Organization and Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2020

Organization and Significant Accounting Policies [Abstract]

Basic Net Income (Loss) per Share

Our basic net income (loss) per share was calculated as follows (in thousands, except per share amounts):

Year Ended December 31, 2020	Weighted Average Shares Owned in Akcea		Akcea’s Net Loss Per Share			Basic Net Loss Per Share Calculation
Akcea’s net loss in the pre-acquisition period attributable to our ownership		77,095	$	(1.45	)	$	(111,775	)
Akcea’s net loss in the post-acquisition period attributable to our ownership							(85,987	)
Akcea’s total net loss attributable to our ownership						$	(197,762	)
Ionis’ stand-alone net loss							(253,725	)
Net loss available to Ionis common stockholders						$	(451,487	)
Weighted average shares outstanding							139,612
Basic net loss per share						$	(3.23	)

Year Ended December 31, 2019	Weighted Average Shares Owned in Akcea		Akcea’s Net Income Per Share		Basic Net Income Per Share Calculation
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			Basic Net Income Per Share Calculation
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

Basic and Diluted Net Income Per Share

For the years ended December 31, 2019 and 2018, 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 each period. 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 ESPP		—		18
	$	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 ESPP		—		6
	$	276,868		134,056	$	2.07

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)
2021	$	2.1
2022	$	2.0
2023	$	1.9
2024	$	1.7
2025	$	1.6

Accrued Liabilities

Our accrued liabilities consisted of the following (in thousands):

	December 31,
	2020		2019
Clinical expenses	$	39,477	$	24,461
In-licensing expenses		8,264		10,289
Commercial expenses		11,559		6,020
Other miscellaneous expenses		30,861		25,999
Total accrued liabilities	$	90,161	$	66,769

Inventory

Our inventory consisted of the following (in thousands):

	December 31,
	2020		2019
Raw materials:
Raw materials- clinical	$	9,206	$	9,363
Raw materials- commercial		7,502		6,520
Total raw materials		16,708		15,883
Work in process		2,252		2,039
Finished goods		3,005		258
Total inventory	$	21,965	$	18,180

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)		2020			2019
Computer software, laboratory, manufacturing and other equipment	3 to 10		$	68,990		$	60,965
Building, building improvements and building systems	15 to 40			137,879			119,830
Land improvements		20		8,391			2,853
Leasehold improvements	5 to 15			17,263			13,600
Furniture and fixtures	5 to 10			12,871			7,354
				245,394			204,602
Less accumulated depreciation				(87,379	)		(74,013	)
				158,015			130,589
Land				23,062			23,062
Total			$	181,077		$	153,651

Changes in Accumulated Other Comprehensive Loss

Accumulated other comprehensive loss is comprised of unrealized gains and losses on investments, net of taxes and currency translation adjustments. The following table summarizes changes in accumulated other comprehensive loss for the years ended December 31, 2020, 2019 and 2018 (in thousands):

	Year Ended December 31,
	2020			2019			2018
Beginning balance accumulated other comprehensive loss	$	(25,290	)	$	(32,016	)	$	(31,759	)
Unrealized gains (losses) on securities, net of tax (1)		3,729			6,633			(280	)
Currency translation adjustment		617			93			23
Adjustments to other comprehensive loss from purchase of noncontrolling interest of Akcea Therapeutics, Inc.		(127	)		—			—
Net other comprehensive loss for the period		4,219			6,726			(257	)
Ending balance accumulated other comprehensive loss	$	(21,071	)	$	(25,290	)	$	(32,016	)

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(1) We did not have tax expense included in our other comprehensive loss for the year ended December 31, 2020. For the years ended December 31, 2019 and 2018, we had a tax benefit $1.4 million and $0.3 million included in other comprehensive loss respectively. 

Assets Measured at Fair Value on a Recurring Basis

The following tables present the major security types we held at December 31, 2020 and 2019 that we regularly measure and carry at fair value. At December 31, 2019, our ProQR investment was subject to trading restrictions until 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. As of December 31, 2020, our ProQR investment was no longer subject to trading restrictions. As of December 31, 2020, we did not have any investments which we valued using Level 3 inputs. The following 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, 2020		Quoted Prices in Active Markets (Level 1)		Significant Other Observable Inputs (Level 2)
Cash equivalents (1)	$	221,125	$	221,125	$	—
Corporate debt securities (2)		846,315		—		846,315
Debt securities issued by U.S. government agencies (4)		174,861		—		174,861
Debt securities issued by the U.S. Treasury (3)		358,497		358,497		—
Debt securities issued by states of the U.S. and political subdivisions of the states (4)		136,309		—		136,309
Other municipal debt securities (4)		6,225		—		6,225
Investment in ProQR Therapeutics N.V. (5)		2,031		2,031		—
Total	$	1,745,363	$	581,653	$	1,163,710

	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 (6)		1,102,568		—		1,102,568		—
Debt securities issued by U.S. government agencies (7)		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

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(1) Included in cash and cash equivalents on our consolidated balance sheet.

(2) $10.0 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) $17.5 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.

(4) Included in short-term investments.

(5) Included in other current assets on our consolidated balance sheet.

(6) $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.

(7) $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.