Vertex Pharmaceuticals (VRTX) 10-Q 1 Aug 16 2016 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2016	Jul. 22, 2016
Document and Entity Information [Abstract]
Entity Registrant Name	VERTEX PHARMACEUTICALS INC / MA
Entity Central Index Key	875,320
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Document Type	10-Q
Document Period End Date	Jun. 30, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q2
Amendment Flag	false
Entity Common Stock, Shares Outstanding		247,778,698

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations (unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Revenues:
Product revenues, net	$ 425,651	$ 160,388	$ 820,061	$ 291,263
Royalty revenues	5,282	5,077	8,878	11,869
Collaborative revenues	675	611	749	1,453
Total revenues	431,608	166,076	829,688	304,585
Costs and expenses:
Cost of product revenues	44,154	15,409	93,943	24,790
Royalty expenses	1,098	1,451	1,958	4,377
Research and development expenses	271,008	223,858	526,868	439,457
Sales, general and administrative expenses	111,652	94,394	216,866	180,254
Restructuring expenses (income), net	343	2,128	1,030	(1,144)
Total costs and expenses	428,255	337,240	840,665	647,734
Income (loss) from operations	3,353	(171,164)	(10,977)	(343,149)
Interest expense, net	(20,155)	(21,111)	(40,853)	(42,418)
Other (expenses) income, net	(1,219)	1,414	3,192	(3,699)
Loss before provision for income taxes	(18,021)	(190,861)	(48,638)	(389,266)
Provision for income taxes	18,130	30,131	23,615	30,430
Net loss	(36,151)	(220,992)	(72,253)	(419,696)
(Income) loss attributable to noncontrolling interest	(28,374)	32,144	(33,903)	32,242
Net loss attributable to Vertex	$ (64,525)	$ (188,848)	$ (106,156)	$ (387,454)
Net loss:
Basic (usd per share)	$ (0.26)	$ (0.78)	$ (0.43)	$ (1.61)
Diluted (usd per share)	$ (0.26)	$ (0.78)	$ (0.43)	$ (1.61)
Shares used in per share calculations:
Basic (in shares)	244,482	240,757	244,124	240,129
Diluted (in shares)	244,482	240,757	244,124	240,129

Condensed Consolidated Stateme3

Condensed Consolidated Statements of Comprehensive Loss (unaudited) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Net loss	$ (36,151)	$ (220,992)	$ (72,253)	$ (419,696)
Changes in other comprehensive loss:
Unrealized holding gains (losses) on marketable securities	(29)	(46)	200	130
Unrealized gains (losses) on foreign currency forward contracts, net of tax	4,999	(4,280)	(213)	(3,974)
Foreign currency translation adjustment	(3,461)	1,828	(5,201)	1,220
Total changes in other comprehensive loss	1,509	(2,498)	(5,214)	(2,624)
Comprehensive loss	(34,642)	(223,490)	(77,467)	(422,320)
Comprehensive (income) loss attributable to noncontrolling interest	(28,374)	32,144	(33,903)	32,242
Comprehensive loss attributable to Vertex	$ (63,016)	$ (191,346)	$ (111,370)	$ (390,078)

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets (unaudited) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Current assets:
Cash and cash equivalents	$ 605,866	$ 714,768
Marketable securities, available for sale	465,570	327,694
Restricted cash and cash equivalents (VIE)	70,513	78,910
Accounts receivable, net	189,356	177,639
Inventories	66,589	57,207
Prepaid expenses and other current assets	56,256	50,935
Total current assets	1,454,150	1,407,153
Property and equipment, net	690,607	697,715
Intangible assets	284,340	284,340
Goodwill	50,384	50,384
Cost method investment in CRISPR	33,213	0
Notes receivable	0	30,000
Restricted cash	22,085	22,083
Other assets	14,203	6,912
Total assets	2,548,982	2,498,587
Current liabilities:
Accounts payable	51,302	74,942
Accrued expenses	275,165	305,820
Deferred revenues, current portion	11,468	16,296
Accrued restructuring expenses, current portion	7,683	7,894
Capital lease obligations, current portion	17,446	15,545
Senior secured term loan, current portion	221,576	71,296
Other liabilities, current portion	38,215	14,374
Total current liabilities	622,855	506,167
Deferred revenues, excluding current portion	7,411	9,714
Accrued restructuring expenses, excluding current portion	4,801	7,464
Capital lease obligations, excluding current portion	34,317	42,923
Deferred tax liability	132,810	110,439
Construction financing lease obligation, excluding current portion	472,374	472,611
Senior secured term loan, net of current portion and discount	74,921	223,863
Other liabilities, excluding current portion	30,648	31,778
Total liabilities	1,380,137	1,404,959
Commitments and contingencies
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000,000 shares authorized; none issued and outstanding at June 30, 2016 and December 31, 2015	0	0
Common stock, $0.01 par value; 500,000,000 and 500,000,000 shares authorized at June 30, 2016 and December 31, 2015, respectively; 247,703,932 and 246,306,818 shares issued and outstanding at June 30, 2016 and December 31, 2015, respectively	2,440	2,427
Additional paid-in capital	6,350,244	6,197,500
Accumulated other comprehensive (loss) income	(3,390)	1,824
Accumulated deficit	(5,367,940)	(5,261,784)
Total Vertex shareholders' equity	981,354	939,967
Noncontrolling interest	187,491	153,661
Total shareholders’ equity	1,168,845	1,093,628
Total liabilities and shareholders’ equity	$ 2,548,982	$ 2,498,587

Condensed Consolidated Balance5

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2016	Dec. 31, 2015
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	247,703,932	246,306,818
Common stock, shares outstanding	247,703,932	246,306,818

Condensed Consolidated Stateme6

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, 2014			241,764
Balance at Dec. 31, 2014	$ 1,096,183	$ 1,075,006	$ 2,385	$ 5,777,154	$ 917	$ (4,705,450)	$ 21,177
Increase (Decrease) in Stockholders' Equity
Other comprehensive loss, net of tax	(2,624)	(2,624)			(2,624)
Net loss	(419,696)	(387,454)				(387,454)	(32,242)
Issuance of common stock under benefit plans (shares)			2,578
Issuance of common stock under benefit plans	87,354	87,354	$ 21	87,333			0
Stock-based compensation expense	122,682	122,682		122,682			0
Noncontrolling interest upon consolidation	164,317						164,317
Balance (shares) at Jun. 30, 2015			244,342
Balance at Jun. 30, 2015	1,048,216	894,964	$ 2,406	5,987,169	(1,707)	(5,092,904)	153,252
Balance (shares) at Dec. 31, 2015			246,307
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	(5,214)	(5,214)			(5,214)
Net loss	(72,253)	(106,156)				(106,156)	33,903
Issuance of common stock under benefit plans (shares)			1,397
Issuance of common stock under benefit plans	33,570	33,570	$ 13	33,557			0
Stock-based compensation expense	119,114	119,187		119,187			(73)
Balance (shares) at Jun. 30, 2016			247,704
Balance at Jun. 30, 2016	$ 1,168,845	$ 981,354	$ 2,440	$ 6,350,244	$ (3,390)	$ (5,367,940)	$ 187,491

Condensed Consolidated Stateme7

Condensed Consolidated Statements of Cash Flows (unaudited) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Cash flows from operating activities:
Net loss	$ (72,253)	$ (419,696)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation expense	117,414	120,645
Depreciation and amortization expense	31,378	30,428
Deferred income taxes	22,858	6,346
Other non-cash items, net	3,436	6,045
Changes in operating assets and liabilities:
Accounts receivable, net	(12,954)	(21,197)
Inventories	(7,779)	(9,426)
Prepaid expenses and other assets	(7,971)	(15,397)
Accounts payable	(23,821)	(3,033)
Accrued expenses and other liabilities	(14,562)	8,098
Accrued restructuring expense	(2,892)	(26,012)
Deferred revenues	(7,131)	(9,303)
Net cash provided by (used in) operating activities	25,723	(332,502)
Cash flows from investing activities:
Purchases of marketable securities	(470,077)	(125,655)
Maturities of marketable securities	332,316	741,725
Payment for acquisition of variable interest entity	0	80,000
Expenditures for property and equipment	(27,892)	(23,978)
Increase in restricted cash and cash equivalents	0	(21,975)
Investment in CRISPR Series B preferred stock	(3,075)	0
Decrease in restricted cash and cash equivalents (VIE)	8,397	2,277
(Increase) decrease in other assets	(159)	87
Net cash (used in) provided by investing activities	(160,490)	492,481
Cash flows from financing activities:
Issuances of common stock under benefit plans	33,702	87,850
Payments on capital lease obligations	(7,538)	(14,441)
Proceeds from capital lease financing	0	13,386
Payments on construction financing lease obligation	(209)	(184)
Net cash provided by financing activities	25,955	86,611
Effect of changes in exchange rates on cash	(90)	(1,306)
Net (decrease) increase in cash and cash equivalents	(108,902)	245,284
Cash and cash equivalents—beginning of period	714,768	625,259
Cash and cash equivalents—end of period	605,866	870,543
Supplemental disclosure of cash flow information:
Cash paid for interest	41,325	42,885
Cash paid for income taxes	1,237	1,022
Issuances of common stock exercises from employee benefit plans receivable	$ 161	$ 166

Basis of Presentation and Accou

Basis of Presentation and Accounting Policies	6 Months Ended
	Jun. 30, 2016
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 June 30, 2016 and 2015 . 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, 2015 , which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 that was filed with the Securities and Exchange Commission (the “SEC”) on February 16, 2016 (the " 2015 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 2015 Annual Report on Form 10-K. Recent Accounting Pronouncements In 2016, the Financial Accounting Standards Board (“FASB”) issued amended guidance applicable to leases that will be effective for the year ending December 31, 2019. Early adoption is permitted. This update requires an entity to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance applicable to share-based compensation to employees that will be effective for the year ending December 31, 2017. Early adoption is permitted. This update 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 Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2015 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the six months ended June 30, 2016 that had a material effect on its condensed consolidated financial statements.

