Income Taxes (Tables)

12 Months Ended

Dec. 31, 2016

A reconciliation of the Company’s effective tax rate to the statutory federal income tax rate is as follows:

	Years Ended December 31,
	2016			2015			2014
Federal income tax at statutory federal rate		35.0	%		35.0	%		35.0	%
State taxes		0.7			1.0			3.1
Permanent differences		(11.6	)		(6.4	)		(9.1	)
Stock-based compensation		(2.2	)		(1.3	)		(1.7	)
Tax credits		28.0			21.3			30.5
Foreign rate differential		—			—			(2.3	)
Change in deferred state tax rate		(0.3	)		(2.3	)		—
Other		4.5			(0.5	)		4.5
Change in valuation allowance		(54.1	)		(46.8	)		(60.0	)
Total		—	%		—	%		—	%

Temporary differences that give rise to significant net deferred tax assets as of December 31, 2016 and 2015 are as follows:

	December 31,
(in thousands)	2016			2015
Deferred tax assets
Net operating losses	$	194,027		$	182,992
Capitalized research and development expenses		15,854			21,444
Credit carryforwards		144,823			93,113
Depreciation		2,557			2,128
Deferred compensation		12,463			11,664
Accrued expenses		3,601			1,807
Deferred revenue		21,935			10,999
Other temporary differences		25,276			17,235
Total gross deferred tax assets		420,536			341,382
Valuation allowance		(414,558	)		(326,577	)
Net deferred tax assets		5,978			14,805
Deferred tax liabilities
Intangible assets		(1,428	)		(2,667	)
Debt discount		(4,550	)		(12,138	)
Net deferred taxes	$	—		$	—

The change in the valuation allowance against the deferred tax assets in the years ended December 31, 2016, 2015 and 2014 was as follows:

(in thousands)	Balance at Beginning of Period		Additions		Deductions		Balance at End of Period
December 31, 2014	$	207,304	$	50,185	$	—	$	257,489
December 31, 2015		257,489		69,088		—		326,577
December 31, 2016		326,577		87,981		—		414,558