0000875320-19-000057 | 10-Q | XBRL Viewer | Vertex Pharmaceuticals INC MA

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Cover Page - shares	9 Months Ended
Cover Page - shares	Sep. 30, 2019	Oct. 18, 2019
Cover page.
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2019
Document Transition Report	false
Entity File Number	000-19319
Entity Registrant Name	VERTEX PHARMACEUTICALS INC / MA
Entity Incorporation, State or Country Code	MA
Entity Tax Identification Number	04-3039129
Entity Address, Address Line One	50 Northern Avenue
Entity Address, City or Town	Boston
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02210
City Area Code	617
Local Phone Number	341-6100
Title of 12(b) Security	Common Stock, $0.01 Par Value Per Share
Trading Symbol	VRTX
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		257,149,588
Entity Central Index Key	0000875320
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	Q3
Amendment Flag	false

Condensed Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Revenues:
Revenues	$ 949,828	$ 784,535	$ 2,749,556	$ 2,177,491
Costs and expenses:
Cost of sales	131,914	111,255	362,746	287,250
Research and development expenses	555,948	330,510	1,274,529	978,595
Sales, general and administrative expenses	159,674	137,295	463,221	404,406
Change in fair value of contingent consideration	2,959	0	2,959	0
Restructuring income	0	(174)	0	(188)
Total costs and expenses	850,495	578,886	2,103,455	1,670,063
Income from operations	99,333	205,649	646,101	507,428
Interest income	17,628	10,543	51,319	24,381
Interest expense	(14,548)	(18,686)	(44,253)	(53,727)
Other (expense) income, net	(31,747)	(60,995)	64,802	89,662
Income before provision for income taxes	70,666	136,511	717,969	567,744
Provision for income taxes	13,148	8,055	124,393	5,737
Net income	57,518	128,456	593,576	562,007
Loss (income) attributable to noncontrolling interest	0	290	0	(15,638)
Net income attributable to Vertex	$ 57,518	$ 128,746	$ 593,576	$ 546,369
Net income:
Basic (in dollars per share)	$ 0.22	$ 0.51	$ 2.32	$ 2.15
Diluted (in dollars per share)	$ 0.22	$ 0.50	$ 2.28	$ 2.11
Shares used in per share calculations:
Basic (in shares)	256,946	254,905	256,289	254,096
Diluted (in shares)	260,473	259,788	260,182	258,972
Product revenues, net
Revenues:
Revenues	$ 949,828	$ 782,511	$ 2,747,461	$ 2,170,152
Collaborative and royalty revenues
Revenues:
Revenues	$ 0	$ 2,024	$ 2,095	$ 7,339

Condensed Consolidated Statements of Comprehensive Income - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Net income (loss)	$ 57,518	$ 128,456	$ 593,576	$ 562,007
Changes in other comprehensive income:
Unrealized holding gains on marketable securities, net	64	224	1,111	137
Unrealized gains on foreign currency forward contracts, net of tax of $2.2 million, zero, $5.5 million and $0.5 million, respectively	12,812		6,814
Unrealized gains on foreign currency forward contracts, net of tax of $2.2 million, zero, $5.5 million and $0.5 million, respectively		4,029		29,062
Foreign currency translation adjustment	9,172	659	10,263	6,800
Total changes in other comprehensive income	22,048	4,912	18,188	35,999
Comprehensive income	79,566	133,368	611,764	598,006
Comprehensive loss (income) attributable to noncontrolling interest	0	290	0	(15,638)
Comprehensive income attributable to Vertex	$ 79,566	$ 133,658	$ 611,764	$ 582,368

Condensed Consolidated Statements of Comprehensive Income (Parenthetical) - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Comprehensive Income (Loss), Net of Tax, Including Portion Attributable to Noncontrolling Interest [Abstract]
Unrealized (losses) gains on foreign currency forward contracts, tax	$ 2.2		$ 5.5
Unrealized (losses) gains on foreign currency forward contracts, tax		$ 0.0		$ 0.5

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 3,397,941	$ 2,650,134
Marketable securities	598,390	518,108
Accounts receivable, net	443,315	409,688
Inventories	162,306	124,360
Prepaid expenses and other current assets	175,142	140,819
Total current assets	4,777,094	3,843,109
Property and equipment, net	733,509	812,005
Goodwill	447,525	50,384
Deferred tax assets	1,415,511	1,499,672
Operating lease assets	60,929
Other assets	79,985	40,728
Total assets	7,514,553	6,245,898
Current liabilities:
Accounts payable	92,528	110,987
Accrued expenses	1,173,783	958,899
Other current liabilities	122,583	50,406
Total current liabilities	1,388,894	1,120,292
Long-term finance lease liabilities	541,561
Long-term finance lease liabilities		581,550
Long-term operating lease liabilities	62,978
Long-term advance from collaborator	85,084	82,573
Long-term contingent consideration	175,000	0
Other long-term liabilities	7,642	26,280
Total liabilities	2,261,159	1,810,695
Commitments and contingencies	0	0
Shareholders’ equity:
Preferred stock, $0.01 par value; 1,000 shares authorized; none issued and outstanding	0	0
Common stock, $0.01 par value; 500,000 shares authorized, 257,265 and 255,172 shares issued and outstanding, respectively	2,571	2,546
Additional paid-in capital	7,668,188	7,421,476
Accumulated other comprehensive income	18,847	659
Accumulated deficit	(2,436,212)	(2,989,478)
Total shareholders’ equity	5,253,394	4,435,203
Total liabilities and shareholders’ equity	$ 7,514,553	$ 6,245,898

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2019	Dec. 31, 2018
Statement of Financial Position [Abstract]
Preferred stock, par value (in dollars 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 (in dollars per share)	$ 0.01	$ 0.01
Common stock, shares authorized	500,000,000	500,000,000
Common stock, shares issued	257,265,000	255,172,000
Common stock, shares outstanding	257,265,000	255,172,000

Condensed Consolidated Statements of Shareholders' Equity and Noncontrolling Interest - USD ($) shares in Thousands, $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive (Loss) Income	Accumulated Deficit	Total Vertex Shareholders’ Equity	Noncontrolling Interest
Balance (shares) at Dec. 31, 2017		253,253
Beginning Balance at Dec. 31, 2017	$ 2,042,306	$ 2,512	$ 7,157,362	$ (11,572)	$ (5,119,723)	$ 2,028,579	$ 13,727
Increase (Decrease) in Stockholders' Equity
Other comprehensive income, net of tax	35,999			35,999		35,999
Net income (loss)	562,007				546,369	546,369	15,638
Repurchases of common stock (in shares)		(1,283)
Repurchases of common stock	(211,038)	$ (13)	(211,025)			(211,038)
Issuance of common stock under benefit plans (shares)		3,641
Issuance of common stock under benefit plans	250,420	$ 52	250,368			250,420
Stock-based compensation expense	246,558		246,558			246,558
Other VIE activity	(1,000)						(1,000)
Balance (shares) at Sep. 30, 2018		255,611
Ending Balance at Sep. 30, 2018	2,934,481	$ 2,551	7,443,263	307	(4,540,005)	2,906,116	28,365
Balance (shares) at Jun. 30, 2018		254,883
Beginning Balance at Jun. 30, 2018	2,714,883	$ 2,542	7,357,042	(4,605)	(4,668,751)	2,686,228	28,655
Increase (Decrease) in Stockholders' Equity
Other comprehensive income, net of tax	4,912			4,912		4,912
Net income (loss)	128,456				128,746	128,746	(290)
Repurchases of common stock (in shares)		(515)
Repurchases of common stock	(92,004)	$ (5)	(91,999)			(92,004)
Issuance of common stock under benefit plans (shares)		1,243
Issuance of common stock under benefit plans	92,793	$ 14	92,779			92,793
Stock-based compensation expense	85,441		85,441			85,441
Balance (shares) at Sep. 30, 2018		255,611
Ending Balance at Sep. 30, 2018	2,934,481	$ 2,551	7,443,263	307	(4,540,005)	2,906,116	28,365
Increase (Decrease) in Stockholders' Equity
Cumulative effect adjustment for adoption of new accounting guidance				(24,120)
Balance (shares) at Dec. 31, 2018		255,172
Beginning Balance at Dec. 31, 2018	4,435,203	$ 2,546	7,421,476	659	(2,989,478)	4,435,203	0
Increase (Decrease) in Stockholders' Equity
Other comprehensive income, net of tax	18,188			18,188		18,188
Net income (loss)	593,576				593,576	593,576
Repurchases of common stock (in shares)		(931)
Repurchases of common stock	(167,954)	$ (9)	(167,945)			(167,954)
Issuance of common stock under benefit plans (shares)		3,024
Issuance of common stock under benefit plans	144,557	$ 34	144,523			144,557
Stock-based compensation expense	270,134		270,134			270,134
Balance (shares) at Sep. 30, 2019		257,265
Ending Balance at Sep. 30, 2019	5,253,394	$ 2,571	7,668,188	18,847	(2,436,212)	5,253,394	0
Balance (shares) at Jun. 30, 2019		256,671
Beginning Balance at Jun. 30, 2019	5,069,965	$ 2,565	7,564,331	(3,201)	(2,493,730)	5,069,965	0
Increase (Decrease) in Stockholders' Equity
Other comprehensive income, net of tax	22,048			22,048		22,048
Net income (loss)	57,518				57,518	57,518
Repurchases of common stock (in shares)		(71)
Repurchases of common stock	(12,105)		(12,105)			(12,105)
Issuance of common stock under benefit plans (shares)		665
Issuance of common stock under benefit plans	30,012	$ 6	30,006			30,012
Stock-based compensation expense	85,956		85,956			85,956
Balance (shares) at Sep. 30, 2019		257,265
Ending Balance at Sep. 30, 2019	$ 5,253,394	$ 2,571	$ 7,668,188	$ 18,847	$ (2,436,212)	$ 5,253,394	$ 0

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018
Cash flows from operating activities:
Net income	$ 593,576	$ 562,007
Adjustments to reconcile net income to net cash provided by operating activities:
Stock-based compensation expense	268,898	246,104
Depreciation expense	80,685	53,594
Change in fair value of contingent consideration	2,959	0
Write-downs of inventories to net realizable value	8,650	13,089
Deferred income taxes	94,175	3,595
Unrealized gains on equity securities	(68,862)	(88,217)
Other non-cash items, net	(12,674)	10,701
Changes in operating assets and liabilities:
Accounts receivable, net	(41,444)	(75,167)
Inventories	(45,280)	(24,461)
Prepaid expenses and other assets	(23,709)	31,797
Accounts payable	(12,210)	23,023
Accrued expenses	255,699	167,647
Other liabilities	22,859	31,996
Net cash provided by operating activities	1,123,322	955,708
Cash flows from investing activities:
Purchases of available-for-sale debt securities	(381,739)	(329,367)
Maturities of available-for-sale debt securities	375,145	308,406
Payment to acquire business, net of cash acquired	(245,824)	0
Expenditures for property and equipment	(58,690)	(79,803)
Investment in equity securities	(27,219)	(60,490)
Net cash used in investing activities	(338,327)	(161,254)
Cash flows from financing activities:
Issuances of common stock under benefit plans	144,630	245,754
Repurchases of common stock	(155,953)	(207,038)
Payments on finance leases	(28,879)
Advance from collaborator	10,000	7,500
Repayments of advanced funding	(4,316)	(3,714)
Proceeds related to capital lease and construction financing lease obligations	1,002	12,983
Payments on capital lease and construction financing lease obligations		(24,658)
Other financing activities	(1,132)	(1,000)
Net cash (used in) provided by financing activities	(34,648)	29,827
Effect of changes in exchange rates on cash	(4,009)	(4,756)
Net increase in cash and cash equivalents	746,338	819,525
Cash, cash equivalents and restricted cash—beginning of period	2,658,253	1,667,526
Cash, cash equivalents and restricted cash—end of period	3,404,591	2,487,051
Supplemental disclosure of cash flow information:
Cash paid for interest	41,704	50,017
Cash paid for income taxes	22,838	10,316
Capitalization of costs related to construction financing lease obligation	0	3,389
Issuances of common stock from employee benefit plans receivable	13	5,509
Accrued share repurchase liability	$ 12,001	$ 4,000

Basis of Presentation and Accounting Policies

9 Months Ended

Sep. 30, 2019

Accounting Policies [Abstract]

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 the Company and its wholly-owned subsidiaries. The Company's condensed consolidated financial statements for the interim period ended September 30, 2018 also include the financial results of BioAxone Biosciences, Inc. (“BioAxone”), a variable interest entity (“VIE”) that the Company consolidated from 2014 through December 31, 2018. All material intercompany balances and transactions have been eliminated. The Company operates in one segment, pharmaceuticals. The Company has reclassified certain items from the prior year’s condensed consolidated financial statements to conform to the current year’s presentation.

Certain information and footnote disclosures normally included in the Company’s 2018 Annual Report on Form 10-K 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 September 30, 2019 and 2018.

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, 2018, which are contained in the Company’s 2018 Annual Report on Form 10-K.

Use of Estimates

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, research and development expenses, goodwill, intangible assets, deferred tax asset valuation allowances, fair value of contingent consideration and the provision for 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.

Recently Adopted Accounting Standards

Leases

In 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) (“ASC 842”), which amends a number of aspects of lease accounting and requires entities to recognize right-of-use assets and liabilities on the balance sheet. ASC 842 became effective on January 1, 2019. The Company has finalized its review of its portfolio of existing leases and current accounting policies and has concluded that the amended guidance results in the recognition of additional assets and corresponding liabilities on its balance sheets. The Company also has finalized changes to its controls to address the adoption and ongoing lease accounting and related disclosure requirements of the new standard.

Until December 31, 2018, the Company applied build-to-suit accounting and was the deemed owner of its leased corporate headquarters in Boston and research site in San Diego, for which it was recognizing depreciation expense over the buildings’ useful lives and imputed interest on the corresponding construction financing lease obligations. Under the amended guidance that became effective January 1, 2019, the Company accounts for these buildings as finance leases, resulting in increased depreciation expense over the respective lease terms of approximately 15 years, which are significantly shorter than the buildings’ useful lives of 40 years. The Company also expects a reduction in its imputed interest expense in the initial years of each finance lease term.

In July 2018, the FASB issued ASU No. 2018-11, Leases (Topic 842): Targeted Improvements (“ASU 2018-11”), which offered a transition option to entities adopting ASC 842. Under ASU 2018-11, entities could elect to apply ASC 842 using a modified-retrospective adoption approach resulting in a cumulative effect adjustment to accumulated deficit at the beginning of the year in which the new lease standard is adopted, rather than adjustments to the earliest comparative period presented in their financial statements. The Company adopted ASC 842 using the modified-retrospective method. As of January 1, 2019, the Company recorded a cumulative effect adjustment to increase its “Accumulated deficit” by $40.3 million related to the adjustments to its build-to-suit leases described in the previous paragraph.

The Company elected the package of transition practical expedients for leases that commenced prior to January 1, 2019, allowing it not to reassess (i) whether any expired or existing contracts contain leases, (ii) the lease classification for any expired or existing leases and (iii) the initial indirect costs for any existing leases.

Additionally, the Company recorded, upon adoption of ASC 842 on January 1, 2019, operating lease assets of $61.7 million and corresponding liabilities of $71.9 million related to its real estate leases that are not treated as finance leases under ASC 842. The difference between these assets and liabilities is primarily attributable to prepaid or accrued lease payments. The Company also reclassified amounts that were recorded as “Capital lease obligations, current portion” and “Capital lease obligations, excluding current portion” as of December 31, 2018 to “Other current liabilities” and “Long-term finance lease liabilities,” respectively, on January 1, 2019. These adjustments had no impact on the Company’s condensed consolidated statement of operations and had no impact on the Company’s accumulated deficit.

The cumulative effect of applying ASC 842 on the Company’s condensed consolidated balance sheet as of January 1, 2019 was as follows:



	Balance as of						Balance as of
	December 31, 2018 ^			Adjustments			January 1, 2019
Assets	(in thousands)
Prepaid expenses and other current assets	$	140,819		$	(2,930	)	$	137,889
Property and equipment, net	812,005			(53,920		)	758,085
Deferred tax assets	1,499,672			11,236			1,510,908
Operating lease assets	—			61,674			61,674
Total assets	$	6,245,898		$	16,060		$	6,261,958
Liabilities and Shareholders’ Equity
Capital lease obligations, current portion	$	9,817		$	(9,817	)	$	—
Other current liabilities	40,589			34,304			74,893
Capital lease obligations, excluding current portion	19,658			(19,658		)	—
Construction financing lease obligation, excluding current portion	561,892			(561,892		)	—
Long-term finance lease liabilities	—			569,487			569,487
Long-term operating lease liabilities	—			64,849			64,849
Other long-term liabilities	26,280			(20,903		)	5,377
Accumulated deficit	(2,989,478		)	(40,310		)	(3,029,788		)
Total liabilities and shareholders’ equity	$	6,245,898		$	16,060		$	6,261,958
^ As reported in the Company’s 2018 Annual Report on Form 10-K.

Please refer to Note K, “Leases,” for further information regarding the Company’s leases as well as certain disclosures required by ASC 842.

Derivatives and Hedging

In 2017, the FASB issued ASU 2017-12, Derivatives and Hedging (Topic 815) (“ASU 2017-12”), which helps simplify certain aspects of hedge accounting and enables entities to more accurately present their risk management activities in their financial statements. ASU 2017-12 became effective January 1, 2019. The adoption of ASU 2017-12 did not have a significant effect on the Company’s condensed consolidated financial statements.

Recently Issued Accounting Standards

Internal-Use Software

In 2018, the FASB issued ASU 2018-15, Intangibles—Goodwill and Other—Internal-Use Software (Subtopic 350-40): Customer’s Accounting for Implementation Costs Incurred in a Cloud Computing Arrangement That Is a Service Contract (“ASU 2018-15”), which clarifies the accounting for implementation costs in cloud computing arrangements. ASU 2018-15 is effective on January 1, 2020. Early adoption is permitted. The Company currently is evaluating the impact the adoption of ASU 2018-15 may have on its condensed consolidated financial statements.