Product Revenues, Net

Product Revenues, Net	6 Months Ended
	Jun. 30, 2016
Product Revenues [Abstract]
Product Revenues, Net	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. The following table summarizes activity in each of the product revenue allowance and reserve categories for the six months ended June 30, 2016 : Trade Rebates, Product Other Total (in thousands) Balance at December 31, 2015 $ 2,089 $ 44,669 $ 1,228 $ 1,310 $ 49,296 Provision related to current period sales 9,935 65,066 1,288 4,220 80,509 Adjustments related to prior period sales (77 ) (1,712 ) (205 ) 5 (1,989 ) Credits/payments made (9,762 ) (44,113 ) (260 ) (4,638 ) (58,773 ) Balance at June 30, 2016 $ 2,185 $ 63,910 $ 2,051 $ 897 $ 69,043 In the three and six months ended June 30, 2016, the Company sold ORKAMBI in France pursuant to early access programs. The Company has not recognized any product revenues based on these sales because the price is not fixed or determinable due to the ongoing negotiations regarding the reimbursement rate for ORKAMBI in France. If the negotiated reimbursement rate in France is lower than the price currently being paid by Customers in France under these programs, the Company would reimburse the difference between such prices to the Customers. The cash received from sales in France is included as a liability on the Company's condensed consolidated balance sheet, and the increase in "other liabilities, current portion" from December 31, 2015 to June 30, 2016 is primarily due to this liability.

Collaborative Arrangements

Collaborative Arrangements	6 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Collaborative Arrangements	Collaborative Arrangements Cystic Fibrosis Foundation Therapeutics Incorporated In April 2011, the Company entered into an amendment (the “April 2011 Amendment”) to its existing collaboration agreement with Cystic Fibrosis Foundation Therapeutics Incorporated (“CFFT”) pursuant to which CFFT agreed to provide financial support for (i) development activities for VX-661, a compound that targets the processing and trafficking defect of the F508del CFTR proteins discovered under the collaboration, and (ii) additional research and development activities directed at discovering new compounds targeting the processing and trafficking defect of the F508del protein. Under the April 2011 Amendment, CFFT agreed to provide the Company with up to $75.0 million in funding over approximately five years for corrector compound research and development activities. The Company retains the right to develop and commercialize KALYDECO (ivacaftor), ORKAMBI (lumacaftor in combination with ivacaftor), lumacaftor and VX-661. The Company recognized no collaborative revenues from this collaboration during the three and six months ended June 30, 2016 and 2015 . In the original agreement, as amended prior to the April 2011 Amendment, the Company agreed to pay CFFT tiered royalties calculated as a percentage, ranging from single digits to sub-teens, of annual net sales of any approved drugs first synthesized or tested during the research term that ended in 2008, including ivacaftor, lumacaftor and VX-661. The April 2011 Amendment provides for a tiered royalty in the same range on net sales of corrector compounds first synthesized or tested during the research term that ended in February 2014. In each of 2012 and 2013, CFFT earned a commercial milestone payment of $9.3 million from the Company upon achievement of certain sales levels for KALYDECO. In each of the fourth quarter of 2015 and 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 related to sales levels for KALYDECO or ORKAMBI. 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 VX-661 until the expiration of patents covering that compound. 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 VX-661 that expire in 2027 and 2028, respectively, subject to potential extension. CRISPR Therapeutics AG On October 26, 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 sheet. In the second quarter of 2016, the Company made an additional preferred stock investment in CRISPR of approximately $3.1 million . 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. 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 milestone and royalty 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 milestone and royalty payments. The following collaborations are reflected in the Company's financial statements as consolidated VIEs: Parion Sciences, Inc. License and Collaboration Agreement On June 4, 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 cystic fibrosis, or CF, and 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 Parion is a VIE based on, among other factors, the significance to Parion of the ENaC inhibitors licensed to the Company pursuant to the Parion Agreement and on the Company's power to direct the activities that most significantly affect the economic performance of 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. 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 difference between the fair value of the consideration and the fair value of Parion's assets (including the fair value of intangible assets) and liabilities was allocated to goodwill. The measurement period for purchase accounting was closed during the quarter. There were no purchase accounting adjustments recorded during the measurement period. BioAxone Biosciences, Inc. In October 2014, the Company entered into a license and collaboration agreement (the “BioAxone Agreement”) with BioAxone Biosciences, Inc. (“BioAxone”), a privately-held biotechnology company, 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 loss attributable to noncontrolling interest related to the Company's VIEs for the three and six months ended June 30, 2016 and 2015 is as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Loss attributable to noncontrolling interest before provision for income taxes $ 2,835 $ 1,293 $ 3,674 $ 1,579 Provision for income taxes 17,511 29,653 20,573 29,590 (Increase) decrease in fair value of contingent milestone and royalty payments (48,720 ) 1,198 (58,150 ) 1,073 Net (income) loss attributable to noncontrolling interest $ (28,374 ) $ 32,144 $ (33,903 ) $ 32,242 The increases in the fair value of the contingent milestone and royalty payments in the three and six months ended June 30, 2016 were primarily due to a Phase 2 clinical trial of VX-371, a compound being developed pursuant to the Parion Agreement, achieving its primary safety endpoint in the second quarter of 2016. The fair value of the contingent milestone and royalty payments also reflects changes in market interest rates and the time value of money. During the three and six months ended June 30, 2016 and 2015 , the increase (decrease) in the fair value of the contingent milestone and royalty payments related to the Company's VIEs was as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Parion $ 48,400 $ (1,621 ) $ 57,400 $ (1,621 ) BioAxone 320 423 750 548 As of June 30, 2016 , the fair value of the contingent milestone and royalty payments related to the Parion Agreement and the BioAxone Agreement was $231.4 million and $28.7 million , respectively. As of December 31, 2015 , the fair value of the contingent milestone and royalty payments related to the Parion collaboration and the BioAxone collaboration was $179.0 million and $28.0 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: June 30, 2016 December 31, 2015 (in thousands) Restricted cash and cash equivalents (VIE) $ 70,513 $ 78,910 Prepaid expenses and other current assets 3,001 3,138 Intangible assets 284,340 284,340 Goodwill 19,391 19,391 Other assets 383 455 Accounts payable 1,129 676 Taxes payable 11,723 24,554 Other current liabilities 7,059 7,100 Deferred tax liability, net 132,810 110,438 Other liabilities 310 300 Noncontrolling interest 187,491 153,661 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. Outlicense Arrangements In the ordinary course of the Company's business, the Company has entered into various agreements pursuant to which it has outlicensed rights to certain drug candidates to third-party collaborators. Although the Company does not consider any of these outlicense arrangements to be material, the most notable of these outlicense arrangements is described below. Pursuant to these outlicense arrangements, our collaborators are responsible for all costs related to the continued development of such drug candidates. Depending on the terms of the arrangements, the Company's collaborators may be required to make upfront payments, milestone payments upon the achievement of certain product research and development objectives and/or pay royalties on future sales, if any, of commercial products resulting from the collaboration. 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 and six months ended June 30, 2016 , the Company recorded reimbursement for these development activities of $4.3 million and $7.8 million , respectively. During the three and six months ended June 30, 2015 , the Company recorded reimbursement for these development activities of $7.1 million and $14.7 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. Subsequent Event 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 made a $20.0 million investment in Moderna pursuant to a convertible promissory note. 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 collaboration, 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.

Earnings Per Share

Earnings Per Share	6 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Earnings Per Share	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 Company did not include the securities in the following table in the computation of the net loss per share attributable to Vertex common shareholders calculations because the effect would have been anti-dilutive during each period: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Stock options 12,231 11,933 12,231 11,933 Unvested restricted stock and restricted stock units 3,506 3,355 3,506 3,355

