0001558370-24-013960 | 10-Q | XBRL Viewer

Material Terms of Trading Arrangement


Name and Title	Action Taken	Type of Trading Arrangement	Nature of Trading Arrangement	Duration of Trading Arrangement	Aggregate Number of Securities
Lonnel Coates (Director)	Adoption August 21, 2024	Trading plan intended to satisfy the affirmative defense conditions of Securities Exchange Act Rule 10b5-1(c)	Sale of the Company’s common stock pursuant to the terms of the trading plan	August 21, 2024 – August 18, 2025	19,824
Kathryn D. Haviland (Chief Executive Officer, Director)	Adoption August 30, 2024	Trading plan intended to satisfy the affirmative defense conditions of Securities Exchange Act Rule 10b5-1(c)	Sale of the Company’s common stock pursuant to the terms of the trading plan	August 30, 2024 – December 31, 2025	13,515
Ariel Hurley (Senior Vice President, Finance & Principal Accounting Officer)	Adoption September 12, 2024	Trading plan intended to satisfy the affirmative defense conditions of Securities Exchange Act Rule 10b5-1(c)	Sale of the Company’s common stock pursuant to the terms of the trading plan	September 12, 2024 – September 15, 2025	15,215
Christopher Murray (Chief Technical Operations & Quality Officer)	Adoption August 20, 2024	Trading plan intended to satisfy the affirmative defense conditions of Securities Exchange Act Rule 10b5-1(c)	Sale of the Company’s common stock pursuant to the terms of the trading plan	August 20, 2024 – August 15, 2025	16,500

Lonnel Coates

Lonnel Coates

Director

true

August 21, 2024

August 18, 2025

19,824

Kathryn D. Haviland

Chief Executive Officer, Director

true

August 30, 2024

December 31, 2025

13,515

Ariel Hurley

Senior Vice President, Finance & Principal Accounting Officer

true

September 12, 2024

September 15, 2025

15,215

Christopher Murray

Chief Technical Operations & Quality Officer

true

Adoption Date

August 20, 2024

Expiration Date

August 15, 2025

Aggregate Available

16,500

Product Revenue - Concentration Risk (Details)	3 Months Ended		9 Months Ended		12 Months Ended
Product Revenue - Concentration Risk (Details)	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2023
Revenue from Contract with Customer Benchmark \| Customer Concentration Risk \| Customer One
Concentration Risk
Concentration risk (as a percent)	38.00%	42.00%	39.00%	42.00%
Revenue from Contract with Customer Benchmark \| Customer Concentration Risk \| Customer Two
Concentration Risk
Concentration risk (as a percent)	14.00%		12.00%
Revenue from Contract with Customer Benchmark \| Customer Concentration Risk \| Customer Three
Concentration Risk
Concentration risk (as a percent)	11.00%	11.00%		11.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer One
Concentration Risk
Concentration risk (as a percent)			27.00%		34.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Two
Concentration Risk
Concentration risk (as a percent)			15.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Three
Concentration Risk
Concentration risk (as a percent)			12.00%		11.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Four
Concentration Risk
Concentration risk (as a percent)					10.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Five
Concentration Risk
Concentration risk (as a percent)					10.00%

Restricted Cash - Tabular Disclosure (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023	Sep. 30, 2023	Dec. 31, 2022
Reconciliation of cash, cash equivalents, and restricted cash
Cash and cash equivalents	$ 89,356	$ 71,286	$ 55,972
Restricted cash	11,503	10,238	9,696
Total cash, cash equivalents, and restricted cash shown in condensed consolidated statements of cash flows	$ 100,859	$ 81,524	$ 65,668	$ 124,904

Stock-based Compensation - Unrecognized Compensation Costs (Details) $ in Millions	Sep. 30, 2024 USD ($)
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock option awards	$ 81.0
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 7 months 6 days
Restricted Stock Units
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock awards	$ 131.0
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 7 months 6 days
Performance-based restricted stock units
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock awards	$ 11.3
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 1 month 6 days

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Cash flows from operating activities
Net loss	$ (17,133)	$ (396,068)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	12,290	10,134
Non-cash lease expense	7,381	6,759
Stock-based compensation	80,529	70,087
Non-cash interest expense	783	11,886
Net (accretion of discount) amortization of premium on investments	(17,172)	(11,527)
Non-cash debt extinguishment gain	(173,676)
Other	(1,677)	2,342
Changes in assets and liabilities:
Accounts receivable	(22,516)	(18,970)
Inventory	(6,055)	(5,195)
Prepaid expenses and other current assets	(7,350)	10,570
Other assets	(9,572)	(1,724)
Accrued expenses and accounts payable	3,447	(10,856)
Other long-term liabilities	(6,199)	(7,235)
Deferred revenue	2,561	(10,280)
Operating lease liabilities	(8,863)	(7,842)
Net cash used in operating activities	(163,222)	(357,919)
Cash flows from investing activities
Purchases of property and equipment	(3,698)	(11,389)
Purchases of investments	(756,662)	(648,705)
Maturities of investments	679,150	855,365
Net cash provided by (used in) investing activities	(81,210)	195,271
Cash flows from financing activities
Proceeds from at-the-market offerings, net of issuance costs	48,936
Net proceeds from stock option exercises and employee stock purchase plan	67,984	5,729
Net proceeds from term loan facility	146,973	97,968
Principal payments for financing arrangements	(541)
Net cash provided by financing activities	263,352	103,697
Net increase (decrease) in cash, cash equivalents, and restricted cash	18,920	(58,951)
Cash, cash equivalents and restricted cash at beginning of period	81,524	124,904
Effect of exchange rate changes on cash, cash equivalents and restricted cash	415	(285)
Cash, cash equivalents and restricted cash at end of period	100,859	65,668
Supplemental cash flow information
Cash paid for interest	56,055	25,455
Property and equipment purchases unpaid at period end	106	1,921
Cash paid for taxes, net	$ 789	$ 762

Leases

9 Months Ended

Sep. 30, 2024

Leases

15. Leases

The Company’s building leases are comprised of office and laboratory spaces under non-cancelable operating leases. The lease agreements contain various clauses for renewal at the Company’s option and only certain exercised renewal options were included in the calculation of the operating lease assets and the operating lease liabilities, as other renewal options were not reasonably certain of being exercised as of September 30, 2024. The lease agreements do not contain residual value guarantees.

Lease costs for the three and nine months ended September 30, 2024 and 2023 were as follows (in thousands):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
Operating leases:	2024		2023		2024		2023
Lease cost	$	5,831	$	5,758	$	17,268	$	17,301

The Company has not entered into any material short-term leases or financing leases as of September 30, 2024.

Supplemental cash flow information related to leases for the nine months ended September 30, 2024 and 2023 is as follows (in thousands):


	Nine Months Ended
	September 30,
	2024		2023
Cash paid for amounts included in the measurement of lease liabilities:	$	13,664	$	13,249
Lease liabilities arising from obtaining right-of-use assets:
Operating leases	$	116	$	109

The weighted average remaining lease term and weighted average discount rate of the operating leases are as follows:


					Operating leases
Weighted average remaining lease term in years					5.1
Weighted average discount rate					7.3%

Product Revenue - Product Revenue Allowance and Reserve (Details) - Valuation Allowances and Reserves, Product Revenue - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Product revenue allowance and reserve
Beginning Balance	$ 19,274	$ 9,788
Provision related to sales in the current period	58,911	25,874
Adjustment related to prior periods sales	(171)	(545)
Credits and payments made	(43,326)	(17,469)
Ending Balance	$ 34,688	$ 17,648

Stock-based Compensation (Tables)

9 Months Ended

Sep. 30, 2024

Summary of stock option activity


		Weighted-Average
	Shares	Exercise Price
Outstanding at December 31, 2023	6,658,444	$	66.48
Granted	1,055,795		95.87
Exercised	(1,034,224)		62.39
Canceled	(181,789)		73.13
Outstanding at September 30, 2024	6,498,226	$	71.83
Exercisable at September 30, 2024	4,413,290	$	71.14

Summary of restricted stock units activity


		Weighted-Average
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2023	2,107,026	$	60.33
Granted	988,769		95.99
Vested	(687,395)		63.48
Forfeited	(134,699)		69.87
Unvested shares at September 30, 2024	2,273,701	$	74.33

Summary of performance-based restricted stock units activity


		Weighted-Average
		Grant Date
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2023	52,500	$	59.32
Granted	90,000		135.84
Vested	—		—
Forfeited	—		—
Unvested shares at September 30, 2024	142,500	$	107.65

Summary of stock-based compensation expense, allocation by type of awards and recognition in statements of operations


	Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2024		2023		2024		2023
Stock options	$	11,301	$	9,998	$	31,537	$	31,195
Restricted stock units		15,548		12,536		45,282		37,389
Performance-based restricted stock units		1,288		261		3,157		605
Employee stock purchase plan		427		417		1,319		1,308
Subtotal		28,564		23,212		81,295		70,497
Capitalized stock-based compensation costs		(282)		(141)		(766)		(410)
Stock-based compensation expense included in total cost and operating expenses	$	28,282	$	23,071	$	80,529	$	70,087


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2024		2023		2024		2023
Research and development	$	12,552	$	11,169	$	35,712	$	31,512
Selling, general and administrative		15,730		11,902		44,817		38,575
Total	$	28,282	$	23,071	$	80,529	$	70,087

Collaboration and Other Agreements - Collaboration Loss Sharing (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2023
Collaboration and Other Agreements
Collaboration loss sharing		$ 1,771	$ 4,301
Collaborative Arrangement \| Roche, Collaboration (Pralsetnib) Agreement
Collaboration and Other Agreements
Collaboration loss sharing	$ 0	$ (1,800)	$ (4,300)

Collaboration and Other Agreements - Transaction Price (Details) - Collaborative Arrangement - USD ($) $ in Millions				7 Months Ended	9 Months Ended
	Jul. 13, 2020	Oct. 15, 2019	Jun. 01, 2018	Sep. 30, 2024	Sep. 30, 2024
Rigel Pharmaceuticals, Inc.
Collaboration and Other Agreements
Collaborative arrangement, transaction price				$ 27.7
Collaborative arrangement, transaction price, upfront payment				10.0
Collaborative arrangement, transaction price, milestone and royalty payments				11.2
Collaborative arrangement, transaction price, inventory				$ 6.5
Roche, Collaboration (Pralsetnib) Agreement
Collaboration and Other Agreements
Collaborative arrangement, transaction price	$ 695.7
Collaborative arrangement, transaction price, upfront payment	675.0
Collaborative arrangement, transaction price, stock issued, premium on sale of stock to counterparty	$ 20.7
Roche, Collaboration and License (Immunotherapy) Agreement
Collaboration and Other Agreements
Collaborative arrangement, transaction price					$ 64.7
Clementia
Collaboration and Other Agreements
Collaborative arrangement, transaction price		$ 46.5
C Stone
Collaboration and Other Agreements
Collaborative arrangement, transaction price			$ 40.0

Stock-based Compensation

9 Months Ended

Sep. 30, 2024

Stock-based Compensation

12. Stock-based Compensation

Stock Plans

In 2015, the Company’s board of directors and stockholders approved the 2015 Stock Option and Incentive Plan (the 2015 Plan), which replaced the Company’s 2011 Stock Option and Grant Plan, as amended (the 2011 Plan). The 2015 Plan includes incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock, restricted stock units, performance-based restricted stock units, unrestricted stock, performance-based awards and cash-based awards. The Company initially reserved a total of 1,460,084 shares of common stock for the issuance of awards under the 2015 Plan. The 2015 Plan provided that the number of shares reserved and available for issuance under the 2015 Plan would be cumulatively increased on January 1 of each calendar year by 4% of the number of shares of common stock issued and outstanding on the immediately preceding December 31 or such lesser amount as specified by the compensation committee of the board of directors. For the calendar year beginning January 1, 2024, the number of shares reserved for issuance under the 2015 Plan was increased by 2,445,889 shares.

In March 2020, the Company’s board of directors adopted the 2020 Inducement Plan (the Inducement Plan), pursuant to which the Company may grant, subject to the terms of the Inducement Plan and Nasdaq rules, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, and other stock-based awards. The Company initially reserved a total of 1,000,000 shares of common stock for the issuance of awards under the Inducement Plan and in June 2022, the Company’s board of directors approved the reservation of an additional 1,500,000 shares of common stock for the issuance of awards under the Inducement Plan.

On June 12, 2024, the Company’s stockholders approved the 2024 Stock Incentive Plan (the 2024 Plan), which replaced the Company’s 2015 Plan and the Inducement Plan. As of September 30, 2024, there were 8,060,501 and 767,490 shares underlying awards outstanding under the 2015 Plan and the Inducement Plan, respectively. No further shares will be granted under the 2015 Plan and the Inducement Plan after the effective date of the 2024 Plan. The 2024 Plan provides for the granting of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock, restricted stock units, performance-based restricted stock units, unrestricted stock and cash-based awards. The 2024 Plan provides for the issuance of up to 9,200,000 shares. Any shares of common stock underlying any awards that are forfeited, canceled, held back upon exercise or settlement of an award to satisfy the exercise price or tax withholding, repurchased, expire or are otherwise terminated by the Company under the 2024 Plan and the 2015 Plan will be added back to the shares of common stock available for issuance under the 2024 Plan. As of September 30, 2024, there were 9,242,424 shares available for future grant under the 2024 Plan.

Employee Stock Purchase Plan

In 2015, the Company’s board of directors and stockholders approved the 2015 Employee Stock Purchase Plan (the 2015 ESPP), which became effective upon the closing of the Company’s initial public offering in May 2015. The Company initially reserved a total of 243,347 shares of common stock for issuance under the 2015 ESPP. The 2015 ESPP provides that the number of shares reserved and available for issuance under the 2015 ESPP will be cumulatively increased on January 1 of each calendar year by 1% of the number of shares of common stock issued and outstanding on the immediately preceding December 31 or such lesser amount as specified by the compensation committee of the board of directors. For the calendar year beginning January 1, 2024, the number of shares reserved for issuance under the 2015 ESPP was increased by 611,472 shares.

Stock options

The following table summarizes the stock option activity for the nine months ended September 30, 2024:


		Weighted-Average
	Shares	Exercise Price
Outstanding at December 31, 2023	6,658,444	$	66.48
Granted	1,055,795		95.87
Exercised	(1,034,224)		62.39
Canceled	(181,789)		73.13
Outstanding at September 30, 2024	6,498,226	$	71.83
Exercisable at September 30, 2024	4,413,290	$	71.14

As of September 30, 2024, the total unrecognized compensation expense related to unvested stock option awards was $81.0 million, which is expected to be recognized over a weighted-average period of approximately 2.6 years.

Restricted stock units

The following table summarizes the restricted stock units activity for the nine months ended September 30, 2024:


		Weighted-Average
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2023	2,107,026	$	60.33
Granted	988,769		95.99
Vested	(687,395)		63.48
Forfeited	(134,699)		69.87
Unvested shares at September 30, 2024	2,273,701	$	74.33

As of September 30, 2024, the total unrecognized compensation expense related to unvested restricted stock units was $131.0 million, which is expected to be recognized over a weighted-average period of approximately 2.6 years.

Performance-based restricted stock units

In 2023, the Company began granting performance-based restricted stock units (PSUs) that will settle in stock. PSUs awarded to employees have a three-year performance period and vest on the third anniversary of the grant date. The vesting of these awards is subject to the respective employee’s continued employment. The number of PSUs granted represents the target number of units that are eligible to be earned based on the achievement of cumulative three-year performance measures established at the beginning of the performance period, which ends on December 31 of the third year of the performance period.

Participants may ultimately earn between zero and 200.0% of the target number of PSUs granted based on the degree of achievement of the performance metric which is measured on a three-year cumulative relative total shareholder return metric. Accordingly, additional PSUs may be issued or currently issued PSUs may be cancelled upon final determination of the number of units earned.

The following table summarizes the PSU activity for the nine months ended September 30, 2024:


		Weighted-Average
		Grant Date
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2023	52,500	$	59.32
Granted	90,000		135.84
Vested	—		—
Forfeited	—		—
Unvested shares at September 30, 2024	142,500	$	107.65

As of September 30, 2024, the total unrecognized compensation expense related to unvested PSUs was $11.3 million, which is expected to be recognized over a weighted-average period of approximately 2.1 years.

The Company values PSUs on the grant date using a lattice model with a Monte Carlo simulation. This valuation methodology utilizes several key assumptions, including defined consecutive trading day average closing stock price on the grant date, valuation date stock price, expected volatilities using historical volatilities, correlation coefficients based on the volatility data, risk-free rates of return and expected dividend yield. The probability of actual shares expected to be earned is considered in the grant date valuation and the expense is not adjusted to reflect the actual units earned.

