Document:

Medarex, Inc. 2002 New Employee Stock Option Plan

  
 Exhibit 10. 1 
  
 Medarex, Inc. 2002 New Employee Stock Option Plan 
  

 

  
 MEDAREX, INC. 
 2002 NEW EMPLOYEE STOCK OPTION PLAN 
  
 Section
1.    Purpose of the Plan.  The purpose of the New Employee Stock Option Plan (the “Plan”) is to aid Medarex, Inc. (the “Corporation”) and its subsidiaries in securing and retaining employees
of outstanding ability and to motivate such persons to exert their best efforts on behalf of the Corporation and its subsidiaries. In addition, the Corporation expects that it will benefit from the added interest which the respective optionees and
participants will have in the welfare of the Corporation as a result of their ownership or increased ownership of the Common Stock of the Corporation (the “Stock”). 
  
 Section 2.    Administration.  (a) the Board of Directors of the Corporation (the “Board”) shall designate a
Committee of not less that two (2) Directors (the “Committee”) who shall serve at the pleasure of the Board. Each member of the Committee shall be a “non-employee” director within the meaning of Rule 16b-3(b) (3)(i) under the
Securities Exchange Act of 1934, as amended (the “Exchange Act”), as such Rule or any other comparable rule may be in effect from time to time, while serving on the Committee. The Board shall fill any vacancies on the Committee and may
remove any member of the Committee at any time with or without cause. The Committee shall select its chairman and hold its meetings at such times and places as it may determine. A majority of the whole Committee present at a meeting at which a
quorum is present, or an act approved in writing by all members of the Committee, shall be an act of the Committee. The Committee shall have full power and authority, subject to such resolutions not inconsistent with the provisions of the Plan as
may from time to time be issued or adopted by the Board (provided the entire Board acting on the matter are Disinterested Persons), to grant to Eligible Persons (as defined herein) pursuant to the provisions of the Plan (i) stock options to purchase
shares, (ii) stock appreciation rights, (iii) restricted stock, (iv) deferred stock, or (v) other Stock-based awards permitted hereunder (each of the foregoing being an “AWARD” and collectively, the “AWARDS”). The Committee shall
also interpret the provisions of the Plan and any AWARD issued under the Plan (and any agreements relating thereto) and supervise the administration of the Plan. 
  
 (b)    The Committee shall:  (i) select the employees of the Corporation and its subsidiaries to whom AWARDS may from time to
time be granted hereunder; (ii) determine whether nonqualified stock options, stock appreciation rights, restricted stock, deferred stock, or other Stock-based awards, or a combination of the foregoing, are to be granted hereunder; (iii) determine
the number of shares to be covered by each AWARD granted hereunder; (iv) determine the terms and conditions, not inconsistent with the provisions of the Plan, of any AWARD granted hereunder (including but not limited to any restriction and
forfeiture condition on such AWARD and/or the shares of Stock relating thereto); (v) determine whether, to what extent and under what circumstances AWARDS may be settled in cash; (vi) determine whether, to what extent, and under what circumstances
Stock and other amounts payable with respect to an AWARD under this Plan shall be deferred either automatically or at the election of the 

 participant; and (vii) determine whether, to what extent, and under what circumstances option grants and/or other AWARDS
under the Plan are to be made, and operate, on a tandem basis. 
  
 (c)     All
decisions made by the Committee pursuant to the provisions of the Plan and related orders or resolutions of the Board (as and to the extent permitted hereunder) shall be final, conclusive and binding on all persons, including the Corporation, its
shareholders, employees and Plan participants. 
  
 (d)     No member of the
Committee shall be liable for any action or determination made in good faith with respect to the Plan or any AWARD thereunder. 
  
 (e)     Anything herein to the contrary notwithstanding, the Committee, by resolution, may delegate to management of the Corporation the right to grant AWARDS with respect to up to
50,000 shares to any one participant without any further action being required by the Committee. 
  
 Section 3.    Stock Subject to the Plan.  Except as otherwise provided by this Section 3, the total number of shares of Stock available for distribution under the Plan is 500,000. The total number
of shares of stock with respect to which AWARDS may be granted to any participant in any calendar year is 200,000 shares. Such shares may consist, in whole or in part, of authorized and unissued shares or treasury shares, except that treasury shares
must be used in the case of restricted stock. If any shares that have been optioned cease to be subject to option because the option has expired or has been deemed to have expired or has been surrendered pursuant to the Plan, or if any shares of
restricted stock are forfeited or such AWARD otherwise terminates without the actual or deemed delivery of such shares, such shares shall again be subject to an AWARD under the Plan. 
  
 In the event of any merger, reorganization, consolidation, recapitalization, stock dividend, extraordinary cash dividend, or other change in corporate
structure affecting the Stock, such adjustment shall be made in the aggregate number of shares which may be delivered under the Plan, in the number and/or option price of shares subject to outstanding options granted under the Plan, and/or in the
number of shares subject to restricted stock, deferred stock, or other Stock-based awards granted under the Plan as may be determined to be appropriate by the Committee, in its sole discretion; provided that the number of shares subject to any
AWARDS shall always be a whole number. Such adjusted option price shall also be used to determine the amount payable by the Corporation upon the exercise of any stock appreciation right associated with any option. In addition, subject to the
limitations provided in Section 11, the Committee is authorized to make adjustments in the terms and conditions of, and performance criteria relating to, AWARDS in recognition of unusual or nonrecurring events (including, without limitation, events
described in this paragraph) affecting the Corporation or the financial statements of the Corporation, or in response to changes in applicable laws, regulations or accounting principles. 

 
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 Section 4.    Eligibility.  Any person who
is an employee of the Corporation or its subsidiaries and who has not previously been an employee or director of the Corporation or any of its subsidiaries is eligible to be granted AWARDS under the Plan as an inducement essential to that
person’s entering into employment with the Corporation or its subsidiaries (each an “Eligible Person” and collectively “Eligible Persons”). The participants under the Plan shall be selected from time to time by the
Committee, in its sole discretion, from among those eligible, and the Committee shall determine, in its sole discretion, the number of shares covered by each stock option, the number of stock appreciation rights (if any) granted to each optionee,
and the number of shares (if any) subject to restricted stock, deferred stock or other Stock-based awards granted to each participant. 
  
 For purposes of the Plan, a subsidiary of the Corporation shall be any corporation which at the time qualifies as a subsidiary thereof under the definition of “subsidiary corporation” in Section 424(f) of the
Internal Revenue Code of 1986, as amended. 
  
 Section 5.    Stock Options.  Any
stock option granted under the Plan shall be in such form as the Committee may from time to time approve. Any such option shall be subject to the following terms and conditions and shall contain such additional terms and conditions, not inconsistent
with the provisions of the Plan, as the Committee shall deem desirable. 
  
 (a)     Option
Price.  The purchase price per share of the Stock purchasable under a stock option shall be determined by the Committee. 
  
 (b)     Option Period.  The term of each stock option shall be fixed by the Committee, but no stock option shall be exercisable after the expiration of 10 years from the date the option
is granted. 
  
 (c)     Exercisability.  (1) Stock options shall be exercisable
at such time or times as determined by the Committee at or subsequent to the date of grant. Unless otherwise determined by the Committee at or subsequent to the date of grant, no stock option shall be exercisable until the first anniversary date of
the granting of the option, except as provided in paragraphs (f), (g) or (h) of this Section 5; provided, however, that notwithstanding the foregoing from and after a Change of Control (as hereinafter defined) all stock options shall become
immediately exercisable to the full extent of the AWARD. 
  
 (2)    As used herein, “Change
of Control” shall mean any of the following events: 
  
   (A)   An
acquisition (other than directly from the Corporation) of any voting securities of the Corporation (the “Voting Securities”) by any “Person” (as the term “person” is used for purposes of Section 13(d) or 14(d) of the
Exchange Act) immediately after which such Person has “Beneficial Ownership” (within the meaning of Rule 13d-3 promulgated under the Exchange Act) of 15% or more of the combined voting power of the Corporation’s then outstanding
Voting Securities; provided, however, that in determining whether a Change of 

 
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 Control has occurred, voting securities which are acquired in a “Non-Control Acquisition” (as hereinafter
defined) shall not constitute an acquisition which would cause a Change of Control. 
  
