SEQUENOM INC. AMENDED AND RESTATED EMPLOYMENT AGREEMENT

Exhibit 10.29

SEQUENOM INC.

AMENDED AND RESTATED EMPLOYMENT AGREEMENT

This Amended and Restated Employment Agreement (this “ Agreement ”) is entered into between Sequenom, Inc. a Delaware corporation (the “ Company ”) and Harry Stylli, Ph.D. (“ Employee ”), on December 15, 2008. This Agreement shall replace and supersede that certain Employment Agreement between Employee and the Company entered into effective as of May 31, 2005 (the “ Prior Agreement ”). In consideration of, and as a condition of Employee’s employment by the Company, and of the compensation to be paid to Employee by the Company, and in recognition of the fact that Employee will have access to the Company’s confidential, proprietary, and trade secret information, the Company and Employee agrees to the terms and conditions set forth in this Agreement as follows:

1. Employment. Director.

1.1 Employment. Employee will continue to be employed by the Company as its President and Chief Executive Officer. Employee previously commenced employment with the Company in June 2005, (such hire date is referred to herein as the “Hire Date” ). Employee agrees that Employee’s employment with the Company is on an at-will basis, is for no specified term and may be terminated by the Company at any time, with or without Cause (as defined in Section 10(c) herein), in accordance with and subject to the terms of Section 10 of this Agreement. Similarly, Employee may terminate employment with the Company at any time for any reason upon written notice as provided in Section 10 of this Agreement. Employee understands and agrees that the at-will nature of Employee’s employment relationship with the Company cannot be changed or modified except by a written agreement signed by the Chairman of the Board of Directors of the Company (the “ Board ”).

1.2 Director. Effective as of the Hire Date, employee was elected to the Board. Employee agrees to resign as a director of the Company, if requested to do so by the Board, upon the termination of his employment with the Company.

2. Duties of Employee. Employee shall report to the Board. Employee shall have overall responsibility for the management, direction, and operations of the Company. Employee shall perform such other duties and have such other responsibilities as may be assigned to Employee from time to time by the Board.

3. Loyalty. As long as Employee is employed by the Company, Employee shall devote full time and efforts to the Company and shall not, without the Company’s prior express written consent, engage directly or indirectly in any employment, consulting or business activity other than for the Company. Notwithstanding the foregoing, the Company agrees that Employee may continue to provide services as a member of the board of directors of Xencor and Molecular Insight Pharmaceuticals, as an advisor to Nanosyn and as a passive owner in a start-up internet business that is tentatively named BIZbt. In addition, Employee may serve as director or trustee of one or more other corporations or foundations (either for-profit or not-for-profit) if such service has been approved by the Board. Employee will refer to the Company all corporate opportunities Employee learns of as a result of service of an employee of the Company.

4. Compensation and Benefits.

4.1 Salary. Employee’s annual base salary shall be $441,000, less standard deductions and withholdings, payable in accordance with the Company’s standard

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payroll policy. Such base salary may be increased, subject to approval by the Compensation Committee of the Board.

4.2 Bonus. Employee shall be eligible for an annual performance bonus of up to 50% of Employee’s applicable annual base salary (the “Target Bonus” ), less standard deductions and withholdings. The amount of the bonus, if any, will be determined by the Company’s and Employee’s performance against specific measurable corporate and personal goals established annually by the Compensation Committee of the Board. The Target Bonus shall be paid during the calendar year that follows the calendar year for which it was earned.

4.3 Inducement Stock Options. Effective as of the Hire Date and as an inducement to join the Company, the Company granted to Employee stock options to purchase an aggregate of 1,000,000 shares of the common stock of the Company, $0.001 par value per share (the “ Common Stock ”). The exercise price for such stock options was equal to the fair market value of the Common Stock on the Hire Date, as determined by the Board. Such stock options have a 10 year term and become exercisable or “vest” as described in the individual stock option agreement (twenty-five percent after one year of employment from the Hire Date, and the balance in 36 equal monthly installments thereafter so long as Employee remains employed by the Company), subject to acceleration as set forth below. In addition, Employee will be permitted to exercise such stock options for up to one year following termination of his employment by the Company (but in any event no later than the end of the maximum permitted term of the option). Such stock options shall not vest during the Consulting Period (as defined in Section 12.1 herein) or any other time that Employee is not employed by the Company. The other terms and conditions of such stock options are as set forth in the individual stock option agreements, which shall be the Company’s standard form of option agreement and consistent with its 1999 Stock Incentive Plan (the “Option Plan” ); provided, however, that such stock options may not be granted pursuant to the Option Plan.

