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Income Taxes (Tables)
12 Months Ended
Dec. 31, 2017
Income Taxes [Abstract]  
Loss Before Income Tax (Benefit) Expense
Loss before income tax (benefit) expense is comprised of (in thousands):

 
Years Ended December 31,
 
 
2017
 
2016
 
2015
 
United States
 
$
(11,802
)
 
$
(83,622
)
 
$
(87,906
)
Foreign
  
(11,474
)
  
   
 
Loss before income tax (benefit) expense
 
$
(23,276
)
 
$
(83,622
)
 
$
(87,906
)

Income Tax (Benefit) Expense

Our income tax (benefit) expense was as follows (in thousands):

  
Years Ended December 31,
 
  
2017
  
2016
  
2015
 
Current:
         
Federal
 
$
(7,460
)
 
$
1,067
  
$
379
 
State
  
1,246
   
1,867
   
(7
)
Foreign
  
234
   
   
 
Total current income tax (benefit) expense
  
(5,980
)
  
2,934
   
372
 
             
Deferred:
            
Federal
  
   
   
 
State
  
   
   
 
Total deferred income tax (benefit) expense
  
   
   
 
Total income tax (benefit) expense
 
$
(5,980
)
 
$
2,934
  
$
372
 

Reconciliation of Statutory to Effective Tax Rate
The reconciliation between our effective tax rate on loss from continuing operations and the statutory U.S. tax rate is as follows (in thousands):

  
Years Ended December 31,
 
  
2017
  
2016
  
2015
 
Pre-tax loss
 
$
(23,276
)
    
$
(83,622
)
    
$
(87,906
)
   
                      
Statutory rate
  
(8,147
)
  
35.0
%
  
(29,268
)
  
35.0
%
  
(30,767
)
  
35.0
%
State income tax net of federal benefit
  
722
   
(3.1
)%
  
(276
)
  
0.3
%
  
1
   
0.0
%
Foreign
  
4,299
   
(18.3
)%
  
   
0.0
%
  
   
0.0
%
Net change in valuation allowance
  
(76,409
)
  
328.3
%
  
55,927
   
(66.9
)%
  
69,499
   
(79.1
)%
Net operating loss expiration
  
3,987
   
(17.0
)%
  
   
0.0
%
  
   
0.0
%
Tax credits
  
(32,769
)
  
140.8
%
  
(26,954
)
  
32.2
%
  
(41,284
)
  
47.0
%
Deferred tax true-up
  
4,848
   
(20.6
)%
  
2,591
   
(3.1
)%
  
1,496
   
(1.7
)%
Tax Cuts and Jobs Act
  
107,323
   
(461.1
)%
  
       
   
0.0
%
Nondeductible items
  
4,123
   
(17.9
)%
  
1,149
   
(1.4
)%
  
1,055
   
(1.2
)%
Akcea deconsolidation adjustment at IPO
  
469
   
(2.0
)%
  
   
0.0
%
  
   
0.0
%
Excess stock-based compensation
  
(14,337
)
  
61.0
%
  
   
0.0
%
  
   
0.0
%
Other
  
(89
)
  
0.6
%
  
(235
)
  
0.4
%
  
372
   
(0.4
)%
Effective rate
 
$
(5,980
)
  
25.7
%
 
$
2,934
   
(3.5
)%
 
$
372
   
(0.4
)%

Deferred Tax Assets and Liabilities
Significant components of our deferred tax assets and liabilities as of December 31, 2017 and 2016 are as follows (in thousands):

  
Years Ended December 31,
 
  
2017
  
2016
 
Deferred Tax Assets:
      
Net operating loss carryovers
 
$
153,575
  
$
194,372
 
R&D credits
  
240,290
   
193,845
 
Deferred revenue
  
42,055
   
54,203
 
Stock-based compensation
  
40,090
   
48,209
 
Intangible and capital assets
  
672
   
 
Other
  
12,164
   
26,228
 
Total deferred tax assets
 
$
488,846
  
$
516,857
 
         
Deferred Tax Liabilities:
        
Convertible debt
 
$
(32,391
)
 
$
(62,669
)
Intangible and capital assets
  
   
(2,030
)
Net deferred tax asset
 
$
456,455
  
$
452,158
 
Valuation allowance
  
(456,455
)
  
(452,158
)
         
Total net deferred tax assets and liabilities
 
$
  
$
 

Gross Unrecognized Tax Benefits
The following table summarizes our gross unrecognized tax benefits (in thousands):

  
Years Ended December 31,
 
  
2017
  
2016
  
2015
 
Beginning balance of unrecognized tax benefits
 
$
66,999
  
$
51,257
  
$
27,365
 
Settlement of prior period tax positions
  
   
(4,033
)
  
 
Increase for prior period tax positions
  
1,520
   
7,928
   
215
 
Increase for current period tax positions
  
9,495
   
11,847
   
23,677
 
Ending balance of unrecognized tax benefits
 
$
78,014
  
$
66,999
  
$
51,257