0001070081-23-000065 | 10-Q | XBRL Viewer

Fair value of financial instruments and investments - Marketable Securities, Unrealized Gains (Losses) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Dec. 31, 2022
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	$ 1,649		$ 1,649		$ 23,104
Gross Unrealized, Gain					5
Gross Unrealized, Loss	(24)		(24)		(499)
Fair Value	1,625		1,625		22,610
Write downs of available for sale debt securities	0	$ 0	0	$ 0
Increase in allowance for credit losses	0	0	0	0
Realized gain (loss) from sale of marketable securities	0	$ (1,300)	(300)	$ (1,600)
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Amortized Cost					12,419
Gross Unrealized, Gain					5
Gross Unrealized, Loss					0
Fair Value					12,424
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Amortized Cost	1,649		1,649		10,685
Gross Unrealized, Gain	0		0
Gross Unrealized, Loss	(24)		(24)		(499)
Fair Value	$ 1,625		$ 1,625		$ 10,186

Fair value of financial instruments and investments - Fair Value Liabilities Measured (Details) - Agilis - Commitments $ in Thousands	Sep. 30, 2023 USD ($)	Dec. 31, 2022 USD ($)	Sep. 30, 2022 USD ($)	Dec. 31, 2021 USD ($)
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Development and Regulatory Milestone \| Minimum
Fair Value Valuation Inputs
Potential milestones	$ 0	$ 0
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Development and Regulatory Milestone \| Maximum
Fair Value Valuation Inputs
Potential milestones	$ 31,000	$ 331,000
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.85	0.25
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.92	0.92
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Probability of Success \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.90
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.069	0.062
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.076	0.083
Development and Regulatory Milestones \| Valuation Technique, Discounted Cash Flow \| Measurement Input, Discount Rate \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.071
Development and Regulatory Milestones \| Significant unobservable inputs (Level 3)
Fair Value Valuation Inputs
Fair value	$ 26,400	$ 82,500	$ 78,500	$ 139,300
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Sales Milestones \| Minimum
Fair Value Valuation Inputs
Potential milestones	0	0
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Sales Milestones \| Maximum
Fair Value Valuation Inputs
Potential milestones	$ 50,000	$ 150,000
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Probability of Success \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.85	0.25
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Probability of Success \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	1	1
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Probability of Success \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.93
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties \| Minimum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement		0.02
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Percentage of Sales for Royalties \| Maximum
Fair Value Valuation Inputs
Rights Exchange Settlement measurement		0.06
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Measurement Input, Discount Rate
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.12	0.115
Net Sales Milestones and Royalties \| Valuation Technique, Option Pricing Model \| Measurement Input, Discount Rate \| Weighted Average
Fair Value Valuation Inputs
Rights Exchange Settlement measurement	0.120
Net Sales Milestones and Royalties \| Significant unobservable inputs (Level 3)
Fair Value Valuation Inputs
Fair value	$ 12,600	$ 81,500	$ 79,200	$ 100,600

Stock award plan - Share-based compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Stock option plan
Share-based compensation expense	$ 26,942	$ 28,670	$ 85,128	$ 82,989
Unrecognized compensation cost	179,300		$ 179,300
Weighted average remaining service period for recognition of unrecognized compensation cost			1 year 10 months 24 days
Research and development
Stock option plan
Share-based compensation expense	13,986	15,063	$ 44,828	41,896
Selling, general and administrative
Stock option plan
Share-based compensation expense	$ 12,956	$ 13,607	$ 40,300	$ 41,093

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 35
-Paragraph 1D
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480483/718-10-35-1D

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org//1943274/2147480483/718-10-35-3

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
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-URI https://asc.fasb.org//1943274/2147480429/718-10-50-2

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
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Reference 5: http://www.xbrl.org/2003/role/disclosureRef
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Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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Reference 7: http://www.xbrl.org/2003/role/disclosureRef
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Reference 8: http://www.xbrl.org/2003/role/disclosureRef
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Reference 9: http://www.xbrl.org/2003/role/disclosureRef
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Reference 12: http://www.xbrl.org/2003/role/disclosureRef
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Reference 13: http://www.xbrl.org/2003/role/disclosureRef
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Reference 14: http://www.xbrl.org/2003/role/disclosureRef
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Reference 15: http://www.xbrl.org/2003/role/disclosureRef
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Reference 16: http://www.xbrl.org/2003/role/disclosureRef
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Reference 17: http://www.xbrl.org/2003/role/disclosureRef
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Reference 18: http://www.xbrl.org/2003/role/disclosureRef
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Reference 19: http://www.xbrl.org/2003/role/disclosureRef
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Reference 24: http://www.xbrl.org/2003/role/disclosureRef
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Reference 25: http://www.xbrl.org/2003/role/disclosureRef
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Reference 26: http://www.xbrl.org/2003/role/disclosureRef
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Reference 27: http://www.xbrl.org/2003/role/disclosureRef
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Reference 28: http://www.xbrl.org/2003/role/disclosureRef
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+ Details

Fair value of financial instruments and investments - (Tables)

9 Months Ended

Sep. 30, 2023

Fair Value Disclosures [Abstract]

Schedule of financial assets and liabilities that are required to be measured at fair value on a recurring basis


	September 30, 2023
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	1,625	$	—	$	1,625	$	—
Marketable securities - equity investments	$	128,028	$	128,028	$	—	$	—
ClearPoint Equity Investments - available for sale	$	4,482	$	4,482	$	—	$	—
ClearPoint convertible debt security	$	10,637	$	—	$	10,637	$	—
Contingent consideration payable- development and regulatory milestones	$	26,400	$		$		$	26,400
Contingent consideration payable- net sales milestones and royalties	$	12,600	$		$		$	12,600


	December 31, 2022
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	22,610	$	—	$	22,610	$	—
Marketable securities - equity investments	$	108,261	$	108,261	$	—	$	—
ClearPoint Equity Investments	$	10,965	$	10,965	$	—	$	—
ClearPoint convertible debt security	$	15,231	$	—	$	15,231	$	—

Contingent consideration payable- development and regulatory milestones		$	82,500		$	—		$	—		$	82,500
Contingent consideration payable- net sales milestones and royalties		$	81,500		$	—		$	—		$	81,500

Summary of marketable securities accounted for as available-for-sale debt securities


	September 30, 2023
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Corporate debt securities	$	1,649	$	—	$	(24)	$	1,625
Total	$	1,649	$	—	$	(24)	$	1,625


	December 31, 2022
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	12,419	$	5	$	—	$	12,424
Corporate debt securities		10,685		—		(499)		10,186
Total	$	23,104	$	5	$	(499)	$	22,610

Summary of unrealized losses and fair values of available-for-sale debt securities in a continuous unrealized loss position


	September 30, 2023
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Corporate debt securities	$	—		—		(24)		1,625		(24)	$	1,625
Total	$	—	$	—	$	(24)	$	1,625	$	(24)	$	1,625


	December 31, 2022
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Corporate debt securities	$	—		—		(499)		10,186		(499)	$	10,186
Total	$	—	$	—	$	(499)	$	10,186	$	(499)	$	10,186

Schedule of marketable securities on the balance sheet


	September 30, 2023
	Less Than		More Than
	12 Months		12 Months
Corporate debt securities	$	1,625	$	—
Total	$	1,625	$	—


	December 31, 2022
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	12,424	$	—
Corporate debt securities		—		10,186
Total	$	12,424	$	10,186

Summary of changes in the fair value of the Company's Level 3 valuation for contingent consideration payable


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2022	$	82,500	$	81,500
Additions		—		—
Change in fair value		(56,100)		(68,900)
Payments		—		—
Ending balance as of September 30, 2023	$	26,400	$	12,600


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2021	$	139,300	$	100,600
Additions		—		—
Change in fair value		(10,800)		(21,400)
Reclass to accounts payable and accrued expenses		(50,000)		—
Payments		—		—
Ending balance as of September 30, 2022	$	78,500	$	79,200

Fair Value Measurement Inputs and Valuation Techniques


	September 30, 2023
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$26,400	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $31 million 85% - 92% 6.9% - 7.6% 2023 - 2026
Contingent considerable payable- net sales milestones and royalties	$12,600	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $50 million 85% - 100% 0% 12% 2025 - 2034


	December 31, 2022
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$82,500	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $331 million 25% - 92% 6.2% - 8.3% 2023 - 2029
Contingent considerable payable- net sales milestones and royalties	$81,500	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $150 million 25% - 100% 2% - 6% 11.5% 2025 - 2041

Revenue recognition - Performance Obligations (Details) - USD ($) $ in Millions	Sep. 30, 2023	Dec. 31, 2022
Remaining Performance Obligation
Remaining performance obligations	$ 1.2	$ 1.4
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2023-10-01
Remaining Performance Obligation
Remaining performance obligations	$ 1.2
Revenue, performance obligation, period	1 year

Stock award plan - Stock Option Activity (Details) - Stock option - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended
	Sep. 30, 2023
Number of options
Outstanding at the beginning of the period (in shares)	11,502,417
Granted (in shares)	1,059,054
Exercised (in shares)	(806,407)
Forfeited/Cancelled (in shares)	(318,281)
Outstanding at the end of the period (in shares)	11,436,783
Vested or Expected to vest at the end of the period (in shares)	2,357,250
Exercisable at the end of the period (in shares)	8,533,144
Weighted- average exercise price
Outstanding at the beginning of the period (in dollars per share)	$ 43.33
Granted (in dollars per share)	41.29
Exercised (in dollars per share)	29.48
Forfeited/Cancelled (in dollars per share)	47.84
Outstanding at the end of the period (in dollars per share)	43.99
Vested or Expected to vest at the end of the period (in dollars per share)	46.72
Exercisable at the end of the period (in dollars per share)	$ 43.18
Weighted- average remaining contractual term
Outstanding at the end of the period	5 years 10 months 13 days
Vested or Expected to vest at the end of the period	8 years 2 months 23 days
Exercisable at the end of the period	5 years 18 days
Aggregate intrinsic value (in thousands)
Outstanding at the end of the period (in dollars)	$ 5,084
Exercisable at the end of the period (in dollars)	$ 5,084

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Statement of Comprehensive Income [Abstract]
Net Income (Loss)	$ (132,970)	$ (109,315)	$ (470,812)	$ (388,128)
Other comprehensive income (loss):
Unrealized gain (loss) on marketable securities, net of tax	19	736	470	(2,333)
Foreign currency translation gain, net of tax	11,021	25,218	4,343	62,820
Comprehensive loss	$ (121,930)	$ (83,361)	$ (465,999)	$ (327,641)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 235
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08(g)(1)(ii))
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480678/235-10-S99-1

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 323
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (c)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481687/323-10-50-3

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 825
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 28
-Subparagraph (f)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482907/825-10-50-28

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 220
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 6
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482765/220-10-50-6

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
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-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147483443/250-10-50-3

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Topic 250
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
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Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Topic 815
-SubTopic 40
-Name Accounting Standards Codification
-Section 65
-Paragraph 1
-Subparagraph (f)
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Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Topic 250
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Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 250
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+ Details

Fair value of financial instruments and investments - Convertible senior notes (Details) - 1.50% Convertible senior notes due 2026 - USD ($)	Sep. 30, 2023	Dec. 31, 2022	Sep. 30, 2019
Long-term debt
Interest rate ( as a percent )	1.50%
Convertible debt
Long-term debt
Principal	$ 287,500,000	$ 287,500,000	$ 287,500,000
Interest rate ( as a percent )	1.50%		1.50%
Convertible debt \| Significant other observable inputs (level 2)
Long-term debt
Fair value of convertible notes	$ 228,800,000	$ 281,700,000

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

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+ Details

Summary of significant accounting policies - Liability for Sale of Future Royalties (Details) - USD ($) $ in Millions		1 Months Ended
	Jul. 17, 2020	Jul. 31, 2020	Sep. 30, 2023
Assigned royalty payments
Cash consideration received from Royalty Purchase Agreement		$ 650.0
Assigned royalty payment, retained percentage	57.067%
Remaining potential milestones that can be achieved			$ 250.0
Royalty Purchase Agreement \| Assigned Royalty Payments
Assigned royalty payments
Assigned royalty payment, percentage	42.933%
Cash consideration received from Royalty Purchase Agreement	$ 650.0
Royalty purchase agreement termination period once there are no further royalty payment obligations	60 days
Royalty purchase agreement, payment maximum	$ 1,300.0

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

Consolidated Statements of Stockholders' (Deficit) Equity - USD ($) $ in Thousands	Common stock	Additional paid-in capital	Accumulated other comprehensive income (loss)	Accumulated deficit	Total
Balance (in shares) at Dec. 31, 2021	70,828,226
Balance at the beginning of the period at Dec. 31, 2021	$ 71	$ 2,123,606	$ (24,282)	$ (2,097,957)	$ 1,438
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	456,399
Exercise of options		13,203			13,203
Restricted stock vesting and issuance (in shares)	479,004
Issuance of common stock in connection with an employee stock purchase plan (in shares)	91,263
Issuance of common stock in connection with an employee stock purchase plan		3,107			3,107
Share-based compensation expense		82,989			82,989
Net Income (Loss)				(388,128)	(388,128)
Comprehensive income			60,487		60,487
Balance (in shares) at Sep. 30, 2022	71,854,892
Balance at the end of the period at Sep. 30, 2022	$ 71	2,222,905	36,205	(2,486,085)	(226,904)
Balance (in shares) at Jun. 30, 2022	71,505,889
Balance at the beginning of the period at Jun. 30, 2022	$ 71	2,184,230	10,251	(2,376,770)	(182,218)
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	331,379
Exercise of options		10,005			10,005
Restricted stock vesting and issuance (in shares)	17,624
Share-based compensation expense		28,670			28,670
Net Income (Loss)				(109,315)	(109,315)
Comprehensive income			25,954		25,954
Balance (in shares) at Sep. 30, 2022	71,854,892
Balance at the end of the period at Sep. 30, 2022	$ 71	2,222,905	36,205	(2,486,085)	(226,904)
Balance (in shares) at Dec. 31, 2022	73,104,692
Balance at the beginning of the period at Dec. 31, 2022	$ 72	2,305,020	4,796	(2,656,974)	(347,086)
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	806,407
Exercise of options	$ 1	23,770			23,771
Restricted stock vesting and issuance (in shares)	773,157
Restricted stock vesting and issuance, net	$ 1				1
Issuance of common stock in connection with an employee stock purchase plan (in shares)	117,304
Issuance of common stock in connection with an employee stock purchase plan		3,805			3,805
Issuance of common stock in connection with a milestone payable (in shares)	657,462
Issuance of common stock in connection with a milestone payable	$ 1	29,569			29,570
Share-based compensation expense		85,128			85,128
Net Income (Loss)				(470,812)	(470,812)
Comprehensive income			4,813		4,813
Balance (in shares) at Sep. 30, 2023	75,459,022
Balance at the end of the period at Sep. 30, 2023	$ 75	2,447,292	9,609	(3,127,786)	(670,810)
Balance (in shares) at Jun. 30, 2023	75,318,233
Balance at the beginning of the period at Jun. 30, 2023	$ 75	2,416,904	(1,431)	(2,994,816)	(579,268)
Increase (Decrease) in Stockholders' Equity
Exercise of options (in shares)	113,795
Exercise of options		3,446			3,446
Restricted stock vesting and issuance (in shares)	26,994
Share-based compensation expense		26,942			26,942
Net Income (Loss)				(132,970)	(132,970)
Comprehensive income			11,040		11,040
Balance (in shares) at Sep. 30, 2023	75,459,022
Balance at the end of the period at Sep. 30, 2023	$ 75	$ 2,447,292	$ 9,609	$ (3,127,786)	$ (670,810)

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Revenues:
Revenue	$ 196,576	$ 217,127	$ 630,766	$ 531,389
Operating expenses:
Cost of product sales, excluding amortization of acquired intangible assets	9,493	14,011	36,368	33,785
Amortization of intangible assets	58,649	31,023	145,461	80,790
Research and development	164,212	165,462	545,210	462,802
Selling, general and administrative	80,886	80,118	256,249	233,280
Change in the fair value of contingent consideration	1,500	(5,300)	(125,000)	(32,200)
Intangible asset impairment			217,800
Total operating expenses	314,740	285,314	1,076,088	778,457
Loss from operations	(118,164)	(68,187)	(445,322)	(247,068)
Interest expense, net	(28,160)	(20,880)	(84,905)	(66,371)
Other expense, net	(20,266)	(38,141)	(8,832)	(84,355)
Loss before income tax benefit	(166,590)	(127,208)	(539,059)	(397,794)
Income tax benefit	33,620	17,893	68,247	9,666
Net loss attributable to common stockholders	$ (132,970)	$ (109,315)	$ (470,812)	$ (388,128)
Weighted-average shares outstanding:
Basic	75,377,997	71,654,671	74,618,611	71,415,849
Diluted	75,377,997	71,654,671	74,618,611	71,415,849
Net loss per share-basic and diluted (in dollars per share)
Basic	$ (1.76)	$ (1.53)	$ (6.31)	$ (5.43)
Diluted	$ (1.76)	$ (1.53)	$ (6.31)	$ (5.43)
Net product revenue
Revenues:
Revenue	$ 144,038	$ 134,186	$ 506,187	$ 407,720
Collaboration revenue
Revenues:
Revenue	0	50,017	6	50,024
Royalty revenue
Revenues:
Revenue	50,173	32,924	117,857	73,645
Manufacturing revenue
Revenues:
Revenue	$ 2,365	$ 0	$ 6,716	$ 0

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022
Cash flows from operating activities
Net Income (Loss)	$ (470,812)	$ (388,128)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	155,885	89,971
Non-cash operating lease expense	8,156	7,505
Non-cash royalty revenue related to sale of future royalties	(50,599)	(31,617)
Non-cash interest expense on liability related to sale of future royalties	56,031	55,778
Intangible asset impairment	217,800
Change in valuation of contingent consideration	(125,000)	(32,200)
Unrealized loss on ClearPoint Equity Investments	3,107	1,113
Unrealized loss on ClearPoint convertible debt security	4,594	2,392
Unrealized (gain) loss on marketable securities - equity investments	(5,484)	11,319
Realized loss for the sale of Clearpoint Equity Investment	782
Non-cash stock consideration, milestone payment	29,570
Disposal of asset	135	81
Amortization of (discounts) premiums on investments, net	(89)	1,792
Deferred income taxes	(50,909)
Amortization of debt issuance costs	1,574	1,316
Share-based compensation expense	85,128	82,989
Unrealized foreign currency transaction losses, net	3,394	71,246
Changes in operating assets and liabilities:
Inventory, net	(14,121)	(768)
Prepaid expenses and other current assets	59,467	(35,615)
Trade and royalty receivables, net	(9,887)	(24,773)
Deposits and other assets	4,597	(3,752)
Accounts payable and accrued expenses	40,434	1,568
Other liabilities	(1,756)	(908)
Deferred revenue	(127)
Net cash used in operating activities	(58,130)	(190,691)
Cash flows from investing activities
Purchases of fixed assets	(22,872)	(23,394)
Purchases of marketable securities - available for sale		(40,429)
Purchases of marketable securities - equity investments	(26,378)	(22,787)
Sale and redemption of marketable securities- available for sale	21,544	341,990
Sale and redemption of marketable securities - equity investments	12,078	104,431
Sale and redemption of ClearPoint Equity Investments	2,594
Acquisition of product rights and licenses	(69,285)	(102,069)
Net cash (used in) provided by investing activities	(82,319)	257,742
Cash flows from financing activities
Proceeds from exercise of options	23,771	13,203
Debt issuance costs related to secured term loan	(282)
Repayment of Convertible Notes		(150,000)
Proceeds from employee stock purchase plan	3,805	3,107
Payment of finance lease principal	(1,379)	(1,276)
Net cash provided by (used in) financing activities	25,915	(134,966)
Effect of exchange rate changes on cash	19	(8,792)
Net decrease in cash and cash equivalents	(114,515)	(76,707)
Cash and cash equivalents, and restricted cash beginning of period	295,925	197,218
Cash and cash equivalents, and restricted cash end of period	181,410	120,511
Supplemental disclosure of cash information
Cash paid for interest	34,020	12,679
Cash paid for income taxes	13,631	4,029
Supplemental disclosure of non-cash investing and financing activity
Unrealized gain (loss) on marketable securities, net of tax	470	(2,333)
Right-of-use assets obtained in exchange for operating lease obligations		35,294
Acquisition of product rights and licenses	44,963	27,828
Milestone payable	$ 2,500	$ 50,000

Commitments and contingencies - Narrative (Details) - USD ($) $ in Thousands		3 Months Ended	9 Months Ended	12 Months Ended
	Apr. 29, 2020	Jun. 30, 2016	Sep. 30, 2023	Dec. 31, 2022	Sep. 30, 2022	May 29, 2020
Other Commitments
Milestone payable			$ 2,500		$ 50,000
Accrued royalties			52,087	$ 40,546
Wellcome Trust
Other Commitments
Development milestone payment obligations				2,500
Milestone obligation payments made		$ 800
Censa
Other Commitments
Asset acquisition, development and regulatory milestones						$ 109,000
Censa \| Maximum
Other Commitments
Asset acquisition, milestone, amount						217,500
Asset acquisition, net sales milestone						$ 160,000
Former Censa Securityholders
Other Commitments
Development milestone obligation payments made			30,000
Development milestone obligation cash payments made			$ 400
Shares issued for milestone payment			657,462
SMA License Agreement \| SMA Foundation
Other Commitments
Royalty expense			$ 40,300
Royalty payments			35,300
Accrued royalties			5,000
SMA License Agreement \| SMA Foundation \| Maximum
Other Commitments
Potential royalty payments due on net product sales			52,500
Agilis
Other Commitments
Development milestone payments which the entity is obligated to pay	$ 40,000		40,000
Potential developmental and regulatory milestones			31,100
Potential sales milestones			50,000
Milestone obligation payments made				$ 50,000
Development milestone obligation payments made			$ 2,400
Agilis \| Minimum
Other Commitments
Product sales (as a percent)			2.00%
Agilis \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay			$ 60,000
Priority review voucher amount			535,000
Potential sales milestones			$ 150,000
Product sales (as a percent)			6.00%
Development milestone payment obligations, net of cancellation and forfeiture			$ 20,000
Contingent liability, milestone, potential achievements, priority review voucher amount, net of cancellation and forfeiture			361,000
Agilis \| Rights Exchange Agreement
Other Commitments
Contingent liability cancellation and forfeiture of potential milestone payments	174,000
Development milestone payment obligations, cancellation and forfeiture	37,600
Contingent liability, cancellation and forfeiture	$ 211,600
BioElectron \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay			200,000
Marathon \| Agilis Merger Agreement
Other Commitments
Milestone obligation payments made			50,000
Net product revenue \| Wellcome Trust \| Maximum
Other Commitments
Development milestone payments which the entity is obligated to pay			$ 14,500

Insider Trading Arrangements

3 Months Ended

Sep. 30, 2023

Trading Arrangements, by Individual

Material Terms of Trading Arrangement

Director and Officer Trading Arrangements

A portion of the compensation of our directors and officers (as defined in Rule 16a-1(f) under the Securities Exchange Act of 1934, as amended, or the Exchange Act) is in the form of equity awards and, from time to time, directors and officers engage in open-market transactions with respect to the securities acquired pursuant to such equity awards or other Company securities, including to satisfy tax withholding obligations when equity awards vest or are exercised, and for diversification or other personal reasons.

