Income Taxes (Tables)

6 Months Ended

Dec. 31, 2016

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):

	Six Months Ended
	December 31,		Year Ended June 30,
	2016		2016		2015		2014
Loss before income tax expense	$	(78,883)	$	(144,817)	$	(60,739)	$	(71,364)
Expected tax benefit at 34%	$	(26,820)	$	(49,238)	$	(20,651)	$	(24,264)
Permanent differences		15		345		818		215
Incentive stock options		1,313		2,501		1,948		1,738
State tax benefit net of federal benefit		(4,157)		(7,954)		(3,252)		(4,062)
Increase in valuation allowance, net		32,922		62,505		27,940		26,011
Federal research credit		(1,232)		(4,109)		(1,407)		(1,002)
Federal orphan drug credit		(2,901)		(4,241)		(5,471)		—
Expired loss and credit carryforwards		—		184		75		1,364
Stock option expirations		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, 2016, and June 30, 2016 and 2015 are as follows (in thousands):

	December 31,		June 30,
	2016		2016		2015
Deferred tax assets:
Net operating loss carryforwards	$	167,869	$	139,791	$	89,362
Research and development tax credit carryforwards		43,096		36,879		25,131
Property and other intangible assets		2,982		2,395		2,532
Deferred revenue		13,205		12,911		16,179
Stock-based compensation		16,794		16,033		11,379
Deferred lease incentive		4,264		4,356		4,279
Other liabilities		2,107		3,726		3,177
Royalty sale		73,973		75,956		78,427
Total deferred tax assets	$	324,290	$	292,047	$	230,466
Deferred tax liabilities:
Accounting method change		—		(492)		(983)
Royalty sale transaction costs		(1,569)		(1,757)		(2,190)
Total deferred tax liabilities	$	(1,569)	$	(2,249)	$	(3,173)
Valuation allowance		(322,721)		(289,798)		(227,293)
Net deferred tax assets/(liabilities)	$	—	$	—	$	—