Fair Value Measurement

In 2018, the FASB issued ASU 2018-13, Fair Value Measurement (Topic 820): Disclosure Framework-Changes to the Disclosure Requirements for Fair Value Measurement (“ASU 2018-13”), which modifies the disclosure requirements for fair value measurements. ASU 2018-13 is effective on January 1, 2020. Early adoption is permitted. The Company currently is evaluating the impact the adoption of ASU 2018-13 may have on its disclosures.

Credit Losses

In 2016, the FASB issued ASU 2016-13, Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments (“ASU 2016-13”), which requires entities to record expected credit losses for certain financial instruments, including trade receivables, as an allowance that reflects the entity's current estimate of credit losses expected to be incurred. For available-for-sale debt securities in unrealized loss positions, ASU 2016-13 requires allowances to be recorded instead of reducing the amortized cost of the investment. ASU 2016-13 is effective on January 1, 2020. Early adoption is permitted. The Company currently is evaluating the impact the adoption of ASU 2016-13 may have on its condensed 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 Company’s 2018 Annual Report on Form 10-K.

Summary of Significant Accounting Policies

The Company’s significant accounting policies are described in Note A, “Nature of Business and Accounting Policies,” in its 2018 Annual Report on Form 10-K. The Company is disclosing changes in its accounting policies related to guidance that became effective January 1, 2019 in this Quarterly Report on Form 10-Q. Specifically, the Company has included its policy pursuant to its adoption of ASC 842 below.

Leases

At the inception of an arrangement, the Company determines whether the arrangement contains a lease. If a lease is identified in an arrangement, the Company recognizes a right-of-use asset and liability on its balance sheet and determines whether the lease should be classified as a finance or operating lease. The Company does not recognize assets or liabilities for leases with lease terms of less than 12 months.

A lease qualifies as a finance lease if any of the following criteria are met at the inception of the lease: (i) there is a transfer of ownership of the leased asset to the Company by the end of the lease term, (ii) the Company holds an option to purchase the leased asset that it is reasonably certain to exercise, (iii) the lease term is for a major part of the remaining economic life of the leased asset, (iv) the present value of the sum of lease payments equals or exceeds substantially all of the fair value of the leased asset, or (v) the nature of the leased asset is specialized to the point that it is expected to provide the lessor no alternative use at the end of the lease term. All other leases are recorded as operating leases.

Finance and operating lease assets and liabilities are recognized at the lease commencement date based on the present value of the lease payments over the lease term using the discount rate implicit in the lease. If the rate implicit is not readily determinable, the Company utilizes its incremental borrowing rate at the lease commencement date. Operating lease assets are further adjusted for prepaid or accrued lease payments. Operating lease payments are expensed using the straight-line method as an operating expense over the lease term. Finance lease assets are amortized to depreciation expense using the

straight-line method over the shorter of the useful life of the related asset or the lease term. Finance lease payments are bifurcated into (i) a portion that is recorded as imputed interest expense and (ii) a portion that reduces the finance liability associated with the lease.

The Company does not separate lease and non-lease components when determining which lease payments to include in the calculation of its lease assets and liabilities. Variable lease payments are expensed as incurred. If a lease includes an option to extend or terminate the lease, the Company reflects the option in the lease term if it is reasonably certain it will exercise the option.

Finance leases are recorded in “Property and equipment, net,” “Other current liabilities” and “Long-term finance lease liabilities” on the Company’s condensed consolidated balance sheet. Operating leases are recorded in “Operating lease assets,” “Other current liabilities” and “Long-term operating lease liabilities” on the Company’s condensed consolidated balance sheet.

Revenue Recognition

9 Months Ended

Sep. 30, 2019

Revenue from Contract with Customer [Abstract]

Revenue Recognition

Disaggregation of Revenue

Revenues by Product

Product revenues, net consisted of the following:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2019		2018		2019		2018
	(in thousands)
SYMDEKO/SYMKEVI	$	403,714	$	254,919	$	1,085,821	$	474,601
ORKAMBI	296,711		281,859		906,159		947,186
KALYDECO	249,403		245,733		755,481		748,365
Total product revenues, net	$	949,828	$	782,511	$	2,747,461	$	2,170,152

Revenues by Geographic Location

Net product revenues are attributed to countries based on the location of the customer. Collaborative and royalty revenues are attributed to countries based on the location of the Company’s subsidiary associated with the collaborative arrangement related to such revenues. Total revenues from external customers and collaborators by geographic region consisted of the following:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2019		2018		2019		2018
	(in thousands)
United States	$	710,323	$	620,485	$	2,052,044	$	1,687,963
Outside of the United States
Europe	184,845		132,876		532,809		400,685
Other	54,660		31,174		164,703		88,843
Total revenues outside of the United States	239,505		164,050		697,512		489,528
Total revenues	$	949,828	$	784,535	$	2,749,556	$	2,177,491

In the three and nine months ended September 30, 2019 and 2018, revenues attributable to Germany contributed the largest amount to the Company’s European revenues.

French Early Access Programs

In 2015, the Company began distributing ORKAMBI through early access programs in France and it continues to be engaged in ongoing discussions regarding the price for ORKAMBI in France. The Company expects that the difference between the amounts it has collected to date based on the invoiced price and the agreed-upon price for ORKAMBI in France will be returned to the French government.

Pursuant to the revenue recognition accounting guidance that was applicable until December 31, 2017, the Company’s ORKAMBI net product revenues for 2015, 2016 and 2017 did not include any net product revenues from sales of ORKAMBI in France because the price was not fixed or determinable at the time of delivery. Upon adopting ASU 2014-09, Revenues from Contracts with Customers (Topic 606), in the first quarter of 2018, the Company began recognizing net product revenues in France based on a transaction price that reflects its estimate of consideration it expects to retain that will not be subject to a significant reversal in amounts recognized. The Company’s refund liability representing the difference between the amounts the Company has collected from the French government and the transaction price is classified as “Accrued expenses” on the Company’s condensed consolidated balance sheets. If the Company’s estimate regarding the amounts it will receive for ORKAMBI supplied pursuant to these early access programs changes, the Company will reflect the effect of the change in estimate in “Product revenues, net” in the period in which the change in estimate occurs.

Contract Liabilities

The Company recorded contract liabilities of $50.2 million and $24.9 million as of September 30, 2019 and December 31, 2018, respectively, related to annual contracts with government-owned and supported customers in international markets that limit the amount of annual reimbursement the Company can receive. Upon exceeding the annual reimbursement amount, products are provided free of charge, which is a material right. These contracts include upfront payments and fees. The Company defers a portion of the consideration received for shipments made up to the annual reimbursement limit as “Other current liabilities.” The deferred amount is recognized as revenue when the free products are shipped. The Company’s product revenue contracts include performance obligations that are one year or less.

In the majority of international markets in which the Company has a contract with an annual reimbursement limit, the annual period associated with the contract is the same as the Company’s fiscal year, resulting in no contract liability balance at the end of the year and no revenues recognized in the current year related to performance obligations satisfied in previous years. Several of the Company’s contract liabilities relate to contracts with annual reimbursement limits in international markets in which the annual period associated with the contract is not the same as the Company’s fiscal year. In these markets, the Company recognizes revenues related to performance obligations satisfied in previous years; however, these amounts are not material to the Company’s financial statements and do not relate to any performance obligations that were satisfied more than 12 months prior to the beginning of the current year.

Collaborative Arrangements and Acquisitions

9 Months Ended

Sep. 30, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Collaborative Arrangements and Acquisitions

The Company has entered into numerous agreements pursuant to which it collaborates with third parties on research, development and commercialization programs, including in-license and out-license agreements. In addition, the Company periodically engages in acquisitions of entities and/or assets.

The Company’s in-license and out-license agreements and acquisitions that had a significant impact on its financial statements for the three and nine months ended September 30, 2019 and 2018, or were new during the three and nine months ended September 30, 2019, are described below. Additional in-license and out-license agreements and acquisitions were described in Note B, “Collaborative Arrangements and Acquisitions,” of the Company’s 2018 Annual Report on Form 10-K.

In-license Agreements

The Company has entered into a number of license agreements in order to advance and obtain access to technologies and services related to its research and early-development activities. The Company is generally required to make an upfront payment upon execution of the license agreement; development, regulatory and commercialization milestones payments upon the achievement of certain product research, development and commercialization objectives; and royalty payments on future sales, if any, of commercial products resulting from the collaboration.

Pursuant to the terms of its in-license agreements, the Company’s collaborators lead the discovery efforts and the Company leads all preclinical, development and commercialization activities associated with the advancement of any drug candidates and funds all expenses unless otherwise described below.

The Company typically can terminate its in-license agreements by providing advance notice to its collaborators; the required length of notice is dependent on whether any product developed under the license agreement has received marketing approval. The Company’s license agreements may be terminated by either party for a material breach by the other, subject to notice and cure provisions. Unless earlier terminated, these license agreements generally remain in effect until the date on which the royalty term and all payment obligations with respect to all products in all countries have expired.

CRISPR Therapeutics AG

In 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 had the exclusive right to license certain CRISPR-Cas9-based targets. In the fourth quarter of 2019, the Company paid an aggregate of $30.0 million in connection with its election to exclusively license three CRISPR-Cas9-based targets, including cystic fibrosis, pursuant to the CRISPR Agreement. For these three targets, the Company leads all development and global commercialization activities and CRISPR has the potential to receive up to an additional $410.0 million in development, regulatory and commercial milestones as well as royalties on net product sales.

In 2017, the Company entered into a co-development and co-commercialization agreement with CRISPR pursuant to the terms of the CRISPR Agreement, under which the Company and CRISPR are co-developing and will co-commercialize CTX001 (the “CTX001 Co-Co Agreement”) for the treatment of hemoglobinopathy, including treatments for sickle cell disease and beta thalassemia. As part of the collaboration, the Company and CRISPR share equally all development costs and potential worldwide revenues related to potential hemoglobinopathy treatments, including treatments for beta thalassemia and sickle cell disease. The Company concluded that the CTX001 Co-Co Agreement is a cost-sharing arrangement, which results in the net impact of the arrangement being recorded in “Research and development expenses” in its condensed consolidated statements of operations. During the three and nine months ended September 30, 2019, the net expense related to the CTX001 Co-Co Agreement was $7.7 million and $22.3 million, respectively. During the three and nine months ended September 30, 2018, the net expense related to the CTX001 Co-Co Agreement was $5.2 million and $14.1 million, respectively.

In June 2019, the Company entered into a separate strategic collaboration and license agreement (the “CRISPR DMD/DM1 Agreement”) with CRISPR, which became effective in July 2019. Pursuant to this agreement, Vertex received an exclusive worldwide license to CRISPR’s existing and future intellectual property for duchenne muscular dystrophy (“DMD”) and myotonic dystrophy type 1 (“DM1”) and the Company made an upfront payment of $175.0 million to CRISPR. The Company concluded that it did not have any alternative future use for acquired in-process research and development and recorded the upfront payment to “Research and development expenses” in the third quarter of 2019. CRISPR has the potential to receive up to $825.0 million in research, development, regulatory and commercial milestones for the DMD and DM1 programs as well as royalties on net product sales. CRISPR has the option to co-develop and co-commercialize all DM1 products globally and forego the milestones and royalties associated with the DM1 program. The Company will fund all expenses associated with the collaboration except for research costs for specified guide RNA research conducted by CRISPR, which the Company and CRISPR will share equally.

In connection with the CRISPR Agreement, the Company made an upfront payment to CRISPR of $75.0 million and an investment in CRISPR’s stock. The Company has made several subsequent investments in CRISPR’s common stock. Please refer to Note F, “Marketable Securities and Equity Investments,” for further information regarding the Company’s investment in CRISPR’s common stock.

Kymera Therapeutics Inc.

In May 2019, the Company entered into a strategic research and development collaboration agreement (the “Kymera Agreement”) with Kymera Therapeutics Inc. (“Kymera”) to advance small molecule protein degraders against multiple targets. Pursuant to the Kymera Agreement, Kymera’s proprietary platform technology is being applied in the collaboration

activities in exchange for an upfront payment of $50.0 million. The Company has the exclusive right to license up to six protein targets, for each of which Kymera may receive up to $170.0 million in payments, including development, regulatory and commercial milestones as well as royalties on net product sales.

In addition to the upfront payment, the Company purchased $20.0 million of Kymera’s preferred stock. The Company determined that the fair value of its investment in Kymera’s preferred stock approximated $20.0 million and classified the investment, which does not have a readily determinable fair value, in “Other assets.”

The Company determined that substantially all of the fair value of the Kymera Agreement was attributable to acquired in-process research and development and no substantive processes were acquired that would constitute a business. The Company concluded that it did not have any alternative future use for the acquired in-process research and development and recorded the $50.0 million upfront payment to “Research and development expenses.”

BioAxone Biosciences, Inc.

The Company has licensed rights to certain drug candidates from these third-party collaborators, which has resulted in the consolidation of certain third-parties’ financial statements into the Company’s condensed consolidated financial statements as VIEs for certain periods of time. As of December 31, 2018, and continuing through the third quarter of 2019, the Company had no consolidated VIEs reflected in its financial statements.

In 2014, the Company entered into a license and collaboration agreement (the “BioAxone Agreement”) with BioAxone, which resulted in the consolidation of BioAxone as a VIE beginning in October 2014. The Company deconsolidated BioAxone as of December 31, 2018 because it determined that it no longer was the primary beneficiary of BioAxone as it no longer had the power to direct the significant activities of BioAxone. Please refer to Note B, “Collaborative Arrangements and Acquisitions,” in the Company’s 2018 Annual Report on Form 10-K for further information on the deconsolidation of BioAxone.

In the nine months ended September 30, 2018, the Company recorded net income attributable to noncontrolling interest of $15.6 million, which was primarily related to a $24.0 million increase in the fair value of the contingent payments payable by Vertex to BioAxone in the first quarter of 2018 due to (i) the expiration of an option held by the Company to purchase BioAxone in the first quarter of 2018 that increased the probability of a $10.0 million license continuation fee for VX-210 (which was ultimately paid in the first quarter of 2018) and (ii) the probability that additional milestone and royalty payments related to the BioAxone Agreement would be paid. Net income attributable to noncontrolling interest also included a $6.0 million provision for income taxes during the nine months ended September 30, 2018 that was primarily related to the increase in the fair value of the contingent payments. In the three months ended September 30, 2018, the net loss attributable to noncontrolling interest was $0.3 million.

Acquisitions

Exonics Therapeutics, Inc.

On July 16, 2019, the Company completed its acquisition of Exonics Therapeutics, Inc. (“Exonics”), a privately held biotechnology company focused on creating transformative gene-editing therapies to repair mutations that cause DMD and other severe neuromuscular diseases, including DM1. The Company acquired Exonics for an upfront payment of approximately $245.0 million, customary working capital adjustments and approximately $70.0 million in deferred payments. Exonics’ equity holders may receive an additional $728.0 million upon the successful achievement of specified development and regulatory milestones for the DMD and DM1 programs.

The Company concluded that Exonics’ intellectual property, assembled workforce and scientific expertise, has the potential to produce therapies for patients with DMD and DM1; therefore, it has accounted for the acquisition as a business combination. The Company determined that the purchase price related to the Exonics business combination was $438.4 million, which consisted of (i) the upfront payment as adjusted for customary working capital adjustments, and (ii) the estimated fair value related to $678.3 million of contingent development and regulatory milestones attributable to the purchase of Exonics’ outstanding shares on July 16, 2019. The remaining portion, or $49.7 million, of the development and

regulatory milestones and the $70.0 million in deferred payments were determined to be compensatory, as they relate to post-acquisition services, and will be expensed to “Research and development expenses” as incurred.

The purchase price consisted of the following:



	(in thousands)
Upfront payment (adjusted for customary working capital adjustments)	$	266,315
Fair value of contingent development and regulatory payments	172,041
Total purchase price	$	438,356

The Company’s methodology for determining the fair value of the contingent development and regulatory payments is described in Note E, “Fair Value Measurements.”

The Company preliminarily allocated the purchase price to the following assets acquired and liabilities assumed:



	July 16, 2019
	(in thousands)
Cash and cash equivalents	$	19,535
Goodwill	397,141
Intangible asset	13,000
Net other assets (liabilities)	8,680
Total purchase price	$	438,356

The “Goodwill” represents the difference between the fair value of the consideration transferred and the fair value of the assets and liabilities acquired. The goodwill was attributable to Exonics’ technological expertise, assembled workforce, the potential additional therapeutic programs that may be discovered utilizing Exonics’ DMD and DM1 programs and synergies from combining these programs with the Company’s current gene-editing capabilities through its collaboration with CRISPR. None of the goodwill is expected to be deductible for income tax purposes. The “Intangible asset,” which is classified within “Other assets” on the Company’s condensed consolidated balance sheet, is a single in-process research and development asset related to Exonics’ DMD and DM1 programs. The fair value of the intangible asset was determined through a discounted cash flow analysis utilizing Level 3 fair value inputs related to the development and commercialization of therapies for DMD and DM1. The Company may adjust “Goodwill” upon completion of certain items reflected within “Net other assets (liabilities)” in the table above. Such adjustments, if any, are not expected to be material to the Company’s condensed consolidated balance sheet.

The Company has not provided pro forma information because the operations of Exonics did not have a material effect on its consolidated financial statements. The Company’s condensed consolidated financial statements reflect the operations of Exonics as of September 30, 2019 and for the period from July 16, 2019 to September 30, 2019.

Semma Therapeutics, Inc.