Transactions in Company securities by directors and officers are required to be made in accordance with our insider trading policy, which requires that the transactions be in accordance with applicable U.S. federal securities laws that prohibit trading while in possession of material nonpublic information. Rule 10b5-1 under the Exchange Act provides an affirmative defense that enables directors and officers to prearrange transactions in Company securities in a manner that avoids concerns about initiating transactions while in possession of material nonpublic information.

The following table describes, for the quarterly period covered by this report, each trading arrangement for the sale or purchase of Company securities adopted or terminated by our directors and officers that is either (1) a contract, instruction or written plan intended to satisfy the affirmative defense conditions of Rule 10b5-1(c), or a “Rule 10b5-1 trading arrangement”, or (2) a “non-Rule 10b5-1 trading arrangement” (as defined in Item 408(c) of Regulation S-K):


Name (Title)	Action Taken (Date of Action)	Type of Trading Arrangement	Nature of Trading Arrangement	Duration of Trading Arrangement	Aggregate Number of Securities
Pierre Gravier (Chief Financial Officer)	Adoption (July 13, 2023)	Rule 10b5-1 trading arrangement for sell-to-cover transactions for RSUs granted on July 13, 2023	Sale	Until final settlement of RSUs on or around July 13, 2027	Indeterminable (1)

(1) The number of shares subject to this RSU grant that will be sold to satisfy applicable tax withholding obligations upon vesting is unknown as the number will vary based on the extent to which vesting conditions are satisfied and the market price of the Company’s common stock at the time of settlement. This trading arrangement provides for the automatic sale of shares that would otherwise be issuable on each settlement date of the RSU in an amount sufficient to satisfy the applicable withholding obligation, with the proceeds of the sale delivered to the Company in satisfaction of the applicable withholding obligation.

Restricted Stock Unit Trading Arrangement | Pierre Gravier

Trading Arrangements, by Individual

Name

Pierre Gravier

Title

Chief Financial Officer

Rule 10b5-1 Arrangement Adopted

true

Adoption Date

July 13, 2023

Expiration Date

July 13, 2027

Debt - Liability for Sale of Future Royalties (Details) - USD ($) $ in Thousands	1 Months Ended	9 Months Ended
	Jul. 31, 2020	Sep. 30, 2023
Debt Disclosure [Abstract]
Proceeds from sale of future royalties	$ 650,000
Beginning balance		$ 757,886
Less: Non-cash royalty revenue payable to RPI		(50,599)
Plus: non-cash interest expense recognized		56,031
Ending balance		$ 763,318
Effective interest rate of the liability component	11.00%	9.30%

Debt

9 Months Ended

Sep. 30, 2023

Debt Disclosure [Abstract]

Debt

9. Debt

Liability for sale of future royalties

In July 2020, the Company entered into the Royalty Purchase Agreement. As RPI’s interest is explicitly limited, the $650.0 million cash consideration was classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability is being amortized using the effective interest method over the life of the arrangement, in accordance with ASC 470 and ASC 835. The initial annual effective interest rate was determined to be 11.0%. The Company utilizes the prospective method to account for subsequent changes in the estimated future payments to be made to RPI and updates the effective interest rate on a quarterly basis. Issuance costs related to the transaction were determined to be immaterial.

The following table shows the activity within the “liability for sale of future royalties- current” and “liability for sale of future royalties- noncurrent” accounts for the nine months ended September 30, 2023:


	Nine Months Ended September 30,
Liability for sale of future royalties- (current and noncurrent)	2023
Beginning balance as of December 31, 2022	$	757,886
Less: Non-cash royalty revenue payable to RPI		(50,599)
Plus: Non-cash interest expense recognized		56,031
Ending balance	$	763,318
Effective interest rate as of September 30, 2023		9.3	%

Non-cash interest expense is recorded in the statement of operations within “Interest expense, net”.

Senior Secured Term Loan

On October 27, 2022 (the “Closing Date”), the Company entered into a credit agreement (the “Blackstone Credit Agreement”) for fundings of up to $950.0 million consisting of a committed loan facility of $450.0 million and further contemplating the potential for up to $500.0 million of additional financing, to the extent that the Company requests such additional financing and subject to the Lenders’ agreement to provide such additional financing and to mutual agreement on terms, among the Company, certain subsidiaries of the Company (together with the Company, the “Loan Parties”) and funds and other affiliated entities advised or managed by Blackstone Life Sciences and Blackstone Credit (collectively, “Blackstone”, and such lenders, together with their permitted assignees, the “Lenders” and each a “Lender”) and Wilmington Trust, National Association, as the administrative agent for the Lenders.

The Blackstone Credit Agreement provides for a senior secured term loan facility funded on the Closing Date in the aggregate principal amount of $300.0 million (the “Initial Loans”) and a committed delayed draw term loan facility of up to $150.0 million (the “Delayed Draw Loans” and, together with the Initial Loans, the “Loans”) to be funded at the Company’s request within 18 months of the Closing Date subject to specified conditions. In addition, the Blackstone Credit Agreement contemplates the potential for further financings by Blackstone, by providing for incremental discretionary uncommitted further financings of up to $500.0 million. The Company capitalized approximately $11.6 million of debt issuance costs which are presented on the balance sheet as a direct deduction from the debt liability and are being amortized over the term of the senior secured term loan facility using the effective interest rate method.

The Loans mature on the date that is seven years from the Closing Date. Borrowings under the Blackstone Credit Agreement bear interest at a variable rate equal to, at the Company’s option, either an adjusted Term SOFR rate plus seven and a quarter percent (7.25%) or the Base Rate plus six and a quarter percent (6.25%), subject to a floor of one percent (1%) and two percent (2%) with respect to Term SOFR rate and Base Rate (each as defined in the Blackstone Credit Agreement), respectively. Payment of the Loans are subject to certain premiums specified in the Blackstone Credit Agreement, in each case, from the date the applicable Loan is funded.

All obligations under the Blackstone Credit Agreement are secured, subject to certain exceptions and specified inclusions, by security interests in certain assets of the Loan Parties, including (1) intellectual property and other assets related to Translarna, Emflaza, Upstaza, sepiapterin and, until certain release conditions are met, vatiquinone, in each case, together with any other forms, formulations, or methods of delivery of any such products, and regardless of trade or brand name, (2) future acquired intellectual property (but not internally developed intellectual property unrelated to other intellectual property collateral) and other related assets, and (3) the equity interests held by the Loan Parties in certain of their subsidiaries. The Blackstone Credit Agreement contains certain negative covenants with which the Company must remain in compliance. The Blackstone Credit Agreement also requires that the Company maintains consolidated liquidity of at least $100.0 million as of the last day of each fiscal quarter, which shall be increased to $200.0 million upon the Company consummating acquisitions meeting certain consolidated thresholds described therein. In addition, the Company will be required under conditions specified in the Blackstone Credit Agreement to fund a reserve account up to certain amounts specified therein, including $50.0 million that the Company funded into the reserve account during the quarter ended March 31, 2023 and was released back to the Company during the quarter ended June 30, 2023. The funds in the reserve

account are available to prepay the Loans at any time at the Company’s option, and are, if funded, subject to release upon certain further conditions. Upon any such release, such funds are freely available for use by the Company subject to the generally applicable terms and conditions of the Blackstone Credit Agreement. The Blackstone Credit Agreement contains certain customary representations and warranties, affirmative covenants and provisions relating to events of default.

The Blackstone Credit Agreement consists of the following:


	September 30, 2023		December 31, 2022
Principal	$	300,000	$	300,000
Less: Debt issuance costs		(10,742)		(11,322)
Net carrying amount	$	289,258	$	288,678

As of September 30, 2023, the remaining contractual life of the Blackstone Credit Agreement is approximately 6.1 years.

The following table sets forth total interest expense recognized related to the Blackstone Credit Agreement:


	Three Months Ended			Nine Months Ended
	September 30,			September 30,
	2023			2023
Contractual interest expense	$	9,554		$	28,087
Amortization of debt issuance costs		280			702
Total	$	9,834		$	28,789
Effective interest rate		13.1	%		13.1	%

2026 Convertible Notes

In September 2019, the Company issued, at par value, $287.5 million aggregate principal amount of 1.50% convertible senior notes due 2026, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes, which was exercised in full by the initial purchasers. The 2026 Convertible Notes bear cash interest at a rate of 1.50% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. The net proceeds to the Company from the offering were $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by the Company.

The 2026 Convertible Notes are governed by an indenture (the "2026 Convertible Notes Indenture") with U.S Bank National Association as trustee (the "2026 Convertible Notes Trustee").

Holders of the 2026 Convertible Notes may convert their 2026 Convertible Notes at their option at any time prior to the close of business on the business day immediately preceding March 15, 2026 only under the following circumstances:

●

during any calendar quarter commencing on or after December 31, 2019 (and only during such calendar quarter), if the last reported sale price of the Company’s common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day;

●

during the five business day period after any five consecutive trading day period (the “measurement period”) in which the trading price (as defined in the 2026 Convertible Notes Indenture) per $1,000 principal amount of 2026 Convertible Notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of the Company’s common stock and the conversion rate on each such trading day;

●

during any period after the Company has issued notice of redemption until the close of business on the scheduled trading day immediately preceding the relevant redemption date; or

●

upon the occurrence of specified corporate events.

On or after March 15, 2026, until the close of business on the business day immediately preceding the maturity date, holders may convert their 2026 Convertible Notes at any time, regardless of the foregoing circumstances. Upon conversion, the Company will pay or deliver, as the case may be, cash, shares of the Company’s common stock or any combination thereof at the Company’s election.

The conversion rate for the 2026 Convertible Notes was initially, and remains, 19.0404 shares of the Company’s common stock per $1,000 principal amount of the 2026 Convertible Notes, which is equivalent to an initial conversion price of approximately $52.52 per share of the Company’s common stock. The conversion rate may be subject to adjustment in some events but will not be adjusted for any accrued and unpaid interest.

The Company was not permitted to redeem the 2026 Convertible Notes prior to September 20, 2023. The Company may redeem for cash all or any portion of the 2026 Convertible Notes, at its option, if the last reported sale price of its common stock has been at least 130% of the conversion price then in effect on the last trading day of, and for at least 19 other trading days (whether or not consecutive) during, any 30 consecutive trading day period ending on, and including, the trading day immediately preceding the date on which the Company provides notice of redemption, at a redemption price equal to 100% of the principal amount of the 2026 Convertible Notes to be redeemed, plus accrued and unpaid interest to, but excluding, the redemption date. No sinking fund is provided for the 2026 Convertible Notes, which means that the Company is not required to redeem or retire the 2026 Convertible Notes periodically.

If the Company undergoes a “fundamental change” (as defined in the 2026 Convertible Notes Indenture), subject to certain conditions, holders of the 2026 Convertible Notes may require the Company to repurchase for cash all or part of their 2026 Convertible Notes at a repurchase price equal to 100% of the principal amount of the 2026 Convertible Notes to be repurchased, plus accrued and unpaid interest to, but excluding, the fundamental change repurchase date.

The 2026 Convertible Notes represent senior unsecured obligations and will rank senior in right of payment to the Company’s future indebtedness that is expressly subordinated in right of payment to the notes, equal in right of payment to the Company’s existing and future unsecured indebtedness that is not so subordinated, effectively junior in right of payment to any of the Company’s secured indebtedness to the extent of the value of the assets securing such indebtedness, and structurally subordinated to all existing and future indebtedness and other liabilities (including trade payables) incurred by the Company’s subsidiaries. The 2026 Convertible Notes Indenture contains customary events of default with respect to the 2026 Convertible Notes, including that upon certain events of default (including the Company’s failure to make any payment of principal or interest on the 2026 Convertible Notes when due and payable) occurring and continuing, the 2026 Convertible Notes Trustee by notice to the Company, or the holders of at least 25% in principal amount of the outstanding 2026 Convertible Notes by notice to the Company and the Convertible Notes Trustee, may, and the 2026 Convertible Notes Trustee at the request of such holders (subject to the provisions of the 2026 Convertible Notes Indenture) shall, declare 100% of the principal of and accrued and unpaid interest, if any, on all the 2026 Convertible Notes to be due and payable. In case of certain events of bankruptcy, insolvency or reorganization, involving the Company or a significant subsidiary, 100% of the principal of and accrued and unpaid interest on the 2026 Convertible Notes will automatically become due and payable. Upon such a declaration of acceleration, such principal and accrued and unpaid interest, if any, will be due and payable immediately.

The 2026 Convertible Notes consist of the following:



	September 30, 2023		December 31, 2022
Principal	$	287,500	$	287,500
Less: Debt issuance costs		(3,584)		(4,456)
Net carrying amount	$	283,916	$	283,044

As of September 30, 2023, the remaining contractual life of the 2026 Convertible Notes is approximately 3.0 years.

The following table sets forth total interest expense recognized related to the 2026 Convertible Notes:

	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
Contractual interest expense	$	1,080		$	1,081		$	3,215		$	3,217
Amortization of debt issuance costs		294			289			872			856
Total	$	1,374		$	1,370		$	4,087		$	4,073
Effective interest rate		1.9	%		1.9	%		1.9	%		1.9	%

In April 2022, under the terms of the 2026 Convertible Notes Indenture, the Company paid additional interest on the 2026 Convertible Notes at a rate equal to 0.5% per annum, for a total interest payment of approximately $2.1 million, for the period beginning September 25, 2020 and ending March 14, 2022. In September 2022, under the terms of the 2026 Convertible Notes Indenture, the Company paid additional interest on the 2026 Convertible Notes at a rate equal to 0.5% per annum, for a total interest payment of approximately $0.1 million, for the period beginning March 15, 2022 and ending April 8, 2022. These amounts are not included in the table above, but were recorded as interest expense, net within the statement of operations for the nine months ended September 30, 2022.

2022 Convertible Notes

In August 2015, the Company issued, at par value, $150.0 million aggregate principal amount of 3.00% convertible senior notes due 2022, (the “2022 Convertible Notes”). On August 15, 2022, the Company repaid the outstanding principal amount and accrued interest, totaling $152.3 million, of the 2022 Convertible Notes that was due upon maturity in accordance with the terms of the notes.

The following table sets forth total interest expense recognized related to the 2022 Convertible Notes:



	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
Contractual interest expense	$	—		$	559		$	—		$	2,800
Amortization of debt issuance costs		—			92			—			460
Total	$	—		$	651		$	—		$	3,260
Effective interest rate		—	%		3.5	%		—	%		3.5	%

Fair value of financial instruments and investments - Marketable Securities, Balance Sheet Disclosures (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Dec. 31, 2022
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	$ 1,625	$ 12,424
Marketable securities, More Than 12 Months		10,186
Commercial paper
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months		12,424
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Marketable securities, Less Than 12 Months	$ 1,625
Marketable securities, More Than 12 Months		$ 10,186

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (aa)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (aaa)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (c)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-2

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-3

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-3

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-3

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (c)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-3

Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Topic 320
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 3
-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-3

+ Details

Accounts payable and accrued expenses

9 Months Ended

Sep. 30, 2023

Payables and Accruals [Abstract]

Accounts payable and accrued expenses

5. Accounts payable and accrued expenses

Accounts payable and accrued expenses at September 30, 2023 and December 31, 2022 consist of the following:


	September 30,		December 31,
	2023		2022
Employee compensation, benefits, and related accruals	$	70,778	$	62,669
Income tax payable		2,822		4,712
Consulting and contracted research		21,236		38,882
Professional fees		3,067		3,093
Sales allowance		72,202		63,787
Sales rebates		119,971		67,355
Royalties		52,087		40,546
Accounts payable		19,152		27,268
Other		9,416		12,054
Total	$	370,731	$	320,366

During the three and nine month periods ended September 30, 2023, the Company incurred $22.6 million and $30.6 million, respectively, of restructuring costs from a reduction in workforce in connection with the Company’s strategic pipeline prioritization and discontinuation of its preclinical and early research programs in its gene therapy platform. The costs are included in research and development and selling, general, and administrative expenses on the Company’s consolidated statement of operations. As of September 30, 2023, the remaining $23.4 million of accrued restructuring costs are included above within employee compensation, benefits, and related accruals.

The Company (Details) $ in Thousands	9 Months Ended
The Company (Details) $ in Thousands	Sep. 30, 2023 USD ($) product	Dec. 31, 2022 USD ($)
Long-term debt
Number of products \| product	2
Retained earnings (accumulated deficit) \| $	$ (3,127,786)	$ (2,656,974)
1.50% Convertible senior notes due 2026
Long-term debt
Interest rate ( as a percent )	1.50%

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

- Definition

Amount of accumulated undistributed earnings (deficit).

+ References + Details

Intangible assets and goodwill - Goodwill (Details) - USD ($) $ in Thousands	61 Months Ended
	Sep. 30, 2023	Dec. 31, 2022	Aug. 23, 2018
Goodwill
Goodwill	$ 82,341	$ 82,341
Changes in goodwill	$ 0
Agilis
Goodwill
Goodwill			$ 82,300

- Definition

Amount after accumulated impairment loss of an asset representing future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized.

+ References + Details

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 2: http://www.xbrl.org/2003/role/exampleRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 55
-Paragraph 24
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482548/350-20-55-24

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (c)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (d)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (e)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (f)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (g)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Subparagraph (h)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1

Reference 11: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 1A
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-1A

Reference 12: http://www.xbrl.org/2003/role/disclosureRef
-Topic 350
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482573/350-20-50-2

+ Details

Intangible assets and goodwill - Definite-lived Intangibles (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Dec. 31, 2022
Definite-lived intangible assets
Milestone Payable	$ 2,500	$ 50,000	$ 2,500	$ 50,000
Accrued royalties	52,087		52,087		$ 40,546
Definite-lived intangibles
Amortization	(58,649)	(31,023)	(145,461)	(80,790)
Finite-Lived Intangible Assets, Net	$ 187,576		$ 187,576
Weighted Average
Definite-lived intangible assets
Remaining amortization period	5 years 3 months 18 days		5 years 3 months 18 days
Emflaza asset acquisition
Definite-lived intangible assets
Milestone obligation payments recorded			$ 76,500
Marathon \| Emflaza asset acquisition \| Accounts payable and accrued expenses
Definite-lived intangible assets
Milestone Payable	$ 43,900		43,900
Akcea \| Waylivra
Definite-lived intangible assets
Royalty payments			200
Akcea \| Waylivra \| Accounts payable and accrued expenses
Definite-lived intangible assets
Accrued royalties	200		200
Akcea \| Tegsedi
Definite-lived intangible assets
Royalty payments			4,300
Akcea \| Tegsedi \| Accounts payable and accrued expenses
Definite-lived intangible assets
Accrued royalties	900		900
Definite-lived intangible assets
Definite-lived intangibles
Beginning balance - Definite-lived assets, Gross			526,228
Additions			80,910
Foreign Currency Translation			(279)
Ending balance - Definite-lived assets, Gross	606,859		606,859
Beginning balance - Accumulated amortization			(273,903)
Amortization	(58,600)	$ (31,000)	(145,461)	$ (80,800)
Foreign Currency Translation - Accumulated amortization			81
Ending balance - Accumulated amortization	(419,283)		(419,283)
Finite-Lived Intangible Assets, Net	187,576		187,576
Definite-lived intangible assets \| Emflaza
Definite-lived intangibles
Beginning balance - Definite-lived assets, Gross			420,253
Additions			76,454
Ending balance - Definite-lived assets, Gross	496,707		496,707
Beginning balance - Accumulated amortization			(266,023)
Amortization			(138,038)
Ending balance - Accumulated amortization	(404,061)		(404,061)
Definite-lived intangible assets \| Waylivra
Definite-lived intangibles
Beginning balance - Definite-lived assets, Gross			9,316
Additions			157
Foreign Currency Translation			(96)
Ending balance - Definite-lived assets, Gross	9,377		9,377
Beginning balance - Accumulated amortization			(2,751)
Amortization			(791)
Foreign Currency Translation - Accumulated amortization			45
Ending balance - Accumulated amortization	(3,497)		(3,497)
Definite-lived intangible assets \| Tegsedi
Definite-lived intangibles
Beginning balance - Definite-lived assets, Gross			7,109
Additions			4,299
Foreign Currency Translation			(183)
Ending balance - Definite-lived assets, Gross	11,225		11,225
Beginning balance - Accumulated amortization			(1,709)
Amortization			(1,035)
Foreign Currency Translation - Accumulated amortization			36
Ending balance - Accumulated amortization	(2,708)		(2,708)
Definite-lived intangible assets \| Upstaza
Definite-lived intangibles
Beginning balance - Definite-lived assets, Gross			89,550
Ending balance - Definite-lived assets, Gross	89,550		89,550
Beginning balance - Accumulated amortization			(3,420)
Amortization			(5,597)
Ending balance - Accumulated amortization	$ (9,017)		$ (9,017)

Fair value of financial instruments and investments - Hierarchy (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Dec. 31, 2022
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	$ 1,625	$ 22,610
Contingent consideration payable	39,000	164,000
Transfers of assets measured between Level 1, Level 2, and Level 3	0	0
Recurring basis
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint Equity Investments	4,482	10,965
ClearPoint convertible debt security	10,637	15,231
Recurring basis \| Quoted prices in active markets for identical assets (Level 1)
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint Equity Investments	4,482	10,965
Recurring basis \| Significant other observable inputs (Level 2)
Financial assets and liabilities measured at fair value on recurring basis
ClearPoint convertible debt security	10,637	15,231
Recurring basis \| Development and Regulatory Milestones
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	26,400	82,500
Recurring basis \| Development and Regulatory Milestones \| Significant unobservable inputs (Level 3)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	26,400	82,500
Recurring basis \| Net Sales Milestones and Royalties
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	12,600	81,500
Recurring basis \| Net Sales Milestones and Royalties \| Significant unobservable inputs (Level 3)
Financial assets and liabilities measured at fair value on recurring basis
Contingent consideration payable	12,600	81,500
Recurring basis \| Marketable securities
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	1,625	22,610
Marketable securities - equity investments	128,028	108,261
Recurring basis \| Marketable securities \| Quoted prices in active markets for identical assets (Level 1)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - equity investments	128,028	108,261
Recurring basis \| Marketable securities \| Significant other observable inputs (Level 2)
Financial assets and liabilities measured at fair value on recurring basis
Marketable securities - available for sale	$ 1,625	$ 22,610

