Income Taxes (Tables)

12 Months Ended

Dec. 31, 2016

Income Tax Disclosure [Abstract]

Significant Components of Deferred Tax Assets

Significant components of our deferred tax assets are as follows:

	December 31,
	2016			2015
Deferred tax assets:	(in thousands)
Federal and state net operating losses	$	68,605		$	68,552
Capitalized research and patent costs		23,575			24,876
Research credits		19,058			19,208
Biopharma Financing Agreement		5,556			10,423
Stock-based compensation costs		6,508			6,246
Other		6,067			4,345
Total deferred tax assets		129,369			133,650
Valuation allowance		(129,369	)		(133,650	)
Net deferred tax assets	$	—		$	—

Reconciliation of Statutory Federal Income Tax Rate to Effective Rate

The following table presents a reconciliation from the statutory federal income tax rate to the effective rate.

	Year ended December 31,
	2016			2015			2014
	(in thousands)
U.S. federal taxes (benefit) at statutory rate	$	2,840		$	(2,178	)	$	(10,670	)
Changes in valuation allowance		(3,679	)		2,495			11,002
Unutilized research credits		(69	)		(445	)		(1,308	)
Non-deductible offset of Orphan Drug Credit		—			—			249
Non-deductible Compensation		2,435			—			—
Stock-based compensation		(1,660	)		6			673
Other		133			122			54
Total	$	—		$	—		$	—

Changes in Balance of Gross Unrecognized Tax Benefits

The aggregate annual changes in the balance of gross unrecognized tax benefits are as follows (in thousands):

	Year ended December 31,
	2016			2015
Beginning Balance	$	4,342		$	—
Increase in tax positions for prior years		222			4,173
Decreases in tax positions for prior years		(1,189	)		—
Increase in tax positions for current year		152			169
Ending Balance	$	3,527		$	4,342