SEQUENOM, INC. CHANGE IN CONTROL SEVERANCE BENEFIT PLAN

Exhibit 99.1

S EQUENOM , I NC .

CHANGE IN CONTROL SEVERANCE BENEFIT PLAN

The Sequenom, Inc. Change in Control Severance Benefit Plan (the “Plan” ) was established effective October 11, 2007 (the “Adoption Date” ). The purpose of the Plan is to provide severance benefits to certain eligible employees of the Company and its Affiliates upon selected terminations of service in connection with a Change in Control (as defined below).

This Plan shall supersede the Change in Control Severance Benefit Plan established effective April 28, 2005 and any generally applicable change in control severance plan, policy, or practice, whether written or unwritten, with respect to each employee who becomes a Participant in the Plan. For the purposes of the foregoing sentence, a “generally applicable change in control severance plan, policy or practice” is a plan, policy or practice in which benefits are not conditioned upon (i) being expressly designated a participant, (ii) receiving an award such as a stock option, or (iii) the employee expressly electing to participate. In consideration for the benefits set forth in this Plan, this Plan shall also supersede and replace the change in control severance benefits in any individually negotiated employment contract or agreement, or any written plans that are not of general application, and, except as set forth in the Participation Notice (as defined below), each Participant’s change in control severance benefits shall be governed solely by the terms of this Plan.

This Plan document is also the Summary Plan Description for the Plan.

The following shall be defined terms for purposes of the Plan:

(a) “Affiliate” means a Parent Corporation or a Subsidiary Corporation.

(b) “ Base Salary ” means a Participant’s monthly base salary in effect immediately prior to the Covered Termination and prior to any reduction in base salary that would permit such Participant to voluntarily terminate employment for Good Reason (as defined below) (including without limitation any compensation that is deferred by Participant into a Company-sponsored retirement or deferred compensation plan, exclusive of any employer matching contributions by the Company associated with any such retirement or deferred compensation plan and exclusive of any other Company contributions) and excludes all bonuses, commissions, expatriate premiums, fringe benefits (including without limitation car allowances), option grants, equity awards, employee benefits and other similar items of compensation.

(c) “ Board ” means the Board of Directors of the Company.

(d) “ Cash Severance Benefits Period ” means 24 months for a Tier I Participant and 12 months for all other Participants.

(e) “ Cash Severance Benefits Reduction Period ” means the 19 ^th through the 24 ^th month following the Covered Termination of a Tier I Participant.

(f) “ Cause ” means, with respect to a Participant, the occurrence of one or more of the following:

(1) Such Participant’s conviction of, or plea of guilty or no contest with respect to, (i) any crime involving fraud, dishonesty or moral turpitude, or (ii) any felony under the laws of the United States or any state thereof;

(2) Such Participant’s commission of, or attempted commission of, or participation in, a fraud or act of dishonesty against the Company that results in (or might reasonably result in) material harm to the Company;

(3) Such Participant’s intentional and material violation of any statutory duty owed to the Company;

(4) Such Participant’s unauthorized use or disclosure of the Company’s material confidential information, material trade secrets or material proprietary information;

(5) Such Participant’s intentional and material violation of a written policy or rule of the Company or intentional violation of a fiduciary duty to the Company; or

(6) Any other definition of “Cause” (or a similar term) set forth in such Participant’s written agreement governing his or her employment by the Company or the termination of such employment that, if met, would allow the Company to terminate such Participant’s employment without the obligation to provide Participant with specified severance benefits or payments.