Cover - shares	9 Months Ended
Cover - shares	Sep. 30, 2023	Oct. 24, 2023
Cover [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2023
Document Transition Report	false
Entity File Number	001-35969
Entity Registrant Name	PTC Therapeutics, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	04-3416587
Entity Address, Address Line One	100 Corporate Court
Entity Address, City or Town	South Plainfield
Entity Address, State or Province	NJ
Entity Address, Postal Zip Code	07080
City Area Code	908
Local Phone Number	222-7000
Title of 12(b) Security	Common Stock, $0.001 par value per share
Trading Symbol	PTCT
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Large Accelerated Filer
Entity Small Business	false
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		75,463,145
Entity Central Index Key	0001070081
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2023
Document Fiscal Period Focus	Q3
Amendment Flag	false

Revenue recognition - Net Product Sales (Details) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023 USD ($) segment country Distributor	Sep. 30, 2022 USD ($) segment country Distributor	Sep. 30, 2023 USD ($) segment country Distributor	Sep. 30, 2022 USD ($) segment country Distributor	Dec. 31, 2022 USD ($)
Revenue recognition
Number of operating segments \| segment	1	1	1	1
Revenue	$ 196,576	$ 217,127	$ 630,766	$ 531,389
Net product revenue \| United States
Revenue recognition
Number of countries exceeding 10% of net product sales \| country	1
Net product revenue \| Geographic concentration risk
Revenue recognition
Number of countries exceeding 10% of net product sales \| country	1	2	3	2
Percentage of net product sales threshold	10.00%	10.00%	10.00%	10.00%
Net product revenue \| Geographic concentration risk \| United States
Revenue recognition
Revenue	$ 67,400	$ 54,800	$ 187,700	$ 160,100
Net product revenue \| Geographic concentration risk \| Russia
Revenue recognition
Revenue		$ 28,300	69,000	$ 57,100
Net product revenue \| Geographic concentration risk \| Brazil
Revenue recognition
Revenue			$ 52,500
Net product revenue \| Customer concentration risk
Revenue recognition
Number of distributors \| Distributor	3	2	2	2
Percentage of net product sales threshold	10.00%	10.00%	10.00%	10.00%
Net product revenue
Revenue recognition
Revenue	$ 144,038	$ 134,186	$ 506,187	$ 407,720
Contract with Customer, Liability	0		0		$ 0
Net product revenue \| Non-US
Revenue recognition
Revenue	76,600	79,400	318,500	247,600
Emflaza \| United States
Revenue recognition
Revenue	67,400	54,800	187,700	160,100
Translarna \| Non-US
Revenue recognition
Revenue	$ 69,000	$ 76,600	$ 280,600	$ 232,900

Intangible assets and goodwill - Indefinite-lived Intangibles (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2023	Dec. 31, 2022
Indefinite-lived intangibles
Impairment	$ (217,800)
Intangible assets, net	423,342	$ 705,891
PTC-FA and PTC-AS
Indefinite-lived intangibles
Impairment	(217,800)
Indefinite-lived intangible assets
Indefinite-lived intangibles
Beginning Balance	453,566
Additions
Impairment	(217,800)
Ending Balance	235,766
Intangible assets, net	423,342
Indefinite-lived intangible assets \| Upstaza
Indefinite-lived intangibles
Beginning Balance	235,766
Additions
Ending Balance	235,766
Indefinite-lived intangible assets \| PTC-FA and PTC-AS
Indefinite-lived intangibles
Impairment	(217,800)
Indefinite-lived intangible assets \| PTC-FA
Indefinite-lived intangibles
Beginning Balance	112,500
Additions
Impairment	(112,500)
Indefinite-lived intangible assets \| PTC-AS
Indefinite-lived intangibles
Beginning Balance	105,300
Additions
Impairment	$ (105,300)

Accounts payable and accrued expenses - Components (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Dec. 31, 2022
Payables and Accruals [Abstract]
Employee compensation, benefits, and related accruals	$ 70,778	$ 62,669
Income tax payable	2,822	4,712
Consulting and contracted research	21,236	38,882
Professional fees	3,067	3,093
Sales allowance	72,202	63,787
Sales rebates	119,971	67,355
Royalties	52,087	40,546
Accounts payable	19,152	27,268
Other	9,416	12,054
Accounts payable and accrued expenses	$ 370,731	$ 320,366

Fair value of financial instruments and investments - Summary of changes in the fair value of the Company's Level 3 valuation (Details) - Significant unobservable inputs (Level 3) - Agilis - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022
PTC-FA and PTC-AS
Changes in the fair value of warrant liability and SARs liability
Change in fair value	$ 129,800
Ending Balance	0
Upstaza
Changes in the fair value of warrant liability and SARs liability
Ending Balance	39,000
Development and Regulatory Milestones \| Commitments
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	82,500	$ 139,300
Additions	0	0
Change in fair value	(56,100)	(10,800)
Reclass to accounts payable and accrued expenses		(50,000)
Rights Exchange settlement	0	0
Ending Balance	26,400	78,500
Net Sales Milestones and Royalties \| Commitments
Changes in the fair value of warrant liability and SARs liability
Beginning Balance	81,500	100,600
Additions	0	0
Change in fair value	(68,900)	(21,400)
Reclass to accounts payable and accrued expenses		0
Rights Exchange settlement	0	0
Ending Balance	$ 12,600	$ 79,200

Summary of significant accounting policies - Reconciliation of cash (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Dec. 31, 2022	Sep. 30, 2022	Dec. 31, 2021
Accounting Policies [Abstract]
Cash and cash equivalents	$ 165,157	$ 279,834
Restricted cash included in deposits and other assets	16,253	16,091
Total Cash, cash equivalents and restricted cash per statement of cash flows	$ 181,410	$ 295,925	$ 120,511	$ 197,218

Leases - Cash flow (Details) - USD ($) $ in Thousands	9 Months Ended
Leases - Cash flow (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Sep. 30, 2022
Leases
Operating cash flows from operating leases	$ 11,479	$ 10,954
Financing cash flows from finance lease	1,379	1,276
Operating cash flows from finance leases	$ 1,621	1,724
Right-of-use assets obtained in exchange for operating lease obligations		$ 35,294

Leases - Lease costs (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Leases - Lease costs (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Leases
Fixed lease cost	$ 5,490	$ 5,377	$ 16,463	$ 14,267
Variable lease cost	1,376	1,151	4,140	3,152
Short-term lease cost	271	262	866	600
Total operating lease cost	$ 7,137	$ 6,790	$ 21,469	$ 18,019

Subsequent events (Details) $ in Millions	Oct. 19, 2023 USD ($)	Oct. 18, 2023 USD ($) Option	Sep. 30, 2023
Royalty Purchase Agreement \| Royalty Pharma
Subsequent Event [Line Items]
Previously assigned royalty payment, percentage			42.933%
Subsequent Event \| Senior Secured Term Loan
Subsequent Event [Line Items]
Outstanding principal and accrued interest repaid	$ 302.1
Prepayment premiums, expenses and other exit fees	$ 82.1
Subsequent Event \| A&R Royalty Purchase Agreement
Subsequent Event [Line Items]
Cash consideration		$ 1,000.0
Retained Royalty Rights percentage sold		38.0447%
Additional cash consideration		$ 500.0
Number of put options held by the company \| Option		5
Maximum number of put options which can be exercised before Royalty Pharma can exercise a call option \| Option		2
Maximum percentage of remaining retained royalty rights that are available upon exercise of call option		50.00%
Royalty purchase agreement termination period once there are no further royalty payment obligations		60 days
Subsequent Event \| A&R Royalty Purchase Agreement \| Royalty Pharma
Subsequent Event [Line Items]
Total percentage of royalty rights assigned		80.9777%
Royalty purchase agreement, payment maximum		$ 1,300.0
Percentage of total royalty payable after threshold royalties received		66.6667%
Percentage of maximum royalty payable until assigned royalty rights		90.4888%
Percentage of maximum royalty payable thereafter assigned royalty rights		83.3333%

Pay vs Performance Disclosure - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Pay vs Performance Disclosure - USD ($) $ in Thousands	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Pay vs Performance Disclosure
Net Income (Loss)	$ (132,970)	$ (109,315)	$ (470,812)	$ (388,128)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

+ Details

Summary of significant accounting policies (Tables)

9 Months Ended

Sep. 30, 2023

Accounting Policies [Abstract]

Reconciliation of cash


	End of			Beginning of
	period-		period-
	September 30,		December 31,
	2023		2022
Cash and cash equivalents	$	165,157	$	279,834
Restricted cash included in deposits and other assets		16,253		16,091
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	181,410	$	295,925

Schedule of Inventory


	September 30, 2023		December 31, 2022
Raw materials	$	907	$	1,078
Work in progress		24,595		14,074
Finished goods		10,250		6,656

Total inventory

35,752

21,808

Accounts payable and accrued expenses - (Tables)

9 Months Ended

Sep. 30, 2023

Payables and Accruals [Abstract]

Schedule of components of accounts payable and accrued expenses


	September 30,		December 31,
	2023		2022
Employee compensation, benefits, and related accruals	$	70,778	$	62,669
Income tax payable		2,822		4,712
Consulting and contracted research		21,236		38,882
Professional fees		3,067		3,093
Sales allowance		72,202		63,787
Sales rebates		119,971		67,355
Royalties		52,087		40,546
Accounts payable		19,152		27,268
Other		9,416		12,054
Total	$	370,731	$	320,366

Debt - Narrative (Details)		1 Months Ended				9 Months Ended	18 Months Ended
Debt - Narrative (Details)	Aug. 15, 2022 USD ($)	Sep. 30, 2022 USD ($)	Apr. 30, 2022 USD ($)	Apr. 08, 2022	Sep. 30, 2019 USD ($) D $ / shares	Sep. 30, 2023 USD ($)	Mar. 14, 2022	Dec. 31, 2022 USD ($)	Aug. 31, 2015 USD ($)
Long-term debt
Long-term debt						$ 573,174,000		$ 571,722,000
Additional paid-in capital						$ 2,447,292,000		2,305,020,000
1.50% Convertible senior notes due 2026
Long-term debt
Interest rate ( as a percent )						1.50%
Incremental interest rate per annum				0.50%			0.50%
Additional interest paid		$ 100,000	$ 2,100,000
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Net carrying amount						$ 283,916,000		283,044,000
Debt principal amount					$ 287,500,000	$ 287,500,000		$ 287,500,000
Debt instrument additional amount available for repurchase					$ 37,500,000
Interest rate ( as a percent )					1.50%	1.50%
Net proceeds from issuance of convertible notes					$ 279,300,000
Trading days, number \| D					20
Consecutive trading days, period \| D					30
Stock price trigger					130.00%
Business days, period					5 days
Consecutive trading-day period					5 days
Maximum product of the closing sale price of shares of the Company's common stock and the applicable conversion rate for such trading day					98.00%
Conversion ratio					19.0404
Conversion price per share (in dollars per share) \| $ / shares					$ 52.52
Redemption price as percent of principal amount					100.00%
Convertible instruments principal and unpaid interest payable upon events of default					100.00%
Minimum percentage of principal held by convertible debt instrument holders required to issue notice for declaration of principal and unpaid interest payable upon events of default					25.00%
Term of the convertible notes						3 years
Convertible debt \| 1.50% Convertible senior notes due 2026 \| Redemption on or after September 20, 2023
Long-term debt
Trading days, number \| D					19
Consecutive trading days, period \| D					30
Stock price trigger					130.00%
Redemption price as percent of principal amount					100.00%
Sinking fund					$ 0
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Debt principal amount									$ 150,000,000.0
Interest rate ( as a percent )									3.00%
Repayment of convertible notes including accrued interest	$ 152,300,000

The Company

9 Months Ended

Sep. 30, 2023

Organization, Consolidation and Presentation of Financial Statements [Abstract]

The Company

1. The Company

PTC Therapeutics, Inc. (the “Company” or “PTC”) is a science-driven global biopharmaceutical company focused on the discovery, development and commercialization of clinically differentiated medicines that provide benefits to patients with rare disorders. PTC’s ability to innovate to identify new therapies and to globally commercialize products is the foundation that drives investment in a robust and diversified pipeline of transformative medicines. PTC’s mission is to provide access to best-in-class treatments for patients who have little to no treatment options. PTC’s strategy is to leverage its strong scientific and clinical expertise and global commercial infrastructure to bring therapies to patients. PTC believes that this allows it to maximize value for all of its stakeholders.

PTC has a portfolio pipeline that includes several commercial products and product candidates in various stages of development, including clinical, pre-clinical and research and discovery stages, focused on the development of new treatments for multiple therapeutic areas for rare diseases relating to neurology, metabolism and oncology.

The Company has two products, Translarna™ (ataluren) and Emflaza® (deflazacort), for the treatment of Duchenne muscular dystrophy (“DMD”), a rare, life threatening disorder. Translarna has marketing authorization in the European Economic Area (the “EEA”) for the treatment of nonsense mutation Duchenne muscular dystrophy (“nmDMD”) in ambulatory patients aged 2 years and older and in Russia for the treatment of nmDMD in patients aged two years and older. Translarna also has marketing authorization in Brazil for the treatment of nmDMD in ambulatory patients two years and older and for continued treatment of patients that become non-ambulatory. In July 2020, the European Commission (“EC”) approved the removal of the statement “efficacy has not been demonstrated in non-ambulatory patients” from the indication statement for Translarna. Emflaza is approved in the United States for the treatment of DMD in patients two years and older.

The Company’s marketing authorization for Translarna in the EEA is subject to annual review and renewal by the EC following reassessment by the European Medicines Agency (“EMA”) of the benefit-risk balance of the authorization, which the Company refers to as the annual EMA reassessment. In September 2022, the Company submitted a Type II variation to the EMA to support conversion of the conditional marketing authorization for Translarna to a standard marketing authorization, which included a report on the placebo-controlled trial of Study 041 and data from the open-label extension. In February 2023, the Company also submitted an annual marketing authorization renewal request to the EMA. In September 2023, the Committee for Medicinal Products for Human Use (“CHMP’), gave a negative opinion on the conversion of the conditional marketing authorization to full marketing authorization of Translarna for the treatment of nmDMD and a negative opinion on the renewal of the existing conditional marketing authorization of Translarna for the treatment of nmDMD. The Company has requested re-examination of the CHMP opinion regarding the renewal of the existing conditional marketing authorization. In re-examination, the Company intends to address concerns raised during the previous review process on the benefit demonstrated in Translarna clinical trials and regarding the robustness of the Strategic Targeting of Registries and International Database of Excellence, or STRIDE, real world registry. In accordance with EMA guidelines, the Company expects the CHMP opinion following the re-examination process to occur in late January 2024, with EC ratification of the opinion within the following 67 days.

Translarna is an investigational new drug in the United States. Following the Company’s announcement of top-line results from the placebo-controlled trial of Study 041 in June 2022, the Company submitted a meeting request to the U.S. Food and Drug Administration (“FDA”) to gain clarity on the regulatory pathway for a potential re-submission of a New Drug Application (“NDA”) for Translarna. The FDA provided initial written feedback that Study 041 does not provide substantial evidence of effectiveness to support an NDA re-submission. The Company then had an informal meeting with the FDA, during which the Company discussed the potential path to an NDA re-submission for Translarna. Based on the meeting discussion, the Company has scheduled an additional Type C meeting with the FDA to review the totality of data

collected to date, including dystrophin and other mechanistic data as well as additional analyses that could support the benefit of Translarna.

The Company has developed Upstaza (eladocagene exuparvovec), a gene therapy used for the treatment of Aromatic L-Amino Acid Decarboxylase (“AADC”) deficiency (“AADC deficiency”), a rare central nervous system (“CNS”) disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. In July 2022, the EC approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the EEA. In November 2022, the Medicines and Healthcare Products Regulatory Agency approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the United Kingdom. The Company is also preparing a biologics license application (“BLA”) for Upstaza for the treatment of AADC deficiency in the United States and anticipates submitting the BLA shortly after its pre-BLA meeting that is scheduled for December 2023, pending the outcome of such meeting.

The Company holds the rights for the commercialization of Tegsedi® (inotersen) and Waylivra® (volanesorsen) for the treatment of rare diseases in countries in Latin America and the Caribbean pursuant to the Collaboration and License Agreement (the “Tegsedi-Waylivra Agreement”), dated August 1, 2018, by and between the Company and Akcea Therapeutics, Inc. (“Akcea”), a subsidiary of Ionis Pharmaceuticals, Inc. Tegsedi has received marketing authorization in the United States, the European Union (the “EU”) and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis (“hATTR amyloidosis”). The Company began to make commercial sales of Tegsedi for the treatment of hATTR amyloidosis in Brazil in the second quarter of 2022 and it continues to make Tegsedi available in certain other countries within Latin America and the Caribbean through early access programs (“EAP Programs”). In August 2021, ANVISA, the Brazilian health regulatory authority, approved Waylivra as the first treatment for familial chylomicronemia syndrome (“FCS”) in Brazil and the Company began to make commercial sales of Waylivra in Brazil in the third quarter of 2022 while continuing to make Waylivra available in certain other countries within Latin America and the Caribbean through EAP Programs. In December 2022, ANVISA approved Waylivra for the treatment of familial partial lipodystrophy (“FPL”). Waylivra has also received marketing authorization in the EU for the treatment of FCS.

The Company also has a spinal muscular atrophy (“SMA”) collaboration with F. Hoffman-La Roche Ltd and Hoffman-La Roche Inc. (referred to collectively as “Roche”) and the Spinal Muscular Atrophy Foundation (“SMA Foundation”). The SMA program has one approved product, Evrysdi® (risdiplam), which was approved by the FDA in August 2020 for the treatment of SMA in adults and children two months and older and by the EC in March 2021 for the treatment of 5q SMA in patients two months and older with a clinical diagnosis of SMA Type 1, Type 2 or Type 3 or with one to four SMN2 copies. Evrysdi also received marketing authorization for the treatment of SMA in Brazil in October 2020 and Japan in June 2021. In May 2022, the FDA approved a label expansion for Evrysdi to include infants under two months old with SMA. In August 2023, the EC approved an extension of the Evrysdi marketing authorization to include infants under two months old in the EU. In addition to the Company’s SMA program, the Company’s splicing platform also includes PTC518, which is being developed for the treatment of Huntington’s disease (“HD”). The Company initiated a Phase 2 study of PTC518 for the treatment of HD in the first quarter of 2022, which consists of an initial 12-week placebo-controlled phase focused on safety, pharmacology and pharmacodynamic effects followed by a nine-month placebo-controlled phase focused on PTC518 biomarker effect. In June 2023, the Company announced interim data from the 12-week placebo-controlled phase. The Company expects the next data update from the Phase 2 study of PTC518 for the treatment of HD in the first half of 2024. In the Phase 2 study, enrollment outside of the United States remains active and ongoing while enrollment within the United States is paused as the FDA requested additional data to allow the Phase 2 study to proceed. The Company had a Type A meeting with the FDA to review the clinical safety data needed to enable resumption of enrollment in the United States. At that meeting, the FDA stated that the existing three-month safety data could support 12-week dosing and that six months of clinical safety data could support dosing in the 12-month Phase 2 study.

The most advanced molecule in the Company’s metabolic platform is sepiapterin, a precursor to intracellular tetrahydrobiopterin, which is a critical enzymatic cofactor involved in metabolism and synthesis of numerous metabolic products, for orphan diseases. In May 2023, the Company announced that the primary endpoint was achieved in its registration-directed Phase 3 trial for sepiapterin for phenylketonuria (“PKU”). The primary endpoint of the study was the achievement of statistically-significant reduction in blood Phe level. The Company participated in a pre-NDA meeting with the FDA in the third quarter of 2023. At that meeting, the FDA stated that the sepiapterin clinical safety and efficacy

data supported NDA submission for the treatment of pediatric and adult PKU patients. However, the FDA has requested that PTC completes a 26-week nonclinical mouse study to assess sepiapterin carcinogenicity potential prior to NDA submission. PTC expects to submit an NDA to the FDA for sepiapterin for the treatment of PKU by the end of the third quarter of 2024 and PTC intends to discuss with the FDA the potential for an earlier submission if PTC is permitted to submit the 26-week mouse study report during the review process of the NDA. Additionally, PTC expects to submit a marketing authorization application (“MAA”) to the EMA for sepiapterin for the treatment of PKU in the EEA in the first half of 2024.

The Company’s Bio-e platform consists of small molecule compounds that target oxidoreductase enzymes that regulate oxidative stress and inflammatory pathways central to the pathology of a number of CNS diseases. The two most advanced molecules in the Company’s Bio-e platform are vatiquinone and utreloxastat. The Company announced topline results from a registration-directed Phase 3 trial of vatiquinone in children and young adults with Friedreich ataxia in May 2023. While the study did not meet its primary endpoint of statistically significant change, the Company participated in a Type C written response only meeting with the FDA in the third quarter of 2023 to discuss the potential for an NDA submission for vatiquinone for the treatment of Friedreich ataxia. In their written response, the FDA stated that while they see the value of upright stability as a clinically meaningful endpoint, they believed a confirmatory study would likely be needed to support NDA submission. PTC has requested a follow-up live meeting to address the issues raised by the FDA. Additionally, PTC is participating in a scientific advice procedure with the EMA to determine if the data from the registration-directed Phase 3 trial of vatiquinone in children and young adults with Friedreich ataxia could support a conditional MAA in the EEA. The Company initiated a Phase 2 trial of utreloxastat for amyotrophic lateral sclerosis in the first quarter of 2022 and enrollment is ongoing.

Unesbulin is the Company’s most advanced oncology agent. The Company completed its Phase 1 trials evaluating unesbulin in leiomyosarcoma (“LMS”) and diffuse intrinsic pontine glioma (“DIPG”) in the fourth quarter of 2021. The Company initiated a registration-directed Phase 2/3 trial of unesbulin for the treatment of LMS in the first quarter of 2022 and enrollment is ongoing. The Company is evaluating its plans for a potential initiation of a registration-directed Phase 2/3 trial of unesbulin for the treatment of DIPG.

In addition, the Company has a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas for rare diseases.

As of September 30, 2023, the Company had an accumulated deficit of approximately $3,127.8 million. The Company has financed its operations to date primarily through the private offerings in September 2019 of 1.50% convertible senior notes due 2026 (see Note 9), public offerings of common stock in February 2014, October 2014, April 2018, January 2019, and September 2019, “at the market offering” of its common stock, its initial public offering of common stock in June 2013, proceeds from the Royalty Purchase Agreement dated as of July 17, 2020, by and among the Company, RPI 2019 Intermediate Finance Trust (“RPI”), and, solely for the limited purposes set forth therein, Royalty Pharma PLC (the “Royalty Purchase Agreement”) (see Note 2), net proceeds from the Company’s’ borrowings under its credit agreement with Blackstone (see Note 9), private placements of its convertible preferred stock and common stock, collaborations, bank and institutional lender debt, other convertible debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by the Company’s product candidates. The Company has also relied on revenue generated from net sales of Translarna for the treatment of nmDMD in territories outside of the United States since 2014, Emflaza for the treatment of DMD in the United States since 2017, and Upstaza for the treatment of AADC deficiency in the EEA since May 2022. The Company has also relied on revenue associated with milestone and royalty payments from Roche pursuant to the License and Collaboration Agreement (the “SMA License Agreement”) dated as of November 23, 2011, by and among the Company, Roche and, for the limited purposes set forth therein, the SMA Foundation, under its SMA program. The Company expects that cash flows from the sales of its products, milestone and royalty payments from Roche, together with the Company’s cash, cash equivalents and marketable securities, will be sufficient to fund its operations for at least the next twelve months.