In August 2019, the Company entered into an agreement to acquire Semma Therapeutics, Inc. (“Semma”), a privately held biotechnology company primarily focused on the use of stem cell-derived human islets as a potentially curative treatment for type 1 diabetes. In October 2019, the acquisition closed upon, among other things, the satisfaction of customary closing conditions and the expiration of the waiting period under the HSR Act, resulting in no financial statement impact during the three and nine months ended September 30, 2019. At closing, the Company acquired all outstanding shares of Semma in exchange for approximately $950.0 million. The Company will account for the acquisition in the fourth quarter of 2019.

Out-license agreements

The Company has entered into licensing agreements pursuant to which it has out-licensed rights to certain drug candidates to third-party collaborators. Pursuant to these out-license agreements, the Company’s collaborators become responsible for all costs related to the continued development of such drug candidates and obtain development and

commercialization rights to these drug candidates. Depending on the terms of the agreements, the Company’s collaborators may be required to make upfront payments, milestone payments upon the achievement of certain product research and development objectives and may also be required to pay royalties on future sales, if any, of commercial products resulting from the collaboration. The termination provisions associated with these collaborations are generally the same as those described above related to the Company’s in-license agreements. None of the Company’s out-license agreements had a significant impact on the Company’s condensed consolidated statement of operations during the three and nine months ended September 30, 2019 and 2018.

Cystic Fibrosis Foundation

The Company has a research, development and commercialization agreement that was originally entered into in 2004 with Cystic Fibrosis Foundation (“CFF”), as successor in interest to the Cystic Fibrosis Foundation Therapeutics, Inc. This agreement was most recently amended in 2016 (the “2016 Amendment”). Pursuant to the agreement, as amended, the Company agreed to pay royalties ranging from low-single digits to mid-single digits on potential sales of certain compounds first synthesized and/or tested between March 1, 2014 and August 31, 2016, including elexacaftor, and tiered royalties ranging from single digits to sub-teens on any approved drugs first synthesized and/or tested during a research term on or before February 28, 2014, including KALYDECO (ivacaftor), ORKAMBI (lumacaftor in combination with ivacaftor) and SYMDEKO/SYMKEVI (tezacaftor in combination with ivacaftor). For combination products, such as ORKAMBI, SYMDEKO and TRIKAFTA (elexacaftor, tezacaftor, and ivacaftor), sales are allocated equally to each of the active pharmaceutical ingredients in the combination product. There are no remaining commercial milestone payments payable by the Company to CFF pursuant to the agreement.

Pursuant to the 2016 Amendment, the Company received an upfront payment of $75.0 million and is receiving development funding from CFF of up to $6.0 million annually. The Company concluded that the upfront payment plus any future development funding represent a form of financing pursuant to ASC 730 and thus records the amounts as a liability on the condensed consolidated balance sheet, primarily reflected in “Long-term advance from collaborator.” The Company reduces this liability over the estimated royalty term of the agreement and reflects the reductions as an offset to “Cost of sales” and as “Interest expense.”

The Company has royalty obligations to CFF for ivacaftor, lumacaftor and tezacaftor until the expiration of patents covering those compounds. The Company has patents in the United States and European Union covering the composition-of-matter of ivacaftor that expire in 2027 and 2025, respectively, subject to potential patent extension. The Company has patents in the United States and European Union covering the composition-of-matter of lumacaftor that expire in 2030 and 2026, respectively, subject to potential extension. The Company has patents in the United States and European Union covering the composition-of-matter of tezacaftor that expire in 2027 and 2028, respectively, subject to potential extension.

Earnings Per Share

9 Months Ended

Sep. 30, 2019

Earnings Per Share [Abstract]

Earnings Per Share

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

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



	Three Months Ended September 30,					Nine Months Ended September 30,
	2019		2018			2019		2018
	(in thousands, except per share amounts)
Basic net income attributable to Vertex per common share calculation:
Net income attributable to Vertex common shareholders	$	57,518	$	128,746		$	593,576	$	546,369
Less: Undistributed earnings allocated to participating securities	—		(14		)	—		(161		)
Net income attributable to Vertex common shareholders—basic	$	57,518	$	128,732		$	593,576	$	546,208

Basic weighted-average common shares outstanding	256,946		254,905			256,289		254,096
Basic net income attributable to Vertex per common share	$	0.22	$	0.51		$	2.32	$	2.15

Diluted net income attributable to Vertex per common share calculation:
Net income attributable to Vertex common shareholders	$	57,518	$	128,746		$	593,576	$	546,369
Less: Undistributed earnings allocated to participating securities	—		(13		)	—		(158		)
Net income attributable to Vertex common shareholders—diluted	$	57,518	$	128,733		$	593,576	$	546,211

Weighted-average shares used to compute basic net income per common share	256,946		254,905			256,289		254,096
Effect of potentially dilutive securities:
Stock options	2,080		2,962			2,297		2,990
Restricted stock and restricted stock units (including PSUs)	1,434		1,896			1,582		1,866
Employee stock purchase program	13		25			14		20
Weighted-average shares used to compute diluted net income per common share	260,473		259,788			260,182		258,972
Diluted net income attributable to Vertex per common share	$	0.22	$	0.50		$	2.28	$	2.11

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



	Three Months Ended September 30,		Nine Months Ended September 30,
	2019	2018	2019	2018
	(in thousands)
Stock options	3,303	2,572	3,116	2,152
Unvested restricted stock and restricted stock units (including PSUs)	13	1	7	4

Fair Value Measurements

9 Months Ended

Sep. 30, 2019

Fair Value Disclosures [Abstract]

Fair Value Measurements

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



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

The Company’s investment strategy is focused on capital preservation. The Company invests in instruments that meet the credit quality standards outlined in the Company’s investment policy. This policy also limits the amount of credit exposure to any one issue or type of instrument. The Company maintains strategic investments separately from the investment policy that governs its other cash, cash equivalents and marketable securities as described in “Note F, “Marketable Securities and Equity Investments.” As of September 30, 2019, the Company’s investments were in money market funds, U.S. Treasury securities, government-sponsored enterprise securities, corporate debt securities, commercial paper and corporate equity securities. Additionally, the Company utilizes foreign currency forward contracts intended to mitigate the effect of changes in foreign exchange rates on its condensed consolidated statement of operations.

As of September 30, 2019, the Company’s financial assets and liabilities that were subject to fair value measurements were valued using both observable and unobservable inputs. The Company’s financial assets valued based on Level 1 inputs consisted of money market funds, U.S. Treasury securities, government-sponsored enterprise securities and corporate equity securities. The Company’s financial assets and liabilities valued based on Level 2 inputs consisted of certain corporate equity securities as described below, corporate debt securities, commercial paper, which consisted of investments in highly-rated investment-grade corporations, and foreign currency forward contracts with reputable and creditworthy counterparties. As discussed further below, the Company’s financial liabilities valued based on Level 3 consisted of acquisition-related contingent milestones. During the three and nine months ended September 30, 2019 and 2018, the Company did not record any other-than-temporary impairment charges related to its financial assets.

The following table sets forth the Company’s financial assets and liabilities subject to fair value measurements (and does not include $1.9 billion and $1.4 billion of cash as of September 30, 2019 and December 31, 2018, respectively):



	Fair Value Measurements as of September 30, 2019
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset positions):
Cash equivalents:
Money market funds	$	1,476,254		$	1,476,254	$	—		$	—
U.S. Treasury securities	5,893			5,893		—			—
Government-sponsored enterprise securities	13,370			13,370		—			—
Commercial paper	50,119			—		50,119			—
Marketable securities:
Corporate equity securities	236,184			220,564		15,620			—
Government-sponsored enterprise securities	14,217			14,217		—			—
Corporate debt securities	265,051			—		265,051			—
Commercial paper	82,938			—		82,938			—
Prepaid expenses and other current assets:
Foreign currency forward contracts	27,253			—		27,253			—
Other assets:
Foreign currency forward contracts	1,806			—		1,806			—
Total financial assets	$	2,173,085		$	1,730,298	$	442,787		$	—
Financial instruments carried at fair value (liability positions):
Other current liabilities:
Foreign currency forward contracts	$	(85	)	$	—	$	(85	)	$	—
Long-term contingent consideration	(175,000		)	—		—			(175,000		)
Other long-term liabilities:
Foreign currency forward contracts	(10		)	—		(10		)	—
Total financial liabilities	$	(175,095	)	$	—	$	(95	)	$	(175,000	)



	Fair Value Measurements as of December 31, 2018
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset positions):
Cash equivalents:
Money market funds	$	1,226,603		$	1,226,603	$	—		$	—
U.S. Treasury securities	5,966			5,966		—			—
Government-sponsored enterprise securities	7,123			7,123		—			—
Commercial paper	58,268			—		58,268			—
Marketable securities:
Corporate equity securities	167,323			153,733		13,590			—
U.S. Treasury securities	6,026			6,026		—			—
Government-sponsored enterprise securities	10,704			10,704		—			—
Corporate debt securities	233,665			—		233,665			—
Commercial paper	100,390			—		100,390			—
Prepaid expenses and other current assets:
Foreign currency forward contracts	19,023			—		19,023			—
Other assets:
Foreign currency forward contracts	1,514			—		1,514			—
Total financial assets	$	1,836,605		$	1,410,155	$	426,450		$	—
Financial instruments carried at fair value (liability positions):
Other current liabilities:
Foreign currency forward contracts	$	(340	)	$	—	$	(340	)	$	—
Other long-term liabilities:
Foreign currency forward contracts	(108		)	—		(108		)	—
Total financial liabilities	$	(448	)	$	—	$	(448	)	$	—

Please refer to Note F, “Marketable Securities and Equity Investments,” for the carrying amount and related unrealized gains (losses) by type of investment.

Fair Value of Moderna Investment

The Company has an investment in the common stock of Moderna, Inc. (“Moderna”), which became a publicly traded company in 2018. The Company has valued its investment in Moderna based on Level 2 inputs due to transfer restrictions subsequent to Moderna’s initial public offering lasting until December 2019. The reduction in fair value recorded on the Company’s condensed consolidated balance sheet related to this transfer restriction is not material to its financial statements.

Fair Value of Contingent Consideration

The Company’s contingent consideration liabilities, which are related to development and regulatory milestones potentially payable to Exonics former shareholders, are classified as Level 3 within the valuation hierarchy. The Company bases its estimates of the probability of achieving the milestones relevant to the fair value of contingent payments on industry data attributable to rare diseases. The discount rates used in the valuation model for contingent payments 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. Due to the uncertainties associated with development and commercialization of a drug candidate in the pharmaceutical industry, the Company's estimates regarding the fair value of contingent consideration will change in the future, resulting in adjustments to the fair value of the Company’s contingent consideration liabilities, and the effect of any such adjustments could be material.

The following table represents a rollforward of the fair value of the Company’s contingent consideration liabilities:



	Nine Months Ended September 30, 2019
	(in thousands)
Balance at December 31, 2018	$	—
Contingent consideration related to acquisition of Exonics	172,041
Increase in fair value of contingent payments	2,959
Balance at September 30, 2019	$	175,000

The “Increase in fair value of contingent payments” in the table above was primarily due to changes in market interest rates and the time value of money.

Fair Value of Intangible Asset

As discussed in Note C, “Collaborative Arrangements and Acquisitions,” the fair value of the Company’s $13.0 million in-process research and development intangible asset related to Exonics’ DMD and DM1 programs was determined through a discounted cash flow analysis utilizing Level 3 fair value inputs.

- Definition

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

+ References + Details

Marketable Securities and Equity Investments

9 Months Ended

Sep. 30, 2019

Investments, Debt and Equity Securities [Abstract]

Marketable Securities and Equity Investments

A summary of the Company’s cash equivalents and marketable securities, which are recorded at fair value (and do not include $1.9 billion and $1.4 billion of cash as of September 30, 2019 and December 31, 2018, respectively), is shown below:



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
As of September 30, 2019
Cash equivalents:
Money market funds	$	1,476,254	$	—	$	—		$	1,476,254
U.S. Treasury securities	5,892		1		—			5,893
Government-sponsored enterprise securities	13,370		—		—			13,370
Commercial paper	50,125		1		(7		)	50,119
Total cash equivalents	1,545,641		2		(7		)	1,545,636
Marketable securities:
Government-sponsored enterprise securities	14,188		29		—			14,217
Corporate debt securities	264,613		465		(27		)	265,051
Commercial paper	82,825		113		—			82,938
Total marketable debt securities	361,626		607		(27		)	362,206
Corporate equity securities	133,157		107,450		(4,423		)	236,184
Total marketable securities	$	494,783	$	108,057	$	(4,450	)	$	598,390

As of December 31, 2018
Cash equivalents:
Money market funds	$	1,226,603	$	—	$	—		$	1,226,603
U.S. Treasury securities	5,967		—		(1		)	5,966
Government-sponsored enterprise securities	7,124		—		(1		)	7,123
Commercial paper	58,271		—		(3		)	58,268
Total cash equivalents	1,297,965		—		(5		)	1,297,960
Marketable securities:
U.S. Treasury securities	6,026		—		—			6,026
Government-sponsored enterprise securities	10,704		—		—			10,704
Corporate debt securities	234,088		27		(450		)	233,665
Commercial paper	100,498		—		(108		)	100,390
Total marketable debt securities	351,316		27		(558		)	350,785
Corporate equity securities	133,157		40,619		(6,453		)	167,323
Total marketable securities	$	484,473	$	40,646	$	(7,011	)	$	518,108

Available-for-sale debt securities were recorded in the Company's condensed consolidated balance sheets at fair value as follows:



	As of September 30, 2019		As of December 31, 2018
	(in thousands)
Cash and cash equivalents	$	1,545,636	$	1,297,960
Marketable securities	362,206		350,785
Total	$	1,907,842	$	1,648,745

Available-for-sale debt securities by contractual maturity were as follows:



	As of September 30, 2019		As of December 31, 2018
	(in thousands)
Matures within one year	$	1,778,426	$	1,647,500
Matures after one year through five years	129,416		1,245
Total	$	1,907,842	$	1,648,745

The Company has a limited number of available-for-sale debt securities in insignificant loss positions as of September 30, 2019, which it does not intend to sell and has concluded it will not be required to sell before recovery of the amortized costs for the investments at maturity. The Company did not record any charges for other-than-temporary declines in the fair value of available-for-sale debt securities or gross realized gains or losses in the three and nine months ended September 30, 2019 and 2018.

The Company maintains strategic investments separately from the investment policy that governs its other cash, cash equivalents and marketable securities. The Company’s investments in the common stock of publicly traded companies, CRISPR and Moderna, as of September 30, 2019 and December 31, 2018, respectively, have readily determinable fair values and are recorded in “Marketable securities” on its condensed consolidated balance sheets. As of September 30, 2019 and December 31, 2018, the total fair value of the Company’s strategic investments in the common stock of publicly traded companies, was $236.2 million and $167.3 million, respectively. The Company records unrealized gains or losses related to its strategic investments, which are primarily attributable to its investment in CRISPR, to “Other (expense) income, net” on its condensed consolidated statements of operations. During the three and nine months ended September 30, 2019, the Company recorded an unrealized loss of $31.2 million and unrealized gain of $68.9 million, respectively. During the three and nine months ended September 30, 2018, the Company recorded an unrealized loss of $61.2 million and an unrealized gain of $88.2 million, respectively.

As of September 30, 2019, the carrying value of the Company’s equity investments without readily determinable fair values, which are recorded in “Other assets” on its condensed consolidated balance sheets, was $40.8 million.

Accumulated Other Comprehensive Income (Loss)

9 Months Ended

Sep. 30, 2019

Equity [Abstract]

Accumulated Other Comprehensive Income (Loss)

The following table summarizes the changes in accumulated other comprehensive income (loss) by component:



				Unrealized Holding Gains (Losses), Net of Tax
	Foreign Currency Translation Adjustment			On Available-For-Sale Debt Securities			On Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2018	$	(11,227	)	$	(536	)	$	12,422		$	659
Other comprehensive income before reclassifications	10,263			1,111			26,663			38,037
Amounts reclassified from accumulated other comprehensive income (loss)	—			—			(19,849		)	(19,849		)
Net current period other comprehensive income	10,263			1,111			6,814			18,188
Balance at September 30, 2019	$	(964	)	$	575		$	19,236		$	18,847



				Unrealized Holding Gains (Losses), Net of Tax
	Foreign Currency Translation Adjustment			On Available-For-Sale Debt Securities			On Equity Securities			On Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2017	$	(21,031	)	$	(594	)	$	25,069		$	(15,016	)	$	(11,572	)
Other comprehensive income before reclassifications	6,800			137			—			21,102			28,039
Amounts reclassified from accumulated other comprehensive income (loss)	—			—			—			7,960			7,960
Net current period other comprehensive income	6,800			137			—			29,062			35,999
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard	949			—			(25,069		)	—			(24,120		)
Balance at September 30, 2018	$	(13,282	)	$	(457	)	$	—		$	14,046		$	307

Hedging

9 Months Ended

Sep. 30, 2019

Derivative Instruments and Hedging Activities Disclosure [Abstract]

Hedging

Foreign currency forward contracts - Designated as hedging instruments

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 recognizes realized gains and losses for the effective portion of such contracts in “Product revenues, net” in its condensed consolidated statements of operations in the same period that it recognizes the product revenues that were impacted by the hedged foreign exchange rate changes.

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. If the Company were to determine 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 September 30, 2019, all hedges were determined to be highly effective.

The Company considers the impact of its counterparties’ credit risk on the fair value of the foreign currency forward contracts. As of September 30, 2019 and December 31, 2018, credit risk did not change the fair value of the Company’s foreign currency forward contracts.

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



	As of September 30, 2019		As of December 31, 2018
Foreign Currency	(in thousands)
Euro	$	460,885	$	335,179
Australian dollar	87,358		52,820
British pound sterling	76,061		73,460
Canadian dollar	47,863		43,759
Total foreign currency forward contracts	$	672,167	$	505,218

Foreign currency forward contracts - Not designated as hedging instruments

The Company also enters into foreign currency forward contracts with contractual maturities of less than one month, which are designed to mitigate the effect of changes in foreign exchange rates on monetary assets and liabilities, including intercompany balances. These contracts are not designated as hedging instruments under GAAP. The Company recognizes realized gains and losses for such contracts in “Other (expense) income, net” in its condensed consolidated statements of operations each period. As of September 30, 2019, the notional amount of the Company’s outstanding foreign currency forward contracts where hedge accounting under GAAP is not applied was $413.2 million.