Stock-based compensation expense

The Company recognized stock-based compensation expense of $28.3 million and $80.5 million for the three and nine months ended September 30, 2024, respectively, and $23.1 million and $70.1 million for the three and nine months ended September 30, 2023, respectively. Stock-based compensation expense by award type included within the unaudited condensed consolidated statements of operations and comprehensive loss was as follows (in thousands):


	Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2024		2023		2024		2023
Stock options	$	11,301	$	9,998	$	31,537	$	31,195
Restricted stock units		15,548		12,536		45,282		37,389
Performance-based restricted stock units		1,288		261		3,157		605
Employee stock purchase plan		427		417		1,319		1,308
Subtotal		28,564		23,212		81,295		70,497
Capitalized stock-based compensation costs		(282)		(141)		(766)		(410)
Stock-based compensation expense included in total cost and operating expenses	$	28,282	$	23,071	$	80,529	$	70,087

Stock-based compensation expense, that is included in operating expenses, by classification within the unaudited condensed consolidated statements of operations and comprehensive loss is as follows (in thousands):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2024		2023		2024		2023
Research and development	$	12,552	$	11,169	$	35,712	$	31,512
Selling, general and administrative		15,730		11,902		44,817		38,575
Total	$	28,282	$	23,071	$	80,529	$	70,087

Financing Arrangements - Royalty and Sales Information (Details) - Sixth Street Partners $ in Millions	Jul. 31, 2022 USD ($)
Financing Arrangements
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, percentage rate (as a percent)	9.75%
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, amount, maximum	$ 900.0
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, cumulative cap of upfront invested capital, ratio	1.45
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, cumulative cap of upfront invested capital, amount	$ 362.5
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, cumulative cap of upfront invested capital, revenue targets not achieved, percentage increase (as a percent)	15.00%
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, cumulative cap of upfront invested capital, revenue targets not achieved, ratio	1.85
Purchase and sale agreement, royalties, future royalty payments, annual worldwide net product sales, cumulative cap of upfront invested capital, revenue targets not achieved, amount	$ 462.5

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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-URI https://asc.fasb.org/1943274/2147481139/470-20-50-1E

Reference 19: http://www.xbrl.org/2003/role/disclosureRef
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-URI https://asc.fasb.org/1943274/2147481139/470-20-50-1E

Reference 20: http://www.xbrl.org/2003/role/disclosureRef
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Reference 21: http://www.xbrl.org/2003/role/disclosureRef
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Reference 22: http://www.xbrl.org/2003/role/disclosureRef
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Reference 23: 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/2009/role/commonPracticeRef
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-URI https://asc.fasb.org/1943274/2147482925/835-30-45-2

Reference 27: http://www.xbrl.org/2009/role/commonPracticeRef
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-Publisher FASB
-URI https://asc.fasb.org/1943274/2147482900/835-30-50-1

Collaboration and Other Agreements - Equity Investment (Details) - USD ($) $ in Thousands		1 Months Ended	3 Months Ended
	Aug. 01, 2022	Jul. 31, 2023	Sep. 30, 2024	Dec. 31, 2023
Equity Investment
Equity investment			$ 28,699	$ 27,789
Collaborative Arrangement \| IDRx, Inc. \| Director
Equity Investment
Equity investment, license agreement, shares received (in shares)	4,509,105	192,282
Equity investment	$ 27,800		28,700
Equity investment, transaction costs	$ 300
Equity investment, change in fair value			$ 900

Restricted Cash

9 Months Ended

Sep. 30, 2024

Restricted Cash

8. Restricted Cash

The following table provides a reconciliation of cash, cash equivalents, and restricted cash reported within the Company's condensed consolidated balance sheets for the nine months ended September 30, 2024 and 2023 (in thousands):


	September 30,		September 30,
	2024		2023
Cash and cash equivalents	$	89,356	$	55,972
Restricted cash		11,503		9,696
Total cash, cash equivalents, and restricted cash shown in condensed consolidated statements of cash flows	$	100,859	$	65,668

As of September 30, 2024 and December 31, 2023, $11.5 million and $10.2 million, respectively, of the Company’s cash is restricted by a financial institution primarily related to funds held to satisfy the requirements of certain government agreements and the security deposits for the lease agreements for the Company’s office and laboratory spaces.

Product Revenue - Product Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Revenues
Revenue	$ 128,184	$ 56,566	$ 362,458	$ 177,423
Product revenue, net
Revenues
Revenue	128,184	54,228	334,825	133,173
Product revenue, net \| United States
Revenues
Revenue	113,133	49,121	297,731	118,355
Product revenue, net \| Rest of World
Revenues
Revenue	$ 15,051	$ 5,107	$ 37,094	$ 14,818

Amount, including 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.

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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Reference 13: http://www.xbrl.org/2003/role/disclosureRef
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Inventory (Tables)

9 Months Ended

Sep. 30, 2024

Schedule of capitalized inventory


	September 30,		December 31,
	2024		2023
Raw materials	$	3,069	$	3,147
Work in process		32,179		29,132
Finished goods		7,210		4,823
Total	$	42,458	$	37,102

Balance sheet classification


	September 30,		December 31,
	2024		2023
Inventory	$	12,528	$	21,223
Other assets		29,930		15,879
Total	$	42,458	$	37,102

Marketable Securities (Tables)

9 Months Ended

Sep. 30, 2024

Schedule of marketable securities


	Amortized		Unrealized		Unrealized		Fair
September 30, 2024	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	133,228	$	292	$	(32)	$	133,488
U.S. treasury obligations		657,530		2,006		(27)		659,509
Total	$	790,758	$	2,298	$	(59)	$	792,997


	Amortized		Unrealized		Unrealized		Fair
December 31, 2023	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	170,194	$	27	$	(418)	$	169,803
U.S. treasury obligations		525,880		588		(386)		526,082
Total	$	696,074	$	615	$	(804)	$	695,885

Summary of the fair value and the number of the available-for-sale securities by their maturities


	September 30, 2024				December 31, 2023
	Amortized		Fair		Amortized		Fair
	Cost		value		Cost		value
Within one year	$	643,209	$	644,817	$	639,881	$	639,355
After one through five years		147,549		148,180		56,193		56,530
Total	$	790,758	$	792,997	$	696,074	$	695,885

Summary of fair value and number of available-for-sale securities in loss positions


	September 30, 2024				December 31, 2023
	Fair		Unrealized		Fair		Unrealized
	value		losses		value		losses
Debt securities in unrealized loss position for 12 months or less	$	75,525	$	(46)	$	267,917	$	(550)
Debt securities in unrealized loss position for more than 12 months		29,942		(13)		64,659		(254)
Total debt securities	$	105,467	$	(59)	$	332,576	$	(804)

Summary of proceeds from maturities of debt securities


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Proceeds from maturities of debt securities	$	231,000	$	237,600	$	679,150	$	855,365

Tabular disclosure of investment in debt security measured at fair value with change in fair value recognized in other comprehensive income (available-for-sale).

Reference 1: http://www.xbrl.org/2009/role/commonPracticeRef
-Topic 320
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Reference 2: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 3: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 4: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 5: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 6: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 7: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 8: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 9: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 10: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 11: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 12: http://www.xbrl.org/2009/role/commonPracticeRef
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Financing Arrangements

9 Months Ended

Sep. 30, 2024

Financing Arrangements

3. Financing Arrangements

Royalty Pharma Purchase and Sale Agreement

On June 30, 2022, the Company entered into a purchase and sale agreement (Royalty Purchase Agreement) with Royalty Pharma Investments 2019 ICAV (Royalty Pharma). Pursuant to the Royalty Purchase Agreement, the Company received an upfront payment of $175.0 million in consideration for the Company’s rights to receive royalty payments on the net sales of GAVRETO worldwide, excluding the CStone Territory (as defined below) and the U.S., under the terms of the Roche pralsetinib collaboration agreement.

Despite selling all rights to receive royalties on GAVRETO net sales of the underlying territories to Royalty Pharma, the Company maintained its involvement in the global co-development of pralsetinib with Roche and was therefore involved in the generation of these future royalties. Due to the Company’s significant continued involvement, any royalties and development and commercialization milestones earned pertaining to the underlying territory under the Roche pralsetinib collaboration agreement were recognized as collaboration revenue on the consolidated statements of operations and comprehensive income (loss) throughout the contract term of the Roche pralsetinib collaboration agreement. The net proceeds received from the transaction were recorded as a liability related to sale of future royalties and revenues on the consolidated balance sheet on June 30, 2022.

In February 2023, the Company received written notice from Roche of their election to terminate for convenience the Roche pralsetinib collaboration agreement. The termination became effective February 2024 and the Company regained commercialization and development rights to GAVRETO from Roche worldwide excluding the CStone Territory. In January 2024, the Company decided to discontinue global development and marketing of GAVRETO in territories excluding the U.S. and the CStone Territory following the termination of the Roche pralsetinib collaboration. In connection with and effective upon the termination of the Roche pralsetinib collaboration agreement, on February 22, 2024 (the Royalty Pharma Termination Date), Royalty Pharma and the Company agreed to terminate the Royalty Purchase Agreement (Royalty Pharma Termination Agreement). Following the termination of the Royalty Purchase Agreement, the Company has no outstanding obligations under the Royalty Purchase Agreement, other than the remaining royalty payment obligation related to GAVRETO net sales through the termination effective date. As of September 30, 2024, the Company had no plan to enter into a new arrangement to commercialize GAVRETO outside of the U.S. and the CStone territory.

The Company has no material outstanding obligations under the Royalty Pharma Termination Agreement and it was accounted for as a debt extinguishment under ASC 470-50 as the terms and conditions of the Royalty Purchase Agreement had undergone a substantial modification and the modified terms are considered substantially different. As a result, during the nine months ended September 30, 2024, the Company recorded a debt extinguishment gain of $173.7 million as other income in the unaudited condensed consolidated statements of operations and comprehensive loss. As of September 30, 2024, the net carrying value of the Company’s liability related to these agreements was $0.7 million, which was determined based on the fair value of the remaining cash flow associated with anticipated future payments outlined in the Royalty Pharma Termination Agreement.

Financing Arrangements with Sixth Street Partners

In July 2022, the Company closed two transactions pursuant to a purchase and sale agreement (Future Revenue Purchase Agreement) and a debt financing transaction for up to $660.0 million (as amended, Financing Agreement) with Sixth Street Partners. Because two transactions were entered into with the same parties and in contemplation of one another, the Company recorded these transactions based on the relative fair values of each freestanding financial instrument and allocated the proceeds in proportion to those fair value amounts.

Sixth Street Partners Purchase and Sale Agreement

Pursuant to the Future Revenue Purchase Agreement, the Company received gross proceeds of $250.0 million in exchange for future royalty payments at a rate of 9.75% on up to $900 million each year of (i) aggregate worldwide annual net product sales of AYVAKIT/AYVAKYT (avapritinib) and (ii), if it is approved, aggregate worldwide annual net product sales of BLU-263 (elenestinib), but excluding sales in Greater China, subject to a cumulative cap of 1.45 times the upfront invested capital or a total of $362.5 million. In the event that certain revenue targets are not achieved

by specified dates, the royalty rate and cumulative cap shall be increased to 15% and 1.85 times the invested capital (or $462.5 million), respectively.

The Company continues to own the research, development, manufacturing and commercialization of AYVAKIT/AYVAKYT and if it is approved, elenestinib, and has significant continuing involvement in the generation of the cash flows under the Future Revenue Purchase Agreement. Therefore, the Company continues to account for any revenue earned from worldwide product sales of AYVAKIT/AYVAKYT and, if it is approved, elenestinib, on its unaudited condensed consolidated statements of operations and comprehensive loss. Net proceeds received from the transaction were recorded as a liability related to sale of future royalties and revenues on the consolidated balance sheet. The Company accretes the $250.0 million, net of transaction costs of $5.4 million, to the total of these future payments as interest expense using the effective interest method over the estimated life of the arrangement.

As payments are made to Sixth Street Partners, the balance of the liability is effectively repaid over the life of the Future Revenue Purchase Agreement. In order to determine the amortization of the liability, the Company estimates the total amount of future revenue payments to be paid to Sixth Street Partners over the life of the arrangement. The exact amount of repayment is likely to change each reporting period. A significant increase or decrease in worldwide product sales of AYVAKIT/AYVAKYT and, if it is approved, elenestinib, will materially impact the liability related to this arrangement, interest expense and the time period for repayment. The Company periodically assesses the expected payments to Sixth Street Partners and prospectively adjusts the amortization of the liability related to this arrangement for material changes in such payments. As of September 30, 2024, the Company’s estimate of this total interest expense resulted in an effective annual interest rate of 10.5%. These estimates contain assumptions that impact the amount recorded and the interest expense that will be recognized in future periods.

As of September 30, 2024, the net carrying value of the liability related to this arrangement was $260.5 million. The following table shows the activity within the liability account (in thousands):


	Nine Months Ended September 30,
	2024		2023
Beginning Balance at January 1	$	266,670	$	254,328
Interest expense recognized		20,721		21,043
Payments		(26,921)		(10,484)
Carrying value as of September 30	$	260,470	$	264,887

Sixth Street Partners Term Loan

The Financing Agreement entered into by the parties in connection with the transaction provides for (i) a senior secured term loan facility of up to $150.0 million and (ii) a senior secured delayed draw term loan facility of up to $250.0 million to be funded in two tranches at the Company’s choice subject to certain terms and conditions. The term loans will mature on June 30, 2028 and bear interest at a variable rate equal to either the Secured Overnight Financing Rate (SOFR) plus 6.50% or the base rate plus 5.50%, subject to a floor of 1% and 2% with respect to the SOFR and base rate, respectively.

The following table shows the proceeds the Company has received under the Financing Agreement with Sixth Street Partners (in thousands):


				Debt discount/
Term loan draw	Date	Gross proceeds		Transaction cost		Net proceeds
Senior Secured Term Loan Facility	July 2022	$	150,000	$	12,214	$	137,786
1st Senior Secured Delayed Draw Term Loan Facility	August 2023		100,000		2,067		97,933
2nd Senior Secured Delayed Draw Term Loan Facility	May 2024		150,000		3,027		146,973
		$	400,000	$	17,308	$	382,692

Debt discounts and transaction costs have been recorded as a reduction to the carrying amount of the debt on the Company’s consolidated balance sheet and are amortized as additional interest expenses using the effective interest

rate method over the period from issuance through maturity. In addition, the Company may at any time request an incremental term loan in an amount not to exceed $260.0 million on terms to be agreed and subject to the consent of Sixth Street Partners providing such incremental term loan. As of September 30, 2024, the Company’s estimate of the total interest expense resulted in an effective annual interest rate of 12.3%. The carrying amount of the debt as of September 30, 2024 is subject to variable interest rates, which are based on current market rates, and as such, approximates fair value.

The following table shows the activity within the liability account (in thousands):


	Nine Months Ended September 30,
	2024		2023
Beginning Balance at January 1	$	238,813	$	139,083
Net proceeds received from the delayed draw term loan		146,973		97,968
Interest expense recognized		29,917		15,557
Payments		(29,134)		(14,230)
Carrying value as of September 30	$	386,569	$	238,378

The Company’s obligations under the Financing Agreement are secured, subject to certain exceptions, by security interests in substantially all assets of the Company and certain of its subsidiaries. The Financing Agreement contains customary negative covenants that, among other things and subject to certain exceptions, could restrict the Company’s ability to incur additional liens, incur additional indebtedness, make investments, including acquisitions, engage in fundamental changes, sell or dispose of assets that constitute collateral, including certain intellectual property, pay dividends or make any distribution or payment on or redeem, retire or purchase any equity interests, amend, modify or waive certain material agreements or organizational documents and make payments of certain subordinated indebtedness. The Financing Agreement also requires the Company to maintain a consolidated liquidity of at least $80.0 million. As of September 30, 2024, the Company was in compliance with the applicable terms and conditions of the covenants under the Financing Agreement.

