FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT NO. COMPX

Exhibit 10.4d

EXECUTION VERSION

FIRST AMENDMENT TO

LOAN AND SECURITY AGREEMENT NO. COMPX

This FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT NO. COMPX (this “Amendment”), dated as of March 25, 2011, amends and provides Lender’s consent under the Loan and Security Agreement No. Compx, dated as of December 17, 2010 (as amended, supplemented, restated or modified from time to time, the “ATEL Loan Agreement”), between COMPLETE GENOMICS, INC., a Delaware corporation (“Borrower”), and ATEL VENTURES, INC., a California corporation (“Lender”). Capitalized terms used herein but not defined herein have the meanings given in the ATEL Loan Agreement and the rules of interpretation set forth therein shall apply hereto. Unless otherwise noted, all section references used herein are to provisions of the ATEL Loan Agreement.

RECITALS

A. Borrower is entering into a Loan and Security Agreement with Oxford Finance Corporation (“Oxford”) dated the date hereof in substantially the form attached hereto as Exhibit A (the “Oxford Loan Agreement”) in order to, among other things, pay off in full the Indebtedness of Borrower owed to Comerica Bank (“Comerica”) under that certain Loan and Security Agreement dated December 17, 2010 between Borrower and Comerica (the “Comerica Loan Agreement”).

B. Borrower requests approval of Lender under the ATEL Loan Agreement to (a) execute, deliver and perform the terms and conditions of the Oxford Loan Agreement and all documents related thereto (the “Oxford Documents”) and (b) pay off all Indebtedness owed to Comerica pursuant to the Comerica Loan Agreement.

NOW, THEREFORE, it is agreed by Borrower and Lender as follows:

a. Lender hereby (a) consents to Borrower entering into the Oxford Documents and performing its obligations thereunder, and (b) agrees that the Indebtedness under the Oxford Loan Agreement shall be considered “Permitted Indebtedness” under the ATEL Loan Agreement and that the Liens securing the Oxford Loan Agreement shall be considered “Permitted Liens” under the ATEL Loan Agreement; and

b. Lender hereby consents pursuant to Section 7.4 of the ATEL Loan Agreement to Borrower prepaying in full the Indebtedness owed to Comerica under the Comerica Loan Agreement.

“Oxford” means Oxford Finance Corporation, a Delaware corporation.

“Oxford Loan Agreement” means that certain Loan and Security Agreement between Borrower and Oxford dated as of March 25, 2011 (as the same may be amended, restated or modified from time to time).

“Oxford Collateral” means the collateral securing the Oxford Indebtedness.

“Oxford Indebtedness” means Indebtedness owing from Borrower to Oxford in the aggregate original principal amount of Twenty Million Dollars ($20,000,000) pursuant to the Oxford Loan Agreement.

“Designated Deposit Account” means account number 33-00497905 maintained with Silicon Valley Bank or another account designated in writing to Lender from time to time held at another financial institution reasonably satisfactory to Lender.

(d) the Oxford Indebtedness;

(iii) Certificates of deposit at a financial institution reasonably satisfactory to Lender maturing no more than one year from the date of investment therein, and

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(iv) money market accounts at a financial institution reasonably agreeable to Lender;

(j) Investments in accordance with the Borrower’s investment policy as in effect on March 25, 2011, as the same may be immaterially amended from time to time.

(e) Liens securing the Oxford Indebtedness.

“Investments. Directly or indirectly acquire or own, or make any Investment in or to any Person, or permit any of its Subsidiaries so to do, other than Permitted Investments, or maintain or invest any of its property with a Person other than a banking institution permitted under the Oxford Loan Agreement (as long as the Oxford Indebtedness is outstanding) or permit any Subsidiary to do so unless such Person has entered into a control agreement with Oxford (as long as the Oxford Indebtedness is outstanding), in form and substance satisfactory to Oxford, or suffer or permit any Subsidiary to be a party to, or be bound by, an agreement that restricts such Subsidiary from paying dividends or otherwise distributing property to Borrower.”

“Oxford Default. If an Event of Default occurs under the Oxford Loan Agreement which remains uncured and un-waived; provided that

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any subsequent cure or waiver of such Event of Default shall be deemed to be a cure or waiver for purposes of a cross default hereunder unless Lender has already commenced its right or remedies hereunder.”

“Total amount of Borrower’s cash and investments maintained with Comerica Bank or any other financial institution permitted under the Agreement.”

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IN WITNESS WHEREOF, the undersigned have caused this Amendment to be duly executed by their officers duly authorized as of the date first set forth above.

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