During the three and nine months ended September 30, 2019 and 2018, the Company recognized the following related to foreign currency forward contacts in its condensed consolidated statements of operations:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2019			2018			2019			2018
	(in thousands)
Designated as hedging instruments - Reclassified from AOCI
Product revenues, net	$	10,304		$	1,721		$	25,381		$	(7,438	)
Not designated as hedging instruments
Other (expense) income, net	$	(8,812	)	$	(782	)	$	(10,874	)	$	1,832

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 its condensed consolidated balance sheets:



As of September 30, 2019
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid expenses and other current assets	$	27,253	Other current liabilities	$	(85	)
Other assets	1,806		Other long-term liabilities	(10		)
Total assets	$	29,059	Total liabilities	$	(95	)



As of December 31, 2018
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid expenses and other current assets	$	19,023	Other current liabilities	$	(340	)
Other assets	1,514		Other long-term liabilities	(108		)
Total assets	$	20,537	Total liabilities	$	(448	)

As of September 30, 2019, the Company expects amounts that are related to foreign exchange forward contracts designated as cash flow hedges under GAAP recorded in “Prepaid expenses and other current assets” and “Other current liabilities” to be reclassified to earnings within twelve months.

The following table summarizes the potential effect of offsetting derivatives by type of financial instrument designated as cash flow hedges under GAAP on the Company’s condensed consolidated balance sheets:



	As of September 30, 2019
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	29,059		$	—	$	29,059		$	(95	)	$	28,964
Total liabilities	$	(95	)	$	—	$	(95	)	$	95		$	—



	As of December 31, 2018
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	20,537		$	—	$	20,537		$	(448	)	$	20,089
Total liabilities	$	(448	)	$	—	$	(448	)	$	448		$	—

Inventories

9 Months Ended

Sep. 30, 2019

Inventory Disclosure [Abstract]

Inventories

Inventories consisted of the following:



	As of September 30, 2019		As of December 31, 2018
	(in thousands)
Raw materials	$	21,293	$	9,677
Work-in-process	105,667		87,944
Finished goods	35,346		26,739
Total	$	162,306	$	124,360

Revolving Credit Facility	9 Months Ended
Revolving Credit Facility	Sep. 30, 2019
Debt Disclosure [Abstract]
Revolving Credit Facility	Revolving Credit Facility In September 2019, the Company and certain of its subsidiaries entered into a Credit Agreement (the “2019 Credit Agreement”) with Bank of America, N.A., as administrative agent and the lenders referred to therein. The 2019 Credit Agreement provides for a $500.0 million unsecured revolving facility, which was not drawn upon at closing. The 2019 Credit Agreement also provides that, subject to satisfaction of certain conditions, the Company may request that the borrowing capacity under the 2019 Credit Agreement be increased by an additional $500.0 million. The 2019 Credit Agreement, which matures on September 17, 2024, supersedes the Company’s credit agreement entered into in 2016 with Bank of America, N.A serving in the same capacity. Direct costs related to the 2019 Credit Agreement, which were not material to the Company’s financial statements, were deferred and will be recorded over the term of the 2019 Credit Agreement. Any amounts borrowed under the 2019 Credit Agreement will bear interest, at the Company’s option, at either a base rate or a Eurocurrency rate, in each case plus an applicable margin. Under the 2019 Credit Agreement, the applicable margins on base rate loans range from 0.125% to 0.50% and the applicable margins on Eurocurrency loans range from 1.125% to 1.50%, in each case based on the Company’s consolidated leverage ratio (the ratio of the Company’s total consolidated funded indebtedness to the Company’s consolidated EBITDA for the most recently completed four fiscal quarter period). Any amounts borrowed pursuant to the 2019 Credit Agreement are guaranteed by certain of the Company’s existing and future domestic subsidiaries, subject to certain exceptions. The 2019 Credit Agreement contains customary representations and warranties and affirmative and negative covenants, including financial covenants to maintain (i) subject to certain limited exceptions, a consolidated leverage ratio of 3.50 to 1.00, subject to an increase to 4.00 to 1.00 following a material acquisition and (ii) a consolidated interest coverage ratio (the ratio of the Company’s consolidated EBITDA to its consolidated interest expenses for the most recently completed four fiscal quarter period) of 2.50 to 1.00, in each case measured on a quarterly basis. The 2019 Credit Agreement also contains customary events of default. In the case of a continuing event of default, the administrative agent would be entitled to exercise various remedies, including the acceleration of amounts due under outstanding loans.

Leases

9 Months Ended

Sep. 30, 2019

Leases [Abstract]

Leases

Finance Leases

The Company’s finance lease assets and liabilities primarily relate to its corporate headquarters in Boston and research site in San Diego (the “Buildings”). These Buildings are classified as finance leases because the present value of the sum of the lease payments associated with the Buildings exceeds substantially all of the fair value of the Buildings. The Company also has outstanding finance leases for equipment.

Prior to the adoption of ASC 842 on January 1, 2019, the Company was deemed for accounting purposes to be the owner of the Buildings during their construction periods and recorded project construction costs incurred by its landlords. Upon completion of the Buildings, the Company determined that the underlying leases did not meet the criteria for “sale-leaseback” treatment. Accordingly, the Company depreciated the Buildings over 40 years and recorded interest expense associated with the financing obligations for the Buildings. The Company bifurcated the lease payments pursuant to the Buildings into (i) a portion that was 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 was treated as an operating lease.

Pursuant to ASC 842, the Company adjusted the amounts recorded on its condensed consolidated balance sheet as of January 1, 2019 for the Buildings to reflect the present value of the lease payments over the remaining lease term related to the Buildings. The finance lease assets associated with the Buildings are amortized to depreciation expense using the straight-line method over the remaining lease term, which is significantly shorter than the Buildings’ useful lives. The Company continues to record interest expense associated with the finance lease liabilities for the Buildings.

Corporate Headquarters

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 in Boston, Massachusetts for a term of 15 years. Base rent payments commenced in December 2013, and will continue through December 2028. The Company utilizes this initial period as its lease term. The Company has an option to extend the lease terms for an additional ten years.

San Diego Lease

In 2015, the Company entered into a lease agreement pursuant to which the Company leases approximately 170,000 square feet of office and laboratory space in San Diego, California for a term of 16 years. Base rent payments commenced in the second quarter of 2019, and will continue through May 2034. The Company utilizes this initial period as its lease term. The Company has an option to extend the lease term for up to two additional five-year terms. The Company placed this building in service in the second quarter of 2018.

Operating Leases

The Company’s operating leases relate to its real estate leases that are not classified as finance leases.

Aggregate Lease Information Related to the Application of ASC 842

The following information is disclosed in accordance with ASC 842, which became effective January 1, 2019. The components of lease cost recorded in the Company’s condensed consolidated statement of operations were as follows:



	Three Months Ended September 30, 2019			Nine Months Ended September 30, 2019
	(in thousands)
Operating lease cost	$	2,796		$	8,064
Finance lease cost
Amortization of leased assets	12,217			36,645
Interest on lease liabilities	13,093			39,917
Variable lease cost	7,427			20,225
Sublease income	(1,702		)	(4,873		)
Net lease cost	$	33,831		$	99,978

The Company’s variable lease cost during the three and nine months ended September 30, 2019 primarily related to operating expenses, taxes and insurance associated with its finance leases. The Company’s sublease income during the three and nine months ended September 30, 2019 primarily related to subleases for an insignificant portion of the Company’s corporate headquarters.

The Company’s leases are included on its condensed consolidated balance sheets as follows:



	As of September 30, 2019		As of December 31, 2018 ^
	(in thousands)
Finance leases
Property and equipment, net	$	449,350	$	640,952
Total finance lease assets	$	449,350	$	640,952

Capital lease obligations, current portion	$	—	$	9,817
Other current liabilities	37,063		5,271
Capital lease obligations, excluding current portion	—		19,658
Construction financing lease obligation, excluding current portion	—		561,892
Long-term finance lease liabilities	541,561		—
Total finance lease liabilities	$	578,624	$	596,638

Operating leases
Operating lease assets	$	60,929	$	—
Total operating lease assets	$	60,929	$	—

Other current liabilities	$	8,199	$	—
Long-term operating lease liabilities	62,978		—
Total operating lease liabilities	$	71,177	$	—
^ As reported in the Company’s 2018 Annual Report on Form 10-K.

Maturities of the Company’s finance and operating lease liabilities in accordance with ASC 842 as of September 30, 2019 were as follows:



Year	Finance Leases			Operating Leases			Total
	(in thousands)
Remainder of 2019	$	16,172		$	2,299		$	18,471
2020	89,159			11,033			100,192
2021	87,525			9,372			96,897
2022	85,177			8,994			94,171
2023	84,253			8,920			93,173
Thereafter	513,206			47,405			560,611
Total lease payments	875,492			88,023			963,515
Less: amount representing interest	(296,868		)	(16,846		)	(313,714		)
Present value of lease liabilities	$	578,624		$	71,177		$	649,801

The weighted-average remaining lease terms and discount rates related to the Company’s leases were as follows:



	As of September 30, 2019
Weighted-average remaining lease term (in years)
Finance leases	10.02
Operating leases	10.41

Weighted-average discount rate
Finance leases	9.11	%
Operating leases	4.01	%

Please refer to Note O, “Additional Cash Flow Information,” for cash flow impact of the Company’s leases.

Additional Lease Information Related to the Application of ASC 840

The following information is disclosed in accordance with ASC 840, Leases (Topic 840) (“ASC 840”), which was applicable until December 31, 2018. As of December 31, 2018, future minimum commitments under the Company’s real estate leases with initial terms of more than one year were as follows:



Year	Fan Pier Leases		San Diego Lease		Other Leases		Total Lease Commitments
	(in thousands)
2019	$	66,540	$	5,324	$	13,207	$	85,071
2020	72,589		9,127		14,270		95,986
2021	72,589		9,127		12,529		94,245
2022	72,589		9,127		12,045		93,761
2023	72,589		9,530		11,952		94,071
Thereafter	389,855		119,864		65,472		575,191
Total minimum lease payments	$	746,751	$	162,099	$	129,475	$	1,038,325

As of December 31, 2018, the Company’s total sublease income to be received related to its facility leases was $6.2 million. During the three and nine months ended September 30, 2018, rental expenses were $4.5 million and $13.3 million, respectively.

As of December 31, 2018, the Company had capital leases for property and equipment of $94.8 million, related to which it had recorded $34.0 million of accumulated depreciation. The capital leases, which were related to equipment and leasehold improvements, bore interest at rates ranging from less than 1% to 6% per year. The Company’s capital lease amortization was included in depreciation expense during the three and nine months ended September 30, 2018. The following table set forth the Company’s future minimum payments due under capital leases as of December 31, 2018:



Year	(in thousands)
2019	$	10,770
2020	7,282
2021	5,649
2022	3,300
2023	1,974
Thereafter	3,085
Total payments	32,060
Less: amount representing interest	(2,585		)
Present value of payments	$	29,475

Leases

Finance Leases

Corporate Headquarters

San Diego Lease

Operating Leases

The Company’s operating leases relate to its real estate leases that are not classified as finance leases.

Aggregate Lease Information Related to the Application of ASC 842



	Three Months Ended September 30, 2019			Nine Months Ended September 30, 2019
	(in thousands)
Operating lease cost	$	2,796		$	8,064
Finance lease cost
Amortization of leased assets	12,217			36,645
Interest on lease liabilities	13,093			39,917
Variable lease cost	7,427			20,225
Sublease income	(1,702		)	(4,873		)
Net lease cost	$	33,831		$	99,978

The Company’s leases are included on its condensed consolidated balance sheets as follows:



	As of September 30, 2019		As of December 31, 2018 ^
	(in thousands)
Finance leases
Property and equipment, net	$	449,350	$	640,952
Total finance lease assets	$	449,350	$	640,952

Capital lease obligations, current portion	$	—	$	9,817
Other current liabilities	37,063		5,271
Capital lease obligations, excluding current portion	—		19,658
Construction financing lease obligation, excluding current portion	—		561,892
Long-term finance lease liabilities	541,561		—
Total finance lease liabilities	$	578,624	$	596,638

Operating leases
Operating lease assets	$	60,929	$	—
Total operating lease assets	$	60,929	$	—

Other current liabilities	$	8,199	$	—
Long-term operating lease liabilities	62,978		—
Total operating lease liabilities	$	71,177	$	—
^ As reported in the Company’s 2018 Annual Report on Form 10-K.

Maturities of the Company’s finance and operating lease liabilities in accordance with ASC 842 as of September 30, 2019 were as follows:



Year	Finance Leases			Operating Leases			Total
	(in thousands)
Remainder of 2019	$	16,172		$	2,299		$	18,471
2020	89,159			11,033			100,192
2021	87,525			9,372			96,897
2022	85,177			8,994			94,171
2023	84,253			8,920			93,173
Thereafter	513,206			47,405			560,611
Total lease payments	875,492			88,023			963,515
Less: amount representing interest	(296,868		)	(16,846		)	(313,714		)
Present value of lease liabilities	$	578,624		$	71,177		$	649,801

The weighted-average remaining lease terms and discount rates related to the Company’s leases were as follows:



	As of September 30, 2019
Weighted-average remaining lease term (in years)
Finance leases	10.02
Operating leases	10.41

Weighted-average discount rate
Finance leases	9.11	%
Operating leases	4.01	%

Please refer to Note O, “Additional Cash Flow Information,” for cash flow impact of the Company’s leases.

Additional Lease Information Related to the Application of ASC 840



Year	Fan Pier Leases		San Diego Lease		Other Leases		Total Lease Commitments
	(in thousands)
2019	$	66,540	$	5,324	$	13,207	$	85,071
2020	72,589		9,127		14,270		95,986
2021	72,589		9,127		12,529		94,245
2022	72,589		9,127		12,045		93,761
2023	72,589		9,530		11,952		94,071
Thereafter	389,855		119,864		65,472		575,191
Total minimum lease payments	$	746,751	$	162,099	$	129,475	$	1,038,325



Year	(in thousands)
2019	$	10,770
2020	7,282
2021	5,649
2022	3,300
2023	1,974
Thereafter	3,085
Total payments	32,060
Less: amount representing interest	(2,585		)
Present value of payments	$	29,475

Stock-based Compensation Expense and Share Repurchase Programs

9 Months Ended

Sep. 30, 2019

Share-based Payment Arrangement [Abstract]

Stock-based Compensation Expense and Share Repurchase

Stock-based Compensation Expense and Share Repurchase Programs

Stock-based compensation expense

During the three and nine months ended September 30, 2019 and 2018, the Company recognized the following stock-based compensation expense:



	Three Months Ended September 30,					Nine Months Ended September 30,
	2019			2018		2019			2018
	(in thousands)
Stock-based compensation expense by type of award:
Restricted stock and restricted stock units (including PSUs)	$	61,175		$	55,482	$	185,651		$	157,397
Stock options	21,737			27,234		76,053			81,880
ESPP share issuances	3,044			2,725		8,430			7,281
Stock-based compensation expense related to inventories	(536		)	91		(1,236		)	(454		)
Total stock-based compensation included in costs and expenses	$	85,420		$	85,532	$	268,898		$	246,104

Stock-based compensation expense by line item:
Cost of sales	$	1,337		$	1,259	$	4,178		$	3,263
Research and development expenses	52,504			52,918		167,851			153,018
Sales, general and administrative expenses	31,579			31,355		96,869			89,823
Total stock-based compensation included in costs and expenses	85,420			85,532		268,898			246,104
Income tax effect	(21,996		)	3,114		(87,638		)	(13,715		)
Total stock-based compensation included in costs and expenses, net of tax	$	63,424		$	88,646	$	181,260		$	232,389

The following table sets forth the Company’s unrecognized stock-based compensation expense as of September 30, 2019, by type of award and the weighted-average period over which that expense is expected to be recognized:



	As of September 30, 2019
	Unrecognized Expense		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Restricted stock and restricted stock units (including PSUs)	$	409,425	2.27
Stock options	$	153,686	2.64
ESPP share issuances	$	3,321	0.46

The following table summarizes information about stock options outstanding and exercisable as of September 30, 2019:



	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$29.07–$40.00	186	1.47	$	36.89	186	$	36.89
$40.01–$60.00	379	2.73	$	50.00	379	$	50.00
$60.01–$80.00	299	4.62	$	73.01	294	$	72.96
$80.01–$100.00	2,183	6.41	$	89.27	1,477	$	89.78
$100.01–$120.00	597	5.37	$	109.29	592	$	109.25
$120.01–$140.00	707	5.89	$	130.24	695	$	130.35
$140.01–$160.00	1,203	8.34	$	155.51	464	$	155.41
$160.01–$180.00	803	8.61	$	167.65	257	$	163.59
$180.01–$189.38	1,733	9.12	$	185.35	346	$	184.58
Total	8,090	7.02	$	128.89	4,690	$	109.42

Share repurchase programs

In January 2018, the Company’s Board of Directors approved a share repurchase program (the “2018 Share Repurchase Program”), pursuant to which the Company was authorized to repurchase up to $500.0 million of its common stock between February 1, 2018 and December 31, 2019. As of September 30, 2019, the Company had repurchased the entire $500.0 million it was authorized to repurchase of its common stock under the 2018 Share Repurchase Program. Under the 2018 Share Repurchase Program, the Company was authorized to purchase shares from time to time through open market or privately negotiated transactions. Such purchases were made pursuant to Rule 10b5-1 plans or other means as determined by the Company’s management and in accordance with the requirements of the SEC.