Stock-based Compensation - Stock-based Compensation Expense - By Type (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Total stock based compensation expense
Subtotal	$ 28,564	$ 23,212	$ 81,295	$ 70,497
Capitalized stock-based compensation costs	(282)	(141)	(766)	(410)
Stock-based compensation expense included in total cost and operating expenses	28,282	23,071	80,529	70,087
Employee Stock Option
Total stock based compensation expense
Subtotal	11,301	9,998	31,537	31,195
Restricted Stock Units
Total stock based compensation expense
Subtotal	15,548	12,536	45,282	37,389
Performance-based restricted stock units
Total stock based compensation expense
Subtotal	1,288	261	3,157	605
Employee Stock
Total stock based compensation expense
Subtotal	$ 427	$ 417	$ 1,319	$ 1,308

Financing Arrangements - Net Proceeds Received (Details) - Secured Debt - USD ($) $ in Thousands	1 Months Ended			9 Months Ended		27 Months Ended
	May 31, 2024	Aug. 31, 2023	Jul. 31, 2022	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024
Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities
Proceeds from (Repayments of) Debt
Gross proceeds						$ 400,000
Debt discount/transaction cost						17,308
Net proceeds				$ 146,973	$ 97,968	$ 382,692
Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facility
Proceeds from (Repayments of) Debt
Gross proceeds			$ 150,000
Debt discount/transaction cost			12,214
Net proceeds			$ 137,786
Sixth Street Partners, Financing Agreement, 1st Senior Secured Delayed Draw Term Loan Facility
Proceeds from (Repayments of) Debt
Gross proceeds		$ 100,000
Debt discount/transaction cost		2,067
Net proceeds		$ 97,933
Sixth Street Partners, Financing Agreement, 2nd Senior Secured Delayed Draw Term Loan Facility
Proceeds from (Repayments of) Debt
Gross proceeds	$ 150,000
Debt discount/transaction cost	3,027
Net proceeds	$ 146,973

Restricted Cash - Additional Information (Details) - USD ($) $ in Millions	Sep. 30, 2024	Dec. 31, 2023
Restricted cash
Restricted cash	$ 11.5	$ 10.2

Net Loss Per Share (Tables)

9 Months Ended

Sep. 30, 2024

Schedule of common stock equivalents excluded from calculation of diluted net loss per share applicable to common stockholders


	September 30,
	2024	2023
Stock options	6,498	6,984
Restricted stock units	2,274	2,093
Performance-based restricted stock units	143	53
ESPP shares	27	47
Total	8,942	9,177

Financing Arrangements - Long-term Debt (Details) - Sale of Future Royalties and Revenues - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023	Sep. 30, 2023	Dec. 31, 2022	Feb. 22, 2022
Royalty Pharma, Royalty Purchase Agreement
Long-term Debt
Long-term debt	$ 0				$ 0
Sixth Street Partners, Future Revenue Purchase Agreement
Long-term Debt
Long-term debt	$ 260,470	$ 266,670	$ 264,887	$ 254,328

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

Fair Value of Financial Instruments (Tables)

9 Months Ended

Sep. 30, 2024

Schedule of financial instruments measured at fair value

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of September 30, 2024 (in thousands):


			Active		Observable		Unobservable
	September 30,		Markets		Inputs		Inputs
Description	2024		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	57,153	$	57,153	$	—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		133,488		—		133,488		—
U.S. treasury obligations		659,509		659,509		—		—
Total	$	850,150	$	716,662	$	133,488	$	—

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2023 (in thousands):


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2023		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	55,412	$	55,412	$	—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		169,803		—		169,803		—
U.S. treasury obligations		526,082		526,082		—		—
Total	$	751,297	$	581,494	$	169,803	$	—

Product Revenue

9 Months Ended

Sep. 30, 2024

Product Revenue

6. Product Revenue

The Company generates product revenue from the sales of AYVAKIT/AYVAKYT in the U.S. and Europe. The following table summarizes net revenue recognized from product sales for the three and nine months ended September 30, 2024 and 2023 (in thousands):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2024		2023		2024		2023
United States	$	113,133	$	49,121	$	297,731	$	118,355
Rest of World		15,051		5,107		37,094		14,818
Total product revenue	$	128,184	$	54,228	$	334,825	$	133,173

The Company primarily sells AYVAKIT/AYVAKYT through specialty distributors and specialty pharmacies. The following table summarizes the customers that represent 10% or greater of gross product revenue for the three and nine months ended September 30, 2024 and 2023 (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Customer 1	38	%	42	%	39	%	42	%
Customer 2	14	%	*	%	12	%	*	%
Customer 3	11	%	11	%	*	%	11	%

* Indicates the customer’s share is under 10%.

The following table summarizes the customers with amounts due that represent 10% or greater of the accounts receivable associated with the Company’s product sales as of September 30, 2024 and December 31, 2023 (in thousands):


	September 30,		December 31,
	2024		2023
Customer 1	27	%	34	%
Customer 2	15	%	*	%
Customer 3	12	%	11	%
Customer 4	*	%	10	%
Customer 5	*	%	10	%

* Indicates the customer’s share is under 10%.

The following table summarizes activity in each of the product revenue allowance and reserve categories for the nine months ended September 30, 2024 and 2023 (in thousands):


	Nine Months Ended September 30,
	2024		2023
Beginning balance at January 1	$	19,274	$	9,788
Provision related to sales in the current period		58,911		25,874
Adjustment related to prior periods sales		(171)		(545)
Credits and payments made		(43,326)		(17,469)
Ending balance at September 30	$	34,688	$	17,648

The total reserves that are included in the Company’s unaudited condensed consolidated balance sheets as of September 30, 2024 and December 31, 2023, are summarized as follows (in thousands):


	September 30,		December 31,
	2024		2023
Reduction of accounts receivable, net	$	3,512	$	1,809
Component of accrued expenses		31,176		17,465
Total revenue-related reserves	$	34,688	$	19,274

Restricted Cash (Tables)

9 Months Ended

Sep. 30, 2024

Reconciliation of cash, cash equivalents, and restricted cash


	September 30,		September 30,
	2024		2023
Cash and cash equivalents	$	89,356	$	55,972
Restricted cash		11,503		9,696
Total cash, cash equivalents, and restricted cash shown in condensed consolidated statements of cash flows	$	100,859	$	65,668

Marketable Securities - Unrealized Loss Positions - Tabular Disclosure (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Unrealized loss position, aggregate fair value
Unrealized loss position for less than 12 months, aggregate fair value	$ 75,525	$ 267,917
Unrealized loss position for more than 12 months, aggregate fair value	29,942	64,659
Unrealized loss position, aggregate fair value	105,467	332,576
Unrealized loss position
Unrealized loss position for less than 12 months	(46)	(550)
Unrealized loss position for more than 12 months	(13)	(254)
Total debt securities in unrealized loss position	$ (59)	$ (804)

Inventory - Write-down (Details) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
Inventory - Write-down (Details) - USD ($) $ in Millions	Sep. 30, 2023	Sep. 30, 2023
Inventory
Inventory write-down	$ 0.1	$ 2.2

Commitments and Contingencies

9 Months Ended

Sep. 30, 2024

Commitments and Contingencies

16. Commitments and Contingencies

Purchase Commitments Associated with Clinical and Commercial Supply Agreements

In connection with the commercialization of AYVAKIT/AYVAKYT, the Company has negotiated manufacturing agreements with certain vendors that require the Company to meet minimum purchase obligations on an annual basis. The Company also has unconditional purchase obligations related to certain clinical manufacturing agreements. The aggregate amount of future unconditional purchase obligations under these manufacturing agreements over the period of next five years is approximately $4.0 million as of September 30, 2024.

Legal Proceedings

In the normal course of business, the Company from time to time is named as a party to various legal claims, actions and complaints, which have included and may include matters involving securities, employment, intellectual property, arising from the use of therapeutics utilizing its technology, or others. The Company records a loss contingency reserve for a legal proceeding when it considers the potential loss probable and it can reasonably estimate the amount of the loss or determine a probable range of loss. The Company provides disclosure when it considers a loss reasonably possible or when it determines that a loss in excess of a reserve is reasonably possible. The Company

provides an estimate of such reasonably possible losses or an aggregate range of such reasonably possible losses, unless the Company believes that such an estimate cannot be made. The Company expenses the costs related to its legal proceedings as they are incurred. As of September 30, 2024, the Company has not recorded any material accruals for loss contingencies.

On June 7, 2024, a purported stockholder filed a putative class action lawsuit against the Company in the Court of Chancery of the State of Delaware, with the caption Johnson v. Blueprint Medicines Corporation, Case No. 2024-0625. Plaintiff claims in the complaint that a “Proxy Access” provision in the Company’s Amended and Restated Bylaws, effective November 30, 2022, is invalid under Delaware law because it allegedly usurps the right of stockholders to select the members of the board of directors, and plaintiff seeks declaratory relief invalidating that provision, as well as attorneys’ fees and costs. On October 7, 2024, the lawsuit was consolidated with twelve other lawsuits against companies with similar bylaw provisions under the caption In re Irrevocable Resignation Bylaw Litigation, Consolidated C.A. No. 2024-0538-JTL. On October 11, 2024, the Company, together with the other companies in the consolidated action, filed an opening brief in support of a motion to dismiss the complaint. The Company does not believe the outcome of this matter will have a material effect on its financial position, results of operations, or liquidity.

Indemnification Agreements

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of its board of directors and senior management that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers of the Company. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. The Company is not aware of any claims under indemnification arrangements, and it has not accrued any liabilities related to such obligations in its condensed consolidated financial statements as of September 30, 2024 or December 31, 2023.

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2024	Dec. 31, 2023
Preferred Stock Disclosures
Preferred stock, par value (in dollars per share)	$ 0.001	$ 0.001
Preferred stock, shares authorized (in shares)	5,000,000	5,000,000
Preferred stock, shares issued (in shares)	0	0
Preferred stock, shares outstanding (in shares)	0	0
Common Stock Disclosures
Common stock, par value (in dollars per share)	$ 0.001	$ 0.001
Common stock, shares authorized (in shares)	120,000,000	120,000,000
Common stock, shares issued (in shares)	63,454,673	61,147,236
Common Stock, shares outstanding (in shares)	63,454,673	61,147,236

Marketable Securities - Realized Gains (Losses) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Realized gains (losses) from maturities of debt securities
Realized gains (losses) from maturities of debt securities	$ 0	$ 0	$ 0	$ 0

Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Revenues:
Revenue	$ 128,184	$ 56,566	$ 362,458	$ 177,423
Cost and operating expenses:
Cost of sales	1,932	2,782	12,716	8,280
Research and development	85,300	110,252	257,761	330,184
Selling, general and administrative	89,926	70,741	262,822	215,826
Collaboration loss sharing		1,771		4,301
Total cost and operating expenses	177,158	185,546	533,299	558,591
Other income (expense):
Interest expense, net	(7,616)	(3,808)	(20,376)	(13,624)
Other income (expense), net	587	(728)	962	(369)
Debt extinguishment gain			173,676
Total other income (expense), net	(7,029)	(4,536)	154,262	(13,993)
Loss before income taxes	(56,003)	(133,516)	(16,579)	(395,161)
Income tax expense	273	197	554	907
Net loss	(56,276)	(133,713)	(17,133)	(396,068)
Other comprehensive loss:
Unrealized gains on available-for-sale investments	2,939	1,443	2,428	7,624
Currency translation adjustments	(119)	95	(4)	136
Comprehensive loss	$ (53,456)	$ (132,175)	$ (14,709)	$ (388,308)
Net loss per share - basic (in dollars per share)	$ (0.89)	$ (2.20)	$ (0.27)	$ (6.55)
Net loss per share - diluted (in dollars per share)	$ (0.89)	$ (2.20)	$ (0.27)	$ (6.55)
Weighted-average number of common shares used in net loss per share - basic (in shares)	63,381	60,688	62,608	60,445
Weighted-average number of common shares used in net loss per share - diluted (in shares)	63,381	60,688	62,608	60,445
Product revenue, net
Revenues:
Revenue	$ 128,184	$ 54,228	$ 334,825	$ 133,173
Collaboration, License and Other
Revenues:
Revenue		$ 2,338	$ 27,633	$ 44,250

Marketable Securities - Unrealized Loss Positions - General Information (Details) - security	Sep. 30, 2024	Dec. 31, 2023
Unrealized loss position, number of positions
Number of held securities in an unrealized loss position	22	62

Accrued Expenses (Tables)

9 Months Ended

Sep. 30, 2024

Schedule of accrued expenses


	September 30,		December 31,
	2024		2023
Research, development and commercial contract costs	$	35,886	$	49,354
Employee compensation		40,267		43,434
Accrued professional fees		16,946		12,522
Revenue-related reserves		31,176		17,465
Other		6,606		5,217
Total	$	130,881	$	127,992

Collaboration and Other Agreements - General Information (Details) $ in Thousands			1 Months Ended		2 Months Ended	3 Months Ended			9 Months Ended		57 Months Ended
	Oct. 15, 2019 USD ($)	Jun. 01, 2018 USD ($) item	Feb. 28, 2022 USD ($)	Oct. 31, 2019 USD ($)	Dec. 31, 2021 USD ($)	Sep. 30, 2024 USD ($) item	Sep. 30, 2023 USD ($)	Sep. 30, 2020 USD ($)	Sep. 30, 2024 USD ($) item	Sep. 30, 2023 USD ($)	Sep. 30, 2024 USD ($) item	Feb. 22, 2024 USD ($)	Dec. 31, 2023 USD ($)	Nov. 08, 2021 USD ($)	Jul. 13, 2020
Collaboration and Other Agreements
Prepaid expenses and other current assets						$ 42,333			$ 42,333		$ 42,333		$ 33,702
Research and development expense						85,300	$ 110,252		257,761	$ 330,184
Collaborative Arrangement \| IDRx, Inc. \| Director
Collaboration and Other Agreements
Collaborative arrangement, milestones, potential contingent payments						217,500			$ 217,500		217,500
Collaborative arrangement, termination, counterparty written notice period									12 months
Collaborative Arrangement \| VantAI
Collaboration and Other Agreements
Collaborative arrangement, upfront payment			$ 20,000
Collaborative arrangement, milestones, potential contingent payments						1,670,000			$ 1,670,000		$ 1,670,000
Research and development expense						$ 1,600	$ 600		$ 5,500	$ 6,200
Collaborative arrangement, jointly research and advance novel protein degrader therapies into development candidates, number \| item						3			3		3
Collaborative Arrangement \| Zai Lab (Shanghai) Co., Ltd.
Collaboration and Other Agreements
Collaborative arrangement, upfront payment, cash payment received					$ 25,000
Collaborative arrangement, milestones, contingent payments eligible to receive														$ 590,000
Collaborative arrangement, termination, counterparty written notice period, period from effective date									2 years
Collaborative arrangement, termination, counterparty written notice period, period from effective date, given after first commercial sale of licensed product in counterparty territory									12 months
Collaborative arrangement, termination, counterparty written notice period, period from effective date, given prior to first commercial sale of licensed product in counterparty territory									9 months
Collaborative Arrangement \| Roche, Collaboration (Pralsetnib) Agreement
Collaboration and Other Agreements
Collaborative arrangement, upfront payment, cash payment received								$ 675,000
Collaborative arrangement, milestones, specified regulatory and commercialization milestones, achieved									$ 105,000		$ 105,000
Collaborative arrangement, percentage of global development costs shared, entity (as a percent)															45.00%
Collaborative arrangement, percentage of global development costs shared, counterparty (as a percent)															55.00%
Collaborative arrangement, selling, general, and administrative expenses, wind-down costs and net transition costs reimbursable						$ 4,200			4,400
Collaborative Arrangement \| Clementia
Collaboration and Other Agreements
Collaborative arrangement, upfront payment, cash payment received	$ 25,000
Collaborative arrangement, milestones, cash payments received				$ 50,000
Collaborative arrangement, milestones, contingent payments eligible to receive	460,000
Collaborative arrangement, inventory purchased by counterparty	$ 1,500
Collaborative arrangement, termination, counterparty written notice period	12 months
Collaborative Arrangement \| C Stone
Collaboration and Other Agreements
Collaborative arrangement, upfront payment, cash payment received		$ 40,000
Collaborative arrangement, milestones, contingent payments eligible to receive		$ 307,500
Collaborative arrangement, milestones, achieved						$ 38,500			$ 38,500		$ 38,500
Collaborative arrangement, licensed product term from first commercial sale		12 years
Collaborative arrangement, license option rights, number \| item		3
Collaborative arrangement, collaboration programs with exclusive commercialization rights, number \| item		3
Arrangement Other than Collaborative, Asset Purchase Agreement \| Rigel Pharmaceuticals, Inc.
Collaboration and Other Agreements
Asset purchase agreement, purchase price, receivable												$ 15,000
Asset purchase agreement, purchase price, receivable, payable upon first commercial sale												10,000
Asset purchase agreement, purchase price, receivable, additional contingent amount payable												5,000
Asset purchase agreement, contingent specified regulatory and commercial milestone payments												$ 102,500
Asset purchase agreement, tiered percentage royalties on annual net sales, low end of range (as a percent)												10.00%
Asset purchase agreement, tiered percentage royalties on annual net sales, high end of range (as a percent)												30.00%

Nature of Business (Details) $ in Millions	Sep. 30, 2024 USD ($)
Cash, cash equivalents and marketable securities
Cash, cash equivalents and marketable securities	$ 882.4

Collaboration and Other Agreements - Change in Contract with Customer, Liability (Details) $ in Millions	9 Months Ended
	Sep. 30, 2023 USD ($)
Collaborative Arrangement \| Roche, Collaboration and License (Immunotherapy) Agreement
Change in Contract with Customer, Liability
Amounts included in the contact liability at the beginning of the period	$ 16.0

Stock-Based Compensation - Stock Plans (Details) - shares		1 Months Ended	9 Months Ended
	Jan. 01, 2024	Jun. 30, 2022	Sep. 30, 2024	Jun. 12, 2024	Mar. 31, 2020	Apr. 08, 2015
2015 Stock Option and Incentive Plan
Stock-based compensation
Initial shares of common stock authorized for issuance of stock awards (in shares)						1,460,084
Increase in number of shares available for grant (as a percent)			4.00%
Increase in number of shares available for grant (in shares)	2,445,889
Shares underlying awards outstanding (in shares)			8,060,501
2020 Inducement Plan
Stock-based compensation
Initial shares of common stock authorized for issuance of stock awards (in shares)					1,000,000
Increase in number of shares available for grant (in shares)		1,500,000
Shares underlying awards outstanding (in shares)			767,490
2024 Stock Incentive Plan
Stock-based compensation
Initial shares of common stock authorized for issuance of stock awards (in shares)				9,200,000
Number of shares available for grant (in shares)			9,242,424

Marketable Securities - Proceeds from Maturities (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Proceeds from the maturities of debt securities
Proceeds from the maturities of debt securities	$ 231,000	$ 237,600	$ 679,150	$ 855,365

Document and Entity Information - $ / shares	9 Months Ended
Document and Entity Information - $ / shares	Sep. 30, 2024	Oct. 28, 2024
Cover [Abstract]
Entity Central Index Key	0001597264
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2024
Document Transition Report	false
Entity File Number	001-37359
Entity Registrant Name	BLUEPRINT MEDICINES CORPORATION
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	26-3632015
Entity Address, Address Line One	45 Sidney Street
Entity Address, City or Town	Cambridge
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02139
City Area Code	617
Local Phone Number	374-7580
Title of 12(b) Security	Common stock, par value $0.001 per share
Trading Symbol	BPMC
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 Listing, Par Value Per Share	$ 0.001
Entity Common Stock, Shares Outstanding		63,525,838
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2024
Document Fiscal Period Focus	Q3
Amendment Flag	false

Income Taxes

9 Months Ended

Sep. 30, 2024

Income Taxes

14. Income Taxes

The Company utilizes the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on the difference between the financial statement carrying amounts and tax basis of assets and liabilities using enacted tax rates in effect for years in which the temporary differences are expected to reverse. The Company provides a valuation allowance when it is more likely than not that deferred tax assets will not be realized.