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	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 June 30, 2016 , the Company’s investments were in money market funds, short-term government-sponsored enterprise securities, U.S. Treasury securities, corporate debt securities and commercial paper. As of June 30, 2016 , 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, short-term government-sponsored enterprise securities and U.S. Treasury 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 Fair Value Hierarchy Total Level 1 Level 2 Level 3 (in thousands) Financial assets carried at fair value: Cash equivalents: Money market funds $ 110,696 $ 110,696 $ — $ — Marketable securities: U.S. Treasury securities 33,142 33,142 — — Government-sponsored enterprise securities 131,900 131,900 — — Corporate debt securities 135,675 — 135,675 — Commercial paper 164,853 — 164,853 — Prepaid and other current assets: Foreign currency forward contracts 9,966 — 9,966 — Other assets: Foreign currency forward contracts 1,604 — 1,604 — Total financial assets $ 587,836 $ 275,738 $ 312,098 $ — Financial liabilities carried at fair value: Other liabilities, current portion: Foreign currency forward contracts $ (7,317 ) $ — $ (7,317 ) $ — Other liabilities, excluding current portion: Foreign currency forward contracts (88 ) — (88 ) — Total financial liabilities $ (7,405 ) $ — $ (7,405 ) $ — Fair Value Measurements as 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 $ 199,507 $ 199,507 $ — $ — Government-sponsored enterprise securities 85,994 85,994 — — Commercial paper 34,889 — 34,889 — Corporate debt securities 11,533 — 11,533 — Marketable securities: Government-sponsored enterprise securities 87,162 87,162 — — Commercial paper 99,123 — 99,123 — Corporate debt securities 141,409 — 141,409 — Prepaid and other current assets: Foreign currency forward contracts 5,161 — 5,161 — Other assets: Foreign currency forward contracts 605 $ — 605 $ — Total financial assets $ 665,383 $ 372,663 $ 292,720 $ — Financial instruments carried at fair value (liability position): Other liabilities, current portion: Foreign currency forward contracts $ (769 ) $ — $ (769 ) $ — Other liabilities, excluding current portion: Foreign currency forward contracts (132 ) — (132 ) — Total financial liabilities $ (901 ) $ — $ (901 ) $ — The Company's VIEs invested in cash equivalents consisting of money market funds of $70.2 million as of June 30, 2016 , 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 milestone and royalty payments , which are valued based on Level 3 inputs. Please refer to Note C, “Collaborative Arrangements,” for further information. As of June 30, 2016 , the fair value and carrying value of the Company's Term Loan was $296.5 million . The fair value of the Company's Term Loan was estimated based on Level 3 inputs computed using the effective interest rate of the Term Loan. The effective interest rate considers the timing and amount of estimated future interest payments as well as current market rates. Please refer to Note K, "Long-term Obligations" for further information regarding the Company's Term Loan.

Marketable Securities

Marketable Securities	6 Months Ended
	Jun. 30, 2016
Cash and Cash Equivalents [Abstract]
Marketable Securities	Marketable Securities A summary of the Company’s cash, cash equivalents and marketable securities is shown below: Amortized Cost Gross Gross Fair Value (in thousands) As of June 30, 2016 Cash and cash equivalents: Cash and money market funds $ 605,866 $ — $ — $ 605,866 Total cash and cash equivalents $ 605,866 $ — $ — $ 605,866 Marketable securities: U.S. Treasury securities (due within 1 year) $ 33,138 $ 4 $ — $ 33,142 Government-sponsored enterprise securities (due within 1 year) 131,868 35 (3 ) 131,900 Commercial paper (due within 1 year) 164,575 278 — 164,853 Corporate debt securities (due within 1 year) 135,663 34 (22 ) 135,675 Total marketable securities $ 465,244 $ 351 $ (25 ) $ 465,570 Total cash, cash equivalents and marketable securities $ 1,071,110 $ 351 $ (25 ) $ 1,071,436 As of December 31, 2015 Cash and cash equivalents: Cash and money market funds $ 582,352 $ — $ — $ 582,352 Government-sponsored enterprise securities 85,994 — — 85,994 Commercial paper 34,889 — — 34,889 Corporate debt securities 11,533 — — 11,533 Total cash and cash equivalents $ 714,768 $ — $ — $ 714,768 Marketable securities: Government-sponsored enterprise securities (due within 1 year) $ 87,176 $ — $ (14 ) $ 87,162 Commercial paper (due within 1 year) 98,877 246 — 99,123 Corporate debt securities (due within 1 year) 141,515 — (106 ) 141,409 Total marketable securities $ 327,568 $ 246 $ (120 ) $ 327,694 Total cash, cash equivalents and marketable securities $ 1,042,336 $ 246 $ (120 ) $ 1,042,462 The Company has a limited number of marketable securities in insignificant loss positions as of June 30, 2016 , 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 and six months ended June 30, 2016 and 2015 .

Accumulated Other Comprehensive

Accumulated Other Comprehensive (Loss) Income	6 Months Ended
	Jun. 30, 2016
Equity [Abstract]
Accumulated Other Comprehensive (Loss) Income	Accumulated Other Comprehensive (Loss) Income A summary of the Company's changes in accumulated other comprehensive (loss) income by component is shown below: Foreign Currency Translation Adjustment Unrealized Holding Gains (Losses) on Marketable Securities Unrealized Gains 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 (5,201 ) 200 1,847 (3,154 ) Amounts reclassified from accumulated other comprehensive loss — — (2,060 ) (2,060 ) Net current period other comprehensive (loss) income $ (5,201 ) $ 200 $ (213 ) $ (5,214 ) Balance at June 30, 2016 $ (7,281 ) $ 326 $ 3,565 $ (3,390 ) Foreign Currency Translation Adjustment Unrealized Holding (Losses) Gains on Marketable Securities Unrealized Gains (Losses) on Foreign Currency Forward Contracts Total (in thousands) Balance at December 31, 2014 $ (971 ) $ (123 ) $ 2,011 $ 917 Other comprehensive (loss) income before reclassifications 1,220 130 (1,370 ) (20 ) Amounts reclassified from accumulated other comprehensive loss — — (2,604 ) (2,604 ) Net current period other comprehensive (loss) income $ 1,220 $ 130 $ (3,974 ) $ (2,624 ) Balance at June 30, 2015 $ 249 $ 7 $ (1,963 ) $ (1,707 )

Hedging

Hedging	6 Months Ended
	Jun. 30, 2016
Derivative Instruments and Hedging Activities Disclosure [Abstract]
Hedging	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 June 30, 2016 , 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 June 30, 2016 As of December 31, 2015 Foreign Currency (in thousands) Euro $ 193,542 $ 103,362 British pound sterling 79,845 78,756 Australian dollar 28,318 27,167 Total foreign currency forward contracts $ 301,705 $ 209,285 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 June 30, 2016 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 9,966 Other liabilities, current portion $ (7,317 ) Other assets 1,604 Other liabilities, excluding current portion (88 ) Total assets $ 11,570 Total liabilities $ (7,405 ) As of December 31, 2015 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 5,161 Other liabilities, current portion $ (769 ) Other assets 605 Other liabilities, excluding current portion (132 ) Total assets $ 5,766 Total liabilities $ (901 ) 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 June 30, 2016 Gross Amounts Recognized Gross Amounts Offset Gross Amounts Presented Gross Amounts Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 11,570 $ — $ 11,570 $ (7,405 ) $ 4,165 Total liabilities $ (7,405 ) $ — $ (7,405 ) $ 7,405 $ — As of December 31, 2015 Gross Amounts Recognized Gross Amounts Offset Gross Amounts Presented Gross Amounts Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 5,766 $ — $ 5,766 $ (901 ) $ 4,865 Total liabilities $ (901 ) $ — $ (901 ) $ 901 $ —

Inventories

Inventories	6 Months Ended
	Jun. 30, 2016
Inventory Disclosure [Abstract]
Inventories	Inventories Inventories consisted of the following: As of June 30, 2016 As of December 31, 2015 (in thousands) Raw materials $ 5,408 $ 8,696 Work-in-process 45,807 40,695 Finished goods 15,374 7,816 Total $ 66,589 $ 57,207

Intangible Assets and Goodwill

Intangible Assets and Goodwill	6 Months Ended
	Jun. 30, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Intangible Assets and Goodwill	Intangible Assets and Goodwill Intangible Assets As of June 30, 2016 and December 31, 2015 , in-process research and development intangible assets of $284.3 million were recorded on the Company's condensed consolidated balance sheet. In June 2015, in connection with entering into the Parion Agreement, the Company recorded an in-process research and development intangible asset of $255.3 million based on the Company’s estimate of the fair value of Parion’s lead investigational ENaC inhibitors, including VX-371 and VX-551, that were licensed by the Company from Parion. The Company aggregated the fair value of the ENaC inhibitors into a single intangible asset because the phase, nature and risks of development as well as the amount and timing of benefits associated with the assets were similar. In October 2014, the Company recorded an in-process research and development intangible asset of $29.0 million based on the Company’s estimate of the fair value of VX-210, a drug candidate for patients with spinal cord injuries that was licensed by the Company from BioAxone. The Company used discount rates of 7.1% and 7.5% in the present-value models to estimate the fair values of the ENaC inhibitors and VX-210 intangible assets, respectively. Goodwill As of June 30, 2016 and December 31, 2015 , goodwill of $50.4 million was recorded on the Company's condensed consolidated balance sheet.

Long-term Obligations

Long-term Obligations	6 Months Ended
	Jun. 30, 2016
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 $495.7 million and $502.3 million as of June 30, 2016 and December 31, 2015 , respectively, related to construction costs for the Buildings. The carrying value of the Company's lease agreement liability for the Buildings was $472.8 million and $473.0 million as of June 30, 2016 and December 31, 2015 , 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 second half of 2017, 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. 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 provides for a $300.0 million senior secured term loan ("Term Loan"). The credit agreement also provides that, subject to satisfaction of certain conditions, the Company may request that the lenders establish an incremental senior secured term loan facility in an aggregate amount not to exceed $200.0 million . The Term 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 bears interest at a rate of LIBOR plus 5.0% per annum during the third year of the term. The maturity date of all loans under the facilities is July 9, 2017. Interest is payable quarterly and on the maturity date. In October 2015, the Company amended the terms of the credit agreement to provide for, among other things, a modification to the repayment schedule of the loan. As amended, the Company is required to repay principal on the Term Loan in quarterly installments of $75 million from October 1, 2016 through the maturity date. The Company may prepay the Term Loan, in whole or in part, at any time; provided that prepayments prior to the July 9, 2016 are subject to a make-whole premium to ensure Macquarie receives approximately the present value of two years of interest payments over the life of the loan. The Company accounted for the amendment as a debt modification, as opposed to an extinguishment of debt, based on an insignificant change to the present value of the future cash flows relating to the credit agreement. The Company's obligations under the Term Loan are unconditionally guaranteed by certain of its domestic subsidiaries. All obligations under the Term Loan, and the guarantees of those obligations, are secured, subject to certain exceptions, by substantially all of the Company's assets and the assets of all guarantors, including the pledge of all or a portion of the equity interests of certain of its subsidiaries. The credit agreement requires that the Company maintain, on a quarterly basis, a minimum level of KALYDECO net revenues. Further, the credit agreement includes negative covenants, subject to exceptions, restricting or limiting the Company's ability and the ability of its subsidiaries to, among other things, incur additional indebtedness, grant liens, engage in certain investment, acquisition and disposition transactions, pay dividends, repurchase capital stock and enter into transactions with affiliates. The credit agreement also contains customary representations and warranties, affirmative covenants and events of default, including payment defaults, breach of representations and warranties, covenant defaults and cross defaults. If an event of default occurs, the administrative agent would be entitled to take various actions, including the acceleration of amounts due under outstanding loans. There have been no events of default as of or during the period ended June 30, 2016 . Based on the Company's evaluation of the Term Loan, the Company determined that the Term Loan contains several embedded derivatives. These embedded derivatives are clearly and closely related to the host instrument because they relate to the Company's credit risk; therefore, they do not require bifurcation from the host instrument, the Term Loan. The Company incurred $5.3 million in fees paid to Macquarie that were recorded as a discount on the Term Loan and are being recorded as interest expense using the effective interest method over the term of the loan in the Company’s condensed consolidated statements of operations . As of June 30, 2016 and December 31, 2015 , the unamortized discount associated with the Term Loan that was included in the senior secured term loan caption on the Company’s condensed consolidated balance sheet was $3.4 million and $4.6 million , respectively.

Stock-based Compensation Expens

Stock-based Compensation Expense	6 Months Ended
	Jun. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-based Compensation Expense	Stock-based Compensation Expense During the three and six months ended June 30, 2016 and 2015 , the Company recognized the following stock-based compensation expense: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Stock-based compensation expense by type of award: Stock options $ 31,826 $ 37,687 $ 58,086 $ 66,646 Restricted stock and restricted stock units 29,608 24,902 57,141 52,071 ESPP share issuances 1,436 1,825 3,960 3,965 Less stock-based compensation expense capitalized to inventories (928 ) (1,153 ) (1,773 ) (2,037 ) Total stock-based compensation included in costs and expenses $ 61,942 $ 63,261 $ 117,414 $ 120,645 Stock-based compensation expense by line item: Research and development expenses $ 40,640 $ 41,632 $ 75,088 $ 79,849 Sales, general and administrative expenses 21,302 21,629 42,326 40,796 Total stock-based compensation included in costs and expenses $ 61,942 $ 63,261 $ 117,414 $ 120,645 The following table sets forth the Company's unrecognized stock-based compensation expense, net of estimated forfeitures, by type of award and the weighted-average period over which that expense is expected to be recognized: As of June 30, 2016 Unrecognized Expense, Weighted-average (in thousands) (in years) Type of award: Stock options $ 176,251 2.66 Restricted stock and restricted stock units $ 201,858 2.57 ESPP share issuances $ 5,546 0.64 The following table summarizes information about stock options outstanding and exercisable at June 30, 2016 : Options Outstanding Options Exercisable Range of Exercise Prices Number Weighted-average Weighted-average Number Weighted-average (in thousands) (in years) (per share) (in thousands) (per share) $18.93–$20.00 137 1.61 $ 18.93 137 $ 18.93 $20.01–$40.00 1,964 3.45 $ 34.24 1,962 $ 34.23 $40.01–$60.00 2,066 6.07 $ 48.14 1,657 $ 48.66 $60.01–$80.00 1,368 7.62 $ 75.90 734 $ 75.39 $80.01–$100.00 3,555 8.60 $ 90.68 1,080 $ 88.91 $100.01–$120.00 1,644 8.57 $ 109.32 500 $ 109.27 $120.01–$134.69 1,497 9.05 $ 130.61 420 $ 129.84 Total 12,231 7.21 $ 79.37 6,490 $ 63.32

Other Arrangements

Other Arrangements	6 Months Ended
	Jun. 30, 2016
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 June 30, 2016 , the Company had $18.9 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

Income Taxes	6 Months Ended
	Jun. 30, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company is subject to United States federal, state, and foreign income taxes. For the three and six months ended June 30, 2016 , the Company recorded a provision for income taxes of $18.1 million and $23.6 million , respectively. The provision for income taxes recorded in the three and six months ended June 30, 2016 included $17.5 million and $20.6 million , respectively, 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 and six months ended June 30, 2015 , the Company recorded a provision for income taxes of $30.1 million and $30.4 million , respectively, primarily related to the Company's VIEs' income tax provision. As of June 30, 2016 and December 31, 2015 , the Company had unrecognized tax benefits of $0.4 million . The Company recognizes interest and penalties related to income taxes as a component of income tax expense. As of June 30, 2016 , 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 June 30, 2016 and December 31, 2015 . In 2016, it is reasonably possible that the Company will reduce the balance of its unrecognized tax benefits by approximately $0.4 million due to the application of statute of limitations and settlements with taxing authorities, all of which would reduce the Company’s effective tax rate. 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. 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 before 2011 or any other major taxing jurisdiction for years before 2009, except where the Company has net operating losses or tax credit carryforwards that originated before 2009. The Company currently is under examination by the Internal Revenue Service for the year ended December 31, 2011 and in Delaware, Canada and Quebec for varying periods including the years ended December 31, 2011 through 2014. No adjustments have been reported. The Company is not under examination by any other jurisdictions for any tax year. The Company concluded audits with Pennsylvania and Texas during 2016 and Massachusetts and New York during 2015 with no material adjustments. The Company currently intends to reinvest the total amount of its unremitted earnings. At June 30, 2016 , 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

Restructuring Liabilities	6 Months Ended
	Jun. 30, 2016
Restructuring and Related Activities [Abstract]
Restructuring Liabilities	Restructuring Liabilities 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 and six months ended June 30, 2016 and 2015 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Liability, beginning of the period $ 7,224 $ 9,506 $ 7,944 $ 11,596 Cash payments (3,833 ) (2,584 ) (7,764 ) (6,569 ) Cash received from subleases 3,008 2,799 6,016 5,275 Restructuring expense (income) (11 ) 203 192 (378 ) Liability, end of the period $ 6,388 $ 9,924 $ 6,388 $ 9,924 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 and six months ended June 30, 2016 and 2015 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Liability, beginning of the period $ 5,449 $ 11,137 $ 5,964 $ 33,390 Cash payments (3,096 ) (3,095 ) (6,252 ) (22,351 ) Cash received from subleases 2,361 — 4,769 — Restructuring expense (income) 149 975 382 (2,022 ) Liability, end of the period $ 4,863 $ 9,017 $ 4,863 $ 9,017 Other Restructuring Activities The Company has engaged in several other restructuring activities that are unrelated to its 2003 Kendall Restructuring and the 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 activities related to the Company's other restructuring liabilities for the three and six months ended June 30, 2016 and 2015 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Liability, beginning of the period $ 1,262 $ 845 $ 1,450 $ 869 Cash payments (234 ) (893 ) (673 ) (1,223 ) Restructuring expense 205 950 456 1,256 Liability, end of the period $ 1,233 $ 902 $ 1,233 $ 902

Commitments and Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Financing Arrangements As of June 30, 2016 , the Company had irrevocable stand-by letters of credit outstanding that were issued in connection with property leases and other similar agreements totaling $21.9 million that are cash collateralized. The cash used to support these letters of credit is included in restricted cash, as of June 30, 2016 , on the Company's condensed consolidated balance sheet. Litigation On May 28, 2014, a purported shareholder class action Local No. 8 IBEW Retirement Plan & Trust v. Vertex Pharmaceuticals Incorporated, et al. was filed in the United States District Court for the District of Massachusetts, naming the Company and certain of the Company's current and former officers and directors as defendants. The lawsuit alleged that the Company made material misrepresentations and/or omissions of material fact in the Company's disclosures during the period from May 7, 2012 through May 29, 2012, all in violation of Section 10(b) of the Securities Exchange Act of 1934, as amended, and Rule 10b-5 promulgated thereunder. The purported class consists of all persons (excluding defendants) who purchased the Company’s common stock between May 7, 2012 and May 29, 2012. The plaintiffs seek unspecified monetary damages, costs and attorneys’ fees as well as disgorgement of the proceeds from certain individual defendants’ sales of the Company’s stock. On October 8, 2014, the Court approved Local No. 8 IBEW Retirement Fund as lead plaintiff, and Scott and Scott LLP as lead counsel for the plaintiff and the putative class. On February 23, 2015, the Company filed a reply to the plaintiffs’ opposition to its motion to dismiss. The court heard oral argument on the motion to dismiss on March 6, 2015 and took the motion under advisement. On September 30, 2015, the court granted the Company's motion to dismiss. On October 15, 2015, the plaintiff filed a notice of appeal. The First Circuit Court of Appeals issued a scheduling order on December 24, 2015. On February 2, 2016, the Plaintiff filed their opening brief and the Company filed its opposition brief on March 7, 2016. On March 24, 2016, the plaintiff filed their reply brief. Oral argument on the appeal took place on July 26, 2016. The Company believes the claims to be without merit and intend to vigorously defend the litigation. As of June 30, 2016 , the Company has not recorded any reserves for this purported class action. 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 June 30, 2016 or December 31, 2015 .