During the nine months ended September 30, 2019, the Company repurchased 832,186 shares of its common stock under the 2018 Share Repurchase Program for an aggregate of $150.0 million including commissions and fees. During the nine months ended September 30, 2018, the Company repurchased 1,282,683 shares of its common stock under the 2018 Share Repurchase Program for an aggregate of $211.0 million including commissions and fees.

In July 2019, the Company’s Board of Directors approved a new share repurchase program (the “2019 Share Repurchase Program”), pursuant to which the Company is authorized to repurchase up to $500.0 million of its common stock between August 1, 2019 and December 31, 2020. The Company expects to fund further repurchases of its common stock through a combination of cash on hand and cash generated by operations. During the nine months ended September 30, 2019, the Company repurchased 70,713 shares of its common stock under the 2019 Share Repurchase Program for an aggregate

of $12.0 million including commissions and fees. As of September 30, 2019, there is a total of $488.0 million remaining for repurchases under the 2019 Share Repurchase Program.

Income Taxes	9 Months Ended
Income Taxes	Sep. 30, 2019
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes The Company is subject to U.S. federal, state, and foreign income taxes. For the three and nine months ended September 30, 2019, the Company recorded provisions for income taxes of $13.1 million and $124.4 million, respectively. The Company’s effective tax rate for the three and nine months ended September 30, 2019 is lower than the U.S. statutory rate primarily due to excess tax benefits related to stock-based compensation. The Company’s provision for income taxes in 2019 has increased compared to historical amounts due to the release of the Company’s valuation allowance on the majority of its net operating losses and other deferred tax assets as of December 31, 2018. Starting in 2019, the Company began recording a provision for income taxes on its pre-tax income using an estimated effective tax rate that approximates statutory rates. Due to the Company's ability to offset its pre-tax income against previously benefited net operating losses, it expects the majority of its tax provision to represent a non-cash expense until its net operating losses have been fully utilized. During the three and nine months ended September 30, 2018, the Company’s income taxes included excess tax benefits related to stock-based compensation, a provision for income taxes related to BioAxone’s income taxes and the Company’s U.S. state and foreign taxes. As noted above, the Company released the valuation allowance on the majority of net operating losses and other deferred tax assets and maintained a valuation allowance of $168.5 million related primarily to U.S. state and foreign tax attributes as of December 31, 2018. On a periodic basis, the Company reassesses any valuation allowances that it maintains on its deferred tax assets, weighing positive and negative evidence to assess the recoverability of the deferred tax assets. The Company has reviewed the tax positions taken, or to be taken, in its tax returns for all tax years currently open to examination by a taxing authority. Unrecognized tax benefits represent the aggregate tax effect of differences between tax return positions and the benefits recognized in the financial statements. As of September 30, 2019 and December 31, 2018, the Company had $29.4 million and $19.5 million, respectively, of gross unrecognized tax benefits, which would affect the Company’s tax rate if recognized. The Company does not expect that its unrecognized tax benefits will materially increase within the next twelve months. The Company accrues interest and penalties related to unrecognized tax benefits as a component of its provision for income taxes. As of September 30, 2019, no significant interest or penalties were accrued. The Company did not recognize any material interest or penalties related to uncertain tax positions during the three and nine months ended September 30, 2019 and 2018. As of September 30, 2019, foreign earnings, which were not significant, have been retained indefinitely by foreign subsidiaries for indefinite reinvestment. Upon repatriation of those earnings, in the form of dividends or otherwise, the Company could be subject to withholding taxes payable to the various foreign countries. The Company files U.S. federal income tax returns and income tax returns in various state, local and foreign jurisdictions. The Company is no longer subject to any tax assessment from an income tax examination in the United States or any other major taxing jurisdiction for years before 2011, except where the Company has net operating losses or tax credit carryforwards that originate before 2011. The Company has various income tax audits ongoing at any time throughout the world. No significant adjustments have been reported for any jurisdiction under audit.

Commitments and Contingencies	9 Months Ended
Commitments and Contingencies	Sep. 30, 2019
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Guaranties and Indemnifications As permitted under Massachusetts law, the Company’s Articles of Organization and By-laws provide that the Company will indemnify certain of its officers and directors for certain claims asserted against them in connection with their service as an officer or director. The maximum potential amount of future payments that the Company could be required to make under these indemnification provisions is unlimited. However, the Company has purchased directors’ and officers’ liability insurance policies that could reduce its monetary exposure and enable it to recover a portion of any future amounts paid. No indemnification claims currently are outstanding, and the Company believes the estimated fair value of these indemnification arrangements is minimal. The Company customarily agrees in the ordinary course of its business to indemnification provisions in agreements with clinical trial investigators and sites in its drug development programs, sponsored research agreements with academic and not-for-profit institutions, various comparable agreements involving parties performing services for the Company and its real estate leases. The Company also customarily agrees to certain indemnification provisions in its drug discovery, development and commercialization collaboration agreements. With respect to the Company’s clinical trials and sponsored research agreements, these indemnification provisions typically apply to any claim asserted against the investigator or the investigator’s institution relating to personal injury or property damage, violations of law or certain breaches of the Company’s contractual obligations arising out of the research or clinical testing of the Company’s compounds or drug candidates. With respect to lease agreements, the indemnification provisions typically apply to claims asserted against the landlord relating to personal injury or property damage caused by the Company, to violations of law by the Company or to certain breaches of the Company’s contractual obligations. The indemnification provisions appearing in the Company’s collaboration agreements are similar to those for the other agreements discussed above, but in addition provide some limited indemnification for its collaborator in the event of third-party claims alleging infringement of intellectual property rights. In each of the cases above, the indemnification obligation generally survives the termination of the agreement for some extended period, although the Company believes the obligation typically has the most relevance during the contract term and for a short period of time thereafter. The maximum potential amount of future payments that the Company could be required to make under these provisions is generally unlimited. The Company has purchased insurance policies covering personal injury, property damage and general liability that reduce its exposure for indemnification and would enable it in many cases to recover all or a portion of any future amounts paid. The Company has never paid any material amounts to defend lawsuits or settle claims related to these indemnification provisions. Accordingly, the Company believes the estimated fair value of these indemnification arrangements is minimal. Other Contingencies The Company has certain contingent liabilities that arise in the ordinary course of its business activities. The Company accrues a reserve for contingent liabilities when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. There were no material contingent liabilities accrued as of September 30, 2019 or December 31, 2018.

Additional Cash Flow Information

9 Months Ended

Sep. 30, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Additional Cash Flow Information

The cash, cash equivalents and restricted cash at the beginning and ending of each period presented in the Company’s condensed consolidated statements of cash flows consisted of the following:



	Nine Months Ended September 30,
	2019				2018
	Beginning of period		End of period		Beginning of period		End of period
	(in thousands)
Cash and cash equivalents	$	2,650,134	$	3,397,941	$	1,665,412	$	2,478,302
Prepaid expenses and other current assets	4,910		6,650		2,114		8,749
Other assets	3,209		—		—		—
Cash, cash equivalents and restricted cash per statement of cash flows	$	2,658,253	$	3,404,591	$	1,667,526	$	2,487,051

Supplemental cash flow information related to the Company’s leases was as follows:



	Nine Months Ended September 30, 2019
	(in thousands)
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	8,062
Operating cash flows from finance leases	$	37,667
Financing cash flows from finance leases	$	28,879

Right-of-use assets obtained in exchange for lease obligations
Operating leases **	$	6,077
Finance leases	$	—
** Includes $5.4 million acquired in July 2019 pursuant to the Company’s acquisition of Exonics.

Basis of Presentation and Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2019

Accounting Policies [Abstract]

Basis of Presentation

Use of Estimates

Recently Adopted Accounting Standards and Recently Issued Accounting Standards

Recently Adopted Accounting Standards

Leases

The cumulative effect of applying ASC 842 on the Company’s condensed consolidated balance sheet as of January 1, 2019 was as follows:



	Balance as of						Balance as of
	December 31, 2018 ^			Adjustments			January 1, 2019
Assets	(in thousands)
Prepaid expenses and other current assets	$	140,819		$	(2,930	)	$	137,889
Property and equipment, net	812,005			(53,920		)	758,085
Deferred tax assets	1,499,672			11,236			1,510,908
Operating lease assets	—			61,674			61,674
Total assets	$	6,245,898		$	16,060		$	6,261,958
Liabilities and Shareholders’ Equity
Capital lease obligations, current portion	$	9,817		$	(9,817	)	$	—
Other current liabilities	40,589			34,304			74,893
Capital lease obligations, excluding current portion	19,658			(19,658		)	—
Construction financing lease obligation, excluding current portion	561,892			(561,892		)	—
Long-term finance lease liabilities	—			569,487			569,487
Long-term operating lease liabilities	—			64,849			64,849
Other long-term liabilities	26,280			(20,903		)	5,377
Accumulated deficit	(2,989,478		)	(40,310		)	(3,029,788		)
Total liabilities and shareholders’ equity	$	6,245,898		$	16,060		$	6,261,958
^ As reported in the Company’s 2018 Annual Report on Form 10-K.

Please refer to Note K, “Leases,” for further information regarding the Company’s leases as well as certain disclosures required by ASC 842.

Derivatives and Hedging

Recently Issued Accounting Standards

Internal-Use Software

Fair Value Measurement

Credit Losses

Summary of Significant Accounting Policies

Leases

Basis of Presentation and Accounting Policies (Tables)

9 Months Ended

Sep. 30, 2019

Accounting Policies [Abstract]

Schedule of new accounting pronouncements and changes in accounting principles

The cumulative effect of applying ASC 842 on the Company’s condensed consolidated balance sheet as of January 1, 2019 was as follows:



	Balance as of						Balance as of
	December 31, 2018 ^			Adjustments			January 1, 2019
Assets	(in thousands)
Prepaid expenses and other current assets	$	140,819		$	(2,930	)	$	137,889
Property and equipment, net	812,005			(53,920		)	758,085
Deferred tax assets	1,499,672			11,236			1,510,908
Operating lease assets	—			61,674			61,674
Total assets	$	6,245,898		$	16,060		$	6,261,958
Liabilities and Shareholders’ Equity
Capital lease obligations, current portion	$	9,817		$	(9,817	)	$	—
Other current liabilities	40,589			34,304			74,893
Capital lease obligations, excluding current portion	19,658			(19,658		)	—
Construction financing lease obligation, excluding current portion	561,892			(561,892		)	—
Long-term finance lease liabilities	—			569,487			569,487
Long-term operating lease liabilities	—			64,849			64,849
Other long-term liabilities	26,280			(20,903		)	5,377
Accumulated deficit	(2,989,478		)	(40,310		)	(3,029,788		)
Total liabilities and shareholders’ equity	$	6,245,898		$	16,060		$	6,261,958
^ As reported in the Company’s 2018 Annual Report on Form 10-K.

Revenue Recognition (Tables)

9 Months Ended

Sep. 30, 2019

Revenue from Contract with Customer [Abstract]

Schedule of disaggregation of revenue

Total revenues from external customers and collaborators by geographic region consisted of the following:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2019		2018		2019		2018
	(in thousands)
United States	$	710,323	$	620,485	$	2,052,044	$	1,687,963
Outside of the United States
Europe	184,845		132,876		532,809		400,685
Other	54,660		31,174		164,703		88,843
Total revenues outside of the United States	239,505		164,050		697,512		489,528
Total revenues	$	949,828	$	784,535	$	2,749,556	$	2,177,491

Product revenues, net consisted of the following:



	Three Months Ended September 30,				Nine Months Ended September 30,
	2019		2018		2019		2018
	(in thousands)
SYMDEKO/SYMKEVI	$	403,714	$	254,919	$	1,085,821	$	474,601
ORKAMBI	296,711		281,859		906,159		947,186
KALYDECO	249,403		245,733		755,481		748,365
Total product revenues, net	$	949,828	$	782,511	$	2,747,461	$	2,170,152

Collaborative Arrangements and Acquisitions (Tables)

9 Months Ended

Sep. 30, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Schedule of business price consideration

The purchase price consisted of the following:



	(in thousands)
Upfront payment (adjusted for customary working capital adjustments)	$	266,315
Fair value of contingent development and regulatory payments	172,041
Total purchase price	$	438,356

Schedule of purchase price assumed assets and liabilities

The Company preliminarily allocated the purchase price to the following assets acquired and liabilities assumed:



	July 16, 2019
	(in thousands)
Cash and cash equivalents	$	19,535
Goodwill	397,141
Intangible asset	13,000
Net other assets (liabilities)	8,680
Total purchase price	$	438,356

Earnings Per Share (Tables)

9 Months Ended

Sep. 30, 2019

Earnings Per Share [Abstract]

Schedule of earnings per share, basic and diluted

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



	Three Months Ended September 30,					Nine Months Ended September 30,
	2019		2018			2019		2018
	(in thousands, except per share amounts)
Basic net income attributable to Vertex per common share calculation:
Net income attributable to Vertex common shareholders	$	57,518	$	128,746		$	593,576	$	546,369
Less: Undistributed earnings allocated to participating securities	—		(14		)	—		(161		)
Net income attributable to Vertex common shareholders—basic	$	57,518	$	128,732		$	593,576	$	546,208

Basic weighted-average common shares outstanding	256,946		254,905			256,289		254,096
Basic net income attributable to Vertex per common share	$	0.22	$	0.51		$	2.32	$	2.15

Diluted net income attributable to Vertex per common share calculation:
Net income attributable to Vertex common shareholders	$	57,518	$	128,746		$	593,576	$	546,369
Less: Undistributed earnings allocated to participating securities	—		(13		)	—		(158		)
Net income attributable to Vertex common shareholders—diluted	$	57,518	$	128,733		$	593,576	$	546,211

Weighted-average shares used to compute basic net income per common share	256,946		254,905			256,289		254,096
Effect of potentially dilutive securities:
Stock options	2,080		2,962			2,297		2,990
Restricted stock and restricted stock units (including PSUs)	1,434		1,896			1,582		1,866
Employee stock purchase program	13		25			14		20
Weighted-average shares used to compute diluted net income per common share	260,473		259,788			260,182		258,972
Diluted net income attributable to Vertex per common share	$	0.22	$	0.50		$	2.28	$	2.11

Potential gross common equivalent shares



	Three Months Ended September 30,		Nine Months Ended September 30,
	2019	2018	2019	2018
	(in thousands)
Stock options	3,303	2,572	3,116	2,152
Unvested restricted stock and restricted stock units (including PSUs)	13	1	7	4

Fair Value Measurements (Tables)

9 Months Ended

Sep. 30, 2019

Fair Value Disclosures [Abstract]

Financial assets subject to fair value measurements (excluding VIE cash and cash equivalents, which are recorded as Restricted cash and cash equivalents (VIE))



	Fair Value Measurements as of September 30, 2019
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset positions):
Cash equivalents:
Money market funds	$	1,476,254		$	1,476,254	$	—		$	—
U.S. Treasury securities	5,893			5,893		—			—
Government-sponsored enterprise securities	13,370			13,370		—			—
Commercial paper	50,119			—		50,119			—
Marketable securities:
Corporate equity securities	236,184			220,564		15,620			—
Government-sponsored enterprise securities	14,217			14,217		—			—
Corporate debt securities	265,051			—		265,051			—
Commercial paper	82,938			—		82,938			—
Prepaid expenses and other current assets:
Foreign currency forward contracts	27,253			—		27,253			—
Other assets:
Foreign currency forward contracts	1,806			—		1,806			—
Total financial assets	$	2,173,085		$	1,730,298	$	442,787		$	—
Financial instruments carried at fair value (liability positions):
Other current liabilities:
Foreign currency forward contracts	$	(85	)	$	—	$	(85	)	$	—
Long-term contingent consideration	(175,000		)	—		—			(175,000		)
Other long-term liabilities:
Foreign currency forward contracts	(10		)	—		(10		)	—
Total financial liabilities	$	(175,095	)	$	—	$	(95	)	$	(175,000	)



	Fair Value Measurements as of December 31, 2018
				Fair Value Hierarchy
	Total			Level 1		Level 2			Level 3
	(in thousands)
Financial instruments carried at fair value (asset positions):
Cash equivalents:
Money market funds	$	1,226,603		$	1,226,603	$	—		$	—
U.S. Treasury securities	5,966			5,966		—			—
Government-sponsored enterprise securities	7,123			7,123		—			—
Commercial paper	58,268			—		58,268			—
Marketable securities:
Corporate equity securities	167,323			153,733		13,590			—
U.S. Treasury securities	6,026			6,026		—			—
Government-sponsored enterprise securities	10,704			10,704		—			—
Corporate debt securities	233,665			—		233,665			—
Commercial paper	100,390			—		100,390			—
Prepaid expenses and other current assets:
Foreign currency forward contracts	19,023			—		19,023			—
Other assets:
Foreign currency forward contracts	1,514			—		1,514			—
Total financial assets	$	1,836,605		$	1,410,155	$	426,450		$	—
Financial instruments carried at fair value (liability positions):
Other current liabilities:
Foreign currency forward contracts	$	(340	)	$	—	$	(340	)	$	—
Other long-term liabilities:
Foreign currency forward contracts	(108		)	—		(108		)	—
Total financial liabilities	$	(448	)	$	—	$	(448	)	$	—

Schedule of fair value of our contingent consideration liabilities

The following table represents a rollforward of the fair value of the Company’s contingent consideration liabilities:



	Nine Months Ended September 30, 2019
	(in thousands)
Balance at December 31, 2018	$	—
Contingent consideration related to acquisition of Exonics	172,041
Increase in fair value of contingent payments	2,959
Balance at September 30, 2019	$	175,000

Marketable Securities and Equity Investments (Tables)

9 Months Ended

Sep. 30, 2019

Investments, Debt and Equity Securities [Abstract]

