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Organization and Significant Accounting Policies (Tables) | 12 Months Ended
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Dec. 31, 2018
Organization and Significant Accounting Policies [Abstract] |
Basic Net Loss per Share | Our basic net income per share for 2018, was calculated as follows (in thousands, except per share amounts):
Year Ended December 31, 2018 |  | Weighted Average Shares Owned in Akcea |  |  | Akcea’s Net Income (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 for 2018 as follows (in thousands except per share amounts):
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 ESPP |  |  | — |  |  |  | 6 |  |  |  |  |
Income available to Ionis common stockholders, plus assumed conversions |  | $ | 276,868 |  |  |  | 134,056 |  |  | $ | 2.07 |
We calculated our diluted net income per share for 2017 as follows (in thousands except per share amounts):
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 ESPP |  |  | — |  |  |  | 4 |  |  |  |  |
Income available to Ionis common stockholders, plus assumed conversions |  | $ | 18,792 |  |  |  | 126,098 |  |  | $ | 0.15 |
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 and 2016 to adopt Topic 606 (in thousands, except per share amounts): Consolidated Balance Sheet
|  | At December 31, 2017 |
|  | As Previously Reported under Topic 605 |  |  | Topic 606 Adjustment |  |  | As Revised |
Current portion of deferred contract revenue |  | $ | 106,465 |  |  | $ | 18,871 |  |  | $ | 125,336 |
Long-term portion of deferred contract 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 |
Consolidated Statements of Operations
|  | Year Ended December 31, 2017 |
|  | As Previously Reported under Topic 605 |  |  | Topic 606 Adjustment |  |  | As Revised |
Revenue: |  |  |  |  |  |  |  |  |
Commercial revenue: |  |  |  |  |  |  |  |  |
SPINRAZA royalties |  | $ | 112,540 |  |  | $ | - |  |  | $ | 112,540 |
Licensing and other royalty revenue |  |  | 9,519 |  |  |  | (2,045 | ) |  |  | 7,474 |
Total commercial revenue |  |  | 122,059 |  |  |  | (2,045 | ) |  |  | 120,014 |
Research and development revenue under collaborative agreements |  |  | 385,607 |  |  |  | 8,558 |  |  |  | 394,165 |
Total revenue |  | $ | 507,666 |  |  | $ | 6,513 |  |  | $ | 514,179 |
Income from operations |  | $ | 24,534 |  |  | $ | 6,513 |  |  | $ | 31,047 |
Net income (loss) |  | $ | (17,296 | ) |  | $ | 6,513 |  |  | $ | (10,783 | )
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders |  | $ | (5,970 | ) |  | $ | 6,316 |  |  | $ | 346 |
Net income per share, basic and diluted |  | $ | 0.08 |  |  | $ | 0.07 |  |  | $ | 0.15 |
|  | Year Ended December 31, 2016 |
|  | As Previously Reported under Topic 605 |  |  | Topic 606 Adjustment |  |  | As Revised |
Revenue: |  |  |  |  |  |  |  |  |
Commercial revenue: |  |  |  |  |  |  |  |  |
SPINRAZA royalties |  | $ | 883 |  |  | $ | — |  |  | $ | 883 |
Licensing and other royalty revenue |  |  | 19,839 |  |  |  | 2,045 |  |  |  | 21,884 |
Total commercial revenue |  |  | 20,722 |  |  |  | 2,045 |  |  |  | 22,767 |
Research and development revenue under collaborative agreements |  |  | 325,898 |  |  |  | 24,111 |  |  |  | 350,009 |
Total revenue |  | $ | 346,620 |  |  | $ | 26,156 |  |  | $ | 372,776 |
Income (loss) from operations |  | $ | (46,316 | ) |  | $ | 26,156 |  |  | $ | (20,160 | )
Net income (loss) |  | $ | (86,556 | ) |  | $ | 26,156 |  |  | $ | (60,400 | )
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders |  | $ | (86,556 | ) |  | $ | 26,156 |  |  | $ | (60,400 | )
Net income (loss) per share, basic and diluted |  | $ | (0.72 | ) |  | $ | 0.22 |  |  | $ | (0.50 | )
Consolidated Statements of Cash Flows
|  | Year Ended December 31, 2017 |
|  | As Previously Reported under Topic 605 |  |  | Topic 606 Adjustment |  |  | As Revised |
Net income (loss) |  | $ | (17,296 | ) |  | $ | 6,513 |  |  | $ | (10,783 | )
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities: |  |  |  |  |  |  |  |  |  |  |  |
Deferred contract revenue |  | $ | 36,695 |  |  | $ | (6,513 | ) |  | $ | 30,182 |
Cash and cash equivalents at beginning of year |  | $ | 84,685 |  |  | $ | — |  |  | $ | 84,685 |
Cash and cash equivalents at end of year |  | $ | 129,630 |  |  | $ | — |  |  | $ | 129,630 |
|  | Year Ended December 31, 2016 |
|  | As Previously Reported under Topic 605 |  |  | Topic 606 Adjustment |  |  | As Revised |
Net income (loss) |  | $ | (86,556 | ) |  | $ | 26,156 |  |  | $ | (60,400 | )
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities: |  |  |  |  |  |  |  |  |  |  |  |
Deferred contract revenue |  | $ | (59,150 | ) |  | $ | (26,156 | ) |  | $ | (85,306 | )
Cash and cash equivalents at beginning of year |  | $ | 128,797 |  |  | $ | — |  |  | $ | 128,797 |
Cash and cash equivalents at end of year |  | $ | 84,685 |  |  | $ | — |  |  | $ | 84,685 |
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 contract revenue |  | $ | 106,465 |  |  | $ | 18,871 |  |  | $ | 125,336 |
Long-term portion of deferred contract revenue |  |  | 72,708 |  |  |  | 35,318 |  |  |  | 108,026 |
Total deferred revenue |  | $ | 179,173 |  |  | $ | 54,189 |  |  | $ | 233,362 |
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:
Years Ending December 31, |  | Amortization (in millions) |
2019 |  | $ | 1.7 |
2020 |  | $ | 1.6 |
2021 |  | $ | 1.5 |
2022 |  | $ | 1.4 |
2023 |  | $ | 1.3 |
Accrued Liabilities | Our accrued liabilities consisted of the following (in thousands):
|  | December 31, |
|  | 2018 |  |  | 2017 |
Clinical expenses |  | $ | 22,125 |  |  | $ | 16,347 |
In-licensing expenses |  |  | 12,298 |  |  |  | 33,790 |
Other miscellaneous expenses |  |  | 13,938 |  |  |  | 16,481 |
Total accrued liabilities |  | $ | 48,361 |  |  | $ | 66,618 |
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) |  |  | 2018 |  |  | 2017 |
Computer software, laboratory, manufacturing and other equipment |  | 3 to 10 |  |  | $ | 53,496 |  |  | $ | 66,558 |
Building, building improvements and building systems |  | 15 to 40 |  |  |  | 97,528 |  |  |  | 92,770 |
Land improvements |  |  | 20 |  |  |  | 2,853 |  |  |  | 2,853 |
Leasehold improvements |  | 5 to 15 |  |  |  | 18,981 |  |  |  | 26,748 |
Furniture and fixtures |  | 5 to 10 |  |  |  | 6,283 |  |  |  | 6,161 |
|  |  |  |  |  |  | 179,141 |  |  |  | 195,090 |
Less accumulated depreciation |  |  |  |  |  |  | (61,474 | ) |  |  | (87,676 | )
|  |  |  |  |  |  | 117,667 |  |  |  | 107,414 |
Land |  |  |  |  |  |  | 14,493 |  |  |  | 14,493 |
Total |  |  |  |  |  | $ | 132,160 |  |  | $ | 121,907 |
Changes in Accumulated Other Comprehensive Income (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, 2018, 2017 and 2016 (in thousands):
|  | Year Ended December 31, |
|  | 2018 |  |  | 2017 |  |  | 2016 |
Beginning balance accumulated other comprehensive loss |  | $ | (31,759 | ) |  | $ | (30,358 | ) |  | $ | (13,565 | )
Unrealized losses on securities, net of tax (1) |  |  | (280 | ) |  |  | (960 | ) |  |  | (17,219 | )
Amounts reclassified from accumulated other comprehensive loss |  |  | — |  |  |  | (374 | ) |  |  | 447 |
Currency translation adjustment |  |  | 23 |  |  |  | (67 | ) |  |  | (21 | )
Net other comprehensive loss for the period |  |  | (257 | ) |  |  | (1,401 | ) |  |  | (16,793 | )
Ending balance accumulated other comprehensive loss |  | $ | (32,016 | ) |  | $ | (31,759 | ) |  | $ | (30,358 | )
(1) | A tax benefit of $0.3 million was included in other comprehensive loss for the year ended December 31, 2018. There was no tax benefit or expense for other comprehensive loss for the years ended December 31, 2017 or 2016.
Assets Measured at Fair Value on a Recurring Basis |
|  | 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 (2) |  |  | 1,252,960 |  |  |  | — |  |  |  | 1,252,960 |  |  |  | — |
Debt securities issued by U.S. government agencies (3) |  |  | 276,612 |  |  |  | — |  |  |  | 276,612 |  |  |  | — |
Debt securities issued by the U.S. Treasury (4) |  |  | 260,154 |  |  |  | 260,154 |  |  |  | — |  |  |  | — |
Debt securities issued by states of the U.S. and political subdivisions of the states (3) |  |  | 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 |
|  | At December 31, 2017 |  |  | Quoted Prices in Active Markets (Level 1) |  |  | Significant Other Observable Inputs (Level 2) |
Cash equivalents (1) |  | $ | 86,262 |  |  | $ | 86,262 |  |  | $ | — |
Corporate debt securities (6) |  |  | 647,461 |  |  |  | — |  |  |  | 647,461 |
Debt securities issued by U.S. government agencies (3) |  |  | 136,325 |  |  |  | — |  |  |  | 136,325 |
Debt securities issued by the U.S. Treasury (3) |  |  | 30,818 |  |  |  | 30,818 |  |  |  | — |
Debt securities issued by states of the U.S. and political subdivisions of the states (7) |  |  | 93,932 |  |  |  | — |  |  |  | 93,932 |
Total |  | $ | 994,798 |  |  | $ | 117,080 |  |  | $ | 877,718 |
(1) | Included in cash and cash equivalents on our consolidated balance sheet.
(2) | $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.
(3) | Included in short-term investments on our consolidated balance sheet.
(4) | $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.
(5) | Included in other current assets on our consolidated balance sheet.
(6) | $11.9 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) | $3.5 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.
Reconciliation of Assets Measured at Fair Value on a Recurring Basis Using Significant Unobservable Inputs (Level 3) | The following is a reconciliation of the potential premium we would have received if Akcea had not completed its IPO, measured at fair value on a recurring basis using significant unobservable inputs (Level 3) for 2017 (in thousands):
|  | Year Ended December 31, 2017 |
Beginning balance of Level 3 instruments |  | $ | — |
Value of the potential premium we will receive from Novartis at inception of the SPA (January 2017) |  |  | 5,035 |
Write-off of premium to other expenses |  |  | (5,035 | )
Ending balance of Level 3 instruments |  | $ | — |

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Data Type: | nonnum:textBlockItemType
Balance Type: | na
Period Type: | duration