Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013
Cash flows from operating activities:
Net loss	$ (8,233)	$ (114,354)
Adjustments to reconcile net loss to net cash used in operating activities:
Recognition of previously received milestone payment which is no longer refundable	(70,000)
Non-cash royalty revenue related to sale of future royalties	(16,753)	(12,744)
Non-cash interest expense on liability related to sale of future royalties	15,725	16,644
Stock-based compensation	12,647	13,165
Depreciation and amortization	9,733	10,882
Other non-cash transactions	313	332
Changes in operating assets and liabilities:
Accounts receivable, net	(43,845)	1,248
Inventory	1,757	3,193
Other assets	679	6,817
Accounts payable	(3,670)	697
Accrued compensation	(501)	5,137
Accrued expenses	1,667	2,741
Accrued clinical trial expenses	(7,262)	(2,261)
Interest payable	(3,750)	(3,916)
Deferred revenue	1,480	(14,914)
Other liabilities	(7,366)	(4,825)
Net cash used in operating activities	(117,379)	(92,158)
Cash flows from investing activities:
Maturities of investments	171,826	274,011
Purchases of investments	(200,160)	(140,569)
Sales of investments	21,661
Purchases of property and equipment	(6,090)	(1,382)
Net cash (used in) provided by investing activities	(12,763)	132,060
Cash flows from financing activities:
Payment of capital lease obligations	(2,578)	(2,201)
Repayment of proceeds from sale of future royalties	(7,000)	(3,000)
Issuance of common stock, net of issuance costs	116,536
Proceeds from shares issued under equity compensation plans	16,168	5,253
Net cash provided by financing activities	123,126	52
Effect of exchange rates on cash and cash equivalents	(43)	20
Net (decrease) increase in cash and cash equivalents	(7,059)	39,974
Cash and cash equivalents at beginning of period	39,067	25,437
Cash and cash equivalents at end of period	32,008	65,411
Supplemental disclosure of cash flow information:
Cash paid for interest	$ 16,487	$ 17,097