Exhibit 10.4

AMENDED AND RESTATED EMPLOYMENT AGREEMENT

THIS AMENDED AND RESTATED EMPLOYMENT AGREEMENT, effective as of April 27, 2001 (this "Agreement"), is made by and between NANOGEN, INC., a
Delaware corporation (hereinafter the "Company"), and VERA P. PARDEE, Esq. (hereinafter "Executive").

RECITALS

WHEREAS, the Company and Executive entered into an Employment Agreement, dated as of November 1, 2000 (the "Previous Employment Agreement"); and

WHEREAS,
the Company and Executive wish to amend and restate the Previous Employment Agreement.

NOW,
THEREFORE, the Company and Executive, in consideration of the Executive's continued employment with the Company, agree as follows:

ARTICLE I.        TERM OF AGREEMENT

A.Commencement Date.The terms of this Agreement shall govern Executive's employment with the Company
from November 1, 2000 ("Commencement Date") and this Agreement shall expire after a period of three (3) years from the Commencement Date, unless terminated earlier pursuant to
Article 6.

B.Renewal.The term of this Agreement shall be automatically renewed for successive, additional three
(3) year terms unless either party delivers written notice to the other at least ninety (90) days prior to the expiration date of this Agreement of an intention to terminate this
Agreement or to renew it for a term of less than three (3) years but not less than (1) year. If the term of this Agreement is renewed for a term of less than three (3) years, then
thereafter the term of this Agreement shall be automatically renewed for successive, additional identical terms unless either party delivers a written notice to the other at least ninety
(90) days prior to a termination date of this Agreement of an intention to terminate this Agreement or to renew it for a different term of not less than one (1) year. Any renewal bonus
will be negotiated as mutually agreed to at the time of any renewal of this Agreement.

If
this Agreement is not renewed at the end of any term hereof by the Company for any reason except death, disability or retirement of Executive, notwithstanding anything herein
elsewhere contained, Executive shall be paid his salary, as provided for in Section 3.A hereof, and receive the other benefits applicable under Article 4 hereof, for an additional six
months after the termination date hereof.

ARTICLE II.        EMPLOYMENT DUTIES

A.Title/Responsibilities.Executive hereby accepts employment with the Company pursuant to the terms
and conditions hereof. Executive agrees to serve the Company in the position of Vice President, Assistant General Counsel and Secretary. Executive shall have the powers and duties commensurate with
such position, including but not limited to, hiring personnel necessary (in the judgment of the Board of Directors) to carry out the responsibilities for such position.

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B.Full Time Attention.Executive shall devote her best efforts and her full business time and
attention to the performance of the services customarily incident to such office and to such other services as the Board may reasonably request.

C.Other Activities.Except upon the prior written consent of the Board of Directors, Executive shall
not during the period of employment engage, directly or indirectly, in any other business activity (whether or not pursued for pecuniary advantage) that is or may be competitive with, or that might
place her in a competing position to that of the Company or any other corporation or entity that directly or indirectly controls, is controlled by, or is under common control with the Company (an
"Affiliated Company"), provided that Executive may own less than two percent of the outstanding securities of any such publicly traded competing corporation.

ARTICLE III.        COMPENSATION

A.Base Salary.Executive shall receive a Base Salary at an annual rate of two hundred thousand dollars
($200,000), payable in accordance with the Company's customary payroll practices. The Company's Board of Directors shall provide Executive with annual performance reviews, and, thereafter, Executive
shall be entitled to such Base Salary as the Board of Directors may from time to time establish in its sole discretion.

B.Achievement Bonus.The Company shall pay Executive an Achievement Bonus of up to 50% of Executive's
Base Salary annually based upon achievement by the Company of its corporate goals as established and determined by the Board of Directors annually and for other achievements by the Company or the
Executive during the year as approved by the Compensation Committee. The Board of Directors or Compensation Committee, as applicable, shall, in their respective sole discretion, determine whether such
corporate or other goals have been attained or other achievements have occurred.

