0001558370-23-012897 | 10-Q | XBRL Viewer

Inventory

7. Inventory

Capitalized inventory consists of the following at June 30, 2023 and December 31, 2022 (in thousands):


	June 30,		December 31,
	2023		2022
Raw materials	$	1,599	$	4,967
Work in process		32,750		28,427
Finished goods		2,589		2,791
Total	$	36,938	$	36,185

Balance sheet classification


	June 30,		December 31,
	2023		2022
Inventory	$	17,016	$	29,697
Other assets		19,922		6,488
Total	$	36,938	$	36,185

Inventory amounts written down as a result of excess, obsolescence, unmarketability or other reasons are charged to cost of sales. The Company recognized a write-down of $0.5 million and $2.0 million for the three and six months ended June 30, 2023, respectively. The Company did not recognize any write-down for the three and six months ended June 30, 2022. Long-term inventory, which primarily consists of work in process and raw materials, is included in other assets in the unaudited condensed consolidated balance sheets.

Stock-based Compensation - Unvested Awards - Activity (Details)	6 Months Ended
	Jun. 30, 2023 $ / shares shares
Restricted Stock Units
Shares
Unvested at beginning of period (in shares) \| shares	1,893,944
Granted (in shares) \| shares	851,876
Vested (in shares) \| shares	(524,345)
Forfeited (in shares) \| shares	(72,401)
Unvested at end of period (in shares) \| shares	2,149,074
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share) \| $ / shares	$ 73.28
Granted (in dollars per share) \| $ / shares	44.07
Vested (in dollars per share) \| $ / shares	72.51
Forfeited (in dollars per share) \| $ / shares	65.62
Unvested at end of period (in dollars per share) \| $ / shares	$ 62.16
Performance-based restricted stock units
Shares
Unvested at beginning of period (in shares) \| shares	0
Granted (in shares) \| shares	52,500
Unvested at end of period (in shares) \| shares	52,500
Weighted-Average Grant Date Fair Value
Unvested at beginning or period (in dollars per share) \| $ / shares	$ 0
Granted (in dollars per share) \| $ / shares	59.32
Unvested at end of period (in dollars per share) \| $ / shares	$ 59.32

Stock-based Compensation - 2015 Stock Option and Incentive Plan (Details) - 2015 Stock Option and Incentive Plan - shares		6 Months Ended
	Jan. 01, 2023	Jun. 30, 2023	Apr. 08, 2015
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)	2,398,356
Number of shares available for grant (in shares)		4,839,806

Condensed Consolidated Statements of Cash Flows (Parenthetical) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022	Jun. 30, 2022	Dec. 31, 2021
Reconciliation of cash, cash equivalents, and restricted cash
Cash and cash equivalents	$ 75,527	$ 119,709	$ 173,399
Restricted cash	6,352	5,195	5,171
Total cash, cash equivalents, and restricted cash shown in condensed consolidated statements of cash flows	$ 81,879	$ 124,904	$ 178,570	$ 215,119

Restricted Cash (Details) - USD ($) $ in Millions	Jun. 30, 2023	Dec. 31, 2022
Restricted cash
Restricted cash	$ 6.4	$ 5.2

Marketable Securities - Unrealized Loss Positions (Details) $ in Thousands	Jun. 30, 2023 USD ($) security	Dec. 31, 2022 USD ($) security
Unrealized loss position, aggregate fair value
Unrealized loss position for less than 12 months, aggregate fair value \| $	$ 625,248	$ 371,746
Unrealized loss position for more than 12 months, aggregate fair value \| $	96,291	550,561
Unrealized loss position, aggregate fair value \| $	$ 721,539	$ 922,307
Unrealized loss position, number of positions
Number of held securities in an unrealized loss position for less than 12 months \| security	110	66
Number of held securities in an unrealized loss position for 12 months or longer \| security	14	56
Number of held securities in an unrealized loss position \| security	124	122

Collaboration and License Agreements - Performance Obligations (Details) - Collaborative Arrangement	6 Months Ended
	Jun. 30, 2023 item component
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 promises, number	1
Collaborative arrangement, material promises, manufacturing activities, term	24 months
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

Income Taxes - Unrecognized Tax Benefits (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Unrecognized tax benefits
Unrecognized tax benefits	$ 200	$ 0

Collaboration and License Agreements - Equity Investment (Details) - USD ($) $ in Thousands	Aug. 01, 2022	Jun. 30, 2023	Dec. 31, 2022
Equity Investment
Equity investment		$ 27,789	$ 27,789
Collaborative Arrangement \| IDRx, Inc. \| Director
Equity Investment
Equity investment, license agreement, shares received (in shares)	4,509,105
Equity investment	$ 27,800	$ 27,800
Equity investment, transaction costs	$ 300

Net Loss Per Share (Tables)

6 Months Ended

Jun. 30, 2023

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


	June 30,
	2023	2022
Stock options	7,070	6,387
Restricted stock units	2,149	1,857
Performance-based restricted stock units	53	—
ESPP shares	47	46
Total	9,319	8,290

Stock-based Compensation - Stock Options - Activity (Details)	6 Months Ended
	Jun. 30, 2023 $ / shares shares
Shares
Outstanding at beginning of period (in shares) \| shares	6,233,451
Granted (in shares) \| shares	1,126,487
Exercised (in shares) \| shares	(97,004)
Cancelled (in shares) \| shares	(192,527)
Outstanding at end of period (in shares) \| shares	7,070,407
Weighted-Average Exercise Price
Outstanding at beginning of period (in dollars per share) \| $ / shares	$ 69.14
Granted (in dollars per share) \| $ / shares	44.54
Exercised (in dollars per share) \| $ / shares	30.48
Cancelled (in dollars per share) \| $ / shares	72.40
Outstanding at end of period (in dollars per share) \| $ / shares	$ 65.67
Additional disclosures
Shares - Exercisable (in shares) \| shares	4,594,568
Weighted-Average Exercise Price - Exercisable (in dollars per share) \| $ / shares	$ 68.34

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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Stock-based Compensation - Performance-based Restricted Stock Units (Details) - Performance-based restricted stock units	6 Months Ended
	Jun. 30, 2023
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%

Accrued Expenses

6 Months Ended

Jun. 30, 2023

Accrued Expenses

9. Accrued Expenses

Accrued expenses consist of the following (in thousands):


	June 30,		December 31,
	2023		2022
Research, development and commercial contract costs	$	40,401	$	66,041
Employee compensation		26,179		30,744
Accrued professional fees		13,516		17,588
Revenue-related reserves		13,555		9,046
Other		7,511		7,704
Total	$	101,162	$	131,123

Collaboration and License Agreements - General Information (Details) $ in Thousands				1 Months Ended		2 Months Ended	3 Months Ended			6 Months Ended		36 Months Ended	86 Months Ended
	Feb. 26, 2022 USD ($) item Program	Oct. 15, 2019 USD ($)	Jun. 01, 2018 USD ($) item	Oct. 31, 2019 USD ($)	Mar. 31, 2016 USD ($) Program Right	Dec. 31, 2021 USD ($)	Jun. 30, 2023 USD ($)	Jun. 30, 2022 USD ($)	Sep. 30, 2020 USD ($)	Jun. 30, 2023 USD ($)	Jun. 30, 2022 USD ($)	Jun. 30, 2023 USD ($)	Apr. 30, 2023 Program	Dec. 31, 2022 USD ($)	Nov. 08, 2021 USD ($)	Jul. 13, 2020
Collaboration Agreements
Prepaid expenses and other current assets							$ 33,418			$ 33,418		$ 33,418		$ 35,024
Research and development expense							110,063	$ 128,466		222,135	$ 231,599
Collaborative Arrangement \| IDRx, Inc. \| Director
Collaboration Agreements
Collaborative arrangement, milestones, potential contingent payments							217,500			$ 217,500		217,500
Collaborative arrangement, termination, counterparty written notice period										12 months
Collaborative Arrangement \| Proteovant
Collaboration Agreements
Collaborative arrangement, upfront payment	$ 20,000
Collaborative arrangement, milestones, potential contingent payments	632,000
Prepaid expenses and other current assets	$ 20,000
Research and development expense							4,300	$ 1,000		$ 5,700	$ 1,500
Collaborative arrangement, jointly research and advance novel protein degrader therapies into development candidates, number \| item	2
Collaborative arrangement, jointly research and advance additional novel protein degrader target programs, number \| Program	2
Collaborative Arrangement \| Zai Lab (Shanghai) Co., Ltd.
Collaboration 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 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 \| Roche, Collaboration and License (Immunotherapy) Agreement
Collaboration Agreements
Collaborative arrangement, upfront payment, cash payment received					$ 45,000
Collaborative arrangement, milestones, cash payments received, aggregate							25,000			25,000		25,000
Collaborative arrangement, milestones, research milestones, achieved							25,000			25,000		25,000
Collaborative arrangement, option rights, maximum \| Right					5
Collaborative arrangement, development programs, terminated \| Program													4
Collaborative arrangement, development programs \| Program					5
Collaborative arrangement, agreement termination, clinical development costs payment commitment reduction										5,300
Collaborative Arrangement \| Clementia
Collaboration 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 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

Commitments and Contingencies

6 Months Ended

Jun. 30, 2023

Commitments and Contingencies

15. Commitments and Contingencies

Purchase Commitments Associated with 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. During the six months ended June 30, 2023, there was a decrease of $7.3 million in the Company’s contractual obligations described in Note 18 to the consolidated financial statements in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2022.

