and Equipment [Line Items]
Construction financing lease obligation, current and noncurrent		472,500	472,600
Fan Pier Leases \| Construction in progress
Property, Plant and Equipment [Line Items]
Property and equipment, net		$ 485,700	$ 489,000

Long-term Obligations - San Diego Lease (Details) - San Diego Lease ft² in Thousands, $ in Millions	Dec. 02, 2015 USD ($) ft² term_extension	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)
Property, Plant and Equipment [Line Items]
Area of real estate property (in square feet) \| ft²	170
Length of lease	16 years
Average yearly aggregate rent	$ 10.2
Amount of optional renewal terms \| term_extension	2
Optional renewal term length	5 years
Capital leased assets		$ 28.9	$ 15.0

Long-term Obligations - Credit Facility (Details)	1 Months Ended		3 Months Ended
Long-term Obligations - Credit Facility (Details)	Feb. 28, 2017 USD ($)	Oct. 31, 2016 USD ($)	Mar. 31, 2017 USD ($)	Mar. 31, 2016 USD ($)
Line of Credit Facility [Line Items]
Proceeds from lines of credit		$ 300,000,000
Line of credit facility additional borrowing capacity		300,000,000.0
Repayments of lines of credit	$ 300,000,000		$ 300,000,000	$ 0
Line of Credit
Line of Credit Facility [Line Items]
Line of credit facility, current borrowing capacity		500,000,000.0
Debt covenant, minimum consolidated EBITDA		$ 200,000,000.0
Debt covenant, consolidated leverage ratio		3.00
Base Rate \| Minimum \| Line of Credit
Line of Credit Facility [Line Items]
Interest rate, stated percentage		0.75%
Base Rate \| Maximum \| Line of Credit
Line of Credit Facility [Line Items]
Interest rate, stated percentage		1.50%
Eurodollar \| Minimum \| Line of Credit
Line of Credit Facility [Line Items]
Interest rate, stated percentage		1.75%
Eurodollar \| Maximum \| Line of Credit
Line of Credit Facility [Line Items]
Interest rate, stated percentage		2.50%

Long-term Obligations - Term Loan (Details) - Senior Secured Term Loan	1 Months Ended
	Jul. 31, 2014 USD ($)
Debt Instrument [Line Items]
Face amount of term loan	$ 300,000,000
Interest rate, stated percentage	7.20%
Unamortized discount on term loan	$ 5,300,000
Minimum
Debt Instrument [Line Items]
Interest rate, stated percentage	6.20%
Minimum \| LIBOR
Debt Instrument [Line Items]
Basis spread on variable rate (percent)	5.00%

Stock-based Compensation Expense - (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Stock-based compensation expense:
Less stock-based compensation expense capitalized to inventories	$ (808)	$ (845)
Total stock-based compensation included in costs and expenses	68,982	55,472
Stock options
Stock-based compensation expense:
Stock-based compensation expense by type of award:	26,981	26,260
Type of award:
Unrecognized Expense	$ 200,906
Weighted-average recognition period (in years)	2 years 7 months 24 days
Restricted stock and restricted stock units
Stock-based compensation expense:
Stock-based compensation expense by type of award:	$ 40,745	27,533
Type of award:
Unrecognized Expense	$ 291,088
Weighted-average recognition period (in years)	2 years 6 months 26 days
ESPP share issuances
Stock-based compensation expense:
Stock-based compensation expense by type of award:	$ 2,064	2,524
Type of award:
Unrecognized Expense	$ 2,016
Weighted-average recognition period (in years)	5 months 5 days
Research and development expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	$ 44,837	34,448
Sales, general and administrative expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	$ 24,145	$ 21,024

Stock-based Compensation Expense - Stock Options Outstanding and Exercisable (Details) shares in Thousands	3 Months Ended
	Mar. 31, 2017 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price range, options outstanding (in shares) \| shares	13,598
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 2 months 9 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 82.60
Exercise price range, options exercisable (in shares) \| shares	7,536
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 71.52
$18.93–$20.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	18.93
Exercise price, high end of range (usd per share)	$ 20.00
Exercise price range, options outstanding (in shares) \| shares	134
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	10 months 6 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 18.93
Exercise price range, options exercisable (in shares) \| shares	134
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 18.93
$20.01–$40.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	20.01
Exercise price, high end of range (usd per share)	$ 40
Exercise price range, options outstanding (in shares) \| shares	1,576
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	2 years 11 months 12 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 33.77
Exercise price range, options exercisable (in shares) \| shares	1,576
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 33.77
$40.01–$60.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	40.01
Exercise price, high end of range (usd per share)	$ 60
Exercise price range, options outstanding (in shares) \| shares	1,678
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	5 years 4 months 2 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 48.36
Exercise price range, options exercisable (in shares) \| shares	1,678
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 48.36
$60.01–$80.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	60.01
Exercise price, high end of range (usd per share)	$ 80
Exercise price range, options outstanding (in shares) \| shares	1,279
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	6 years 10 months 17 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 75.86
Exercise price range, options exercisable (in shares) \| shares	924
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 75.61
$80.01–$100.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	80.01
Exercise price, high end of range (usd per share)	$ 100
Exercise price range, options outstanding (in shares) \| shares	5,932
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 7 months 24 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 89.51
Exercise price range, options exercisable (in shares) \| shares	1,757
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 89.81
$100.01–$120.00
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	100.01
Exercise price, high end of range (usd per share)	$ 120
Exercise price range, options outstanding (in shares) \| shares	1,572
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 9 months 15 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 109.33
Exercise price range, options exercisable (in shares) \| shares	799
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 109.30
$120.01–$134.69
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price, low end of range (usd per share)	120.01
Exercise price, high end of range (usd per share)	$ 134.69
Exercise price range, options outstanding (in shares) \| shares	1,427
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 2 months 19 days
Exercise price range, options outstanding, weighted-average exercise price (usd per share)	$ 130.53
Exercise price range, options exercisable (in shares) \| shares	668
Exercise price range, options exercisable, weighted-average exercise price (usd per share)	$ 130.27

Other Arrangements (Details) - USD ($)	12 Months Ended
Other Arrangements (Details) - USD ($)	Dec. 31, 2008	Mar. 31, 2017
Sale of HIV Protease Inhibitor Royalty Stream
Gross proceeds from sale of royalty rights receivable from GlaxoSmithKline	$ 160,000,000.0
Deferred revenue royalty purchase agreement		$ 11,800,000

Income Taxes (Details) - USD ($)	3 Months Ended		12 Months Ended
Income Taxes (Details) - USD ($)	Mar. 31, 2017	Mar. 31, 2016	Dec. 31, 2016
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes	$ 3,985,000	$ 5,485,000
Income tax liability associated with variable interest entity	0
Unrecognized tax benefits	0		$ 0
Income taxes, interest and penalties accrued	0
Increase in unrecognized tax benefits is reasonably possible	0
Effective income tax rate reconciliation, share-based compensation, excess tax benefit, amount	400,000
Income taxes, material interest or penalties related to uncertain tax positions	0		0
Amount of unrecognized deferred tax liability, undistributed earnings of foreign subsidiaries	0
Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes	400,000	$ 3,100,000
Accounting Standards Update 2016-09, Excess Tax Benefit
Schedule of Collaborative Arrangement Agreements [Line Items]
Operating loss carryforwards	410,800,000
Deferred income tax assets, net			3,400,000
Domestic Tax Authority \| Accounting Standards Update 2016-09, Excess Tax Benefit
Schedule of Collaborative Arrangement Agreements [Line Items]
Operating loss carryforwards	404,700,000
State and Local Jurisdiction \| Accounting Standards Update 2016-09, Excess Tax Benefit
Schedule of Collaborative Arrangement Agreements [Line Items]
Operating loss carryforwards	$ 6,100,000
Retained Earnings \| Accounting Standards Update 2016-09, Forfeiture Rate Component
Schedule of Collaborative Arrangement Agreements [Line Items]
Cumulative effect of new accounting principle in period of adoption			9,371,000
Additional Paid-in Capital \| Accounting Standards Update 2016-09, Forfeiture Rate Component
Schedule of Collaborative Arrangement Agreements [Line Items]
Cumulative effect of new accounting principle in period of adoption			$ (9,371,000)

Restructuring Liabilities - Narrative (Details) ft² in Thousands	1 Months Ended	3 Months Ended		12 Months Ended
	Feb. 28, 2017 position facility	Mar. 31, 2015 ft² lease	Sep. 30, 2014 facility	Dec. 31, 2003	Mar. 31, 2017 USD ($)	Dec. 31, 2016 USD ($)	Mar. 31, 2016 USD ($)	Dec. 31, 2015 USD ($)
Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring Reserve					$ 3,727,000	$ 0
Restructuring and related cost, number of facilities expected to close \| facility	1
Restructuring and related cost, number of positions eliminated \| position	70
Kendall Restructuring
Restructuring Cost and Reserve [Line Items]
Lease term (in years)				15 years
Restructuring and related activities, leased office space, maximum percentage used - not more than				50.00%
Fan Pier Move Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring Reserve					1,995,000	$ 3,626,000	$ 5,449,000	$ 5,964,000
Number of facilities decommissioned \| facility			3
Number of leases terminated \| lease		2
Area of real estate property (in square feet) \| ft²		120
Discount rate related to leases (percent)		9.00%
Other Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring Reserve					0		$ 1,262,000	$ 1,450,000
Employee Severance \| Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring and related cost, expected cost					6,800,000
Asset Impairments \| Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring and related cost, expected cost					2,000,000
Minimum \| Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring and related cost, expected cost					11,300,000
Minimum \| Facility Closing \| Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring and related cost, expected cost					2,500,000
Maximum \| Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring and related cost, expected cost					13,000,000
Maximum \| Facility Closing \| Research and Development Restructuring
Restructuring Cost and Reserve [Line Items]
Restructuring and related cost, expected cost					$ 4,200,000

Restructuring Liabilities - Activity Related to Restructuring Liability (Details) - USD ($)	3 Months Ended
	Mar. 31, 2017	Mar. 31, 2016
Restructuring activities
Restructuring expense (income)	$ 9,999,000	$ 687,000
2003 Restructuring
Restructuring activities
Liability, beginning of the period	4,328,000	7,944,000
Restructuring expense (income)	485,000	203,000
Cash payments	(5,264,000)	(3,931,000)
Cash received from subleases	2,976,000	3,008,000
Liability, end of the period	2,525,000	7,224,000
Fan Pier Move Restructuring
Restructuring activities
Liability, beginning of the period	3,626,000	5,964,000
Restructuring expense (income)	296,000	233,000
Cash payments	(4,405,000)	(3,156,000)
Cash received from subleases	2,478,000	2,408,000
Liability, end of the period	1,995,000	5,449,000
Other Restructuring
Restructuring activities
Liability, beginning of the period		1,450,000
Restructuring expense (income)		251,000
Cash payments		(439,000)
Liability, end of the period	0	$ 1,262,000
Research and Development Restructuring
Restructuring activities
Liability, beginning of the period	0
Restructuring expense (income)	9,218,000
Cash payments	(3,258,000)
Asset impairments and other non-cash expense	(2,233,000)
Liability, end of the period	$ 3,727,000

Commitments and Contingencies (Details) - USD ($) $ in Thousands	Mar. 31, 2017	Dec. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Contingent liabilities	$ 0	$ 0
Indemnification claims	$ 0