(g) “ Change in Control ” means the occurrence of any of the following events prior to the automatic termination of this Plan as provided in Section 6(b):

(1) The consummation of a merger or consolidation of the Company with or into another entity or any other corporate reorganization, if more than 50% of the combined voting power of the continuing or surviving entity’s securities outstanding immediately after such merger, consolidation or other reorganization is not owned by persons who were stockholders of the Company immediately prior to such merger, consolidation or other reorganization, in substantially the same relative proportions as their ownership of the combined voting power of the Company immediately prior to such merger, consolidation or other reorganization;

(2) There is consummated a sale, lease, exclusive license or other disposition of all or substantially all of the assets of the Company, other than a sale, lease, license or other disposition of all or substantially all of the consolidated assets of the Company to an entity, more than 50% of the combined voting power of the voting securities of which are owned by stockholders of the Company in substantially the same proportions as their ownership of the outstanding voting securities of the Company immediately prior to such sale, lease, license or other disposition;

(3) When a majority of the incumbent directors on the Board are replaced by new directors within any 18-month period; provided, however, that each director (i) whose election has been approved by a vote of at least a majority of the directors who were either incumbent directors at the beginning of the period or elected or nominated in accordance with clause (i) or (ii) of this Section 2(f)(3) during such period or (ii) whose nomination for election by the Company’s stockholders has been approved by a committee of the Board, a majority of whose members are directors who were either incumbent directors at the beginning of the period or elected or nominated in accordance with clause (i) or (ii) of this Section 2(f)(3) during such period shall be deemed to be an “incumbent director” and not a “new director” for purposes of this Section 2(f)(3); or

(4) Any “person” that (as such term is used in sections 13(d) and 14(d) of the Securities Exchange Act of 1934, as amended) by the acquisition or aggregation of securities is or becomes the beneficial owner, directly or indirectly, of securities of the Company representing 50% or more of the combined voting power of the Company’s then outstanding securities ordinarily (and apart from rights accruing under special circumstances) having the right to vote at elections of directors (the “Base Capital Stock” ); except that any change in the relative beneficial ownership of the Company’s securities by any person resulting solely from a reduction in the aggregate number of outstanding shares of Base Capital Stock, and any decrease thereafter in such person’s ownership of securities, shall be disregarded until such person increases in any manner, directly or indirectly, such person’s beneficial ownership of any securities of the Company.

The term “Change in Control” shall not include a transaction, the sole purpose of which is to change the state of the Company’s incorporation.

(h) “ Company ” means Sequenom, Inc. or, following a Change in Control, the surviving entity resulting from such transaction or the parent company of such surviving entity.

(i) “Compensation Committee” means the Compensation Committee of the Board.

(j) “ Covered Termination ” means, with respect to a Participant who immediately prior to a termination of employment was an employee of the Company, such Participant’s termination of employment by the Company without Cause or a voluntary resignation of employment by the Participant for Good Reason; either of which occurring within the one-month period ending on the date of a Change in Control or 11-month period following a Change in Control.

(k) “ Good Reason ” means, with respect to a Participant, the occurrence of one or more of the following events, if applicable, without such Participant’s express written consent:

(1) A material reduction in such Participant’s authority, duties or responsibilities (and not simply a change in title or reporting relationships;

(2) A material reduction by the Company in such Participant’s Base Salary;

(3) A material adverse change by the Company to Participant’s Target Bonus or to the criteria, milestones or objectives related to such Participant’s Target Bonus that is reasonably likely to result in the Participant earning less than his or her Target Bonus during the subsequent applicable period;

(4) Any requirement, as a condition to continued service, that the Participant enter into any agreement with the Company regarding confidentiality, non-competition, non-solicitation or other similar restrictive covenant that is materially more restrictive than the Participant’s written obligations with the Company under which the Participant is then bound;

(5) Any Board action or assignment related to such Participant that is contrary to applicable law, regulatory guidelines or accounting standards or which constitutes an unethical business practice; or

(6) A relocation of the Participant’s principal place of work to a location that would increase the Participant’s one-way commute from his or her personal residence to the new principal place of work by more than 15 miles.

Notwithstanding the foregoing, a Participant shall have “Good Reason” for his or her resignation only if: (a) the Participant notifies the Company in writing, within 30 days after the occurrence of one of the foregoing events, that he or she intends to terminate his or her employment no earlier than 30 days after providing such notice; (b) the Company does not cure such condition within 30 days following its receipt of such notice or states unequivocally in writing that it does not intend to attempt to cure such condition; and (c) the Participant resigns from employment within 30 days following the end of the period within which the Company was entitled to remedy the condition constituting Good Reason but failed to do so.

