Research & Development Collaboration Agreement

EXHIBIT 10.60


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.


Research & Development Collaboration Agreement


F. Hoffmann-La Roche Ltd.


and


Affymetrix, Inc.


dated


January 29, 2003


TABLE OF CONTENTS


Section 1

Statement of Purpose


Section 2

Common Terms and Definitions


Section 3

Management


Section 4

Project Proposals and Implementation


Section 5

Projects for Diagnostic Products


Section 6

Market Development Activities.


Section 7

Performance of Collaboration Projects for Instrumentation and Other Products


Section 8

License Grants


Section 9

General Applicable Provisions


Section 10

Warranty Disclaimers


Section 11

Infringement, Indemnity, Etc.


Section 12

Term and Termination


Section 13

Limitation of Liability


Section 14

No Implied Obligations


2


RESEARCH & DEVELOPMENT COLLABORATION AGREEMENT

January 29, 2003


THIS RESEARCH & DEVELOPMENT COLLABORATION AGREEMENT (" Agreement") is effective as of the date first written above (the " Effective Date") between F. Hoffmann-La Roche Ltd. (" Roche") and Affymetrix, Inc., a Delaware corporation (" Affymetrix").

R E C I T A L S

A. The Parties desire to collaborate (the " Collaboration" as more specifically defined in the " Common Terms Agreement" dated as of even date herewith, between Affymetrix and Roche) in the development and commercialization of diagnostic products in connection with and in the field of DNA chip technology and in the development of certain instrumentation and related software for use with microarrays using Affymetrix Technology. In connection with such Collaboration, the Parties are entering into the Collaboration Agreements.

B. Pursuant to the Collaboration, the Parties desire that Affymetrix, upon Roche's request in accordance with the terms of this Agreement, shall undertake mutually agreed research and development projects, in collaboration with Roche, focusing on the development and validation of specific Diagnostic Products for Diagnostic Use.

C. The Parties further desire that Roche (and/or its Affiliates), pursuant to the Collaboration, will undertake research and development activities in collaboration with Affymetrix to develop instrumentation for use with Arrays which shall have a cost and throughput which makes feasible the widespread use of such instrumentation by Customers and other purchasers of Diagnostic Products. The Parties also contemplate that they may undertake related collaborative research and development activities to develop improved chip packaging based on Affymetrix' Existing Technology as well as analytical software for use with Roche's instruments.

D. In connection with such research and development projects, the Parties will combine certain of their scientific, intellectual property, development and financial resources as specified herein and under the Collaboration Agreements, to (i) facilitate the development of such specific Diagnostic Products for Diagnostic Use, which Diagnostic Products will be commercialized as described in the Collaboration Agreements; and (ii) to facilitate the development by the Parties of instrumentation for use with Arrays and such improved chip packaging and analytical software for use with such instruments.

E. The Parties intend that the research and development goals and the responsibilities for any given research and development project pursuant to this Agreement shall be formulated by the Parties on a project-by-project basis, and that all research and development activities between the Parties shall be governed by and conducted in accordance with the terms and conditions set forth in this Agreement, subject to any express modifications made in a Project Plan.


3


A G R E E M E N T

NOW, THEREFORE, in consideration of the foregoing and the mutual covenants, promises and undertakings set forth herein, the Parties agree as follows:

Section 1 Statement of Purpose


The Parties wish to pursue collaborative activities in the development and commercialization of Diagnostic Products, chip packaging, instrumentation and related software in connection with and in the field of DNA chip technology. This Agreement, together with the Collaboration Agreements, provides the terms, conditions and covenants which will govern their relationship for purposes of such research and development, both with respect to specifically identified projects and general cooperative research and development undertakings.

Section 2 Common Terms and Definitions


2.1 Common Terms

(a) All capitalized terms not otherwise defined herein shall have the meanings set forth in the Common Terms Agreement.

(b) This Agreement shall be governed by and subject to the provisions contained in the Common Terms Agreement, in accordance with its terms.

2.2 Definitions

(a) " Hosted Employees" means, as applicable, employees of either Affymetrix or Roche, or their respective Affiliates, who are invited to participate in research, development or other activities located at the other Party's or its Affiliate's facilities and who participate in such activities. "Hosted Employees" means all Hosted Employees, Affymetrix' Hosted Employees or Roche's Hosted Employees, as the context may require.

(b) " Jointly-Owned IP" shall have the meaning set forth in Section 9.3(a).

(c) " Project Managers" means those individuals so designated in accordance with Section 3.2.

(d) " Standard Fully Loaded FTE" means (i) [***], such as [***], incurred in a period related to an activity plus (ii) [***] (i.e., [***] and [***]), plus [***], [***] and [***] for the equivalent number of full-time employees in a 12-month period (with the portion of a full-time equivalent year devoted by an employee to the Collaboration determined by dividing the number of days during any 12-month period devoted by such employee to the Collaboration by the total number of working days during the 12-month period, with appropriate proportional adjustment for normal vacation and holiday days).

4


Section 3 Management


3.1 Joint Research Management Committee . The Parties shall establish and maintain a Joint Research Management Committee (the " Joint Research Management Committee" or " JRMC") in accordance with the following provisions:

(a) The JRMC shall consist of six members, three members to be appointed by each of Affymetrix and Roche, with one of the three designated each Party's JRMC primary contact (a " Primary Contact"). Each Party may, with notice to the other Party, replace any of its members serving on the JRMC. The Parties shall designate their respective members within ten (10) days of the Effective Date. The JRMC shall propose recommendations to the Parties regarding the Project Plans. All recommendations of the JRMC shall be made unanimously. No chairperson shall be appointed and each member of the JRMC shall have only one vote.

