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Significant Accounting Policies (Tables)
 6 Months Ended
Jun. 30, 2021
Significant Accounting Policies [Abstract]  
Inventory

Our inventory consisted of the following (in thousands):

 
June 30, 2021
  
December 31, 2020
Raw materials:
          
Raw materials- clinical
$
11,987
  
$
9,206
Raw materials- commercial
  
9,599
    
7,502
Total raw materials
  
21,586
    
16,708
Work in process
  
954
    
2,252
Finished goods
  
1,559
    
3,005
Total inventory
$
24,099
  
$
21,965
Basic Net Loss per Share

We calculated our basic net loss per share for the three months ended June 30, 2020 as follows (in thousands, except per share amounts):

Three months ended June 30, 2020
  
Weighted
Average Shares
Owned in Akcea
    
Akcea’s
Net Loss
Per Share
    
Basic
Net Loss Per
Share Calculation
(as revised*)
  
Ionis’ portion of Akcea’s net loss
    
77,095
    
$
(0.49
)
  
$
(37,665
)
Akcea’s net loss attributable to our ownership
                  
$
(37,665
)
Ionis’ stand-alone net income
                    
12,016
  
Net loss available to Ionis common stockholders
                  
$
(25,649
)
Weighted average shares outstanding
                    
139,352
  
Basic net loss per share
                  
$
(0.18
)
Adoption of ASU 2020-06

The following table summarizes the adjustments we made to the condensed consolidated balance sheet we originally reported at December 31, 2020 to adopt ASU 2020-06 (in thousands):

  
December 31, 2020
  
   
As Previously
Reported
    
ASU 2020-06
Adjustment
    
As Revised
  
1 percent convertible senior notes
  
$
293,161
    
$
15,648
    
$
308,809
  
0.125 percent convertible senior notes
  
$
455,719
    
$
84,417
    
$
540,136
  
Additional paid-in-capital
  
$
2,113,646
    
$
(218,127
)
  
$
1,895,519
  
Accumulated deficit
  
$
(1,249,368
)
  
$
118,062
    
$
(1,131,306
)


The following tables summarize the adjustments we made to the condensed consolidated statement of operations we originally reported for the three and six months ended June 30, 2020 to adopt ASU 2020-06 (in thousands):

  
Three Months Ended June 30, 2020
  
   
As Previously
Reported
    
ASU 2020-06
Adjustment
    
As Revised
  
Interest expense
  
$
(11,173
)
  
$
8,732
    
$
(2,441
)
Loss before income tax benefit
  
$
(44,208
)
  
$
8,732
    
$
(35,476
)
Income tax benefit (expense)
  
$
439
    
$
(2,523
)
  
$
(2,084
)
Net loss
  
$
(43,769
)
  
$
6,209
    
$
(37,560
)
Net loss attributable to Ionis Pharmaceuticals, Inc. common stockholders
  
$
(31,845
)
  
$
6,209
    
$
(25,636
)
Basic and diluted net loss per share
  
$
(0.23
)
  
$
0.05
    
$
(0.18
)

 
Six Months Ended June 30, 2020
  
   
As Previously
Reported
    
ASU 2020-06
Adjustment
    
As Revised
  
Interest expense
  
$
(22,163
)
  
$
17,515
    
$
(4,648
)
Loss before income tax benefit
  
$
(105,945
)
  
$
17,515
    
$
(88,430
)
Income tax benefit
  
$
3,696
    
$
(2,708
)
  
$
988
  
Net loss
  
$
(102,249
)
  
$
14,807
    
$
(87,442
)
Net loss attributable to Ionis Pharmaceuticals, Inc. common stockholders
  
$
(80,071
)
  
$
14,807
    
$
(65,264
)
Basic and diluted net loss per share
  
$
(0.58
)
  
$
0.11
    
$
(0.47
)

The following tables summarize the adjustments we made to our condensed consolidated statements of stockholders’ equity we originally reported at December 31, 2020 and 2019 to adopt ASU 2020-06 (in thousands):
December 31, 2020
  
 
As Previously
Reported
  
ASU 2020-06
Adjustment
  
As Revised
  
Additional paid-in-capital
  
$
2,113,646
    
$
(218,127
)
  
$
1,895,519
  
Accumulated deficit
  
$
(1,249,368
)
  
$
118,062
    
$
(1,131,306
)
Total stockholders’ equity
  
$
843,347
    
$
(100,065
)
  
$
743,282
  

December 31, 2019
  
 
As Previously
Reported
  
ASU 2020-06
Adjustment
  
As Revised
  
Additional paid-in-capital
  
$
2,203,778
    
$
(218,128
)
  
$
1,985,650
  
Accumulated deficit
  
$
(707,534
)
  
$
111,039
    
$
(596,495
)
Total stockholders’ equity
  
$
1,684,547
    
$
(107,089
)
  
$
1,577,458
  
Weighted-Average Assumptions for Stock Options

Employee Stock Options:
  
Six Months Ended
June 30,
  
   
2021
    
2020
  
Risk-free interest rate
    
0.5
%
    
1.6
%
Dividend yield
    
0.0
%
    
0.0
%
Volatility
    
54.8
%
    
58.9
%
Expected life
  
4.9 years
    
4.7 years
  
Weighted-Average Assumptions for ESPP

ESPP:
  
Six Months Ended
June 30,
  
   
2021
    
2020
  
Risk-free interest rate
    
0.1
%
    
1.1
%
Dividend yield
    
0.0
%
    
0.0
%
Volatility
    
39.1
%
    
47.2
%
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, 2021 and 2020 (in thousands).

 
Three Months Ended
June 30,
    
Six Months Ended
June 30,
  
 
2021
    
2020
    
2021
    
2020
  
Cost of sales
  
$
—
    
$
350
    
$
182
    
$
587
  
Research, development and patent expense
    
22,748
      
26,016
      
48,647
      
51,573
  
Selling, general and administrative expense
    
7,274
      
22,076
      
19,053
      
37,073
  
Total non-cash stock-based compensation expense
  
$
30,022
    
$
48,442
    
$
67,882
    
$
89,233