Basis of Presentation and Acc24

Basis of Presentation and Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2016
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 June 30, 2016 and 2015 . 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, 2015 , which are contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 that was filed with the Securities and Exchange Commission (the “SEC”) on February 16, 2016 (the " 2015 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 2016, the Financial Accounting Standards Board (“FASB”) issued amended guidance applicable to leases that will be effective for the year ending December 31, 2019. Early adoption is permitted. This update requires an entity to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. In 2016, the FASB issued amended guidance applicable to share-based compensation to employees that will be effective for the year ending December 31, 2017. Early adoption is permitted. This update 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 Company is in the process of evaluating the new guidance and determining the expected effect on its consolidated financial statements. For a discussion of other recent accounting pronouncements please refer to Note A, “Nature of Business and Accounting Policies—Recent Accounting Pronouncements,” in the 2015 Annual Report on Form 10-K. The Company did not adopt any new accounting pronouncements during the six months ended June 30, 2016 that had a material effect on its condensed consolidated financial statements.

Product Revenues, Net (Tables)

Product Revenues, Net (Tables)	6 Months Ended
	Jun. 30, 2016
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 six months ended June 30, 2016 : Trade Rebates, Product Other Total (in thousands) Balance at December 31, 2015 $ 2,089 $ 44,669 $ 1,228 $ 1,310 $ 49,296 Provision related to current period sales 9,935 65,066 1,288 4,220 80,509 Adjustments related to prior period sales (77 ) (1,712 ) (205 ) 5 (1,989 ) Credits/payments made (9,762 ) (44,113 ) (260 ) (4,638 ) (58,773 ) Balance at June 30, 2016 $ 2,185 $ 63,910 $ 2,051 $ 897 $ 69,043

Collaborative Arrangements (Tab

Collaborative Arrangements (Tables)	6 Months Ended
	Jun. 30, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Schedule of Collaborative Arrangement Activity Net Loss Attributable to Noncontrolling Interest	An aggregate summary of net loss attributable to noncontrolling interest related to the Company's VIEs for the three and six months ended June 30, 2016 and 2015 is as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Loss attributable to noncontrolling interest before provision for income taxes $ 2,835 $ 1,293 $ 3,674 $ 1,579 Provision for income taxes 17,511 29,653 20,573 29,590 (Increase) decrease in fair value of contingent milestone and royalty payments (48,720 ) 1,198 (58,150 ) 1,073 Net (income) loss attributable to noncontrolling interest $ (28,374 ) $ 32,144 $ (33,903 ) $ 32,242
Changes In Fair Value Of Contingent Consideration [Table Text Block]	During the three and six months ended June 30, 2016 and 2015 , the increase (decrease) in the fair value of the contingent milestone and royalty payments related to the Company's VIEs was as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Parion $ 48,400 $ (1,621 ) $ 57,400 $ (1,621 ) BioAxone 320 423 750 548
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: June 30, 2016 December 31, 2015 (in thousands) Restricted cash and cash equivalents (VIE) $ 70,513 $ 78,910 Prepaid expenses and other current assets 3,001 3,138 Intangible assets 284,340 284,340 Goodwill 19,391 19,391 Other assets 383 455 Accounts payable 1,129 676 Taxes payable 11,723 24,554 Other current liabilities 7,059 7,100 Deferred tax liability, net 132,810 110,438 Other liabilities 310 300 Noncontrolling interest 187,491 153,661

Earnings Per Share (Tables)

Earnings Per Share (Tables)	6 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Potential gross common equivalent shares	The Company did not include the securities in the following table in the computation of the net loss per share attributable to Vertex common shareholders calculations because the effect would have been anti-dilutive during each period: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Stock options 12,231 11,933 12,231 11,933 Unvested restricted stock and restricted stock units 3,506 3,355 3,506 3,355

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2016
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 Fair Value Hierarchy Total Level 1 Level 2 Level 3 (in thousands) Financial assets carried at fair value: Cash equivalents: Money market funds $ 110,696 $ 110,696 $ — $ — Marketable securities: U.S. Treasury securities 33,142 33,142 — — Government-sponsored enterprise securities 131,900 131,900 — — Corporate debt securities 135,675 — 135,675 — Commercial paper 164,853 — 164,853 — Prepaid and other current assets: Foreign currency forward contracts 9,966 — 9,966 — Other assets: Foreign currency forward contracts 1,604 — 1,604 — Total financial assets $ 587,836 $ 275,738 $ 312,098 $ — Financial liabilities carried at fair value: Other liabilities, current portion: Foreign currency forward contracts $ (7,317 ) $ — $ (7,317 ) $ — Other liabilities, excluding current portion: Foreign currency forward contracts (88 ) — (88 ) — Total financial liabilities $ (7,405 ) $ — $ (7,405 ) $ — Fair Value Measurements as 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 $ 199,507 $ 199,507 $ — $ — Government-sponsored enterprise securities 85,994 85,994 — — Commercial paper 34,889 — 34,889 — Corporate debt securities 11,533 — 11,533 — Marketable securities: Government-sponsored enterprise securities 87,162 87,162 — — Commercial paper 99,123 — 99,123 — Corporate debt securities 141,409 — 141,409 — Prepaid and other current assets: Foreign currency forward contracts 5,161 — 5,161 — Other assets: Foreign currency forward contracts 605 $ — 605 $ — Total financial assets $ 665,383 $ 372,663 $ 292,720 $ — Financial instruments carried at fair value (liability position): Other liabilities, current portion: Foreign currency forward contracts $ (769 ) $ — $ (769 ) $ — Other liabilities, excluding current portion: Foreign currency forward contracts (132 ) — (132 ) — Total financial liabilities $ (901 ) $ — $ (901 ) $ —

Marketable Securities (Tables)

Marketable Securities (Tables)	6 Months Ended
	Jun. 30, 2016
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 Gross Fair Value (in thousands) As of June 30, 2016 Cash and cash equivalents: Cash and money market funds $ 605,866 $ — $ — $ 605,866 Total cash and cash equivalents $ 605,866 $ — $ — $ 605,866 Marketable securities: U.S. Treasury securities (due within 1 year) $ 33,138 $ 4 $ — $ 33,142 Government-sponsored enterprise securities (due within 1 year) 131,868 35 (3 ) 131,900 Commercial paper (due within 1 year) 164,575 278 — 164,853 Corporate debt securities (due within 1 year) 135,663 34 (22 ) 135,675 Total marketable securities $ 465,244 $ 351 $ (25 ) $ 465,570 Total cash, cash equivalents and marketable securities $ 1,071,110 $ 351 $ (25 ) $ 1,071,436 As of December 31, 2015 Cash and cash equivalents: Cash and money market funds $ 582,352 $ — $ — $ 582,352 Government-sponsored enterprise securities 85,994 — — 85,994 Commercial paper 34,889 — — 34,889 Corporate debt securities 11,533 — — 11,533 Total cash and cash equivalents $ 714,768 $ — $ — $ 714,768 Marketable securities: Government-sponsored enterprise securities (due within 1 year) $ 87,176 $ — $ (14 ) $ 87,162 Commercial paper (due within 1 year) 98,877 246 — 99,123 Corporate debt securities (due within 1 year) 141,515 — (106 ) 141,409 Total marketable securities $ 327,568 $ 246 $ (120 ) $ 327,694 Total cash, cash equivalents and marketable securities $ 1,042,336 $ 246 $ (120 ) $ 1,042,462

Accumulated Other Comprehensi30

Accumulated Other Comprehensive (Loss) Income (Tables)	6 Months Ended
	Jun. 30, 2016
Equity [Abstract]
Accumulated Other Comprehensive (Loss) Income	A summary of the Company's changes in accumulated other comprehensive (loss) income by component is shown below: Foreign Currency Translation Adjustment Unrealized Holding Gains (Losses) on Marketable Securities Unrealized Gains 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 (5,201 ) 200 1,847 (3,154 ) Amounts reclassified from accumulated other comprehensive loss — — (2,060 ) (2,060 ) Net current period other comprehensive (loss) income $ (5,201 ) $ 200 $ (213 ) $ (5,214 ) Balance at June 30, 2016 $ (7,281 ) $ 326 $ 3,565 $ (3,390 ) Foreign Currency Translation Adjustment Unrealized Holding (Losses) Gains on Marketable Securities Unrealized Gains (Losses) on Foreign Currency Forward Contracts Total (in thousands) Balance at December 31, 2014 $ (971 ) $ (123 ) $ 2,011 $ 917 Other comprehensive (loss) income before reclassifications 1,220 130 (1,370 ) (20 ) Amounts reclassified from accumulated other comprehensive loss — — (2,604 ) (2,604 ) Net current period other comprehensive (loss) income $ 1,220 $ 130 $ (3,974 ) $ (2,624 ) Balance at June 30, 2015 $ 249 $ 7 $ (1,963 ) $ (1,707 )

Hedging (Tables)

Hedging (Tables)	6 Months Ended
	Jun. 30, 2016
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 June 30, 2016 As of December 31, 2015 Foreign Currency (in thousands) Euro $ 193,542 $ 103,362 British pound sterling 79,845 78,756 Australian dollar 28,318 27,167 Total foreign currency forward contracts $ 301,705 $ 209,285
Schedule of Foreign Exchange Contracts	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 June 30, 2016 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 9,966 Other liabilities, current portion $ (7,317 ) Other assets 1,604 Other liabilities, excluding current portion (88 ) Total assets $ 11,570 Total liabilities $ (7,405 ) As of December 31, 2015 Assets Liabilities Classification Fair Value Classification Fair Value (in thousands) Prepaid and other current assets $ 5,161 Other liabilities, current portion $ (769 ) Other assets 605 Other liabilities, excluding current portion (132 ) Total assets $ 5,766 Total liabilities $ (901 )
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 June 30, 2016 Gross Amounts Recognized Gross Amounts Offset Gross Amounts Presented Gross Amounts Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 11,570 $ — $ 11,570 $ (7,405 ) $ 4,165 Total liabilities $ (7,405 ) $ — $ (7,405 ) $ 7,405 $ — As of December 31, 2015 Gross Amounts Recognized Gross Amounts Offset Gross Amounts Presented Gross Amounts Not Offset Legal Offset Foreign currency forward contracts (in thousands) Total assets $ 5,766 $ — $ 5,766 $ (901 ) $ 4,865 Total liabilities $ (901 ) $ — $ (901 ) $ 901 $ —

Inventories (Tables)

Inventories (Tables)	6 Months Ended
	Jun. 30, 2016
Inventory Disclosure [Abstract]
Schedule of Inventories by Type	Inventories consisted of the following: As of June 30, 2016 As of December 31, 2015 (in thousands) Raw materials $ 5,408 $ 8,696 Work-in-process 45,807 40,695 Finished goods 15,374 7,816 Total $ 66,589 $ 57,207

Stock-based Compensation Expe33

Stock-based Compensation Expense (Tables)	6 Months Ended
	Jun. 30, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-based compensation expense by line item	During the three and six months ended June 30, 2016 and 2015 , the Company recognized the following stock-based compensation expense: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Stock-based compensation expense by type of award: Stock options $ 31,826 $ 37,687 $ 58,086 $ 66,646 Restricted stock and restricted stock units 29,608 24,902 57,141 52,071 ESPP share issuances 1,436 1,825 3,960 3,965 Less stock-based compensation expense capitalized to inventories (928 ) (1,153 ) (1,773 ) (2,037 ) Total stock-based compensation included in costs and expenses $ 61,942 $ 63,261 $ 117,414 $ 120,645 Stock-based compensation expense by line item: Research and development expenses $ 40,640 $ 41,632 $ 75,088 $ 79,849 Sales, general and administrative expenses 21,302 21,629 42,326 40,796 Total stock-based compensation included in costs and expenses $ 61,942 $ 63,261 $ 117,414 $ 120,645
Unrecognized stock-based compensation expense, net of estimated forfeitures	The following table sets forth the Company's unrecognized stock-based compensation expense, net of estimated forfeitures, by type of award and the weighted-average period over which that expense is expected to be recognized: As of June 30, 2016 Unrecognized Expense, Weighted-average (in thousands) (in years) Type of award: Stock options $ 176,251 2.66 Restricted stock and restricted stock units $ 201,858 2.57 ESPP share issuances $ 5,546 0.64
Stock options outstanding and exercisable	The following table summarizes information about stock options outstanding and exercisable at June 30, 2016 : Options Outstanding Options Exercisable Range of Exercise Prices Number Weighted-average Weighted-average Number Weighted-average (in thousands) (in years) (per share) (in thousands) (per share) $18.93–$20.00 137 1.61 $ 18.93 137 $ 18.93 $20.01–$40.00 1,964 3.45 $ 34.24 1,962 $ 34.23 $40.01–$60.00 2,066 6.07 $ 48.14 1,657 $ 48.66 $60.01–$80.00 1,368 7.62 $ 75.90 734 $ 75.39 $80.01–$100.00 3,555 8.60 $ 90.68 1,080 $ 88.91 $100.01–$120.00 1,644 8.57 $ 109.32 500 $ 109.27 $120.01–$134.69 1,497 9.05 $ 130.61 420 $ 129.84 Total 12,231 7.21 $ 79.37 6,490 $ 63.32

Restructuring Liabilities (Tabl

Restructuring Liabilities (Tables)	6 Months Ended
	Jun. 30, 2016
Kendall Restructuring
Restructuring Cost and Reserve [Line Items]
Activity related to restructuring liability	The activities related to the restructuring liability for the three and six months ended June 30, 2016 and 2015 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Liability, beginning of the period $ 7,224 $ 9,506 $ 7,944 $ 11,596 Cash payments (3,833 ) (2,584 ) (7,764 ) (6,569 ) Cash received from subleases 3,008 2,799 6,016 5,275 Restructuring expense (income) (11 ) 203 192 (378 ) Liability, end of the period $ 6,388 $ 9,924 $ 6,388 $ 9,924
Fan Pier Move Restructuring
Restructuring Cost and Reserve [Line Items]
Activity related to restructuring liability	The activities related to the restructuring liability for the three and six months ended June 30, 2016 and 2015 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Liability, beginning of the period $ 5,449 $ 11,137 $ 5,964 $ 33,390 Cash payments (3,096 ) (3,095 ) (6,252 ) (22,351 ) Cash received from subleases 2,361 — 4,769 — Restructuring expense (income) 149 975 382 (2,022 ) Liability, end of the period $ 4,863 $ 9,017 $ 4,863 $ 9,017
Other Restructuring
Restructuring Cost and Reserve [Line Items]
Activity related to restructuring liability	The activities related to the Company's other restructuring liabilities for the three and six months ended June 30, 2016 and 2015 were as follows: Three Months Ended June 30, Six Months Ended June 30, 2016 2015 2016 2015 (in thousands) Liability, beginning of the period $ 1,262 $ 845 $ 1,450 $ 869 Cash payments (234 ) (893 ) (673 ) (1,223 ) Restructuring expense 205 950 456 1,256 Liability, end of the period $ 1,233 $ 902 $ 1,233 $ 902

Basis of Presentation and Acc35

Basis of Presentation and Accounting Policies (Details)	6 Months Ended
	Jun. 30, 2016segment
Accounting Policies [Abstract]
Number of operating segments	1

Product Revenues, Net (Details)

Product Revenues, Net (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2016USD ($)
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	$ 49,296
Provision related to current period sales	80,509
Adjustments related to prior period sales	(1,989)
Credits/payments made	(58,773)
Balance at June 30, 2016	69,043
Trade Allowances
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	2,089
Provision related to current period sales	9,935
Adjustments related to prior period sales	(77)
Credits/payments made	(9,762)
Balance at June 30, 2016	2,185
Rebates, Chargebacks and Discounts
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	44,669
Provision related to current period sales	65,066
Adjustments related to prior period sales	(1,712)
Credits/payments made	(44,113)
Balance at June 30, 2016	63,910
Product Returns
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	1,228
Provision related to current period sales	1,288
Adjustments related to prior period sales	(205)
Credits/payments made	(260)
Balance at June 30, 2016	2,051
Other Incentives
Product Revenue Allowance and Reserve [Roll Forward]
Balance at December 31, 2015	1,310
Provision related to current period sales	4,220
Adjustments related to prior period sales	5
Credits/payments made	(4,638)
Balance at June 30, 2016	$ 897

Collaborative Arrangement - Cys

Collaborative Arrangement - Cystic Fibrosis Foundation Therapeutics Incorporated (Details) - USD ($)	1 Months Ended	3 Months Ended				6 Months Ended		12 Months Ended
	Apr. 30, 2011	Jun. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2013	Dec. 31, 2012
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative revenues		$ 675,000			$ 611,000	$ 749,000	$ 1,453,000
Cystic Fibrosis Foundation Therapeutics Incorporated
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative funding	$ 75,000,000
Number of years over which funding will be made (in years)	5 years
Collaborative revenues						$ 0	$ 0
Milestone Revenues			$ 13,900,000	$ 13,900,000				$ 9,300,000	$ 9,300,000

Collaborative Arrangements - CR

Collaborative Arrangements - CRISPR Therapeutics AG (Details) - CRISPR Therapeutics	Oct. 26, 2015USD ($)target	Jun. 30, 2016USD ($)
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	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 - Pa

Collaborative Arrangements - Parion Sciences, Inc. (Details) - USD ($)	Jun. 04, 2015	Jun. 30, 2016	Dec. 31, 2015
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
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
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
Intangible assets	$ 255,300,000
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 Coll

Collaborative Arrangements Collaborative Arrangements - 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
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 - Ag

