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Significant Accounting Policies (Tables)
 6 Months Ended
Jun. 30, 2018
Significant Accounting Policies [Abstract]  
Adjustments Made to Adopt New Revenue Accounting Guidance
The following tables summarize the adjustments we were required to make to amounts we originally reported in 2017 to adopt Topic 606 (in thousands, except per share amounts):

Condensed Consolidated Balance Sheet

  
At December 31, 2017
 
  
As Previously
Reported under
Topic 605
  
Topic 606
Adjustment
  
As Revised
 
Current portion of deferred revenue
 
$
106,465
  
$
18,871
  
$
125,336
 
Long-term portion of deferred revenue
 
$
72,708
  
$
35,318
  
$
108,026
 
Accumulated deficit
 
$
(1,187,398
)
 
$
(53,636
)
 
$
(1,241,034
)
   Noncontrolling interest in Akcea Therapeutics, Inc.
 
$
87,847
  
$
(3,580
)
 
$
84,267
 
Total stockholders’ equity
 
$
418,719
  
$
(53,439
)
 
$
365,280
 

Condensed Consolidated Statement of Operations

  
Three Months Ended June 30, 2017
 
  
As Previously
Reported under
Topic 605
  
Topic 606
Adjustment
  
As Revised
 
Revenue:
         
Commercial revenue:
         
SPINRAZA royalties
 
$
22,366
  
$
—
  
$
22,366
 
Licensing and other royalty revenue
  
557
   
765
   
1,322
 
Total commercial revenue
  
22,923
   
765
   
23,688
 
Research and development revenue under collaborative agreements
  
81,229
   
7,356
   
88,585
 
Total revenue
 
$
104,152
  
$
8,121
  
$
112,273
 
Income (loss) from operations
 
$
(1,671
)
 
$
8,121
  
$
6,450
 
Net income (loss)
 
$
(11,206
)
 
$
8,121
  
$
(3,085
)
Net income (loss) per share, basic and diluted
 
$
(0.09
)
 
$
0.07
  
$
(0.02
)

  
Six Months Ended June 30, 2017
 
  
As Previously
Reported under
Topic 605
  
Topic 606
Adjustment
  
As Revised
 
Revenue:
         
Commercial revenue:
         
SPINRAZA royalties
 
$
27,577
  
$
—
  
$
27,577
 
Licensing and other royalty revenue
  
4,103
   
(191
)
  
3,912
 
Total commercial revenue
  
31,680
   
(191
)
  
31,489
 
Research and development revenue under collaborative agreements
  
182,776
   
13,808
   
196,584
 
Total revenue
 
$
214,456
  
$
13,617
  
$
228,073
 
Income from operations
 
$
12,318
  
$
13,617
  
$
25,935
 
Net income (loss)
 
$
(7,739
)
 
$
13,617
  
$
5,878
 
Net income (loss) per share, basic and diluted
 
$
(0.06
)
 
$
0.11
  
$
0.05
 

Condensed Consolidated Statement of Cash Flows

  
Six Months Ended June 30, 2017
 
  
As Previously
Reported under
Topic 605
  
Topic 606
Adjustment
  
As Revised
 
Net income (loss)
 
$
(7,739
)
 
$
13,617
  
$
5,878
 
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
            
Deferred contract revenue
 
$
69,205
  
$
(13,617
)
 
$
55,588
 
Cash and cash equivalents at beginning of period
 
$
84,685
  
$
—
  
$
84,685
 
Cash and cash equivalents at end of period
 
$
132,991
  
$
—
  
$
132,991
 


The following table summarizes the adjustments we were required to make to our deferred revenue amounts to adopt Topic 606 (in thousands):

 
At December 31, 2017
 
 
As Previously
Reported under
Topic 605
 
Topic 606
Adjustment
 
As Revised
 
Current portion of deferred revenue
 
$
106,465
  
$
18,871
  
$
125,336
 
Long-term portion of deferred revenue
  
72,708
   
35,318
   
108,026
 
Total deferred revenue
 
$
179,173
  
$
54,189
  
$
233,362
 
Basic Net Loss per Share
Our basic net loss per share for the three months ended June 30, 2018, was calculated as follows (in thousands, except per share amounts):

Three months ended June 30, 2018
 
Weighted
Average Shares
Owned in Akcea
  
Akcea’s
Net Income (Loss)
Per Share
  
Ionis’ Portion of
Akcea’s Net Loss
 
          
Common shares
  
60,832
  
$
(0.72
)
 
