Income Taxes (Tables)

12 Months Ended

Dec. 31, 2016

Income Tax Disclosure [Abstract]

Loss Before Provision (Benefit) for Income Taxes

Loss before provision (benefit) for income taxes includes the following components (in thousands):

	Year Ended December 31,
	2016			2015			2014
Domestic	$	(155,375	)	$	(81,931	)	$	(56,414	)
Foreign		2,727			1,260			1,986
Loss before provision (benefit) for income taxes	$	(152,648	)	$	(80,671	)	$	(54,428	)

Provision (Benefit) for Income Taxes

The provision (benefit) for income taxes consists of the following (in thousands):

	Year Ended December 31,
	2016			2015			2014
Current:
Federal	$	—		$	—		$	—
State		(1	)		(1	)		1
Foreign		992			529			(482	)
Total Current		991			528			(481	)
Deferred:
Federal		—			—			—
State		—			—			—
Foreign		(115	)		(22	)		(31	)
Total Deferred		(115	)		(22	)		(31	)
Provision (benefit) for income taxes	$	876		$	506		$	(512	)

Income Tax Provision Related to Continuing Operations

Income tax provision related to continuing operations differs from the amount computed by applying the statutory income tax rate of 35% to pretax loss as follows (in thousands):

	Year Ended December 31,
	2016			2015			2014
U.S. federal provision (benefit)
At statutory rate	$	(53,427	)	$	(28,235	)	$	(19,050	)
Change in valuation allowance		51,981			22,210			11,831
Non-cash interest expense on liability related to sale of    future royalties		6,899			7,217			7,311
Stock-based compensation		528			674			2,832
Foreign tax deduction		—			1,773			—
Research credits		(4,543	)		(4,529	)		(2,933	)
Other		(562	)		1,396			(503	)
Provision (benefit) for income taxes	$	876		$	506		$	(512	)

Significant Components of Deferred Tax Assets and Liabilities

Significant components of our deferred tax assets for federal and state income taxes are as follows (in thousands):

	December 31,
	2016			2015
Deferred tax assets:
Net operating loss carryforwards	$	508,406		$	447,761
Research and other credits		74,917			70,258
Stock-based compensation		26,357			22,832
Deferred revenue		23,035			29,658
Reserves and accruals		12,269			8,309
Capitalized research expenses		11,587			12,440
Property, plant and equipment		6,882			6,451
Sale of future royalties		1,611			12,319
Other		750			3,158
Deferred tax assets before valuation allowance		665,814			613,186
Valuation allowance for deferred tax assets		(665,514	)		(612,996	)
Total deferred tax assets		300			190
Total deferred tax liabilities		—			—
Net deferred tax assets	$	300		$	190

Unrecognized Tax Benefits

We have the following activity relating to unrecognized tax benefits (in thousands):

	December 31,
	2016		2015			2014
Beginning balance	$	17,384	$	27,522		$	16,363
Tax positions related to current year
Additions:
Federal		530		529			502
State		499		443			6,141
Reductions		—		—			—
Tax positions related to prior year
Additions:
Federal		—		—			—
State		—		—			5,258
Foreign		—		—			—
Reductions		—		(11,110	)		(742	)
Settlements		—		—			—
Lapses in statute of limitations		—		—			—
Ending balance	$	18,413	$	17,384		$	27,522