Summary of cash equivalents and marketable securities



	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Fair Value
	(in thousands)
As of September 30, 2019
Cash equivalents:
Money market funds	$	1,476,254	$	—	$	—		$	1,476,254
U.S. Treasury securities	5,892		1		—			5,893
Government-sponsored enterprise securities	13,370		—		—			13,370
Commercial paper	50,125		1		(7		)	50,119
Total cash equivalents	1,545,641		2		(7		)	1,545,636
Marketable securities:
Government-sponsored enterprise securities	14,188		29		—			14,217
Corporate debt securities	264,613		465		(27		)	265,051
Commercial paper	82,825		113		—			82,938
Total marketable debt securities	361,626		607		(27		)	362,206
Corporate equity securities	133,157		107,450		(4,423		)	236,184
Total marketable securities	$	494,783	$	108,057	$	(4,450	)	$	598,390

As of December 31, 2018
Cash equivalents:
Money market funds	$	1,226,603	$	—	$	—		$	1,226,603
U.S. Treasury securities	5,967		—		(1		)	5,966
Government-sponsored enterprise securities	7,124		—		(1		)	7,123
Commercial paper	58,271		—		(3		)	58,268
Total cash equivalents	1,297,965		—		(5		)	1,297,960
Marketable securities:
U.S. Treasury securities	6,026		—		—			6,026
Government-sponsored enterprise securities	10,704		—		—			10,704
Corporate debt securities	234,088		27		(450		)	233,665
Commercial paper	100,498		—		(108		)	100,390
Total marketable debt securities	351,316		27		(558		)	350,785
Corporate equity securities	133,157		40,619		(6,453		)	167,323
Total marketable securities	$	484,473	$	40,646	$	(7,011	)	$	518,108

Available-for-sale debt securities were recorded in the Company's condensed consolidated balance sheets at fair value as follows:



	As of September 30, 2019		As of December 31, 2018
	(in thousands)
Cash and cash equivalents	$	1,545,636	$	1,297,960
Marketable securities	362,206		350,785
Total	$	1,907,842	$	1,648,745

Available-for-sale debt securities by contractual maturity were as follows:



	As of September 30, 2019		As of December 31, 2018
	(in thousands)
Matures within one year	$	1,778,426	$	1,647,500
Matures after one year through five years	129,416		1,245
Total	$	1,907,842	$	1,648,745

Accumulated Other Comprehensive Income (Loss) (Tables)

9 Months Ended

Sep. 30, 2019

Equity [Abstract]

Accumulated Other Comprehensive Income (Loss)

The following table summarizes the changes in accumulated other comprehensive income (loss) by component:



				Unrealized Holding Gains (Losses), Net of Tax
	Foreign Currency Translation Adjustment			On Available-For-Sale Debt Securities			On Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2018	$	(11,227	)	$	(536	)	$	12,422		$	659
Other comprehensive income before reclassifications	10,263			1,111			26,663			38,037
Amounts reclassified from accumulated other comprehensive income (loss)	—			—			(19,849		)	(19,849		)
Net current period other comprehensive income	10,263			1,111			6,814			18,188
Balance at September 30, 2019	$	(964	)	$	575		$	19,236		$	18,847



				Unrealized Holding Gains (Losses), Net of Tax
	Foreign Currency Translation Adjustment			On Available-For-Sale Debt Securities			On Equity Securities			On Foreign Currency Forward Contracts			Total
	(in thousands)
Balance at December 31, 2017	$	(21,031	)	$	(594	)	$	25,069		$	(15,016	)	$	(11,572	)
Other comprehensive income before reclassifications	6,800			137			—			21,102			28,039
Amounts reclassified from accumulated other comprehensive income (loss)	—			—			—			7,960			7,960
Net current period other comprehensive income	6,800			137			—			29,062			35,999
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard	949			—			(25,069		)	—			(24,120		)
Balance at September 30, 2018	$	(13,282	)	$	(457	)	$	—		$	14,046		$	307

Hedging (Tables)

9 Months Ended

Sep. 30, 2019

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 under GAAP:



	As of September 30, 2019		As of December 31, 2018
Foreign Currency	(in thousands)
Euro	$	460,885	$	335,179
Australian dollar	87,358		52,820
British pound sterling	76,061		73,460
Canadian dollar	47,863		43,759
Total foreign currency forward contracts	$	672,167	$	505,218

Schedule of Foreign Exchange Contracts, Condensed Consolidated Statements of Operations



	Three Months Ended September 30,						Nine Months Ended September 30,
	2019			2018			2019			2018
	(in thousands)
Designated as hedging instruments - Reclassified from AOCI
Product revenues, net	$	10,304		$	1,721		$	25,381		$	(7,438	)
Not designated as hedging instruments
Other (expense) income, net	$	(8,812	)	$	(782	)	$	(10,874	)	$	1,832

Schedule of Foreign Exchange Contracts



As of September 30, 2019
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid expenses and other current assets	$	27,253	Other current liabilities	$	(85	)
Other assets	1,806		Other long-term liabilities	(10		)
Total assets	$	29,059	Total liabilities	$	(95	)



As of December 31, 2018
Assets			Liabilities
Classification	Fair Value		Classification	Fair Value
(in thousands)
Prepaid expenses and other current assets	$	19,023	Other current liabilities	$	(340	)
Other assets	1,514		Other long-term liabilities	(108		)
Total assets	$	20,537	Total liabilities	$	(448	)

Offsetting liabilities



	As of September 30, 2019
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	29,059		$	—	$	29,059		$	(95	)	$	28,964
Total liabilities	$	(95	)	$	—	$	(95	)	$	95		$	—



	As of December 31, 2018
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	20,537		$	—	$	20,537		$	(448	)	$	20,089
Total liabilities	$	(448	)	$	—	$	(448	)	$	448		$	—

Offsetting assets



	As of September 30, 2019
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	29,059		$	—	$	29,059		$	(95	)	$	28,964
Total liabilities	$	(95	)	$	—	$	(95	)	$	95		$	—



	As of December 31, 2018
	Gross Amounts Recognized			Gross Amounts Offset		Gross Amounts Presented			Gross Amounts Not Offset			Legal Offset
Foreign currency forward contracts	(in thousands)
Total assets	$	20,537		$	—	$	20,537		$	(448	)	$	20,089
Total liabilities	$	(448	)	$	—	$	(448	)	$	448		$	—

Inventories (Tables)

9 Months Ended

Sep. 30, 2019

Inventory Disclosure [Abstract]

Schedule of Inventories by Type

Inventories consisted of the following:



	As of September 30, 2019		As of December 31, 2018
	(in thousands)
Raw materials	$	21,293	$	9,677
Work-in-process	105,667		87,944
Finished goods	35,346		26,739
Total	$	162,306	$	124,360

Leases (Tables)

9 Months Ended

Sep. 30, 2019

Leases [Abstract]

Lease cost

The components of lease cost recorded in the Company’s condensed consolidated statement of operations were as follows:



	Three Months Ended September 30, 2019			Nine Months Ended September 30, 2019
	(in thousands)
Operating lease cost	$	2,796		$	8,064
Finance lease cost
Amortization of leased assets	12,217			36,645
Interest on lease liabilities	13,093			39,917
Variable lease cost	7,427			20,225
Sublease income	(1,702		)	(4,873		)
Net lease cost	$	33,831		$	99,978

Components of lease in balance sheets

The Company’s leases are included on its condensed consolidated balance sheets as follows:



	As of September 30, 2019		As of December 31, 2018 ^
	(in thousands)
Finance leases
Property and equipment, net	$	449,350	$	640,952
Total finance lease assets	$	449,350	$	640,952

Capital lease obligations, current portion	$	—	$	9,817
Other current liabilities	37,063		5,271
Capital lease obligations, excluding current portion	—		19,658
Construction financing lease obligation, excluding current portion	—		561,892
Long-term finance lease liabilities	541,561		—
Total finance lease liabilities	$	578,624	$	596,638

Operating leases
Operating lease assets	$	60,929	$	—
Total operating lease assets	$	60,929	$	—

Other current liabilities	$	8,199	$	—
Long-term operating lease liabilities	62,978		—
Total operating lease liabilities	$	71,177	$	—
^ As reported in the Company’s 2018 Annual Report on Form 10-K.

Finance lease, liability, maturity

Maturities of the Company’s finance and operating lease liabilities in accordance with ASC 842 as of September 30, 2019 were as follows:



Year	Finance Leases			Operating Leases			Total
	(in thousands)
Remainder of 2019	$	16,172		$	2,299		$	18,471
2020	89,159			11,033			100,192
2021	87,525			9,372			96,897
2022	85,177			8,994			94,171
2023	84,253			8,920			93,173
Thereafter	513,206			47,405			560,611
Total lease payments	875,492			88,023			963,515
Less: amount representing interest	(296,868		)	(16,846		)	(313,714		)
Present value of lease liabilities	$	578,624		$	71,177		$	649,801

Lessee, operating lease, liability, maturity

Maturities of the Company’s finance and operating lease liabilities in accordance with ASC 842 as of September 30, 2019 were as follows:



Year	Finance Leases			Operating Leases			Total
	(in thousands)
Remainder of 2019	$	16,172		$	2,299		$	18,471
2020	89,159			11,033			100,192
2021	87,525			9,372			96,897
2022	85,177			8,994			94,171
2023	84,253			8,920			93,173
Thereafter	513,206			47,405			560,611
Total lease payments	875,492			88,023			963,515
Less: amount representing interest	(296,868		)	(16,846		)	(313,714		)
Present value of lease liabilities	$	578,624		$	71,177		$	649,801

Weighted-average remaining lease terms and discount rates

The weighted-average remaining lease terms and discount rates related to the Company’s leases were as follows:



	As of September 30, 2019
Weighted-average remaining lease term (in years)
Finance leases	10.02
Operating leases	10.41

Weighted-average discount rate
Finance leases	9.11	%
Operating leases	4.01	%

Schedule of future minimum rental payments for operating leases



Year	Fan Pier Leases		San Diego Lease		Other Leases		Total Lease Commitments
	(in thousands)
2019	$	66,540	$	5,324	$	13,207	$	85,071
2020	72,589		9,127		14,270		95,986
2021	72,589		9,127		12,529		94,245
2022	72,589		9,127		12,045		93,761
2023	72,589		9,530		11,952		94,071
Thereafter	389,855		119,864		65,472		575,191
Total minimum lease payments	$	746,751	$	162,099	$	129,475	$	1,038,325

Schedule of future minimum lease payments for capital leases

The following table set forth the Company’s future minimum payments due under capital leases as of December 31, 2018:



Year	(in thousands)
2019	$	10,770
2020	7,282
2021	5,649
2022	3,300
2023	1,974
Thereafter	3,085
Total payments	32,060
Less: amount representing interest	(2,585		)
Present value of payments	$	29,475

Stock-based Compensation Expense and Share Repurchase Programs (Tables)

9 Months Ended

Sep. 30, 2019

Share-based Payment Arrangement [Abstract]

Stock-based compensation expense by line item

During the three and nine months ended September 30, 2019 and 2018, the Company recognized the following stock-based compensation expense:



	Three Months Ended September 30,					Nine Months Ended September 30,
	2019			2018		2019			2018
	(in thousands)
Stock-based compensation expense by type of award:
Restricted stock and restricted stock units (including PSUs)	$	61,175		$	55,482	$	185,651		$	157,397
Stock options	21,737			27,234		76,053			81,880
ESPP share issuances	3,044			2,725		8,430			7,281
Stock-based compensation expense related to inventories	(536		)	91		(1,236		)	(454		)
Total stock-based compensation included in costs and expenses	$	85,420		$	85,532	$	268,898		$	246,104

Stock-based compensation expense by line item:
Cost of sales	$	1,337		$	1,259	$	4,178		$	3,263
Research and development expenses	52,504			52,918		167,851			153,018
Sales, general and administrative expenses	31,579			31,355		96,869			89,823
Total stock-based compensation included in costs and expenses	85,420			85,532		268,898			246,104
Income tax effect	(21,996		)	3,114		(87,638		)	(13,715		)
Total stock-based compensation included in costs and expenses, net of tax	$	63,424		$	88,646	$	181,260		$	232,389

Unrecognized stock-based compensation expense, net of estimated forfeitures



	As of September 30, 2019
	Unrecognized Expense		Weighted-average Recognition Period
	(in thousands)		(in years)
Type of award:
Restricted stock and restricted stock units (including PSUs)	$	409,425	2.27
Stock options	$	153,686	2.64
ESPP share issuances	$	3,321	0.46

Stock options outstanding and exercisable

The following table summarizes information about stock options outstanding and exercisable as of September 30, 2019:



	Options Outstanding				Options Exercisable
Range of Exercise Prices	Number Outstanding	Weighted-average Remaining Contractual Life	Weighted-average Exercise Price		Number Exercisable	Weighted-average Exercise Price
	(in thousands)	(in years)	(per share)		(in thousands)	(per share)
$29.07–$40.00	186	1.47	$	36.89	186	$	36.89
$40.01–$60.00	379	2.73	$	50.00	379	$	50.00
$60.01–$80.00	299	4.62	$	73.01	294	$	72.96
$80.01–$100.00	2,183	6.41	$	89.27	1,477	$	89.78
$100.01–$120.00	597	5.37	$	109.29	592	$	109.25
$120.01–$140.00	707	5.89	$	130.24	695	$	130.35
$140.01–$160.00	1,203	8.34	$	155.51	464	$	155.41
$160.01–$180.00	803	8.61	$	167.65	257	$	163.59
$180.01–$189.38	1,733	9.12	$	185.35	346	$	184.58
Total	8,090	7.02	$	128.89	4,690	$	109.42

Additional Cash Flow Information (Tables)

9 Months Ended

Sep. 30, 2019

Organization, Consolidation and Presentation of Financial Statements [Abstract]

Condensed Cash Flow Statement

The cash, cash equivalents and restricted cash at the beginning and ending of each period presented in the Company’s condensed consolidated statements of cash flows consisted of the following:



	Nine Months Ended September 30,
	2019				2018
	Beginning of period		End of period		Beginning of period		End of period
	(in thousands)
Cash and cash equivalents	$	2,650,134	$	3,397,941	$	1,665,412	$	2,478,302
Prepaid expenses and other current assets	4,910		6,650		2,114		8,749
Other assets	3,209		—		—		—
Cash, cash equivalents and restricted cash per statement of cash flows	$	2,658,253	$	3,404,591	$	1,667,526	$	2,487,051

Lease, Supplemental Cash Flow Information

Supplemental cash flow information related to the Company’s leases was as follows:



	Nine Months Ended September 30, 2019
	(in thousands)
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	8,062
Operating cash flows from finance leases	$	37,667
Financing cash flows from finance leases	$	28,879

Right-of-use assets obtained in exchange for lease obligations
Operating leases **	$	6,077
Finance leases	$	—
** Includes $5.4 million acquired in July 2019 pursuant to the Company’s acquisition of Exonics.

Basis of Presentation and Accounting Policies - Additional Information (Details) $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2019 USD ($) segment	Dec. 31, 2018	Jan. 01, 2019 USD ($)	Jan. 01, 2018 USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Number of operating segments \| segment	1
Length of lease			15 years
Cumulative effect adjustment to accumulated deficit			$ (40,310)	$ 9,229
Operating lease assets	$ 60,929		61,674
Present value of lease liabilities	$ 71,177
Accumulated Deficit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect adjustment to accumulated deficit			(40,310)	$ 33,349
Accounting Standards Update 2016-02
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Operating lease assets			61,674
Present value of lease liabilities			71,900
Accounting Standards Update 2016-02 \| Accumulated Deficit
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Cumulative effect adjustment to accumulated deficit			$ (40,300)
Building
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Useful life	40 years	40 years

Basis of Presentation and Accounting Policies - Cumulative Effect of Applying ASC 842 to the Condensed Consolidated Balance Sheet (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Prepaid expenses and other current assets	$ 175,142	$ 137,889	$ 140,819
Property and equipment, net	733,509	758,085	812,005
Deferred tax assets	1,415,511	1,510,908	1,499,672
Operating lease assets	60,929	61,674
Total assets	7,514,553	6,261,958	6,245,898
Capital lease obligations, current portion			9,817
Other current liabilities		74,893	40,589
Capital lease obligations, excluding current portion			19,658
Construction financing lease obligation, excluding current portion			561,892
Long-term finance lease liabilities	541,561	569,487
Long-term operating lease liabilities	62,978	64,849
Other long-term liabilities	7,642	5,377	26,280
Accumulated deficit	(2,436,212)	(3,029,788)	(2,989,478)
Total liabilities and shareholders’ equity	$ 7,514,553	6,261,958	$ 6,245,898
Accounting Standards Update 2016-02
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Prepaid expenses and other current assets		(2,930)
Property and equipment, net		(53,920)
Deferred tax assets		11,236
Operating lease assets		61,674
Total assets		16,060
Capital lease obligations, current portion		(9,817)
Other current liabilities		34,304
Capital lease obligations, excluding current portion		(19,658)
Construction financing lease obligation, excluding current portion		(561,892)
Long-term finance lease liabilities		569,487
Long-term operating lease liabilities		64,849
Other long-term liabilities		(20,903)
Accumulated deficit		(40,310)
Total liabilities and shareholders’ equity		$ 16,060

Revenue Recognition - Schedule of Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	$ 949,828	$ 784,535	$ 2,749,556	$ 2,177,491
United States
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	710,323	620,485	2,052,044	1,687,963
Europe
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	184,845	132,876	532,809	400,685
Other
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	54,660	31,174	164,703	88,843
Total revenues outside of the United States
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	239,505	164,050	697,512	489,528
Product revenues, net
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	949,828	782,511	2,747,461	2,170,152
SYMDEKO/SYMKEVI
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	403,714	254,919	1,085,821	474,601
ORKAMBI
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	296,711	281,859	906,159	947,186
KALYDECO
Disaggregation of Revenue [Line Items]
Disaggregation of revenue	$ 249,403	$ 245,733	$ 755,481	$ 748,365

Revenue Recognition - Narrative (Details) - USD ($) $ in Millions	Sep. 30, 2019	Dec. 31, 2018
Revenue from Contract with Customer [Abstract]
Contract liabilities	$ 50.2	$ 24.9

Collaborative Arrangements and Acquisitions - CRISPR Therapeutics AG (Details) $ in Millions	1 Months Ended	3 Months Ended			9 Months Ended		12 Months Ended
	Jul. 31, 2019 USD ($)	Dec. 31, 2019 USD ($) target	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Sep. 30, 2019 USD ($)	Sep. 30, 2018 USD ($)	Dec. 31, 2015 USD ($)
CRISPR Therapeutics
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Collaborative arrangement, development and regulatory potential milestone payments maximum	$ 825.0				$ 410.0
Collaborative arrangement, up-front payment	$ 175.0						$ 75.0
CRISPR Therapeutics \| Forecast
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Collaborative arrangement, aggregate payments		$ 30.0
Collaborative arrangement, right to exclusively license, number of targets \| target		3
CTX001 Co-Co
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Collaborative arrangement research and development expenses			$ 7.7	$ 5.2	$ 22.3	$ 14.1

Collaborative Arrangements and Acquisitions - Kymera Therapeutics (Details) - Kymera Therapeutics $ in Millions	1 Months Ended
	May 31, 2019 USD ($) target
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Collaborative arrangement, up-front payment	$ 50.0
Collaborative arrangement, right to exclusively license, number of targets \| target	6
Collaborative arrangement, development and regulatory potential milestone payments maximum	$ 170.0
Collaborative Arrangement, Investment in Collaborative Partner, Amount	$ 20.0

Collaborative Arrangements and Acquisitions - BioAxone Biosciences, Inc. (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Net loss (income) attributable to noncontrolling interest	$ 0	$ 290	$ 0	$ (15,638)
Increase in fair value of contingent payments	2,959	0	2,959	0
Provision for income taxes	$ 13,148	8,055	$ 124,393	5,737
BioAxone Biosciences Inc.
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Increase in fair value of contingent payments				24,000
Collaborative arrangement, up-front payment		$ 10,000
Provision for income taxes				$ 6,000

Collaborative Arrangements and Acquisitions - Exonics Therapeutics - Additional Information (Details) - Exonics Therapeutics $ in Thousands	Jul. 16, 2019 USD ($)
Business Acquisition [Line Items]
Payments to acquire businesses	$ 245,000
Future payments to acquire businesses	70,000
Acquisition Related Development And Regulatory Potential Milestone Payments Maximum	728,000
Total purchase price	438,356
Non Compensatory [Member]
Business Acquisition [Line Items]
Acquisition Related Development And Regulatory Potential Milestone Payments Maximum	678,300
Compensatory [Member]
Business Acquisition [Line Items]
Acquisition Related Development And Regulatory Potential Milestone Payments Maximum	$ 49,700

Collaborative Arrangements and Acquisitions - Exonics Therapeutics (Details) - USD ($) $ in Thousands		9 Months Ended
	Jul. 16, 2019	Sep. 30, 2019	Dec. 31, 2018
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Fair value of contingent development and regulatory payments		$ 172,041
Goodwill		$ 447,525	$ 50,384
Exonics Therapeutics
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Upfront payment (adjusted for customary working capital adjustments)	$ 266,315
Fair value of contingent development and regulatory payments	172,041
Total purchase price	438,356
Cash and cash equivalents	19,535
Goodwill	397,141
Intangible asset	13,000
Net other assets (liabilities)	8,680
Goodwill, and liabilities assumed, net	$ 438,356

Collaborative Arrangements and Acquisitions - Semma Therapeutics (Details) $ in Millions	1 Months Ended
	Oct. 31, 2019 USD ($)
Semma \| Subsequent Event
Business Acquisition [Line Items]
Payments to acquire businesses	$ 950.0

Collaborative Arrangements and Acquisitions - Cystic Fibrosis Foundation Therapeutics Incorporated (Details) - Cystic Fibrosis Foundation Therapeutics Incorporated - USD ($)	9 Months Ended	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2016
Collaborative Arrangement and Arrangement Other than Collaborative [Line Items]
Additional milestone payments	$ 0
Collaborative funding		$ 75,000,000.0
Additional collaborative funding		$ 6,000,000.0

Earnings Per Share - Schedule of Earnings Per Share Computation Statement (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Antidilutive Securities Excluded from Computation of Earnings Per Share
Net income attributable to Vertex common shareholders	$ 57,518	$ 128,746	$ 593,576	$ 546,369
Basic net income attributable to Vertex per common share calculation:
Less: Undistributed earnings allocated to participating securities	0	(14)	0	(161)
Net income attributable to Vertex common shareholders—basic	$ 57,518	$ 128,732	$ 593,576	$ 546,208
Basic weighted-average common shares outstanding (in shares)	256,946	254,905	256,289	254,096
Basic net income attributable to Vertex per common share (in dollars per share)	$ 0.22	$ 0.51	$ 2.32	$ 2.15
Diluted net income attributable to Vertex per common share calculation:
Less: Undistributed earnings allocated to participating securities	$ 0	$ (13)	$ 0	$ (158)
Net income attributable to Vertex common shareholders—diluted	$ 57,518	$ 128,733	$ 593,576	$ 546,211
Effect of potentially dilutive securities:
Employee stock purchase program (in shares)	13	25	14	20
Weighted-average shares used to compute diluted net income per common share (in shares)	260,473	259,788	260,182	258,972
Diluted net income attributable to Vertex per common share (in dollars per share)	$ 0.22	$ 0.50	$ 2.28	$ 2.11
Stock options
Effect of potentially dilutive securities:
Share-based payment arrangements (in shares)	2,080	2,962	2,297	2,990
Restricted stock and restricted stock units (including PSUs)
Effect of potentially dilutive securities:
Share-based payment arrangements (in shares)	1,434	1,896	1,582	1,866

Earnings Per Share - Potential Gross Common Equivalent Shares (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Stock options
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	3,303	2,572	3,116	2,152
Unvested restricted stock and restricted stock units (including PSUs)
Antidilutive Securities Excluded from Computation of Earnings Per Share
Antidilutive securities excluded from computation of earnings per share (in shares)	13	1	7	4

Fair Value Measurements - Additional Information (Details) - USD ($) $ in Billions	Sep. 30, 2019	Dec. 31, 2018
Fair Value Disclosures [Abstract]
Cash	$ 1.9	$ 1.4

Fair Value Measurements - Financial Assets and Liabilities Subject to Fair Value Measurements (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Financial instruments carried at fair value (liability positions):
Long-term contingent consideration	$ (175,000)	$ 0
Recurring basis
Financial instruments carried at fair value (asset positions):
Total financial assets	2,173,085	1,836,605
Financial instruments carried at fair value (liability positions):
Total financial liabilities	(175,095)	(448)
Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Total financial assets	1,730,298	1,410,155
Financial instruments carried at fair value (liability positions):
Total financial liabilities	0	0
Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Total financial assets	442,787	426,450
Financial instruments carried at fair value (liability positions):
Total financial liabilities	(95)	(448)
Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Total financial assets	0	0
Financial instruments carried at fair value (liability positions):
Total financial liabilities	(175,000)	0
Other current liabilities \| Recurring basis
Financial instruments carried at fair value (liability positions):
Long-term contingent consideration	(175,000)
Other current liabilities \| Recurring basis \| Level 1
Financial instruments carried at fair value (liability positions):
Long-term contingent consideration	0
Other current liabilities \| Recurring basis \| Level 2
Financial instruments carried at fair value (liability positions):
Long-term contingent consideration	0
Other current liabilities \| Recurring basis \| Level 3
Financial instruments carried at fair value (liability positions):
Long-term contingent consideration	(175,000)
Money market funds \| Recurring basis
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	1,476,254	1,226,603
Money market funds \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	1,476,254	1,226,603
Money market funds \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Money market funds \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
U.S. Treasury securities \| Recurring basis
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	5,893	5,966
Marketable securities		6,026
U.S. Treasury securities \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	5,893	5,966
Marketable securities		6,026
U.S. Treasury securities \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Marketable securities		0
U.S. Treasury securities \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Marketable securities		0
Government-sponsored enterprise securities \| Recurring basis
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	13,370	7,123
Marketable securities	14,217	10,704
Government-sponsored enterprise securities \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	13,370	7,123
Marketable securities	14,217	10,704
Government-sponsored enterprise securities \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Marketable securities	0	0
Government-sponsored enterprise securities \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Marketable securities	0	0
Commercial paper \| Recurring basis
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	50,119	58,268
Marketable securities	82,938	100,390
Commercial paper \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Marketable securities	0	0
Commercial paper \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	50,119	58,268
Marketable securities	82,938	100,390
Commercial paper \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Cash and cash equivalents	0	0
Marketable securities	0	0
Corporate equity securities \| Recurring basis
Financial instruments carried at fair value (asset positions):
Marketable securities	236,184	167,323
Corporate equity securities \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Marketable securities	220,564	153,733
Corporate equity securities \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Marketable securities	15,620	13,590
Corporate equity securities \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Marketable securities	0	0
Corporate debt securities \| Recurring basis
Financial instruments carried at fair value (asset positions):
Marketable securities	265,051	233,665
Corporate debt securities \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Marketable securities	0	0
Corporate debt securities \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Marketable securities	265,051	233,665
Corporate debt securities \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Marketable securities	0	0
Foreign currency forward contracts \| Other current liabilities \| Recurring basis
Financial instruments carried at fair value (liability positions):
Derivative liability current	(85)	(340)
Foreign currency forward contracts \| Other current liabilities \| Recurring basis \| Level 1
Financial instruments carried at fair value (liability positions):
Derivative liability current	0	0
Foreign currency forward contracts \| Other current liabilities \| Recurring basis \| Level 2
Financial instruments carried at fair value (liability positions):
Derivative liability current	(85)	(340)
Foreign currency forward contracts \| Other current liabilities \| Recurring basis \| Level 3
Financial instruments carried at fair value (liability positions):
Derivative liability current	0	0
Foreign currency forward contracts \| Other long-term liabilities \| Recurring basis
Financial instruments carried at fair value (liability positions):
Derivative liability, noncurrent	(10)	(108)
Foreign currency forward contracts \| Other long-term liabilities \| Recurring basis \| Level 1
Financial instruments carried at fair value (liability positions):
Derivative liability, noncurrent	0	0
Foreign currency forward contracts \| Other long-term liabilities \| Recurring basis \| Level 2
Financial instruments carried at fair value (liability positions):
Derivative liability, noncurrent	(10)	(108)
Foreign currency forward contracts \| Other long-term liabilities \| Recurring basis \| Level 3
Financial instruments carried at fair value (liability positions):
Derivative liability, noncurrent	0	0
Foreign currency forward contracts \| Prepaid expenses and other current assets \| Recurring basis
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	27,253	19,023
Foreign currency forward contracts \| Prepaid expenses and other current assets \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	0	0
Foreign currency forward contracts \| Prepaid expenses and other current assets \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	27,253	19,023
Foreign currency forward contracts \| Prepaid expenses and other current assets \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	0	0
Foreign currency forward contracts \| Other assets \| Recurring basis
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	1,806
Total financial assets		1,514
Foreign currency forward contracts \| Other assets \| Recurring basis \| Level 1
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	0
Total financial assets		0
Foreign currency forward contracts \| Other assets \| Recurring basis \| Level 2
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	1,806
Total financial assets		1,514
Foreign currency forward contracts \| Other assets \| Recurring basis \| Level 3
Financial instruments carried at fair value (asset positions):
Foreign currency forward contracts	$ 0
Total financial assets		$ 0

Fair Value Measurements - Fair Value of Contingent Consideration Liabilities (Details) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended
	Jul. 16, 2019	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Balance at December 31, 2018				$ 0
Contingent consideration related to acquisition of Exonics				172,041
Increase in fair value of contingent payments		$ 2,959	$ 0	2,959	$ 0
Balance at September 30, 2019		$ 175,000		$ 175,000
Exonics Therapeutics
Fair Value, Assets Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Contingent consideration related to acquisition of Exonics	$ 172,041
Intangible assets	$ 13,000

Marketable Securities and Equity Investments - Additional Information (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Summary of cash, cash equivalents and marketable securities
Cash	$ 1,900,000,000		$ 1,900,000,000		$ 1,400,000,000
Other-than-temporary declines in fair value of available-for-sale debt securities	0	$ 0	0	$ 0
Gross realized gain (loss)	0	0	0	0
Unrealized gain (loss)	(31,200,000)	$ (61,200,000)	68,900,000	$ 88,200,000
Corporate equity securities
Summary of cash, cash equivalents and marketable securities
Fair value	236,184,000		236,184,000		$ 167,323,000
Other assets
Summary of cash, cash equivalents and marketable securities
Equity securities without readily determinable fair value, amount	$ 40,800,000		$ 40,800,000

Marketable Securities and Equity Investments - Summary of Cash Equivalents and Marketable Securities (Details) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Sep. 30, 2019	Dec. 31, 2018
Available-for-sale Debt Securities
Fair Value	$ 1,907,842	$ 1,648,745
Equity Securities, FV-NI and without Readily Determinable Fair Value [Abstract]
Amortized Cost	494,783	484,473
Gross Unrealized Gains	108,057	40,646
Gross Unrealized Losses	(4,450)	(7,011)
Fair Value	598,390	518,108
Money market funds
Summary of cash, cash equivalents and marketable securities
Amortized Cost	1,476,254	1,226,603
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Fair Value	1,476,254	1,226,603
U.S. Treasury securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	5,892	5,967
Gross Unrealized Gains	1	0
Gross Unrealized Losses	0	(1)
Fair Value	5,893	5,966
Available-for-sale Debt Securities
Amortized Cost		6,026
Gross Unrealized Gains		0
Gross Unrealized Losses		0
Fair Value		6,026
Government-sponsored enterprise securities
Summary of cash, cash equivalents and marketable securities
Amortized Cost	13,370	7,124
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	(1)
Fair Value	13,370	7,123
Available-for-sale Debt Securities
Amortized Cost	14,188	10,704
Gross Unrealized Gains	29	0
Gross Unrealized Losses	0	0
Fair Value	14,217	10,704
Commercial paper
Summary of cash, cash equivalents and marketable securities
Amortized Cost	50,125	58,271
Gross Unrealized Gains	1	0
Gross Unrealized Losses	(7)	(3)
Fair Value	50,119	58,268
Available-for-sale Debt Securities
Amortized Cost	82,825	100,498
Gross Unrealized Gains	113	0
Gross Unrealized Losses	0	(108)
Fair Value	82,938	100,390
Cash equivalents
Summary of cash, cash equivalents and marketable securities
Amortized Cost	1,545,641	1,297,965
Gross Unrealized Gains	2	0
Gross Unrealized Losses	(7)	(5)
Fair Value	1,545,636	1,297,960
Corporate debt securities
Available-for-sale Debt Securities
Amortized Cost	264,613	234,088
Gross Unrealized Gains	465	27
Gross Unrealized Losses	(27)	(450)
Fair Value	265,051	233,665
Marketable securities
Available-for-sale Debt Securities
Amortized Cost	361,626	351,316
Gross Unrealized Gains	607	27
Gross Unrealized Losses	(27)	(558)
Fair Value	362,206	350,785
Corporate equity securities
Equity Securities, FV-NI and without Readily Determinable Fair Value [Abstract]
Amortized Cost	133,157	133,157
Gross Unrealized Gains	107,450	40,619
Gross Unrealized Losses	(4,423)	(6,453)
Fair Value	$ 236,184	$ 167,323

Marketable Securities and Equity Investments - Available-for-Sale Debt Securities at Fair Value (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Debt Securities, Available-for-sale [Line Items]
Debt securities	$ 1,907,842	$ 1,648,745
Cash and cash equivalents
Debt Securities, Available-for-sale [Line Items]
Cash and cash equivalents	1,545,636	1,297,960
Marketable securities
Debt Securities, Available-for-sale [Line Items]
Debt securities	$ 362,206	$ 350,785

Marketable Securities and Equity Investments - Available-for-Sale Debt Securities by Contractual Maturity (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Investments, Debt and Equity Securities [Abstract]
Matures within one year	$ 1,778,426	$ 1,647,500
Matures after one year through five years	129,416	1,245
Total	$ 1,907,842	$ 1,648,745

Accumulated Other Comprehensive Income (Loss) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Jan. 01, 2019	Jan. 01, 2018
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	$ 5,069,965	$ 2,714,883	$ 4,435,203	$ 2,042,306
Total changes in other comprehensive income	22,048	4,912	18,188	35,999
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard					$ (40,310)	$ 9,229
Ending Balance	5,253,394	2,934,481	5,253,394	2,934,481
Foreign Currency Translation Adjustment
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance			(11,227)	(21,031)
Other comprehensive income before reclassifications			10,263	6,800
Amounts reclassified from accumulated other comprehensive income (loss)			0	0
Total changes in other comprehensive income			10,263	6,800
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard		949		949
Ending Balance	(964)	(13,282)	(964)	(13,282)
On Available-For-Sale Debt Securities
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance			(536)	(594)
Other comprehensive income before reclassifications			1,111	137
Amounts reclassified from accumulated other comprehensive income (loss)			0	0
Total changes in other comprehensive income			1,111	137
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard		0		0
Ending Balance	575	(457)	575	(457)
On Equity Securities
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance				25,069
Other comprehensive income before reclassifications				0
Amounts reclassified from accumulated other comprehensive income (loss)				0
Total changes in other comprehensive income				0
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard		(25,069)		(25,069)
Ending Balance		0		0
On Foreign Currency Forward Contracts
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance			12,422	(15,016)
Other comprehensive income before reclassifications			26,663	21,102
Amounts reclassified from accumulated other comprehensive income (loss)			(19,849)	7,960
Total changes in other comprehensive income			6,814	29,062
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard		0		0
Ending Balance	19,236	14,046	19,236	14,046
Total
AOCI Attributable to Parent, Net of Tax [Roll Forward]
Beginning Balance	(3,201)	(4,605)	659	(11,572)
Other comprehensive income before reclassifications			38,037	28,039
Amounts reclassified from accumulated other comprehensive income (loss)			(19,849)	7,960
Total changes in other comprehensive income	22,048	4,912	18,188	35,999
Amounts reclassified to accumulated deficit pursuant to adoption of new accounting standard		(24,120)		(24,120)		$ (24,120)
Ending Balance	$ 18,847	$ 307	$ 18,847	$ 307