 A
“Non-Control Acquisition” shall mean an acquisition by (i) an employee benefit plan (or a trust forming a part thereof) maintained by (x) the Corporation or (y) any corporation or other Person of which a majority of its voting power or its
equity securities or equity interest is owned directly or indirectly by the Corporation (a “Subsidiary”), (ii) the Corporation or any Subsidiary, or (iii) any Person in connection with a Non-Control Transaction (as defined below);

  
 (B)    The individuals who, as of January 1, 2002 were members of the Board
(the “Incumbent Board”), cease for any reason to constitute at least 66 2/3% of the Board; provided, however, that if the election, or nomination for election by the Corporation’s stockholders, of any new director was approved by a
vote of at least 66 2/3% of the Incumbent Board, such new director shall be considered as a member of the Incumbent Board; provided, further, however, that no individual shall be considered a member of the Incumbent Board if such individual
initially assumed office as a result of either an actual or threatened “Election Contest” (as described in Rule 14a-11 promulgated under the Exchange Act) or other actual or threatened solicitation of proxies or consents by or on behalf of
a Person other than the Board (a “Proxy Contest”) including by reason of any agreement intended to avoid or settle any Election Contest or Proxy Contest; or 
  
 (C)    Approval of the Corporation’s shareholders of: (1) a merger, consolidation or reorganization involving the Corporation,
unless (i) the stockholders of the Corporation, immediately before such merger, consolidation or reorganization, own, directly or indirectly immediately following such merger, consolidation or reorganization, at least 66 2/3% of the combined voting
power of the outstanding Voting Securities of the Corporation resulting from such merger or consolidation or reorganization (the “Surviving Corporation”) in substantially the same proportion as their ownership of the Voting Securities
immediately before such merger, consolidation or reorganization, (ii) the individuals who were members of the Incumbent Board immediately prior to the execution of the agreement providing for such merger, consolidation or reorganization constitute
at least 66 2/3% of the members of the board of directors of the Surviving Corporation, and (iii) no Person, other than the Corporation, any Subsidiary, any employee benefit plan (or any trust forming a part thereof) maintained by the Corporation,
the Surviving Corporation or any Subsidiary, or any Person who, immediately prior to such merger, consolidation or reorganization had Beneficial Ownership of 15% or more of the then outstanding Voting Securities of the Corporation, has Beneficial
Ownership of 15% or more of the combined voting power of the Surviving Corporation’s then outstanding voting securities (a transaction described in clause (i) through (iii) shall herein be referred to as a “Non-Control Transaction”);
(2) a complete liquidation or dissolution of the Corporation; or (3) an agreement for the sale or other disposition of all or substantially all of the assets of the Corporation to any Person (other than a transfer to a Subsidiary). 

 
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 Notwithstanding the foregoing, a Change of Control shall not be
deemed to occur solely because any Person (the “Subject Person”) acquired Beneficial Ownership of more than the permitted amount of the outstanding Voting Securities as a result of the acquisition of Voting Securities by the Corporation
which, by reducing the number of Voting Securities outstanding, increases the proportional number of shares Beneficially Owned by the Subject Person, provided that if a Change of Control would occur (but for the operation of this sentence) as a
result of the acquisition of Voting Securities by the Corporation, and after such share acquisition, the Subject Person becomes the Beneficial Owner of any additional Voting Securities which increases the percentage of the then outstanding Voting
Securities Beneficially Owned by the Subject Person, then a Change of Control shall occur. 
  
 (d)    Method of Exercise.  Stock options may be exercised, in whole or in part, by giving written notice of exercise to the Corporation specifying the number of shares to be purchased. Such
notice shall be accompanied by payment in full of the purchase price in cash, either by certified or bank check; provided, however, that after a Change of Control an optionee, during the 60-day period from and after a Change of Control, shall have
the right, in lieu of the payment of the full purchase price of the shares of the Stock being purchased under the stock option and by giving written notice to the Corporation, to elect (within such respective periods) to surrender all or part of the
stock option to the Corporation and to receive in cash an amount equal to the amount by which the fair market value per share of the Stock on the date of exercise shall exceed the purchase price per share under the stock option multiplied by the
number of shares of the Stock granted under the stock option as to which the right granted by this proviso shall have been exercised. 
  
 The written notice provided by the optionee shall specify the optionee’s election to purchase shares subject to the stock option or to receive the cash payment herein provided. 
  