The realization of deferred income tax assets is dependent on the generation of sufficient taxable income during future periods in which temporary differences are expected to reverse. Where the realization of such assets does not meet the more likely than not criterion, the Company applies a valuation allowance against the deferred income tax asset under consideration. The valuation allowance is reviewed periodically and if the assessment of the more likely than not criterion changes, the valuation allowance is adjusted accordingly. As of September 30, 2024, the Company has a full valuation allowance applied against its U.S. and foreign deferred tax assets.

On June 30, 2022, the Company entered into a Royalty Purchase Agreement with Royalty Pharma and a Future Revenue Purchase Agreement with Sixth Street Partners. Pursuant to the agreements, the Company received gross proceeds of $175.0 million from Royalty Pharma in June 2022 and $250.0 million from Sixth Street Partners in July 2022 upon the transactions closing. The total cash consideration of $425.0 million, in its entirety, was considered taxable income for calendar year ended December 31, 2022. In connection with and effective upon the termination of the Roche collaboration agreement, on February 22, 2024, Royalty Pharma and the Company entered into the Royalty Pharma Termination Agreement to terminate the Royalty Purchase Agreement. The Company accounted for the Royalty Pharma Termination Agreement as a debt extinguishment. As a result, during the nine months ended September 30, 2024 the Company recorded $173.7 million as a debt extinguishment gain in its condensed consolidated financial statements. For additional information, see Note 3, Financing Arrangements, to our unaudited condensed consolidated financial statements. For tax purposes, the debt extinguishment gain was excluded from the December 31, 2024 estimated taxable income calculation since it was already included in taxable income during the year ended December 31, 2022.

As of September 30, 2024, the Company expects to be in a taxable loss position for the calendar year ended December 31, 2024, and has recorded an income tax expense of $0.3 million and $0.6 million for the three and nine months ended September 30, 2024, respectively. The Company recorded an income tax provision despite forecasting a taxable loss due to state income tax and taxable income from the jurisdictions in which the Company is subject to tax.

The Company recognizes interest and penalties related to unrecognized tax benefits in the provision for income taxes. As of September 30, 2024, the Company did not have any gross unrecognized tax benefit.

The entire disclosure for income tax.

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Collaboration and Other Agreements - Contract Assets and Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Contract Assets
Accounts receivable, net	$ 65,814	$ 42,827
Contract Liabilities
Contract liabilities, current	4,118	812
Contract liabilities, noncurrent	7,916	4,792
Accrued expenses, current	35,886	49,354
Collaborative Arrangement \| Rigel Pharmaceuticals, Inc.
Contract Assets
Contract assets, current	2,680
Contract assets, noncurrent	8,389
Contract assets	11,069
Contract Liabilities
Contract liabilities, noncurrent	3,562
Contract liabilities	3,562
Collaborative Arrangement \| VantAI
Prepaid Assets
Prepaid assets, current	6,067	6,581
Prepaid assets, noncurrent	3,087	6,581
Prepaid assets, total	9,154	13,162
Collaborative Arrangement \| Roche, Collaboration (Pralsetnib) Agreement
Other Assets
Other current assets		361
Contract Liabilities
Accrued expenses	4,314	7,388
Collaborative Arrangement \| Roche, Collaboration and License (Immunotherapy) Agreement
Contract Liabilities
Contract liabilities	0	0
Collaborative Arrangement \| Clementia
Contract Liabilities
Contract liabilities	0	0
Collaborative Arrangement \| C Stone
Contract Liabilities
Contract liabilities	3,165	604
Accrued expenses	$ 841	$ 1,863

Collaboration and Other Agreements

9 Months Ended

Sep. 30, 2024

Collaboration and Other Agreements

10. Collaboration and Other Agreements

Rigel

On February 22, 2024, the Company entered into an Asset Purchase Agreement with Rigel Pharmaceuticals, Inc. (“Rigel”) for Rigel to purchase certain assets from the Company comprising the U.S. rights to research, develop, manufacture and commercialize GAVRETO (pralsetinib). Such assets include, among other things, applicable intellectual property related to pralsetinib in the U.S, including patents, copyrights and trademarks, as well as clinical regulatory and commercial data and records. Simultaneously and in connection with entering into the Asset Purchase Agreement, the parties also entered into certain supporting agreements, including a customary transition agreement, (such agreements collectively, the Rigel Agreement), pursuant to which, the Company transitioned certain inventory and regulatory and distribution responsibilities for pralsetinib to Rigel.

Under the terms of the Rigel Agreement, the Company has the right to receive a purchase price of $15.0 million, with $10.0 million paid upon first commercial sale of GAVRETO by Rigel and an additional $5.0 million as a delayed purchase price payable on the later of (i) the first anniversary of the closing date of the transaction, or (ii) the completion of certain transition activities. The Company is also eligible to receive up to $102.5 million in contingent specified regulatory and commercial milestone payments, in addition to tiered percentage royalties ranging from 10 percent to 30 percent on annual net sales of GAVRETO in the U.S. The royalties will be payable until the later of (i) the expiration of the royalty term, as defined in the agreement, which begins on the date of the first commercial sale of GAVRETO in the U.S., (ii) the date of expiration of the last valid patent claim within the Company’s IP that covers GAVRETO in the U.S., and (iii) the expiration of the last regulatory exclusivity for GAVRETO in the U.S.

The Company determined that the Rigel Agreement is a transaction with a customer and therefore accounted for the transaction in accordance with ASC 606. As of the effective date, the Company determined that the agreement includes three performance obligations: the delivery of (1) the U.S. rights to GAVRETO; (2) additional pralsetinib clinical data; and (3) GAVRETO product to be purchased from Genentech.

The transaction price under ASC 606 was fully constrained at the inception of the Rigel Agreement due to the pending completion of key transition activities stipulated in the agreement, including the transfer of the new drug application (NDA). These key transition activities, including the transfer of the NDA, related patents, and GAVRETO product, were completed in the second quarter of 2024. The performance obligations related to the U.S. rights to GAVRETO and the delivery of GAVRETO product were satisfied at a point in time upon the completion of these key transition activities. The transaction price was determined to be $27.7 million, which consisted of $6.5 million consideration for the GAVRETO product, $10.0 million upfront purchase price payment, and $11.2 million in the

milestone and royalty payments that were considered probable of achievement and not subject to significant subsequent reversal of revenue. The transaction price was allocated to the three performance obligations on a relative stand-alone selling price basis.

During the nine months ended September 30, 2024, the Company recognized total revenue of $24.3 million which is primarily comprised of GAVRETO product consideration of $6.5 million and the transaction price allocated to the U.S. rights to GAVRETO performance obligation of $17.6 million. The additional clinical data performance obligation will be satisfied at a point in time once the transfer of such data to Rigel is completed, and the allocated transaction price of $3.6 million was recorded as deferred revenue on the condensed consolidated financial statements as of September 30, 2024. During the three months ended September 30, 2024, insignificant revenue was recognized under the Rigel agreements.

The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal.

The following table summarizes the assets and liabilities under the Rigel agreements as of September 30, 2024 (in thousands):


	September 30, 2024
	Current		Noncurrent		Total
Contract assets	$	2,680	$	8,389	$	11,069
Contract liabilities	$	—	$	3,562	$	3,562

IDRx

In August 2022, the Company entered into a license agreement with IDRx, Inc. (IDRx), pursuant to which the Company granted IDRx an exclusive, worldwide, royalty-bearing license to exploit the Company’s internally discovered KIT exon 13 inhibitor IDRX-73 (IDRx License Agreement). IDRx is a clinical-stage biopharmaceutical company and among IDRx’s founders are Alexis Borisy, George Demetri, M.D., and Nicholas Lydon, Ph.D., who were each a member of the Company’s board of directors at the time. Due to these relationships, the transaction with IDRx is a related party transaction.

In connection with the IDRx License Agreement, the Company also entered into a stock purchase agreement with IDRx (IDRx Stock Purchase Agreement), pursuant to which the Company received 4,509,105 shares of IDRx’s Series A preferred stock with the right to receive additional shares of IDRx’s Series A preferred stock through an anti-dilution provision subject to a defined financing cap. In July 2023, the Company received 192,282 additional shares under the anti-dilution provision. The shares are restricted from reselling unless IDRx subsequently proposes a resale registered under the Securities Act or if an exemption from registration is otherwise available.

The Company is also eligible to receive up to $217.5 million in contingent cash payments, including specified development, regulatory and sales-based milestone payments. In addition, IDRx is obligated to pay to the Company royalties on aggregate annual worldwide net sales of licensed products at tiered percentage rates up to low-teens, subject to adjustments in specified circumstances under the IDRx License Agreement.

Unless earlier terminated, the IDRx License Agreement will expire on a country-by-country, licensed product-by-licensed product basis upon the latest of: (a) the expiration of the last valid claim within the licensed patents covering such licensed product in a such country, (b) the expiration of the regulatory exclusivity period for such licensed product in such country, or (c) the 10th anniversary of the first commercial sale of such licensed product in such country. Following the end of the term for any such licensed product and in such region by expiration, the license granted to IDRx will become exclusive, perpetual, irrevocable, fully paid-up and royalty-free. IDRx may terminate the IDRx License Agreement for convenience at any time upon at least twelve months’ prior written notice to the Company. Either party may also terminate the IDRx License Agreement for material breach of the other party or for insolvency, and the

Company may terminate the IDRx License Agreement for IDRx’s breach of the anti-dilution provision in the IDRx Stock Purchase Agreement. Upon termination of the license agreement in its entirety, all rights and obligations under the license agreement will terminate and revert back to the Company, and the Company has a license under certain intellectual property of IDRx to continue to exploit the compound and terminated product, subject to a royalty that will be negotiated at the time of termination.

The Company considered the ASC 606 criteria for combining contracts and determined the IDRx License Agreement and the IDRx Stock Purchase Agreement should be combined into a single contract because they were negotiated and entered into in contemplation of one another. Therefore, the Company determined that the 4,509,105 shares of IDRx’s Series A preferred stock and the anti-dilution right to receive additional shares should be attributed to the transaction price of the IDRx License Agreement.

The Company evaluated the IDRx License Agreement under ASC 606. The Company identified the following material promises under the agreement: (1) the exclusive license and (2) the initial know-how transfer. The Company determined that the exclusive license and the initial know-how transfer were not distinct from each other, as the exclusive license has limited value without the corresponding know-how transfer. As such, for the purposes of ASC 606, the Company determined that these two material promises, the exclusive license and the initial know-how transfer, should be combined into one distinct performance obligation. The Company concluded that the license is a functional intellectual property license. The Company determined that IDRx benefited from the license along with the initial know-how transfer at the time of grant, and therefore the related performance obligation is satisfied at a point in time.

For the purposes of ASC 606, the transaction price of the IDRx License Agreement at the contract inception was determined to be $27.5 million and recorded as license revenue-related party on the consolidated statements of operations and comprehensive loss during 2022. The fair value was derived from IDRx’s most recent financing transaction with unrelated investors. All potential milestone payments that the Company is eligible to receive under the IDRx License Agreement have been excluded from the transaction price. The Company reevaluates the transaction price for inclusion of milestone payments and royalties at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal. Additionally, the Company is entitled to sales milestones and royalties from the sales of the licensed products, and revenue are recognized when the related sales occur.

The Company concluded the preferred stock investment should be accounted for as an equity investment as it is not mandatorily redeemable nor does the Company have the unilateral right to redeem the preferred stock, and the Company, along with its related parties, do not have a controlling financial interest in IDRx nor have the ability to influence the financial and operating policies through the ownership of preferred stock. IDRx’s preferred stock is not exchange-traded and does not have a readily determinable fair value. Therefore, the preferred stock investment was accounted for under the measurement alternative for equity investments that do not have a readily determinable fair value, at cost of $27.8 million including transaction costs of $0.3 million. If observable price changes in orderly transactions for the identical or similar investment are identified, the Company will adjust the carrying value of the investment to its fair value as of the transaction date. During the three months ended September 30, 2024, IDRx completed a Series B preferred stock financing and accordingly, the Company adjusted the carrying value of its investment in IDRx to $28.7 million. The $0.9 million investment gain was recorded as other income on the Company’s unaudited condensed consolidated statements of operations and comprehensive loss. No revenue was recorded under the IDRx License Agreement during the three and nine months ended September 30, 2024 and 2023.

VantAI

In February 2022, the Company entered into an exclusive collaboration agreement with Oncopia Therapeutics, Inc. d/b/a Proteovant Therapeutics, Inc. (Proteovant) (the 2022 Agreement) to jointly research and advance certain protein degrader therapies into development candidates, with VantAI, Inc. (VantAI) performing computational chemistry services on behalf of Proteovant under the agreement. In December 2023, the Company entered into an Amended and Restated Collaboration and License Agreement (the A&R Agreement) with VantAI and Proteovant, which amended and restated and replaced in its entirety the 2022 Agreement. Under the A&R Agreement, Proteovant ceased its role under the 2022 Agreement and VantAI provides expanded computational support directly to the Company, including

computational biology and expanded computational chemistry to advance three novel protein degrader programs, and the Company has the option, at its sole discretion, to expand the collaboration to include a fourth target program.

Under the A&R Agreement, VantAI is eligible to receive up to $1.67 billion in contingent payments including specified research, development, regulatory and commercialization milestones for all the target programs. The Company will be obligated to pay VantAI tiered percentage royalties on a licensed product-by-licensed product basis ranging from the mid-single digits on annual net sales of each licensed product in the applicable territory, subject to adjustment in specified circumstances.

Under the 2022 Agreement, the Company paid Proteovant an upfront payment of $20.0 million in connection with the execution of the 2022 Agreement. This upfront payment was recorded as a prepaid asset on the Company’s consolidated balance sheet and was amortized as research and development expense over the expected research period because the Company concluded that Proteovant was providing the Company with research services throughout such period. The Company determined to continue to amortize the remaining prepaid asset balance as research and development expense over the expected research period of the A&R Agreement as VantAI continued to provide such research and development services. During the three and nine months ended September 30, 2024, the Company recorded research and development expense of $1.6 million and $5.5 million, respectively, under the A&R Agreement. During the three and nine months ended September 30, 2023, research and development expense recorded under the 2022 Agreement was $0.6 million and $6.2 million, respectively. The following table summarizes the prepaid assets associated with the A&R Agreement as of September 30, 2024 and December 31, 2023 (in thousands):


	September 30, 2024						December 31, 2023
	Current		Noncurrent		Total		Current		Noncurrent		Total
Prepaid assets	$	6,067	$	3,087	$	9,154	$	6,581	$	6,581	$	13,162

The Company reevaluates the expected research period at the end of each reporting period and prospectively adjusts the amortization of the asset for changes in the expected research period. Each research and development milestone payment is accrued and expensed when probable.

Zai Lab

In November 2021, the Company entered into a collaboration (the Zai Lab agreement) with Zai Lab (Shanghai) Co., Ltd., (Zai Lab) to develop and commercialize certain licensed products for the treatment of EGFR-driven non-small cell lung cancer in Greater China, including Mainland China, Hong Kong, Macau and Taiwan (collectively, the Zai Lab Territory), which currently include BLU-945 and BLU-525. In January 2024, the Company decided to discontinue further investment in the early clinical-stage therapies for EGFR-mutant NSCLC globally. Zai Lab retains its rights to BLU-945 and BLU-525 under the agreement. The Company retains exclusive rights to the licensed products outside the Zai Lab Territory. The decision to deprioritize the licensed products does not have an impact on the Company’s accounting treatment related to the Zai Lab agreement.

Under the Zai Lab agreement, the Company received an upfront cash payment of $25.0 million and, in addition to the upfront payment received, the Company is eligible to receive up to $590.0 million in contingent payments, including specified development, regulatory and sales-based milestones and tiered percentage royalties on a licensed product-by-licensed product basis ranging from the low-teens to mid-teens on annual net sales of each licensed product in the Zai Lab Territory, subject to adjustment in specified circumstances. Zai Lab is responsible for costs related to clinical trials in the Zai Lab Territory, other than the specified shared services costs as defined in the Zai Lab agreement which are shared by the Company and Zai Lab.

Pursuant to the terms of the Zai Lab agreement, Zai Lab is responsible for conducting all development and commercialization activities in the Zai Lab Territory related to the licensed drug candidates. In addition, under the Zai Lab agreement, each party has granted the other party specified intellectual property licenses to enable the other party to perform its obligations and exercise its rights under the Zai Lab agreement, including license grants to enable each party to conduct research, development and commercialization activities pursuant to the terms of the Zai Lab agreement.

