Exhibit 10.2

AMENDMENT AND CONSENT

THIS AMENDMENT AND CONSENT (this “Agreement” or “Amendment and Consent”) dated
as of March 27, 2008, is made by and between Nanogen, Inc., a Delaware
corporation (the “Company”), and the undersigned holder (the “Holder”).

WHEREAS, the Company and The Bank of New York, as trustee (the “Trustee”)
executed and delivered that certain Indenture, dated as of August 27, 2007 (the
“Initial Indenture”), by and between Nanogen, Inc., a Delaware corporation (the
“Company”), as amended and supplemented by that certain First Supplemental
Indenture, dated as of August 27, 2007 (the “First Supplemental Indenture,” and
together with the Initial Indenture as so supplemented, the “Indenture”),
pursuant to which the Company issued to the Holder its 6.25% Senior Convertible
Notes Due 2010 (the “Notes”).

WHEREAS, the Company and the Holder entered into that certain Amendment and
Exchange Agreement dated as of March 13, 2008 (the “Amendment Agreement”)
pursuant to which the Holder and the Company have agreed to exchange, supercede
and replace certain portions of the Notes and in exchange therefore to issue to
such holders certain 9.75% Senior Secured Convertible Notes (the “Exchanged
Note”) (such transaction, the “Note Exchange”).

WHEREAS, the Holder executed a Consent and Agreement dated March 13, 2008
(“Consent”) pursuant to which the Holder consented to certain amendments to the
Indenture and the execution of a Second Supplemental Indenture between the
Company and the Trustee.

WHEREAS, the Company and Holder agree to amend certain terms of the Amendment
Agreement, the form of the Exchanged Note attached to the Amendment Agreement
and the Consent.

NOW, THEREFORE, each Holder hereby agrees as follows:

Capitalized terms used herein (including the recitals) and not defined herein
shall have the meanings assigned to such terms in the Indenture.

1. The definition of “Permitted Lien” in the form of the Exchanged Note is
hereby amended by deleting the word “and” immediately prior to clause (x) in
such definition and inserting the following clauses at the end of clause (x) in
such definition:

“(xi) those certain Liens in debts, accounts, moneys and choses in action owing
to or owned by Company or its Subsidiaries in respect of “Products” and
“Licensed Products”, where Products and Licensed Products refer to are any
diagnostic kits and components and materials therefore defined by one of more
claims of the “Patents” or derived from “Inventions and Technology” referred to
in that certain Memorandum of an Agreement made as of January 18, 1991 between
Dr. George Jackowski and Spectral Diagnostic Inc. pursuant to which
Dr. Jackowski assigned his right, title and interest in the Patents, Inventions
and Technology to Spectral Diagnostics Inc. in return for, among other things, a
royalty payment, and which Memorandum of Agreement was assigned by Spectral
Diagnostics Inc. to the Company; and (xii) any Liens granted in favor of or held
for the benefit of the Company.”

 

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2. The Consent is hereby amended by

(a) inserting the following clauses (4) and (5) in Schedule 1 attached to the
Consent:

“(4) The Holder waives any Events of Default which may have been occasioned by
the grant of those certain Liens in debts, accounts, moneys and choses in action
owing to or owned by Company or its Subsidiaries in respect of “Products” and
“Licensed Products”, where Products and Licensed Products refer to diagnostic
kits and components and materials therefore defined by one of more claims of the
“Patents” or derived from the “Inventions and Technology” referred to in that
certain Memorandum of an Agreement made as of January 18, 1991 between
Dr. George Jackowski and Spectral Diagnostic Inc. pursuant to which
Dr. Jackowski assigned his right, title and interest in the Patents, Inventions
and Technology to Spectral Diagnostics Inc. in return for, among other things, a
royalty payment and which Memorandum of Agreement was assigned by Spectral
Diagnostics Inc. to the Company.

(5) The Holder waives any Events of Default which may have been occasioned by
the existence of Liens granted to, or held for the benefit of, the Company.”

and

(b) deleting the word “and” immediately prior to clause (x) in the definition of
“Permitted Lien” in the form of Second Supplemental Indenture attached as
Exhibit A to the Consent, and inserting the following clauses immediately after
the end of clause (x) in such definition:

“(xi) those certain Liens in debts, accounts, moneys and choses in action owing
to or owned by Company or its Subsidiaries in respect of “Products” and
“Licensed Products”, where Products and Licensed Products refer to are any
diagnostic kits and components and materials therefore defined by one of more
claims of the “Patents” or derived from “Inventions and Technology” referred to
in that certain Memorandum of an Agreement made as of January 18, 1991 between
Dr. George Jackowski and Spectral Diagnostic Inc. pursuant to which
Dr. Jackowski assigned his right, title and interest in the Patents, Inventions
and Technology to Spectral Diagnostics Inc. in return for, among other things, a
royalty payment, and which Memorandum of Agreement was assigned by Spectral
Diagnostics Inc. to the Company; and (xii) any Liens granted in favor of, or
held for the benefit of, the Company.”