Accounts payable and accrued expenses - Restructuring (Details) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2023 USD ($)	Sep. 30, 2023 USD ($)
Restructuring costs
Restructuring costs	$ 22.6	$ 30.6
Accrued restructuring costs	$ 23.4	$ 23.4

Summary of significant accounting policies - Inventory (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Dec. 31, 2022
Accounting Policies [Abstract]
Raw materials		$ 907		$ 1,078
Work in progress		24,595		14,074
Finished goods		10,250		6,656
Total inventory		35,752		$ 21,808
Inventory write-down	$ 300	$ 400	$ 1,200

Leases - Supplemental lease terms (Details)	Sep. 30, 2023	Dec. 31, 2022
Leases
Weighted-average remaining lease terms - operating leases (years)	11 years 7 months 9 days	11 years 7 months 9 days
Weighted-average discount rate - operating leases	8.67%	8.61%
Weighted-average remaining lease terms - finance lease (years)	9 years 3 months 3 days	10 years 3 days
Weighted-average discount rate - finance lease	7.80%	7.80%

Summary of significant accounting policies - Narrative (Details) $ in Thousands		1 Months Ended			3 Months Ended		9 Months Ended		12 Months Ended
	Dec. 22, 2017	May 31, 2023 USD ($)	Jun. 30, 2022 USD ($)	Jul. 31, 2020 USD ($)	Sep. 30, 2023 USD ($) segment country	Sep. 30, 2022 USD ($) segment country	Sep. 30, 2023 USD ($) segment country	Sep. 30, 2022 USD ($) segment country	Dec. 31, 2019 USD ($)	Mar. 31, 2023 USD ($)	Dec. 31, 2022 USD ($)	Dec. 31, 2018 USD ($)
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Number of operating segments \| segment					1	1	1	1
Allowance for credit loss					$ 0	$ 0	$ 0	$ 0
Increase in allowance for credit losses					0	0	0	0
Allowance for doubtful accounts receivable					1,000		1,000				$ 300
Bad debt expense					400		700
Revenue					196,576	$ 217,127	630,766	$ 531,389
Cash consideration received from Royalty Purchase Agreement				$ 650,000
Income taxes
Federal income tax statutory rate	21.00%
Deferred tax benefit		$ 50,900					50,909
Impairment of indefinite-lived intangibles excluding goodwill							217,800
PTC-FA and PTC-AS
Income taxes
Impairment of indefinite-lived intangibles excluding goodwill							217,800
Indefinite-lived intangible assets
Income taxes
Impairment of indefinite-lived intangibles excluding goodwill							217,800
Indefinite-lived intangible assets \| PTC-FA and PTC-AS
Income taxes
Impairment of indefinite-lived intangibles excluding goodwill							217,800
Agilis
Income taxes
Deferred tax liability												$ 122,000
Deposits and other assets
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Bank guarantee					$ 600		$ 600
Blackstone Credit Agreement
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Credit agreement reserve										$ 50,000
Hopewell Campus
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Period after which letter of credit may be reduced if lease is not in default									5 years
Hopewell Campus \| Minimum
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Term for letter of credit (in years)									5 years
Hopewell Campus \| Deposits and other assets
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of credit									$ 7,500
Hopewell Campus \| Fifth Anniversary
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of credit									$ 3,800
Warren Premises
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Period after which letter of credit may be reduced if lease is not in default			5 years
Warren Premises \| Deposits and other assets
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of credit			$ 8,100
Warren Premises \| Fifth Anniversary
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Letters of credit			$ 4,100
Net product revenue \| United States
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Number of countries exceeding 10% of net product sales \| country					1
Net product revenue \| Geographic concentration risk
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Number of countries exceeding 10% of net product sales \| country					1	2	3	2
Percentage of net product sales threshold					10.00%	10.00%	10.00%	10.00%
Net product revenue \| Geographic concentration risk \| Russia
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue						$ 28,300	$ 69,000	$ 57,100
Net product revenue \| Geographic concentration risk \| Brazil
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue							52,500
Net product revenue \| Geographic concentration risk \| United States
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue					$ 67,400	54,800	187,700	160,100
Net product revenue
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue					144,038	134,186	506,187	407,720
Net product revenue \| Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue					76,600	79,400	318,500	247,600
Emflaza \| United States
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue					67,400	54,800	187,700	160,100
Translarna \| Non-US
New Accounting Pronouncements or Change in Accounting Principle [Line Items]
Revenue					$ 69,000	$ 76,600	$ 280,600	$ 232,900

Capitalization - Narrative (Details) - Sales Agreement - USD ($) $ in Millions	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Aug. 31, 2019
Common stock
Number of shares issued in transaction (in shares)	0	0	0	0
Maximum
Common stock
Value of shares available to be issued and sold in transaction					$ 125.0
Aggregate value of remaining shares to be issued and sold			$ 93.0

Net loss per share - (Tables)

9 Months Ended

Sep. 30, 2023

Earnings Per Share [Abstract]

Schedule of computation of basic and diluted net loss available to common stockholders


	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
Numerator
Net loss	$	(132,970)		$	(109,315)		$	(470,812)		$	(388,128)
Denominator
Denominator for basic and diluted net loss per share		75,377,997			71,654,671			74,618,611			71,415,849
Net loss per share:
Basic and diluted	$	(1.76)	*	$	(1.53)	*	$	(6.31)	*	$	(5.43)	*

* In the three and nine months ended September 30, 2023 and 2022, the Company experienced a net loss and therefore did not report any dilutive share impact.

Schedule of historical dilutive common share equivalents outstanding


	As of September 30,
	2023	2022
Stock Options	11,436,783	11,478,421
Unvested restricted stock awards and units	3,414,102	2,488,944
Total	14,850,885	13,967,365

Intangible assets and goodwill

9 Months Ended

Sep. 30, 2023

Goodwill and Intangible Assets Disclosure [Abstract]

Intangible assets and goodwill

12. Intangible assets and goodwill

Definite-lived intangibles

Definite-lived intangible assets consisted of the following at September 30, 2023 and December 31, 2022:


		Ending Balance at				Reclass from				Foreign		Ending Balance at
Definite-lived		December 31,				Indefinite Lived to				currency		September 30,
intangibles assets, gross		2022		Additions		Definite Lived		Impairment		translation		2023
Emflaza	$	420,253	$	76,454	$	—	$	—	$	—	$	496,707
Waylivra		9,316		157		—		—		(96)		9,377
Tegsedi		7,109		4,299		—		—		(183)		11,225
Upstaza		89,550		—		—		—		—		89,550
Total definite-lived intangibles, gross	$	526,228	$	80,910	$	—	$	—	$	(279)	$	606,859

Ending Balance at

Foreign

Ending Balance at

Definite-lived

December 31,

currency

September 30,

intangibles assets, accumulated amortization

2022

Amortization

translation

2023

Emflaza

(266,023)

(138,038)

—

(404,061)

Waylivra		(2,751)		(791)		45		(3,497)
Tegsedi		(1,709)		(1,035)		36		(2,708)
Upstaza		(3,420)		(5,597)		—		(9,017)
Total definite-lived intangibles, accumulated amortization	$	(273,903)	$	(145,461)	$	81	$	(419,283)

Total definite-lived intangibles, net							$	187,576

Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza beginning in 2018, up to a specified aggregate maximum amount over the expected commercial life of the asset. In accordance with the guidance for an asset acquisition, the Company records the milestone payment when it becomes payable to Marathon and increases the cost basis for the Emflaza rights intangible asset. For the nine months ended September 30, 2023, total milestone payments of $76.5 million were recorded. These payments are being amortized over the remaining useful life of the Emflaza rights asset on a straight line basis. As of September 30, 2023, a milestone payable to Marathon of $43.9 million was recorded on the consolidated balance sheet within accounts payable and accrued expenses.

Akcea is also entitled to receive royalty payments subject to certain terms set forth in the Tegsedi-Waylivra Agreement related to sales of Waylivra and Tegsedi. In accordance with the guidance for an asset acquisition, the Company records royalty payments when they become payable to Akcea and increase the cost basis for the Waylivra and Tegsedi intangible assets. For the nine months ended September 30, 2023, royalty payments of $4.3 million and $0.2 million were recorded for Tegsedi and Waylivra, respectively. As of September 30, 2023, a royalty payable of $0.9 million and $0.2 million for Tegsedi and Waylivra, respectively, was recorded on the consolidated balance sheet within accounts payable and accrued expenses.

For the three months ended September 30, 2023 and 2022, the Company recognized amortization expense of $58.6 million and $31.0 million, respectively, related to the Emflaza rights, Upstaza, Waylivra, and Tegsedi intangible assets. For the nine months ended September 30, 2023 and 2022, the Company recognized amortization expense of $145.5 million and $80.8 million, respectively, related to the Emflaza rights, Upstaza, Waylivra, and Tegsedi intangible assets. The estimated future amortization of the Emflaza rights, Upstaza, Waylivra, and Tegsedi intangible assets is expected to be as follows:


	As of September 30, 2023
2023	$	58,640
2024		46,557
2025		10,041
2026		10,041
2027 and thereafter		62,297
Total	$	187,576

The weighted average remaining amortization period of the definite-lived intangibles as of September 30, 2023 is 5.3 years.

Indefinite-lived intangibles

Indefinite-lived intangible assets consisted of the following at September 30, 2023 and December 31, 2022:


		Ending Balance at				Reclass from				Foreign		Ending Balance at
Indefinite-lived		December 31,				Indefinite Lived to				currency		September 30,
intangibles assets		2022		Additions		Definite Lived		Impairment		translation		2023
Upstaza	$	235,766	$	—	$	—	$	—	$	—	$	235,766
PTC-FA		112,500		—		—		(112,500)		—		—
PTC-AS		105,300		—		—		(105,300)		—		—
Total indefinite-lived intangibles	$	453,566	$	—	$	—	$	(217,800)	$	—	$	235,766

Total intangible assets, net											$	423,342

In connection with the acquisition of the Company’s gene therapy platform from Agilis, the Company acquired rights to Upstaza, for the treatment of AADC deficiency. AADC deficiency is a rare CNS disorder arising from reductions in the enzyme AADC that result from mutations in the dopa decarboxylase gene. The gene therapy platform also includes PTC-FA, an asset targeting Friedreich ataxia, a rare and life-shortening neurodegenerative disease caused by a single defect in the FXN gene which causes reduced production of the frataxin protein. Additionally, the gene therapy platform includes two other programs targeting CNS disorders, including PTC-AS for Angelman syndrome, a rare, genetic, neurological disorder characterized by severe developmental delays.

In accordance with the acquisition method of accounting, the Company allocated the acquisition cost for the Agilis Merger to the underlying assets acquired and liabilities assumed, based upon the estimated fair values of those assets and liabilities at the date of acquisition. The Company classified the fair value of the acquired IPR&D as indefinite lived intangible assets until the successful completion or abandonment of the associated research and development efforts. As of December 31, 2022, the value allocated to the indefinite lived intangible assets was $453.6 million.

In May 2023, as part of the Company’s strategic portfolio prioritization, the Company decided to discontinue its preclinical and early research programs in its gene therapy platform, which included PTC-FA and PTC-AS. As a result, the Company determined that the PTC-FA and PTC-AS indefinite-lived intangible assets were fully impaired and recorded impairment expense of $217.8 million during the nine month period ended September 30, 2023, which is recorded as intangible asset impairment in the statement of operations. As of September 30, 2023, the remaining indefinite lived intangible asset balance is $235.8 million, consisting solely of Upstaza, which the Company plans to continue to develop and commercialize.

Goodwill

As a result of the Agilis Merger on August 23, 2018, the Company recorded $82.3 million of goodwill. As of September 30, 2023, there have been no changes to the balance of goodwill since the date of the Agilis Merger. Accordingly, the goodwill balance as of September 30, 2023 is $82.3 million.

Subsequent events

9 Months Ended

Sep. 30, 2023

Subsequent Events [Abstract]

Subsequent events

13. Subsequent events

Royalty Purchase Agreement

On October 18, 2023, the Company, Royalty Pharma Investments 2019 ICAV (“Royalty Pharma”), and, for the limited purposes set forth in the agreement, Royalty Pharma plc, entered into an Amended and Restated Royalty Purchase Agreement (the “A&R Royalty Purchase Agreement”), which amends and restates in its entirety the Royalty Purchase Agreement. Pursuant to the A&R Royalty Purchase Agreement, the Company has sold or agreed to sell to Royalty Pharma certain portions of the Company’s remaining Royalty on worldwide net sales of Evrysdi and any other product (the “Products”) developed pursuant to the SMA License Agreement (all such retained Royalty rights of the Company, the “Retained Royalty Rights,” and all such Royalty rights that are sold to Royalty Pharma pursuant to the A&R Royalty Purchase Agreement, the “A&R Assigned Royalty Rights”). At closing, Royalty Pharma paid the Company $1.0 billion in cash consideration for 38.0447% of the Company’s Retained Royalty Rights (which is in addition to the 42.9330% assigned to Royalty Pharma in connection with the Royalty Purchase Agreement, for a total of 80.9777% of the total Royalty) until such time as Royalty Pharma has received payments in respect of the A&R Assigned Royalty Rights equal to $1.3 billion in the aggregate, and thereafter 66.6667% of the total Royalty. In addition, the Company may sell to Royalty Pharma the remainder of the Company’s Retained Royalty Rights in exchange for an aggregate of $500.0 million in additional cash consideration after the closing of the A&R Royalty Purchase Agreement, less royalties received in respect of the Retained Royalty Rights put to Royalty Pharma, which will be payable by Royalty Pharma pursuant to five put options held by the Company that are exercisable at the Company’s option between January 1, 2024 and December 31, 2025. If the Company exercises two or fewer of the put options, Royalty Pharma may exercise a call option during the period from and after January 1, 2026 until and including March 31, 2026 for up to 50% of the remainder of the Company’s Retained Royalty Rights less amounts exercised by the Company via its put options at a purchase price that is proportional to the purchase price of the Company’s unexercised put options. Royalty Pharma’s exercise of the call option would result in Royalty Pharma owning 90.4888% of the total Royalty until such time as Royalty Pharma has received payments in respect of the A&R Assigned Royalty Rights equal to $1.3 billion in the aggregate, and thereafter 83.3333% of the total Royalty. The Company is evaluating the accounting impact of the A&R Royalty Purchase Agreement.

Under the A&R Royalty Purchase Agreement, and in connection with its sale of the A&R Assigned Royalty Rights, the Company has agreed to specified negative and affirmative covenants with respect to the exercise of its rights under the SMA License Agreement, including the Company’s right to amend, modify, assign or terminate the SMA License Agreement. Subject to certain customary exceptions, the Company has agreed not to grant a security interest in its interest in the SMA License Agreement, the Products or the patent rights that cover the Products. The A&R Royalty Purchase Agreement also contains representations and warranties, covenants and other provisions, including information rights and confidentiality obligations, customary for transactions of this nature.

The A&R Royalty Purchase Agreement will terminate 60 days following the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the License Agreement.

Senior Secured Term Loan Termination

On October 19, 2023, the Company terminated the Blackstone Credit Agreement. In connection with the termination of the Blackstone Credit Agreement, the Company repaid outstanding principal and accrued interest thereunder totaling $302.1 million and paid an additional $82.1 million in prepayment premiums, expenses and other exit fees. All liens and security interests securing the loans made pursuant to the Blackstone Credit Agreement were released upon termination.

Net loss per share - Antidilutive (Details) - shares	9 Months Ended
Net loss per share - Antidilutive (Details) - shares	Sep. 30, 2023	Sep. 30, 2022
Net loss per share
Total shares excluded from calculation (in shares)	14,850,885	13,967,365
Employee Stock Option
Net loss per share
Total shares excluded from calculation (in shares)	11,436,783	11,478,421
Restricted stock awards and units
Net loss per share
Total shares excluded from calculation (in shares)	3,414,102	2,488,944

Summary of significant accounting policies

9 Months Ended

Sep. 30, 2023

Accounting Policies [Abstract]

Summary of significant accounting policies

2. Summary of significant accounting policies

The Company’s complete listing of significant accounting policies is set forth in Note 2 of the notes to the Company’s audited financial statements as of December 31, 2022 included in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (the "SEC") on February 21, 2023 (the "2022 Form 10-K"). Selected significant accounting policies are discussed in further detail below.

Basis of presentation

The accompanying financial information as of September 30, 2023 and for the three and nine months ended September 30, 2023 and 2022 has been prepared by the Company, without audit, pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with generally accepted accounting principles in the United States ("GAAP") have been condensed or omitted pursuant to such rules and regulations. These interim financial statements should be read in conjunction with the Company’s audited financial statements as of December 31, 2022 and notes thereto included in the 2022 Form 10-K.

In the opinion of management, the unaudited financial information as of September 30, 2023 and for the three and nine months ended September 30, 2023 and 2022 reflects all adjustments, which are normal recurring adjustments, necessary to present a fair statement of financial position, results of operations, stockholders’ (deficit) equity, and cash flows. The results of operations for the three and nine months ended September 30, 2023 are not necessarily indicative of the results to be expected for the year ended December 31, 2023 or for any other interim period or for any other future year.

Use of estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Significant estimates in these consolidated financial statements have been made in connection with the calculation of net product sales, royalty revenue, certain accruals related to the Company’s research and development expenses, valuation procedures for liability for sale of future royalties, valuation procedures for convertible notes, fair value of the contingent consideration, and the provision for or benefit from income taxes. Actual results could differ from those estimates. Changes in estimates are reflected in reported results in the period in which they become known.

Restricted cash

Restricted cash included in deposits and other assets on the consolidated balance sheet contains an unconditional, irrevocable and transferable letter of credit that was entered into during the twelve-month period ended December 31, 2019 in connection with obligations under a facility lease for the Company’s leased biologics manufacturing facility in Hopewell Township, New Jersey. The amount of the letter of credit is $7.5 million, is to be maintained for a term of not less than five years and has the potential to be reduced to $3.8 million if after five years the Company is not in default of its lease. Restricted cash also contains an unconditional, irrevocable and transferable letter of credit that was entered into during June 2022 in connection with obligations for the Company’s new facility lease in Warren, New Jersey. The amount of the letter of credit is $8.1 million and has the potential to be reduced to $4.1 million if after five years the Company is not in default of its lease. Both amounts are classified within deposits and other assets on the consolidated balance sheet due to the long-term nature of the respective letters of credit. Restricted cash also includes a bank guarantee of $0.6 million denominated in a foreign currency.

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the consolidated balance sheet that sum to the total of the same amounts shown in the statement of cash flows:


	End of			Beginning of
	period-		period-
	September 30,		December 31,
	2023		2022
Cash and cash equivalents	$	165,157	$	279,834
Restricted cash included in deposits and other assets		16,253		16,091
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	181,410	$	295,925

Marketable securities

The Company’s marketable securities consists of both debt securities and equity investments. The Company considers its investments in debt securities with original maturities of greater than 90 days to be available for sale securities. Securities under this classification are recorded at fair value and unrealized gains and losses within accumulated other comprehensive income. The estimated fair value of the available for sale securities is determined based on quoted market prices or rates for similar instruments. In addition, the cost of debt securities in this category is adjusted for amortization of premium and accretion of discount to maturity. For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. If the criteria are not met, the Company evaluates whether the decline in fair value has resulted from a credit loss or other factors. In making this assessment, management considers, among other factors, the extent to which fair value is less than amortized cost, any changes to the rating of the security by a rating agency, and adverse conditions specifically related to the security. If this assessment indicates that a credit loss exists, the present value of cash flows expected to be collected from the security are compared to the amortized cost basis of the security. If the present value of the cash flows expected to be collected is less than the amortized cost basis, a credit loss exists and an allowance for credit losses is recorded for the credit loss, limited by the amount that the fair value is less than the amortized costs basis. Any impairment that has not been recorded through an allowance for credit losses is recognized in other comprehensive income. For the three and nine months ended September 30, 2023 and 2022, no allowance was recorded for credit losses.

Marketable securities that are equity investments are measured at fair value, as it is readily available, and as such are classified as Level 1 assets. Unrealized holding gains and losses for these equity investments are components of other (expense) income, net within the consolidated statement of operations.

Inventory and cost of product sales

Inventory

Inventories are stated at the lower of cost and net realizable value with cost determined on a first-in, first-out basis by product. The Company capitalizes inventory costs associated with products following regulatory approval when future commercialization is considered probable and the future economic benefit is expected to be realized. Products which may be used in clinical development programs are included in inventory and charged to research and development expense when the product enters the research and development process and no longer can be used for commercial purposes. Inventory used for marketing efforts are charged to selling, general and administrative expense. Amounts related to clinical development programs and marketing efforts are immaterial.

The following table summarizes the components of the Company’s inventory for the periods indicated:


	September 30, 2023		December 31, 2022
Raw materials	$	907	$	1,078
Work in progress		24,595		14,074
Finished goods		10,250		6,656

Total inventory

35,752

21,808

The Company periodically reviews its inventories for excess amounts or obsolescence and writes down obsolete or otherwise unmarketable inventory to its estimated net realizable value. For the three months ended September 30, 2023, the Company’s inventory write-downs were immaterial. For the nine months ended September 30, 2023, the Company recorded inventory write-downs of $0.4 million primarily related to product approaching expiration. For the three and nine months ended September 30, 2022, the Company recorded inventory write-downs of $0.3 million and $1.2 million, respectively, primarily related to product approaching expiration. Additionally, though the Company’s product is subject to strict quality control and monitoring which it performs throughout the manufacturing processes, certain batches or units of product may not meet quality specifications resulting in a charge to cost of product sales. For the three and nine months ended September 30, 2023 and 2022, these amounts were immaterial.

Cost of product sales

Cost of product sales consists of the cost of inventory sold, manufacturing and supply chain costs, storage costs, amortization of the acquired intangible asset, royalty payments associated with net product sales, and royalty payments to collaborative partners associated with royalty revenues and collaboration revenue related to milestones. Production costs are expensed as cost of product sales when the related products are sold or royalty revenues and collaboration revenue milestones are earned.

Revenue recognition

Net product revenue

The Company’s net product revenue primarily consists of sales of Translarna in territories outside of the U.S. for the treatment of nmDMD and sales of Emflaza in the U.S. for the treatment of DMD. The Company recognizes revenue when its performance obligations with its customers have been satisfied. The Company’s performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when the Company’s customer obtains control of the product, which is typically upon delivery. The Company invoices its customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of the invoice date. The Company determines the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods the Company has yet to provide. As the Company has identified only one distinct performance obligation, the transaction price is allocated entirely to product sales. In determining the transaction price, a significant financing component does not exist since the timing from when the Company delivers product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.

The Company records product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. The Company uses the expected value or most likely amount method when estimating its variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained.