The Zai Lab agreement will continue on a licensed product-by-product and region-by-region basis until the later of (i) the 12^th anniversary of the date of the first commercial sale of a licensed product in the Zai Lab Territory, (ii) the date of expiration of the last valid patent claim related to the Company’s patent rights of the product in the Zai Lab Territory, and (iii) the expiration of the last regulatory exclusivity for that product in a region in the Zai Lab Territory. Zai Lab may terminate the agreement for convenience by giving a written notice after the second anniversary of the effective date (a) at least 12 months after the date of notice, in the event such notice is given after the first commercial sale of a licensed product in the Zai Lab Territory or (b) at least nine months after the date of such notice, in the event such notice is given prior to the first commercial sale of the first licensed product in the Zai Lab Territory. Either party may terminate the Zai Lab agreement for the other party’s uncured material breach or insolvency. Upon termination, all licenses and all other rights granted by the Company to Zai Lab will terminate. Each party will retain its joint ownership interests in any joint collaboration technology.

The Company concluded that the Zai Lab agreement is a collaborative agreement under ASC 808 as both parties are active participants in the clinical trials and are exposed to significant risks and rewards of those activities under the Zai Lab agreement. The Company determined that the Zai Lab agreement contained two material components: (i) licenses granted to Zai Lab to exploit and develop each licensed product in the Zai Lab Territory and related activities in the Zai Lab Territory, including manufacturing, and (ii) global development of the licensed products. The Company concluded that Zai Lab is the Company’s customer for the licenses and related activities in the Zai Lab Territory under ASC 606, whereas payments received by the Company for global development activities, including manufacturing, are accounted for as a reduction of related expenses. The Company did not record any reductions of expenses under the Zai Lab agreement during the three and nine months ended September 30, 2024 and 2023.

The Company evaluated the Zai Lab Territory specific licenses and related activities under ASC 606 and identified three material promises at the outset of the Zai Lab agreement, which consists of the following for each licensed product: (1) the exclusive license, (2) the initial know-how transfer and (3) manufacturing activities related to development and commercial supply of the licensed product in the Zai Lab Territory. The Company determined that the exclusive license and the initial know-how transfer were not distinct from each other, as the exclusive license has limited value without the corresponding know-how transfer. As such, for the purposes of ASC 606, the Company determined that these two material promises, the exclusive license and the initial know-how, should be combined into one distinct performance obligation. The manufacturing activities were excluded as performance obligation at the outset of the arrangement because it represented a customer option that was not a material right.

The Company determined that the license is a functional intellectual property license as Zai Lab benefited from the license along with the initial know-how transfer at the time of grant, and therefore the related performance obligation is satisfied at a point in time. The transaction price of the Zai Lab agreement at the outset of the arrangement was determined to be $25.0 million and the Company satisfied the performance obligation upon delivery of the licenses and initial know-how transfer and accordingly, the upfront payment of $25.0 million was recognized as revenue in 2021. Revenue from sales-based milestones and royalties will be recognized when the related sales occur. The other potential milestone payments that the Company is eligible to receive were excluded from the transaction price, as all milestone amounts were fully constrained based on the probability of achievement. Costs that are incurred associated with Zai Lab Territory specific activities are reimbursable from Zai Lab and are recognized as revenue. The Company did not record any revenue under the Zai Lab agreement during the three and nine months ended September 30, 2024. Revenue recorded during the three and nine months ended September 30, 2023 was negligible.

Roche – Pralsetinib Collaboration

In July 2020, the Company entered into a collaboration agreement (the Roche pralsetinib collaboration agreement) with F. Hoffmann-La Roche Ltd and Genentech, Inc., a member of the Roche Group (collectively, Roche), pursuant to which the Company granted Roche exclusive rights to develop and commercialize the Company’s drug candidate pralsetinib worldwide, excluding the CStone Territory (as defined below), and a co-exclusive license in the U.S. to develop and commercialize pralsetinib. In February 2023, the Company received written notice from Roche of their election to terminate for convenience the Roche pralsetinib collaboration agreement. The termination became effective on February 22, 2024 (the collaboration termination effective date), at which time the Company regained commercialization and development rights to GAVRETO from Roche worldwide excluding the CStone Territory. In January 2024, the Company decided to discontinue global development and marketing of GAVRETO in territories excluding the U.S. and the CStone Territory, due to a lack of an alternate partner in these regions. The Company and Roche continued to perform their respective obligations under the Roche pralsetinib collaboration agreement through the collaboration termination effective date. On February 22, 2024, the Company and Roche entered into a transition agreement (the Roche transition agreement) in connection with the termination of the Roche pralsetinib collaboration agreement.

Under the Roche pralsetinib collaboration agreement, the Company received an upfront cash payment of $675.0 million. Through the collaboration termination effective date, the Company received an aggregate of $105.0 million in specified regulatory and commercialization milestones under the Roche pralsetinib collaboration agreement. In connection with the Roche pralsetinib collaboration agreement, in July 2020, the Company also entered into a stock purchase agreement with Roche Holdings, Inc. (Roche Holdings) pursuant to which the Company issued and sold an aggregate of 1,035,519 shares of common stock to Roche Holdings at a purchase price of $96.57 per share for a consideration of $100.0 million. The fair market value of the common stock issued to Roche Holdings was $79.3 million on the date of issuance. The Company determined that the premium of $20.7 million paid by Roche Holdings for the common stock should be attributed to the transaction price of the Roche pralsetinib collaboration agreement.

In the U.S., the Company and Roche co-commercialized pralsetinib and shared responsibilities, profits and losses equally. In addition, the Company received tiered royalties on annual net sales of pralsetinib outside the U.S., excluding the CStone Territory (the Roche Territory). The Company and Roche shared global development costs for pralsetinib at a rate of 45 percent for the Company and 55 percent for Roche.

The Company determined that the Roche pralsetinib collaboration agreement contained four material components: (i) licenses granted to Roche to develop and commercialize pralsetinib worldwide, excluding the CStone Territory (pralsetinib license); (ii) the Roche Territory-specific commercialization activities for pralsetinib, including manufacturing (Roche Territory activities); (iii) the parties’ joint development activities for pralsetinib worldwide, excluding the CStone Territory; and (iv) the parties’ joint commercialization activities for pralsetinib in the U.S.

The Company evaluated the Roche pralsetinib license under ASC 606 and concluded that the pralsetinib license was a functional intellectual property license and a distinct performance obligation. The Company determined that Roche benefited from the pralsetinib license at the time of grant, and therefore the related performance obligation was satisfied at a point in time. Costs incurred associated with the Roche Territory activities were reimbursable from Roche and were recognized as revenue.

The transaction price of the Roche pralsetinib collaboration agreement at the outset of the arrangement was determined to be $695.7 million, which consisted of the upfront cash payment of $675.0 million and the $20.7 million premium on the sale of common stock to Roche Holdings, which was allocated to the performance obligation related to the pralsetinib licenses. Through the collaboration termination effective date, the Company achieved an aggregate of $105.0 million in specified regulatory and commercialization milestones which were added to the estimated transaction price of the Roche pralsetinib collaboration agreement.

Roche was the principal for recording product sales to customers in the U.S., and the Company recognized a portion of the profit as revenue and losses as collaboration loss sharing in its consolidated statements of operations and comprehensive income (loss). During the nine months ended September 30, 2024, the Company recorded revenue of $1.4 million derived from profit sharing on Roche sales of GAVRETO in the U.S. and no collaboration profit or loss sharing was recorded during the three months ended September 30, 2024 due to the termination of the Roche pralsetinib

collaboration agreement. During the three and nine months ended September 30, 2023, the Company recorded a collaboration loss sharing expense of $1.8 million and $4.3 million on Roche’s sales of GAVRETO in the U.S., respectively.

During the three months ended September 30, 2024, no revenue was recognized related to the Roche pralsetinib collaboration agreement, and during the nine months ended September 30, 2024, revenue of $0.5 million was recognized related to Roche Territory specific activities and royalty revenue through the collaboration termination effective date. During the three and nine months ended September 30, 2023, the Company recorded revenue of $0.5 million and $1.7 million, respectively, related to the Roche Territory specific activities and royalty revenue.

For the parties’ participation in global development for pralsetinib and the U.S. commercialization activities for GAVRETO, the Company concluded that those activities and cost-sharing payments related to such activities were within the scope of ASC 808, as both parties were active participants in the development, manufacturing and commercialization activities and are exposed to significant risks and rewards of those activities under the Roche pralsetinib collaboration agreement. Payments to or reimbursements from Roche related to the global development activities were accounted for either as an increase or reduction of research and development expenses.

No operating expenses were recorded under the Roche pralsetinib collaboration since June 30, 2024. During the nine months ended September 30, 2024, the Company recorded $1.0 million reduction to selling, general and administrative expenses in connection with the commercialization of GAVRETO in the U.S and $1.1 million increase in research and development expenses related to global development activities for pralsetinib under the Roche pralsetinib collaboration. During the three and nine months ended September 30, 2023, the Company recorded $3.1 million and $8.6 million, respectively, as reductions in selling, general and administrative expenses in connection with the commercialization of GAVRETO in the U.S. and $7.6 million and $21.2 million, respectively, as increases in research and development expenses in connection with global development activities for pralsetinib.

Upon termination of the Roche pralsetinib collaboration agreement, the Company chose not to assume responsibility for any ongoing pralsetinib clinical trials, and under the terms of the Roche pralsetinib collaboration agreement, Roche bears sole responsibility for all costs associated with the wind-down of these trials.

Pursuant to the Roche transition agreement, the Company is obligated to reimburse Roche for wind-down costs associated with the marketing and commercialization activities occurred for Roche Territory until December 31, 2026. Additionally, the Company is obligated to reimburse Roche for any U.S. transition related costs that exceeds GAVRETO’s net sales in the U.S., and any remaining net profit are shared equally between the Company and Roche until December 31, 2025. The Company has concluded that such activities and associated payments to Roche are not within the scope of ASC 808 as only the Company is exposed to significant risks and awards associated with those activities. The Company records those wind-down costs and the net amount of U.S. transition costs reimbursable to Roche as selling, general, and administrative expenses when they are incurred. During the three and nine months ended September 30, 2024, the Company recorded $4.2 million and $4.4 million, respectively, in such costs.

The following table summarizes the assets and liabilities associated with the Roche pralsetinib agreements as of September 30, 2024 and December 31, 2023 (in thousands):


	September 30,		December 31,
	2024		2023
Other current assets	$	—	$	361
Accrued expenses	$	4,314	$	7,388

Clementia

In October 2019, the Company entered into a license agreement (the Clementia agreement) with Clementia Pharmaceuticals, Inc. (Clementia), a wholly-owned subsidiary of Ipsen S.A. Under the Clementia agreement, the Company granted an exclusive, worldwide, royalty-bearing license to Clementia to develop and commercialize BLU-782, the Company’s oral, highly selective investigational ALK2 inhibitor in Phase 1 clinical development for the treatment of fibrodysplasia ossificans progressiva (FOP), as well as specified other compounds related to the BLU-782 program.

Under the Clementia agreement, the Company received an upfront cash payment of $25.0 million and through September 30, 2024, the Company has received an aggregate of $50.0 million in cash milestone payments. Subject to the terms of the Clementia agreement, in addition to the upfront and milestone payments received through September 30, 2024, the Company is eligible to receive up to $460.0 million in contingent payments, including specified development, regulatory and sales-based milestones for licensed products. In addition, Clementia is obligated to pay to the Company royalties on aggregate annual worldwide net sales of licensed products at tiered percentage rates ranging from the low- to mid-teens, subject to adjustment in specified circumstances under the Clementia agreement, and Clementia purchased specified manufacturing inventory from the Company for a total of $1.5 million.

Unless earlier terminated in accordance with the terms of the Clementia agreement, the agreement will expire on a country-by-country, licensed product-by-licensed product basis on the date when no royalty payments are or will become due. Clementia may terminate the agreement at any time upon at least 12 months’ prior written notice to the Company. Either party may terminate the agreement for the other party’s uncured material breach or insolvency and in certain other circumstances agreed to by the parties. In certain termination circumstances, the Company is entitled to retain specified licenses to be able to continue to exploit the Clementia licensed products.

The Company evaluated the Clementia agreement under ASC 606, as the agreement represented a transaction with a customer. The Company identified the following material promises under the agreement: (1) the exclusive license to develop, manufacture and commercialize BLU-782; (2) the technology transfer of BLU-782 program; (3) the transfer of existing manufacturing inventory; and (4) the transfer of in-process manufacturing inventory. In addition, the Company determined that the exclusive license and technology transfer were not distinct from each other, as the exclusive license has limited value without the corresponding technology transfer. As such, for the purposes of ASC 606, the Company determined that these four material promises, described above, should be combined into three performance obligations: (1) the exclusive license and the technology transfer; (2) the transfer of existing manufacturing inventory; and (3) the transfer of in-process manufacturing inventory.

The Company determined that the transaction price at the outset of the arrangement was $46.5 million, which was allocated to the three performance obligations on a relative stand-alone selling price basis, and was recognized as revenue during 2019 and 2020.

During the three and nine months ended September 30, 2024 and 2023, no revenue was recognized from the Clementia agreement. All potential milestone payments that the Company is eligible to receive were excluded from the transaction price, as the amounts were fully constrained based on the probability of achievement. The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal.

There was no revenue deferred as a contract liability associated with the Clementia agreement as of September 30, 2024 and December 31, 2023.

CStone Pharmaceuticals

In June 2018, the Company entered into a collaboration and license agreement (the CStone agreement) with CStone Pharmaceuticals (CStone) pursuant to which the Company granted CStone exclusive rights to develop and commercialize the Company’s drug candidates avapritinib, pralsetinib and fisogatinib, including back-up and other forms thereof, in Mainland China, Hong Kong, Macau and Taiwan (each, a CStone region and collectively, the CStone Territory), either as a monotherapy or as part of a combination therapy.

The Company received an upfront cash payment of $40.0 million, and through September 30, 2024, the Company has achieved an aggregate of $38.5 million in milestones under this collaboration. Subject to the terms of the CStone agreement, in addition to the upfront payments received and milestones achieved through September 30, 2024, the Company will be eligible to receive up to $307.5 million in contingent payments, including specified development, regulatory and sales-based milestones for licensed products. In addition, CStone is obligated to pay the Company tiered percentage royalties on a licensed product-by-licensed product basis ranging from the mid-teens to low twenties on annual net sales of each licensed product in the CStone Territory, subject to adjustment in specified circumstances.

CStone is responsible for costs related to the development of the licensed products in the CStone Territory, other than specified costs related to the development of fisogatinib as a combination therapy in the CStone Territory that are shared by the Company and CStone.

Pursuant to the terms of the CStone agreement, CStone is responsible for conducting all development and commercialization activities in the CStone Territory related to the licensed products. Subject to specified exceptions, during the term of the CStone agreement, each party has agreed that neither it nor its affiliates will conduct specified development and commercialization activities in the CStone Territory related to selective inhibitors of FGFR4, KIT, PDGFRA and RET. In addition, under the CStone agreement, each party has granted the other party specified intellectual property licenses to enable the other party to perform its obligations and exercise its rights under the CStone agreement, including license grants to enable each party to conduct research, development and commercialization activities pursuant to the terms of the CStone agreement.

The CStone agreement will continue on a licensed product-by-licensed product and CStone region-by-CStone region basis until the later of (i) 12 years after the first commercial sale of a licensed product in a CStone region in the CStone Territory and (ii) the date of expiration of the last valid patent claim related to the Company’s patent rights or any joint collaboration patent rights for the licensed product that covers the composition of matter, method of use or method of manufacturing such licensed product in such region. Subject to the terms of the CStone agreement, CStone may terminate the CStone agreement in its entirety or with respect to one or more licensed products for convenience by providing written notice to the Company, and CStone may terminate the CStone agreement with respect to a licensed product for convenience at any time by providing written notice to the Company following the occurrence of specified events. In addition, the Company may terminate the CStone agreement under specified circumstances if CStone or certain other parties challenges the Company’s patent rights or any joint collaboration patent rights or if CStone or its affiliates do not conduct any material development or commercialization activities with respect to one or more licensed products for a specified period of time, subject to specified exceptions. Either party may terminate the CStone agreement for the other party’s uncured material breach or insolvency. In certain termination circumstances, the parties are entitled to retain specified licenses to be able to continue to exploit the licensed products, and in the event of termination by CStone for the Company’s uncured material breach, the Company will be obligated to pay CStone a low single digit percentage royalty on a licensed product-by-licensed product basis on annual net sales of such licensed product in the CStone Territory, subject to a cap and other specified exceptions.

The Company evaluated the CStone agreement to determine whether it is a collaborative arrangement for purposes of ASC 808. The Company determined that there were two material components of the CStone agreement: (i) the CStone Territory-specific license and related activities in the CStone Territory, and (ii) the parties’ participation in global development of the licensed products. The Company concluded that the CStone Territory-specific license and related activities in the CStone Territory are not within the scope of ASC 808 because the Company is not exposed to significant risks and rewards. The Company concluded that CStone is a customer with regard to the component that includes the CStone Territory-specific license and related activities in CStone Territory, which include manufacturing. For the parties’ participation in global development of the licensed products, the Company concluded that the research and development activities and cost-sharing payments related to such activities are within the scope of ASC 808 as both parties are active participants exposed to the risk of the activities under the CStone agreement. The Company concluded that CStone is not a customer with regard to the global development component in the context of the CStone agreement. Therefore, net payments received by the Company for global development activities under the CStone agreement, including manufacturing, are accounted for as a reduction of related expenses.

