Exhibit 10.3

THIRD AMENDMENT

TO

LOAN AND SECURITY AGREEMENT

THIS THIRD AMENDMENT to Loan and Security Agreement (this “Amendment”) is
entered into as of September 15, 2012, by and between OXFORD FINANCE LLC
(successor in interest to Oxford Finance Corporation; in its individual
capacity, “Oxford”; and in its capacity as Collateral Agent, “Collateral
Agent”), the Lenders a party thereto from time to time including Oxford in its
capacity as a Lender (each a “Lender” and collectively, the “Lenders”) and
COMPLETE GENOMICS, INC., a Delaware corporation (“Borrower”).

RECITALS

A. Collateral Agent, Lender and Borrower have entered into that certain Loan and
Security Agreement dated as of March 25, 2011 (as amended from time to time,
including by that certain First Amendment to Loan and Security Agreement dated
as of August 22, 2011 and that certain Second Amendment to Loan and Security
Agreement dated as of February 28, 2012, as the same may from time to time be
further amended, modified, supplemented or restated, the “Loan Agreement”).

B. Lender has extended credit to Borrower for the purposes permitted in the Loan
Agreement.

C. Borrower has requested that Collateral Agent and Lender amend the Loan
Agreement to make certain revisions to the Loan Agreement as more fully set
forth herein.

D. Borrower, Collateral Agent and Lender have agreed to so amend certain
provisions of the Loan Agreement, but only to the extent, in accordance with the
terms, subject to the conditions and in reliance upon the representations and
warranties set forth below.

AGREEMENT

NOW, THEREFORE, in consideration of the foregoing recitals and other good and
valuable consideration, the receipt and adequacy of which is hereby
acknowledged, and intending to be legally bound, the parties hereto agree as
follows:

1. Definitions. Capitalized terms used but not defined in this Amendment shall
have the meanings given to them in the Loan Agreement.

2. Amendments to Loan Agreement.

2.1 Section 6.13 (Financial Covenant). A new Section 6.13 hereby is added to the
Loan Agreement to read as follows:

“6.13 Financial Covenant. From and after Borrower’s incurrence of any
Indebtedness from BGI-HONGKONG CO., LIMITED pursuant to the terms of that
certain $30,000,000 Convertible Subordinated Promissory Note by Borrower in
favor of BGI-HONGKONG CO., LIMITED dated as of September 15, 2012, Borrower
shall maintain a Liquidity Ratio of not less than 0.90 to 1.00 at all times.”

2.2 Section 13.1 (Definitions). The following term and its respective definition
hereby is added to Section 13.1 of the Loan Agreement as follows:

“Liquidity Ratio” means a ratio of (i) Borrower’s unrestricted cash and Cash
Equivalents to (ii) the aggregate amount of Borrower’s Obligations to Collateral
Agent and Lenders plus the Atel Indebtedness.

 

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2.3 Exhibit C attached to the Loan Agreement hereby is replaced with Exhibit C
attached hereto.

3. Limitation of Amendments.

3.1 The amendments set forth in Section 2, above, are effective for the purposes
set forth herein and shall be limited precisely as written and shall not be
deemed to (a) be a consent to any amendment, waiver or modification of any other
term or condition of any Loan Document, or (b) otherwise prejudice any right or
remedy which Collateral Agent or any Lender may now have or may have in the
future under or in connection with any Loan Document.

3.2 This Amendment shall be construed in connection with and as part of the Loan
Documents and all terms, conditions, representations, warranties, covenants and
agreements set forth in the Loan Documents, except as herein amended, are hereby
ratified and confirmed and shall remain in full force and effect.

4. Representations and Warranties. To induce Collateral Agent and Lender to
enter into this Amendment, Borrower hereby represents and warrants to Collateral
Agent and Lender as follows:

4.1 Immediately after giving effect to this Amendment (a) the representations
and warranties contained in the Loan Documents are true, accurate and complete
in all material respects as of the date hereof (except as previously disclosed
in writing to Lender and except to the extent such representations and
warranties relate to an earlier date, in which case they are true and correct as
of such date), and (b), no Event of Default has occurred and is continuing;

4.2 Borrower has the power and authority to execute and deliver this Amendment
and to perform its obligations under the Loan Agreement, as amended by this
Amendment;

4.3 The organizational documents of Borrower delivered to Collateral Agent and
Lender on the Effective Date, or thereafter are true, accurate and complete and
have not been amended, supplemented or restated and are and continue to be in
full force and effect;

4.4 The execution and delivery by Borrower of this Amendment and the performance
by Borrower of its obligations under the Loan Agreement, as amended by this
Amendment, have been duly authorized;