For the three months ended September 30, 2023 and 2022, net product sales outside of the United States were $76.6 million and $79.4 million, respectively, consisting of sales of Translarna, Tegsedi, Waylivra, and Upstaza. Translarna net revenues made up $69.0 million and $76.6 million of the net product sales outside of the United States for the three months ended September 30, 2023 and 2022, respectively. For the three months ended September 30, 2023 and 2022, net product sales in the United States were $67.4 million and $54.8 million, respectively, consisting solely of sales of Emflaza. During the three months ended September 30, 2023, one country, the United States, accounted for at least 10% of the Company’s net product sales, representing $67.4 million of net product sales. During the three months ended September 30, 2022, two

countries, the United States and Russia, accounted for at least 10% of the Company’s net product sales, representing $54.8 million and $28.3 million of net product sales, respectively.

For the nine months ended September 30, 2023 and 2022, net product sales outside of the United States were $318.5 million and $247.6 million, respectively, consisting of Translarna, Tegsedi, Waylivra, and Upstaza. Translarna net revenues made up $280.6 million and $232.9 million of the net product sales outside of the United States for the nine months ended September 30, 2023 and 2022, respectively. For the nine months ended September 30, 2023 and 2022, net product sales in the United States were $187.7 million and $160.1 million, respectively, consisting solely of Emflaza. During the nine months ended September 30, 2023, three countries, the United States, Russia, and Brazil, accounted for at least 10% of the Company’s net product sales, representing $187.7 million, $69.0 million, and $52.5 million of net product sales, respectively. During the nine months ended September 30, 2022, two countries, the United States and Russia, accounted for at least 10% of the Company’s net product sales, representing $160.1 million and $57.1 million of net product sales, respectively.

In relation to customer contracts, the Company incurs costs to fulfill a contract but does not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. The Company considers any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Collaboration and royalty revenue

The terms of these agreements typically include payments to the Company of one or more of the following: nonrefundable, upfront license fees; milestone payments; research funding and royalties on future product sales. In addition, the Company generates service revenue through agreements that generally provide for fees for research and development services and may include additional payments upon achievement of specified events.

At the inception of a collaboration arrangement, the Company needs to first evaluate if the arrangement meets the criteria in Financial Accounting Standards Board (“FASB”) Accounting Standards Codification (“ASC”) Topic 808 “Collaborative Arrangements” to then determine if ASC Topic 606 is applicable by considering whether the collaborator meets the definition of a customer. If the criteria are met, the Company assesses the promises in the arrangement to identify distinct performance obligations.

For licenses of intellectual property, the Company assesses, at contract inception, whether the intellectual property is distinct from other performance obligations identified in the arrangement. If the licensing of intellectual property is determined to be distinct, revenue is recognized for nonrefundable, upfront license fees when the license is transferred to the customer and the customer can use and benefit from the license. If the licensing of intellectual property is determined not to be distinct, then the license will be bundled with other promises in the arrangement into one distinct performance obligation. The Company needs to determine if the bundled performance obligation is satisfied over time or at a point in time. If the Company concludes that the nonrefundable, upfront license fees will be recognized over time, the Company will need to assess the appropriate method of measuring proportional performance.

For milestone payments, the Company assesses, at contract inception, whether the development or sales-based milestones are considered probable of being achieved. If it is probable that a significant revenue reversal will occur, the Company will not record revenue until the uncertainty has been resolved. Milestone payments that are contingent upon regulatory approval are not considered probable of being achieved until the applicable regulatory approvals or other external conditions are obtained as such conditions are not within the Company’s control. If it is probable that a significant revenue reversal will not occur, the Company will estimate the milestone payments using the most likely amount method. The Company will re-assess the development and sales-based milestones each reporting period to determine the probability of achievement. The Company recognizes royalties from product sales at the later of when the related sales occur or when the performance obligation to which the royalty has been allocated has been satisfied. If it is probable that a significant revenue reversal will not occur, the Company will estimate the royalty payments using the most likely amount method.

The Company recognizes revenue for reimbursements of research and development costs under collaboration agreements as the services are performed. The Company records these reimbursements as revenue and not as a reduction of research and development expenses as the Company has the risks and rewards as the principal in the research and development activities.

For the three months ended September 30, 2023, the Company did not recognize collaboration revenue related to the SMA License Agreement with Roche. For the three months ended September 30, 2022, the Company recognized $50.0 million of collaboration revenue related to the SMA License Agreement. For the nine months ended September 30, 2023, the amounts recognized for the collaboration revenue related to the SMA License Agreement with Roche were immaterial. For the nine months ended September 30, 2022, the Company recognized $50.0 million of collaboration revenue related to the SMA License Agreement with Roche. In September 2022, the Company recognized a sales milestone of $50.0 million for the achievement of $750.0 million in worldwide annual net sales from Evrysdi.

For the three and nine months ended September 30, 2023, the Company has recognized $50.2 million and $117.9 million of royalty revenue, respectively, related to Evrysdi. For the three and nine months ended September 30, 2022, the Company has recognized $32.9 million and $73.6 million of royalty revenue, respectively, related to Evrysdi.

Manufacturing Revenue

The Company has manufacturing services related to the production of plasmid deoxyribonucleic acid (“DNA”) and adeno-associated virus (“AAV”) vectors for gene therapy applications for external customers. Performance obligations vary but may include manufacturing plasmid DNA and/or AAV vectors, material testing, stability studies, and other services related to material development. The transaction prices for these arrangements are fixed and include amounts stated in the contracts for each promised service. Typically, the performance obligations within a manufacturing contract are highly interdependent, in which case, the Company will combine them into a single performance obligation. The Company has determined that the assets created have no alternative use to the Company, and the Company has an enforceable right to payment for the performance completed to date, therefore revenue related to these services are recognized over time and is measured using an output method based on performance of manufacturing milestones completed to date.

Manufacturing service contracts may also include performance obligations related to project management services or obtaining materials from third parties. The Company has determined that these are separate performance obligations for which revenue is recognized at the point in time the services are performed. For performance obligations related to obtaining third party materials, the Company has determined that it is the principal as the Company has control of the materials and has discretion in setting the price. Therefore, the Company recognizes revenue on a gross basis related to obtaining third party materials.

Certain arrangements require a portion of the contract consideration to be received in advance at the commencement of the contract, and such advance payment is initially recorded as a contract liability. A contract asset may be recognized in the event the Company’s satisfaction of performance obligations outpaces customer billings.

For the three and nine months ended September 30, 2023, the Company recognized $2.4 million and $6.7 million of manufacturing revenue, respectively, related to plasmid DNA and AAV vector production for external customers. No manufacturing revenue was recognized for the three and nine months ended September 30, 2022. As of September 30, 2023, the Company has contract assets of $1.4 million and remaining performance obligations of $1.2 million related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. For the period ended December 31, 2022, the Company had remaining performance obligations of $1.4 million and no contracts assets related to plasmid DNA and AAV production for external customers.

Allowance for doubtful accounts

The Company maintains an allowance for estimated losses resulting from the inability of its customers to make required payments. The Company estimates uncollectible amounts based upon current customer receivable balances, the age of customer receivable balances, the customer’s financial condition and current economic trends. The Company also assesses whether an allowance for expected credit losses may be required which includes a review of the Company’s receivables

portfolio, which are pooled on a customer basis or country basis. In making its assessment of whether an allowance for credit losses is required, the Company considers its historical experience with customers, current balances, levels of delinquency, regulatory and legal environments, and other relevant current and future forecasted economic conditions. For the three and nine months ended September 30, 2023 and 2022, no allowance was recorded for credit losses. The allowance for doubtful accounts was $1.0 million as of September 30, 2023 and $0.3 million as of December 31, 2022. For the three and nine months ended September 30, 2023, bad debt expense was $0.4 million and $0.7 million, respectively. For the three and nine months ended September 30, 2022, bad debt expense was immaterial.

Liability for sale of future royalties

On July 17, 2020, the Company, RPI, and, for the limited purposes set forth in the agreement, Royalty Pharma PLC, entered into the Royalty Purchase Agreement. Pursuant to the Royalty Purchase Agreement, the Company sold to RPI 42.933% (the “Assigned Royalty Rights”) of the Company’s right to receive sales-based royalty payments (the “Royalty”) on worldwide net sales of Evrysdi and any other product developed pursuant to the SMA License Agreement. In consideration for the sale of the Assigned Royalty Rights, RPI paid the Company $650.0 million in cash consideration. The Company has retained a 57.067% interest in the Royalty and all economic rights to receive the remaining potential regulatory and sales milestone payments under the SMA License Agreement, which remaining milestone payments equal $250.0 million in the aggregate as of September 30, 2023. The Royalty Purchase Agreement will terminate 60 days following the earlier of the date on which Roche is no longer obligated to make any payments of the Royalty pursuant to the SMA License Agreement and the date on which RPI has received $1.3 billion in respect of the Assigned Royalty Rights.

The cash consideration obtained pursuant to the Royalty Purchase Agreement is classified as debt and is recorded as “liability for sale of future royalties-current” and “liability for sale of future royalties-noncurrent” on the Company’s consolidated balance sheet based on the timing of the expected payments to be made to RPI. The fair value for the liability for sale of future royalties at the time of the transaction was based on the Company’s estimates of future royalties expected to be paid to RPI over the life of the arrangement, which was determined using forecasts from market data sources, which are considered Level 3 inputs. The liability is being amortized using the effective interest method over the life of the arrangement, in accordance with the respective guidance. The Company utilizes the prospective method to account for subsequent changes in the estimated future payments to be made to RPI. Refer to Note 9 for further details.

Indefinite-lived intangible assets

Indefinite-lived intangible assets consist of in process research and development ("IPR&D"). IPR&D acquired directly in a transaction other than a business combination is capitalized if the projects will be further developed or have an alternative future use; otherwise they are expensed. The fair values of IPR&D projects and license agreement assets acquired in business combinations are capitalized. Several methods may be used to determine the estimated fair value of the IPR&D and license agreement asset acquired in a business combination. The Company utilizes the "income method" and uses estimated future net cash flows that are derived from projected sales revenues and estimated costs. These projections are based on factors such as relevant market size, patent protection, and expected pricing and industry trends. The estimated future net cash flows are then discounted to the present value using an appropriate discount rate. These assets are treated as indefinite-lived intangible assets until completion or abandonment of the projects, at which time the assets are amortized over the remaining useful life or written off, as appropriate. Intangible assets with indefinite lives, including IPR&D, are tested for impairment if impairment indicators arise and, at a minimum, annually. However, an entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that an indefinite-lived intangible asset’s fair value is less than its carrying amount. Otherwise, no further impairment testing is required. The indefinite-lived intangible asset impairment test consists of a one-step analysis that compares the fair value of the intangible asset with its carrying amount. If the carrying amount of an intangible asset exceeds its fair value, an impairment loss is recognized in an amount equal to that excess. The Company considers many factors in evaluating whether the value of its intangible assets with indefinite lives may not be recoverable, including, but not limited to, expected growth rates, the cost of equity and debt capital, general economic conditions, the Company’s outlook and market performance of the Company’s industry and recent and forecasted financial performance.

Goodwill

Goodwill represents the amount of consideration paid in excess of the fair value of net assets acquired as a result of the Company’s business acquisitions accounted for using the acquisition method of accounting. Goodwill is not amortized and is subject to impairment testing at a reporting unit level on an annual basis or when a triggering event occurs that may indicate the carrying value of the goodwill is impaired. The Company reassesses its reporting units as part of its annual segment review. An entity is permitted to first assess qualitative factors to determine if a quantitative impairment test is necessary. Further testing is only required if the entity determines, based on the qualitative assessment, that it is more likely than not that the fair value of the reporting unit is less than its carrying amount.

Income Taxes

The Organization for Economic Co-operation and Development (“OECD”), the European Community (“the EC”), and individual taxing jurisdictions where the Company and its affiliates do business have recently focused on issues related to the taxation of multinational corporations. The OECD has released its comprehensive plan to create an agreed set of international rules for fighting base erosion and profit shifting. In addition, the OECD, the EC and individual taxing jurisdictions are examining changes to how taxing rights should be allocated among countries considering the digital economy. As a result, the tax laws in the U.S. and other countries in which the Company and its affiliates do business could change on a prospective or retroactive basis and any such changes could materially adversely affect the Company’s business.

On December 22, 2017, the U.S. government enacted the 2017 Tax Act, which significantly revised U.S. tax law by, among other provisions, lowering the U.S. federal statutory corporate income tax rate to 21%, imposing a mandatory one-time transition tax on previously deferred foreign earnings, and eliminating or reducing certain income tax deductions. The Global Intangible Low-Taxed Income ("GILTI") provisions of the 2017 Tax Act require the Company to include in its U.S. income tax return foreign subsidiary earnings in excess of an allowable return on the foreign subsidiary’s tangible assets. The Company has elected to account for GILTI tax in the period in which it is incurred, and therefore has not provided any deferred tax impacts of GILTI in its consolidated financial statements for the period ended September 30, 2023.

Starting in 2022, TCJA amendments to IRC Section 174 no longer permits an immediate deduction for research and development (R&D) expenditures in the tax year that such costs are incurred. Instead, these IRC Section 174 development costs must now be capitalized and amortized over either a five- or 15-year period, depending on the location of the activities performed. The new amortization period begins with the midpoint of any taxable year that IRC Section 174 costs are first incurred, regardless of whether the expenditures were made prior to or after July 1, and runs until the midpoint of year five for activities conducted in the United States or year 15 in the case of development conducted on foreign soil.

Deferred tax assets and liabilities are recognized for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and net operating loss and credit carryforwards. Deferred tax assets and liabilities are measured at rates expected to apply to taxable income in the years in which those temporary differences and carryforwards are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the statement of operations in the period that includes the enactment date. A valuation allowance is recorded when it is not more likely than not that all or a portion of the net deferred tax assets will be realized.

On August 23, 2018, the Company completed its acquisition of Agilis Biotherapeutics, Inc. (“Agilis”), pursuant to an Agreement and Plan of Merger, dated as of July 19, 2018 (the “Agilis Merger Agreement”), by and among the Company,

Agility Merger Sub, Inc., a Delaware corporation and the Company’s wholly owned, indirect subsidiary, Agilis and, solely in its capacity as the representative, agent and attorney-in-fact of the equityholders of Agilis, Shareholder Representative Services LLC, (the “Agilis Merger”). The Company recorded a deferred tax liability in conjunction with the Agilis Merger of $122.0 million in 2018, related to the tax basis difference in the IPRD indefinite-lived intangibles acquired. The Company’s policy is to record a deferred tax liability related to acquired IPR&D which may eventually be realized either upon amortization of the asset when the research is completed, and a product is successfully launched or the write-off of the asset if it is abandoned or unsuccessful. In July 2022, the Company received EMEA approval for a portion of the IPR&D assets, and thus, began the amortization of the intangible.

In May 2023, the Company announced the discontinuation of its preclinical and early research programs in gene therapy as part of a strategic portfolio prioritization. In conjunction with the announcement, the Company recorded an impairment to its indefinite-lived intangible for IP research and development relating to the Friedreich ataxia and Angelman syndrome gene therapy assets. As a result of the impairment, the Company recorded a deferred tax benefit of $50.9 million.

Leases

The Company determines if an arrangement is a lease at inception. This determination generally depends on whether the arrangement conveys to the Company the right to control the use of an explicitly or implicitly identified fixed asset for a period of time in exchange for consideration. Control of an underlying asset is conveyed to the Company if the Company obtains the rights to direct the use of and to obtain substantially all of the economic benefits from using the underlying asset. The Company has lease agreements which include lease and non-lease components, which the Company accounts for as a single lease component for all leases. Operating and finance leases are classified as right of use ("ROU") assets, short term lease liabilities, and long term lease liabilities. Operating and finance lease ROU assets and lease liabilities are recognized at the commencement date based on the present value of lease payments over the lease term. ROU assets are amortized and lease liabilities accrete to yield straight-line expense over the term of the lease. Lease payments included in the measurement of the lease liability are comprised of fixed payments.

Variable lease payments associated with the Company’s leases are recognized when the event, activity, or circumstance in the lease agreement on which those payments are assessed occurs. Variable lease payments are presented in the Company’s consolidated statements of operations in the same line item as expense arising from fixed lease payments for operating leases.

Leases with an initial term of 12 months or less are not recorded on the consolidated balance sheet and the Company recognizes lease expense for these leases on a straight-line basis over the lease term. The Company applies this policy to all underlying asset categories.

A lessee is required to discount its unpaid lease payments using the interest rate implicit in the lease or, if that rate cannot be readily determined, its incremental borrowing rate. As most of the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on the information available at the commencement date in determining the present value of lease payments. The Company gives consideration to its recent debt issuances as well as publicly available data for instruments with similar characteristics when calculating its incremental borrowing rates.

The lease term for all of the Company’s leases includes the non-cancellable period of the lease plus any additional periods covered by either a Company option to extend (or not to terminate) the lease that the Company is reasonably certain to exercise, or an option to extend (or not to terminate) the lease controlled by the lessor. Leasehold improvements are capitalized and depreciated over the lesser of useful life or lease term. See Note 3 Leases for additional information.

Debt - Senior Secured Term Loan (Details) - USD ($) $ in Thousands		3 Months Ended	9 Months Ended
	Oct. 27, 2022	Sep. 30, 2023	Sep. 30, 2023	Sep. 30, 2022	Mar. 31, 2023	Dec. 31, 2022	Jul. 31, 2020
Interest expense
Amortization of debt issuance costs			$ 1,574	$ 1,316
Effective interest rate		9.30%	9.30%				11.00%
Blackstone Credit Agreement
Debt Facility
Maximum borrowing capacity	$ 950,000
Debt issuance costs capitalized	11,600
Credit agreement reserve					$ 50,000
Principal		$ 300,000	$ 300,000			$ 300,000
Less: Debt issuance costs		(10,742)	(10,742)			(11,322)
Net carrying amount		289,258	$ 289,258			$ 288,678
Loan term			6 years 1 month 6 days
Interest expense
Contractual interest expense		9,554	$ 28,087
Amortization of debt issuance costs		280	702
Total		$ 9,834	$ 28,789
Effective interest rate		13.10%	13.10%
Blackstone Credit Agreement \| Minimum
Debt Facility
Minimum consolidated liquidity covenant	100,000
Increased minimum consolidated liquidity covenant after consummation of acquisitions meeting specified thresholds	$ 200,000
Blackstone Credit Agreement \| Adjusted Term SOFR
Debt Facility
Basis spread on variable rate	7.25%
Floor interest rate	1.00%
Blackstone Credit Agreement \| Base Rate
Debt Facility
Basis spread on variable rate	6.25%
Floor interest rate	2.00%
Committed Loan Facility
Debt Facility
Maximum borrowing capacity	$ 450,000
Fund draw term	18 months
Loan term	7 years
Senior Secured Term Loan
Debt Facility
Principal	$ 300,000
Committed Delayed Draw Term Loan Facility
Debt Facility
Maximum borrowing capacity	150,000
Uncommitted Incremental Facility
Debt Facility
Maximum borrowing capacity	$ 500,000

Stock award plan

9 Months Ended

Sep. 30, 2023

Share-based Payment Arrangement [Abstract]

Stock award plan

8. Stock award plan

In May 2013, the Company’s Board of Directors and stockholders approved the 2013 Long-Term Incentive Plan, which became effective upon the closing of the Company’s initial public offering. On June 8, 2022 (the “Restatement Effective Date”), the Company’s stockholders approved the Amended and Restated 2013 Long-Term Incentive Plan (the “Amended 2013 LTIP”). The Amended 2013 LTIP provides for the grant of incentive stock options, nonstatutory stock options, restricted stock units and other stock-based awards. The number of shares of common stock reserved for issuance under the Amended 2013 LTIP is the sum of (A) the number of shares of the Company’s common stock (up to 16,724,212 shares) that is equal to the sum of (1) the number of shares issued under the 2013 Long-Term Incentive Plan prior to the Restatement Effective Date, (2) the number of shares that remain available for issuance under the 2013 Long-Term Incentive Plan immediately prior to the Restatement Effective Date and (3) the number of shares subject to awards granted under the 2013 Long-Term Incentive Plan prior to the Restatement Effective Date that are outstanding as of the Restatement Effective Date, plus (B) from and after the Restatement Effective Date, an additional 8,475,000 shares of Common Stock. As of September 30, 2023, awards for 6,802,210 shares of common stock are available for issuance under the Amended 2013 LTIP.

There are no additional shares of common stock available for issuance under the Company’s 1998 Employee, Director and Consultant Stock Option Plan, 2009 Equity and Long Term Incentive Plan or 2013 Stock Incentive Plan.

In January 2020, the Company’s Board of Directors approved the 2020 Inducement Stock Incentive Plan. The 2020 Inducement Stock Incentive Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards and other stock-based awards for, initially, up to at the time, an aggregate of 1,000,000 shares of common stock. Any grants made under the 2020 Inducement Stock Incentive Plan must be made pursuant to the Nasdaq Listing Rule 5635(c)(4) inducement grant exception as a material component of the Company’s new hires’ employment compensation. In December 2020, the Company’s Board of Directors approved an additional 1,000,000 shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan. In April 2022, the Company’s Board of Directors approved a reduction in the total number of shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan to 1,300,000 shares. In December 2022, the Company’s Board of Directors approved an additional 1,700,000 shares of common stock that may be issued under the 2020 Inducement Stock Incentive Plan. As of September 30, 2023, awards for 1,705,941 shares of common stock were available for issuance under the 2020 Inducement Stock Incentive Plan.

The Board of Directors has the authority to select the individuals to whom options are granted and determine the terms of each option, including (i) the number of shares of common stock subject to the option; (ii) the date on which the option becomes exercisable; (iii) the option exercise price, which, in the case of incentive stock options, must be at least 100% (110% in the case of incentive stock options granted to a stockholder owning in excess of 10% of the Company’s stock) of the fair market value of the common stock as of the date of grant; and (iv) the duration of the option (which, in the case of incentive stock options, may not exceed ten years). Options typically vest over a four-year period.

Inducement stock option awards

From January 1, 2023 through September 30, 2023, the Company issued a total of 1,059,054 stock options to various employees. Of those, 121,460 were inducement grants for non-statutory stock options, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan.

Stock option activity—A summary of stock option activity is as follows:


				Weighted-
		Weighted-		average		Aggregate
		average		remaining		intrinsic
	Number of	exercise		contractual		value(in
	options	price		term		thousands)

Outstanding at December 31, 2022	11,502,417	$	43.33
Granted	1,059,054	$	41.29
Exercised	(806,407)	$	29.48
Forfeited/Cancelled	(318,281)	$	47.84
Outstanding at September 30, 2023	11,436,783	$	43.99	5.87	years	$	5,084
Vested or Expected to vest at September 30, 2023	2,357,250	$	46.72	8.23	years	$	—
Exercisable at September 30, 2023	8,533,144	$	43.18	5.05	years	$	5,084

The fair value of grants made in the nine months ended September 30, 2023 was contemporaneously estimated on the date of grant using the following assumptions:


		Nine months ended
		September 30, 2023
Risk-free interest rate		3.54% - 3.91%
Expected volatility		53% - 54%
Expected term		5.5 years

The Company assumed no expected dividends for all grants. The weighted average grant date fair value of options granted during the nine months ended September 30, 2023 was $21.83 per share.