The Company did not have significant manufacturing and research and development services related to the global development activities during the three and nine months ended September 30, 2024 and 2023.

The Company evaluated the CStone Territory-specific license and related activities in the CStone Territory under ASC 606, as these transactions are considered transactions with a customer. The Company identified the following material promises under the arrangement: (1) the three exclusive licenses granted in the CStone Territory to develop, manufacture and commercialize the three licensed products; (2) the initial know-how transfer for each licensed product; (3) manufacturing activities related to development and commercial supply of the licensed products; (4) participation in the joint steering committee (JSC) and joint project teams (JPT); (5) regulatory responsibilities; and (6) manufacturing technology and continuing know-how transfers. The Company determined that each licensed product is distinct from the other licensed products. In addition, the Company determined that the exclusive licenses and initial know-how transfers

for each licensed product were not distinct from each other, as each exclusive license has limited value without the corresponding initial know-how transfer. For purposes of ASC 606, the Company determined that participation on the JSC and JPTs, the regulatory responsibilities and the manufacturing technology and continuing know-how transfers are qualitatively and quantitatively immaterial in the context of the CStone agreement and therefore are excluded from performance obligations. As such, the Company determined that these six material promises, described above, should be combined into one performance obligation for each of the three candidates.

The Company evaluated the provision of manufacturing activities related to development and commercial supply of the licensed products as an option for purposes of ASC 606 to determine whether these manufacturing activities provide CStone with any material rights. The Company concluded that the manufacturing activities were not issued at a significant and incremental discount, and therefore do not provide CStone with any material rights. As such, the manufacturing activities are excluded as performance obligations at the outset of the arrangement.

Based on these assessments, the Company identified three distinct performance obligations at the outset of the CStone agreement, which consists of the following for each licensed product: (1) the exclusive license and (2) the initial know-how transfer.

Under the CStone agreement, in order to evaluate the transaction price for purposes of ASC 606, the Company determined that the upfront amount of $40.0 million constituted the entirety of the consideration to be included in the transaction price at the outset of the arrangement, which was allocated to the three performance obligations. The potential milestone payments that the Company is eligible to receive were excluded from the transaction price, as all milestone amounts were fully constrained based on the probability of achievement. The Company satisfied the performance obligations upon delivery of the licenses, initial know-how transfers and product trademark and recognized the upfront payment of $40.0 million as revenue in 2018.

The Company did not achieve any milestones under the CStone agreement during the three and nine months ended September 30, 2024 and during the three months ended September 30, 2023. During the nine months ended September 30, 2023, cash consideration associated with the achieved regulatory milestone of $9.0 million was added to the estimated transaction price for the CStone agreement and recognized as revenue. The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal.

Subsequent to the CStone agreement, the Company entered into various commercial supply and manufacturing technology transfer agreements for avapritinib and pralsetinib related to supply of active pharmaceutical ingredient (API), drug substance and commercialization activities conducted specifically for the CStone Territory. The manufacturing activities in these agreements were considered as distinct performance obligations from the CStone collaboration agreement and collaboration revenue is recognized upon delivery of the supply to CStone. Considerations payable to CStone related to the Company’s obligations in connection with commercial supply of pralsetinib for the CStone Territory was recognized as a reduction of collaboration revenue.

A summary of revenue recognized under the CStone agreement during the three and nine months ended September 30, 2024 and 2023 is as follows (in thousands):


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2024		2023		2024		2023
License milestone revenue	$	—	$	—	$	—	$	9,000
Manufacturing services and royalty revenue related to CStone territory-specific activities		(148)		1,820		1,424		7,861
Total CStone collaboration revenue	$	(148)	$	1,820	$	1,424	$	16,861

The Company did not have any contract assets related to the CStone collaboration as of September 30, 2024 and December 31, 2023. The following table presents the contract liabilities associated with the CStone collaboration as of September 30, 2024 and December 31, 2023 (in thousands):


	September 30,		December 31,
	2024		2023
Contract liabilities	$	3,165	$	604
Accrued expenses	$	841	$	1,863

The Company’s liabilities associated with the CStone collaboration as of September 30, 2024 and December 31, 2023 resulted primarily from the Company’s obligations in connection with commercial supply of pralsetinib for the CStone Territory.

Roche – Immunotherapy Collaboration

In March 2016, the Company entered into a collaboration and license agreement (as amended, the Roche immunotherapy agreement) with F. Hoffmann-La Roche Ltd and Hoffmann-La Roche Inc. (collectively, Roche) for the discovery, development and commercialization of small molecule therapeutics targeting kinases believed to be important in cancer immunotherapy, as single products or possibly in combination with other therapeutics. On April 30, 2023, the Company and Roche entered into a mutual termination agreement to terminate the Roche immunotherapy agreement. Certain licenses granted by Roche to the Company survived and became exclusive, worldwide, perpetual, royalty-free and irrevocable and the Company retained ownership of all the targets developed under the collaboration.

The Roche immunotherapy agreement represented a vendor-customer relationship under ASC 606 as the Company performed its one performance obligation at the outset of the Roche immunotherapy agreement, which consisted of: (1) the non-exclusive license; (2) the research and development activities through Phase 1; and (3) regulatory responsibilities under Phase 1 clinical trials.

The aggregate net transaction price of the Roche immunotherapy agreement was $64.7 million. The Company recognized revenue associated with the performance obligation using an input method, based on the costs incurred for the research and development activities on each program and the costs expected to be incurred in the future to satisfy the performance obligation for each respective period. The amounts received that had not yet been recognized as revenue were deferred as a contract liability on the Company’s consolidated balance sheet and recognized over the remaining research and development period until the performance obligation was satisfied. The performance obligation was completely satisfied as of June 30, 2023 and no revenue was recognized thereafter for this agreement. During the nine months ended September 30, 2023, the Company recognized research and development services revenue of $25.7 million under the Roche immunotherapy agreement, of which $16.0 million resulted from changes in contract liability balances at the beginning of the period. There was no revenue deferred as a contract liability associated with the Roche immunotherapy agreement as of September 30, 2024 and December 31, 2023.

Pay vs Performance Disclosure - USD ($) $ in Thousands	3 Months Ended						9 Months Ended
Pay vs Performance Disclosure - USD ($) $ in Thousands	Sep. 30, 2024	Jun. 30, 2024	Mar. 31, 2024	Sep. 30, 2023	Jun. 30, 2023	Mar. 31, 2023	Sep. 30, 2024	Sep. 30, 2023
Pay vs Performance Disclosure
Net Income (Loss)	$ (56,276)	$ (49,994)	$ 89,136	$ (133,713)	$ (132,794)	$ (129,560)	$ (17,133)	$ (396,068)

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

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Stock-based Compensation - Performance-based Restricted Stock Units (Details) - Performance-based restricted stock units	9 Months Ended
	Sep. 30, 2024
Stock-based compensation
Award service period	3 years
Award vesting period	3 years
Performance metric, cumulative relative total shareholder return, period	3 years
Minimum
Stock-based compensation
Award grants, percentage of target (as a percent)	0.00%
Maximum
Stock-based compensation
Award grants, percentage of target (as a percent)	200.00%

Product Revenue - Revenue-related Reserves (Details) - Valuation Allowances and Reserves, Product Revenue - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023	Sep. 30, 2023	Dec. 31, 2022
Product revenue allowance and reserve
Total revenue-related reserves	$ 34,688	$ 19,274	$ 17,648	$ 9,788
Accounts Receivable, Net
Product revenue allowance and reserve
Total revenue-related reserves	3,512	1,809
Accrued Expenses
Product revenue allowance and reserve
Total revenue-related reserves	$ 31,176	$ 17,465

Collaboration and Other Agreements - Sale of Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended			9 Months Ended
	Jul. 31, 2020	Sep. 30, 2024	Mar. 31, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Sale of Stock
Stock issued (in shares)		0		0	544,719	0
Issuance of common stock			$ 48,936
Private Placement
Sale of Stock
Stock issued (in shares)	1,035,519
Share price (in dollars per share)	$ 96.57
Purchase consideration	$ 100,000
Issuance of common stock	79,300
Share purchase consideration, premium	$ 20,700

Equity impact of the value of new stock issued during the period. Includes shares issued in an initial public offering or a secondary public offering.

Nature of Business

9 Months Ended

Sep. 30, 2024

Nature of Business

1. Nature of Business

Blueprint Medicines Corporation (the Company), a Delaware corporation incorporated on October 14, 2008, is a global fully-integrated biopharmaceutical company that invents life-changing medicines in two core focus areas: allergy/inflammation and oncology/hematology. The Company’s approach targets the root causes of disease, using deep scientific knowledge in the Company’s core focus areas and drug discovery expertise across multiple therapeutic modalities.

The Company has a track record of success with two approved medicines, including AYVAKIT®/AYVAKYT® (avapritinib), which the Company is bringing to patients living with systemic mastocytosis (SM) and PDGFRA Exon 18 mutant GIST in the U.S. and Europe. Leveraging the Company’s established research, development, and commercial capability and infrastructure, the Company now aims to significantly scale its impact by advancing a broad pipeline of programs ranging from early science to advanced clinical trials in mast cell diseases including SM and chronic urticaria, breast cancer and other solid tumors.

As of September 30, 2024, the Company had cash, cash equivalents and marketable securities of $882.4 million. Based on the Company’s current operating plans, the Company anticipates that its existing cash, cash equivalents and marketable securities will be sufficient to enable it to fund its current operations for at least the next twelve months from the issuance of the financial statements.

Stock-based Compensation - Stock Options - Activity (Details)	9 Months Ended
	Sep. 30, 2024 $ / shares shares
Shares
Outstanding at beginning of period (in shares) \| shares	6,658,444
Granted (in shares) \| shares	1,055,795
Exercised (in shares) \| shares	(1,034,224)
Cancelled (in shares) \| shares	(181,789)
Outstanding at end of period (in shares) \| shares	6,498,226
Weighted-Average Exercise Price
Outstanding at beginning of period (in dollars per share) \| $ / shares	$ 66.48
Granted (in dollars per share) \| $ / shares	95.87
Exercised (in dollars per share) \| $ / shares	62.39
Cancelled (in dollars per share) \| $ / shares	73.13
Outstanding at end of period (in dollars per share) \| $ / shares	$ 71.83
Additional disclosures
Shares - Exercisable (in shares) \| shares	4,413,290
Weighted-Average Exercise Price - Exercisable (in dollars per share) \| $ / shares	$ 71.14

Marketable Securities - Impairment (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Marketable Securities
Marketable debt securities, charges for credit-related impairments	$ 0	$ 0	$ 0	$ 0

Inventory - Capitalized (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Inventory
Raw materials	$ 3,069	$ 3,147
Work in process	32,179	29,132
Finished goods	7,210	4,823
Total	$ 42,458	$ 37,102

Marketable Securities - Tabular Disclosure (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Marketable securities, available-for-sale:
Amortized cost	$ 790,758	$ 696,074
Unrealized gain	2,298	615
Unrealized losses	(59)	(804)
Fair value	792,997	695,885
U.S. government agency securities
Marketable securities, available-for-sale:
Amortized cost	133,228	170,194
Unrealized gain	292	27
Unrealized losses	(32)	(418)
Fair value	133,488	169,803
U.S. Treasury obligations
Marketable securities, available-for-sale:
Amortized cost	657,530	525,880
Unrealized gain	2,006	588
Unrealized losses	(27)	(386)
Fair value	$ 659,509	$ 526,082

Amount of investment in debt security measured at fair value with change in fair value recognized in other comprehensive income (available-for-sale).

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Leases (Tables)

9 Months Ended

Sep. 30, 2024

Summary of lease expenses and cash flow and weighted average information


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
Operating leases:	2024		2023		2024		2023
Lease cost	$	5,831	$	5,758	$	17,268	$	17,301


	Nine Months Ended
	September 30,
	2024		2023
Cash paid for amounts included in the measurement of lease liabilities:	$	13,664	$	13,249
Lease liabilities arising from obtaining right-of-use assets:
Operating leases	$	116	$	109


					Operating leases
Weighted average remaining lease term in years					5.1
Weighted average discount rate					7.3%

Collaboration and Other Agreements (Tables)

9 Months Ended

Sep. 30, 2024

Summary of prepaid assets


	September 30, 2024						December 31, 2023
	Current		Noncurrent		Total		Current		Noncurrent		Total
Prepaid assets	$	6,067	$	3,087	$	9,154	$	6,581	$	6,581	$	13,162

Rigel Pharmaceuticals, Inc. | Collaboration, License and Other

Summary of contract assets and/or contract liabilities


	September 30, 2024
	Current		Noncurrent		Total
Contract assets	$	2,680	$	8,389	$	11,069
Contract liabilities	$	—	$	3,562	$	3,562

Roche, Collaboration (Pralsetnib) Agreement | Collaboration, License and Other

Summary of contract assets and/or contract liabilities


	September 30,		December 31,
	2024		2023
Other current assets	$	—	$	361
Accrued expenses	$	4,314	$	7,388

C Stone | Collaboration, License and Other

Summary of revenue recognized


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2024		2023		2024		2023
License milestone revenue	$	—	$	—	$	—	$	9,000
Manufacturing services and royalty revenue related to CStone territory-specific activities		(148)		1,820		1,424		7,861
Total CStone collaboration revenue	$	(148)	$	1,820	$	1,424	$	16,861

Summary of contract assets and/or contract liabilities


	September 30,		December 31,
	2024		2023
Contract liabilities	$	3,165	$	604
Accrued expenses	$	841	$	1,863

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Current assets:
Cash and cash equivalents	$ 89,356	$ 71,286
Marketable securities	644,817	639,355
Accounts receivable	65,814	42,827
Inventory	12,528	21,223
Prepaid expenses and other current assets	42,333	33,702
Total current assets	854,848	808,393
Marketable securities	148,180	56,530
Property and equipment, net	37,850	41,959
Operating lease right-of-use assets, net	66,416	73,691
Restricted cash	11,503	10,238
Equity investment	28,699	27,789
Other assets	52,153	30,650
Total assets	1,199,649	1,049,250
Current liabilities:
Accounts payable	4,716	4,710
Accrued expenses	130,881	127,992
Current portion of operating lease liabilities	13,011	11,933
Current portion of deferred revenue	4,118	812
Current portion of liabilities related to the sale of future royalties and revenues	59,903	39,198
Current portion of term loan	45,032	30,278
Total current liabilities	257,661	214,923
Operating lease liabilities, net of current portion	71,916	81,751
Deferred revenue, net of current portion	7,916	4,792
Liabilities related to the sale of future royalties and revenues, net of current portion	201,304	402,427
Term loan, net of current portion	341,537	208,535
Other long-term liabilities	6,167	6,213
Total liabilities	886,501	918,641
Commitments and Contingencies (Note 16)
Stockholders' equity:
Preferred stock, $0.001 par value; 5,000,000 shares authorized; no shares issued and outstanding
Common stock, $0.001 par value; 120,000,000 shares authorized; 63,454,673 and 61,147,236 shares issued and outstanding at September 30, 2024 and December 31, 2023, respectively	63	61
Additional paid-in capital	2,671,231	2,473,985
Accumulated other comprehensive loss	(1,070)	(3,495)
Accumulated deficit	(2,357,076)	(2,339,942)
Total stockholders' equity	313,148	130,609
Total liabilities and stockholders' equity	$ 1,199,649	$ 1,049,250

Financing Arrangements - Roll Forward (Details) - USD ($) $ in Thousands	9 Months Ended		27 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024
Sale of Future Royalties and Revenues \| Sixth Street Partners, Future Revenue Purchase Agreement
Long-term Debt
Carrying value, beginning balance	$ 266,670	$ 254,328
Interest expense recognized	20,721	21,043
Payments	(26,921)	(10,484)
Carrying value, ending balance	260,470	264,887	$ 260,470
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities
Long-term Debt
Carrying value, beginning balance	238,813	139,083
Net proceeds received	146,973	97,968	382,692
Interest expense recognized	29,917	15,557
Payments	(29,134)	(14,230)
Carrying value, ending balance	$ 386,569	$ 238,378	$ 386,569

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

Commitments and Contingencies - Purchase Commitments (Details) - Clinical Manufacturing Agreements $ in Millions	9 Months Ended
	Sep. 30, 2024 USD ($)
Clinical and Commercial Supply Agreements
Unrecorded unconditional purchase obligation, term	5 years
Unrecorded unconditional purchase obligation, future minimum purchase obligations	$ 4.0

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Details)	Sep. 30, 2024
Accounting Standards Update 2023-07
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false
Accounting Standards Update 2023-09
Summary of Significant Accounting Policies and Recent Accounting Pronouncements
Change in Accounting Principle, Accounting Standards Update, Adopted	false

Indicates (true false) whether accounting standards update was adopted.