3. The Amendment Agreement is amended by:

(a). amending and restating Recital D thereof as follows:

As additional consideration for the transactions contemplated hereby, any
Exchanged Notes issued hereunder will be secured by a first priority, perfected
security interest in certain of the assets of the Company and the stock and
assets of each of the Company’s

 

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subsidiaries, as evidenced by the security agreement attached hereto as Exhibit
B (the “Security Agreement”, and together with any other ancillary documents
related thereto and the Subordination Agreement (as defined below), collectively
the “Security Documents”).

(b). amending and restating Section 2(a)(i) thereof as follows:

All references to “Notes” shall include the “Exchanged Notes” (as defined in
those certain Amendment and Exchange Agreements, each by and between the Company
and a Buyer, dated as of March 13, 2008 (as amended from time to time, the
“Amendment Agreements”);

(c). amending and restating Section 2(a)(iii) thereof as follows:

The defined term “Transaction Documents” is hereby amended to include the
Amendment Agreements, the Security Documents and those certain Amendment and
Consent Agreements, each by and between the Company and a Buyer, dated as of
March 27, 2008 (the “Amendment and Consent Agreements”);

(d). adding the following as paragraph (f) of Section 3 thereof:

“(f) The Company represents and warrants to the Investor that (i) it acquired
all of the Subordinated Secured Debentures issued pursuant to that certain Trust
Indenture dated as of July 4, 2003 (as amended to date, the “Canadian
Indenture”) between Synx Pharma Inc and The Canada Trust Company, as trustee (in
such capacity, the “Canadian Trustee”) and remains the sole owner of such
Debentures, (ii) other than the Debentures, no indebtedness remains outstanding
pursuant to the Canadian Indenture, (iii) the security interest granted by Synx
Pharma Inc to the Canadian Trustee securing the obligations under the Canadian
Indenture is, to the extent such security interest remains in existence, held by
the Canadian Trustee solely for the benefit of the Company and (iv) other than
the Company and the Canadian Trustee (solely to the extent of any fees and
expenses due and payable to the Canadian Trustee pursuant to the Canadian
Indenture, which as of the date hereof do not, in the aggregate, exceed
$30,000), no Person has any obligations secured by any liens arising under or
relating to the Canadian Indenture.”

(e). adding the following as paragraph (s) of Section 7 thereof:

(s) Canadian Indenture. The Company covenants that it will cause the Canadian
Trustee to terminate any security interests, or filings in respect of security
interests, held by the Canadian Trustee in any assets of the Company and any its
Subsidiaries and will cause such releases or terminations, as applicable, in
form and substance reasonably satisfactory to the Collateral Agent, to be filed
with any applicable governmental authorities no later than 21 calendar days
after the Closing Date.”

(f). adding the following as paragraph (t) of Section 7 thereof:

(t) Jackowski Subordination Agreement. The Company hereby covenants that it
shall, no later than thirty (30) calendar days after the Closing Date, deliver
to the Collateral Agent a

 

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subordination agreement in form and substance reasonably satisfactory to the
Collateral Agent, duly executed by Dr. George Jackowski and Drug Royalty
Corporation (the “Junior Secured Parties”) (or any applicable successor or
assigns of the Junior Secured Parties in accordance with the Memorandum of
Agreement (as defined below)) for the benefit of the Collateral Agent (as
defined in the Securities Purchase Agreement) (the “Subordination Agreement”),
whereby the Junior Secured parties shall agree (x) to subordinate any payment
obligations owed to them by the Company and any liens in the assets (the
“Subordinated Assets”) of the Company arising under that certain Memorandum of
an Agreement made as of January 18, 1991 between Dr. Jackowski and Spectral
Diagnostic Inc. (the “Memorandum of Agreement”) to the Company’s payment
obligations under the Exchanged Notes and the lien granted to the holders of
such Exchanged Notes pursuant to the Transaction Documents and (y) to permit the
Collateral Agent to exercise any rights or remedies with respect to the
Subordinated Assets as permitted under the Security Agreement, including,
without limitation, to liquidate any assets of the Company, without the consent
of the Junior Secured Parties in the event of a bankruptcy of the Company.
Without the prior written consent of the Required Holders (as defined in the
Exchanged Notes), the Company shall not pay any additional consideration to the
Junior Secured Parties with respect to such Subordination Agreement or amend any
term or condition in the Memorandum of Agreement in any manner adverse to the
Company or any of its Subsidiaries.

4. The amendment and consent provided herein is effective only in one instance
and only with respect to the matters set forth herein. The amendment and consent
set forth herein is limited precisely as written and shall not be deemed (a) to
be a consent to, or waiver of, any other term or condition of the Indenture, the
Securities or any of the agreements, instruments and documents referred to
therein or executed in connection therewith or (b) to prejudice any contractual,
legal or other right or rights which the undersigned may have or may have in the
future under or in connection with the Indenture, the Securities or any
agreements, instruments and documents referred to therein or executed in
connection therewith. The undersigned Holder hereby reserves all of its rights
and remedies under applicable law and under the Indenture, the Securities or any
of the agreements, instruments and documents referred to therein or executed in
connection therewith with respect to any matters other than those addressed in
this Agreement.

5. The execution, delivery and performance by the undersigned Holder of this
Agreement has been duly authorized by all necessary action on the part of such
Holder. This Agreement has been duly executed by such Holder.

6. All questions concerning the construction, validity, enforcement and
interpretation of this Agreement shall be governed by the internal laws of the
State of New York, without giving effect to any choice of law or conflict of law
provision or rule (whether of the State of New York or any other jurisdictions)
that would cause the application of the laws of any jurisdictions other than the
State of New York. Each party hereby irrevocably submits to the exclusive
jurisdiction of the state and federal courts sitting in The City of New York,
Borough of Manhattan, for the adjudication of any dispute hereunder or in
connection herewith or with any transaction contemplated hereby or discussed
herein, and hereby irrevocably waives, and agrees not to assert in any suit,
action or proceeding, any claim that it is not personally subject to the
jurisdiction of any such court, that such suit, action or proceeding is brought
in an

 

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inconvenient forum or that the venue of such suit, action or proceeding is
improper. Each party hereby irrevocably waives personal service of process and
consents to process being served in any such suit, action or proceeding by
mailing a copy thereof to such party at the address for such notices to it under
this Agreement and agrees that such service shall constitute good and sufficient
service of process and notice thereof. Nothing contained herein shall be deemed
to limit in any way any right to serve process in any manner permitted by law.
EACH PARTY HEREBY IRREVOCABLY WAIVES ANY RIGHT IT MAY HAVE, AND AGREES NOT TO
REQUEST, A JURY TRIAL FOR THE ADJUDICATION OF ANY DISPUTE HEREUNDER OR IN
CONNECTION WITH OR ARISING OUT OF THIS AGREEMENT OR ANY TRANSACTION CONTEMPLATED
HEREBY.

7. This Agreement is intended for the benefit of the parties hereto and their
respective permitted successors and assigns, and is not for the benefit of, nor
may any provision hereof be enforced by, any other Person.

8. This Agreement shall be binding upon and inure to the benefit of the parties
and their respective successors and assigns in accordance with the terms of this
Agreement.

9. The obligations of the Holder under this Agreement are several and not joint
with the obligations of any other Holder, and the Holder shall not be
responsible in any way for the performance of the obligations of any other
Holder under the Agreement. Nothing contained herein or in this Agreement, and
no action taken by the Holder pursuant hereto, shall be deemed to constitute
such Holder and other Holders as a partnership, an association, a joint venture
or any other kind of entity, or create a presumption that such Holder and the
other Holders are in any way acting in concert or as a group with respect to
such obligations or the transactions contemplated by this Agreement and the
Company acknowledges that the Holders are not acting in concert or as a group
with respect to such obligations or the transactions contemplated by this
Agreement. The Company and the Holder confirms that the Holder has independently
participated in the negotiation of the transactions contemplated hereby with the
advice of its own counsel and advisors. The Holder shall be entitled to
independently protect and enforce its rights arising out of this Agreement, and
it shall not be necessary for any other Holder to be joined as an additional
party in any proceeding for such purpose.

10. This Agreement may be executed in two or more identical counterparts, all of
which shall be considered one and the same agreement and shall become effective
when counterparts have been signed by each party and delivered to the other
party; provided that a facsimile signature shall be considered due execution and
shall be binding upon the signatory thereto with the same force and effect as if
the signature were an original, not a facsimile signature.

[signature page follows]

 

 

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IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the date
first above written.

 

HOLDER: By:      

Name:

Title:

 

[Signature Page to Consent and Agreement]

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IN WITNESS WHEREOF, the undersigned has executed this Agreement as of the date
first above written.

 

COMPANY:

 

NANOGEN, INC.

By:      

Name:

Title: