Income Taxes (Tables)

12 Months Ended

Dec. 31, 2018

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):

					Six Months Ended		Year Ended
	Years Ended December 31,				December 31,		June 30,
	2018		2017		2016		2016
Loss before income tax expense	$	(168,843)	$	(96,012)	$	(78,883)	$	(144,817)
Expected tax benefit at 21%,  34%,  34% and 34%, respectively	$	(35,457)	$	(32,644)	$	(26,820)	$	(49,238)
Permanent differences		(103)		25		15		345
Incentive stock options		1,144		1,528		1,313		2,501
State tax benefit net of federal benefit		(10,622)		(3,537)		(4,157)		(7,954)
Change in valuation allowance, net		53,706		(63,238)		32,922		62,505
Federal research credit		(2,466)		(2,204)		(1,232)		(4,109)
Federal orphan drug credit		(6,934)		(7,118)		(2,901)		(4,241)
Expired loss and credit carryforwards		—		—		—		184
Change in U.S. tax law		—		97,479		—		—
Debt inducement		—		8,044		—		—
Lease incentive		109		—		—		—
Stock option expirations		623		1,665		860		7
Benefit for income taxes	$	—	$	—	$	—	$	—

Schedule of significant components of deferred tax assets

Significant components of the Company’s deferred tax assets and liabilities as of December 31, 2018 and 2017 are as follows (in thousands):

	December 31,
	2018		2017
Deferred tax assets:
Net operating loss carryforwards	$	171,437	$	118,672
Research and development tax credit carryforwards		69,710		58,606
Property and other intangible assets		297		2,272
Deferred revenue		22,075		25,997
Stock-based compensation		12,849		12,125
Deferred lease incentive		2,639		2,889
Other liabilities		2,920		3,037
Royalty sale		38,593		47,143
Total deferred tax assets	$	320,520	$	270,741
Deferred tax liabilities:
Stock-based compensation		(156)		—
Royalty sale transaction costs		(625)		(859)
Total deferred tax liabilities	$	(781)	$	(859)
Valuation allowance		(319,739)		(269,882)
Net deferred tax assets/(liabilities)	$	—	$	—