CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities:
Net (loss) income	$ 28,234	$ (171,285)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation, amortization and impairment charges	11,617	9,019
Stock-based compensation	14,659	29,009
Repayment of interest related to facility lease obligation	(5,338)	0
Reclassification of elements of accumulated other comprehensive income (loss) to earnings upon sale of sale of European operations	2,939	0
Gain on the Incyte transaction	(131,734)	0
Deferred income tax benefit	0	(6,086)
Increase (decrease) from:
Accounts receivable	(17,317)	(7,078)
Inventory	(2,279)	(539)
Other current assets	1,917	10,021
Other assets	1,327	(1,301)
Accounts payable	(5,778)	(2,161)
Accrued compensation and benefits	(7,576)	(3,224)
Accrued product development expenses	(3,179)	8,016
Other accrued expenses	10,113	7,041
Other liabilities	(22,466)	5,350
Deferred revenue	3,425	2,560
Net cash used in operating activities	(121,436)	(120,658)
Cash flows from investing activities:
Investment in property and equipment	(39,572)	(4,446)
Proceeds from the Incyte transaction, net of $4,484 of cash transferred	143,149	0
Net cash provided by (used in) investing activities	103,577	(4,446)
Cash flows from financing activities:
Repayment of long-term debt	(4,813)	(313)
Reimbursements of amounts related to facility lease obligation	34,173	1,816
Proceeds from royalty financing	50,000	50,000
Proceeds from issuance of common stock pursuant to stock option and purchase plans	14,234	3,596
Payment of tax withholding obligations related to stock compensation	(1,541)	(321)
Net cash provided by financing activities	92,053	54,778
Effect of exchange rates on cash	(44)	(175)
Net increase (decrease) in cash and cash equivalents	74,150	(70,501)
Cash and cash equivalents, beginning of period	230,888	352,688
Cash and cash equivalents, end of period	305,038	282,187
Supplemental disclosures:
Capitalization of construction-in-progress related to facility lease obligation	10,254	26,634
Non-cash transaction – property and equipment included in accounts payable or accruals	3,430	1,106
Non-cash transaction - deferred financing costs included in accounts payable or accruals	0	3,846
Non-cash transaction – sublease tenant improvements related to facility lease obligation	12,379	0
Non-cash transaction – marketable equity securities recorded at fair market value	$ (1,780)	$ 15,138