Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities:
Net loss	$ (111,325)	$ (27,040)
Adjustments to reconcile net loss to net cash (used in) provided by operating activities:
Non-cash royalty revenue related to sale of future royalties	(22,341)	(14,752)
Non-cash interest expense on liability related to sale of future royalties	14,929	15,428
Stock-based compensation	18,793	14,499
Depreciation and amortization	11,502	9,109
Other non-cash transactions	(2,190)	(1,448)
Changes in operating assets and liabilities:
Accounts receivable, net	5,698	641
Inventory	592	2,600
Other assets	6,041	3,843
Accounts payable	4,799	(525)
Accrued compensation	9,735	7,056
Accrued clinical trial expenses	2,726	3,394
Other accrued expenses	2,386	949
Interest payable	0	(3,750)
Liability related to refundable upfront payment	12,500	0
Deferred revenue	(12,665)	(11,832)
Other liabilities	(5,793)	3,854
Net cash (used in) provided by operating activities	(64,613)	2,026
Cash flows from investing activities:
Purchases of investments	(142,972)	(202,870)
Maturities of investments	201,449	155,683
Sales of investments	4,969	23,778
Release of restricted cash	0	25,000
Purchases of property, plant and equipment	(3,741)	(8,722)
Net cash provided by (used in) investing activities	59,705	(7,131)
Cash flows from financing activities:
Payment of capital lease obligations	(5,376)	(3,798)
Proceeds from shares issued under equity compensation plans	18,041	15,516
Net cash provided by financing activities	12,665	11,718
Effect of exchange rates on cash and cash equivalents	(32)	(159)
Net increase in cash and cash equivalents	7,725	6,454
Cash and cash equivalents at beginning of period	55,570	12,365
Cash and cash equivalents at end of period	63,295	18,819
Supplemental disclosure of cash flow information:
Cash paid for interest	15,513	16,095
Supplemental schedule of non-cash investing and financing activities:
Accrued debt issuance costs	$ 0	$ 8,503