EXHIBIT 10.1

Confidential treatment has been requested for portions of this exhibit.  The
copy filed herewith omits the information subject to the confidentiality
request.  Omissions are designated as [***].  A complete version of this exhibit
has been filed separately with the Securities and Exchange Commission.

Amendment Agreement

December 22, 2006

This Amendment Agreement (this “Amendment”) dated as of the date first written
above is entered into by F. Hoffmann-La Roche Ltd., a Swiss corporation
(“Roche”), Roche Molecular Systems, Inc., a Delaware corporation (“RMS”), and
Affymetrix, Inc., a Delaware corporation (“Affymetrix”).  RMS is a wholly-owned
direct subsidiary of Roche.  Roche, RMS and Affymetrix are each a “Party” and
collectively the “Parties.”

Roche and Affymetrix have entered into the following agreements (collectively,
together with this Amendment, the “Collaboration Agreements”) on January 29,
2003:  (i) the Common Terms Agreement, (ii) the License Agreement, (iii) the
Supply Agreement, (iv) the Affymetrix Instrument Agency Agreement, (v) the
Diagnostic Product Agency Agreement, (vi) the Standstill Agreement and (vii) the
R&D Agreement.  The Collaboration Agreements also include the P450 Addendum
Agreement among the Parties dated June 24, 2003, the Amendment Agreement among
the Parties dated February 17, 2004, and the Amendment Agreement among the
Parties dated December 8, 2004.  All capitalized terms not otherwise defined
herein shall have the meanings set forth in the Common Terms Agreement.

The Parties now desire to amend and supplement the Collaboration Agreements on
the terms set forth herein.

The Parties therefore agree as follows:

1.               Installment Payments. Roche is hereby relieved of its
obligations to pay License Installment Payments under Section III(b) of the
License Agreement (as amended), and such section is hereby deleted in its
entirety.

2.               Most Favorable Terms and Conditions. Affymetrix is hereby
relieved of its obligations under Section IV(k)(i), IV(k)(ii) and IV(k)(iii) of
the License Agreement (as amended), and such sections are hereby deleted in
their entirety. In addition, Affymetrix’ notice obligations under Section
IV(k)(v) of the License Agreement (as amended) shall apply only with respect to
the running royalty rate in a Third Party license and, if the Third Party
license was entered into in conjunction with a chip supply arrangement, the Chip
transfer or sales price.

3.               Milestone Payments.

(a)                                  Section III(d)(i) of the License Agreement
(as amended) is hereby further amended to read in full as follows:

(i) Upon the earlier to occur of (A) initial Regulatory Approval for a
particular Diagnostic Product in any of the United States, Japan or Germany, or
(B) commercial aggregate gross sales for a particular Diagnostic Product in the
United States of at least $[***] over four consecutive calendar quarters, then
for such Diagnostic Product:

(1)                                  US$[***] if Affymetrix has contributed
substantially to the Content of such Diagnostic Product; or

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(2)                                  US$[***] if Affymetrix has not contributed
substantially to the Content of such Diagnostic Product; and

(b)                                 The US$[***] aggregate maximum on Milestone
Payments payable under Section III(d) of the License Agreement (as amended) is
removed, but the Parties hereby agree that, notwithstanding clauses (i) and (ii)
(as amended) in such Section III(d),

(i) if the aggregate amount of all prior Milestone Payments does not exceed
US$[***] but an additional Milestone Payment will bring the aggregate amount of
all Milestone Payments above $[***], then the portion of the additional
Milestone Payment which causes such amount to be exceeded shall be the lesser of
(x) the amount otherwise due without regard to this clause (ii) and (y) an
amount to be negotiated by the Parties that shall in no event be less than
US$[***] nor more than US$[***], and

(ii) if the aggregate amount of all prior Milestone Payments exceeds US$[***]
then the amount of each additional Milestone Payment shall be an amount to be
negotiated by the Parties that shall in no event be less than US$[***] nor more
than US$[***], and

(iii) if the aggregate amount of all prior Milestone Payments exceeds US$[***],
then any additional Milestone Payment shall only be achieved and payable if and
when initial Regulatory Approval for the relevant Diagnostic Product has been
achieved in the United States and Germany, and commercial aggregate gross sales
for such Diagnostic Product have reached at least $[***] worldwide.

(c)                                  The Milestone Payments defined in Section
III(d)(i) (as amended) already reflect the [***]% reduction described in Section
3(a) of the December 08, 2004 Amendment Agreement. Accordingly, no portion of
such Milestone Payments shall be deleted or creditable against future royalties
payable under Section III(c) of the License Agreement.

(d)                                 Nothing in this Section 3(b) of this
Amendment shall alter the provisions of Section 3(b) of the December 08, 2004
Amendment Agreement with regards to the maximum quarterly Milestone Payments.

4.               Roche Discretion.  By entering into this Amendment, Roche has
elected not to give an Early Termination Notice with respect to the optional
termination effective date of December 31, 2007. Accordingly, Roche hereby
waives its early termination rights (including full termination and Partial
Termination) as provided in Section VI(b) of the License Agreement (as
supplemented and amended) with respect to such date. For clarity, nothing in
this Amendment shall in any way limit Roche’s complete discretion to give an
Early Termination Notice (whether relating to a full termination or a Partial
Termination) with respect to any subsequent optional termination effective dates
in accordance with the Collaboration Agreements (as amended) for any or no
reason.

5.               General Provisions.

(a)          Collaboration Agreement.  For all purposes of the Collaboration
Agreements, this Amendment shall constitute a Collaboration Agreement, and the
definition of the term “Collaboration Agreements” in the Common Terms Agreement
is hereby amended accordingly.  Without limiting the generality of the
foregoing, Section VI (General) of the Common Terms Agreement shall apply to
this Amendment and is incorporated by reference as if fully set forth herein.

(b)         Relation to Other Collaboration Agreements.  As amended by this
Amendment, the Collaboration Agreements remain in full force and effect.

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IN WITNESS WHEREOF the Parties have executed this Amendment.

AFFYMETRIX, INC.

 

F. HOFFMANN-LA ROCHE LTD.

 

 

 

 

 

 

 

 

 

By:

/s/ Noel Doheny

 

By:

  /s/ Florian Zabel

 

Name:

Noel Doheny

 

 

Name:

Florian Zabel

 

Title:

Senior Vice President,
Molecular Diagnostics

 

 

Title:

Legal Counsel

 

 

 

 

By:

  /s/ Robert Yates

 

 

 

 

 

Name:

Robert Yates

 

 

 

 

 

Title:

Head of Business Development

 

 

 

 

 

ROCHE MOLECULAR SYSTEMS, INC.

 

 

 

 

 

 

 

 

By:

/s/ Daniel P. O’Day

 

 

 

Name:  Daniel P. O’Day

 

 

 

Title:

 

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