The expected term of options was estimated based on the Company’s historical exercise data and the expected volatility of options was estimated based on the Company’s historical stock volatility. The risk-free rate of the options was based on U.S. Government Securities Treasury Constant Maturities yields at the date of grant for a term similar to the expected term of the option.

Restricted Stock Awards and Restricted Stock Units—Restricted stock awards and restricted stock units are granted subject to certain restrictions, including in some cases service or time conditions (restricted stock). The grant-date fair value of restricted stock awards and restricted stock units, which have been determined based upon the market value of the Company’s shares on the grant date, are expensed over the vesting period. From January 1, 2023, through September 30, 2023, the Company issued a total of 1,973,973 restricted stock units to various employees. Of those, 83,210 were inducement grants for restricted stock units, all of which were made pursuant to the 2020 Inducement Stock Incentive Plan.

The following table summarizes information on the Company’s restricted stock awards and units:


	Restricted Stock Awards and Units
		Weighted
		Average
		Grant
	Number of	Date
	Shares	Fair Value
Unvested at December 31, 2022	2,516,336	$	45.67
Granted	1,973,973		40.00
Vested	(778,442)		46.34
Forfeited	(297,765)		42.65
Unvested at September 30, 2023	3,414,102	$	42.50

Employee Stock Purchase Plan—In June 2016, the Company established an Employee Stock Purchase Plan (as amended, “ESPP” or the "Plan”), for certain eligible employees. The Plan is administered by the Company’s Board of Directors or a committee appointed by the Company’s Board of Directors. In June 2021, the Plan was amended to increase the total number of shares available for purchase under the Plan from one million shares to two million shares of the Company’s common stock. Employees may participate over a six month period through payroll withholdings and may purchase, at the end of the six month period, the Company’s common stock at a purchase price of at least 85% of the closing price of a share of the Company’s common stock on the first business day of the offering period or the closing price of a share of the Company’s common stock on the last business day of the offering period, whichever is lower. No participant will be granted a right to purchase the Company’s common stock under the Plan if such participant would own more than 5% of the total combined voting power of the Company or any subsidiary of the Company after such purchase. For the three and nine months ended September 30, 2023, the Company recorded $0.7 million and $2.0 million, respectively, in compensation expense related to the ESPP.

The Company recorded share-based compensation expense in the statement of operations related to incentive stock options, nonstatutory stock options, restricted stock awards, restricted stock units and the ESPP as follows:


	Three Months Ended September 30,				Nine Months Ended September 30,
	2023		2022		2023		2022
Research and development	$	13,986	$	15,063	$	44,828	$	41,896
Selling, general and administrative		12,956		13,607		40,300		41,093
Total	$	26,942	$	28,670	$	85,128	$	82,989

As of September 30, 2023, there was approximately $179.3 million of total unrecognized compensation cost related to unvested share-based compensation arrangements granted under the Company’s equity award plans. This cost is expected to be recognized as share-based compensation expense over the weighted average remaining service period of approximately 1.9 years.

Revenue recognition - Collaboration and Royalty Revenue (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Nov. 30, 2011
Revenue recognition
Remaining potential milestones that can be achieved		$ 250,000		$ 250,000
Revenue		196,576	$ 217,127	630,766	$ 531,389
Collaboration revenue
Revenue recognition
Revenue		0	50,017	6	50,024
Royalty revenue
Revenue recognition
Revenue		50,173	32,924	117,857	73,645
SMA License Agreement \| Collaboration revenue
Revenue recognition
Revenue		0
SMA License Agreement \| Royalty revenue
Revenue recognition
Revenue		50,200	$ 32,900	117,900	$ 73,600
Research And Development Event Milestones \| SMA License Agreement
Revenue recognition
Remaining potential milestones that can be achieved		0		0
Sales Milestones \| SMA License Agreement
Revenue recognition
Remaining potential milestones that can be achieved		$ 250,000		$ 250,000
Milestone payments due	$ 50,000
Net sales milestone threshold achieved	$ 750,000
Maximum \| Research And Development Event Milestones \| SMA License Agreement
Revenue recognition
Remaining potential milestones that can be achieved						$ 135,000
Maximum \| Sales Milestones \| SMA License Agreement
Revenue recognition
Remaining potential milestones that can be achieved						$ 325,000

Revenue recognition

9 Months Ended

Sep. 30, 2023

Revenue from Contract with Customer [Abstract]

Revenue recognition

11. Revenue recognition

Net product sales

The Company views its operations and manages its business in one operating segment.

During the three months ended September 30, 2023 and 2022, net product sales outside of the United States were $76.6 million and $79.4 million, respectively, consisting of sales of Translarna, Tegsedi, Waylivra, and Upstaza. Translarna net revenues made up $69.0 million and $76.6 million of the net product sales outside of the United States for the three months ended September 30, 2023 and 2022, respectively. During the three months ended September 30, 2023, and 2022, net product sales in the United States were $67.4 million and $54.8 million, respectively, consisting solely of sales of Emflaza. During the three months ended September 30, 2023, one country, the United States, accounted for at least 10% of the Company’s net product sales, representing $67.4 million of the net product sales. During the three months ended September 30, 2022, two countries, the United States and Russia, accounted for at least 10% of the Company’s net product sales, representing $54.8 million and $28.3 million of the net product sales, respectively. For the three months ended September 30, 2023 and 2022, the Company had a total of three and two distributors, respectively, that each accounted for over 10% of the Company’s net product sales.

During the nine months ended September 30, 2023 and 2022, net product sales outside of the United States were $318.5 million and $247.6 million, respectively, consisting of Translarna, Tegsedi, Waylivra, and Upstaza. Translarna net revenues made up $280.6 million and $232.9 million of the net product sales outside of the United States for the nine months ended September 30, 2023 and 2022, respectively. For the nine months ended September 30, 2023 and 2022, net product sales in the United States were $187.7 million and $160.1 million, respectively, consisting solely of Emflaza. During the nine months ended September 30, 2023, three countries, the United States, Russia, and Brazil, accounted for at least 10% of the Company’s net product sales, representing $187.7 million, $69.0 million, and $52.5 million of net product sales, respectively. During the nine months ended September 30, 2022, two countries, the United States and Russia, accounted for at least 10% of the Company’s net product sales, representing $160.1 million and $57.1 million of net product sales, respectively. For the nine months ended September 30, 2023 and 2022, the Company had a total of two and two distributors, respectively, that each accounted for over 10% of the Company's net product sales.

As of September 30, 2023 and December 31, 2022, the Company does not have a contract liabilities balance related to net product sales, and has not made significant changes to the judgments made in applying ASC Topic 606.

Collaboration and Royalty revenue

In November 2011, the Company and the SMA Foundation entered into the SMA License Agreement with Roche. Under the terms of the SMA License Agreement, Roche acquired an exclusive worldwide license to the Company’s SMA program.

Under the SMA License Agreement, the Company is eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product.

The SMA program currently has one approved product, Evrysdi, which was approved in August 2020 by the FDA for the treatment of SMA in adults and children two months and older. As of September 30, 2023, the Company does not have any remaining research and development event milestones that can be received. The remaining potential sales milestones that can be received is $250.0 million.

to the SMA License Agreement. In September 2022, the Company recognized a sales milestone of $50.0 million for the achievement of $750.0 million in worldwide annual net sales from Evrysdi.

In addition to research and development and sales milestones, the Company is eligible to receive up to double-digit royalties on worldwide annual net sales of a commercial product under the SMA License Agreement. For the three and nine months ended September 30, 2023, the Company has recognized $50.2 million and $117.9 million of royalty revenue related to Evrysdi, respectively. For the three and nine months ended September 30, 2022, the Company has recognized $32.9 million and $73.6 million of royalty revenue, respectively, related to Evrysdi.

Manufacturing Revenue

For the three and nine months ended September 30, 2023, the Company recognized $2.4 million and $6.7 million of manufacturing revenue, respectively, related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. No manufacturing revenue was recognized for the three and nine months ended September 30, 2022. The Company has not made significant changes to the judgments made in applying ASC Topic 606 for the three and nine months ended September 30, 2023 and 2022.

As of September 30, 2023 and December 31, 2022, the Company has a contract liabilities balance of $1.2 million and $1.4 million, respectively, related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers, which is recorded within deferred revenue on the consolidated balance sheet. For the three-month period ended September 30, 2023, the Company did not recognize any revenue related to the amount included in the contract liability balance at the beginning of the period. For the nine-month period ended September 30, 2023, the Company recognized $1.4 million related to the amounts included in the contract liability balance at the beginning of the period.

As of September 30, 2023, the Company has contract assets of $1.4 million related to plasmid DNA and AAV production for external customers, which is recorded within prepaid expenses and other current assets on the consolidated balance sheet. The Company did not have any contract assets for the period ending December 31, 2022.

Remaining performance obligations

As of September 30, 2023 and December 31, 2022, the Company has remaining performance obligations of $1.2 million and $1.4 million, respectively, related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. The Company expects to recognize revenue over the next one year, as the specific timing for satisfying the performance obligations is contingent upon a number of factors, including customers’ needs and schedules.

- Definition

The entire disclosure of revenue from contract with customer to transfer good or service and to transfer nonfinancial asset. Includes, but is not limited to, disaggregation of revenue, credit loss recognized from contract with customer, judgment and change in judgment related to contract with customer, and asset recognized from cost incurred to obtain or fulfill contract with customer. Excludes insurance and lease contracts.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 606
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 9
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147479806/606-10-50-9

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 606
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-Paragraph 10
-Publisher FASB
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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 606
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-Section 50
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Reference 4: http://www.xbrl.org/2003/role/disclosureRef
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Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 606
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-Subparagraph (b)
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Reference 6: http://www.xbrl.org/2003/role/disclosureRef
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Reference 8: http://www.xbrl.org/2003/role/disclosureRef
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-Topic 606
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Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Name Accounting Standards Codification
-Topic 606
-Publisher FASB
-URI https://asc.fasb.org//606/tableOfContent

+ Details

Debt - (Tables)

9 Months Ended

Sep. 30, 2023

Debt Instrument, Redemption [Line Items]

Summary of liability for sale of future royalties


	Nine Months Ended September 30,
Liability for sale of future royalties- (current and noncurrent)	2023
Beginning balance as of December 31, 2022	$	757,886
Less: Non-cash royalty revenue payable to RPI		(50,599)
Plus: Non-cash interest expense recognized		56,031
Ending balance	$	763,318
Effective interest rate as of September 30, 2023		9.3	%

1.50% Convertible senior notes due 2026

Debt Instrument, Redemption [Line Items]

Summary of convertible notes



	September 30, 2023		December 31, 2022
Principal	$	287,500	$	287,500
Less: Debt issuance costs		(3,584)		(4,456)
Net carrying amount	$	283,916	$	283,044

Summary of interest expense recognized related to the Convertible Notes

	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
Contractual interest expense	$	1,080		$	1,081		$	3,215		$	3,217
Amortization of debt issuance costs		294			289			872			856
Total	$	1,374		$	1,370		$	4,087		$	4,073
Effective interest rate		1.9	%		1.9	%		1.9	%		1.9	%

3.00% Convertible senior notes due 2022

Debt Instrument, Redemption [Line Items]

Summary of interest expense recognized related to the Convertible Notes



	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
Contractual interest expense	$	—		$	559		$	—		$	2,800
Amortization of debt issuance costs		—			92			—			460
Total	$	—		$	651		$	—		$	3,260
Effective interest rate		—	%		3.5	%		—	%		3.5	%

Blackstone Credit Agreement

Debt Instrument, Redemption [Line Items]

Schedule of credit agreement


	September 30, 2023		December 31, 2022
Principal	$	300,000	$	300,000
Less: Debt issuance costs		(10,742)		(11,322)
Net carrying amount	$	289,258	$	288,678

Summary of interest expense recognized related to debt


	Three Months Ended			Nine Months Ended
	September 30,			September 30,
	2023			2023
Contractual interest expense	$	9,554		$	28,087
Amortization of debt issuance costs		280			702
Total	$	9,834		$	28,789
Effective interest rate		13.1	%		13.1	%

Net loss per share - Numerator and Denominator (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Numerator
Net loss - Basic	$ (132,970)	$ (109,315)	$ (470,812)	$ (388,128)
Net loss - Diluted	$ (132,970)	$ (109,315)	$ (470,812)	$ (388,128)
Denominator
Basic	75,377,997	71,654,671	74,618,611	71,415,849
Diluted	75,377,997	71,654,671	74,618,611	71,415,849
Net loss per share - Basic	$ (1.76)	$ (1.53)	$ (6.31)	$ (5.43)
Net loss per share - Diluted	$ (1.76)	$ (1.53)	$ (6.31)	$ (5.43)

- Definition

The amount of net income (loss) for the period per each share of common stock or unit outstanding during the reporting period.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 250
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
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Reference 4: http://www.xbrl.org/2003/role/disclosureRef
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+ Details

- Definition

The amount of net income (loss) for the period available to each share of common stock or common unit outstanding during the reporting period and to each share or unit that would have been outstanding assuming the issuance of common shares or units for all dilutive potential common shares or units outstanding during the reporting period.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 250
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- Definition

Amount, after deduction of tax, noncontrolling interests, dividends on preferred stock and participating securities, and addition from assumption of issuance of common shares for dilutive potential common shares; of income (loss) available to common shareholders.

+ References + Details

Capitalization

9 Months Ended

Sep. 30, 2023

Stockholders' Equity Note [Abstract]

Capitalization

6. Capitalization

In August 2019, the Company entered into an At the Market Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald and RBC Capital Markets, LLC (together, the “Sales Agents”), pursuant to which, the Company may offer and sell shares of its common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended. No shares were sold during the three and nine months ended September 30, 2023 and 2022. The remaining shares of the Company’s common stock available to be issued and sold, under the At the Market Offering, have an aggregate offering price of up to $93.0 million as of September 30, 2023.

- Definition

The entire disclosure for equity.

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+ Details

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2023	Dec. 31, 2022
Current assets:
Cash and cash equivalents	$ 165,157	$ 279,834
Marketable securities	129,653	130,871
Trade and royalty receivables, net	165,718	155,614
Inventory, net	35,752	21,808
Prepaid expenses and other current assets	44,082	105,658
Total current assets	540,362	693,785
Fixed assets, net	85,031	72,590
Intangible assets, net	423,342	705,891
Goodwill	82,341	82,341
Operating lease ROU assets	94,072	102,430
Deposits and other assets	34,737	48,582
Total assets	1,259,885	1,705,619
Current liabilities:
Accounts payable and accrued expenses	370,731	320,366
Deferred revenue	1,224	1,351
Operating lease liabilities- current	11,703	9,370
Finance lease liabilities- current	2,611	3,000
Liability for sale of future royalties - current	105,849	72,149
Total current liabilities	492,118	406,236
Long-term debt	573,174	571,722
Contingent consideration payable	39,000	164,000
Deferred tax liability	51,927	102,834
Operating lease liabilities- noncurrent	99,682	100,860
Finance lease liabilities- noncurrent	17,184	18,675
Liability for sale of future royalties- noncurrent	657,469	685,737
Other long-term liabilities	141	2,641
Total liabilities	1,930,695	2,052,705
Stockholders' deficit:
Common stock, $0.001 par value. Authorized 250,000,000 shares; issued and outstanding 75,459,022 shares at September 30, 2023. Authorized 250,000,000 shares; issued and outstanding 73,104,692 shares at December 31, 2022	75	72
Additional paid-in capital	2,447,292	2,305,020
Accumulated other comprehensive income	9,609	4,796
Accumulated deficit	(3,127,786)	(2,656,974)
Total stockholders' deficit	(670,810)	(347,086)
Total liabilities and stockholders' deficit	$ 1,259,885	$ 1,705,619

Leases - (Tables)

9 Months Ended

Sep. 30, 2023

Leases

Schedule of lease costs


	Three Months Ended		Three Months Ended		Nine Months Ended		Nine Months Ended
		September 30, 2023		September 30, 2022		September 30, 2023		September 30, 2022
Operating Lease Cost
Fixed lease cost	$	5,490	$	5,377	$	16,463	$	14,267
Variable lease cost		1,376		1,151		4,140		3,152
Short-term lease cost		271		262		866		600
Total operating lease cost	$	7,137	$	6,790	$	21,469	$	18,019


	September 30, 2023		December 31, 2022
Weighted-average remaining lease terms - operating leases (years)	11.61		11.61
Weighted-average discount rate - operating leases	8.67	%	8.61	%
Weighted-average remaining lease terms - finance lease (years)	9.26		10.01
Weighted-average discount rate - finance lease	7.80	%	7.80	%

Schedule of supplemental cash flow information related to leases


	Nine Months Ended September 30,
	2023		2022
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	11,479	$	10,954
Financing cash flows from finance lease		1,379		1,276
Operating cash flows from finance lease		1,621		1,724

Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	—	$	35,294

Schedule of future lease payments - Operating leases


	Operating Leases		Finance Lease
2023 (excludes the nine months ended September 30, 2023)	$	5,077	$	—
2024		18,369		3,000
2025		20,438		3,000
2026		19,988		3,000
2027 and thereafter		193,792		18,000
Total lease payments		257,664		27,000
Less: Imputed Interest expense		146,279		7,205
Total	$	111,385	$	19,795

Schedule of future lease payments - Finance leases


	Operating Leases		Finance Lease
2023 (excludes the nine months ended September 30, 2023)	$	5,077	$	—
2024		18,369		3,000
2025		20,438		3,000
2026		19,988		3,000
2027 and thereafter		193,792		18,000
Total lease payments		257,664		27,000
Less: Imputed Interest expense		146,279		7,205
Total	$	111,385	$	19,795

Summary of significant accounting policies - Manufacturing Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Dec. 31, 2022
Revenue recognition
Revenue	$ 196,576	$ 217,127	$ 630,766	$ 531,389
Remaining performance obligations	1,200		1,200		$ 1,400
Manufacturing revenue
Revenue recognition
Revenue	2,365	$ 0	6,716	$ 0
Contract with customer, asset	$ 1,400		$ 1,400		$ 0

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References + Details

- Definition

Amount, excluding tax collected from customer, of revenue from satisfaction of performance obligation by transferring promised good or service to customer. Tax collected from customer is tax assessed by governmental authority that is both imposed on and concurrent with specific revenue-producing transaction, including, but not limited to, sales, use, value added and excise.

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+ Details

Leases - Narrative (Details) $ in Thousands		1 Months Ended	3 Months Ended		9 Months Ended		12 Months Ended
Leases - Narrative (Details) $ in Thousands	Jul. 01, 2020 USD ($) ft² item	May 31, 2022 USD ($) ft² period building	Sep. 30, 2023 USD ($) lease	Sep. 30, 2022 USD ($)	Sep. 30, 2023 USD ($) lease	Sep. 30, 2022 USD ($)	Dec. 31, 2020 USD ($)	Dec. 31, 2022 USD ($)	Jun. 19, 2020 USD ($)
Leases
Number of operating leases \| lease			2		2
Operating lease, expense			$ 7,100	$ 6,800	$ 21,500	$ 18,000
Finance Lease, Liability			19,795		19,795
Finance lease liabilities- current			2,611		2,611			$ 3,000
Finance lease liabilities- noncurrent			17,184		17,184			18,675
Aggregate rent, Initial term			257,664		257,664
Operating lease ROU assets			94,072		94,072			102,430
Operating Lease, Liability			111,385		111,385
Research and development			164,212	165,462	545,210	462,802
MassBio
Leases
Finance lease cost			400	$ 400	1,100	$ 1,200
Finance Lease, Liability									$ 41,400
Finance lease liabilities- current			2,600		2,600			3,000
Finance lease liabilities- noncurrent			$ 17,200		$ 17,200			$ 18,700
Finance lease ROU asset									$ 41,400
Finance lease, term of contract									12 years 6 months
Research and development							$ 41,400
Minimum
Leases
Operating lease, term of contract			4 months 24 days		4 months 24 days
Maximum
Leases
Operating lease, term of contract			15 years 8 months 12 days		15 years 8 months 12 days
Renewal term			20 years		20 years
Hopewell Campus
Leases
Operating lease, term of contract	15 years
Area of real estate property \| ft²	220,500
Renewal term	10 years
Number of renewable terms \| item	2
Lessee, Operating Lease, Existence of Option to Extend [true false]	true
Aggregate rent, Initial term	$ 111,500
Percent of market rate	95.00%
Warren Premises
Leases
Operating lease, term of contract		17 years
Number of buildings leased \| building		2
Area of real estate property \| ft²		360,000
Renewal term		5 years
Number of renewable terms \| period		3
Lessee, Operating Lease, Existence of Option to Extend [true false]		true
Aggregate rent, Initial term		$ 163,000
Operating lease ROU assets		28,900
Operating Lease, Liability		$ 28,900
Base rent abatement period		3 years
Base rent abatement		$ 18,600
Aggregate rent net of base rate abatement, initial term		144,400
Allowance for lease improvements		36,200
Commitment to fund construction account		3,600
Payment due from lessor at issuance of temporary certificate of occupancy		$ 5,000

Leases - Lease payments (Details) $ in Thousands	Sep. 30, 2023 USD ($)
Operating leases
2023 (excludes the nine months ended September 30, 2023)	$ 5,077
2024	18,369
2025	20,438
2026	19,988
2027 and thereafter	193,792
Total lease payments	257,664
Less: Imputed Interest expense	146,279
Total	111,385
Finance leases
2024	3,000
2025	3,000
2026	3,000
2027 and thereafter	18,000
Total lease payments	27,000
Less: Imputed Interest expense	7,205
Total	$ 19,795

Leases

9 Months Ended

Sep. 30, 2023

Leases

Leases

3. Leases

The Company leases office space in South Plainfield, New Jersey for its principal office under two noncancelable operating leases through August 2024, in addition to office and laboratory space in Bridgewater, New Jersey and other locations throughout the United States and office space in various countries for international employees primarily through workspace providers.

The Company also leases approximately 220,500 square feet of office, manufacturing and laboratory space at a facility located in Hopewell Township, New Jersey pursuant to a Lease Agreement (the “Hopewell Lease”) with Hopewell Campus Owner LLC. The rental term of the Hopewell Lease commenced on July 1, 2020 and has an initial term of fifteen years (the “Hopewell Initial Term”), with two consecutive ten year renewal periods, each at the Company’s option. The aggregate rent for the Hopewell Initial Term will be approximately $111.5 million. The rental rate for the renewal periods will be 95% of the Prevailing Market Rate (as defined in the Hopewell Lease) and determined at the time of the exercise of the renewal. The Company is also responsible for maintaining certain insurance and the payment of proportional taxes, utilities and common area operating expenses. The Hopewell Lease contains customary events of default, representations, warranties and covenants.