(l) “ Health Severance Benefits Period ” means 18 months for a Tier I Participant and 12 months for all other Participants.

(m) “Parent Corporation” means any corporation (other than the Company) in an unbroken ownership chain of corporations ending with the Company, provided each corporation in the unbroken ownership chain (other than the Company) owns, at the time of the determination, stock possessing 50% or more of the total combined voting power of all classes of stock in one of the other corporations in such ownership chain.

(n) “ Participant ” means an individual who (i) is employed by the Company or its Affiliates, (ii) has been designated eligible to participate in the Plan by the Plan Administrator in its sole discretion (either by a specific designation or by virtue of being a member of a class of employees who have been so designated) and (iii) who has received a Participation Notice from the Company and elected to participate in the Plan by executing and returning such Participation Notice to the Company within the time period set forth therein. The Participation Notice shall designate the Participant as either a “Tier I Participant”, “Tier II Participant” or “Tier III Participant”; provided that, in the absence of such specific designation,

the Participant shall be deemed a Tier III Participant for purposes of the Plan. The determination of whether an employee is eligible to be a Participant and the designation of either a Tier I Participant, Tier II Participant or Tier III Participant, shall be made by the Plan Administrator, in its sole discretion, and such determination shall be binding and conclusive on all persons.

(o) “ Participation Notice ” means the latest notice delivered by the Company to a Participant substantially in the form of Exhibit A hereto or such other form as may be approved by the Plan Administrator.

(p) “Payment Commencement Date” means, with respect to a Participant, (i) if such Covered Termination occurs prior to the applicable Change in Control, the later of (A) such Change in Control or (B) the effective date of the Release (as defined below) or (ii) if such Covered Termination occurs on or after the applicable Change in Control, the later of (X) the date of such Covered Termination or (Y) the effective date of the Release.

(q) “Plan Administrator” means the Compensation Committee.

(r) “ Qualified Plan ” means a plan sponsored by the Company or an Affiliate that is intended to be qualified under Section 401(a) of the Internal Revenue Code.

(s) “Subsidiary Corporation” means any corporation (other than the Company) in an unbroken ownership chain of corporations beginning with the Company, provided each corporation (other than the last corporation) in the unbroken ownership chain owns, at the time of the determination, stock possessing 50% or more of the total combined voting power of all classes of stock in one of the other corporations in such ownership chain.

(t) “Target Bonus” means the target bonus (i.e., the annual bonus amount payable to a Participant in cash, common stock or other property if exactly 100% of all performance goals are achieved) most recently approved by the Compensation Committee or the Board for such Participant prior to the earlier of (i) the Payment Commencement Date and (ii) any reduction in Target Bonus that would permit such Participant to voluntarily terminate employment for Good Reason.

(u) “Vesting Acceleration Benefit” means (i) the remainder of all vesting installments, whether time-based or performance-based, for a Tier I Participant, (ii) the next 24 monthly time-based vesting installments following the Covered Termination for a Tier II Participant and (iii) the next 12 monthly time-based vesting installments following the Covered Termination for a Tier III Participant.

The following additional terms are defined in the Section identified below:

Subject to the requirements set forth in this Section, the Company shall provide change in control severance benefits under the Plan to the Participants. In order to be eligible to receive benefits under the Plan, a Participant must (i) experience a Covered Termination and (ii) execute a general waiver and release (the “Release” ) in substantially the form attached hereto as Exhibit B , Exhibit C , or Exhibit D , as appropriate (or as then may be required by law to effect a release of claims), and such Release must become effective in accordance with its terms; provided, however, that no such Release shall require the Participant to forego any unpaid salary, any accrued but unpaid vacation pay or any benefits payable pursuant to this Plan. With respect to any outstanding option held by the Participant, no provision set forth in this Plan granting the Participant additional rights to exercise the option can be exercised unless and until the Release becomes effective.

