Income Taxes (Tables)

12 Months Ended

Dec. 31, 2019

Income Taxes

Reconciliation of the Company's expected tax benefit, as computed by applying the U.S. federal corporate tax rate to loss before the benefit for income taxes, and actual tax

The difference between the Company’s expected tax benefit, as computed by applying the applicable U.S. federal corporate tax rate to loss before the benefit for income taxes, and actual tax is reconciled in the following chart (in thousands):

	Years Ended December 31,
	2019		2018		2017
Loss before income tax expense	$	(104,133)	$	(168,843)	$	(96,012)
Expected tax benefit at 21%, 34%, 34% and 34%, respectively	$	(21,868)	$	(35,457)	$	(32,644)
Permanent differences		320		(103)		25
Incentive stock options		569		1,144		1,528
State tax benefit net of federal benefit		(6,726)		(10,622)		(3,537)
Change in valuation allowance, net		27,812		53,706		(63,238)
Federal research credit		(1,652)		(2,466)		(2,204)
Federal orphan drug credit		(4,426)		(6,934)		(7,118)
Expired loss and credit carryforwards		500		—		—
Change in U.S. tax law		—		—		97,479
Debt inducement		—		—		8,044
Lease incentive		—		109		—
Stock option expirations		5,471		623		1,665
Benefit for income taxes	$	—	$	—	$	—

Schedule of significant components of deferred tax assets

	December 31,
	2019		2018
Deferred tax assets:
Net operating loss carryforwards	$	191,744	$	171,437
Research and development tax credit carryforwards		75,084		69,710
Property and other intangible assets		809		297
Deferred revenue		36,008		22,075
Stock-based compensation		9,630		12,849
Operating Lease Liability		6,767		2,639
Other liabilities		2,255		2,920
Royalty sale		30,030		38,593
Total deferred tax assets	$	352,327	$	320,520
Deferred tax liabilities:
Stock-based compensation		(110)		(156)
Operating lease right of use asset		(4,258)		—
Royalty sale transaction costs		(408)		(625)
Total deferred tax liabilities	$	(4,776)	$	(781)
Valuation allowance		(347,551)		(319,739)
Net deferred tax assets/(liabilities)	$	—	$	—