In May 2022, the Company entered into a Lease Agreement (the “Warren Lease”) with Warren CC Acquisitions, LLC (the “Warren Landlord”) relating to the lease of two entire buildings comprised of approximately 360,000 square feet of shell condition, modifiable space (the “Warren Premises”) at a facility located in Warren, New Jersey. The rental term of the Warren Lease commenced on June 1, 2022, with an initial term of seventeen years (the “Warren Initial Term”), followed by three consecutive five-year renewal periods at the Company’s option. The aggregate base rent for the Warren Initial Term will be approximately $163.0 million; provided, however, that if the Company is not subject to an Event of Default (as defined in the Warren Lease), the Company will be entitled to a base rent abatement over the first three years of the Warren Initial Term of approximately $18.6 million, reducing the Company’s total base rent obligation to $144.4 million. The rental rate for the renewal periods will be at the Fair Market Rental Value (as defined in the Warren Lease) and determined at the time of the exercise of the renewal. Beginning in the second lease year, the Company is also responsible for the payment of all taxes and operating expenses for the Warren Premises. As a result, the Company recorded an operating lease ROU asset of $28.9 million and an operating lease ROU liability of $28.9 million as of the commencement date.

The Company is developing the Warren Premises into office and laboratory space. The Company is entitled to an allowance of approximately $36.2 million to be provided by the Warren Landlord to be used towards such improvements. The Landlord is providing the allowance to cover those assets that are real property improvements, such as structural components, roofs, flooring, etc., whose useful lives are typically longer in nature. The Company evaluated the leasehold improvements under ASC 842 and determined that the Company will be the owner of the improvements, and therefore the $36.2 million allowance and $5.0 million due from the Landlord were treated as lease incentives at the commencement of the lease and included in the calculation of the lease ROU asset and lease ROU liability, effectively reducing both at Commencement Date. In connection with the execution of the Warren Lease, the Company also committed to fund a construction account with $3.6 million to go towards the Company’s improvements of the Warren Premises. Subject to the terms of the Warren Lease, the Company has a right of first offer to purchase the Warren Premises if the Warren Landlord receives a bona fide third party offer to purchase the Warren Premises or the Warren Landlord decides to sell the Warren Premises.

On June 19, 2020, the Company entered into a commercial manufacturing service agreement for a term of 12.5 years with MassBiologics of the University of Massachusetts Medical School ("MassBio"). The Company determined that the agreement was a finance lease, for which the Company recorded a finance lease ROU asset for $41.4 million and corresponding finance lease liability for $41.4 million at the onset of the lease agreement. Given that the leased asset is designed for the production of PTC’s AADC program and would not have an alternate use outside the PTC gene therapy platform without incurring significant costs, the Company determined that the lease should be treated as research and development expense under ASC 730. Accordingly, the full $41.4 million relating to the finance lease ROU asset was written off and expensed to research and development during the year ended December 31, 2020. As of September 30, 2023, the balance of the finance lease liabilities-current and finance lease liabilities-noncurrent are $2.6 million and $17.2 million, respectively, and are directly related to the Company’s MassBio agreement. As of December 31, 2022, the balance of the finance lease liabilities-current and finance lease liabilities-noncurrent were $3.0 million and $18.7 million, respectively. Additionally, the Company recorded finance lease costs of $0.4 million and $1.1 million related to interest on the lease liability during the three and nine months ended September 30, 2023, respectively. The Company recorded finance lease costs of $0.4 million and $1.2 million related to interest on the lease liability during the three and nine months ended September 30, 2022, respectively.

The Company also leases certain vehicles, lab equipment, and office equipment under operating leases. The Company’s leases have remaining operating lease terms ranging from 0.4 years to 15.7 years and certain of the leases include renewal options to extend the lease for up to 20 years. Rent expense was $7.1 million and $6.8 million for the three months ended September 30, 2023 and 2022, respectively. Rent expense was $21.5 million and $18.0 million for the nine months ended September 30, 2023 and 2022, respectively.

The components of operating lease expense were as follows:


	Three Months Ended		Three Months Ended		Nine Months Ended		Nine Months Ended
		September 30, 2023		September 30, 2022		September 30, 2023		September 30, 2022
Operating Lease Cost
Fixed lease cost	$	5,490	$	5,377	$	16,463	$	14,267
Variable lease cost		1,376		1,151		4,140		3,152
Short-term lease cost		271		262		866		600
Total operating lease cost	$	7,137	$	6,790	$	21,469	$	18,019

Total operating lease cost is a component of operating expenses on the consolidated statements of operations.

Supplemental lease term and discount rate information related to leases was as follows as September 30, 2023 and December 31, 2022:


	September 30, 2023		December 31, 2022
Weighted-average remaining lease terms - operating leases (years)	11.61		11.61
Weighted-average discount rate - operating leases	8.67	%	8.61	%
Weighted-average remaining lease terms - finance lease (years)	9.26		10.01
Weighted-average discount rate - finance lease	7.80	%	7.80	%

Supplemental cash flow information related to leases was as follows as of September 30, 2023 and 2022:


	Nine Months Ended September 30,
	2023		2022
Cash paid for amounts included in the measurement of lease liabilities:
Operating cash flows from operating leases	$	11,479	$	10,954
Financing cash flows from finance lease		1,379		1,276
Operating cash flows from finance lease		1,621		1,724

Right-of-use assets obtained in exchange for lease obligations:
Operating leases	$	—	$	35,294

Future minimum lease payments under non-cancelable leases as of September 30, 2023 were as follows:


	Operating Leases		Finance Lease
2023 (excludes the nine months ended September 30, 2023)	$	5,077	$	—
2024		18,369		3,000
2025		20,438		3,000
2026		19,988		3,000
2027 and thereafter		193,792		18,000
Total lease payments		257,664		27,000
Less: Imputed Interest expense		146,279		7,205
Total	$	111,385	$	19,795

Net loss per share

9 Months Ended

Sep. 30, 2023

Earnings Per Share [Abstract]

Net loss per share

7. Net loss per share

Basic and diluted net loss per share is computed by dividing net loss by the weighted-average number of common shares outstanding. Potentially dilutive securities were excluded from the diluted calculation because their effect would be anti-dilutive.

The following tables set forth the computation of basic and diluted net loss per share:


	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
Numerator
Net loss	$	(132,970)		$	(109,315)		$	(470,812)		$	(388,128)
Denominator
Denominator for basic and diluted net loss per share		75,377,997			71,654,671			74,618,611			71,415,849
Net loss per share:
Basic and diluted	$	(1.76)	*	$	(1.53)	*	$	(6.31)	*	$	(5.43)	*

* In the three and nine months ended September 30, 2023 and 2022, the Company experienced a net loss and therefore did not report any dilutive share impact.

The following table shows historical dilutive common share equivalents outstanding, which are not included in the above historical calculation, as the effect of their inclusion is anti-dilutive during each period.


	As of September 30,
	2023	2022
Stock Options	11,436,783	11,478,421
Unvested restricted stock awards and units	3,414,102	2,488,944
Total	14,850,885	13,967,365

Summary of significant accounting policies - Collaboration and Royalty Revenue (Details) - USD ($) $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022
Collaboration and royalty revenue
Revenue		$ 196,576	$ 217,127	$ 630,766	$ 531,389
Collaboration revenue
Collaboration and royalty revenue
Revenue		0	50,017	6	50,024
Royalty revenue
Collaboration and royalty revenue
Revenue		50,173	32,924	117,857	73,645
SMA License Agreement \| Collaboration revenue
Collaboration and royalty revenue
Revenue		0
SMA License Agreement \| Royalty revenue
Collaboration and royalty revenue
Revenue		$ 50,200	$ 32,900	$ 117,900	$ 73,600
SMA License Agreement \| Sales Milestones
Collaboration and royalty revenue
Milestone payments due	$ 50,000
Net sales milestone threshold achieved	$ 750,000

- Definition

+ References

+ Details

Stock award plan - Restricted Stock (Details) - Restricted stock awards and units	9 Months Ended
	Sep. 30, 2023 $ / shares shares
Number of Shares
Balance at the beginning of the period (in shares) \| shares	2,516,336
Granted (in shares) \| shares	1,973,973
Vested (in shares) \| shares	(778,442)
Forfeited (in shares) \| shares	(297,765)
Balance at the end of the period (in shares) \| shares	3,414,102
Weighted Average Grant Date Fair Value
Balance at the beginning of the period (in dollars per share) \| $ / shares	$ 45.67
Granted (in dollars per share) \| $ / shares	40.00
Vested (in dollars per share) \| $ / shares	46.34
Forfeited (in dollars per share) \| $ / shares	42.65
Balance at the end of the period (in dollars per share) \| $ / shares	$ 42.50

Intangible assets and goodwill - (Tables)

9 Months Ended

Sep. 30, 2023

Goodwill and Intangible Assets Disclosure [Abstract]

Schedule of definite lived intangible assets

Definite-lived intangible assets consisted of the following at September 30, 2023 and December 31, 2022:


		Ending Balance at				Reclass from				Foreign		Ending Balance at
Definite-lived		December 31,				Indefinite Lived to				currency		September 30,
intangibles assets, gross		2022		Additions		Definite Lived		Impairment		translation		2023
Emflaza	$	420,253	$	76,454	$	—	$	—	$	—	$	496,707
Waylivra		9,316		157		—		—		(96)		9,377
Tegsedi		7,109		4,299		—		—		(183)		11,225
Upstaza		89,550		—		—		—		—		89,550
Total definite-lived intangibles, gross	$	526,228	$	80,910	$	—	$	—	$	(279)	$	606,859

Ending Balance at

Foreign

Ending Balance at

Definite-lived

December 31,

currency

September 30,

intangibles assets, accumulated amortization

2022

Amortization

translation

2023

Emflaza

(266,023)

(138,038)

—

(404,061)

Waylivra		(2,751)		(791)		45		(3,497)
Tegsedi		(1,709)		(1,035)		36		(2,708)
Upstaza		(3,420)		(5,597)		—		(9,017)
Total definite-lived intangibles, accumulated amortization	$	(273,903)	$	(145,461)	$	81	$	(419,283)

Total definite-lived intangibles, net							$	187,576

Schedule of estimated future amortization of intangible assets


	As of September 30, 2023
2023	$	58,640
2024		46,557
2025		10,041
2026		10,041
2027 and thereafter		62,297
Total	$	187,576

Schedule of indefinite lived intangible assets

Indefinite-lived intangible assets consisted of the following at September 30, 2023 and December 31, 2022:


		Ending Balance at				Reclass from				Foreign		Ending Balance at
Indefinite-lived		December 31,				Indefinite Lived to				currency		September 30,
intangibles assets		2022		Additions		Definite Lived		Impairment		translation		2023
Upstaza	$	235,766	$	—	$	—	$	—	$	—	$	235,766
PTC-FA		112,500		—		—		(112,500)		—		—
PTC-AS		105,300		—		—		(105,300)		—		—
Total indefinite-lived intangibles	$	453,566	$	—	$	—	$	(217,800)	$	—	$	235,766

Total intangible assets, net											$	423,342

Debt - Convertible Notes (Details) - 1.50% Convertible senior notes due 2026 - Convertible debt - USD ($)	Sep. 30, 2023	Dec. 31, 2022	Sep. 30, 2019
Long-term debt
Principal	$ 287,500,000	$ 287,500,000	$ 287,500,000
Less: Debt issuance costs	(3,584,000)	(4,456,000)
Net carrying amount	$ 283,916,000	$ 283,044,000

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

- Definition

Amount, after deduction of unamortized premium (discount) and debt issuance cost, of long-term debt. Excludes lease obligation.

+ References + Details

Stock award plan - (Tables)

9 Months Ended

Sep. 30, 2023

Share-based Payment Arrangement [Abstract]

Summary of stock option activity


				Weighted-
		Weighted-		average		Aggregate
		average		remaining		intrinsic
	Number of	exercise		contractual		value(in
	options	price		term		thousands)

Outstanding at December 31, 2022	11,502,417	$	43.33
Granted	1,059,054	$	41.29
Exercised	(806,407)	$	29.48
Forfeited/Cancelled	(318,281)	$	47.84
Outstanding at September 30, 2023	11,436,783	$	43.99	5.87	years	$	5,084
Vested or Expected to vest at September 30, 2023	2,357,250	$	46.72	8.23	years	$	—
Exercisable at September 30, 2023	8,533,144	$	43.18	5.05	years	$	5,084

Schedule of assumptions used to estimate fair values of grants made on the date of grant


		Nine months ended
		September 30, 2023
Risk-free interest rate		3.54% - 3.91%
Expected volatility		53% - 54%
Expected term		5.5 years

Summary of information on the Company's restricted stock


	Restricted Stock Awards and Units
		Weighted
		Average
		Grant
	Number of	Date
	Shares	Fair Value
Unvested at December 31, 2022	2,516,336	$	45.67
Granted	1,973,973		40.00
Vested	(778,442)		46.34
Forfeited	(297,765)		42.65
Unvested at September 30, 2023	3,414,102	$	42.50

Schedule of share-based compensation expense recorded in the statement of operations


	Three Months Ended September 30,				Nine Months Ended September 30,
	2023		2022		2023		2022
Research and development	$	13,986	$	15,063	$	44,828	$	41,896
Selling, general and administrative		12,956		13,607		40,300		41,093
Total	$	26,942	$	28,670	$	85,128	$	82,989

Intangible assets and goodwill - Future Amortization (Details) $ in Thousands	Sep. 30, 2023 USD ($)
Goodwill and Intangible Assets Disclosure [Abstract]
2023	$ 58,640
2024	46,557
2025	10,041
2026	10,041
2027 and thereafter	62,297
Total	$ 187,576

Fair value of financial instruments and investments

9 Months Ended

Sep. 30, 2023

Fair Value Disclosures [Abstract]

Fair value of financial instruments and investments

4. Fair value of financial instruments and marketable securities

The Company follows the fair value measurement rules, which provideguidance on the use of fair value in accounting and disclosure for assets and liabilities when such accounting and disclosure is called for by other accounting literature. These rules establish a fair value hierarchy for inputs to be used to measure fair value of financial assets and liabilities. This hierarchy prioritizes the inputs to valuation techniques used to measure fair value into three levels: Level 1 (highest priority), Level 2, and Level 3 (lowest priority).

●

Level 1—Unadjusted quoted prices in active markets for identical assets or liabilities that the Company has the ability to access at the balance sheet date.

●

Level 2—Inputs other than quoted prices included within Level 1 that are observable for the asset or liability, either directly or indirectly. Level 2 inputs include quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, inputs other than quoted prices that are observable for the asset or liability (i.e., interest rates, yield curves, etc.), and inputs that are derived principally from or corroborated by observable market data by correlation or other means (market corroborated inputs).

●

Level 3—Inputs are unobservable and reflect the Company’s assumptions as to what market participants would use in pricing the asset or liability. The Company develops these inputs based on the best information available.

Cash equivalents and marketable securities are reflected in the accompanying financial statements at fair value. The carrying amount of receivables and accounts payable and accrued expenses approximates fair value due to the short-term nature of those instruments.

The Company owns common stock in ClearPoint Neuro, Inc. (“ClearPoint”) (formerly MRI Interventions, Inc.), a publicly traded medical device company. The ClearPoint equity investments (collectively, the “ClearPoint Equity Investments”) represent financial instruments, and therefore, are recorded at fair value, which is readily determinable. The ClearPoint Equity Investments are components of prepaids and other current assets on the consolidated balance sheet as of September 30, 2023, and deposits and other assets as of December 31, 2022. During three and nine months ended September 30, 2023, the Company recorded unrealized losses of $2.0 million and $3.1 million, respectively. During the three and nine months ended September 30, 2022, the Company recorded unrealized losses of $3.5 million and $1.1 million, respectively. During the three months ended September 30, 2023, the Company did not record any realized gains or losses for the sale of ClearPoint Equity Investments. During the nine months ended September 30, 2023, the Company recorded a realized loss of $0.8 million for the sale of ClearPoint Equity Investments. During the three and nine months ended September 30, 2022, the Company did not record any realized gains or losses for the sale of Clearpoint Equity Investments. These unrealized and realized losses are components of other expense, net within the consolidated statement of operations. The fair value of the ClearPoint Equity Investments was $4.5 million and $11.0 million as of September 30, 2023 and December 31, 2022, respectively. The Company classifies the ClearPoint Equity Investments as Level 1 assets within the fair value hierarchy, as the value is based on a quoted market price in an active market, which is not adjusted.

In January 2020, the Company purchased a $10.0 million convertible note from ClearPoint that the Company can convert into ClearPoint shares at a conversion rate of $6.00 per share at any point throughout the term of the loan, which matures five years from the purchase date. The Company determined that the convertible note represents an available for sale debt security and the Company has elected to record it at fair value under ASC 825. The Company classifies its ClearPoint convertible debt security as a Level 2 asset within the fair value hierarchy, as the value is based on inputs other than quoted prices that are observable. The fair value of the ClearPoint convertible debt security is determined at each reporting period by utilizing a Black-Scholes option pricing model, as well as a present value of expected cash flows from the debt security utilizing the risk free rate and the estimated credit spread as of the valuation date as the discount rate. During the three and nine months ended September 30, 2023, the Company recorded unrealized losses of $3.1 million and $4.6 million, respectively. During the three and nine months ended September 30, 2022, the Company recorded unrealized losses of $4.4 million and $2.4 million, respectively. These unrealized gains and losses are components of other expense, net within the consolidated statement of operations. The fair value of the convertible debt security was $10.6 million and $15.2

million as of September 30, 2023 and December 31, 2022, respectively. The convertible debt security is considered to be long term and is included as a component of deposits and other assets on the consolidated balance sheet. Other than the ClearPoint Equity Investments and the ClearPoint convertible debt security, no other items included in deposits and other assets and prepaids and other current assets on the consolidated balance sheets are fair valued.

The Company has investments in mutual funds, including one that is denominated in a foreign currency. All of these are equity investments and are classified as marketable securities on the Company’s consolidated balance sheets. These equity investments are reported at fair value, as they are readily available, and as such are classified as Level 1 assets. Unrealized holding gains and losses for these equity investments are included as components of other expense, net within the consolidated statement of operations. For the three and nine months ended September 30, 2023, the Company had unrealized gains of $1.1 million and of $5.5 million, respectively, relating to the equity investments still held at the reporting date. For the three and nine months ended September 30, 2022, the Company had unrealized gains of $0.1 million and unrealized losses of $11.3 million relating to the equity investments still held at the reporting date, respectively. For the three and nine months ended September 30, 2023, the Company had redemptions of $7.8 million and $12.1 million, respectively, which were primarily due to liquidation of one of the mutual funds. For the three and nine months ended September 30, 2022, the Company had redemptions of $100.8 million and $104.4 million, respectively, which were primarily due to liquidation of one of the mutual funds. For the three months ended September 30, 2023, the Company had foreign currency unrealized losses of $1.4 million relating to these equity investments. For the nine months ended September 30, 2023, the amounts recognized for foreign currency unrealized losses relating to these investments were immaterial. For the three and nine months ended September 30, 2022, the Company had foreign currency unrealized losses of $1.4 million and $1.0 million, respectively, relating to these equity investments.

Fair value of marketable securities that are classified as available for sale debt securities is based upon market prices using quoted prices in active markets for identical assets quoted on the last day of the period. In establishing the estimated fair value of the remaining available for sale debt securities, the Company used the fair value as determined by its investment advisors using observable inputs other than quoted prices.

The following represents the fair value using the hierarchy described above for the Company’s financial assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2023 and December 31, 2022:


	September 30, 2023
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	1,625	$	—	$	1,625	$	—
Marketable securities - equity investments	$	128,028	$	128,028	$	—	$	—
ClearPoint Equity Investments - available for sale	$	4,482	$	4,482	$	—	$	—
ClearPoint convertible debt security	$	10,637	$	—	$	10,637	$	—
Contingent consideration payable- development and regulatory milestones	$	26,400	$		$		$	26,400
Contingent consideration payable- net sales milestones and royalties	$	12,600	$		$		$	12,600


	December 31, 2022
			Quoted prices		Significant
			in active		other		Significant
			markets for		observable		unobservable
			identical assets		inputs		inputs
	Total		(level 1)		(level 2)		(level 3)
Marketable securities - available for sale	$	22,610	$	—	$	22,610	$	—
Marketable securities - equity investments	$	108,261	$	108,261	$	—	$	—
ClearPoint Equity Investments	$	10,965	$	10,965	$	—	$	—
ClearPoint convertible debt security	$	15,231	$	—	$	15,231	$	—

Contingent consideration payable- development and regulatory milestones		$	82,500		$	—		$	—		$	82,500
Contingent consideration payable- net sales milestones and royalties		$	81,500		$	—		$	—		$	81,500

No transfers of assets between Level 1, Level 2, or Level 3 of the fair value measurement hierarchy occurred during the periods ended September 30, 2023 and December 31, 2022.

The following is a summary of marketable securities accounted for as available for sale debt securities at September 30, 2023 and December 31, 2022:


	September 30, 2023
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Corporate debt securities	$	1,649	$	—	$	(24)	$	1,625
Total	$	1,649	$	—	$	(24)	$	1,625


	December 31, 2022
	Amortized		Gross Unrealized
	Cost		Gains		Losses		Fair Value
Commercial paper	$	12,419	$	5	$	—	$	12,424
Corporate debt securities		10,685		—		(499)		10,186
Total	$	23,104	$	5	$	(499)	$	22,610

For available for sale debt securities in an unrealized loss position, the Company assesses whether it intends to sell or if it is more likely than not that the Company will be required to sell the security before recovery of its amortized cost basis. If either of the criteria regarding intent or requirement to sell is met, the security’s amortized cost basis is written down to fair value. For the three and nine months ended September 30, 2023 and 2022, no write downs occurred. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost basis, which may be maturity. The Company also reviews its available for sale debt securities in an unrealized loss position and evaluates whether the decline in fair value has resulted from credit losses or other factors. This review is subjective, as it requires management to evaluate whether an event or change in circumstances has occurred in that period that may be related to credit issues. For the three and nine months ended September 30, 2023 and 2022, no allowance was recorded for credit losses. Unrealized gains and losses are reported as a component of accumulated other comprehensive (loss) income in stockholders’ equity.

For the three months ended September 30, 2023, the Company did not have any realized gains or losses from the sale of available for sale debt securities. For the nine months ended September 30, 2023, the Company had $0.3 million of realized losses from the sale of available for sale debt securities. For the three and nine months ended September 30, 2022, the Company had $1.3 million and $1.6 million of realized losses from the sale of available for sale debt securities, respectively. Realized gains and losses are reported as a component of interest expense, net in the consolidated statement of operations. Reclassified amounts from other comprehensive items were determined using the actual realized gains and losses from the sales of marketable securities.

