Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2016	Dec. 31, 2015	Dec. 31, 2014
Cash flows from operating activities:
Net loss	$ (84,031)	$ (588,181)	$ (742,745)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Stock-based compensation expense	237,705	231,025	177,542
Depreciation and amortization expense	61,398	62,343	63,257
Deferred income taxes	16,961	3,283	281
Impairment of property and equipment	0	2,516	1,689
Excess tax benefit from share-based payment arrangements	0	0	(2,160)
Other non-cash items, net	6,140	9,532	0
Changes in operating assets and liabilities, excluding the effects of the acquisition and deconsolidation of variable interest entities:
Accounts receivable, net	(33,027)	(104,847)	7,428
Inventories	(16,450)	(23,146)	(16,469)
Prepaid expenses and other assets	(8,699)	(9,260)	(15,771)
Accounts payable	(11,745)	(1,709)	25,048
Accrued expenses and other liabilities	88,649	102,746	(63,183)
Accrued restructuring expense	(7,426)	(30,492)	17,502
Deferred revenues	(13,372)	(19,242)	(25,531)
Net cash provided by provided by (used in) operating activities	236,103	(365,432)	(573,112)
Cash flows from investing activities:
Maturities of marketable securities	757,562	1,067,443	1,557,938
Purchases of marketable securities	(616,625)	(633,041)	(1,424,172)
Payment for acquisition of variable interest entity	0	(80,000)	(10,000)
Expenditures for property and equipment	(56,563)	(45,302)	(51,201)
Investment in note receivable	(20,000)	(30,000)	0
Investment in CRISPR	(13,075)	0	0
(Decrease) increase in restricted cash and cash equivalents	22,029	(21,981)	0
Decrease in restricted cash and cash equivalents (VIE)	31,148	11,685	1,638
Increase (decrease) in other assets	(7)	52	(244)
Payments returned related to construction financing lease obligation	0	0	8,050
Net cash provided by investing activities	104,469	268,856	82,009
Cash flows from financing activities:
Issuances of common stock under benefit plans	68,230	185,592	274,615
Payments on construction financing lease obligation	(432)	(381)	(336)
Proceeds from lease financing	11,208	23,662	0
Payments on capital lease financing	(17,597)	(19,954)	(21,443)
Proceeds from senior secured term loan	0	0	294,243
Payments on senior secured term loan	(75,000)	0	0
Proceeds from revolving credit facility	74,965	0	0
Payments of debt issuance costs	(3,103)	0	0
Advance from CFFT	75,000	0	0
Excess tax benefit from share-based payment arrangements	0	0	2,160
Net cash provided by financing activities	133,271	188,919	549,239
Effect of changes in exchange rates on cash	(4,666)	(2,834)	(2,176)
Net increase in cash and cash equivalents	469,177	89,509	55,960
Cash and cash equivalents—beginning of period	714,768	625,259	569,299
Cash and cash equivalents—end of period	1,183,945	714,768	625,259
Supplemental disclosure of cash flow information:
Cash paid for interest	83,656	85,613	68,963
Cash (received from) paid for income taxes	(2,579)	1,806	1,210
Non-cash investing and financing activities:
Capitalization of costs related to construction financing lease obligation	14,238	0	25,564
Assets acquired under capital lease obligations	0	0	9,188
Issuances of common stock exercises from employee benefit plans receivable	68	361	637
Proceeds from revolving credit facility directly paid to settle all outstanding obligations under the term loan	$ 225,000	$ 0	$ 0