Legal Proceedings

The Company is not currently a party to any material legal proceedings. At each reporting date, the Company evaluates whether or not a potential loss amount or a potential range of loss is probable and reasonably estimable under the provisions of the authoritative guidance that addresses accounting for contingencies. The Company expenses the costs related to its legal proceedings as they are incurred.

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 June 30, 2023 or December 31, 2022.

Marketable Securities

6 Months Ended

Jun. 30, 2023

Marketable Securities

4. Marketable Securities

Marketable securities consisted of the following at June 30, 2023 and December 31, 2022 (in thousands):


	Amortized		Unrealized		Unrealized		Fair
June 30, 2023	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	241,322		—		(1,795)	$	239,527
U.S. treasury obligations		523,485		7		(1,980)		521,512
Total	$	764,807	$	7	$	(3,775)	$	761,039


	Amortized		Unrealized		Unrealized		Fair
December 31, 2022	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	377,519		—		(4,848)	$	372,671
U.S. treasury obligations		591,193		22		(5,123)		586,092
Total	$	968,712	$	22	$	(9,971)	$	958,763

The following table summarizes the estimated fair value (in thousands) and number of the Company’s available-for-sale securities that are in loss position as of June 30, 2023 and December 31, 2022 by the length of time the security has been in loss position:


	June 30, 2023				December 31, 2022
	Fair		Number of		Fair		Number of
	value		securities		value		securities
Debt securities in unrealized loss position for 12 months or less	$	625,248		110	$	371,746		66
Debt securities in unrealized loss position for more than 12 months		96,291		14		550,561		56
Total debt securities in unrealized loss position	$	721,539		124	$	922,307		122

The Company has the intent and ability to hold its debt securities until recovery. As a result, the Company did not record any charges for credit-related impairments for its marketable debt securities for the three and six months ended June 30, 2023 and 2022.

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 June 30, 2023 and December 31, 2022 (in thousands):


	June 30, 2023				December 31, 2022
	Amortized		Fair		Amortized		Fair
	Cost		value		Cost		value
Within one year	$	649,622	$	647,107	$	834,440	$	825,283
After one through five years		115,185		113,932		134,272		133,480
Total	$	764,807	$	761,039	$	968,712	$	958,763

The following table summarizes the proceeds from maturities of debt securities during the three and six months ended June 30, 2023 and 2022 (in thousands):


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Proceeds from maturities of debt securities	$	309,515	$	79,623	$	617,765	$	79,623

The Company did not realize any gains or losses from maturities of debt securities for the three and six months ended June 30, 2023 and 2022.

Product Revenue Reserves and Allowances - Concentration Risk (Details)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022	Dec. 31, 2022
Revenue from Contract with Customer Benchmark \| Customer Concentration Risk \| Customer One
Concentration Risk
Concentration risk (as a percent)	41.00%	44.00%	42.00%	46.00%
Revenue from Contract with Customer Benchmark \| Customer Concentration Risk \| Customer Two
Concentration Risk
Concentration risk (as a percent)	11.00%	11.00%	11.00%	11.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer One
Concentration Risk
Concentration risk (as a percent)			34.00%		33.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Two
Concentration Risk
Concentration risk (as a percent)			11.00%		15.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Three
Concentration Risk
Concentration risk (as a percent)					12.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Three \| Maximum
Concentration Risk
Concentration risk (as a percent)			10.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Four
Concentration Risk
Concentration risk (as a percent)			10.00%
Accounts Receivable, Net \| Credit Concentration Risk \| Customer Four \| Maximum
Concentration Risk
Concentration risk (as a percent)					10.00%

Collaboration and License Agreements - Reduction in Expenses (Details) - Collaborative Arrangement - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Roche, Collaboration (Pralsetnib) Agreement
Collaboration Agreements
Collaborative arrangement, commercialization, reduction in selling, general and administrative expenses	$ 2,774	$ 4,416	$ 5,555	$ 9,248
Collaborative arrangement, global development activities, increases in research and development expenses	$ 5,347	3,714	$ 13,623	3,704
C Stone
Collaboration Agreements
Collaborative arrangement, reduction in manufacturing and research and development expenses		$ 600		$ 1,200

Commitments and Contingencies - Indemnification Agreements (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Indemnification Agreement
Indemnification Agreements
Loss contingency accrual	$ 0	$ 0

Marketable Securities - Realized Gains (Losses) (Details) - USD ($) $ in Thousands	3 Months Ended
	Jun. 30, 2023	Jun. 30, 2022
Realized gains (losses) from maturities of debt securities
Realized gains (losses) from maturities of debt securities	$ 0	$ 0

Financing Arrangements

6 Months Ended

Jun. 30, 2023

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. 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 U.S. territory under the terms of the Roche pralsetinib collaboration agreement.

Although the Company sold all of the rights to receive royalties on the net sales of GAVRETO worldwide excluding the CStone Territory and U.S. territory to Royalty Pharma, the Company continues to co-develop pralsetinib with Roche globally and is therefore involved in the generation of these future royalties. Due to the Company’s significant continuing involvement, the Company continues to account for any royalties and development and commercialization milestones earned related to the underlying territory under the Roche pralsetinib collaboration agreement as collaboration revenue on its consolidated statements of operations and comprehensive loss. Net proceeds 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 $175.0 million, net of transaction costs of $3.8 million, to the total of these royalties as interest expense using the effective interest method over the estimated life of the arrangement. These

estimates contain assumptions that impact the amount recorded and the interest expense that will be recognized in future periods.

As payments are made to Royalty Pharma, the balance of the liability will be effectively repaid over the life of the Royalty Purchase Agreement. In order to determine the amortization of the liability, the Company estimates the total amount of future royalty payments to be paid to Royalty Pharma over the life of the arrangement. The exact amount of repayment is likely to change each reporting period. A significant increase or decrease in GAVRETO’s net revenue of the underlying territory will impact interest expense and the liability related to this arrangement. The Company periodically assesses the expected payments to Royalty Pharma and prospectively adjusts the amortization of the liability related to this arrangement for material changes in such payments including the prospective impact around the uncertainty related to GAVRETO’s commercial outlook in the underlying territory during the life of the arrangement.

In February 2023, the Company received written notice from Roche of their election to terminate for convenience the Roche pralsetinib collaboration agreement. The termination will become effective February 2024, at which time the Company will regain commercialization and development rights to GAVRETO from Roche worldwide excluding the CStone Territory. As of June 30, 2023, none of the derecognition conditions under ASC 405 Liabilities were met, and in consideration of the significant uncertainties related to GAVRETO’s commercial outlook in the underlying territory during the life of the arrangement caused by the termination of the Roche pralsetinib collaboration agreement, during the three and six months ended June 30, 2023, the Company did not accrete any interest expenses related to the liability. As of June 30, 2023, the net carrying value of the liability related to this arrangement was $175.6 million.

Pursuant to the Royalty Purchase Agreement, the Company is eligible to receive certain milestone payments totaling up to $165.0 million, subject to the achievement of specified net sales milestones by Roche. However, following the termination of the Roche pralsetinib collaboration agreement, if the specified net sales milestone thresholds under the Royalty Purchase Agreement with Royalty Pharma are not otherwise met, the Company may no longer be eligible to receive any of the contingent milestone payments under the Royalty Purchase Agreement. The potential milestone payments will be added to the carrying value of the liability related to this arrangement when and if the milestones are achieved and received.

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 financing transaction for up to $660.0 million (as amended, Financing Agreement) with Sixth Street Partners (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 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 June 30, 2023, the Company’s estimate of this total interest expense resulted in an effective annual interest rate of 10.8%. These estimates contain assumptions that impact the amount recorded and the interest expense that will be recognized in future periods.

As of June 30, 2023, the net carrying value of the liability related to this arrangement was $261.7 million. The following table shows the activity within the liability account (in thousands):


Carrying value as of January 1, 2023	$	254,328
Interest expense recognized		14,021
Payments		(6,644)
Carrying value as of June 30, 2023	$	261,705

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.

As part of the Financing Agreement with Sixth Street Partners, the Company received gross proceeds of $150.0 million in July 2022 and incurred an aggregate of $12.2 million of debt discounts and transaction costs, which 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. As of June 30, 2023, the Company’s estimate of the total interest expense resulted in an effective annual interest rate of 13.6%. The carrying amount of the debt as of June 30, 2023 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):


Carrying value as of January 1, 2023	$	139,083
Interest expense recognized		9,443
Payments		(8,523)
Carrying value as of June 30, 2023	$	140,003

The Company’s obligations under the Financing Agreement are secured, subject to certain exceptions, by security interests in the substantially all of the Company’s assets and the Company’s certain 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 (i) $50.0 million during the period commencing from the date on which the term loans are funded to the date which is the day before the next term loans are funded and (ii) $80.0 million for each day thereafter. As of

June 30, 2023, the Company was in compliance with the applicable terms and conditions of the covenants under the Financing Arrangement.

Inventory - Capitalized (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Inventory
Raw materials	$ 1,599	$ 4,967
Work in process	32,750	28,427
Finished goods	2,589	2,791
Total	$ 36,938	$ 36,185

Accrued Expenses (Tables)

6 Months Ended

Jun. 30, 2023

Schedule of accrued expenses


	June 30,		December 31,
	2023		2022
Research, development and commercial contract costs	$	40,401	$	66,041
Employee compensation		26,179		30,744
Accrued professional fees		13,516		17,588
Revenue-related reserves		13,555		9,046
Other		7,511		7,704
Total	$	101,162	$	131,123

Collaboration and License Agreements - Sale of Stock (Details) - Private Placement $ / shares in Units, $ in Millions	Jul. 13, 2020 USD ($) $ / shares shares
Sale of Stock
Stock issued (in shares) \| shares	1,035,519
Share price (in dollars per share) \| $ / shares	$ 96.57
Purchase consideration	$ 100.0
Issuance of common stock	79.3
Share purchase consideration, premium	$ 20.7

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

6 Months Ended

Jun. 30, 2023

Nature of Business

1. Nature of Business

Blueprint Medicines Corporation (the Company), a Delaware corporation incorporated on October 14, 2008, is a precision therapy company focused on genomically defined cancers and blood disorders. The Company’s approach is to leverage its novel research engine to systematically and reproducibly identify drivers of diseases in genomically defined patient populations, and to craft highly selective and potent drug candidates that are intended to provide significant and durable clinical responses to patients.

The Company has two approved precision therapies and is globally advancing multiple programs for systemic mastocytosis (SM), lung cancer, breast cancer and other genomically defined cancers, and cancer immunotherapy. The Company is devoting substantially all of its efforts to research and development for current and future drug candidates and commercialization of AYVAKIT/AYVAKYT, GAVRETO and any current or future drug candidates that obtain marketing approval.

As of June 30, 2023, the Company had cash, cash equivalents and marketable securities of $836.6 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.

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022
Cash flows from operating activities
Net loss	$ (262,354)	$ (265,709)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization	7,262	3,098
Non-cash lease expense	4,457	4,107
Stock-based compensation	47,017	48,746
Non-cash interest expense	8,297
Other	(3,611)	550
Changes in assets and liabilities:
Accounts receivable	(13,105)	(2,128)
Unbilled accounts receivable	10,291	9,591
Inventory	(8,112)	(14,694)
Prepaid expenses and other current assets	1,678	(16,314)
Other assets	(1,419)	(13,188)
Accounts payable	4,218	6,589
Accrued expenses	(25,694)	441
Other long-term liabilities	(7,238)	6,157
Deferred revenue	(9,963)	(14,438)
Operating lease liabilities	(5,160)	(3,790)
Net cash used in operating activities	(253,436)	(250,982)
Cash flows from investing activities
Purchases of property and equipment	(5,138)	(3,709)
Purchases of investments	(407,770)	(39,937)
Maturities of investments	617,765	79,623
Net cash provided by investing activities	204,857	35,977
Cash flows from financing activities
Gross proceeds from the sale of future royalties		175,000
Net proceeds from stock option exercises and employee stock purchase plan	5,298	3,762
Net cash provided by financing activities	5,298	178,762
Net decrease in cash, cash equivalents, and restricted cash	(43,281)	(36,243)
Cash, cash equivalents and restricted cash at beginning of period	124,904	215,119
Effect of exchange rate changes on cash, cash equivalents and restricted cash	256	(306)
Cash, cash equivalents and restricted cash at end of period	81,879	178,570
Supplemental cash flow information
Cash paid for interest	15,167
Debt issuance costs incurred but unpaid at period end		5,022
Property and equipment purchases unpaid at period end	2,603	1,829
Cash paid for taxes, net	$ 676	$ 771

Product Revenue Reserves and Allowances - Revenue-related Reserves (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022	Jun. 30, 2022	Dec. 31, 2021
Revenue-related reserves
Revenue-related reserves	$ 14,812	$ 9,788	$ 7,063	$ 4,345
Accounts Receivable, Net
Revenue-related reserves
Revenue-related reserves	1,257	742
Accrued Expenses
Revenue-related reserves
Revenue-related reserves	$ 13,555	$ 9,046

Stock-based Compensation

6 Months Ended

Jun. 30, 2023

Stock-based Compensation

11. Stock-based Compensation

2015 Stock Option and Incentive Plan

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 provides that the number of shares reserved and available for issuance under the 2015 Plan will 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, 2023, the number of shares reserved for issuance under the 2015 Plan was increased by 2,398,356 shares. In addition, the total number of shares reserved for issuance is subject to adjustment in the event of a stock split, stock dividend or other change in the Company’s capitalization. As of June 30, 2023, there were 4,839,806 shares available for future grant under the 2015 Plan.

2020 Inducement Plan

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. 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. The number of shares reserved and available for issuance under the Inducement Plan can be increased at any time with the approval of the Company’s board of directors. The Inducement Plan permits the board of directors or a committee thereof to use the stock-based awards available under the Inducement Plan to attract key employees for the growth of the Company. As of June 30, 2023, there were 1,382,793 shares available for future grant under the Inducement Plan.

Stock options

The following table summarizes the stock option activity for the six months ended June 30, 2023:


		Weighted-Average
	Shares		Exercise Price
Outstanding at December 31, 2022	6,233,451	$	69.14
Granted	1,126,487		44.54
Exercised	(97,004)		30.48
Canceled	(192,527)		72.40
Outstanding at June 30, 2023	7,070,407	$	65.67
Exercisable at June 30, 2023	4,594,568	$	68.34

As of June 30, 2023, the total unrecognized compensation expense related to unvested stock option awards was $78.2 million, which is expected to be recognized over a weighted-average period of approximately 2.75 years.

Restricted stock units

The following table summarizes the restricted stock units activity for the six months ended June 30, 2023:


		Weighted-Average
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2022	1,893,944	$	73.28
Granted	851,876		44.07
Vested	(524,345)		72.51
Forfeited	(72,401)		65.62
Unvested shares at June 30, 2023	2,149,074	$	62.16

As of June 30, 2023, the total unrecognized compensation expense related to unvested restricted stock units was $112.5 million, which is expected to be recognized over a weighted-average period of approximately 2.75 years.

Performance-based restricted stock units

During the first quarter of 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 based 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 six months ended June 30, 2023:


		Weighted-Average
		Grant Date
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2022	—	$	—
Granted	52,500		59.32
Vested	—		—
Forfeited	—		—
Unvested shares at June 30, 2023	52,500	$	59.32

As of June 30, 2023, the total unrecognized compensation expense related to unvested PSUs was $2.8 million, which is expected to be recognized over a weighted-average period of approximately 2.67 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.

2015 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, 2023, the number of shares reserved for issuance under the 2015 ESPP was increased by 599,589 shares.

Stock-based compensation expense

The Company recognized stock-based compensation expense of $23.8 million and $47.0 million for the three and six months ended June 30, 2023, respectively, and $25.3 million and $48.7 million for the three and six months ended June 30, 2022, 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				Six Months Ended
		June 30,				June 30,
		2023		2022		2023		2022
Stock options	$	10,337	$	12,811	$	21,197	$	25,755
Restricted stock units		12,913		12,396		24,853		22,782
Performance-based restricted stock units		257		—		344
Employee stock purchase plan		438		317		891		596
Subtotal		23,945		25,524		47,285		49,133
Capitalized stock-based compensation costs		(124)		(177)		(268)		(387)
Stock-based compensation expense included in total cost and operating expenses	$	23,821	$	25,347	$	47,017	$	48,746

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				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Research and development	$	10,227	$	10,497	$	20,344	$	20,538
Selling, general and administrative		13,594		14,850		26,673		28,208
Total	$	23,821	$	25,347	$	47,017	$	48,746

Commitments and Contingencies - Purchase Commitments (Details) $ in Millions	6 Months Ended
	Jun. 30, 2023 USD ($)
Manufacturing Agreement, October 2020
Manufacturing Agreements
Unrecorded unconditional purchase obligation, period increase (decrease)	$ (7.3)

Income Taxes - Financing Arrangements (Details) - Sale of Future Royalties and Revenues - USD ($) $ in Millions		1 Months Ended	12 Months Ended
	Jun. 30, 2022	Jul. 31, 2022	Dec. 31, 2022
Gross Proceeds
Gross proceeds			$ 425.0
Royalty Pharma, Royalty Purchase Agreement
Gross Proceeds
Gross proceeds	$ 175.0
Sixth Street Partners, Future Revenue Purchase Agreement
Gross Proceeds
Gross proceeds		$ 250.0

Leases - Weighted Average Remaining Lease-term and Weighted Average Discount Rate (Details)	Jun. 30, 2023
Leases
Weighted average remaining lease term in years	6 years 3 months 18 days
Weighted average discount rate	7.40%

Inventory - Write-down (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
Inventory - Write-down (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Inventory
Inventory write-down	$ 500	$ 0	$ 2,000	$ 0

Stock-based Compensation - Employee Stock Purchase Plan (Details) - Employee Stock - shares	1 Months Ended
	May 31, 2015	Jan. 01, 2023
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)		599,589

Collaboration and License Agreements - Transaction Price (Details) - Collaborative Arrangement - USD ($) $ in Millions				1 Months Ended	2 Months Ended	6 Months Ended
	Jul. 13, 2020	Oct. 15, 2019	Jun. 01, 2018	Mar. 31, 2016	Dec. 31, 2021	Jun. 30, 2023	Jun. 30, 2022
Zai Lab (Shanghai) Co., Ltd.
Collaboration Agreements
Collaborative arrangement, transaction price					$ 25.0
Roche, Collaboration (Pralsetnib) Agreement
Collaboration 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 Agreements
Collaborative arrangement, transaction price				$ 45.0
Collaborative arrangement, transaction price, payment commitment reduction							$ 15.0
Collaborative arrangement, transaction price, increase						$ 9.7
Clementia
Collaboration Agreements
Collaborative arrangement, transaction price		$ 46.5
C Stone
Collaboration Agreements
Collaborative arrangement, transaction price			$ 40.0

Financing Arrangements - Additional Information (Details) $ in Millions	Jun. 30, 2022 USD ($)
Debt Financing
Royalty Purchase Agreement, milestone payments, achievement of specified net sales milestones, maximum	$ 165.0

Leases - Components of Lease Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Operating leases:
Lease cost	$ 5,662	$ 4,942	$ 11,543	$ 10,911
Sublease income		(600)		(1,381)
Net lease cost	$ 5,662	$ 4,342	$ 11,543	$ 9,530

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)	6 Months Ended
	Jun. 30, 2023
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 United States (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, 2022 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2022, filed with the SEC on February 16, 2023 (2022 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 June 30, 2023, the results of its operations for the three and six months ended June 30, 2023 and 2022, stockholder’s equity for the three and six months ended June 30, 2023 and 2022 and cash flows for six months ended June 30, 2023 and 2022. Such adjustments are of a normal and recurring nature. The results for the three and six months ended June 30, 2023 are not necessarily indicative of the results for the year ending December 31, 2023 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. The Russian invasion of Ukraine has not had a material impact on the Company’s business, results of operations and financial condition.
Significant Accounting Policies	Significant Accounting Policies The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and six months ended June 30, 2023 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2022 Annual Report on Form 10-K, with the exception of the below new policy.
Performance-Based Restricted Stock Unit Awards	Performance-Based Restricted Stock Unit Awards Fair value of performance-based restricted stock unit awards (PSUs) at the grant date are estimated 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. The PSUs cliff vest at the end of the service period and the compensation expense for PSUs is recognized straight-line over the applicable service period.
New Accounting Pronouncements	New 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. 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.

Disclosure of accounting policy for award under share-based payment arrangement. Includes, but is not limited to, methodology and assumption used in measuring cost.

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Pay vs Performance Disclosure - USD ($) $ in Thousands	3 Months Ended				6 Months Ended
Pay vs Performance Disclosure - USD ($) $ in Thousands	Jun. 30, 2023	Mar. 31, 2023	Jun. 30, 2022	Mar. 31, 2022	Jun. 30, 2023	Jun. 30, 2022
Pay vs Performance Disclosure
Net Income (Loss)	$ (132,793)	$ (129,560)	$ (159,709)	$ (105,999)	$ (262,354)	$ (265,709)

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

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Fair Value of Financial Instruments

6 Months Ended

Jun. 30, 2023

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 June 30, 2023 (in thousands):


			Active		Observable		Unobservable
	June 30,		Markets		Inputs		Inputs
Description	2023		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	62,861		62,861		—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		239,527		—		239,527		—
U.S. treasury obligations		521,512		521,512		—		—
Total	$	823,900	$	584,373	$	239,527	$	—

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2022 (in thousands):


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2022		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	95,198	$	95,198	$	—	$	—
U.S. treasury obligations		4,989		4,989		—		—
Marketable securities, available-for-sale:
U.S. government agency securities		372,671		—		372,671		—
U.S. treasury obligations		586,092		586,092		—		—
Total	$	1,058,950	$	686,279	$	372,671	$	—

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.

Sixth Street Partners, Future Revenue Purchase Agreement

Condensed Consolidated Statements of Operations and Comprehensive Loss - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Revenues:
Revenue	$ 57,570	$ 36,547	$ 120,857	$ 99,278
Cost and operating expenses:
Cost of sales	2,323	4,886	5,498	9,964
Research and development	110,063	128,466	222,135	231,599
Selling, general and administrative	71,931	58,688	142,882	115,747
Collaboration loss sharing	1,234	2,145	2,530	5,410
Total cost and operating expenses	185,551	194,185	373,045	362,720
Other income (expense):
Interest income (expense), net	(3,996)	427	(9,815)	869
Other income (expense), net	(626)	632	359	177
Total other income (expense), net	(4,622)	1,059	(9,456)	1,046
Loss before income taxes	(132,603)	(156,579)	(261,644)	(262,396)
Income tax expense	190	3,130	710	3,313
Net loss	(132,793)	(159,709)	(262,354)	(265,709)
Other comprehensive loss:
Unrealized gains (losses) on available-for-sale investments	361	(2,308)	6,181	(10,328)
Currency translation adjustments	20	170	41	213
Comprehensive loss	$ (132,412)	$ (161,847)	$ (256,132)	$ (275,824)
Net loss per share - basic (in dollars per share)	$ (2.19)	$ (2.68)
Net loss per share - diluted (in dollars per share)	$ (2.19)	$ (2.68)	$ (4.35)	$ (4.47)
Weighted-average number of common shares used in net loss per share - basic (in shares)	60,516	59,617
Weighted-average number of common shares used in net loss per share - diluted (in shares)	60,516	59,617	60,322	59,465
Product revenue, net
Revenues:
Revenue	$ 39,876	$ 28,454	$ 78,945	$ 52,295
Collaboration and license revenue
Revenues:
Revenue	$ 17,694	$ 8,093	$ 41,912	$ 46,983

Marketable Securities - Tabular Disclosure (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Marketable securities, available-for-sale:
Amortized cost	$ 764,807	$ 968,712
Unrealized gain	7	22
Unrealized losses	(3,775)	(9,971)
Fair value	761,039	958,763
U.S. government agency securities
Marketable securities, available-for-sale:
Amortized cost	241,322	377,519
Unrealized losses	(1,795)	(4,848)
Fair value	239,527	372,671
U.S. Treasury obligations
Marketable securities, available-for-sale:
Amortized cost	523,485	591,193
Unrealized gain	7	22
Unrealized losses	(1,980)	(5,123)
Fair value	$ 521,512	$ 586,092

Net Loss Per Share (Details) - shares shares in Thousands	3 Months Ended
Net Loss Per Share (Details) - shares shares in Thousands	Jun. 30, 2023	Jun. 30, 2022
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	9,319	8,290
Employee Stock Option [Member]
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	7,070	6,387
Restricted Stock Units
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	2,149	1,857
Performance-based restricted stock units
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	53
Employee Stock
Antidilutive securities excluded from computation of earnings per share
Antidilutive securities excluded from computation of earnings per share	47	46

Financing Arrangements (Tables)

6 Months Ended

Jun. 30, 2023

Schedule of activity within the liability account


Carrying value as of January 1, 2023	$	254,328
Interest expense recognized		14,021
Payments		(6,644)
Carrying value as of June 30, 2023	$	261,705

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

Schedule of activity within the liability account


Carrying value as of January 1, 2023	$	139,083
Interest expense recognized		9,443
Payments		(8,523)
Carrying value as of June 30, 2023	$	140,003

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://www.xbrl.org/2003/role/exampleRef
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Reference 2: http://www.xbrl.org/2003/role/exampleRef
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Reference 3: http://www.xbrl.org/2009/role/commonPracticeRef
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Fair Value of Financial Instruments (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Fair Value of Financial Instruments
Marketable securities, available-for-sale	$ 761,039	$ 958,763
U.S. government agency securities
Fair Value of Financial Instruments
Marketable securities, available-for-sale	239,527	372,671
U.S. Treasury obligations
Fair Value of Financial Instruments
Marketable securities, available-for-sale	521,512	586,092
Recurring
Fair Value of Financial Instruments
Total	823,900	1,058,950
Recurring \| U.S. government agency securities
Fair Value of Financial Instruments
Marketable securities, available-for-sale	239,527	372,671
Recurring \| U.S. Treasury obligations
Fair Value of Financial Instruments
Marketable securities, available-for-sale	521,512	586,092
Recurring \| Money market funds
Fair Value of Financial Instruments
Cash equivalents	62,861	95,198
Recurring \| U.S. Treasury obligations
Fair Value of Financial Instruments
Cash equivalents		4,989
Recurring \| Active Markets (Level 1)
Fair Value of Financial Instruments
Total	584,373	686,279
Recurring \| Active Markets (Level 1) \| U.S. Treasury obligations
Fair Value of Financial Instruments
Marketable securities, available-for-sale	521,512	586,092
Recurring \| Active Markets (Level 1) \| Money market funds
Fair Value of Financial Instruments
Cash equivalents	62,861	95,198
Recurring \| Active Markets (Level 1) \| U.S. Treasury obligations
Fair Value of Financial Instruments
Cash equivalents		4,989
Recurring \| Observable Inputs (Level 2)
Fair Value of Financial Instruments
Total	239,527	372,671
Recurring \| Observable Inputs (Level 2) \| U.S. government agency securities
Fair Value of Financial Instruments
Marketable securities, available-for-sale	$ 239,527	$ 372,671

Financing Arrangements - Long-term Debt (Details) - Sale of Future Royalties and Revenues - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Royalty Pharma, Royalty Purchase Agreement
Long-term Debt
Long-term debt	$ 175,600
Sixth Street Partners, Future Revenue Purchase Agreement
Long-term Debt
Long-term debt	$ 261,705	$ 254,328

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

Financing Arrangements - Roll Forward (Details) - USD ($) $ in Thousands		1 Months Ended	6 Months Ended	12 Months Ended
	Jun. 30, 2022	Jul. 31, 2022	Jun. 30, 2023	Dec. 31, 2022
Sale of Future Royalties and Revenues
Long-term Debt
Sale of future royalties / borrowings				$ 425,000
Sale of Future Royalties and Revenues \| Royalty Pharma, Royalty Purchase Agreement
Long-term Debt
Sale of future royalties / borrowings	$ 175,000
Carrying value, ending balance			$ 175,600
Sale of Future Royalties and Revenues \| Sixth Street Partners, Future Revenue Purchase Agreement
Long-term Debt
Carrying value, beginning balance			254,328
Sale of future royalties / borrowings		$ 250,000
Interest expense recognized			14,021
Payments			(6,644)
Carrying value, ending balance			261,705	254,328
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facility
Long-term Debt
Carrying value, beginning balance			139,083
Sale of future royalties / borrowings		$ 150,000
Interest expense recognized			9,443
Payments			(8,523)
Carrying value, ending balance			$ 140,003	$ 139,083

Collaboration and License Agreements (Tables)

6 Months Ended

Jun. 30, 2023

Schedule of collaboration loss sharing


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
The Company's share of loss in the U.S. for pralsetinib	$	1,234	$	2,145	$	2,530	$	5,410

Schedule of amounts recognized as reductions to expenses


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Reductions to selling, general and administrative expenses	$	2,774	$	4,416	$	5,555	$	9,248
Increases in research and development expenses	$	5,347	$	3,714	$	13,623	$	3,704

Roche, Collaboration (Pralsetnib) Agreement

Summary of contract assets and/or contract liabilities


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Manufacturing and research and development services related to ex-US territory-specific activities	$	229	$	35	$	356	$	691
Royalty revenue		366		313		803		600
Total Roche pralsetinib collaboration revenue	$	595	$	348	$	1,159	$	1,291


	June 30,		December 31,
	2023		2022
Unbilled accounts receivable	$	380	$	—
Accrued expenses	$	4,573	$	6,519

Roche, Collaboration and License (Immunotherapy) Agreement

Roche, Collaboration and License (Immunotherapy) Agreement | Collaboration revenue


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Roche collaboration research and development services revenue	$	3,709	$	1,183	$	25,705	$	(765)

Summary of contract assets and/or contract liabilities


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Amounts included in the contract liability at the beginning of the period	$	221	$	1,395	$	16,025	$	2,405


	June 30, 2023						December 31, 2022
	Current		Noncurrent		Total		Current		Noncurrent		Total
Deferred revenue	$	—	$	—	$	—	$	2,402	$	13,624	$	16,026
Accrued expenses	$	55	$	—	$	55	$	3,970	$	7,238	$	11,208

C Stone

C Stone | Collaboration revenue


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
License milestone revenue	$	9,000	$	—	$	9,000	$	4,000
Manufacturing services and royalty revenue related to CStone Territory-specific activities		4,390		6,082		6,042		11,294
Total CStone collaboration revenue	$	13,390	$	6,082	$	15,042	$	15,294

Summary of contract assets and/or contract liabilities


	June 30,		December 31,
	2023		2022
Accounts receivable, net	$	11,219	$	4,991
Unbilled accounts receivable		2,850		1,529
Contract liability		3,328		2,265

Collaboration and License Agreements - Collaboration Loss Sharing (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Collaboration Agreements
Collaboration loss sharing	$ 1,234	$ 2,145	$ 2,530	$ 5,410
Collaborative Arrangement \| Roche, Collaboration (Pralsetnib) Agreement
Collaboration Agreements
Collaboration loss sharing	$ 1,234	$ 2,145	$ 2,530	$ 5,410

Product Revenue Reserves and Allowances (Tables)

6 Months Ended

Jun. 30, 2023

Schedules of concentration of risk


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Customer 1	41	%	44	%	42	%	46	%
Customer 2	11	%	11	%	11	%	11	%


	June 30,		December 31,
	2023		2022
Customer 1	34	%	33	%
Customer 2	11	%	15	%
Customer 3	*		12	%
Customer 4	10	%	*

Product revenue, net

Schedule of product revenue allowance and reserve categories


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
United States	$	34,307	$	24,682	$	69,234	$	45,834
Rest of World		5,569		3,772		9,711		6,461
Total product revenue	$	39,876	$	28,454	$	78,945	$	52,295


	Six Months Ended June 30,
	2023		2022
Beginning balance at January 1	$	9,788	$	4,345
Provision related to sales in the current period		16,108		9,408
Adjustment related to prior periods sales		(531)		(570)
Credits and payments made		(10,553)		(6,120)
Ending balance at June 30	$	14,812	$	7,063


	June 30,		December 31,
	2023		2022
Reduction of accounts receivable, net	$	1,257	$	742
Component of accrued expenses		13,555		9,046
Total revenue-related reserves	$	14,812	$	9,788

Nature of Business - General Information (Details)	Jun. 30, 2023 item
Approved precision therapies
Approved precision therapies, number	2

Stock-based Compensation - Stock-based Compensation Expense - General Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Total stock based compensation expense
Stock-based compensation expense	$ 23,821	$ 25,347	$ 47,017	$ 48,746

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Current assets:
Cash and cash equivalents	$ 75,527	$ 119,709
Marketable securities	647,107	825,283
Accounts receivable	35,147	23,525
Unbilled accounts receivable	3,120	13,413
Inventory	17,016	29,697
Prepaid expenses and other current assets	33,418	35,024
Total current assets	811,335	1,046,651
Marketable securities	113,932	133,480
Property and equipment, net	36,957	33,344
Operating lease right-of-use assets, net	77,529	81,854
Restricted cash	6,352	5,195
Equity investment	27,789	27,789
Other assets	32,551	21,589
Total assets	1,106,445	1,349,902
Current liabilities:
Accounts payable	6,979	2,729
Accrued expenses	101,162	131,123
Current portion of operating lease liabilities	11,292	10,579
Current portion of deferred revenue	3,328	4,667
Current portion of liabilities related to the sale of future royalties and revenues	28,410	17,285
Current portion of term loan	17,857	16,851
Total current liabilities	169,028	183,234
Operating lease liabilities, net of current portion	87,049	92,789
Deferred revenue, net of current portion	5,000	13,624
Liabilities related to the sale of future royalties and revenues, net of current portion	408,931	413,045
Term loan, net of current portion	122,146	122,232
Other long-term liabilities	3,161	10,301
Total liabilities	795,315	835,225
Commitments and Contingencies (Note 15)
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; 60,638,275 and 59,958,919 shares issued and outstanding at June 30, 2023 and December 31, 2022, respectively	61	60
Additional paid-in capital	2,410,601	2,358,018
Accumulated other comprehensive loss	(4,221)	(10,443)
Accumulated deficit	(2,095,311)	(1,832,958)
Total stockholders' equity	311,130	514,677
Total liabilities and stockholders' equity	$ 1,106,445	$ 1,349,902

Product Revenue Reserves and Allowances

6 Months Ended

Jun. 30, 2023

Product Revenue Reserves and Allowances

6. Product Revenue Reserves and Allowances

In January 2020, the U.S. Food and Drug Administration (FDA) approved AYVAKIT for the treatment of adults with unresectable or metastatic gastrointestinal stromal tumor (GIST) harboring a PDGFRA exon 18 mutation, including PDGFRA D842V mutations. In September 2020, the European Commission granted conditional marketing authorization to AYVAKYT as a monotherapy for the treatment of adult patients with unresectable or metastatic GIST harboring the PDGFRA D842V mutation. In June 2021, the FDA granted a subsequent approval for AYVAKIT, expanding the labeled indications to include adult patients with advanced SM, including aggressive SM (ASM), SM with an associated hematological neoplasm (SM-AHN) and mast cell leukemia (MCL). In March 2022, the European Commission expanded the marketing authorization for AYVAKYT to include the treatment of adult patients with ASM, SM-AHN, or MCL, after at least one systemic therapy. In May 2023, the FDA approved AYVAKIT for the treatment of adult patients with indolent SM.

The following table summarizes revenue recognized from product sales for the three and six months ended June 30, 2023 and 2022 (in thousands):


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
United States	$	34,307	$	24,682	$	69,234	$	45,834
Rest of World		5,569		3,772		9,711		6,461
Total product revenue	$	39,876	$	28,454	$	78,945	$	52,295

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 six months ended June 30, 2023, and 2022 (in thousands):


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Customer 1	41	%	44	%	42	%	46	%
Customer 2	11	%	11	%	11	%	11	%

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 June 30, 2023 and December 31, 2022 (in thousands):


	June 30,		December 31,
	2023		2022
Customer 1	34	%	33	%
Customer 2	11	%	15	%
Customer 3	*		12	%
Customer 4	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 six months ended June 30, 2023 and 2022 (in thousands):


	Six Months Ended June 30,
	2023		2022
Beginning balance at January 1	$	9,788	$	4,345
Provision related to sales in the current period		16,108		9,408
Adjustment related to prior periods sales		(531)		(570)
Credits and payments made		(10,553)		(6,120)
Ending balance at June 30	$	14,812	$	7,063

The total reserves that are included in the Company’s unaudited condensed consolidated balance sheets as of June 30, 2023 and December 31, 2022, are summarized as follows (in thousands):


	June 30,		December 31,
	2023		2022
Reduction of accounts receivable, net	$	1,257	$	742
Component of accrued expenses		13,555		9,046
Total revenue-related reserves	$	14,812	$	9,788

Product Revenue Reserves and Allowances - Product Revenue Allowance and Reserve (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022
Product revenue allowance and reserve
Beginning balance	$ 9,788	$ 4,345
Provision related to sales in the current period	16,108	9,408
Adjustment related to prior periods sales	(531)	(570)
Credits and payments made	(10,553)	(6,120)
Ending balance	$ 14,812	$ 7,063

Accrued Expenses (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Accrued Expenses
External research and development	$ 40,401	$ 66,041
Employee compensation	26,179	30,744
Accrued professional fees	13,516	17,588
Revenue-related reserves	13,555	9,046
Other	7,511	7,704
Total	$ 101,162	$ 131,123

Collaboration and License Agreements - Contract Assets and Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Contract Assets
Accounts receivable, net	$ 35,147	$ 23,525
Unbilled accounts receivable	3,120	13,413
Contract Liabilities
Contract liabilities, current	3,328	4,667
Contract liabilities, noncurrent	5,000	13,624
Accrued expenses, current	40,401	66,041
Collaborative Arrangement \| Roche, Collaboration (Pralsetnib) Agreement
Contract Assets
Unbilled accounts receivable	380
Contract Liabilities
Accrued expenses	4,573	6,519
Collaborative Arrangement \| Roche, Collaboration and License (Immunotherapy) Agreement
Contract Liabilities
Contract liabilities	0	16,026
Contract liabilities, current	0	2,402
Contract liabilities, noncurrent	0	13,624
Accrued expenses	55	11,208
Accrued expenses, current	55	3,970
Accrued expenses, noncurrent	0	7,238
Collaborative Arrangement \| Clementia
Contract Liabilities
Contract liabilities	0	0
Collaborative Arrangement \| C Stone
Contract Assets
Accounts receivable, net	11,219	4,991
Unbilled accounts receivable	2,850	1,529
Contract Liabilities
Contract liabilities	$ 3,328	$ 2,265

Income Taxes

6 Months Ended

Jun. 30, 2023

Income Taxes

13. 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 June 30, 2023, the Company has a full valuation allowance applied against its U.S. and foreign deferred tax assets.

Effective January 1, 2022, a provision of the Tax Cuts and Jobs Act (TCJA) has taken effect creating a significant change to the treatment of research and experimental (R&E) expenditures under Section 174 of the IRC (Sec. 174 expenses). Historically, businesses have had the option of deducting Sec. 174 expenses in the year incurred or capitalizing and amortizing the costs over five years. The new TCJA provision, however, eliminates this option and will require Sec. 174 expenses associated with research conducted in the U.S to be capitalized and amortized over a five-year period. For expenses associated with research outside of the United States, Sec. 174 expenses will be capitalized and amortized over a 15-year period. The Company has included the tax impact of capitalizing and amortizing these costs over the required periods for the six months ended June 30, 2023.

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. Therefore, the $425.0 million was included in the estimated taxable income calculation when estimating the Company’s forecasted 2022 annual effective tax rate. As of June 30, 2022, the Company expected to be in a taxable income position for the calendar year ended December 31, 2022, and recorded an income tax expense of $3.1 million and $3.3 million for the three and six months ended June 30, 2022, respectively.

On August 16, 2022, President Biden signed the Inflation Reduction Act (IRA) of 2022 (H.R. 5376) into law. It includes income tax incentives designed to encourage investment in renewable and alternative energy sources, adoption of electric vehicles, and improvement in the energy efficiency of buildings and communities. To finance these incentives, the law imposes a 15% corporate alternative minimum tax (CAMT) on adjusted financial statement income of corporations with profits over $1 billion. It also introduces a new excise tax on corporate stock buybacks of public US companies. The CAMT is effective for tax years beginning after December 31, 2022 while the excise tax on corporate stock buybacks is effective for repurchases of stock after December 31, 2022. The Company does not anticipate the IRA having a significant impact on the effective tax rate or income tax payable and deferred income tax positions.

As of June 30, 2023, the Company expects to be in a taxable loss position for the calendar year ended December 31, 2023, and has recorded an income tax expense of $0.2 million and $0.7 million for the three and six

months ended June 30, 2023. The Company recorded an income tax provision despite forecasting a taxable loss due to the impact of recording unfavorable discrete items in the period, and taxable income from the jurisdictions in which the Company is subject to tax.

As of June 30, 2023, the Company had gross unrecognized tax benefit, excluding interest and penalties of approximately $0.2 million. As of December 31, 2022, the Company did not have any gross unrecognized tax benefit. The company recognizes interest and penalties related to unrecognized tax benefits in the provision for income taxes. As of June 30, 2023, the Company has accrued an insignificant amount of interest and penalties related to uncertain tax positions.

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 946
-SubTopic 20
-Name Accounting Standards Codification
-Section 50
-Paragraph 13
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480990/946-20-50-13

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 235
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08(h)(2))
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480678/235-10-S99-1

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-Name Accounting Standards Codification
-Publisher FASB
-URI https://asc.fasb.org//740/tableOfContent

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 14
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482685/740-10-50-14

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 21
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482685/740-10-50-21

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 270
-Name Accounting Standards Codification
-Section 50
-Paragraph 1
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482526/740-270-50-1

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 17
-Subparagraph (b)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482685/740-10-50-17

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 1
-Subparagraph (SAB TOPIC 6.I.5.Q1)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147479360/740-10-S99-1

Reference 9: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 10
-Name Accounting Standards Codification
-Section S99
-Paragraph 2
-Subparagraph (SAB Topic 11.C)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147479360/740-10-S99-2

Reference 10: http://www.xbrl.org/2003/role/disclosureRef
-Topic 740
-SubTopic 30
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147482603/740-30-50-2

Collaboration and License Agreements - Revenue Recognized (Details) - USD ($) $ in Thousands		3 Months Ended		6 Months Ended		12 Months Ended		24 Months Ended
	Aug. 01, 2022	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022	Dec. 31, 2021	Dec. 31, 2018	Dec. 31, 2020
Revenues
Revenue		$ 57,570	$ 36,547	$ 120,857	$ 99,278
License revenue \| IDRx, Inc. \| Director
Revenues
Revenue	$ 27,500
Collaborative Arrangement \| Zai Lab (Shanghai) Co., Ltd.
Revenues
Revenue						$ 25,000
Collaborative Arrangement \| Clementia
Revenues
Revenue		0			30,000			$ 46,500
Collaborative Arrangement \| Collaboration revenue \| Roche, Collaboration (Pralsetnib) Agreement
Revenues
Revenue		595	348	1,159	1,291
Collaborative Arrangement \| Collaboration revenue \| Roche, Collaboration and License (Immunotherapy) Agreement
Revenues
Revenue		3,709		25,705	(765)
Revenue, net			1,183
Cumulative revenue catch-up		3,500		25,100
Collaborative Arrangement \| Collaboration revenue \| C Stone
Revenues
Revenue		13,390	6,082	15,042	15,294		$ 40,000
Collaborative Arrangement \| License milestone revenue \| C Stone
Revenues
Revenue		9,000	0	9,000	4,000
Collaborative Arrangement \| Territory-specific activities \| Zai Lab (Shanghai) Co., Ltd.
Revenues
Revenue		0	500	0	600
Collaborative Arrangement \| Territory-specific activities, manufacturing services and royalty \| C Stone
Revenues
Revenue		4,390	6,082	6,042	11,294
Collaborative Arrangement \| Territory-specific activities, manufacturing and research and development services \| Roche, Collaboration (Pralsetnib) Agreement
Revenues
Revenue		229	35	356	691
Collaborative Arrangement \| Royalty \| Roche, Collaboration (Pralsetnib) Agreement
Revenues
Revenue		$ 366	$ 313	$ 803	$ 600

Marketable Securities - Proceeds from Maturities (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Proceeds from the maturities of debt securities
Proceeds from the maturities of debt securities	$ 309,515	$ 79,623	$ 617,765	$ 79,623

Stock-based Compensation - Stock-based Compensation Expense - By Classification (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Total stock based compensation expense
Stock-based compensation expense	$ 23,821	$ 25,347	$ 47,017	$ 48,746
Research and Development
Total stock based compensation expense
Stock-based compensation expense	10,227	10,497	20,344	20,538
General and Administrative Expense
Total stock based compensation expense
Stock-based compensation expense	$ 13,594	$ 14,850	$ 26,673	$ 28,208

Inventory (Tables)

6 Months Ended

Jun. 30, 2023

Schedule of capitalized inventory


	June 30,		December 31,
	2023		2022
Raw materials	$	1,599	$	4,967
Work in process		32,750		28,427
Finished goods		2,589		2,791
Total	$	36,938	$	36,185

Balance sheet classification


	June 30,		December 31,
	2023		2022
Inventory	$	17,016	$	29,697
Other assets		19,922		6,488
Total	$	36,938	$	36,185

Marketable Securities - Impairment (Details) - USD ($) $ in Thousands	3 Months Ended
	Jun. 30, 2023	Jun. 30, 2022
Marketable Securities
Marketable debt securities, charges for credit-related impairments	$ 0	$ 0

Restricted Cash

6 Months Ended

Jun. 30, 2023

Restricted Cash

8. Restricted Cash

At June 30, 2023 and December 31, 2022, $6.4 million and $5.2 million, respectively, of the Company’s cash is restricted by a financial institution primarily related to security deposits for the lease agreements for the Company’s office and laboratory spaces.

Marketable Securities - Maturities (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Amortized cost
Within one year, amortized cost	$ 649,622	$ 834,440
After one through five years, amortized cost	115,185	134,272
Amortized cost	764,807	968,712
Fair value
Within one year, fair value	647,107	825,283
After one through five years, fair value	113,932	133,480
Investments, available-for-sale	$ 761,039	$ 958,763

Financing Arrangements - General Information (Details) $ in Thousands		1 Months Ended	3 Months Ended	12 Months Ended
	Jun. 30, 2022 USD ($)	Jul. 31, 2022 USD ($) tranche Transaction	Jun. 30, 2023 USD ($)	Dec. 31, 2022 USD ($)
Sixth Street Partners, Financing Arrangements
Debt Financing
Debt instrument, transactions, number \| Transaction		2
Sale of Future Royalties and Revenues
Gross Proceeds
Gross proceeds				$ 425,000
Sale of Future Royalties and Revenues \| Royalty Pharma, Royalty Purchase Agreement
Debt Financing
Debt instrument, issuance date	Jun. 30, 2022
Debt instrument, face amount	$ 175,000
Transaction costs, gross	3,800
Debt instrument, interest expense accretion			$ 0
Gross Proceeds
Gross proceeds	$ 175,000
Sale of Future Royalties and Revenues \| Sixth Street Partners, Future Revenue Purchase Agreement
Debt Financing
Debt instrument, face amount		$ 250,000
Transaction costs, gross		5,400
Gross Proceeds
Gross proceeds		250,000
Effective Interest Rate
Debt instrument, interest rate, effective percentage (as a percent)			10.80%
Loans Payable \| Sixth Street Partners, Financing Agreement
Debt Financing
Debt instrument, face amount, potential amount		660,000
Debt instrument, covenants, consolidated liquidity, period commencing from date term loan funded to date day before next term loans funded		50,000
Debt instrument, covenants, consolidated liquidity, period commencing from date term loan funded to date day before next term loans funded, each day thereafter		$ 80,000
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities
Debt Financing
Debt instrument, maturity date		Jun. 30, 2028
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Term Loan Facilities \| Secured Overnight Financing Rate (SOFR) Overnight Index Swap Rate
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		$ 150,000
Debt discounts and transaction costs		12,200
Gross Proceeds
Gross proceeds		150,000
Effective Interest Rate
Debt instrument, interest rate, effective percentage (as a percent)			13.60%
Secured Debt \| Sixth Street Partners, Financing Agreement, Senior Secured Delayed Draw Term Loan Facility
Debt Financing
Debt instrument, face amount, potential amount		$ 250,000
Debt instrument, tranches, number \| tranche		2

Summary of Significant Accounting Policies and Recent Accounting Pronouncements

6 Months Ended

Jun. 30, 2023

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 United States (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, 2022 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2022, filed with the SEC on February 16, 2023 (2022 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 June 30, 2023, the results of its operations for the three and six months ended June 30, 2023 and 2022, stockholder’s equity for the three and six months ended June 30, 2023 and 2022 and cash flows for six months ended June 30, 2023 and 2022. Such adjustments are of a normal and recurring nature. The results for the three and six months ended June 30, 2023 are not necessarily indicative of the results for the year ending December 31, 2023 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. The Russian invasion of Ukraine has not had a material impact on the Company’s business, results of operations and financial condition.

Significant Accounting Policies

The significant accounting policies used in preparation of these condensed consolidated financial statements for the three and six months ended June 30, 2023 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2022 Annual Report on Form 10-K, with the exception of the below new policy.

Performance-Based Restricted Stock Unit Awards

Fair value of performance-based restricted stock unit awards (PSUs) at the grant date are estimated 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. The PSUs cliff vest at the end of the service period and the compensation expense for PSUs is recognized straight-line over the applicable service period.

New 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. 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.

Leases

6 Months Ended

Jun. 30, 2023

Leases

14. 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 June 30, 2023. The lease agreements do not contain residual value guarantees and the components of lease cost for the three and six months ended June 30, 2023 and 2022 were as follows (in thousands):


	Three Months Ended				Six Months Ended
	June 30,				June 30,
Operating leases:	2023		2022		2023		2022
Lease cost	$	5,662	$	4,942	$	11,543	$	10,911
Sublease income		—		(600)		—		(1,381)
Net lease cost	$	5,662	$	4,342	$	11,543	$	9,530

The Company’s sublease agreements for the 38 Sidney Street property expired in 2022. The Company has not entered into any material short-term leases or financing leases as of June 30, 2023.

Supplemental cash flow information related to leases for the six months ended June 30, 2023 and 2022 is as follows (in thousands):


	Six Months Ended
	June 30,
	2023		2022
Cash paid for amounts included in the measurement of lease liabilities:	$	8,812	$	7,763
Lease liabilities arising from obtaining right-of-use assets:
Operating leases	$	112	$	—

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					6.3
Weighted average discount rate					7.4%

Nature of Business - Cash and Cash Equivalents and Marketable Securities (Details) $ in Millions	Jun. 30, 2023 USD ($)
Cash, cash equivalents and marketable securities
Cash, cash equivalents and marketable securities	$ 836.6

Collaboration and License Agreements - Change in Contract with Customer, Liability (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
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	$ 221	$ 1,395	$ 16,025	$ 2,405

Net Loss Per Share

6 Months Ended

Jun. 30, 2023

Net Loss Per Share

12. Net Loss per Share

Basic net loss per share is calculated by dividing net loss by the weighted average shares outstanding during the period, without consideration for 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 dilutive net loss per share calculation, stock options, unvested restricted stock units, PSUs and ESPP shares are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share, as their effect would be anti-dilutive; therefore, basic and diluted net loss per share were the same for all periods presented as a result of the Company’s net loss.

The following common stock equivalents were excluded from the calculation of diluted net loss per share for the six months ended June 30, 2023 and 2022 because including them would have had an anti-dilutive effect (in thousands):


	June 30,
	2023	2022
Stock options	7,070	6,387
Restricted stock units	2,149	1,857
Performance-based restricted stock units	53	—
ESPP shares	47	46
Total	9,319	8,290

Fair Value of Financial Instruments (Tables)

6 Months Ended

Jun. 30, 2023

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 June 30, 2023 (in thousands):


			Active		Observable		Unobservable
	June 30,		Markets		Inputs		Inputs
Description	2023		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	62,861		62,861		—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		239,527		—		239,527		—
U.S. treasury obligations		521,512		521,512		—		—
Total	$	823,900	$	584,373	$	239,527	$	—

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2022 (in thousands):


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2022		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	95,198	$	95,198	$	—	$	—
U.S. treasury obligations		4,989		4,989		—		—
Marketable securities, available-for-sale:
U.S. government agency securities		372,671		—		372,671		—
U.S. treasury obligations		586,092		586,092		—		—
Total	$	1,058,950	$	686,279	$	372,671	$	—

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, 2021	$ 59	$ 2,250,250	$ (4,133)	$ (1,275,441)	$ 970,735
Beginning Balance (in shares) at Dec. 31, 2021	59,141,086
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan	$ 1	1,297			1,298
Issuance of common stock under stock plan (in shares)	414,888
Stock-based compensation expense		23,609			23,609
Other comprehensive income (loss)			(7,977)		(7,977)
Net loss				(105,999)	(105,999)
Ending Balance at Mar. 31, 2022	$ 60	2,275,156	(12,110)	(1,381,440)	881,666
Ending Balance (in shares) at Mar. 31, 2022	59,555,974
Beginning Balance at Dec. 31, 2021	$ 59	2,250,250	(4,133)	(1,275,441)	970,735
Beginning Balance (in shares) at Dec. 31, 2021	59,141,086
Increase (Decrease) in Stockholders' Equity
Net loss					(265,709)
Ending Balance at Jun. 30, 2022	$ 60	2,303,087	(14,248)	(1,541,149)	747,750
Ending Balance (in shares) at Jun. 30, 2022	59,688,295
Beginning Balance at Mar. 31, 2022	$ 60	2,275,156	(12,110)	(1,381,440)	881,666
Beginning Balance (in shares) at Mar. 31, 2022	59,555,974
Increase (Decrease) in Stockholders' Equity
Issuance of common stock under stock plan and stock purchase plan		2,407			2,407
Issuance of common stock under stock plan and stock purchase plan (in shares)	132,321
Stock-based compensation expense		25,524			25,524
Other comprehensive income (loss)			(2,138)		(2,138)
Net loss				(159,709)	(159,709)
Ending Balance at Jun. 30, 2022	$ 60	2,303,087	(14,248)	(1,541,149)	747,750
Ending Balance (in shares) at Jun. 30, 2022	59,688,295
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				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 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				59,958,919
Increase (Decrease) in Stockholders' Equity
Net loss					$ (262,354)
Ending Balance at Jun. 30, 2023	$ 61	2,410,601	(4,221)	(2,095,311)	$ 311,130
Ending Balance (in shares) at Jun. 30, 2023	60,638,275				60,638,275
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 loss				(132,793)	(132,793)
Ending Balance at Jun. 30, 2023	$ 61	$ 2,410,601	$ (4,221)	$ (2,095,311)	$ 311,130
Ending Balance (in shares) at Jun. 30, 2023	60,638,275				60,638,275

Insider Trading Arrangements

6 Months Ended

Jun. 30, 2023

Trading Arrangements, by Individual

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
Jefferey W. Albers (Chairman of the Board of Directors)	Adoption (5/26/23)	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 plan	5/26/23 – 5/31/24	135,073
Christopher Murray (Chief Technical Operations and Quality Officer)	Adoption (6/5/23)	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 plan	6/5/23 – 6/5/24	11,821

Jefferey W. Albers

Trading Arrangements, by Individual

Name

Jefferey W. Albers

Title

Chairman of the Board of Directors

Rule 10b5-1 Arrangement Adopted

true

5/26/23

5/31/24

135,073

Trading Arrangements, by Individual

Name

Christopher Murray

Title

Chief Technical Operations and Quality Officer

Rule 10b5-1 Arrangement Adopted

true

Adoption Date

6/5/23

Termination Date

6/5/24

Aggregate Available

11,821

Stock-based Compensation - 2020 Inducement Plan (Details) - 2020 Inducement Plan - shares	1 Months Ended
	Jun. 30, 2022	Jun. 30, 2023	Mar. 31, 2020
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
Number of shares available for grant (in shares)		1,382,793

Marketable Securities (Tables)

6 Months Ended

Jun. 30, 2023

Schedule of marketable securities


	Amortized		Unrealized		Unrealized		Fair
June 30, 2023	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	241,322		—		(1,795)	$	239,527
U.S. treasury obligations		523,485		7		(1,980)		521,512
Total	$	764,807	$	7	$	(3,775)	$	761,039


	Amortized		Unrealized		Unrealized		Fair
December 31, 2022	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	377,519		—		(4,848)	$	372,671
U.S. treasury obligations		591,193		22		(5,123)		586,092
Total	$	968,712	$	22	$	(9,971)	$	958,763

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


	June 30, 2023				December 31, 2022
	Fair		Number of		Fair		Number of
	value		securities		value		securities
Debt securities in unrealized loss position for 12 months or less	$	625,248		110	$	371,746		66
Debt securities in unrealized loss position for more than 12 months		96,291		14		550,561		56
Total debt securities in unrealized loss position	$	721,539		124	$	922,307		122

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


	June 30, 2023				December 31, 2022
	Amortized		Fair		Amortized		Fair
	Cost		value		Cost		value
Within one year	$	649,622	$	647,107	$	834,440	$	825,283
After one through five years		115,185		113,932		134,272		133,480
Total	$	764,807	$	761,039	$	968,712	$	958,763

Summary of proceeds from maturities of debt securities


	Three Months Ended				Six Months Ended
	June 30,				June 30,
	2023		2022		2023		2022
Proceeds from maturities of debt securities	$	309,515	$	79,623	$	617,765	$	79,623

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
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 9
-Subparagraph (a)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147481800/320-10-50-9

Reference 2: http://www.xbrl.org/2009/role/commonPracticeRef
-Topic 320
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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 12: http://www.xbrl.org/2009/role/commonPracticeRef
-Topic 320
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-URI https://asc.fasb.org//1943274/2147481800/320-10-50-3

Stock-based Compensation - Unrecognized Compensation Costs (Details) $ in Millions	Jun. 30, 2023 USD ($)
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock option awards	$ 78.2
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 9 months
Restricted Stock Units
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock awards	$ 112.5
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 9 months
Performance-based restricted stock units
Stock-based compensation
Total unrecognized compensation cost related to non-vested stock awards	$ 2.8
Weighted-average period over which unrecognized compensation cost will be recognized	2 years 8 months 1 day

Document and Entity Information - $ / shares	6 Months Ended
Document and Entity Information - $ / shares	Jun. 30, 2023	Jul. 28, 2023
Cover [Abstract]
Entity Central Index Key	0001597264
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Jun. 30, 2023
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		60,664,749
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2023
Document Fiscal Period Focus	Q2
Amendment Flag	false

Income Taxes - Expense (Benefit) (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Income tax expense (benefit)
Income tax expense	$ 190	$ 3,130	$ 710	$ 3,313

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

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Jun. 30, 2023	Dec. 31, 2022
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)	60,638,275	59,958,919
Common Stock, shares outstanding (in shares)	60,638,275	59,958,919

Leases (Tables)

6 Months Ended

Jun. 30, 2023

Summary of lease expenses and cash flow and weighted average information


	Three Months Ended				Six Months Ended
	June 30,				June 30,
Operating leases:	2023		2022		2023		2022
Lease cost	$	5,662	$	4,942	$	11,543	$	10,911
Sublease income		—		(600)		—		(1,381)
Net lease cost	$	5,662	$	4,342	$	11,543	$	9,530


	Six Months Ended
	June 30,
	2023		2022
Cash paid for amounts included in the measurement of lease liabilities:	$	8,812	$	7,763
Lease liabilities arising from obtaining right-of-use assets:
Operating leases	$	112	$	—


					Operating leases
Weighted average remaining lease term in years					6.3
Weighted average discount rate					7.4%

Stock-based Compensation - Stock-based Compensation Expense - By Type (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Total stock based compensation expense
Subtotal	$ 23,945	$ 25,524	$ 47,285	$ 49,133
Capitalized stock-based compensation costs	(124)	(177)	(268)	(387)
Stock-based compensation expense included in total cost and operating expenses	23,821	25,347	47,017	48,746
Employee Stock Option [Member]
Total stock based compensation expense
Subtotal	10,337	12,811	21,197	25,755
Restricted Stock Units
Total stock based compensation expense
Subtotal	12,913	12,396	24,853	22,782
Performance-based restricted stock units
Total stock based compensation expense
Subtotal	257		344
Employee Stock
Total stock based compensation expense
Subtotal	$ 438	$ 317	$ 891	$ 596

Product Revenue Reserves and Allowances - Product Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2023	Jun. 30, 2022	Jun. 30, 2023	Jun. 30, 2022
Revenues
Revenue	$ 57,570	$ 36,547	$ 120,857	$ 99,278
Product revenue, net
Revenues
Revenue	39,876	28,454	78,945	52,295
AYVAKIT and AYVAKYT
Revenues
Revenue	34,307	24,682	69,234	45,834
GAVRETO
Revenues
Revenue	$ 5,569	$ 3,772	$ 9,711	$ 6,461

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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Inventory - Balance Sheet Classification (Details) - USD ($) $ in Thousands	Jun. 30, 2023	Dec. 31, 2022
Inventory
Inventory	$ 17,016	$ 29,697
Other assets	19,922	6,488
Total	$ 36,938	$ 36,185

Collaboration and License Agreements

6 Months Ended

Jun. 30, 2023