The unrealized losses and fair values of available for sale debt securities that have been in an unrealized loss position for a period of less than and greater than or equal to 12 months as of September 30, 2023 are as follows:


	September 30, 2023
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Corporate debt securities	$	—		—		(24)		1,625		(24)	$	1,625
Total	$	—	$	—	$	(24)	$	1,625	$	(24)	$	1,625


	December 31, 2022
	Securities in an unrealized loss				Securities in an unrealized loss
	position less than 12 months				position greater than or equal to 12 months				Total
	Unrealized losses		Fair Value		Unrealized losses		Fair Value		Unrealized losses		Fair Value
Corporate debt securities	$	—		—		(499)		10,186		(499)	$	10,186
Total	$	—	$	—	$	(499)	$	10,186	$	(499)	$	10,186

Available for sale debt securities at September 30, 2023 and December 31, 2022 mature as follows:


	September 30, 2023
	Less Than		More Than
	12 Months		12 Months
Corporate debt securities	$	1,625	$	—
Total	$	1,625	$	—


	December 31, 2022
	Less Than		More Than
	12 Months		12 Months
Commercial paper	$	12,424	$	—
Corporate debt securities		—		10,186
Total	$	12,424	$	10,186

The Company classifies all of its marketable securities as current as they are all either available for sale debt securities or equity investments and are available for current operations.

Convertible senior notes

In September 2019, the Company issued $287.5 million of 1.50% convertible senior notes due September 15, 2026 (the “2026 Convertible Notes,”). The fair value of the 2026 Convertible Notes, which differs from their carrying values, is influenced by interest rates, the Company’s stock price and stock price volatility and is determined by prices for the 2026 Convertible Notes observed in market trading which are Level 2 inputs. The estimated fair value of the 2026 Convertible Notes at September 30, 2023 and December 31, 2022 was $228.8 million and $281.7 million, respectively.

Level 3 valuation

The contingent consideration payable is fair valued each reporting period with the change in fair value recorded as a gain or loss within the change in the fair value of contingent consideration on the consolidated statements of operations. The fair value of the development and regulatory milestones is estimated utilizing a probability adjusted, discounted cash flow approach. The discount rates are estimated utilizing Corporate B rated bonds maturing in the years of expected payments based on the Company’s estimated development timelines for the acquired product candidate. The fair value of the net sales milestones is determined utilizing a valuation framework that estimates net sales volatility to simulate a range of possible payment scenarios. The average of the payments in these scenarios is then discounted to calculate present fair value.

In May 2023, as part of the Company’s strategic portfolio prioritization, the Company decided to discontinue its preclinical and early research programs in its gene therapy platform, which included Friedreich ataxia and Angelman syndrome. As a result, the Company fully impaired the Friedreich ataxia and Angelman syndrome intangible assets and determined that the fair value for all of the contingent consideration payable related to Friedreich ataxia and Angelman syndrome was $0. The change in fair value for the contingent consideration payable related to Friedreich ataxia and Angelman syndrome for the nine months ended September 30, 2023 was $129.8 million and is included in the change in fair value of the contingent consideration in the statement of operations. The remaining contingent consideration as of September 30, 2023 is $39.0 million, which is solely related to the development and regulatory milestones, and net sales milestones, for Upstaza.

As of September 30, 2023, the weighted average discount rate for the Upstaza development and regulatory milestones was 7.1% and the weighted average probability of success was 90%. As of September 30, 2023, the weighted average discount rate for the Upstaza net sales milestones was 12.0% and the weighted average probability of success for the net sales milestones was 93%.

The table presented below is a summary of changes in the fair value of the Company’s Level 3 valuations for the contingent consideration payable for the periods ended September 30, 2023 and September 30, 2022:


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2022	$	82,500	$	81,500
Additions		—		—
Change in fair value		(56,100)		(68,900)
Payments		—		—
Ending balance as of September 30, 2023	$	26,400	$	12,600


	Level 3 liabilities
	Contingent consideration payable-		Contingent consideration payable-
	development and regulatory		net sales milestones and royalties
	milestones
Beginning balance as of December 31, 2021	$	139,300	$	100,600
Additions		—		—
Change in fair value		(10,800)		(21,400)
Reclass to accounts payable and accrued expenses		(50,000)		—
Payments		—		—
Ending balance as of September 30, 2022	$	78,500	$	79,200

The following significant unobservable inputs were used in the valuation of the contingent consideration payable for the periods ended September 30, 2023 and December 31, 2022:


	September 30, 2023
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$26,400	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $31 million 85% - 92% 6.9% - 7.6% 2023 - 2026
Contingent considerable payable- net sales milestones and royalties	$12,600	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $50 million 85% - 100% 0% 12% 2025 - 2034


	December 31, 2022
	Fair Value	Valuation Technique	Unobservable Input	Range
Contingent consideration payable- development and regulatory milestones	$82,500	Probability-adjusted discounted cash flow	Potential development and regulatory milestones Probabilities of success Discount rates Projected years of payments	$0 - $331 million 25% - 92% 6.2% - 8.3% 2023 - 2029
Contingent considerable payable- net sales milestones and royalties	$81,500	Option-pricing model with Monte Carlo simulation	Potential net sales milestones Probabilities of success Potential percentage of net sales for royalties Discount rate Projected years of payments	$0 - $150 million 25% - 100% 2% - 6% 11.5% 2025 - 2041

The contingent consideration payables are classified Level 3 liabilities as their valuation requires substantial judgment and estimation of factors that are not currently observable in the market. If different assumptions were used for the various inputs to the valuation approaches, including but not limited to, assumptions involving probability adjusted sales estimates

for the gene therapy platform and estimated discount rates, the estimated fair value could be significantly higher or lower than the fair value determined.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Fair value of financial instruments and investments - Marketable Securities (Details) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jan. 31, 2020 USD ($) $ / shares	Sep. 30, 2023 USD ($)	Sep. 30, 2022 USD ($)	Sep. 30, 2023 USD ($) fund	Sep. 30, 2022 USD ($) fund	Dec. 31, 2022 USD ($)
Equity Investments
Purchase of marketable securities - equity investments				$ 26,378	$ 22,787
Net unrealized gain (loss) on equity investments				5,484	(11,319)
Redemption of marketable securities- equity investments				12,078	104,431
ClearPoint Convertible note
Purchase of convertible note					40,429
Unrealized gain (loss) on convertible note				(4,594)	(2,392)
ClearPoint Equity Investment
Equity Investments
Net unrealized gain (loss) on equity investments		$ (2,000)	$ (3,500)	(3,100)	(1,100)
Loss on sale of equity investments		0		800
ClearPoint Equity Investment \| Quoted prices in active markets for identical assets (Level 1)
Equity Investments
Fair value of equity investment		4,500		4,500		$ 11,000
ClearPoint convertible debt
ClearPoint Convertible note
Purchase of convertible note	$ 10,000
Conversion price - convertible note \| $ / shares	$ 6.00
Term of convertible note	5 years
Unrealized gain (loss) on convertible note		(3,100)	(4,400)	(4,600)	$ (2,400)
ClearPoint convertible debt \| Recurring basis \| Significant other observable inputs (Level 2) \| Deposits and Other Assets, Noncurrent
ClearPoint Convertible note
ClearPoint convertible debt security		10,600		$ 10,600		$ 15,200
Mutual Funds
Equity Investments
Number of mutual funds denominated in a foreign currency \| fund				1
Number of mutual funds liquidated \| fund					1
Net unrealized gain (loss) on equity investments		1,100	100	$ 5,500	$ (11,300)
Redemption of marketable securities- equity investments		7,800	100,800	$ 12,100	104,400
Unrealized foreign currency gains (losses) on equity investments		$ (1,400)	$ (1,400)		$ (1,000)

Stock award plan - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands		1 Months Ended			3 Months Ended		9 Months Ended
	Jun. 08, 2022	Dec. 31, 2022	Dec. 31, 2020	Jun. 30, 2016	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Apr. 30, 2022	Jun. 30, 2021	May 31, 2021	Jan. 31, 2020
Stock option plan
Share-based compensation expense					$ 26,942	$ 28,670	$ 85,128	$ 82,989
Unrecognized compensation cost					179,300		$ 179,300
Weighted average remaining service period for recognition of unrecognized compensation cost							1 year 10 months 24 days
Stock option
Stock option plan
Granted (in shares)							1,059,054
Expected dividend yield (as a percent)							0.00%
Weighted average grant date fair value (in dollars per share)							$ 21.83
Restricted stock units
Stock option plan
Granted (in shares)							1,973,973
Employee Stock Purchase Plan
Stock option plan
Number of shares authorized (in shares)										2,000,000	1,000,000
Award requisite service period				6 months
Purchase price of common stock, percent				85.00%
Employee stock purchase plan, voting percentage limit				5.00%
Share-based compensation expense					$ 700		$ 2,000
1998 Employee, Director, and Consultant Stock Option Plan, 2009 Equity and Long-term Incentive Plan, and 2013 Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance					0		0
Amended 2013 LTIP
Stock option plan
Number of shares available for issuance					6,802,210		6,802,210
Number of additional shares authorized (in shares)	8,475,000
Amended 2013 LTIP \| Maximum
Stock option plan
Number of shares authorized (in shares)	16,724,212
2020 Inducement Stock Incentive Plan \| Common stock
Stock option plan
Number of shares available for issuance					1,705,941		1,705,941
Number of additional shares authorized (in shares)		1,700,000	1,000,000
2020 Inducement Stock Incentive Plan \| Common stock \| Maximum
Stock option plan
Number of shares authorized (in shares)									1,300,000			1,000,000
2020 Inducement Stock Incentive Plan \| Stock option
Stock option plan
Stockholder's specified ownership percentage					10.00%		10.00%
Inducement grants for non-statutory stock options (in shares)							121,460
Vesting period							4 years
2020 Inducement Stock Incentive Plan \| Stock option \| Minimum
Stock option plan
Stock options granted, exercise price as percentage of the fair market value of common stock at grant date					100.00%		100.00%
2020 Inducement Stock Incentive Plan \| Stock option \| Maximum
Stock option plan
Stock options granted to stockholder with specified ownership percentage, exercise price as percentage of the fair market value of common stock at grant date					110.00%		110.00%
Expiration period							10 years
2020 Inducement Stock Incentive Plan \| Restricted stock units
Stock option plan
Granted (in shares)							83,210

Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2023	Dec. 31, 2022
Statement of Financial Position [Abstract]
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, authorized shares (in shares)	250,000,000	250,000,000
Common stock, issued shares (in shares)	75,459,022	73,104,692
Common stock, outstanding shares (in shares)	75,459,022	73,104,692

Fair value of financial instruments and investments - Available-for-sale securities (Details) - USD ($) $ in Thousands	Sep. 30, 2023	Dec. 31, 2022
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position greater than 12 months - Unrealized losses	$ (24)	$ (499)
Securities in an unrealized loss position greater than 12 months - Fair Value	1,625	10,186
Total - Unrealized losses	(24)	(499)
Total - Fair Value	1,625	10,186
Corporate debt securities
Debt Securities, Available-for-sale [Line Items]
Securities in an unrealized loss position greater than 12 months - Unrealized losses	(24)	(499)
Securities in an unrealized loss position greater than 12 months - Fair Value	1,625	10,186
Total - Unrealized losses	(24)	(499)
Total - Fair Value	$ 1,625	$ 10,186

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

Stock award plan - Assumptions Used (Details)	9 Months Ended
Stock award plan - Assumptions Used (Details)	Sep. 30, 2023
Valuation assumptions
Expected term (in years)	5 years 6 months
Stock option \| Minimum
Valuation assumptions
Risk-free interest rate (as a percent)	3.54%
Expected volatility (as a percent)	53.00%
Stock option \| Maximum
Valuation assumptions
Risk-free interest rate (as a percent)	3.91%
Expected volatility (as a percent)	54.00%

Summary of significant accounting policies (Policies)

9 Months Ended

Sep. 30, 2023

Accounting Policies [Abstract]

Basis of presentation

Use of estimates

Restricted Cash

Restricted cash


	End of			Beginning of
	period-		period-
	September 30,		December 31,
	2023		2022
Cash and cash equivalents	$	165,157	$	279,834
Restricted cash included in deposits and other assets		16,253		16,091
Total Cash, cash equivalents and restricted cash per statement of cash flows	$	181,410	$	295,925

Marketable securities

Inventory and cost of product sales

Inventory

The following table summarizes the components of the Company’s inventory for the periods indicated:


	September 30, 2023		December 31, 2022
Raw materials	$	907	$	1,078
Work in progress		24,595		14,074
Finished goods		10,250		6,656

Total inventory

35,752

21,808

Cost of product sales

Revenue recognition

Net product revenue

countries, the United States and Russia, accounted for at least 10% of the Company’s net product sales, representing $54.8 million and $28.3 million of net product sales, respectively.

Collaboration and royalty revenue

Manufacturing Revenue

Allowance for doubtful accounts

Liability for sale of future royalties

Indefinite-lived intangible assets

Goodwill

Income Taxes

Leases

Debt - Convertible Notes Interest Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Jul. 31, 2020
Long-term debt
Amortization of debt issuance costs			$ 1,574	$ 1,316
Effective interest rate of the liability component	9.30%		9.30%		11.00%
Convertible debt \| 3.00% Convertible senior notes due 2022
Long-term debt
Contractual interest expense		$ 559		2,800
Amortization of debt issuance costs		92		460
Total		$ 651		$ 3,260
Effective interest rate of the liability component		3.50%		3.50%
Convertible debt \| 1.50% Convertible senior notes due 2026
Long-term debt
Contractual interest expense	$ 1,080	$ 1,081	$ 3,215	$ 3,217
Amortization of debt issuance costs	294	289	872	856
Total	$ 1,374	$ 1,370	$ 4,087	$ 4,073
Effective interest rate of the liability component	1.90%	1.90%	1.90%	1.90%

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

+ Details

Revenue recognition - Manufacturing Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2023	Sep. 30, 2022	Sep. 30, 2023	Sep. 30, 2022	Dec. 31, 2022
Revenue recognition
Revenue	$ 196,576	$ 217,127	$ 630,766	$ 531,389
Manufacturing revenue
Revenue recognition
Revenue	2,365	$ 0	6,716	$ 0
Contract with customer, asset	1,400		1,400		$ 0
Contract liability revenues recognized in period	0		1,400
Manufacturing revenue \| Deferred revenue
Revenue recognition
Contract with customer, liability	1,200		1,200		$ 1,400
Manufacturing revenue \| Prepaids and other current assets
Revenue recognition
Contract with customer, asset	$ 1,400		$ 1,400

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References + Details

- Definition

+ References

+ Details

Commitments and contingencies

9 Months Ended

Sep. 30, 2023

Commitments and Contingencies Disclosure [Abstract]

Commitments and contingencies

10. Commitments and contingencies

Under various agreements, the Company will be required to pay royalties and milestone payments upon the successful development and commercialization of products. The Company has entered into funding agreements with The Wellcome Trust Limited ("Wellcome Trust") for the research and development of small molecule compounds in connection with the Company’s oncology and antibacterial programs. As the Company has discontinued development under its antibacterial program, it no longer expects that milestone and royalty payments from the Company to Wellcome Trust will apply under that agreement, resulting in a change to the total amount of development and regulatory milestone payments the Company may become obligated to pay for this program. Under the oncology program funding agreement, to the extent that the Company develops and commercializes program intellectual property on a for-profit basis itself or in collaboration with a partner (provided the Company retains overall control of worldwide commercialization), the Company may become obligated to pay to Wellcome Trust development and regulatory milestone payments and single-digit royalties on sales of any research program product. The Company’s obligation to pay such royalties would continue on a country-by-country basis until the longer of the expiration of the last patent in the program intellectual property in such country covering the research program product and the expiration of market exclusivity of such product in such country. The Company made the first development milestone payment of $0.8 million to Wellcome Trust under the oncology platform funding agreement during the second quarter of 2016. During the year ended December 31, 2022, the Company incurred $2.5 million of development milestones in connection with the enrollment of patients in the registration-directed Phase 2/3 trial of unesbulin for the treatment of LMS, which is recorded in accounts payable and accrued expenses on the balance sheet and will be payable upon the earlier to occur of the first dose administered to the last patient enrolled in the study or the

termination of dosing of all patients in the study. Additional milestone payments of up to an aggregate of $14.5 million may become payable by the Company to Wellcome Trust under this agreement.

The Company has also entered into a collaboration agreement with the SMA Foundation. The Company is obligated to pay the SMA Foundation single-digit royalties on worldwide net product sales of any collaboration product that is successfully developed and subsequently commercialized or, with respect to collaboration products the Company outlicenses, including Evrysdi, a specified percentage of certain payments the Company receives from its licensee. Since inception, the SMA Foundation has earned $40.3 million, $35.3 million which was paid and $5.0 million which was accrued as of September 30, 2023. The Company’s obligation to make such payments would end upon the Company’s payment to the SMA Foundation of an aggregate of $52.5 million.

Pursuant to the asset purchase agreement ("Asset Purchase Agreement") between the Company and Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC) (“Marathon”), Marathon is entitled to receive contingent payments from the Company based on annual net sales of Emflaza up to a specified aggregate maximum amount over the expected commercial life of the asset. In addition, Marathon received a $50.0 million sales-based milestone during the nine months ended September 30, 2022.

Pursuant to the Agilis Merger Agreement, Agilis equityholders were previously entitled to receive contingent consideration payments from the Company based on (i) the achievement of certain development milestones up to an aggregate maximum amount of $60.0 million, (ii) the achievement of certain regulatory approval milestones together with a milestone payment following the receipt of a priority review voucher up to an aggregate maximum amount of $535.0 million, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $150.0 million, and (iv) a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2%-6%. The Company was required to pay $40.0 million of the development milestone payments upon the passing of the second anniversary of the closing of the Agilis Merger, regardless of whether the applicable milestones have been achieved.

Pursuant to the terms of the Rights Exchange Agreement, the Participating Rightholders canceled and forfeited their rights under the Agilis Merger Agreement to receive (i) $174.0 million, in the aggregate, of potential milestone payments based on the achievement of certain regulatory milestones and (ii) $37.6 million, in the aggregate, of $40.0 million in development milestone payments that would have been due upon the passing of the second anniversary of the closing of the Agilis Merger, regardless of whether the milestones are achieved.

The Rights Exchange Agreement has no effect on the Agilis Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightholders’ rights to receive $211.6 million, in the aggregate, of the milestone payments described above. As a result, all other rights and obligations under the Agilis Merger Agreement remain in effect pursuant to their terms, including the Company’s obligation to pay up to an aggregate maximum amount of $20.0 million upon the achievement of certain development milestones (representing the remaining portion of potential development milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement while excluding the remaining $2.4 million milestone payment that was due and paid upon the passing of the second anniversary of the closing of the Agilis Merger), up to an aggregate maximum amount of $361.0 million upon the achievement of certain regulatory milestones (representing the remaining portion of potential regulatory milestone payments for which rights were not canceled and forfeited pursuant to the Rights Exchange Agreement), up to a maximum aggregate amount of $150.0 million upon the achievement of certain net sales milestones and a percentage of annual net sales for Friedreich ataxia and Angelman syndrome during specified terms, ranging from 2% to 6%, pursuant to the terms of the Agilis Merger Agreement.

In July 2022, the European Commission approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the EEA. As a result of such approval, the Company paid the former equityholders of Agilis $50.0 million in accordance with the terms of the Agilis Merger Agreement in the year ended December 31, 2022. In May 2023, as part of the Company’s strategic portfolio prioritization, the Company decided to discontinue its preclinical and early research programs in its gene therapy platform, which included Friedreich ataxia and Angelman syndrome. As a result, the Company does not expect the milestones related to Friedreich ataxia and Angelman syndrome to be achieved. In addition, the Company does not expect to pay the 2% to 6% royalties on annual net sales related to Friedreich ataxia and Angelman syndrome. As of September 30, 2023, the remaining potential development and regulatory milestones the Company

expects to achieve is $31.1 million, and the remaining potential sales milestones the Company expects to achieve is $50.0 million, both of which relate solely to Upstaza.

On October 25, 2019, the Company completed the acquisition of substantially all of the assets of BioElectron Technology Corporation (“BioElectron”), a Delaware corporation, including certain compounds that the Company has begun to develop as part of its Bio-e platform, pursuant to an asset purchase agreement by and between the Company and BioElectron, dated October 1, 2019 (the “BioElectron Asset Purchase Agreement”). BioElectron was a private company with a pipeline focused on inflammatory and central nervous system (CNS) disorders. The lead program, vatiquinone, is in late stage development for CNS disorders with substantial unmet need and significant commercial opportunity that are complementary to PTC’s existing pipeline.

Subject to the terms and conditions of the BioElectron Asset Purchase Agreement, BioElectron may become entitled to receive contingent milestone payments of up to $200.0 million (in cash or in shares of the Company’s common stock, as determined by the Company) from the Company based on the achievement of certain regulatory and net sales milestones. Subject to the terms and conditions of the BioElectron Asset Purchase Agreement, BioElectron may also become entitled to receive contingent payments based on a percentage of net sales of certain products.

Subject to the terms and conditions of the Agreement and Plan of Merger, dated as of May 5, 2020 (the “Censa Merger Agreement”) by and among the Company, Hydro Merger Sub, Inc., the Company’s wholly owned, indirect subsidiary, and, solely in its capacity as the representative, agent and attorney-in-fact of the securityholders of Censa, Shareholder Representative Services LLC (such merger pursuant thereto, the “Censa Merger”), former Censa securityholders may become entitled to receive contingent payments from the Company based on (i) the achievement of certain development and regulatory milestones up to an aggregate maximum amount of $217.5 million for sepiapterin’s two most advanced programs and receipt of a priority review voucher from the FDA as set forth in the Censa Merger Agreement, (ii) $109.0 million in development and regulatory milestones for each additional indication of sepiapterin, (iii) the achievement of certain net sales milestones up to an aggregate maximum amount of $160.0 million, (iv) a percentage of annual net sales during specified terms, ranging from single to low double digits of the applicable net sales threshold amount, and (v) any sublicense fees paid to the Company in consideration of any sublicense of Censa’s intellectual property to commercialize sepiapterin, on a country-by-country basis, which contingent payment shall equal to a mid-double digit percentage of any such sublicense fees.

In February 2023, the Company completed enrollment of its Phase 3 placebo-controlled clinical trial for sepiapterin for PKU. In connection with this event and pursuant to the Censa Merger Agreement, the Company paid a $30.0 million development milestone to the former Censa securityholders during the nine months ended September 30, 2023. The Company elected to pay this milestone in the form of shares of its common stock, less certain cash payments in accordance with the Censa Merger Agreement. Pursuant to such election, the Company issued 657,462 shares of its common stock and paid $0.4 million to the former Censa securityholders.

The Company also has the Tegsedi-Waylivra Agreement for the commercialization of Tegsedi and Waylivra, and products containing those compounds in countries in Latin America and the Caribbean. Akcea is entitled to receive royalty payments subject to certain terms set forth in the Tegsedi-Waylivra Agreement.

The Company has employment agreements with certain employees which require the funding of a specific level of payments, if certain events, such as a change in control or termination without cause, occur. Additionally, the Company has royalty payments associated with Translarna, Emflaza, and Upstaza net product revenue, payable quarterly or annually in accordance with the terms of the related agreements.

From time to time in the ordinary course of its business, the Company is subject to claims, legal proceedings and disputes. The Company is not currently aware of any material legal proceedings against it.