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	$ (153,524)	$ (81,177)	$ (53,916)
Adjustments to reconcile net loss to net cash used in operating activities:
Non-cash royalty revenue related to sale of future royalties	(30,158)	(22,058)	(21,937)
Non-cash interest expense on liability related to sale of future royalties	19,712	20,619	20,888
Stock-based compensation	25,850	19,669	17,017
Depreciation and amortization	15,351	12,855	12,927
Loss from redemption premium and incremental interest on 12% senior secured notes	0	12,500	0
Write-off of deferred financing costs on 12% senior secured notes	0	1,579	0
Other non-cash transactions	(2,185)	(2,365)	(560)
Changes in assets and liabilities:
Accounts receivable, net	4,269	(16,340)	(1,378)
Inventory	237	1,606	500
Other assets	(312)	(825)	(3,294)
Accounts payable	518	(412)	(6,359)
Accrued compensation	12,282	249	(8,505)
Accrued clinical trial expenses	(262)	512	(9,197)
Other accrued expenses	191	(2,278)	273
Interest payable	0	(2,719)	0
Liability related to refundable upfront payment	12,500	0	0
Deferred revenue	(17,615)	(17,530)	(4,664)
Liability related to receipt of refundable milestone payment	0	0	(70,000)
Other liabilities	(3,878)	3,032	(13,801)
Net cash used in operating activities	(117,024)	(73,083)	(142,006)
Cash flows from investing activities:
Purchases of investments	(334,659)	(297,608)	(297,251)
Maturities of investments	253,682	226,923	247,995
Sales of investments	4,969	42,544	21,661
Release of restricted cash	0	25,000	0
Purchases of property, plant and equipment	(6,392)	(11,195)	(9,976)
Net cash used in investing activities	(82,400)	(14,336)	(37,571)
Cash flows from financing activities:
Payment of capital lease obligations	(5,945)	(5,187)	(3,536)
Issuance of common stock, net of issuance costs	189,276	0	116,536
Proceeds from shares issued under equity compensation plans	20,287	32,208	46,984
Proceeds from issuance of 7.75% senior secured notes, net of issuance costs	0	241,262	0
Repayment of 12% senior secured notes	0	(125,000)	0
Payment of redemption premium and incremental interest on 12% senior secured notes	0	(12,500)	0
Repayment of proceeds from sale of future royalties	0	0	(7,000)
Net cash provided by financing activities	203,618	130,783	152,984
Effect of exchange rates on cash and cash equivalents	(124)	(159)	(109)
Net increase (decrease) in cash and cash equivalents	4,070	43,205	(26,702)
Cash and cash equivalents at beginning of year	55,570	12,365	39,067
Cash and cash equivalents at end of year	59,640	55,570	12,365
Supplemental disclosure of cash flow information:
Cash paid for interest	20,589	20,225	17,445
Cash paid for income taxes	757	860	964
Supplemental schedule of non-cash investing and financing activities:
Property and equipment acquired through capital leases and other financing	$ 1,568	$ 93	$ 5,231