 Notwithstanding the foregoing, the Committee may, in its sole discretion, authorize payment in whole or in part of the purchase price to
be made in unrestricted stock already owned by the optionee, or in restricted stock, or deferred stock subject to an AWARD hereunder (based upon the fair market value of the Stock on the date the option is exercised as determined by the Committee).
The Committee may authorize such payment at or after grant. No shares of Stock shall be issued until full payment therefor has been made. Subject to paragraph (i) of this Section 5, an optionee shall have the rights to dividends or other rights of a
stockholder with respect to shares subject to the option when the optionee has given written notice of exercise, has paid in full for such shares, and, if requested, has given the representation described in paragraph (a) of Section 14.

  
 As used in this paragraph (d) of Section 5, the fair market value of the Stock on the date of exercise shall
mean, with respect to an election by an optionee to receive cash in respect of a stock option, the “Change of Control Fair Market Value,” as defined below. 
  
 (e)    Restrictions on Transferability.  The Committee, in its sole discretion, may impose such restrictions on the transferability of
stock options granted hereunder as it deems 

 
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 appropriate. Any such restrictions shall be set forth in the stock option agreement with respect to such
stock options. 
  
 (f)    Termination by Death.  Except to the extent otherwise
provided by the Committee at or after the time of grant, if an optionee’s relationship with or employment by the Corporation and/or any of its subsidiaries terminates by reason of death, the stock option may thereafter be immediately exercised
in full by the legal representative of the estate or by the legatee of the optionee under the will of the optionee, for a period of 15 months from the date of such death or until the expiration of the stated period of the option whichever period is
the shorter. 
  
 (g)    Termination by Reason of Retirement or Permanent
Disability.  Except to the extent otherwise provided by the Committee at or after the time of grant, if an optionee’s relationship with or employment by the Corporation and/or any of its subsidiaries terminates by reason of
retirement or permanent disability, any stock option held by such optionee may thereafter be exercised in full, but may not be exercised after three years from the date of such termination or the expiration of the stated period of the option,
whichever period is the shorter; provided, however, that if the optionee dies within such three-year period, any unexercised stock option held by such optionee shall thereafter be exercisable to the extent to which it was exercisable at the time of
death for a period of 12 months from the date of the optionee’s death or for the stated period of the option, whichever period is the shorter. 
  
 (h)    Other Termination.  Unless otherwise determined by the Committee at or after grant, if an optionee’s relationship with or employment by the Corporation
terminates for any reason other than death, permanent disability or retirement, the stock option shall thereupon terminate; provided, however, that if such termination is by action of the Corporation and other than discharge for reason of willful
violation of the rules of the Corporation or by voluntary resignation of the optionee, in either case within 18 months following a Change of Control, any stock options held by the optionee may be exercised by the optionee until the earlier of six
months and one day after such termination or the expiration of such options in accordance with their terms. 
  
 (i)    Option Buyout.  The Committee may at any time offer to repurchase an option based on such terms and conditions as the Committee shall establish and communicate to the optionee at the time
that such offer is made. 
  
 (j)    Form of Settlement.  In its sole discretion,
the Committee may provide, at the time of grant, that the shares to be issued upon an option’s exercise shall be in the form of restricted stock or deferred stock, or may reserve the right to so provide after the time of grant. 

 
 Section 6.    Stock Appreciation Rights.  (a)  Grant and
Exercise.  Stock appreciation rights may be granted in conjunction with (or in accordance with Section 9, separated from) all or part of any stock option granted under the Plan, either at the time of the grant of such option or at any
subsequent time during the term of the option. A “stock appreciation right” is a right to receive cash or Stock, as provided in this Section 6, in lieu of the purchase of a share under a related option. A stock appreciation right, or
applicable portion thereof, shall terminate and no longer be exercisable upon the termination or 

 
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 exercise of the related stock option, except that a stock appreciation right granted with respect to less than the full number of shares covered
by a related stock option shall not be reduced until the exercise or termination of the related stock option exceeds the number of shares not covered by the stock appreciation right. A stock appreciation right may be exercised by an optionee, in
accordance with paragraph (b) of this Section 6, by surrendering the applicable portion of the related stock option. Upon such exercise and surrender, the optionee shall be entitled to receive an amount determined in the manner prescribed in
paragraph (b) of this Section 6. Options which have been so surrendered, in whole or in part, shall no longer be exercisable to the extent the related stock appreciation rights have been exercised. 
  
