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Income Taxes (Tables) | 12 Months Ended
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Dec. 31, 2019
Income Taxes [Abstract] |
Income (Loss) Before Income Taxes | Income (loss) before income taxes is comprised of (in thousands):
|  | Year Ended December 31, |
|  | 2019 |  |  | 2018 |  |  | 2017 |
United States |  | $ | 344,280 |  |  | $ | (69,576 | ) |  | $ | (5,289 | )
Foreign |  |  | 2,489 |  |  |  | (6,580 | ) |  |  | (11,474 | )
Income (loss) before income taxes |  | $ | 346,769 |  |  | $ | (76,156 | ) |  | $ | (16,763 | )
Income Tax Expense (Benefit) | Our income tax expense (benefit) was as follows (in thousands):
|  | Year Ended December 31, |
|  | 2019 |  |  | 2018 |  |  | 2017 |
Current: |  |  |  |  |  |  |  |  |
Federal |  | $ | 35,861 |  |  | $ | 438 |  |  | $ | (7,460 | )
State |  |  | 14,329 |  |  |  | (1,442 | ) |  |  | 1,246 |
Foreign |  |  | 413 |  |  |  | 374 |  |  |  | 234 |
Total current income tax expense (benefit) |  |  | 50,603 |  |  |  | (630 | ) |  |  | (5,980 | )
Deferred: |  |  |  |  |  |  |  |  |  |  |  |
Federal |  |  | (7,096 | ) |  |  | (290,511 | ) |  |  | — |
State |  |  | — |  |  |  | — |  |  |  | — |
Total deferred income tax benefit |  |  | (7,096 | ) |  |  | (290,511 | ) |  |  | — |
Total income tax expense (benefit) |  | $ | 43,507 |  |  | $ | (291,141 | ) |  | $ | (5,980 | )
Reconciliation of Statutory to Effective Tax Rate | Our expense (benefit) for income taxes differs from the amount computed by applying the U.S. federal statutory rate to income (loss) before taxes. The sources and tax effects of the differences are as follows (in thousands):
|  | Year Ended December 31, |
|  | 2019 |  |  | 2018 |  |  | 2017 |
Pre-tax income (loss) |  | $ | 346,769 |  |  |  |  |  | $ | (76,156 | ) |  |  |  |  | $ | (16,763 | ) |  |  |
Statutory rate |  |  | 72,822 |  |  |  | 21.0 | % |  |  | (15,993 | ) |  |  | 21.0 | % |  |  | (5,867 | ) |  |  | 35.0 | %
State income tax net of federal benefit |  |  | 49,119 |  |  |  | 14.2 | % |  |  | (2,202 | ) |  |  | 2.9 | % |  |  | 820 |  |  |  | (4.9 | )%
Foreign |  |  | 340 |  |  |  | 0.1 | % |  |  | 1,735 |  |  |  | (2.3 | )% |  |  | 4,299 |  |  |  | (25.6 | )%
Net change in valuation allowance |  |  | (37,765 | ) |  |  | (10.9 | )% |  |  | (277,924 | ) |  |  | 364.9 | % |  |  | (86,296 | ) |  |  | 514.8 | %
Net operating loss expiration |  |  | — |  |  |  | 0.0 | % |  |  | 8,864 |  |  |  | (11.6 | )% |  |  | 3,987 |  |  |  | (23.8 | )%
TEGSEDI licensing gain |  |  | — |  |  |  | 0.0 | % |  |  | 59,583 |  |  |  | (78.2 | )% |  |  | — |  |  |  | 0.0 | %
Impact from outside basis differences |  |  | (16,344 | ) |  |  | (4.7 | )% |  |  | — |  |  |  | 0.0 | % |  |  | — |  |  |  | 0.0 | %
Tax credits |  |  | (22,296 | ) |  |  | (6.4 | )% |  |  | (73,362 | ) |  |  | 96.3 | % |  |  | (32,769 | ) |  |  | 195.5 | %
Deferred tax true-up |  |  | 646 |  |  |  | 0.2 | % |  |  | 9,947 |  |  |  | (13.1 | )% |  |  | 4,848 |  |  |  | (28.9 | )%
Tax rate change |  |  | 1,811 |  |  |  | 0.5 | % |  |  | (1,808 | ) |  |  | 2.4 | % |  |  | 114,832 |  |  |  | (685.0 | )%
Non-deductible compensation |  |  | 3,361 |  |  |  | 1.0 | % |  |  | 3,154 |  |  |  | (4.1 | )% |  |  | 1,575 |  |  |  | (9.4 | )%
Other non-deductible items |  |  | 329 |  |  |  | 0.1 | % |  |  | (569 | ) |  |  | 0.7 | % |  |  | 2,548 |  |  |  | (15.2 | )%
Akcea deconsolidation adjustment at IPO |  |  | — |  |  |  | 0.0 | % |  |  | — |  |  |  | 0.0 | % |  |  | 469 |  |  |  | (2.8 | )%
Stock-based compensation |  |  | (4,837 | ) |  |  | (1.4 | )% |  |  | (4,199 | ) |  |  | 5.5 | % |  |  | (14,337 | ) |  |  | 85.5 | %
Foreign-derived intangible income benefit |  |  | (2,071 | ) |  |  | (0.6 | )% |  |  | — |  |  |  | 0.0 | % |  |  | — |  |  |  | 0.0 | %
Other |  |  | (1,608 | ) |  |  | (0.5 | )% |  |  | 1,633 |  |  |  | (2.1 | )% |  |  | (89 | ) |  |  | 0.5 | %
Effective rate |  | $ | 43,507 |  |  |  | 12.6 | % |  | $ | (291,141 | ) |  |  | 382.3 | % |  | $ | (5,980 | ) |  |  | 35.7 | %
Deferred Tax Assets and Liabilities | Significant components of our deferred tax assets and liabilities as of December 31, 2019 and 2018 are as follows (in thousands):
|  | Year Ended December 31, |
|  | 2019 |  |  | 2018 |
Deferred Tax Assets: |  |  |  |  |  |
Net operating loss carryovers |  | $ | 20,191 |  |  | $ | 89,717 |
R&D credits |  |  | 210,455 |  |  |  | 313,652 |
Deferred revenue |  |  | 127,763 |  |  |  | 27,381 |
Stock-based compensation |  |  | 65,703 |  |  |  | 61,027 |
Intangible and capital assets |  |  | 77,861 |  |  |  | 49,007 |
Other |  |  | 12,510 |  |  |  | 8,275 |
Total deferred tax assets |  | $ | 514,483 |  |  | $ | 549,059 |
Deferred Tax Liabilities: |  |  |  |  |  |  |  |
Convertible debt |  | $ | (6,110 | ) |  | $ | (24,018 | )
Fixed assets |  |  | (1,958 | ) |  |  | — |
Other |  |  | (3,884 | ) |  |  | — |
Net deferred tax asset |  | $ | 502,531 |  |  | $ | 525,041 |
Valuation allowance |  |  | (196,974 | ) |  |  | (234,245 | )
Total net deferred tax assets and liabilities |  | $ | 305,557 |  |  | $ | 290,796 |
Gross Unrecognized Tax Benefits | The following table summarizes our gross unrecognized tax benefits (in thousands):
|  | Year Ended December 31, |
|  | 2019 |  |  | 2018 |  |  | 2017 |
Beginning balance of unrecognized tax benefits |  | $ | 68,301 |  |  | $ | 78,014 |  |  | $ | 66,999 |
Decrease for prior period tax positions |  |  | (867 | ) |  |  | (12,814 | ) |  |  | — |
Increase for prior period tax positions |  |  | 736 |  |  |  | — |  |  |  | 1,520 |
Increase for current period tax positions |  |  | 1,614 |  |  |  | 3,101 |  |  |  | 9,495 |
Ending balance of unrecognized tax benefits |  | $ | 69,784 |  |  | $ | 68,301 |  |  | $ | 78,014 |

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