Hedging - Narrative (Details) - Foreign currency forward contracts $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2019 USD ($)	Sep. 30, 2019 USD ($)
Not designated as hedging instruments
Derivative [Line Items]
Derivative term	1 month
Cash flow hedging \| Not designated as hedging instruments
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 413.2	$ 413.2
Cash flow hedging \| Minimum
Derivative [Line Items]
Derivative term		1 month
Cash flow hedging \| Maximum
Derivative [Line Items]
Derivative term		18 months

Hedging - Notional Amount (Details) - Foreign currency forward contracts - Designated as hedging instruments - Cash flow hedging - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 672,167	$ 505,218
Euro
Derivative [Line Items]
Notional amount of foreign currency forward contract	460,885	335,179
Australian dollar
Derivative [Line Items]
Notional amount of foreign currency forward contract	87,358	52,820
British pound sterling
Derivative [Line Items]
Notional amount of foreign currency forward contract	76,061	73,460
Canadian dollar
Derivative [Line Items]
Notional amount of foreign currency forward contract	$ 47,863	$ 43,759

Hedging - Cash Flow Hedging Instruments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Derivative Instruments, Gain (Loss) [Line Items]
Revenues	$ 949,828	$ 784,535	$ 2,749,556	$ 2,177,491
Other (expense) income	(31,747)	(60,995)	64,802	89,662
Unrealized Holding Gains (Losses), Net of Tax, On Foreign Currency Forward Contracts \| Reclassification out of Accumulated Other Comprehensive Income \| Foreign currency forward contracts \| Not designated as hedging instruments
Derivative Instruments, Gain (Loss) [Line Items]
Other (expense) income	(8,812)	(782)	(10,874)	1,832
Product revenues, net
Derivative Instruments, Gain (Loss) [Line Items]
Revenues	949,828	782,511	2,747,461	2,170,152
Product revenues, net \| Unrealized Holding Gains (Losses), Net of Tax, On Foreign Currency Forward Contracts \| Reclassification out of Accumulated Other Comprehensive Income \| Foreign currency forward contracts \| Designated as hedging instruments
Derivative Instruments, Gain (Loss) [Line Items]
Revenues	$ 10,304	$ 1,721	$ 25,381	$ (7,438)

Hedging - Derivative Fair Value (Details) - Designated as hedging instruments - Foreign currency forward contracts - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Cash flow hedging
Derivative [Line Items]
Total assets	$ 29,059	$ 20,537
Total liabilities	(95)	(448)
Prepaid expenses and other current assets \| Cash flow hedging
Derivative [Line Items]
Fair Value - assets	27,253	19,023
Other current liabilities
Derivative [Line Items]
Fair Value - liabilities	(85)
Other current liabilities \| Cash flow hedging
Derivative [Line Items]
Fair Value - liabilities		(340)
Other assets \| Cash flow hedging
Derivative [Line Items]
Fair Value - assets	1,806	1,514
Other long-term liabilities
Derivative [Line Items]
Fair Value - liabilities	$ (10)
Other long-term liabilities \| Cash flow hedging
Derivative [Line Items]
Fair Value - liabilities		$ (108)

Hedging - Offsetting Derivatives (Details) - Cash flow hedging - Designated as hedging instruments - Foreign currency forward contracts - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Offsetting Derivative Assets [Abstract]
Gross Amounts Recognized	$ 29,059	$ 20,537
Gross Amounts Offset	0	0
Gross Amounts Presented	29,059	20,537
Gross Amounts Not Offset	(95)	(448)
Legal Offset	28,964	20,089
Offsetting Derivative Liabilities [Abstract]
Gross Amounts Recognized	(95)	(448)
Gross Amounts Offset	0	0
Gross Amounts Presented	(95)	(448)
Gross Amounts Not Offset	95	448
Legal Offset	$ 0	$ 0

Inventories (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Inventory Disclosure [Abstract]
Raw materials	$ 21,293	$ 9,677
Work-in-process	105,667	87,944
Finished goods	35,346	26,739
Total Inventories	$ 162,306	$ 124,360

Revolving Credit Facility (Details)	1 Months Ended
Revolving Credit Facility (Details)	Sep. 30, 2019 USD ($)
Line of Credit Facility [Line Items]
Line of credit facility additional borrowing capacity	$ 500,000,000.0
Line of Credit
Line of Credit Facility [Line Items]
Line of credit facility, current borrowing capacity	$ 500,000,000.0
Debt covenant, consolidated leverage ratio	3.50
Acquisition, Interest Coverage Ratio	4.00
Debt covenant, interest coverage ratio	2.50
Line of Credit \| Base Rate \| Minimum
Line of Credit Facility [Line Items]
Interest rate, stated percentage	0.125%
Line of Credit \| Base Rate \| Maximum
Line of Credit Facility [Line Items]
Interest rate, stated percentage	0.50%
Line of Credit \| Eurodollar \| Minimum
Line of Credit Facility [Line Items]
Interest rate, stated percentage	1.125%
Line of Credit \| Eurodollar \| Maximum
Line of Credit Facility [Line Items]
Interest rate, stated percentage	1.50%

Leases - Additional Information (Details) ft² in Thousands, $ in Millions	3 Months Ended	9 Months Ended		12 Months Ended
	Sep. 30, 2018 USD ($)	Sep. 30, 2019	Sep. 30, 2018 USD ($)	Dec. 31, 2018 USD ($)	Dec. 31, 2015 ft² term_extension	Dec. 31, 2011 ft² lease building	Jan. 01, 2019
Property, Plant and Equipment [Line Items]
Length of lease							15 years
Sublease income related to facility leases				$ 6.2
Rent expense	$ 4.5		$ 13.3
Total capital leased assets, gross				94.8
Capital leases accumulated depreciation				$ 34.0
Fan Pier Leases
Property, Plant and Equipment [Line Items]
Number of leases \| lease						2
Area of real estate property (in square feet) \| ft²						1,100
Number of buildings under lease agreement \| building						2
Length of lease						15 years
Option to extend lease term						10 years
San Diego Lease
Property, Plant and Equipment [Line Items]
Area of real estate property (in square feet) \| ft²					170
Length of lease					16 years
Amount of optional renewal terms \| term_extension					2
Optional renewal term length					5 years
Minimum
Property, Plant and Equipment [Line Items]
Capital lease, interest rate				1.00%
Maximum
Property, Plant and Equipment [Line Items]
Capital lease, interest rate				6.00%
Building
Property, Plant and Equipment [Line Items]
Useful life (over)		40 years		40 years

Leases - Components of Lease Expense (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2019	Sep. 30, 2019
Leases [Abstract]
Operating lease cost	$ 2,796	$ 8,064
Amortization of leased assets	12,217	36,645
Interest on lease liabilities	13,093	39,917
Variable lease cost	7,427	20,225
Sublease income	(1,702)	(4,873)
Net lease cost	$ 33,831	$ 99,978

Leases - Balance Sheet Classification of Lease Assets and Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Jan. 01, 2019	Dec. 31, 2018
Leases [Abstract]
Property and equipment, net	$ 449,350		$ 640,952
Total finance lease assets	449,350		640,952
Capital lease obligations, current portion			9,817
Other current liabilities	37,063		5,271
Capital lease obligations, excluding current portion			19,658
Construction financing lease obligation, excluding current portion			561,892
Long-term finance lease liabilities	541,561	$ 569,487
Total finance lease liabilities	578,624		$ 596,638
Operating lease assets	60,929	61,674
Other current liabilities	8,199
Long-term operating lease liabilities	62,978	$ 64,849
Total operating lease liabilities	$ 71,177

Leases - Maturities of Operating and Financing Lease Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018
Finance Leases
Remainder of 2019	$ 16,172
2020	89,159
2021	87,525
2022	85,177
2023	84,253
Thereafter	513,206
Total lease payments	875,492
Less: amount representing interest	(296,868)
Present value of lease liabilities	578,624	$ 596,638
Operating Leases
Remainder of 2019	2,299
2020	11,033
2021	9,372
2022	8,994
2023	8,920
Thereafter	47,405
Total lease payments	88,023
Less: amount representing interest	(16,846)
Present value of lease liabilities	71,177
Total
Remainder of 2019	18,471
2020	100,192
2021	96,897
2022	94,171
2023	93,173
Thereafter	560,611
Total lease payments	963,515
Less: amount representing interest	(313,714)
Present value of lease liabilities	$ 649,801

Leases - Weighted-Average Remaining Lease Terms and Discount Rates (Details)	Sep. 30, 2019
Leases [Abstract]
Weighted average remaining lease term, finance leases	10 years 7 days
Weighted-average remaining lease term, operating leases	10 years 4 months 28 days
Weighted average discount rate, finance leases	9.11%
Weighted average discount rate, operating leases	4.01%

Leases - Future Minimum Commitments Under Real Estate Leases (Details) $ in Thousands	Dec. 31, 2018 USD ($)
Property Subject to or Available for Operating Lease [Line Items]
2019	$ 85,071
2020	95,986
2021	94,245
2022	93,761
2023	94,071
Thereafter	575,191
Total minimum lease payments	1,038,325
Fan Pier Leases
Property Subject to or Available for Operating Lease [Line Items]
2019	66,540
2020	72,589
2021	72,589
2022	72,589
2023	72,589
Thereafter	389,855
Total minimum lease payments	746,751
San Diego Lease
Property Subject to or Available for Operating Lease [Line Items]
2019	5,324
2020	9,127
2021	9,127
2022	9,127
2023	9,530
Thereafter	119,864
Total minimum lease payments	162,099
Other Leases
Property Subject to or Available for Operating Lease [Line Items]
2019	13,207
2020	14,270
2021	12,529
2022	12,045
2023	11,952
Thereafter	65,472
Total minimum lease payments	$ 129,475

Leases - Capital Leases (Details) $ in Thousands	Dec. 31, 2018 USD ($)
Leases [Abstract]
2019	$ 10,770
2020	7,282
2021	5,649
2022	3,300
2023	1,974
Thereafter	3,085
Total payments	32,060
Less: amount representing interest	(2,585)
Present value of payments	$ 29,475

Stock-based Compensation Expense and Share Repurchase Programs - Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	$ 85,420	$ 85,532	$ 268,898	$ 246,104
Stock-based compensation expense related to inventories	(536)	91	(1,236)	(454)
Share-based compensation expense by type of award	85,420	85,532	268,898	246,104
Income tax effect	(21,996)	3,114	(87,638)	(13,715)
Total stock-based compensation included in costs and expenses, net of tax	63,424	88,646	181,260	232,389
Cost of sales
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	1,337	1,259	4,178	3,263
Research and development expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	52,504	52,918	167,851	153,018
Sales, general and administrative expenses
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	31,579	31,355	96,869	89,823
Restricted stock and restricted stock units (including PSUs)
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	61,175	55,482	185,651	157,397
Type of award:
Unrecognized Expense	409,425		$ 409,425
Weighted-average Recognition Period			2 years 3 months 7 days
Stock options
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	21,737	27,234	$ 76,053	81,880
Type of award:
Unrecognized Expense	153,686		$ 153,686
Weighted-average Recognition Period			2 years 7 months 20 days
ESPP share issuances
Stock-based compensation expense:
Total stock-based compensation included in costs and expenses	3,044	$ 2,725	$ 8,430	$ 7,281
Type of award:
Unrecognized Expense	$ 3,321		$ 3,321
Weighted-average Recognition Period			14 days

Stock-based Compensation Expense and Share Repurchase Programs - Stock Options Outstanding and Exercisable (Details) shares in Thousands	9 Months Ended
	Sep. 30, 2019 $ / shares shares
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price range, options outstanding (in shares) \| shares	8,090
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	7 years 7 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 128.89
Exercise price range, options exercisable (in shares) \| shares	4,690
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 109.42
$29.07–$40.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	29.07
Exercise price, high end of range (in dollars per share)	$ 40
Exercise price range, options outstanding (in shares) \| shares	186
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	1 year 5 months 19 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 36.89
Exercise price range, options exercisable (in shares) \| shares	186
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 36.89
$40.01–$60.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	40.01
Exercise price, high end of range (in dollars per share)	$ 60
Exercise price range, options outstanding (in shares) \| shares	379
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	2 years 8 months 23 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 50.00
Exercise price range, options exercisable (in shares) \| shares	379
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 50.00
$60.01–$80.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	60.01
Exercise price, high end of range (in dollars per share)	$ 80
Exercise price range, options outstanding (in shares) \| shares	299
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	4 years 7 months 13 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 73.01
Exercise price range, options exercisable (in shares) \| shares	294
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 72.96
$80.01–$100.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	80.01
Exercise price, high end of range (in dollars per share)	$ 100
Exercise price range, options outstanding (in shares) \| shares	2,183
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	6 years 4 months 28 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 89.27
Exercise price range, options exercisable (in shares) \| shares	1,477
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 89.78
$100.01–$120.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	100.01
Exercise price, high end of range (in dollars per share)	$ 120
Exercise price range, options outstanding (in shares) \| shares	597
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	5 years 4 months 13 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 109.29
Exercise price range, options exercisable (in shares) \| shares	592
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 109.25
$120.01–$140.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	120.01
Exercise price, high end of range (in dollars per share)	$ 140.00
Exercise price range, options outstanding (in shares) \| shares	707
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	5 years 10 months 20 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 130.24
Exercise price range, options exercisable (in shares) \| shares	695
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 130.35
$140.01–$160.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	140.01
Exercise price, high end of range (in dollars per share)	$ 160.00
Exercise price range, options outstanding (in shares) \| shares	1,203
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 4 months 2 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 155.51
Exercise price range, options exercisable (in shares) \| shares	464
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 155.41
$160.01–$180.00
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	160.01
Exercise price, high end of range (in dollars per share)	$ 180.00
Exercise price range, options outstanding (in shares) \| shares	803
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	8 years 7 months 9 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 167.65
Exercise price range, options exercisable (in shares) \| shares	257
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 163.59
$180.01–$189.38
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]
Exercise price, low end of range (in dollars per share)	180.01
Exercise price, high end of range (in dollars per share)	$ 189.38
Exercise price range, options outstanding (in shares) \| shares	1,733
Exercise price range, options outstanding, weighted-average remaining contractual life (in years)	9 years 1 month 13 days
Exercise price range, options outstanding, weighted-average exercise price (in dollars per share)	$ 185.35
Exercise price range, options exercisable (in shares) \| shares	346
Exercise price range, options exercisable, weighted-average exercise price (in dollars per share)	$ 184.58

Stock-based Compensation Expense and Share Repurchase Programs - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Jul. 31, 2019	Jan. 31, 2018
Equity, Class of Treasury Stock [Line Items]
Amount of shares repurchased	$ 12,105	$ 92,004	$ 167,954	$ 211,038
Share Repurchase Program 2018
Equity, Class of Treasury Stock [Line Items]
Number of shares authorized to be repurchased	500,000,000.0		500,000,000.0			500,000,000.0
Shares repurchased (in shares)			832,186	1,282,683
Amount of shares repurchased			$ 150,000	$ 211,000
Share Repurchase Program 2019
Equity, Class of Treasury Stock [Line Items]
Number of shares authorized to be repurchased					500,000,000.0
Shares repurchased (in shares)			70,713
Amount of shares repurchased			$ 12,000
Stock repurchase program, remaining amount	$ 488,000		$ 488,000

Income Taxes (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Sep. 30, 2018	Sep. 30, 2019	Sep. 30, 2018	Dec. 31, 2018
Income Tax Disclosure [Abstract]
Provision for income taxes	$ 13,148	$ 8,055	$ 124,393	$ 5,737
Deferred tax assets, valuation allowance					$ 168,500
Unrecognized tax benefits	29,400		29,400		$ 19,500
Increase unrecognized tax benefits	$ 0		$ 0

Commitments and Contingencies (Details)	Sep. 30, 2019 USD ($)
Commitments and Contingencies Disclosure [Abstract]
Indemnification claims	$ 0

Additional Cash Flow Information - Condensed Consolidated Statements of Cash Flows (Details) - USD ($) $ in Thousands	Sep. 30, 2019	Dec. 31, 2018	Sep. 30, 2018	Dec. 31, 2017
Restricted Cash and Cash Equivalents Items [Line Items]
Cash and cash equivalents	$ 3,397,941	$ 2,650,134	$ 2,478,302	$ 1,665,412
Cash, cash equivalents and restricted cash per statement of cash flows	3,404,591	2,658,253	2,487,051	1,667,526
Prepaid expenses and other current assets
Restricted Cash and Cash Equivalents Items [Line Items]
Restricted cash and cash equivalents	6,650	4,910	8,749	2,114
Other assets
Restricted Cash and Cash Equivalents Items [Line Items]
Restricted cash and cash equivalents	$ 0	$ 3,209	$ 0	$ 0

Additional Cash Flow Information - Supplemental Cash Flow Information Related to Leases (Details) - USD ($) $ in Thousands		1 Months Ended	9 Months Ended
	Jul. 16, 2019	Jul. 31, 2019	Sep. 30, 2019
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases			$ 8,062
Operating cash flows from finance leases			37,667
Financing cash flows from finance leases			28,879
Right-of-use assets obtained in exchange for lease obligations
Operating leases			6,077
Finance leases			$ 0
Exonics Therapeutics
Right-of-use assets obtained in exchange for lease obligations
Operating leases		$ 5,400
Payments to acquire businesses	$ 245,000

Label	Element	Value
Parent [Member]
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ 9,229,000
Cumulative Effect of New Accounting Principle in Period of Adoption	us-gaap_CumulativeEffectOfNewAccountingPrincipleInPeriodOfAdoption	$ (40,310,000)