4.4 Contingent Stock Options. Upon the closing of the sale by the Company of any equity financing (which may include one or more related closings for the sale of newly issued shares of Common Stock or preferred stock or other securities convertible into or exercisable for Common Stock) for aggregate gross proceeds of at least $10 million prior to July 1, 2006, the Company shall grant to Employee pursuant to the Option Plan additional stock options to purchase that number of shares of Common Stock necessary for Employee to retain an equivalent ownership position, on a fully diluted basis (assuming the exercise and conversion of all outstanding securities convertible into or exercisable for Common Stock), as that held by Employee immediately prior to such closing. Such additional stock options, if granted, shall have an exercise price equal to the fair market value of the Common Stock on the date of such closing, as determined by the Board. Such additional stock options, if granted, shall have a 10 year term and vest as described in the individual grant option agreement (twenty-five percent after one year of employment from the date of grant, and the balance in 36 equal monthly installments thereafter so long as Employee remains employed by the Company), subject to acceleration as set forth below. In addition, Employee will be permitted to exercise such stock options for up to one year following termination of his employment by the Company (but in any event no later than the end of the maximum permitted term of the option). Such additional stock options shall not vest during the Consulting Period or any other time that Employee is not employed by the Company. The other terms and conditions of such stock options shall be governed by the Option Plan and the individual stock option agreements.

4.5 Change in Control Plan. Employee shall be an eligible “Participant” in the Company’s Change in Control Severance Benefit Plan (the “ Change in Control Plan ”.

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4.6 Other Benefits. Employee shall receive the following employee benefits:

(a) participation for Employee and his family in the Company’s group health insurance programs;

(b) term life insurance coverage of $1,000,000;

(c) disability insurance providing long-term coverage of $20,000 per month; and

(d) 8 Company-wide holidays, 8 individual floating holidays and 17 paid vacation days (excluding individual floating holidays) per calendar year.

In the case of clauses (a), (b) and (c) above, with insurance companies and on such other terms, including but not limited to eligibility, exclusions and coverage limitations, as are reasonably acceptable to Employee; provided, however, that the aggregate additional cost to the Company of the insurance coverage described in clauses (b) and (c) in excess of that provided to employees of the Company generally shall not exceed $15,000 per year and if such cost would exceed $15,000, Employee shall be entitled to adjust the coverage so that such aggregate additional cost shall not exceed $15,000. In addition, Employee shall be entitled to participate in such employee benefit plans and to receive such other fringe benefits as are customarily afforded the Company’s employees. Employee understands that, except when prohibited by applicable law, the Company’s employee benefit plans and fringe benefits, including the Option Plan, may be amended, enlarged, diminished or terminated by the Company from time to time, in its sole discretion.

4.7 Expense Reimbursement. Upon submission of itemized expense statements in the manner specified by the Company, the Company will pay Employee’s reasonable travel and other reasonable business expenses incurred by Employee in the furtherance of and in connection with Employee’s employment hereunder, provided that Employee submits receipts or other documentation for such expenses no later than ninety (90) days after incurring such expenses. The Company shall reimburse all such eligible expenses promptly, but in no event later than ninety (90) after receiving such documentation.

5. Employee’s Performance .

5.1 Rules, Procedures and Standards. Employee shall use best efforts to perform assigned duties diligently, loyally, conscientiously, and with reasonable skill, and shall comply with all rules, procedures and standards promulgated from time to time by the Company. Among such rules, procedures and standards are those governing ethical and other professional standards for dealing with customers, government agencies, vendors, competitors, consultants, fellow employees, and the public-at-large; security provisions designed to protect the Company’s property and the personal security of the Company’s employees; rules respecting attendance, punctuality, and hours of work; and, rules and procedures designed to protect the confidentiality of the Company’s proprietary and trade secret information. The Company agrees to make reasonable efforts to inform Employee of such rules, standards and procedures as are in effect from time to time.

5.2 Employee Handbook. The employment relationship between the Company and Employee shall be governed by the policies and practices established by the Company and the Board. Employee will acknowledge in writing that he has read the

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Company’s Employee Handbook, which will govern the terms and conditions of his employment with the Company, along with this Agreement. In the event that the terms of this Agreement differ from or are in conflict with the Company’s policies or practices or the Company’s Employee Handbook, this Agreement shall control.

5.3 Additional Representations. Employee hereby represents and warrants that (i) Employee has the full right to enter into this Agreement and perform the services required of hereunder, without any restriction whatsoever, and (ii) in the course of performing services hereunder, Employee will not violate the terms or conditions of any agreement between Employee and any third party. It is the understanding of both the Company and Employee that Employee shall not divulge to the Company or any of its subsidiaries any confidential information or trade secrets belonging to others, including Employee ’s former employers, nor shall the Company or any of its affiliates seek to elicit from Employee any such information. Consistent with the foregoing, Employee shall not provide to the Company or any of its affiliates, and the Company and its affiliates shall not request, any documents or copies of documents containing such information.

6. The Company’s Management Rights. The Company retains its full management prerogatives and discretion to manage and direct its business affairs, including the adoption, amendment or modification of research, development, production or marketing decisions as it sees fit, notwithstanding any individual interest in, or expectation, Employee may have regarding a particular business program or product.

7. Nondisclosure of Confidential, Proprietary or Trade Secret Information . As a condition of continued employment, Employee agrees to continue to abide by the Proprietary Information and Inventions Agreement previously entered into in conjunction with the Prior Agreement (the “ Inventions Agreement ”). The termination of employment shall not release Employee from Employee’s obligations under the Inventions Agreement or as established by applicable laws or the Company’s policies.

8. No Solicitation of Customers or Employees. Employee acknowledges that the Company has invested substantial time, effort and expense in compiling its confidential, proprietary and trade secret information and in assembling its present staff of personnel. In order to protect the business value of the Company’s confidential, proprietary and trade secret information, during Employee’s employment with the Company and for one year immediately following the termination of that employment with the Company:

(a) Employee agrees that information regarding all customers and all prospective customers of the Company, of which Employee learns during Employee’s employment with the Company, may constitute “Proprietary Information” of the Company as defined in the Inventions Agreement.

(b) Employee agrees not to, directly or indirectly, induce or solicit any of the Company’s employees to leave their employment with the Company.

9. Return of Property . Upon the termination of Employee’s employment with the Company or at any other time upon request of the Company, Employee shall promptly return any and all customer or prospective customer lists, other customer or prospective customer information or related materials, formulas, computer data and programs, specifications, drawings, blueprints, data storage devices, reproductions, sketches, notes, memoranda, reports, records, proposals, business plans, or copies of them, other documents, materials,

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tools, equipment, and all other property belonging to the Company or its customers which Employee then possesses. Employee further agrees, that upon termination of his employment, Employee shall not take any documents or data of any description containing or pertaining to the Company’s Proprietary Information or Inventions, as those terms are defined in the Inventions Agreement. Upon leaving the Company’s employment, Employee agrees to sign a Termination Certificate confirming that Employee has complied with the requirements of this Section 9 and that Employee is aware that certain restrictions imposed by this Agreement continue after termination of Employee’s employment. Employee further understands that Employee’s continuing obligations under the Inventions Agreement will continue even if Employee does not sign a Termination Certificate.

10. Termination. Employee’s employment hereunder shall terminate upon the occurrence of any of the following events:

(a) The death or legal incapacity of Employee.

(b) Written notice from the Company to Employee of Employee’s employment termination as a result of Employee’s permanent disability. For purposes of this Agreement, Employee’s “permanent disability” shall be deemed to have occurred if Employee shall become physically or mentally incapacitated or disabled and unable fully to discharge his duties hereunder by reason of any medically determinable physical or mental impairment for a period of 180 consecutive calendar days; provided that in no event shall Employee’s permanent disability be deemed to have occurred if Employee is not then eligible to receive the long-term disability insurance benefits described in Section 4.6 of this Agreement. The existence of Employee’s permanent disability shall be determined on the advice of a physician mutually acceptable to the Company and Employee (or Employee’s legal representative).

(c) Written notice from the Company to Employee of Employee’s employment termination by the Company for Cause (as hereafter defined). The Company shall have “Cause” for termination of Employee’s employment if any of the following occur: