Exhibit 10.51

***Text Omitted and Filed Separately with the Securities and Exchange Commission.

Confidential Treatment Requested Under

17 C.F.R. Sections 200.80(b)(4) and 240.24b-2

DATED 3rd November 2009

ISIS INNOVATION LIMITED

AND

SEQUENOM, INC.

THIRD AMENDMENT AGREEMENT

THIS THIRD AMENDMENT AGREEMENT is made on 3rd November, 2009 (The “Third Amendment Agreement Effective Date”).

BETWEEN:

BACKGROUND:

AGREEMENT:

Except as otherwise provided in this Third Amendment Agreement, words and expressions used in this Agreement have the same meaning as in the Licence.

In consideration of the waiver, release and discharge given by the Licensor in clause 4 below, the Licensee enters into the covenants in this Third Amendment Agreement and the Licensee shall pay to the Licensor the sum of one million US dollars (USD 1,000,000) by wire transfer within […***…] of the Third Amendment Agreement Effective Date. The sum is expressed as being exclusive of VAT which if applicable shall be paid at the prevailing rate in force.

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With effect on and from the Third Amendment Agreement Effective Date the following amendments are made to the Licence:

“The Licensee will pay to the Licensor a royalty equal to the Royalty Rate on all Net Sales of Licensed Products. Royalty payments under this clause 8.2 shall be made by Licensee to Licensor within […***…] of the expiration of each Licence Year during the Agreement save that in respect of Royalties payable in respect of the final twelve (12) months of this Agreement (calculated in accordance with clause 11.1) (“Final Twelve Months”) in consideration for the benefits that Licensee is receiving under this Third Amendment Agreement, Licensee agrees that it shall pay to the Licensor a royalty equal to […***…], on Net Sales of Licensed Products occurring during the Final Twelve Months.”

“The Licensee must use its reasonable endeavors throughout the duration of the Licence to develop, exploit and Market the Licensed Technology to maximize the financial return for both parties.”

“The Licensee undertakes to:

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Minimum Sum (clause 8.4):

Milestones and Milestone Fee (clause 8.6):

The Licensor hereby irrevocably waives, releases and discharges the Licensee from and against any and all claims and causes including the Licensor’s rights to damages, rights to terminate the Licence or to convert the Licence from exclusive to a non-exclusive basis arising as a result of Licensee’s past performance under the Licence up to and including the Third Amendment Agreement Effective Date relating to the Licensee’s failure to achieve certain developmental and commercial Milestones as originally contemplated by the parties.

English Law governs this Third Amendment Agreement, and the parties submit to the exclusive jurisdiction of the English Courts for the resolution of any dispute which may arise out of or in connection with this Agreement save for injunctive relief which may be sought in any court of competent jurisdiction.

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AS WITNESS this agreement has been executed by the duly authorized representatives of the parties, respectively, the date(s) written below.