Collaborative Arrangements - Aggregate VIE Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015	Jun. 04, 2015
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Provision for income taxes	$ 18,130	$ 30,131	$ 23,615	$ 30,430
Net (income) loss attributable to noncontrolling interest	(28,374)	32,144	(33,903)	32,242
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Restricted cash and cash equivalents (VIE)	70,513		70,513		$ 78,910
Prepaid expenses and other current assets	56,256		56,256		50,935
Intangible assets	284,340		284,340		284,340
Goodwill	50,384		50,384		50,384
Other assets	14,203		14,203		6,912
Accounts payable	51,302		51,302		74,942
Other current liabilities	275,165		275,165		305,820
Deferred tax liability, net	132,810		132,810		110,439
Other liabilities	30,648		30,648		31,778
Noncontrolling interest	187,491		187,491		153,661
BioAxone Biosciences Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Contingent consideration, liability	28,700		28,700		28,000
Parion Sciences, Inc
Variable Interest Entity, Primary Beneficiary, Does Not Hold Majority Voting Interest, Disclosures [Abstract]
Provision for income taxes	17,500		20,600
Contingent consideration, liability	231,400		231,400		179,000
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	2,835	1,293	3,674	1,579
Provision for income taxes	17,511	29,653	20,573	29,590
(Increase) decrease in fair value of contingent milestone and royalty payments	48,720	(1,198)	58,150	(1,073)
Net (income) loss attributable to noncontrolling interest	(28,374)	32,144	(33,903)	32,242
Variable Interest Entity, Consolidated, Carrying Amount, Assets and Liabilities, Net:
Restricted cash and cash equivalents (VIE)	70,513		70,513		78,910
Prepaid expenses and other current assets	3,001		3,001		3,138
Intangible assets	284,340		284,340		284,340
Goodwill	19,391		19,391		19,391
Other assets	383		383		455
Accounts payable	1,129		1,129		676
Taxes payable	11,723		11,723		24,554
Other current liabilities	7,059		7,059		7,100
Deferred tax liability, net	132,810		132,810		110,438
Other liabilities	310		310		300
Noncontrolling interest	187,491		187,491		$ 153,661
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	320	423	750	548
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	$ 48,400	$ (1,621)	$ 57,400	$ (1,621)

Collaborative Arrangements Co42

Collaborative Arrangements Collaborative Arrangements - Janssen Pharmaceuticals, Inc. (Details) - Janssen - USD ($) $ in Millions	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2014
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Up-front payment					$ 35
Reimbursement for development and commercialization of compounds	$ 4.3	$ 7.1	$ 7.8	$ 14.7
Time period of notice required to terminate			6 months

Collaborative Arrangements Co43

Collaborative Arrangements Collaborative Arrangements - Moderna Therapeutics, Inc. (Details) - Subsequent Event - Moderna Therapeutics, Inc. $ in Millions	1 Months Ended
	Jul. 31, 2016USD ($)
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative Arrangement Up-front License Fee	$ 20
Collaborative Arrangement, Investment in Collaborative Partner, Amount	20
Collaborative arrangement development and regulatory potential milestone payments maximum	275
Collaborative Arrangement Approval and Reimbursement Milestones	$ 220

Earnings Per Share (Details)

Earnings Per Share (Details) - shares shares in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	12,231	11,933	12,231	11,933
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)	3,506	3,355	3,506	3,355

Fair Value Measurements (Detail

Fair Value Measurements (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Level 3
Financial instruments carried at fair value (liability position):
Term loan fair value	$ 296,500
Recurring basis
Financial assets carried at fair value:
Total financial assets	587,836	$ 665,383
Financial instruments carried at fair value (liability position):
Total financial liabilities	(7,405)	(901)
Recurring basis | Money market funds
Financial assets carried at fair value:
Cash equivalents	110,696	199,507
Recurring basis | Commercial paper
Financial assets carried at fair value:
Cash equivalents		34,889
Marketable securities	164,853	99,123
Recurring basis | U.S. Treasury securities
Financial assets carried at fair value:
Marketable securities	33,142
Recurring basis | Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		85,994
Marketable securities	131,900	87,162
Recurring basis | Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		11,533
Marketable securities	135,675	141,409
Recurring basis | Level 1
Financial assets carried at fair value:
Total financial assets	275,738	372,663
Financial instruments carried at fair value (liability position):
Total financial liabilities	0	0
Recurring basis | Level 1 | Money market funds
Financial assets carried at fair value:
Cash equivalents	110,696	199,507
Recurring basis | Level 1 | Commercial paper
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis | Level 1 | U.S. Treasury securities
Financial assets carried at fair value:
Marketable securities	33,142
Recurring basis | Level 1 | Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		85,994
Marketable securities	131,900	87,162
Recurring basis | Level 1 | Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis | Level 2
Financial assets carried at fair value:
Total financial assets	312,098	292,720
Financial instruments carried at fair value (liability position):
Total financial liabilities	(7,405)	(901)
Recurring basis | Level 2 | Money market funds
Financial assets carried at fair value:
Cash equivalents	0	0
Recurring basis | Level 2 | Commercial paper
Financial assets carried at fair value:
Cash equivalents		34,889
Marketable securities	164,853	99,123
Recurring basis | Level 2 | U.S. Treasury securities
Financial assets carried at fair value:
Marketable securities	0
Recurring basis | Level 2 | Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis | Level 2 | Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		11,533
Marketable securities	135,675	141,409
Recurring basis | Level 3
Financial assets carried at fair value:
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 assets carried at fair value:
Cash equivalents	0	0
Recurring basis | Level 3 | Commercial paper
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis | Level 3 | U.S. Treasury securities
Financial assets carried at fair value:
Marketable securities	0
Recurring basis | Level 3 | Government-sponsored enterprise securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Recurring basis | Level 3 | Corporate debt securities
Financial assets carried at fair value:
Cash equivalents		0
Marketable securities	0	0
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	9,966	5,161
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis | Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	9,966	5,161
Prepaid and other current assets | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Other Assets | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	1,604	605
Other Assets | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Other Assets | Foreign currency forward contracts | Recurring basis | Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	1,604	605
Other Assets | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0	0
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	(7,317)
Financial instruments carried at fair value (liability position):
Derivative liability current		(769)
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
Financial instruments carried at fair value (liability position):
Derivative liability current		0
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis | Level 2
Financial assets carried at fair value:
Foreign currency forward contracts	(7,317)
Financial instruments carried at fair value (liability position):
Derivative liability current		(769)
Other liabilities, current portion | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
Financial instruments carried at fair value (liability position):
Derivative liability current		0
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis
Financial assets carried at fair value:
Foreign currency forward contracts	(88)
Financial instruments carried at fair value (liability position):
Derivative liability noncurrent		(132)
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis | Level 1
Financial assets carried at fair value:
Foreign currency forward contracts	0
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 assets carried at fair value:
Foreign currency forward contracts	(88)
Financial instruments carried at fair value (liability position):
Derivative liability noncurrent		(132)
Other liabilities, excluding current portion | Foreign currency forward contracts | Recurring basis | Level 3
Financial assets carried at fair value:
Foreign currency forward contracts	0
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	$ 70,200

Marketable Securities (Details)

Marketable Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Summary of cash, cash equivalents and marketable securities
Amortized Cost	$ 1,071,110	$ 1,042,336
Gross Unrealized Gains	351	246
Gross Unrealized Losses	(25)	(120)
Fair Value	1,071,436	1,042,462
Total cash and cash equivalents
Summary of cash, cash equivalents and marketable securities
Amortized Cost	605,866	714,768
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	605,866	714,768
Cash and money market funds
Summary of cash, cash equivalents and marketable securities
Amortized Cost	605,866	582,352
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	605,866	582,352
Government-sponsored enterprise securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost		85,994
Gross Unrealized Gains		0
Gross Unrealized Losses		0
Fair Value		85,994
Commercial paper
Summary of cash, cash equivalents and marketable securities
Amortized Cost		34,889
Gross Unrealized Gains		0
Gross Unrealized Losses		0
Fair Value		34,889
Corporate debt securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost		11,533
Gross Unrealized Gains		0
Gross Unrealized Losses		0
Fair Value		11,533
Total marketable securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	465,244	327,568
Gross Unrealized Gains	351	246
Gross Unrealized Losses	(25)	(120)
Fair Value	465,570	327,694
U.S. Treasury securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	33,138
Gross Unrealized Gains	4
Gross Unrealized Losses	0
Fair Value	33,142
Government-sponsored enterprise securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	131,868	87,176
Gross Unrealized Gains	35	0
Gross Unrealized Losses	(3)	(14)
Fair Value	131,900	87,162
Commercial paper (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	164,575	98,877
Gross Unrealized Gains	278	246
Gross Unrealized Losses	0	0
Fair Value	164,853	99,123
Corporate debt securities (due within 1 year)
Summary of cash, cash equivalents and marketable securities
Amortized Cost	135,663	141,515
Gross Unrealized Gains	34	0
Gross Unrealized Losses	(22)	(106)
Fair Value	$ 135,675	$ 141,409

Accumulated Other Comprehensi47

Accumulated Other Comprehensive (Loss) Income Accumulated Other Comprehensive (Loss) Income (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			$ 1,824	$ 917
Other comprehensive (loss) income before reclassifications			(3,154)	(20)
Amounts reclassified from accumulated other comprehensive loss			(2,060)	(2,604)
Total changes in other comprehensive loss	$ 1,509	$ (2,498)	(5,214)	(2,624)
Balance at balance sheet date	(3,390)	(1,707)	(3,390)	(1,707)
Foreign Currency Translation Adjustment
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			(2,080)	(971)
Other comprehensive (loss) income before reclassifications			(5,201)	1,220
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			(5,201)	1,220
Balance at balance sheet date	(7,281)	249	(7,281)	249
Unrealized Holding Gains (Losses) on Marketable Securities
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			126	(123)
Other comprehensive (loss) income before reclassifications			200	130
Amounts reclassified from accumulated other comprehensive loss			0	0
Total changes in other comprehensive loss			200	130
Balance at balance sheet date	326	7	326	7
Unrealized Gains on Foreign Currency Forward Contracts, net of tax
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Balance at balance sheet date			3,778	2,011
Other comprehensive (loss) income before reclassifications			1,847	(1,370)
Amounts reclassified from accumulated other comprehensive loss			(2,060)	(2,604)
Total changes in other comprehensive loss			(213)	(3,974)
Balance at balance sheet date	$ 3,565	$ (1,963)	$ 3,565	$ (1,963)