 (b)    Terms and Conditions.  Stock appreciation rights shall be subject to such terms and
conditions, not inconsistent with the provisions of the Plan, as shall be determined from time to time by the Committee, including the following: 
  
 (i)    Stock appreciation rights shall be exercisable only at such time or times and to the extent that the stock options to which they relate shall be exercisable. Except as
otherwise provided in Section 5, a person who is required to file reports under Section 16(a) of the Exchange Act (an “Insider”) may only settle a stock appreciation right by satisfying either of the following conditions: 

 
 (A)  the stock appreciation right is settled at least six (6) months after its date of grant; or

  
 (B)  the settlement of the stock appreciation right is made pursuant to an irrevocable
election to settle the right no earlier than six (6) months after the date of such election. 
  
 None
of the conditions of this Section 6(i) shall be applicable in the event of death or permanent disability of the optionee. 
  
 (ii)    Upon the exercise of a stock appreciation right, an optionee shall be entitled to receive up to, but no more than, an amount in cash or whole shares of the Stock as determined by the Committee in
its sole discretion equal to the excess of the fair market value of one share of Stock over the option price per share specified in the related stock option multiplied by the number of shares in respect of which the stock appreciation right shall
have been exercised; provided, however, that the payment in settlement of stock appreciation rights during the period from and after a Change of Control shall be entirely in cash. Each stock appreciation right may be exercised only at the time and
so long as a related option, if any, would be exercisable or as otherwise permitted by applicable law; provided however, that no stock appreciation right granted under the Plan to an Insider then subject to Section 16 of the Exchange Act shall be
exercised during the first six months of its term. The fair market value of the Stock on the date of exercise of a stock appreciation right shall be determined in the same manner as the fair market value 

 
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 of the Stock on the date of grant of a stock option is determined pursuant to paragraph (a) of Section 5 of the Plan;
provided, however, that during the 60-day period from and after a Change of Control, the fair market value of the Stock on the date of exercise shall mean, with respect to the exercise of a stock appreciation right accompanying an option, the
“Change of Control Fair Market Value.” 
  
 For purposes of this Plan, the “Change of
Control Fair Market Value” shall mean the higher of (x) the highest reported sale price, regular way, of a share of the Stock on the Composite Tape for New York Stock Exchange Listed Stock during the 60-day period prior to the date of the
Change of Control or, if such security is not listed or admitted to trading on the New York Stock Exchange, on the principal national securities exchange on which such security is listed or admitted to trading or, if not listed or admitted to
trading on any national securities exchange, on the Nasdaq National Market or, if such security is not quoted on such Nasdaq National Market, the average of the closing bid and asked prices during such 60-day period in the over-the-counter market as
reported by the National Association of Securities Dealers Automated Quotation system (“NASDAQ”) or, if bid and asked prices for such security during such period shall not have been reported through NASDAQ, the average of the bid and asked
prices for such period as furnished by any New York Stock Exchange member firm regularly making a market in such security selected for such purpose by the Board of Directors of the Corporation or a committee thereof or, if such security is not
publicly traded, the fair market value thereof as determined by an independent investment banking or appraisal firm experienced in the valuation of such securities selected in good faith by the Board of Directors of the Corporation or a committee
thereof or, if no such investment banking or appraisal firm is in the good faith judgment of the Board of Directors or such committee available to make such determination, as determined in good faith by the Board of Directors of the Corporation or
such committee and (y) if the Change of Control is the result of a transaction or series of transactions described in paragraph (i) or (iii) of the definition of Change of Control set forth in Section 5(c), the highest price per share of the Stock
paid in such transaction or series of transactions (in the case of a Change of Control described in such paragraph (i) of Section 5(c), as reflected in any Schedule 13D filed by the person having made the acquisition). 
  
 (iii)  The Committee, in its sole discretion, may impose such restrictions on the transferability of stock
appreciation rights as it deems appropriate. Any such restrictions shall be set forth in the written agreement between the Corporation and the optionee with respect to such rights. 
  
 (iii)  Upon the exercise of a stock appreciation right, the stock option or part thereof to which such stock appreciation right is related shall
be deemed to have been exercised for the purpose of the limitation of the number of shares of the Stock to be issued under the Plan, as set forth in Section 3 of the Plan. 

 
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 Section 7.    Restricted
Stock.  (a)  Stock and Administration.    Shares of restricted stock may be issued either alone or in addition to stock options, stock appreciation rights, deferred stock or other Stock-based awards
granted under the Plan. The Committee shall determine the employees of the Corporation and its subsidiaries to whom, and the time or times at which, grants of restricted stock will be made, the number of shares to be awarded, the time or times
within which such AWARDS may be subject to forfeiture, and all other conditions of the AWARDS. The provisions of restricted stock AWARDS need not be the same with respect to each recipient. 
  