C.Transaction Bonus.In addition, in the event of a transaction involving a Change in Control, in a
transaction approved by the Company's Board of Directors, which transaction results in the receipt by the Company's stockholders of consideration with a value representing, in the sole judgment of the
Board of Directors, a significant premium over the average of the closing prices per share of the Company's common stock as quoted on the Nasdaq National Market for 20 trading days ending one day
prior to the public announcement of such transaction (a "Change in Control Transaction"), Executive shall be paid a Transaction Bonus at the closing of such a transaction in the amount equal to one
(1) times 50% of Executive's Base Salary in effect immediately preceding the closing of such a transaction. Executive shall also be paid said Transaction Bonus if the Company enters into a
transaction approved by the Board of Directors which is not a Change in Control Transaction, but which, nonetheless, involves a significant change in the ownership of the Company or the composition of
the Board of Directors of the Company, and which results in significant additional value for the Company's stockholders, as determined by the Board of Directors in its sole discretion and as
specifically designated a significant event by the Board of Directors (a "Significant Event"). In the event Executive receives a Transaction Bonus, no Achievement Bonus will be paid to Executive in
the year in which such Transaction Bonus is paid.

If
the Company enters into a transaction which is a Change in Control Transaction, then all of the Executive's stock options received before the effective date of the transaction
shall become exercisable in full and all of the shares of the common stock of the Company awarded to Executive under the Company's 1997 Stock Incentive Plan shall become fully vested. If the Company
enters into a transaction which is not a Change in Control Transaction but which is a Significant Event, then the Board of Directors may, in its sole discretion, determine that all, or a portion, of
the Executive's stock options received before the effective date of the transaction shall become exercisable in full and all, or

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a portion, of the shares of the common stock of the Company awarded to Executive under the Company's 1997 Stock Incentive Plan shall become fully vested.

D.Withholdings.All compensation and benefits to Executive hereunder shall be subject to all federal,
state, local and other withholdings and similar taxes and payments required by applicable law.

ARTICLE IV.        EXPENSE ALLOWANCES AND FRINGE BENEFITS

A.Vacation.Executive shall be entitled to three (3) weeks, plus one (1) additional day
for each completed year of employment with the Company, of annual paid vacation during the term of this Agreement.

B.Benefits.During the term of this Agreement, the Company shall also provide Executive with the usual
health insurance benefits it generally provides to its other senior management employees, other than life insurance (which shall be paid directly by Executive). As Executive becomes eligible in
accordance with criteria to be adopted by the Company, the Company shall provide Executive with the right to participate in and to receive benefits from accident, disability, medical, pension, bonus,
stock, profit-sharing and savings plans and similar benefits made available generally to employees of the Company as such plans and benefits may be adopted by the Company, provided that Executive
shall during the term of this Agreement be entitled to receive at a minimum standard medical and dental benefits similar to those typically afforded to Chief Executive Officers in similar sized
biotechnology companies,
excluding life insurance. The amount and extent of benefits to which Executive is entitled shall be governed by the specific benefit plan as it may be amended from time to time.

C.Business Expense Reimbursement.During the term of this Agreement, Executive shall be entitled to
receive proper reimbursement for all reasonable out-of-pocket expenses incurred by her (in accordance with the policies and procedures established by the Company for its senior
executive officers) in performing services hereunder, provided Executive properly accounts therefor.

ARTICLE V.        CONFIDENTIALITY

A.Proprietary Information.Executive represents and warrants that she has executed and delivered to
the Company the Company's standard Proprietary Information and Inventions Agreement in form acceptable to the Company's counsel.

B.Return of Property.All documents, records, apparatus, equipment and other physical property which
is furnished to or obtained by Executive in the course of her employment with the Company shall be and remain the sole property of the Company. Executive agrees that, upon the termination of her
employment, she shall return all such property (whether or not it pertains to Proprietary Information as defined in the Proprietary Information and Inventions Agreement), and agrees not to make or
retain copies, reproductions or summaries of any such property.

ARTICLE VI.        TERMINATION

A.By Death.The period of employment shall terminate automatically upon the death of Executive. In
such event, the Company shall pay to Executive's beneficiaries or her estate, as the case may be, any accrued Base Salary, any bonus compensation to the extent earned, any vested deferred compensation
(other than pension plan or profit-sharing plan benefits which will be paid in accordance with the
applicable plan), any benefits under any plans of the Company in which Executive is a participant to the full extent of Executive's rights under such plans, any accrued vacation pay and any

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appropriate business expenses incurred by Executive in connection with her duties hereunder, all to the date of termination (collectively "Accrued Compensation"), but no other compensation or
reimbursement of any kind, including, without limitation, severance compensation, and thereafter, the Company's obligations hereunder shall terminate.

B.By Disability.If Executive is prevented from properly performing her duties hereunder by reason of
any physical or mental incapacity for a period of more than 90 days in the aggregate in any 365-day period, then, to the extent permitted by law, the Company may terminate the
employment on the 90th day of such incapacity. In such event, the Company shall pay to Executive all Accrued Compensation, and shall continue to pay to Executive the Base Salary until such time (but
not more than 90 days following termination), as Executive shall become entitled to receive disability insurance payments under the disability insurance policy maintained by the Company, which
disability policy shall provide for full payment of Executive's Base Salary during the period of disability, but no other compensation or reimbursement of any kind, including without limitation,
severance compensation, and thereafter the Company's obligations hereunder shall terminate. Nothing in this Section shall affect Executive's rights under any disability plan in which she is a
participant.

C.By Company for Cause.The Company may terminate Executive's employment for Cause (as defined below)
without liability at any time with or without advance notice to Executive. The Company shall pay Executive all Accrued Compensation, but no other compensation or reimbursement of any kind, including
without limitation, severance compensation, and thereafter the Company's obligations hereunder shall terminate. Termination shall be for "Cause" in the event of the occurrence of any of the following:
(a) any intentional action or intentional failure to act by Executive which was performed in bad faith and to the material detriment of the Company; (b) Executive intentionally refuses
or intentionally fails to act in accordance with any lawful and proper direction or order of the Board; (c) gross negligence by Executive in carrying out the duties of employment; or
(d) Executive is convicted of a felony crime involving moral turpitude, provided that in the event that any of the foregoing events is capable of being cured, the Company shall provide written
notice to Executive describing the nature of such event and Executive shall thereafter have five (5) business days to cure such event.

D.At Will.At any time, the Company may terminate Executive's employment without liability other than
as set forth below, for any reason not specified in Section 6.C above, by giving thirty (30) days advance written notice to Executive. If the Company elects to terminate Executive
pursuant to this Section 6.D prior to a Change in Control, the Company shall pay to Executive all Accrued Compensation and shall continue to pay to Executive as provided herein Executive's
Salary for six (6) months from the date of such termination as severance compensation. If the Company or its successor elects to terminate Executive pursuant to this Section after a Change in
Control, the Company (or its successor) shall continue to pay to Executive as provided herein Executive's Salary for twelve (12) months from the date of such termination as severance
compensation. Upon payment of the severance benefits described herein, all obligations of the Company (or its successor) shall terminate.

During
the period when such severance compensation is being paid to Executive, Executive shall not (i) engage, directly or indirectly, in any other business activity that is
competitive with, or that places him in a competing position to that of the Company or any Affiliated Company (provided that Executive may own less than two percent (2%) of the outstanding securities
of any publicly traded corporation), or (ii) hire, solicit, or attempt to hire on behalf of herself or any other party any employee or exclusive consultant of the Company. If the Company
terminates this Agreement or the employment of Executive with the Company other than pursuant to Section 6.A, 6.B or 6.C, then this Section 6.D shall apply.

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E.Constructive Termination.In the event that the Company shall materially reduce the powers and
duties of employment of Executive resulting in a material decrease in the responsibilities of Executive which are inconsistent with Executive acting as Vice President and Assistant General Counsel of
the Company, such action shall be deemed to be a termination of employment of Executive without cause pursuant to Section 6.D. In the event of a Change in Control of the Company in which the
Company shall become a division or subsidiary of a larger organization, references to the Vice President and Assistant General Counsel Science of the Company shall be deemed to mean the Vice President
and Assistant General Counsel of such division or subsidiary for purposes of this Section 6.E.





ARTICLE VII.        GENERAL PROVISIONS

A.Governing Law.The validity, interpretation, construction and performance of this Agreement and the
rights of the parties thereunder shall be interpreted and enforced under California law without reference to principles of conflicts of laws. The parties expressly agree that inasmuch as the Company's
headquarters and principal place of business are located in California, it is appropriate that California law govern this Agreement.

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B.Assignment; Successors; Binding Agreement.



C.No Waiver of Breach.The waiver by any party of the breach of any provision of this Agreement shall
not be deemed to be a waiver of any subsequent breach.

D.Notice.For the purposes of this Agreement, notices and all other communications provided for in
this Agreement shall be in writing and shall be deemed to have been duly given when delivered or mailed by certified or registered mail, return receipt requested, postage prepaid, addressed to the
respective addresses set forth below or to such other address as either party may have furnished to the other in writing in accordance herewith, except that notice of change of address shall be
effective only upon receipt.

| | To the Company: |  | Nanogen, Inc.
10398 Pacific Center Court
San Diego, CA 92121
Attn: Chief Executive Officer
| | --------------- |  | ------------------------------------------------------------------------------------------
| | To Executive:   |  | Vera P. Pardee, Esq.
c/o Nanogen, Inc.
10398 Pacific Center Court
San Diego, CA 92121     

E.Modification; Waiver; Entire Agreement.No provisions of this Agreement may be modified, waived or
discharged unless such waiver, modification or discharge is agreed to in writing signed by Executive and such officer as may be specifically designated by the Board of the Company. No waiver by either
party hereto at any time of any breach by the other party of, or compliance with, any condition or provision of this Agreement to be performed by such other party shall be deemed a waiver of similar
or dissimilar provisions or conditions at the same or any prior or subsequent time. No agreements or representations, oral or otherwise, express or implied, with respect to the subject matter hereof
have been made by either party which are not expressly set forth in this Agreement.

F.Validity.The invalidity or unenforceability of any provision of this Agreement shall not affect the
validity or enforceability of any other provision of this Agreement, which shall remain in full force and effect.

G.Controlling Document.This Agreement supersedes any and all prior employment agreements between the
Company and Executive, but does not supersede any other agreements between Company and Executive, including but not limited to, the Nanogen Inc. Restricted Stock Purchase Agreement, any stock
option agreements or common stock purchase agreements entered into pursuant to the

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Company's 1997 Stock Incentive Plan, and the Nanogen Employees' Handbook and Policies, except as expressly provided herein. In case of conflict between any of the terms and conditions of this
Agreement and the documents herein referred to, the terms and conditions of this Agreement shall control.

H.Executive Acknowledgment.Executive acknowledges (a) that she has consulted with or has had
the opportunity to consult with independent counsel of her own choice concerning this Agreement, and has been advised to do so by the Company, and (b) that she has read and understands the
Agreement, is fully aware of its legal effect, and has entered into it freely based on her own judgment.

I.Remedies.



J.Counterparts.This Agreement may be executed in one or more counterparts, all of which taken
together shall constitute one and the same Agreement.

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Executed by the parties as of the day and year first above written.

| |  | NANOGEN, INC.
| |  | -------------
| |  | By:          
| |  | EXECUTIVE:   
| |  | By:          

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