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Organization and Significant Accounting Policies (Tables) | 12 Months Ended
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Dec. 31, 2019
Organization and Significant Accounting Policies [Abstract] |
Basic Net Income per Share | Our basic net income per share, was calculated as follows (in thousands, except per share amounts):
Year Ended December 31, 2019 |  | Weighted Average Shares Owned in Akcea |  |  | Akcea’s Net Income Per Share |  |  | Ionis’ Portion of Akcea’s Net Income |
Common shares |  |  | 70,100 |  |  | $ | 0.49 |  |  | $ | 34,073 |
Akcea’s net income attributable to our ownership |  |  |  |  |  |  |  |  |  | $ | 34,073 |
Ionis’ stand-alone net income |  |  |  |  |  |  |  |  |  |  | 262,490 |
Net income available to Ionis common stockholders |  |  |  |  |  |  |  |  |  | $ | 296,563 |
Weighted average shares outstanding |  |  |  |  |  |  |  |  |  |  | 139,998 |
Basic net income per share |  |  |  |  |  |  |  |  |  | $ | 2.12 |
Year Ended December 31, 2018 |  | Weighted Average Shares Owned in Akcea |  |  | Akcea’s Net Loss Per Share |  |  | Ionis’ Portion of Akcea’s Net Loss |
Common shares |  |  | 59,812 |  |  | $ | (2.74 | ) |  | $ | (163,938 | )
Akcea’s net loss attributable to our ownership |  |  |  |  |  |  |  |  |  | $ | (163,938 | )
Ionis’ stand-alone net income |  |  |  |  |  |  |  |  |  |  | 440,806 |
Net income available to Ionis common stockholders |  |  |  |  |  |  |  |  |  | $ | 276,868 |
Weighted average shares outstanding |  |  |  |  |  |  |  |  |  |  | 132,320 |
Basic net income per share |  |  |  |  |  |  |  |  |  | $ | 2.09 |
We calculated our basic net income per share for 2017 as follows (in thousands, except per share amounts):
Year Ended December 31, 2017 |  | Weighted Average Shares Owned in Akcea |  |  | Akcea’s Net Loss Per Share |  |  | Ionis’ Portion of Akcea’s Net Loss |
Common shares |  |  | 20,669 |  |  | $ | (3.08 | ) |  | $ | (63,638 | )
Preferred shares |  |  | 15,748 |  |  |  | (1.80 | ) |  |  | (28,346 | )
Akcea’s net loss attributable to our ownership |  |  |  |  |  |  |  |  |  | $ | (91,984 | )
Ionis’ stand-alone net income |  |  |  |  |  |  |  |  |  |  | 110,776 |
Net income available to Ionis common stockholders |  |  |  |  |  |  |  |  |  | $ | 18,792 |
Weighted average shares outstanding |  |  |  |  |  |  |  |  |  |  | 124,016 |
Basic net income per share |  |  |  |  |  |  |  |  |  | $ | 0.15 |
Basic and Diluted Net Income Per Share | We calculated our diluted net income per share as follows (in thousands except per share amounts):
Year Ended December 31, 2019 |  | Income (Numerator) |  |  | Shares (Denominator) |  |  | Per-Share Amount |
Net income available to Ionis common stockholders |  | $ | 296,563 |  |  |  | 139,998 |  |  | $ | 2.12 |
Effect of dilutive securities: |  |  |  |  |  |  |  |  |  |  |  |
Shares issuable upon exercise of stock options |  |  | — |  |  |  | 2,090 |  |  |  |  |
Shares issuable upon restricted stock award issuance |  |  | — |  |  |  | 766 |  |  |  |  |
Shares issuable related to our Employee Stock Purchase Plan |  |  | — |  |  |  | 18 |  |  |  |  |
Income available to Ionis common stockholders, plus assumed conversions |  | $ | 296,563 |  |  |  | 142,872 |  |  | $ | 2.08 |
Year Ended December 31, 2018 |  | Income (Numerator) |  |  | Shares (Denominator) |  |  | Per-Share Amount |
Net income available to Ionis common stockholders |  | $ | 276,868 |  |  |  | 132,320 |  |  | $ | 2.09 |
Effect of dilutive securities: |  |  |  |  |  |  |  |  |  |  |  |
Shares issuable upon exercise of stock options |  |  | — |  |  |  | 1,216 |  |  |  |  |
Shares issuable upon restricted stock award issuance |  |  | — |  |  |  | 514 |  |  |  |  |
Shares issuable related to our Employee Stock Purchase Plan |  |  | — |  |  |  | 6 |  |  |  |  |
Income available to Ionis common stockholders, plus assumed conversions |  | $ | 276,868 |  |  |  | 134,056 |  |  | $ | 2.07 |
Year Ended December 31, 2017 |  | Income (Numerator) |  |  | Shares (Denominator) |  |  | Per-Share Amount |
Net income available to Ionis common stockholders |  | $ | 18,792 |  |  |  | 124,016 |  |  | $ | 0.15 |
Effect of dilutive securities: |  |  |  |  |  |  |  |  |  |  |  |
Shares issuable upon exercise of stock options |  |  | — |  |  |  | 1,619 |  |  |  |  |
Shares issuable upon restricted stock award issuance |  |  | — |  |  |  | 459 |  |  |  |  |
Shares issuable related to our Employee Stock Purchase Plan |  |  | — |  |  |  | 4 |  |  |  |  |
Income available to Ionis common stockholders, plus assumed conversions |  | $ | 18,792 |  |  |  | 126,098 |  |  | $ | 0.15 |
Amortization Expense for Patents | Based on our existing patents, we estimate amortization expense related to patents in each of the next five years to be the following:
Year Ending December 31, |  | Amortization (in millions) |
2020 |  | $ | 1.8 |
2021 |  | $ | 1.8 |
2022 |  | $ | 1.7 |
2023 |  | $ | 1.6 |
2024 |  | $ | 1.4 |
Accrued Liabilities | Our accrued liabilities consisted of the following (in thousands):
|  | December 31, |
|  | 2019 |  |  | 2018 |
Clinical expenses |  | $ | 24,461 |  |  | $ | 22,125 |
In-licensing expenses |  |  | 10,289 |  |  |  | 12,298 |
Other miscellaneous expenses |  |  | 32,019 |  |  |  | 13,080 |
Total accrued liabilities |  | $ | 66,769 |  |  | $ | 47,503 |
Inventory | Our inventory consisted of the following (in thousands):
|  | December 31, |
|  | 2019 |  |  | 2018 |
Raw materials: |  |  |  |  |  |
Raw materials- clinical |  | $ | 9,363 |  |  | $ | 8,497 |
Raw materials- commercial |  |  | 6,520 |  |  |  | — |
Total raw materials |  |  | 15,883 |  |  |  | 8,497 |
Work in process |  |  | 2,039 |  |  |  | — |
Finished goods |  |  | 258 |  |  |  | 85 |
Total inventory |  | $ | 18,180 |  |  | $ | 8,582 |
Property, Plant and Equipment | We carry our property, plant and equipment at cost and depreciate it on the straight-line method over its estimated useful life, which consists of the following (in thousands):
|  | Estimated Useful Lives |  |  | December 31, |
|  | (in years) |  |  | 2019 |  |  | 2018 |
Computer software, laboratory, manufacturing and other equipment |  | 3 to 10 |  |  | $ | 60,965 |  |  | $ | 53,496 |
Building, building improvements and building systems |  | 15 to 40 |  |  |  | 119,830 |  |  |  | 97,528 |
Land improvements |  |  | 20 |  |  |  | 2,853 |  |  |  | 2,853 |
Leasehold improvements |  | 5 to 15 |  |  |  | 13,600 |  |  |  | 18,981 |
Furniture and fixtures |  | 5 to 10 |  |  |  | 7,354 |  |  |  | 6,283 |
|  |  |  |  |  |  | 204,602 |  |  |  | 179,141 |
Less accumulated depreciation |  |  |  |  |  |  | (74,013 | ) |  |  | (61,474 | )
|  |  |  |  |  |  | 130,589 |  |  |  | 117,667 |
Land |  |  |  |  |  |  | 23,062 |  |  |  | 14,493 |
Total |  |  |  |  |  | $ | 153,651 |  |  | $ | 132,160 |
Changes in Accumulated Other Comprehensive Loss | Accumulated other comprehensive loss is primarily comprised of unrealized gains and losses on investments, net of taxes and adjustments we made to reclassify realized gains and losses on investments from other accumulated comprehensive loss to our Consolidated Statement of Operations. The following table summarizes changes in accumulated other comprehensive loss for the years ended December 31, 2019, 2018 and 2017 (in thousands):
|  | Year Ended December 31, |
|  | 2019 |  |  | 2018 |  |  | 2017 |
Beginning balance accumulated other comprehensive loss |  | $ | (32,016 | ) |  | $ | (31,759 | ) |  | $ | (30,358 | )
Unrealized gains (losses) on securities, net of tax (1) |  |  | 6,633 |  |  |  | (280 | ) |  |  | (960 | )
Amounts reclassified from accumulated other comprehensive loss |  |  | — |  |  |  | — |  |  |  | (374 | )
Currency translation adjustment |  |  | 93 |  |  |  | 23 |  |  |  | (67 | )
Net other comprehensive loss for the period |  |  | 6,726 |  |  |  | (257 | ) |  |  | (1,401 | )
Ending balance accumulated other comprehensive loss |  | $ | (25,290 | ) |  | $ | (32,016 | ) |  | $ | (31,759 | )
(1) | A tax benefit of $1.4 million and $0.3 million was included in other comprehensive loss for the years ended December 31, 2019 and 2018, respectively. There was no tax benefit or expense for other comprehensive loss for the year ended December 31, 2017.
Assets Measured at Fair Value on a Recurring Basis | The following tables present the major security types we held at December 31, 2019 and 2018 that we regularly measure and carry at fair value. At December 31, 2019, a portion of our ProQR investment was subject to trading restrictions through the fourth quarter of 2020, as a result we included a lack of marketability discount in valuing this investment, which is a Level 3 input. At December 31, 2018, our ProQR investment was subject to trading restrictions through the fourth quarter of 2019, as a result we included a lack of marketability discount in valuing this investment, which is a Level 3 input. The tables segregate each security type by the level within the fair value hierarchy of the valuation techniques we utilized to determine the respective securities’ fair value (in thousands):
|  | At December 31, 2019 |  |  | Quoted Prices in Active Markets (Level 1) |  |  | Significant Other Observable Inputs (Level 2) |  |  | Significant Unobservable Inputs (Level 3) |
Cash equivalents (1) |  | $ | 418,406 |  |  | $ | 418,406 |  |  | $ | — |  |  | $ | — |
Corporate debt securities (2) |  |  | 1,102,568 |  |  |  | — |  |  |  | 1,102,568 |  |  |  | — |
Debt securities issued by U.S. government agencies (3) |  |  | 329,404 |  |  |  | — |  |  |  | 329,404 |  |  |  | — |
Debt securities issued by the U.S. Treasury (4) |  |  | 363,694 |  |  |  | 363,694 |  |  |  | — |  |  |  | — |
Debt securities issued by states of the U.S. and political subdivisions of the states (4) |  |  | 40,407 |  |  |  | — |  |  |  | 40,407 |  |  |  | — |
Investment in ProQR Therapeutics N.V. (5) |  |  | 4,506 |  |  |  | — |  |  |  | — |  |  |  | 4,506 |
Total |  | $ | 2,258,985 |  |  | $ | 782,100 |  |  | $ | 1,472,379 |  |  | $ | 4,506 |
|  | At December 31, 2018 |  |  | Quoted Prices in Active Markets (Level 1) |  |  | Significant Other Observable Inputs (Level 2) |  |  | Significant Unobservable Inputs (Level 3) |
Cash equivalents (1) |  | $ | 146,281 |  |  | $ | 146,281 |  |  | $ | — |  |  | $ | — |
Corporate debt securities (6) |  |  | 1,252,960 |  |  |  | — |  |  |  | 1,252,960 |  |  |  | — |
Debt securities issued by U.S. government agencies (4) |  |  | 276,612 |  |  |  | — |  |  |  | 276,612 |  |  |  | — |
Debt securities issued by the U.S. Treasury (7) |  |  | 260,154 |  |  |  | 260,154 |  |  |  | — |  |  |  | — |
Debt securities issued by states of the U.S. and political subdivisions of the states (4) |  |  | 79,942 |  |  |  | — |  |  |  | 79,942 |  |  |  | — |
Investment in ProQR Therapeutics N.V. (5) |  |  | 1,349 |  |  |  | — |  |  |  | — |  |  |  | 1,349 |
Total |  | $ | 2,017,298 |  |  | $ | 406,435 |  |  | $ | 1,609,514 |  |  | $ | 1,349 |
________________
(1) | Included in cash and cash equivalents on our consolidated balance sheet.
(2) | $19.0 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.
(3) | $0.8 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.
(4) | Included in short-term investments.
(5) | Included in other current assets on our consolidated balance sheet.
(6) | $50.2 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.
(7) | $14.2 million included in cash and cash equivalents on our consolidated balance sheet, with the difference included in short-term investments on our consolidated balance sheet.

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