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Consolidated Statements of Cash Flows - USD ($)
$ in Thousands
 12 Months Ended
Dec. 31, 2017
Dec. 31, 2016
Dec. 31, 2015
Cash flows from operating activities:      
Net loss $ (96,692) $ (153,524) $ (81,177)
Adjustments to reconcile net loss to net cash used in operating activities:      
Non-cash royalty revenue related to sale of future royalties (30,531) (30,158) (22,058)
Non-cash interest expense on liability related to sale of future royalties 18,869 19,712 20,619
Stock-based compensation 36,615 25,850 19,669
Depreciation and amortization 14,741 15,351 12,855
Loss from redemption premium and incremental interest on 12% senior secured notes 0 0 12,500
Write-off of deferred financing costs on 12% senior secured notes 0 0 1,579
Impairment of equipment from terminated program 15,081 0 0
Other non-cash transactions (881) (2,185) (2,365)
Changes in operating assets and liabilities:      
Accounts receivable, net 10,664 4,269 (16,340)
Inventory 383 237 1,606
Other assets (4,800) (312) (825)
Accounts payable 2,074 518 (412)
Accrued compensation (10,017) 12,282 249
Accrued clinical trial expenses 1,503 (262) 512
Other accrued expenses 5,774 191 (2,278)
Interest payable 0 0 (2,719)
Liability related to refundable upfront payment (12,500) 12,500 0
Deferred revenue (28,269) (17,615) (17,530)
Other liabilities (2,428) (3,878) 3,032
Net cash used in operating activities (80,414) (117,024) (73,083)
Cash flows from investing activities:      
Purchases of investments (404,425) (334,659) (297,608)
Maturities of investments 347,743 253,682 226,923
Sales of investments 37,549 4,969 42,544
Release of restricted cash 0 0 25,000
Purchases of property, plant and equipment (9,676) (6,392) (11,195)
Net cash used in investing activities (28,809) (82,400) (14,336)
Cash flows from financing activities:      
Payment of capital lease obligations (5,131) (5,945) (5,187)
Proceeds from shares issued under equity compensation plans 59,522 20,287 32,208
Issuance of common stock, net of issuance costs 0 189,276 0
Proceeds from issuance of 7.75% senior secured notes, net of issuance costs 0 0 241,262
Repayment of 12% senior secured notes 0 0 (125,000)
Payment of redemption premium and incremental interest on 12% senior secured notes 0 0 (12,500)
Net cash provided by financing activities 54,391 203,618 130,783
Effect of exchange rates on cash and cash equivalents (46) (124) (159)
Net increase (decrease) in cash and cash equivalents (54,878) 4,070 43,205
Cash and cash equivalents at beginning of year 59,640 55,570 12,365
Cash and cash equivalents at end of year 4,762 59,640 55,570
Supplemental disclosure of cash flow information:      
Cash paid for interest 20,116 20,589 20,225
Cash paid for income taxes $ 556 $ 757 $ 860