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Stock-based Compensation - Stock-based Compensation Expense - General Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Total stock based compensation expense
Stock-based compensation expense	$ 28,282	$ 23,071	$ 80,529	$ 70,087

Collaboration and Other Agreements - Revenue Recognized (Details) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended		12 Months Ended		24 Months Ended
	Aug. 01, 2022	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2021	Dec. 31, 2018	Dec. 31, 2020
Revenues
Revenue		$ 128,184	$ 56,566	$ 362,458	$ 177,423
Collaboration, License and Other
Revenues
Revenue			2,338	27,633	44,250
Collaboration, License and Other \| Rigel Pharmaceuticals, Inc.
Revenues
Revenue				24,300
Collaboration, License and Other \| Zai Lab (Shanghai) Co., Ltd.
Revenues
Revenue		0	0	0	0	$ 25,000
Collaboration, License and Other \| Roche, Collaboration (Pralsetnib) Agreement
Revenues
Revenue		0
Collaboration, License and Other \| Roche, Collaboration and License (Immunotherapy) Agreement
Revenues
Revenue		0		0
Collaboration, License and Other \| Clementia
Revenues
Revenue		0	0	0	0			$ 46,500
Collaboration, License and Other \| C Stone
Revenues
Revenue		(148)	1,820	1,424	16,861		$ 40,000
License milestone revenue \| C Stone
Revenues
Revenue		0	0	0	9,000
Territory-specific activities, manufacturing services and royalty \| Roche, Collaboration (Pralsetnib) Agreement
Revenues
Revenue			500	500	1,700
Territory-specific activities, manufacturing services and royalty \| C Stone
Revenues
Revenue		(148)	1,820	1,424	7,861
Territory-specific activities, research and development services \| Roche, Collaboration and License (Immunotherapy) Agreement
Revenues
Revenue					25,700
GAVRETO Product Consideration \| Rigel Pharmaceuticals, Inc.
Revenues
Revenue		6,500
GAVRETO profit share in the U.S. \| Roche, Collaboration (Pralsetnib) Agreement
Revenues
Revenue				1,400
GAVRETO Performance Obligation Rights in the U.S. \| Rigel Pharmaceuticals, Inc.
Revenues
Revenue		17,600
License \| IDRx, Inc. \| Director
Revenues
Revenue	$ 27,500	$ 0	$ 0	$ 0	$ 0

Leases - Cash Flow Information (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Leases
Cash paid for amounts included in the measurement of lease liabilities, operating cash flows from operating leases	$ 13,664	$ 13,249
Lease liabilities arising from obtaining right-of-use assets, operating leases	$ 116	$ 109

Marketable Securities - Maturities (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Amortized cost
Within one year, amortized cost	$ 643,209	$ 639,881
After one through five years, amortized cost	147,549	56,193
Amortized cost	790,758	696,074
Fair value
Within one year, fair value	644,817	639,355
After one through five years, fair value	148,180	56,530
Investments, available-for-sale	$ 792,997	$ 695,885

Amount of investment in debt security measured at fair value with change in fair value recognized in other comprehensive income (available-for-sale).

Inventory

9 Months Ended

Sep. 30, 2024

Sixth Street Partners, Future Revenue Purchase Agreement

Inventory

7. Inventory

Capitalized inventory consists of the following at September 30, 2024 and December 31, 2023 (in thousands):


	September 30,		December 31,
	2024		2023
Raw materials	$	3,069	$	3,147
Work in process		32,179		29,132
Finished goods		7,210		4,823
Total	$	42,458	$	37,102

Balance sheet classification


	September 30,		December 31,
	2024		2023
Inventory	$	12,528	$	21,223
Other assets		29,930		15,879
Total	$	42,458	$	37,102

Inventory amounts written down as a result of excess, obsolescence, unmarketability or other reasons are charged to cost of sales. The Company recognized an insignificant write-down for both the three and nine months ended September 30, 2024. The Company recognized a write-down of $0.1 million and $2.2 million for the three and nine months ended September 30, 2023, respectively. Long-term inventory, which consists of work in process, is included in other assets in the unaudited condensed consolidated balance sheets.

Income Taxes - Financing Arrangements (Details) - USD ($) $ in Thousands		1 Months Ended	3 Months Ended	9 Months Ended	12 Months Ended
	Jun. 30, 2022	Jul. 31, 2022	Sep. 30, 2024	Sep. 30, 2024	Dec. 31, 2022
Gain (Loss) on Extinguishment of Debt
Debt extinguishment gain				$ 173,676
Sale of Future Royalties and Revenues
Gross Proceeds
Gross proceeds					$ 425,000
Sale of Future Royalties and Revenues \| Royalty Pharma, Royalty Purchase Agreement
Gross Proceeds
Gross proceeds	$ 175,000
Gain (Loss) on Extinguishment of Debt
Debt extinguishment gain			$ 173,700	$ 173,700
Sale of Future Royalties and Revenues \| Sixth Street Partners, Future Revenue Purchase Agreement
Gross Proceeds
Gross proceeds		$ 250,000

Net Loss Per Share (Details) - shares shares in Thousands	3 Months Ended		9 Months Ended
Net Loss Per Share (Details) - shares shares in Thousands	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	8,942	9,177	8,942	9,177
Employee Stock Option
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	6,498	6,984	6,498	6,984
Restricted Stock Units
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	2,274	2,093	2,274	2,093
Performance-based restricted stock units
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	143	53	143	53
Employee Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	27	47	27	47

Fair Value of Financial Instruments (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Fair Value of Financial Instruments
Marketable securities, available-for-sale	$ 792,997	$ 695,885
U.S. government agency securities
Fair Value of Financial Instruments
Marketable securities, available-for-sale	133,488	169,803
U.S. Treasury obligations
Fair Value of Financial Instruments
Marketable securities, available-for-sale	659,509	526,082
Recurring
Fair Value of Financial Instruments
Total	850,150	751,297
Recurring \| U.S. government agency securities
Fair Value of Financial Instruments
Marketable securities, available-for-sale	133,488	169,803
Recurring \| U.S. Treasury obligations
Fair Value of Financial Instruments
Marketable securities, available-for-sale	659,509	526,082
Recurring \| Money market funds
Fair Value of Financial Instruments
Cash equivalents	57,153	55,412
Recurring \| Active Markets (Level 1)
Fair Value of Financial Instruments
Total	716,662	581,494
Recurring \| Active Markets (Level 1) \| U.S. Treasury obligations
Fair Value of Financial Instruments
Marketable securities, available-for-sale	659,509	526,082
Recurring \| Active Markets (Level 1) \| Money market funds
Fair Value of Financial Instruments
Cash equivalents	57,153	55,412
Recurring \| Observable Inputs (Level 2)
Fair Value of Financial Instruments
Total	133,488	169,803
Recurring \| Observable Inputs (Level 2) \| U.S. government agency securities
Fair Value of Financial Instruments
Marketable securities, available-for-sale	$ 133,488	$ 169,803

Inventory - Balance Sheet Classification (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Inventory
Inventory	$ 12,528	$ 21,223
Other assets	29,930	15,879
Total	$ 42,458	$ 37,102

Financing Arrangements (Tables)

9 Months Ended

Sep. 30, 2024

Schedule of activity within the liability account and proceeds received


	Nine Months Ended September 30,
	2024		2023
Beginning Balance at January 1	$	266,670	$	254,328
Interest expense recognized		20,721		21,043
Payments		(26,921)		(10,484)
Carrying value as of September 30	$	260,470	$	264,887

Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities

Schedule of activity within the liability account and proceeds received


				Debt discount/
Term loan draw	Date	Gross proceeds		Transaction cost		Net proceeds
Senior Secured Term Loan Facility	July 2022	$	150,000	$	12,214	$	137,786
1st Senior Secured Delayed Draw Term Loan Facility	August 2023		100,000		2,067		97,933
2nd Senior Secured Delayed Draw Term Loan Facility	May 2024		150,000		3,027		146,973
		$	400,000	$	17,308	$	382,692


	Nine Months Ended September 30,
	2024		2023
Beginning Balance at January 1	$	238,813	$	139,083
Net proceeds received from the delayed draw term loan		146,973		97,968
Interest expense recognized		29,917		15,557
Payments		(29,134)		(14,230)
Carrying value as of September 30	$	386,569	$	238,378

Tabular disclosure of long-debt instruments or arrangements, including identification, terms, features, collateral requirements and other information necessary to a fair presentation. These are debt arrangements that originally required repayment more than twelve months after issuance or greater than the normal operating cycle of the entity, if longer.

Reference 1: http://fasb.org/us-gaap/role/ref/legacyRef
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Reference 2: http://www.xbrl.org/2003/role/exampleRef
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Reference 3: http://www.xbrl.org/2003/role/exampleRef
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Reference 4: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 5: http://www.xbrl.org/2009/role/commonPracticeRef
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Reference 7: http://fasb.org/us-gaap/role/ref/legacyRef
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Financing Arrangements - General Information (Details) $ in Millions		1 Months Ended	12 Months Ended
	Jun. 30, 2022 USD ($)	Jul. 31, 2022 USD ($) tranche Transaction	Dec. 31, 2022 USD ($)	Sep. 30, 2024
Sixth Street Partners, Financing Arrangements
Debt Financing
Debt instrument, transactions, number \| Transaction		2
Sale of Future Royalties and Revenues
Gross Proceeds
Gross proceeds			$ 425.0
Sale of Future Royalties and Revenues \| Royalty Pharma, Royalty Purchase Agreement
Debt Financing
Debt instrument, issuance date	Jun. 30, 2022
Gross Proceeds
Gross proceeds	$ 175.0
Sale of Future Royalties and Revenues \| Sixth Street Partners, Future Revenue Purchase Agreement
Debt Financing
Debt instrument, face amount		$ 250.0
Transaction costs, gross		5.4
Gross Proceeds
Gross proceeds		250.0
Effective Interest Rate
Debt instrument, interest rate, effective percentage (as a percent)				10.50%
Loans Payable \| Sixth Street Partners, Financing Agreement
Debt Financing
Debt instrument, face amount, potential amount		660.0
Debt instrument, covenants, consolidated liquidity, period commencing from date term loan funded to date day before next term loans funded, each day thereafter		$ 80.0
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities
Debt Financing
Debt instrument, maturity date		Jun. 30, 2028
Effective Interest Rate
Debt instrument, interest rate, effective percentage (as a percent)				12.30%
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities \| Secured Overnight Financing Rate (SOFR)
Debt Financing
Debt instrument, basis spread on variable rate		6.50%
Debt instrument, variable rate floor		1.00%
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities \| Base Rate
Debt Financing
Debt instrument, basis spread on variable rate		5.50%
Debt instrument, variable rate floor		2.00%
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facility
Debt Financing
Debt instrument, face amount		$ 150.0
Secured Debt \| Sixth Street Partners, Financing Agreement, 1st Senior Secured Delayed Draw Term Loan Facility
Debt Financing
Debt instrument, face amount, potential amount		$ 250.0
Debt instrument, tranches, number \| tranche		2
Secured Debt \| Sixth Street Partners, Financing Agreement, Incremental Term Loan
Debt Financing
Debt instrument, face amount, potential amount		$ 260.0

Leases - Weighted Average Remaining Lease-term and Weighted Average Discount Rate (Details)	Sep. 30, 2024
Leases
Weighted average remaining lease term in years	5 years 1 month 6 days
Weighted average discount rate	7.30%

Financing Arrangements - Debt Extinguishment (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2024	Feb. 22, 2022
Gain (Loss) on Extinguishment of Debt
Debt extinguishment gain		$ 173,676
Sale of Future Royalties and Revenues \| Royalty Pharma, Royalty Purchase Agreement
Gain (Loss) on Extinguishment of Debt
Debt extinguishment gain	$ 173,700	173,700
Long-term Debt
Debt reacquisition liability, current	700	700
Long-term debt	$ 0	$ 0	$ 0

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

Summary of Significant Accounting Policies and Recent Accounting Pronouncements

9 Months Ended

Sep. 30, 2024

Summary of Significant Accounting Policies and Recent Accounting Pronouncements

2. Summary of Significant Accounting Policies and Recent Accounting Pronouncements

Basis of Presentation

The unaudited interim condensed consolidated financial statements of the Company included herein have been prepared in accordance with accounting principles generally accepted in the U.S. (GAAP) as found in the Accounting Standards Codification (ASC), Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB) and the rules and regulations of the Securities and Exchange Commission (SEC). Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the financial statements as of and for the year ended December 31, 2023 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, filed with the SEC on February 15, 2024 (2023 Annual Report on Form 10-K).

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements, and updated, as necessary, in this report. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments that are necessary to present fairly the Company’s financial position as of September 30, 2024, the results of its operations for the three and nine months ended September 30, 2024 and 2023, stockholders’ equity for the three and nine months ended September 30, 2024 and 2023 and cash flows for the nine months ended September 30, 2024 and 2023. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended September 30, 2024 are not necessarily indicative of the results for the year ending December 31, 2024 or for any future period.

The accompanying unaudited interim condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell and hold securities, Blueprint Medicines (Switzerland) GmbH, Blueprint Medicines (Netherlands) B.V., Blueprint Medicines (UK) Ltd., Blueprint Medicines (Germany) GmbH, Blueprint Medicines (Spain) S.L., Blueprint Medicines (France) SAS, and Blueprint Medicines (Italy) S.r.L. All intercompany transactions and balances have been eliminated.

Use of Estimates

The preparation of financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies and in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates. Estimates are used in the following areas, among others: revenue recognition, inventory, operating lease right-of-use assets, operating lease liabilities, stock-based compensation expense, accrued expenses, liabilities related to the sale of future royalties and future revenues, equity investment, and income taxes. Actual results may differ from these estimates.

Significant Accounting Policies

The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and nine months ended September 30, 2024 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2023 Annual Report on Form 10-K, with the exception of the below new policy.

Modification of debt instruments

When the Company’s debt instrument, where the Company is the debtor, is modified or exchanged, the Company shall analyze whether the modification should be accounted for as a modification or an extinguishment. Modified terms are considered substantially different if, after an exchange or modification of debt instruments with the same creditor, the present value of cash flows under the terms of the new debt instrument differs by at least 10% from the present value of the remaining cash flows under the terms of the original debt instrument. If the modified instrument is considered substantially different from the original debt instrument, the modification or exchange is accounted for as an extinguishment. The new instrument is recorded at its fair value and that fair value is used to determine the extinguishment gain or loss.

Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, the Company does not believe that the adoption of recently issued standards have or may have a material impact on its condensed consolidated financial statements and disclosures.

In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures, which is intended to improve reportable segment disclosure requirements, primarily through additional disclosures about significant segment expenses. The standard is effective for fiscal years beginning after December 15, 2023, and interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The amendments will be applied retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the disclosure requirements related to this new standard.

In December 2023, the FASB issued ASU 2023-09, Improvements to Income Tax Disclosures, which requires entities to disclose disaggregated information about their effective tax rate reconciliation and income taxes paid. The disclosure requirements will be applied on a prospective basis, with the option to apply them retrospectively. The standard is effective for fiscal years beginning after December 15, 2024, with early adoption permitted. The Company is currently evaluating the disclosure requirements related to this new standard.

Reclassification

Certain items in the prior year’s condensed consolidated financial statements have been reclassified to conform to the current presentation.

Collaboration and Other Agreements - Performance Obligations (Details) - Collaborative Arrangement	9 Months Ended
	Sep. 30, 2024 item component
Rigel Pharmaceuticals, Inc.
Performance Obligations
Revenue, performance obligation, performance obligations, number	3
IDRx, Inc. \| Director
Performance Obligations
Collaborative arrangement, material promises, number	2
Collaborative arrangement, material promises, combined into distinct performance obligation, number	1
Zai Lab (Shanghai) Co., Ltd.
Performance Obligations
Collaborative arrangement, material promises, number	3
Collaborative arrangement, material promises, combined into distinct performance obligation, number	2
Collaborative arrangement, material components, number \| component	2
Roche, Collaboration (Pralsetnib) Agreement
Performance Obligations
Collaborative arrangement, material components, number \| component	4
Roche, Collaboration and License (Immunotherapy) Agreement
Performance Obligations
Revenue, performance obligation, performance obligations, number	1
Clementia
Performance Obligations
Collaborative arrangement, material promises, number	4
Revenue, performance obligation, performance obligations, number	3
C Stone
Performance Obligations
Collaborative arrangement, material promises, number	6
Collaborative arrangement, material components, number \| component	2
Revenue, performance obligation, performance obligations, number	3

Accrued Expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Accrued Expenses
Research, development and commercial contract costs	$ 35,886	$ 49,354
Employee compensation	40,267	43,434
Accrued professional fees	16,946	12,522
Revenue-related reserves	31,176	17,465
Other	6,606	5,217
Total	$ 130,881	$ 127,992

Stock-based Compensation - Employee Stock Purchase Plan (Details) - Employee Stock - shares	1 Months Ended
	May 31, 2015	Jan. 01, 2024
Stock-based compensation
Number of common shares reserved for future issuance (in shares)	243,347
Annual increase for common stock for issuance (as a percent)	1.00%
Increase of common shares reserved for future issuance (in shares)		611,472

Collaboration and Other Agreements - Reduction in Expenses (Details) - Collaborative Arrangement - Roche, Collaboration (Pralsetnib) Agreement - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Collaboration and Other Agreements
Collaborative arrangement, commercialization, reduction in selling, general and administrative expenses	$ 0	$ 3,100	$ 1,000	$ 8,600
Collaborative arrangement, global development activities, increase (reduction) in research and development expenses	$ 0	$ 7,600	$ 1,100	$ 21,200

Leases - Components of Lease Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Operating leases:
Lease cost	$ 5,831	$ 5,758
Net lease cost	$ 5,831	$ 5,758	$ 17,268	$ 17,301

Income Taxes - Expense (Benefit) (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Income tax expense (benefit)
Income tax expense	$ 273	$ 197	$ 554	$ 907

Amount of current income tax expense (benefit) and deferred income tax expense (benefit) pertaining to continuing operations.

