Income Taxes (Tables)

12 Months Ended

Dec. 31, 2017

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 U.S. federal corporate tax rate of 34% to loss before the benefit for income taxes, and actual tax is reconciled in the following chart (in thousands):

	Year Ended		Six Months Ended
	December 31,		December 31,		Year Ended June 30,
	2017		2016		2016		2015
Loss before income tax expense	$	(96,012)	$	(78,883)	$	(144,817)	$	(60,739)
Expected tax benefit at 34%	$	(32,644)	$	(26,820)	$	(49,238)	$	(20,651)
Permanent differences		25		15		345		818
Incentive stock options		1,528		1,313		2,501		1,948
State tax benefit net of federal benefit		(3,537)		(4,157)		(7,954)		(3,252)
Change in valuation allowance, net		(63,238)		32,922		62,505		27,940
Federal research credit		(2,204)		(1,232)		(4,109)		(1,407)
Federal orphan drug credit		(7,118)		(2,901)		(4,241)		(5,471)
Expired loss and credit carryforwards		—		—		184		75
Change in U.S. tax law		97,479		—		—		—
Debt inducement		8,044		—		—		—
Stock option expirations		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, 2017 and 2016 are as follows (in thousands):

	December 31,
	2017		2016
Deferred tax assets:
Net operating loss carryforwards	$	118,672	$	167,869
Research and development tax credit carryforwards		58,606		43,096
Property and other intangible assets		2,272		2,982
Deferred revenue		25,997		13,205
Stock-based compensation		12,125		16,794
Deferred lease incentive		2,889		4,264
Other liabilities		3,037		2,107
Royalty sale		47,143		73,973
Total deferred tax assets	$	270,741	$	324,290
Deferred tax liabilities:
Royalty sale transaction costs		(859)		(1,569)
Total deferred tax liabilities	$	(859)	$	(1,569)
Valuation allowance		(269,882)		(322,721)
Net deferred tax assets/(liabilities)	$	—	$	—