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SCHEDULE 13D/A 0001315863-25-000377 0001822257 XXXXXXXX LIVE 9 Class A common stock, par value $0.0001 per share 08/22/2025 false 0001818331 81663L200 GeneDx Holdings Corp. 333 Ludlow Street North Tower, 8th Floor Stamford CT 06902 Eli Casdin and Keith Meister (212) 474-6700 c/o Corvex Management LP 667 Madison Avenue New York NY 10065 0001822257 N CMLS Holdings LLC OO N DE 0.00 537285.00 0.00 537285.00 537285.00 N 1.9 OO 0001822233 N C-LSH LLC OO N DE 0.00 537285.00 0.00 537285.00 537285.00 N 1.9 HC OO 0001822736 N M-LSH LLC OO N DE 0.00 537285.00 0.00 537285.00 537285.00 N 1.9 HC OO 0001534261 N Casdin Capital, LLC AF N DE 0.00 3007164.00 0.00 3007164.00 3007164.00 N 10.5 IA 0001534265 N Casdin Partners Master Fund, L.P. WC N E9 0.00 3007164.00 0.00 3007164.00 3007164.00 N 10.5 PN 0001534260 N Casdin Partners GP, LLC AF N DE 0.00 3026411.00 0.00 3026411.00 3026411.00 N 10.5 OO 0001534264 N Eli Casdin AF N X1 35975.00 3563696.00 35975.00 3563696.00 3599671.00 N 12.4 IN HC 0001307631 N Keith A. Meister OO N X1 34912.00 3595914.00 34912.00 3595914.00 3630826.00 N 12.5 IN HC 0001535472 N Corvex Management LP AF N DE 0.00 3058629.00 0.00 3058629.00 3058629.00 N 10.6 IN PN Class A common stock, par value $0.0001 per share GeneDx Holdings Corp. 333 Ludlow Street North Tower, 8th Floor Stamford CT 06902 This Amendment No. 9 (the "Amendment") supplements the information set forth in the Schedule 13D (the "Schedule 13D") filed with the United States Securities and Exchange Commission (the "SEC") on August 2, 2021, as amended as of January 19, 2022, May 3, 2022, December 5, 2022, February 1, 2023, April 20, 2023, November 17, 2023, May 31, 2024 and May 7, 2025 by CMLS Holdings LLC, Keith Meister, Eli Casdin and the other Reporting Persons named therein, relating to the shares of Class A common stock, par value $0.0001 per share ("Shares"), of GeneDx Holdings Corp. (formerly known as Sema4 Holdings Corp., the "Issuer"). Capitalized terms used but not defined herein shall have the meanings ascribed to them in the Schedule 13D. The information set forth in response to each separate Item below shall be deemed to be a response to all Items where such information is relevant. Item 3 and 5 to the Schedule 13D are supplementally amended as follows. Information with respect to each Reporting Person is given solely by such Reporting Person and no Reporting Person assumes responsibility for the accuracy or completeness of the information furnished by another Reporting Person, except as otherwise provided in Rule 13d-1(k). The funds for the purchase of the Shares listed in Exhibit B came from the working capital of Casdin Partners Master Fund, L.P, an investment fund advised by Casdin Capital, LLC, of which Mr. Casdin is the managing member. No borrowed funds were used to purchase the Shares, other than borrowed funds used for working capital purposes in the ordinary course of business. The information set forth in the facing pages of this Schedule 13D with respect to the sole and shared beneficial ownership and percentage of beneficial ownership of Shares by the Reporting Persons is hereby incorporated by reference into this Item 5. The information in Item 5(b) below is hereby incorporated by reference into this Item 5(a). References to percentage ownership of Shares in this Statement are based upon the 28,726,248 Shares stated to be outstanding as of July 24, 2025 in the Issuer's Form 10-Q filed with the SEC on July 29, 2025. The filing of this Statement shall not be construed as an admission that a Reporting Person beneficially owns those Shares held by any other Reporting Person Eli Casdin has the sole power to vote or direct the vote and sole power to dispose or to direct the disposition of 35,975 Shares and shared power to vote or to direct the vote and shared power to dispose or to direct the disposition of 3,563,696 Shares. The Shares reflected as beneficially owned by Mr. Casdin include 333,144 Shares and 204,141 Shares issuable upon the exercise of 204,141 private placement warrants of the Issuer. On September 3, 2021, each private placement warrant became exercisable to purchase one Share at a price of $379.50 per share, subject to adjustment, as described in the definitive proxy statement of the Issuer (File No. 001-39482) filed with the SEC on July 2, 2021. CMLS Holdings LLC is the record holder of these Shares and warrants. The Board of Managers of CMLS Holdings LLC is comprised of Mr. Casdin and Mr. Meister who share voting and investment discretion with respect to the Shares held of record by CMLS Holdings LLC. C-LSH LLC and M-LSH LLC are the members of CMLS Holdings LLC, and Mr. Casdin is the managing member of C-LSH LLC. As such, each of the foregoing may be deemed to have or share beneficial ownership of the Shares held directly by CMLS