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
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Reference 2: http://www.xbrl.org/2003/role/disclosureRef
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Reference 3: http://www.xbrl.org/2003/role/disclosureRef
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Reference 4: http://www.xbrl.org/2003/role/exampleRef
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Reference 5: http://www.xbrl.org/2003/role/disclosureRef
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Stock-based Compensation - Stock-based Compensation Expense - By Classification (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Total stock based compensation expense
Stock-based compensation expense	$ 28,282	$ 23,071	$ 80,529	$ 70,087
Research and Development
Total stock based compensation expense
Stock-based compensation expense	12,552	11,169	35,712	31,512
General and Administrative Expense
Total stock based compensation expense
Stock-based compensation expense	$ 15,730	$ 11,902	$ 44,817	$ 38,575

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	9 Months Ended
	Sep. 30, 2024
Policy Text Blocks
Basis of Presentation	Basis of Presentation The unaudited interim condensed consolidated financial statements of the Company included herein have been prepared in accordance with accounting principles generally accepted in the U.S. (GAAP) as found in the Accounting Standards Codification (ASC), Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB) and the rules and regulations of the Securities and Exchange Commission (SEC). Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the financial statements as of and for the year ended December 31, 2023 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, filed with the SEC on February 15, 2024 (2023 Annual Report on Form 10-K). The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements, and updated, as necessary, in this report. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments that are necessary to present fairly the Company’s financial position as of September 30, 2024, the results of its operations for the three and nine months ended September 30, 2024 and 2023, stockholders’ equity for the three and nine months ended September 30, 2024 and 2023 and cash flows for the nine months ended September 30, 2024 and 2023. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended September 30, 2024 are not necessarily indicative of the results for the year ending December 31, 2024 or for any future period. The accompanying unaudited interim condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell and hold securities, Blueprint Medicines (Switzerland) GmbH, Blueprint Medicines (Netherlands) B.V., Blueprint Medicines (UK) Ltd., Blueprint Medicines (Germany) GmbH, Blueprint Medicines (Spain) S.L., Blueprint Medicines (France) SAS, and Blueprint Medicines (Italy) S.r.L. All intercompany transactions and balances have been eliminated.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies and in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates. Estimates are used in the following areas, among others: revenue recognition, inventory, operating lease right-of-use assets, operating lease liabilities, stock-based compensation expense, accrued expenses, liabilities related to the sale of future royalties and future revenues, equity investment, and income taxes. Actual results may differ from these estimates.
Significant Accounting Policies	Significant Accounting Policies The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and nine months ended September 30, 2024 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2023 Annual Report on Form 10-K, with the exception of the below new policy. Modification of debt instruments When the Company’s debt instrument, where the Company is the debtor, is modified or exchanged, the Company shall analyze whether the modification should be accounted for as a modification or an extinguishment. Modified terms are considered substantially different if, after an exchange or modification of debt instruments with the same creditor, the present value of cash flows under the terms of the new debt instrument differs by at least 10% from the present value of the remaining cash flows under the terms of the original debt instrument. If the modified instrument is considered substantially different from the original debt instrument, the modification or exchange is accounted for as an extinguishment. The new instrument is recorded at its fair value and that fair value is used to determine the extinguishment gain or loss.
Recent Accounting Pronouncements	Recent Accounting Pronouncements From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, the Company does not believe that the adoption of recently issued standards have or may have a material impact on its condensed consolidated financial statements and disclosures. In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures, which is intended to improve reportable segment disclosure requirements, primarily through additional disclosures about significant segment expenses. The standard is effective for fiscal years beginning after December 15, 2023, and interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The amendments will be applied retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the disclosure requirements related to this new standard. In December 2023, the FASB issued ASU 2023-09, Improvements to Income Tax Disclosures, which requires entities to disclose disaggregated information about their effective tax rate reconciliation and income taxes paid. The disclosure requirements will be applied on a prospective basis, with the option to apply them retrospectively. The standard is effective for fiscal years beginning after December 15, 2024, with early adoption permitted. The Company is currently evaluating the disclosure requirements related to this new standard.
Reclassification	Reclassification Certain items in the prior year’s condensed consolidated financial statements have been reclassified to conform to the current presentation.

Stockholders' Equity (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
Stockholders' Equity (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Feb. 28, 2022
Proceeds from Issuance or Sale of Equity [Abstract]
At-the-market facility, aggregate offering price					$ 300,000
At-the-market offerings, net of issuance costs (in shares)	0	0	544,719	0
Proceeds from at-the-market offerings, net of issuance costs			$ 48,936

Stock-based Compensation - Unvested Awards - Activity (Details)	9 Months Ended
	Sep. 30, 2024 $ / shares shares
Restricted Stock Units
Shares
Unvested at beginning of period (in shares) \| shares	2,107,026
Granted (in shares) \| shares	988,769
Vested (in shares) \| shares	(687,395)
Forfeited (in shares) \| shares	(134,699)
Unvested at end of period (in shares) \| shares	2,273,701
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share) \| $ / shares	$ 60.33
Granted (in dollars per share) \| $ / shares	95.99
Vested (in dollars per share) \| $ / shares	63.48
Forfeited (in dollars per share) \| $ / shares	69.87
Unvested at end of period (in dollars per share) \| $ / shares	$ 74.33
Performance-based restricted stock units
Shares
Unvested at beginning of period (in shares) \| shares	52,500
Granted (in shares) \| shares	90,000
Unvested at end of period (in shares) \| shares	142,500
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share) \| $ / shares	$ 59.32
Granted (in dollars per share) \| $ / shares	135.84
Unvested at end of period (in dollars per share) \| $ / shares	$ 107.65

Net Loss Per Share

9 Months Ended

Sep. 30, 2024

Net Loss Per Share

13. Net Loss per Share

Basic net loss per share is calculated by dividing net loss by the weighted average number of shares of common stock outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period. For purposes of the diluted net loss per share calculation, the effect of stock options, unvested restricted stock units, PSUs and ESPP shares on the weighted average number of shares is calculated using the treasury stock method. In periods with reported net operating losses, all common stock equivalents are deemed anti-dilutive such that basic net loss per share and diluted net loss per share are equal.

The following table sets forth the potential shares excluded from the calculation of net loss per share for the three and nine months ended September 30, 2024 and 2023 because their inclusion would be anti-dilutive (in thousands):


	September 30,
	2024	2023
Stock options	6,498	6,984
Restricted stock units	2,274	2,093
Performance-based restricted stock units	143	53
ESPP shares	27	47
Total	8,942	9,177

Product Revenue (Tables)

9 Months Ended

Sep. 30, 2024

Schedules of concentration of risk


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Customer 1	38	%	42	%	39	%	42	%
Customer 2	14	%	*	%	12	%	*	%
Customer 3	11	%	11	%	*	%	11	%

* Indicates the customer’s share is under 10%.


	September 30,		December 31,
	2024		2023
Customer 1	27	%	34	%
Customer 2	15	%	*	%
Customer 3	12	%	11	%
Customer 4	*	%	10	%
Customer 5	*	%	10	%

* Indicates the customer’s share is under 10%.

Product revenue, net

Summary of revenue recognized


	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2024		2023		2024		2023
United States	$	113,133	$	49,121	$	297,731	$	118,355
Rest of World		15,051		5,107		37,094		14,818
Total product revenue	$	128,184	$	54,228	$	334,825	$	133,173

Schedule of product revenue allowance and reserve categories


	Nine Months Ended September 30,
	2024		2023
Beginning balance at January 1	$	19,274	$	9,788
Provision related to sales in the current period		58,911		25,874
Adjustment related to prior periods sales		(171)		(545)
Credits and payments made		(43,326)		(17,469)
Ending balance at September 30	$	34,688	$	17,648


	September 30,		December 31,
	2024		2023
Reduction of accounts receivable, net	$	3,512	$	1,809
Component of accrued expenses		31,176		17,465
Total revenue-related reserves	$	34,688	$	19,274

Condensed Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Total
Beginning Balance at Dec. 31, 2022	$ 60	$ 2,358,018	$ (10,443)	$ (1,832,958)	$ 514,677
Beginning Balance (in shares) at Dec. 31, 2022	59,958,919
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan (in shares)	457,416
Stock-based compensation expense		23,340			23,340
Other comprehensive income (loss)			5,841		5,841
Net income (loss)				(129,560)	(129,560)
Ending Balance at Mar. 31, 2023	$ 60	2,381,358	(4,602)	(1,962,518)	414,298
Ending Balance (in shares) at Mar. 31, 2023	60,416,335
Beginning Balance at Dec. 31, 2022	$ 60	2,358,018	(10,443)	(1,832,958)	$ 514,677
Beginning Balance (in shares) at Dec. 31, 2022	59,958,919
Increase (Decrease) in Stockholders' Equity
At-the-market offerings, net of issuance costs (in shares)					0
Net income (loss)					$ (396,068)
Ending Balance at Sep. 30, 2023	$ 61	2,434,258	(2,683)	(2,229,025)	202,611
Ending Balance (in shares) at Sep. 30, 2023	60,740,744
Beginning Balance at Mar. 31, 2023	$ 60	2,381,358	(4,602)	(1,962,518)	414,298
Beginning Balance (in shares) at Mar. 31, 2023	60,416,335
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan and stock purchase plan	$ 1	5,298			5,299
Issuance of common stock under stock plan and stock purchase plan (in shares)	221,940
Stock-based compensation expense		23,945			23,945
Other comprehensive income (loss)			381		381
Net income (loss)				(132,794)	(132,794)
Ending Balance at Jun. 30, 2023	$ 61	2,410,601	(4,221)	(2,095,312)	311,129
Ending Balance (in shares) at Jun. 30, 2023	60,638,275
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		445			$ 445
Issuance of common stock under stock plan (in shares)	102,469
At-the-market offerings, net of issuance costs (in shares)					0
Stock-based compensation expense		23,212			$ 23,212
Other comprehensive income (loss)			1,538		1,538
Net income (loss)				(133,713)	(133,713)
Ending Balance at Sep. 30, 2023	$ 61	2,434,258	(2,683)	(2,229,025)	202,611
Ending Balance (in shares) at Sep. 30, 2023	60,740,744
Beginning Balance at Dec. 31, 2023	$ 61	2,473,985	(3,495)	(2,339,942)	$ 130,609
Beginning Balance (in shares) at Dec. 31, 2023	61,147,236				61,147,236
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan	$ 1	17,900			$ 17,901
Issuance of common stock under stock plan (in shares)	902,292
At-the-market offerings, net of issuance costs	$ 1	48,935			48,936
At-the-market offerings, net of issuance costs (in shares)	544,719
Stock-based compensation expense		24,457			24,457
Other comprehensive income (loss)			(352)		(352)
Net income (loss)				89,136	89,136
Ending Balance at Mar. 31, 2024	$ 63	2,565,277	(3,847)	(2,250,806)	310,687
Ending Balance (in shares) at Mar. 31, 2024	62,594,247
Beginning Balance at Dec. 31, 2023	$ 61	2,473,985	(3,495)	(2,339,942)	$ 130,609
Beginning Balance (in shares) at Dec. 31, 2023	61,147,236				61,147,236
Increase (Decrease) in Stockholders' Equity
At-the-market offerings, net of issuance costs (in shares)					544,719
Net income (loss)					$ (17,133)
Ending Balance at Sep. 30, 2024	$ 63	2,671,231	(1,070)	(2,357,076)	$ 313,148
Ending Balance (in shares) at Sep. 30, 2024	63,454,673				63,454,673
Beginning Balance at Mar. 31, 2024	$ 63	2,565,277	(3,847)	(2,250,806)	$ 310,687
Beginning Balance (in shares) at Mar. 31, 2024	62,594,247
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan and stock purchase plan		31,337			31,337
Issuance of common stock under stock plan and stock purchase plan (in shares)	571,478
Stock-based compensation expense		28,275			28,275
Other comprehensive income (loss)			(43)		(43)
Other		(21)			(21)
Net income (loss)				(49,994)	(49,994)
Ending Balance at Jun. 30, 2024	$ 63	2,624,868	(3,890)	(2,300,800)	320,241
Ending Balance (in shares) at Jun. 30, 2024	63,165,725
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan		17,799			$ 17,799
Issuance of common stock under stock plan (in shares)	288,948
At-the-market offerings, net of issuance costs (in shares)					0
Stock-based compensation expense		28,564			$ 28,564
Other comprehensive income (loss)			2,820		2,820
Net income (loss)				(56,276)	(56,276)
Ending Balance at Sep. 30, 2024	$ 63	$ 2,671,231	$ (1,070)	$ (2,357,076)	$ 313,148
Ending Balance (in shares) at Sep. 30, 2024	63,454,673				63,454,673

Marketable Securities

9 Months Ended

Sep. 30, 2024

Marketable Securities

4. Marketable Securities

Marketable securities consisted of the following at September 30, 2024 and December 31, 2023 (in thousands):


	Amortized		Unrealized		Unrealized		Fair
September 30, 2024	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	133,228	$	292	$	(32)	$	133,488
U.S. treasury obligations		657,530		2,006		(27)		659,509
Total	$	790,758	$	2,298	$	(59)	$	792,997


	Amortized		Unrealized		Unrealized		Fair
December 31, 2023	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	170,194	$	27	$	(418)	$	169,803
U.S. treasury obligations		525,880		588		(386)		526,082
Total	$	696,074	$	615	$	(804)	$	695,885

The following table summarizes the amortized cost basis and estimated fair value of the Company’s available-for-sale securities by contractual maturity as of September 30, 2024 and December 31, 2023 (in thousands):


	September 30, 2024				December 31, 2023
	Amortized		Fair		Amortized		Fair
	Cost		value		Cost		value
Within one year	$	643,209	$	644,817	$	639,881	$	639,355
After one through five years		147,549		148,180		56,193		56,530
Total	$	790,758	$	792,997	$	696,074	$	695,885

As of September 30, 2024 and December 31, 2023, the Company held 22 and 62 debt securities, respectively, that were in an unrealized loss position. The following table summarizes the estimated fair value and the aggregate unrealized loss of the Company’s available-for-sale securities that are in loss position as of September 30, 2024 and December 31, 2023 by the length of time the security has been in loss position (in thousands):


	September 30, 2024				December 31, 2023
	Fair		Unrealized		Fair		Unrealized
	value		losses		value		losses
Debt securities in unrealized loss position for 12 months or less	$	75,525	$	(46)	$	267,917	$	(550)
Debt securities in unrealized loss position for more than 12 months		29,942		(13)		64,659		(254)
Total debt securities	$	105,467	$	(59)	$	332,576	$	(804)

The Company has the intent and ability to hold its debt securities until recovery of amortized cost basis. As a result, the Company did not recognize any differences between the fair value and amortized cost basis as a loss in its condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2024 and 2023. The Company did not record any credit-related impairments for its available-for-sale securities for the three and nine months ended September 30, 2024 and 2023.

The following table summarizes the proceeds from maturities of debt securities during the three and nine months ended September 30, 2024 and 2023 (in thousands):


	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Proceeds from maturities of debt securities	$	231,000	$	237,600	$	679,150	$	855,365

The Company did not realize any gains or losses from maturities of debt securities for the three and nine months ended September 30, 2024 and 2023.

Stockholders' Equity

9 Months Ended

Sep. 30, 2024

Stockholders' Equity

11. Stockholders’ Equity

In February 2022, the Company entered into an at-the-market (ATM) Facility with Cowen and Company, LLC (Cowen), pursuant to which the Company may offer and sell, from time to time at its sole discretion, shares of its common stock having an aggregate offering price of up to $300.0 million through Cowen as sales agent. The Company did not issue any shares under the ATM Facility during the three months ended September 30, 2024. During the nine months ended September 30, 2024, the Company issued and sold 544,719 shares of its common stock under the ATM Facility and received net proceeds of $48.9 million. The Company did not issue any shares under the ATM Facility during the three and nine months ended September 30, 2023.

The entire disclosure for equity.

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
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Fair Value of Financial Instruments

9 Months Ended

Sep. 30, 2024

Fair Value of Financial Instruments

5. Fair Value of Financial Instruments

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of September 30, 2024 (in thousands):


			Active		Observable		Unobservable
	September 30,		Markets		Inputs		Inputs
Description	2024		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	57,153	$	57,153	$	—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		133,488		—		133,488		—
U.S. treasury obligations		659,509		659,509		—		—
Total	$	850,150	$	716,662	$	133,488	$	—

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2023 (in thousands):


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2023		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	55,412	$	55,412	$	—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		169,803		—		169,803		—
U.S. treasury obligations		526,082		526,082		—		—
Total	$	751,297	$	581,494	$	169,803	$	—

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.

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