The Participant must execute the Release within the time period set forth therein, but in no event later than (x) if a Change in Control shall have occurred prior to such Covered Termination, 45 days following termination of employment or (y) if a Change in Control shall not have occurred prior to such Covered Termination, the later of (A) 45 days following termination of employment or (B) ten days following such Change in Control, and such release must become effective in accordance with its terms.

Unless a Change in Control has occurred, the Plan Administrator, in its sole discretion, may modify the form of the required Release to comply with applicable law and shall determine the form of the required Release, which may be incorporated into a termination agreement or other agreement with the Participant; provided, that, after a Change in Control occurs, the Plan Administrator may modify the form of required Release only if necessary to comply with applicable law.

(a) Subject to the limitations and reductions provided in this Plan, benefits under this Plan, if any, shall be provided to the Participants described in Section 3 in the following amounts. Effective commencing with the Payment Commencement Date, such Participant shall receive the following severance package:

(1) Cash Severance Benefits . At the end of each month during the Cash Severance Benefit Period, which shall commence with the first full month following the Payment Commencement Date, the Participant shall receive a payment in an amount equal to the Participant’s Base Salary.

(2) Bonus Severance Benefits . The Company shall make a cash severance payment to the Participant in an amount equal to a percentage of such Participant’s Target Bonus as set forth in the following table:

Any such bonus payment pursuant to this Section 4(a)(2) shall be in a single lump sum to be paid within 10 days following the Payment Commencement Date.

(3) COBRA Benefits. If such Participant timely elects to continue coverage under the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended ( “COBRA” ), then during the Health Severance Benefits Period, the Company will (i) pay all premiums for group medical, dental and vision coverage elected by such Participant for the Participant and his or her eligible dependents under (A) COBRA and, to the extent applicable, any similar applicable state statute, and (B) to the extent that such coverage under COBRA and any such applicable state statute has been exhausted or is no longer available, then under any individual policy providing group medical, dental and vision benefits substantially similar to those provided to Participant immediately prior to his or her termination of Service, and (ii) if Participant is eligible for benefits under the Exec-U-Care plan, reimburse all other out-of-pocket costs associated with Participant’s participation in such plan. In addition, if Participant does not timely elect to continue coverage group medical, dental or vision coverage under COBRA, then the Company will pay Participant in a lump sum the equivalent cash value of the COBRA payments that otherwise would have been made pursuant to this Section 4(a)(3). Such payment shall be made within 30 days following the expiration date of the COBRA election period. For purposes of this Section 4(a)(3), references to COBRA premiums shall not include any amounts payable by the Participant under an Internal Revenue Code Section 125 health care reimbursement plan. Notwithstanding the foregoing, no such premium payments (or any other payments for health, dental, or vision coverage by the Company) shall be made following the Participant’s death or the effective date of the Participant’s coverage by a health, dental, or vision insurance plan of a subsequent employer.

(4) Equity Award Acceleration. The vesting and exercisability of all outstanding options to purchase the Company’s common stock issued pursuant to any equity incentive plan of the Company or any Affiliate that are then held by the Participant on such date shall be accelerated to the extent applicable so that the Participant shall receive the Vesting Acceleration Benefit, any reacquisition or repurchase rights held by the Company in respect of

common stock issued pursuant to any other stock award granted to the Participant by the Company shall lapse so that the Participant shall receive the Vesting Acceleration Benefit, and the vesting of any other stock awards granted to the Participant by the Company, and any issuance of shares triggered by the vesting of such stock awards, shall be accelerated so that the Participant shall receive the Vesting Acceleration Benefit. If the Covered Termination occurs prior to the applicable Change in Control, such vesting acceleration shall be deemed effective as of the date of the Covered Termination. Notwithstanding the foregoing, this Section 4(a)(4) shall not apply to stock awards issued under or held in any Qualified Plan. Notwithstanding the provisions of this Section 4(a)(4), in the event that the provisions of this Section 4(a)(4) regarding acceleration of vesting of an option would adversely affect a Participant’s option (including, without limitation, its status as an incentive stock option under Section 422 of the Code) that is outstanding on the date the Participant commences participation in the Plan, such acceleration of vesting shall be deemed null and void as to such option unless the affected Participant consents in writing to such acceleration of vesting as to such option at the time he or she becomes a Participant.

(b) Certain Reductions. Notwithstanding any other provision of the Plan to the contrary, any benefits payable to a Participant under Sections 4(a)(1) and 4(a)(2) of this Plan shall not be reduced by any severance benefits payable by the Company or an affiliate of the Company to such Participant under any contract or agreement (including an employment agreement) between such Participant and the Company, covering such Participant; provided, however , that this Plan shall supersede and replace the change in control severance benefits in any individually negotiated employment contract or agreement, or any written plans, and, except as set forth in the Participation Notice, each Participant’s change in control severance benefits shall be governed by the terms of this Plan.

(c) Mitigation. If, during a Tier I Participant’s Cash Severance Benefits Period, such Tier I Participant begins full-time employment with another employer, then (i) the amount payable by the Company to the Tier I Participant pursuant to Section 4(a)(1) above during the Cash Severance Benefits Reduction Period shall be reduced by the amount of any compensation paid to (or payable to) the Participant from such other employer during the Cash Severance Benefits Period (but in any case such amount payable by the Company during the Cash Severance Benefits Reduction Period shall not be reduced below zero).

(d) Application of Section 409A . Severance benefits payable under the Plan are intended to be payable pursuant to a window program pursuant to Section 1.409A-1(b)(9)(iii) of the Internal Revenue Service Treasury Regulations, to the maximum extent permitted by said provision, with any excess amount being regarded as subject to the distribution requirements of Section 409A(a)(2)(A) of the Internal Revenue Code of 1986, as amended (the “Code” ), including, without limitation, the requirement of Section 409A(a)(2)(B)(i) of the Code that payment to Participant be delayed, if necessary, until six months after the Participant’s separation from service if Participant is a “specified employee” within the meaning of the aforesaid section of the Code at the time of such separation from service.

(e) Withholding . All payments under the Plan will be subject to all applicable withholding obligations of the Company, including, without limitation, obligations to withhold for federal, state and local income and employment taxes.

(a) Termination of Benefits. Benefits under the Plan shall terminate immediately if the Participant, at any time, (i) engages in the unauthorized use or disclosure of the Company’s material confidential information, material trade secrets or material proprietary information under any written agreement under which the Participant has such an obligation to the Company that survives the Participant’s termination of service to the Company, (ii) engages in any prohibited or unauthorized competitive activities, or prohibited or unauthorized solicitation or recruitment of employees, in violation of any written agreement under which Participant has such an obligation to the Company that survives the Participant’s termination of service to the Company; (iii) violates any material term or condition of this Plan, or (iv) violates any term of the Release.

(b) Non-Duplication of Benefits. No Participant is eligible to receive benefits under this Plan more than one time.

(c) Indebtedness of Participants. To the extent permitted by law, if a Participant is indebted to the Company or an affiliate of the Company on the date of his or her termination of employment or service, the Company reserves the right to offset any severance benefits payable in cash under the Plan by the amount of such indebtedness. A Participant may be required to execute an agreement to such effect if requested by the Company.

(d) Parachute Payments. If any payment or benefit a Participant would receive in connection with a Change in Control from the Company or otherwise (a “Payment” ) would (i) constitute a “parachute payment” within the meaning of Section 280G of the Code, and (ii) but for this sentence, be subject to the excise tax imposed by Section 4999 of the Code (the “ Excise Tax ”), then such Payment shall be equal to the Reduced Amount. The “Reduced Amount” shall be either (x) the largest portion of the Payment that would result in no portion of the Payment being subject to the Excise Tax or (y) the largest portion of the Payment, up to and including the total Payment, whichever amount, after taking into account all applicable federal, state and local employment taxes, income taxes, and the Excise Tax (all computed at the highest applicable marginal rate), results in the Participant’s receipt, on an after-tax basis, of the greater amount of the Payment notwithstanding that all or some portion of the Payment may be subject to the Excise Tax. If a reduction in paym