(b) The JRMC shall be responsible for negotiating, preparing, executing, implementing, managing and reviewing compliance with the Project Plans and shall in particular: (i) evaluate projects proposed by either Party and make recommendations to the Parties regarding projects selected for approval; (ii) negotiate, prepare and execute Project Plans, including, without limitation, schedules of work and budgets for each such Project Plan; (iii) review and propose amendments to the Project Plans from time to time in such manner as may be appropriate; (iv) monitor progress of the Project Plans; (v) report regularly to the Executive Representatives of the Parties upon the progress of the Project Plans; and (vi) via each Party's Primary Contact, be the initial medium for transfer of information between the Parties regarding current or proposed projects.

3.2 Appointment of Managers . Each Party will designate Project Managers to represent and lead that Party in the day-to-day activities associated with each project undertaken pursuant to this Agreement or a Project Plan. The Project Managers will lead their respective development teams in the day-to-day development work to be performed under the Agreement, including: planning and coordination of all technical efforts; reviewing and responding to proposals presented by the other Party's Project Managers; helping in the preparation of Project Plans; reporting to the JRMC; and working together to resolve any conflicts that may arise in connection with a project. Either Party may change its Project Managers upon written notice to the other Party, but, as with their Executive Representatives, the Parties agree to exercise this right with restraint to help ensure reasonable continuity in management of the relationship.

3.3 JRMC Meetings

(a) The JRMC shall meet as needed at any time upon the reasonable request of either Party during the term of the Project Plans, and in any event no less frequently than quarterly, to review the current status of the Collaboration, to consider potential additional areas of cooperation, and to resolve any escalations. The Project Managers will assist the Primary Contacts in the preparation of agendas for the JRMC meetings. Additionally, the Project Managers will present information concerning progress on areas of Collaboration as requested by the JRMC, as well as provide input on potential areas for future cooperation between the Parties.

5


(b) Unless otherwise agreed by the Parties, all meetings of the JRMC shall be held by teleconference or in person in Alameda or Santa Clara Counties, California or as may be otherwise agreed. Meetings shall be scheduled with at least thirty (30) day's notice (provided that conference calls may be scheduled with at least fifteen (15) day's notice); the Primary Contact of the Party that seeks to convene a particular meeting shall be responsible for the meeting notice and scheduling. The quorum for JRMC meetings shall be at least two members from each Party.

3.4 Technical Reports and Access to Information . Each Party will keep and maintain adequate records containing technical and laboratory data generated in the course of the performance of such Party's responsibilities under the Project Plans to enable it to furnish complete and accurate information to the other Party regarding such Project Plans activities and results. Each Party shall provide reasonably-detailed written reports describing the results of the development work performed by such Party pursuant to the Project Plans. Such reports shall be delivered to the other Party at the JRMC meetings within forty-five (45) days following each March 31, June 30, September 30 and December 31, after commencement of the initial project plan, or at such other time(s) as the JRMC requires. Without limiting the foregoing, each Party agrees to provide the other Party reasonable access to appropriate data and information relating to the Collaboration hereunder, and to give required notices and to respond to inquiries in a reasonable timeframe in order to facilitate the timely completion of the Project Plans contemplated herein.

Section 4 Project Proposals and Implementation


4.1 Proposal and Evaluation of Projects . Either Party may, from time to time, deliver to the JRMC a non-binding proposal regarding an area of cooperation between the Parties. Such proposal shall be in writing and shall be sent by the proposing Party to the JRMC and the other Party's Executive Representative. The JRMC shall promptly evaluate the proposal in good faith and the Parties shall mutually agree whether to proceed with such proposal based on the recommendation of the JRMC.

4.2 Implementation of Projects . In the event that the Parties agree to pursue a proposed area of cooperation, the JRMC shall proceed in good faith to negotiate, prepare and document the cooperative undertaking in a Project Plan according to the processes set out in this Agreement. It shall be the responsibility of the JRMC in consultation with the Project Managers of the Parties to negotiate, prepare, agree to and execute Project Plans prior to initiation of proposed projects. The Project Managers shall cooperate and consult with the JRMC in good faith to prepare Project Plan(s) as appropriate for the activities contemplated by the Parties under this Agreement. The Project Managers and/or the JRMC may associate such other personnel as they or it may deem desirable in connection with negotiation, preparation and agreement of Project Plans and may, from time to time, add to, delete from and/or modify the Project Plans as agreed.

4.3 Hosted Employees . During the course of the relationship established by this Agreement, it is anticipated that the Parties may choose to allow Hosted Employees to visit and/or work on the Parties' or their respective Affiliates' respective premises. Each Hosted Employee shall retain his or her status as an employee of his or her respective company while

6


assigned to work at the hosting Party's premises. Each assigning Party shall have sole and exclusive discretion and control in selecting those of its employees assigned as Hosted Employees, but shall exercise such discretion and control in good faith and with the goal of providing competent and productive personnel capable of promoting and advancing the objectives of the particular assignment.

4.4 Responsibility for Hosted Employees . Each Party shall be solely responsible for all wages and other compensation, and for all U.S., Swiss or other federal, state, cantonal, local, FICA and other similar withholding and payments required in connection with all its employees assigned as Hosted Employees at the ot ...