Hedging (Details)

Hedging (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Dec. 31, 2015
Offsetting Derivative Assets [Abstract]
Gross Amounts Recognized	$ 11,570	$ 5,766
Gross Amounts Offset	0	0
Gross Amounts Presented	11,570	5,766
Gross Amounts Not Offset	(7,405)	(901)
Legal Offset	4,165	4,865
Offsetting Derivative Liabilities [Abstract]
Gross Amounts Recognized	(7,405)	(901)
Gross Amounts Offset	0	0
Gross Amounts Presented	(7,405)	(901)
Gross Amounts Not Offset	7,405	901
Legal Offset	0	0
Prepaid and other current assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	9,966	5,161
Other liabilities, current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(7,317)	(769)
Other assets
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - assets	1,604	605
Other liabilities, excluding current portion
Foreign Currency Cash Flow Hedge Derivative at Fair Value [Abstract]
Fair Value - liabilities	(88)	(132)
Designated as hedging instrument | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	301,705	209,285
Designated as hedging instrument | Euro | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	193,542	103,362
Designated as hedging instrument | British pound sterling | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	79,845	78,756
Designated as hedging instrument | Australian dollar | Foreign Currency Forward Contract | Cash Flow Hedging
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 28,318	$ 27,167
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 Inven

Inventories - Schedule of Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Inventory Disclosure [Abstract]
Raw materials	$ 5,408	$ 8,696
Work-in-process	45,807	40,695
Finished goods	15,374	7,816
Total	$ 66,589	$ 57,207

Intangible Assets and Goodwill

Intangible Assets and Goodwill (Details) - USD ($) $ in Thousands	1 Months Ended
	Oct. 31, 2014	Jun. 30, 2016	Dec. 31, 2015	Jun. 04, 2015
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]
Intangible assets		284,340	284,340
Goodwill		$ 19,391	$ 19,391
Variable Interest Entity, Primary Beneficiary | BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
In-process research and development intangible asset	$ 29,000
Indefinite-lived Intangible Assets | Variable Interest Entity, Primary Beneficiary | Parion Sciences, Inc
Indefinite-Lived Intangible Assets [Line Items]
Fair value inputs, discount rate (percent)	7.10%
Indefinite-lived Intangible Assets | Variable Interest Entity, Primary Beneficiary | BioAxone Biosciences Inc
Indefinite-Lived Intangible Assets [Line Items]
Fair value inputs, discount rate (percent)	7.50%

Long-term Obligations - Fan Pie

Long-term Obligations - Fan Pier Leases (Details) $ in Thousands, ft² in Millions	12 Months Ended
	Dec. 31, 2011ft²leasebuilding	Jun. 30, 2016USD ($)	Dec. 31, 2015USD ($)
Property, Plant and Equipment [Line Items]
Property and equipment, net		$ 690,607	$ 697,715
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		472,800	473,000
Fan Pier Leases | Construction in progress
Property, Plant and Equipment [Line Items]
Property and equipment, net		$ 495,700	$ 502,300

Long-term Obligations - San Die

Long-term Obligations - San Diego Lease (Details) - San Diego Lease ft² in Thousands, $ in Millions	Dec. 02, 2015USD ($)ft²term_extension
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

Long-term Obligations - Term Lo

Long-term Obligations - Term Loan (Details) - USD ($)	1 Months Ended
	Oct. 31, 2015	Jul. 31, 2014	Jun. 30, 2016	Dec. 31, 2015
Senior Secured Term Loan
Debt Instrument [Line Items]
Face amount of term loan		$ 300,000,000
Interest rate, stated percentage		7.20%
Contingent interest rate (percent)		6.20%
Amount of principal repayment on quarterly installment payments from October 1, 2016 through maturity	$ 75,000,000
Debt instrument, repayment provision, period over which present value of interest payments is determined (in years)	2 years
Unamortized discount on term loan		$ 5,300,000	$ 3,400,000	$ 4,600,000
Senior Secured Term Loan Facility
Debt Instrument [Line Items]
Maximum borrowing capacity		$ 200,000,000
Minimum | Senior Secured Term Loan | LIBOR
Debt Instrument [Line Items]
Basis spread on variable rate (percent)		5.00%

Stock-based Compensation Expe54

Stock-based Compensation Expense - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Stock-based compensation expense:
Less stock-based compensation expense capitalized to inventories	$ (928)	$ (1,153)	$ (1,773)	$ (2,037)
Total stock-based compensation included in costs and expenses	61,942	63,261	117,414	120,645
Stock options
Stock-based compensation expense:
Stock-based compensation expense by type of award:	31,826	37,687	58,086	66,646
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	176,251		$ 176,251
Weighted-average recognition period (in years)			2 years 7 months 28 days
Restricted stock and restricted stock units
Stock-based compensation expense:
Stock-based compensation expense by type of award:	29,608	24,902	$ 57,141	52,071
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	201,858		$ 201,858
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:	1,436	1,825	$ 3,960	3,965
Type of award:
Unrecognized Expense, Net of Estimated Forfeitures	5,546		$ 5,546
Weighted-average recognition period (in years)			7 months 21 days
Research and development expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	40,640	41,632	$ 75,088	79,849
Sales, general and administrative expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	$ 21,302	$ 21,629	$ 42,326	$ 40,796

Stock-based Compensation Expe55

Stock-based Compensation Expense - Stock Options Outstanding and Exercisable (Details) shares in Thousands	6 Months Ended
	Jun. 30, 2016$ / sharesshares
Share-based Compensation Arrangement by Share-based Payment Award
Exercise price range, options outstanding (in shares) | shares	12,231
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 2 months 16 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 79.37
Exercise price range, options exercisable (in shares) | shares	6,490
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 63.32
$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
Exercise price range, options outstanding (in shares) | shares	137
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	1 year 7 months 10 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 18.93
Exercise price range, options exercisable (in shares) | shares	137
Exercise price range, options exercisable, weighted-average exercise price (in dollars 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	1,964
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	3 years 5 months 12 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 34.24
Exercise price range, options exercisable (in shares) | shares	1,962
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 34.23
$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	2,066
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	6 years 26 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 48.14
Exercise price range, options exercisable (in shares) | shares	1,657
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 48.66
$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	1,368
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 7 months 13 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 75.90
Exercise price range, options exercisable (in shares) | shares	734
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 75.39
$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	3,555
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 7 months 6 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 90.68
Exercise price range, options exercisable (in shares) | shares	1,080
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 88.91
$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	1,644
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 6 months 26 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 109.32
Exercise price range, options exercisable (in shares) | shares	500
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 109.27
$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	1,497
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 18 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 130.61
Exercise price range, options exercisable (in shares) | shares	420
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 129.84

Other Arrangements (Details)

Other Arrangements (Details) - USD ($)	12 Months Ended
	Dec. 31, 2008	Jun. 30, 2016
Sale of HIV Protease Inhibitor Royalty Stream
Gross proceeds from sale of royalty rights receivable from GlaxoSmithKline	$ 160,000,000
Deferred revenue royalty purchase agreement		$ 18,900,000

Income Taxes (Details)

Income Taxes (Details) - USD ($)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes	$ 18,130,000	$ 30,131,000	$ 23,615,000	$ 30,430,000
Unrecognized tax benefits	400,000		400,000		$ 400,000
Income taxes, interest and penalties accrued	0		0
Income taxes, material interest or penalties related to uncertain tax positions			0		$ 0
Estimated reduction in unrecognized tax benefits in next fiscal year	400,000		400,000
Parion Sciences, Inc
Schedule of Collaborative Arrangement Agreements [Line Items]
Provision for income taxes	$ 17,500,000		$ 20,600,000

Restructuring Liabilities - Nar

Restructuring Liabilities - Narrative (Details) ft² in Thousands	3 Months Ended		12 Months Ended
	Jun. 30, 2015ft²lease	Sep. 30, 2014facility	Dec. 31, 2003
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]
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%

Restructuring Liabilities - Act

Restructuring Liabilities - Activity Related to Restructuring Liability (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Restructuring activities
Restructuring expense (income)	$ 343	$ 2,128	$ 1,030	$ (1,144)
Kendall Restructuring
Restructuring activities
Liability, beginning of the period	7,224	9,506	7,944	11,596
Cash payments	(3,833)	(2,584)	(7,764)	(6,569)
Cash received from subleases	3,008	2,799	6,016	5,275
Restructuring expense (income)	(11)	203	192	(378)
Liability, end of the period	6,388	9,924	6,388	9,924
Fan Pier Move Restructuring
Restructuring activities
Liability, beginning of the period	5,449	11,137	5,964	33,390
Cash payments	(3,096)	(3,095)	(6,252)	(22,351)
Cash received from subleases	2,361	0	4,769	0
Restructuring expense (income)	149	975	382	(2,022)
Liability, end of the period	4,863	9,017	4,863	9,017
Other Restructuring
Restructuring activities
Liability, beginning of the period	1,262	845	1,450	869
Cash payments	(234)	(893)	(673)	(1,223)
Restructuring expense (income)	205	950	456	1,256
Liability, end of the period	$ 1,233	$ 902	$ 1,233	$ 902

Commitments and Contingencies (

Commitments and Contingencies (Details) $ in Millions	Jun. 30, 2016USD ($)
Commitments and Contingencies Disclosure [Abstract]
Restricted cash and cash equivalents	$ 21.9