$
(43,814
)
Akcea’s net loss attributable to our ownership
         
$
(43,814
)
Ionis’ stand-alone net income
          
5,882
 
Net loss available to Ionis common stockholders
         
$
(37,932
)
Weighted average shares outstanding
          
128,712
 
Basic net loss per share
         
$
(0.29
)
Basic and Diluted Net Income Per Share

For the six months ended June 30, 2017, we had net income available to Ionis common stockholders. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during those periods. Diluted common equivalent shares for the six months ended June 30, 2017 consisted of the following (in thousands except per share amounts):

Six months ended June 30, 2017
 
Income
(Numerator)
  
Shares
(Denominator)
  
Per-Share
Amount
 
          
Net income available to Ionis common stockholders
 
$
5,878
   
123,428
  
$
0.05
 
Effect of dilutive securities:
            
Shares issuable upon exercise of stock options
  
—
   
1,659
     
Shares issuable upon restricted stock award issuance
  
—
   
401
     
Shares issuable related to our ESPP
  
—
   
23
     
Income available to Ionis common stockholders, plus assumed conversions
 
$
5,878
   
125,511
  
$
0.05
 

For the six months ended June 30, 2017, the calculation excluded the 1 percent and 2¾ percent notes because the effect on diluted earnings per share was anti-dilutive.
Changes in Accumulated Other Comprehensive Income (Loss)
We include unrealized gains and losses on investments, net of taxes, in accumulated other comprehensive income (loss) along with adjustments we make to reclassify realized gains and losses on investments from other accumulated comprehensive income (loss) to our condensed consolidated statement of operations. The following table summarizes changes in accumulated other comprehensive income (loss) for the three and six months ended June 30, 2018 and 2017 (in thousands):

 
 
Three Months Ended
June 30,
  
Six Months Ended
June 30,
 
 
 
2018
  
2017
  
2018
  
2017
 
Beginning balance accumulated other comprehensive loss
 
$
(33,234
)
 
$
(30,460
)
 
$
(31,759
)
 
$
(30,358
)
Unrealized gains (losses) on securities (1)
  
563
   
130
   
(967
)
  
396
 
Amounts reclassified from accumulated other comprehensive loss
  
—
   
—
   
—
   
(374
)
Currency translation adjustment
  
37
   
(42
)
  
92
   
(36
)
Net current period other comprehensive income (loss)
  
600
   
88
   
(875
)
  
(14
)
Ending balance accumulated other comprehensive loss
 
$
(32,634
)
 
$
(30,372
)
 
$
(32,634
)
 
$
(30,372
)

(1)
There was no income tax expense or benefit related to elements of other comprehensive income (loss) for the three and six months ended June 30, 2018 and 2017.
Weighted-Average Assumptions for Stock Options
We use the Black-Scholes model to estimate the fair value of stock options granted and stock purchase rights under our ESPP. The expected term of stock options granted represents the period of time that we expect them to be outstanding. We estimate the expected term of options granted based on historical exercise patterns. For the six months ended June 30, 2018 and 2017, we used the following weighted-average assumptions in our Black-Scholes calculations:

Employee Stock Options:
 
Six Months Ended
June 30,
 
2018
 
2017
Risk-free interest rate
 
2.3%
  
1.8%
Dividend yield
 
0.0%
  
0.0%
Volatility
 
63.1%
  
66.1%
Expected life
 
4.6 years
  
4.5 years
Weighted-Average Assumptions for ESPP
ESPP:
 
Six Months Ended
June 30,
 
2018
 
2017
Risk-free interest rate
 
1.6%
  
0.7%
Dividend yield
 
0.0%
  
0.0%
Volatility
 
44.4%
  
66.5%
Expected life
 
6 months
  
6 months
Stock-Based Compensation Expense
The following table summarizes stock-based compensation expense for the three and six months ended June 30, 2018 and 2017 (in thousands). Our consolidated non-cash stock-based compensation expense includes $12.1 million and $3.9 million of stock-based compensation expense for Akcea for the three months ended June 30, 2018 and 2017, respectively, and $18.5 million and $7.1 million for the six months ended June 30, 2018 and 2017, respectively.

Three Months Ended
June 30,
 
Six Months Ended
June 30,
 
 
2018
 
2017
 
2018
 
2017
 
Research, development and patent
 
$
19,236
  
$
16,140
  
$
38,918
  
$
32,262
 
Selling, general and administrative
  
14,640
   
5,118
   
23,409
   
9,908
 
Total non-cash stock-based compensation expense
 
$
33,876
  
$
21,258
  
$
62,327
  
$
42,170