4.5 The execution and delivery by Borrower of this Amendment and the performance
by Borrower of its obligations under the Loan Agreement, as amended by this
Amendment, do not and will not contravene (a) any law or regulation binding on
or affecting Borrower, (b) any contractual restriction with a Person binding on
Borrower, (c) any order, judgment or decree of any court or other governmental
or public body or authority, or subdivision thereof, binding on Borrower, or
(d) the organizational documents of Borrower;

4.6 The execution and delivery by Borrower of this Amendment and the performance
by Borrower of its obligations under the Loan Agreement, as amended by this
Amendment, do not require any order, consent, approval, license, authorization
or validation of, or filing, recording or registration with, or exemption by any
governmental or public body or authority, or subdivision thereof, binding on
Borrower, except as already has been obtained or made; and

4.7 This Amendment has been duly executed and delivered by Borrower and is the
binding obligation of Borrower, enforceable against Borrower in accordance with
its terms, except as such enforceability may be limited by bankruptcy,
insolvency, reorganization, liquidation, moratorium or other similar laws of
general application and equitable principles relating to or affecting creditors’
rights.

5. Counterparts. This Amendment may be executed in any number of counterparts
and all of such counterparts taken together shall be deemed to constitute one
and the same instrument.

 

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6. Effectiveness. This Amendment shall be deemed effective upon (i) the due
execution and delivery to Collateral Agent and Lender of this Amendment by each
party hereto; (ii) the due execution and delivery to Collateral Agent of updated
Borrowing Resolutions, in substantially the form attached hereto as Annex I;
(iii) the due execution and delivery of a subordination agreement entered into
by BGI-HONGKONG CO., LIMITED in favor of, and in form and substance satisfactory
to, Collateral Agent; (iv) copies of all documents, instruments, certificates
and/or agreements necessary to, related to, or executed in connection with,
Borrower’s Indebtedness to BGI-HONGKONG CO., LIMITED, and (v) Borrower’s payment
of all Lender’s Expenses incurred through the date of this Amendment.

[Balance of Page Intentionally Left Blank]

 

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IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly
executed and delivered as of the date first written above.

 

COLLATERAL AGENT:     BORROWER: OXFORD FINANCE LLC     COMPLETE GENOMICS, INC.
By:  

/s/ Mark Davis

    By:  

/s/ Clifford A. Reid

Name:  

Mark Davis

    Name:  

Clifford A. Reid

Title:  

VP - Finance, Secretary & Treasurer

    Title:  

Chief Executive Officer

LENDER:      

OXFORD FINANCE FUNDING TRUST 2012-01

By: Oxford Finance LLC, as servicer

      By:  

/s/ Mark Davis

      Name:  

Mark Davis

      Title:  

VP- Finance, Secretary & Treasurer

     

[Signature Page to Third Amendment to Loan and Security Agreement]

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EXHIBIT C

COMPLIANCE CERTIFICATE

 

TO:        OXFORD FINANCE CORPORATION, as Collateral Agent

   Date: ________        

FROM:        COMPLETE GENOMICS, INC., as Borrower

  

The undersigned authorized officer of Complete Genomics, Inc. (“Borrower”)
certifies that under the terms and conditions of the Loan and Security Agreement
between Borrower and Lender (as amended, restated, supplemented or otherwise
modified from time to time, the “Agreement”), (1) Borrower is in complete
compliance for the period ending _______________ with all required covenants
except as noted below, (2) there are no Events of Default, (3) all
representations and warranties in the Agreement are true and correct in all
material respects on this date except as noted below; provided, however, that
such materiality qualifier shall not be applicable to any representations and
warranties that already are qualified or modified by materiality in the text
thereof; and provided, further that those representations and warranties
expressly referring to a specific date shall be true, accurate and complete in
all material respects as of such date, (4) Borrower, and each of its
Subsidiaries, has timely filed all required tax returns and reports, and
Borrower has timely paid all foreign, federal, state and local taxes,
assessments, deposits and contributions owed by Borrower except as otherwise
permitted pursuant to the terms of Section 5.8 of the Agreement, and (5) no
Liens have been levied or claims made against Borrower or any of its
Subsidiaries relating to unpaid employee payroll or benefits of which Borrower
has not previously provided written notification to Lender. Attached are the
required documents supporting the certification. The undersigned certifies, in
the capacity as an officer of the Borrower, that these are prepared in
accordance with GAAP consistently applied from one period to the next except as
explained in an accompanying letter or footnotes. The undersigned acknowledges,
in the capacity as an officer of the Borrower, that no borrowings may be
requested at any time or date of determination that Borrower is not in
compliance with any of the terms of the Agreement, and that compliance is
determined not just at the date this certificate is delivered. Capitalized terms
used but not otherwise defined herein shall have the meanings given them in the
Agreement.

Please indicate compliance status by circling Yes/No under “Complies” column.

 

Reporting Covenant

  

Required

  

Complies

 

Monthly Financial Statements

  

Monthly within 30 days

     Yes         No   

Compliance Certificate

        

Audited Financial Statements

  

Annually within 90 days after FYE

     Yes         No   

Board Approved Projections

  

Annually within 45 days after FYE

     Yes         No   

Financial Covenant

  

Required

  

Complies

 

Liquidity Ratio

  

0.90:1.00

     Yes         No   

The following are the exceptions with respect to the certification above: (If no
exceptions exist, state “No exceptions to note.”)

 

 

 

     LENDER USE ONLY COMPLETE GENOMICS, INC.    Received by:
__________________________                                     AUTHORIZED SIGNER
By: ____________________________________    Date:
_______________________________ Name: __________________________________   
Title: ___________________________________    Verified:
______________________________                                     AUTHORIZED
SIGNER    Date: _______________________________    Compliance
Status:            Yes        No

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ANNEX I

CORPORATE BORROWING CERTIFICATE

 

BORROWER:  

COMPLETE GENOMICS, INC.

   DATE: September __, 2012 COLLATERAL  

OXFORD FINANCE LLC

   AGENT:      LENDER:  

OXFORD FINANCE FUNDING TRUST 2012-01

  

I hereby certify as follows, as of the date set forth above:

1. I am the Secretary, Assistant Secretary or other officer of Borrower. My
title is as set forth below.

2. Borrower’s exact legal name is set forth above. Borrower is a corporation
existing under the laws of the State of Delaware.

3. Attached hereto as Exhibit A and Exhibit B, respectively, are true, correct
and complete copies of (i) Borrower’s Certificate of Incorporation (including
amendments), as filed with the Secretary of State of the state in which Borrower
is incorporated as set forth in paragraph 2 above; and (ii) Borrower’s Bylaws.
Neither such Certificate of Incorporation nor such Bylaws have been amended,
annulled, rescinded, revoked or supplemented, and such Certificate of
Incorporation and such Bylaws remain in full force and effect as of the date
hereof.

4. The following resolutions were duly and validly adopted by Borrower’s Board
of Directors at a duly held meeting of such directors (or pursuant to a
unanimous written consent or other authorized corporate action). Such
resolutions are in full force and effect as of the date hereof and have not been
in any way modified, repealed, rescinded, amended or revoked, and the Lenders
may rely on them until each Lender receives written notice of revocation from
Borrower.

RESOLVED, that any one of the following officers or employees of Borrower, whose
names, titles and signatures are below, may act on behalf of Borrower:

 

Name

  

Title

  

Signature

  

Authorized to

Add or Remove

Signatories

 

  

 

  

 

  

¨

 

  

 

  

 

  

¨

 

  

 

  

 

  

¨

 

  

 

  

 

  

¨

RESOLVED FURTHER, that any one of the persons designated above with a checked
box beside his or her name may, from time to time, add or remove any individuals
to and from the above list of persons authorized to act on behalf of Borrower.

RESOLVED FURTHER, that such individuals may, on behalf of Borrower:

Borrow Money. Borrow money from the Lenders.

Execute Loan Documents. Execute any loan documents any Lender requires.

Grant Security. Grant Collateral Agent a security interest in any of Borrower’s
assets.

Negotiate Items. Negotiate or discount all drafts, trade acceptances, promissory
notes, or other indebtedness in which Borrower has an interest and receive cash
or otherwise use the proceeds.

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Further Acts. Designate other individuals to request advances, pay fees and
costs and execute other documents or agreements (including documents or
agreement that waive Borrower’s right to a jury trial) they believe to be
necessary to effectuate such resolutions.

RESOLVED FURTHER, that all acts authorized by the above resolutions and any
prior acts relating thereto are ratified.

5. The persons listed above are Borrower’s officers or employees with their
titles and signatures shown next to their names.

 

By:     Name:     Title:    

*** If the Secretary, Assistant Secretary or other certifying officer executing
above is designated by the resolutions set forth in paragraph 4 as one of the
authorized signing officers, this Certificate must also be signed by a second
authorized officer or director of Borrower.

I, the __________________________ of Borrower, hereby certify as to paragraphs 1
through 5 above, as of the date set

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forth above.

 

By:     Name:     Title: