First Amendment to Amended and Restated Investor Rights Agreement by and among Genoptix, Inc. and Investors

Exhibit 4.10

GENOPTIX, INC.

FIRST AMENDMENT TO
AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT

        This FIRST AMENDMENT TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT (this "Amendment") by and among GENOPTIX, INC., a Delaware corporation (the "Company") and the investors listed on the signature pages hereof (each, an "Investor", and together, the "Investors") dated as of May 9, 2005 (the "Investor Rights Agreement") is entered into as of August 3, 2005 by and among the Company and the Investors. Capitalized terms used herein which are not defined herein shall have the definition ascribed to them in the Investor Rights Agreement.

RECITALS

        WHEREAS, the Company and the Investors have previously entered into the Investor Rights Agreement, pursuant to which the Investors possess certain registration, right of first refusal, information and other investor rights;

        WHEREAS, the Company is entering into a Follow-On Series 1-D Preferred Stock Purchase Agreement with the purchasers named therein (the "Purchasers" and each individually, a "Purchaser") of even date herewith (the "Follow-On Purchase Agreement"), pursuant to which the Purchasers will purchase up to an aggregate of 12,618,296 shares of the Company's Series 1-D Preferred Stock at the Closing (as defined in the Follow-On Purchase Agreement);

        WHEREAS, in connection with the Follow-On Purchase Agreement, the Company and Investors desire to amend the Investor Rights Agreement so to include the Purchasers as "Investors" therein and to make the other changes described herein;

        WHEREAS, the Purchasers desire to become parties to the Investor Rights Agreement as amended by this Amendment;

        WHEREAS, Section 5.6 of the Investor Rights Agreement provides that the Investor Rights Agreement may be amended with the written consent of the Company and the holders of a majority of the Registrable Securities (as defined in the Investor Rights Agreement); and

        WHEREAS, the undersigned Investors are the holders of at least a majority of all of the Registrable Securities.

AGREEMENT

        NOW, THEREFORE, in consideration of the foregoing and the promises and covenants contained herein and in the Investor Rights Agreement, and for other good and valuable consideration, the receipt of which is hereby acknowledged, the parties hereto agree as follows:

        1.    Amendments.    

        (a)   Section 2.11 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with the following:

        "2.11    Amendment of Registration Rights.    Any provision of this Section 2 may be amended and the observance thereof may be waived (either generally or in a particular instance and either retroactively or prospectively), only with the written consent of the Company and the Holders of at least fifty-five percent (55%) of the Registrable Securities then outstanding. Any amendment or waiver effected in accordance with this Section 2.11

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shall be binding upon each Holder and the Company. By acceptance of any benefits under this Section 2, Holders of Registrable Securities hereby agree to be bound by the provisions hereunder."

        (b)   Section 2.12 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with the following:

        "2.12    Limitation on Subsequent Registration Rights.    Other than as provided in Section 5.11, after the date of this Agreement, the Company shall not, without the prior written consent of the Holders of at least fifty-five percent (55%) of the Registrable Securities then outstanding, enter into any agreement with any holder or prospective holder of any securities of the Company that would grant such holder registration rights pari pasu with or senior to those granted to the Holders hereunder, other than the right to a Special Registration Statement."

        (c)   Section 5.6 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with the following:

        "5.6    Amendment and Waiver.    

        (a)   Except as otherwise expressly provided, this Agreement may be amended or modified only upon the written consent of the Company and the holders of at least fifty-five percent (55%) of the Registrable Securities.

        (b)   Except as otherwise expressly provided, the obligations of the Company and the rights of the Holders under this Agreement may be waived only with the written consent of the holders of at least fifty-five percent (55%) of the Registrable Securities.

        (c)   For the purposes of determining the number of Holder or Investors entitled to vote or exercise any rights hereunder, the Company shall be entitled to rely solely on the list of record holders of its stock as maintained by or on behalf of the Company."

        (d)   Section 5.11 of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with the following:

        "5.11    Additional Investors.    Notwithstanding anything to the contrary contained herein, if the Company shall issue Equity Securities in accordance with Section 4.5(c), (f), (h) or (i) of this Agreement, any purchaser of such Equity Securities may become a party to this Agreement by executing and delivering an additional counterpart signature page to this Agreement and shall be deemed an "Investor," a "Holder" and a party hereunder."

        (e)   Exhibit A of the Investor Rights Agreement is hereby deleted and replaced and superseded in its entirety with Exhibit A attached hereto.

        2.    Waiver of Rights of First Refusal.    The rights set forth in Section 4.1 of the Investor Rights Agreement to purchase shares of Equity Securities (as defined in the Investor Rights Agreement) of the Company are hereby waived, for and on behalf of all Major Investors (as defined in the Investor Rights Agreement) with respect to the issuance of 12,618,296 shares of Series 1-D Preferred at the Closing pursuant to the Follow-On Purchase Agreement.

        3.    Counterpart Signature Page.    By executing this Amendment, each of the Purchasers agrees to be bound by the provisions of the Investor Rights Agreement, as amended by this Amendment, and to be deemed "Investors," "Holders" and parties hereunder and thereunder.

        4.    Effect of Amendment.    Except as expressly modified by this Amendment, the Investor Rights Agreement shall remain unmodified and in full force and effect.

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        5.    Governing Law.    This Amendment shall be governed by and construed in accordance with the laws of the State of Delaware as applied to agreements among Delaware residents entered into and to be performed entirely within the State of Delaware.

        6.    Counterparts.    This Amendment may be executed in any number of counterparts and signatures delivered by facsimile, each of which shall be deemed an original, but all of which together shall constitute one instrument.

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        IN WITNESS WHEREOF, the parties have executed this FIRST AMENDMENT TO AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT as of the date set forth above.

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EXHIBIT A

SCHEDULE OF INVESTORS

A-1

(1)

Represents shares issuable upon exercise of that certain Warrant dated November 26, 2002, originally issued to purchase 12,000 shares of Series B Preferred Stock that was amended in connection with the Series B-2 Preferred Stock financing to become a warrant to purchase 12,000 shares of Series B-1 Preferred, and further amended in connection with the Series 1-C Preferred financing to become a warrant to purchase 12,000 shares of Series 1-A Preferred. Such shares are not included in the "Totals" set forth below.

(2)

Represents shares issuable upon exercise of that certain Warrant dated November 26, 2002 to purchase 16,798 shares of Series B-2 Preferred that was amended in connection with the Series 1-C Preferred financing to become a warrant exercisable for 16,798 shares of Series 1-B Preferred. Such shares are not included in the "Totals" set forth below.

(3)

Represents shares issuable upon exercise of that certain Warrant to purchase 276,025 shares of Series 1-D Preferred issued to Comerica Bank in connection with the Debt Financing. Such shares are not included in the "Totals" set forth below.

A-2

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Exhibit 4.10