Holdings LLC. Casdin Partners Master Fund, LP is the record holder of 3,007,164 Shares reported herein. Casdin Capital, LLC is the investment adviser to Casdin Partners Master Fund, LP and may be deemed to have or share beneficial ownership of the 3,007,164 Shares held by Casdin Partners Master Fund, LP. Casdin Partners GP, LLC is the general partner of Casdin Partners Master Fund LP and may be deemed to have or share beneficial ownership of the 3,007,164 Shares held by Casdin Partners Master Fund, LP, and Casdin Partners GP, LLC is also the direct beneficial owner of 19,247 Shares. Eli Casdin is the managing member of Casdin Capital, LLC and Casdin Partners GP, LLC. As such, each of the foregoing may be deemed to have or share beneficial ownership of the Shares held directly by Casdin Partners Master Fund, LP and Eli Casdin may be deemed the beneficial owner of the 19,247 Shares held by Casdin Partners GP, LLC. The Shares reflected as solely beneficially owned by Mr. Casdin also include 11,882 Shares issuable upon the exercise of fully vested options, 20,518 Shares that were issued upon the vesting of restricted stock units, and 3,576 Shares to be issued upon vesting of restricted stock units, in each case that were granted to Mr. Casdin in connection with his service on the board of directors of the Issuer. Keith Meister has the sole power to vote or to direct the vote and sole power to dispose or to direct the disposition of 34,912 Shares and shared power to vote or direct the vote and shared power to dispose or to direct the disposition of 3,595,914 Shares. The Shares reflected as beneficially owned by Mr. Meister include 333,144 Shares and 204,141 Shares issuable upon the exercise of 204,141 private placement warrants of the Issuer. On September 3, 2021, each private placement warrant became exercisable to purchase one Share at a price of $379.50 per share, subject to adjustment, as described in the definitive proxy statement of the Issuer (File No. 001-39482) filed with the SEC on July 2, 2021. CMLS Holdings LLC is the record holder of these Shares and warrants. The Board of Managers of CMLS Holdings LLC is comprised of Mr. Casdin and Mr. Meister who share voting and investment discretion with respect to the Shares held of record by CMLS Holdings LLC. C-LSH LLC and M-LSH LLC are the members of CMLS Holdings LLC, and Mr. Meister is the managing member of M-LSH LLC. As such, each of the foregoing may be deemed to have or share beneficial ownership of the Shares held directly by CMLS Holdings LLC. The Shares reflected as beneficially owned by Mr. Meister include 3,058,629 Shares owned by investment funds advised by Corvex Management LP, which may be deemed to be indirectly beneficially owned by Keith Meister by virtue of Mr. Meister's control of the general partner of Corvex Management LP. The Shares reflected as beneficially owned by Mr. Meister also include 11,207 Shares issuable upon the exercise of fully vested options, 20,129 Shares that were issued upon the vesting of restricted stock units, and 3,576 Shares to be issued upon vesting of restricted stock units, in each case that were granted to Mr. Meister in connection with his service on the board of directors of the Issuer. The transactions by the Reporting Persons in the securities of the Issuer during the past sixty days are set forth in Exhibit B. All such transactions were carried out in open market transactions. No person other than the Reporting Persons is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the Shares beneficially owned by the Reporting Persons. Not applicable. Exhibit A: Joint Filing Agreement Exhibit B: Schedule of Transactions in Shares CMLS Holdings LLC By: /s/ Eli Casdin Eli Casdin, Manager 08/26/2025 C-LSH LLC By: /s/ Eli Casdin Eli Casdin, Managing Member 08/26/2025 M-LSH LLC By: /s/ Keith A. Meister Keith A. Meister, Managing Member 08/26/2025 Casdin Capital, LLC By: /s/ Eli Casdin Eli Casdin, Managing Member 08/26/2025 Casdin Partners Master Fund, L.P. By: /s/ Eli Casdin Eli Casdin, Managing Member of its General Partner 08/26/2025 Casdin Partners GP, LLC By: /s/ Eli Casdin Eli Casdin, Managing Member 08/26/2025 Eli Casdin By: /s/ Eli Casdin Eli Casdin 08/26/2025 Keith A. Meister By: /s/ Keith A. Meister Keith A. Meister 08/26/2025 Corvex Management LP By: /s/ Keith A. Meister Keith Meister, Managing Partner 08/26/2025 * This reporting person disclaims beneficial ownership of these reported securities except to the extent of its pecuniary interest therein, and this report shall not be deemed an admission that any such person is the beneficial owner of these securities for purposes of Section 16 of the U.S. Securities Exchange Act of 1934, as amended, or for any other purpose. Attention: Intentional misstatements or omissions of fact constitute Federal criminal violations (see 18 U.S.C. 1001).