 (b)    Awards and Certificates.    The prospective recipient of an AWARD of shares of restricted stock shall not, with
respect to such AWARD, be deemed to have become a participant, or to have any rights with respect to such AWARD, until and unless such recipient shall have executed an agreement or other instrument evidencing the AWARD and delivered a fully executed
copy thereof to the Corporation and otherwise complied with the then applicable terms and conditions. 
  
 (i)     Each participant shall be issued a stock certificate in respect of shares of restricted stock awarded under the Plan. Such certificate shall be registered in the name of the participant, and shall
bear an appropriate legend referring to the terms, conditions, and restrictions applicable to such AWARD, substantially in the following form: 
  
 “The transferability of this certificate and the shares of stock represented hereby are subject to the terms and conditions (including forfeiture) of the Medarex, Inc. 2002 New Employee Stock
Option Plan and an Agreement entered into between the registered owner and Medarex, Inc. Copies of such Plan and Agreement are on file in the offices of Medarex, Inc., 707 State Road, Princeton, New Jersey 08540.” 
  
 (ii)    The Committee shall require that the stock certificates evidencing such shares be held in
custody by the Corporation until the restrictions thereon shall have lapsed, and shall require, as a condition of any restricted stock AWARD, that the participant shall have delivered a stock power, endorsed in blank, relating to the Stock covered
by such AWARD. 
  
 (c)    Restrictions and Conditions.    The shares
of restricted stock awarded pursuant to the Plan shall be subject to the following restrictions and conditions: 
  
 (i)     subject to the provisions of this Plan during a period set by the Committee commencing with the date of such AWARD (the “restriction period”), the participant shall not be permitted to sell,
transfer, pledge, or assign shares of restricted stock awarded under the Plan. Within these limits the Committee may provide for the lapse of such restrictions in installments where deemed appropriate. 
  
 (ii)    Except as provided in paragraph (c) of this Section 7, the participants shall have, with
respect to the shares of restricted stock, all of the rights of a stockholder of the Corporation, including the right to vote the restricted stock and the right to receive any 

 
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 cash dividends. The Committee, in its sole discretion, may permit or require the payment of cash dividends to be deferred
and, if the Committee so determines, reinvested in additional restricted stock or otherwise reinvested. Certificates for shares of unrestricted stock shall be delivered to the participant promptly after, and only after, the period of forfeiture
shall expire without forfeiture in respect of such shares of restricted stock. 
  
 (iii)    Subject to the provisions of paragraph (c)(iv) of this Section 7, upon termination of employment of any reason during the restriction period, all shares still subject to restriction shall be forfeited by
the participant and reacquired by the Corporation. 
  
 (iv)    In the event of a
participant’s retirement, permanent disability, or death, or in cases of special circumstances, the Committee may, in its sole discretion, when it finds that a waiver would be in the best interests of the Corporation, waive in whole or in part
any or all remaining restrictions with respect to such participant’s shares of restricted stock. 
  
 (v)     Notwithstanding anything in the foregoing to the contrary, upon a Change of Control any and all restrictions on restricted stock shall lapse regardless of the restriction period established by the
Committee and all such restricted stock shall become fully vested and nonforfeitable. 
  
 Section
8.      Deferred Stock Awards.  (a)  Stock and Administration.    AWARDS of the right to receive Stock that is not to be distributed to the participant until after a
specified deferral period (such AWARD and the deferred stock delivered thereunder hereinafter as the context shall require, referred to as the “deferred stock”) may be made either alone or in addition to stock options, stock appreciation
rights, or restricted stock, or other Stock-based awards granted under the Plan. The Committee shall determine the employees of the Corporation and its subsidiaries to whom and the time or times at which deferred stock shall be awarded, the number
of shares of deferred stock to be awarded to any participant, the duration of the period (the “Deferral Period”) during which, and the conditions under which, receipt of the Stock will be deferred, and the terms and conditions of the AWARD
in addition to those contained in paragraph (b) of this Section 8. In its sole discretion, in lieu of delivering shares, the Committee may provide for a minimum payment to the participant at the end of the applicable Deferral Period based on a
stated percentage of the fair market value on the date of grant of the number of shares covered by a deferred stock AWARD. The Committee may also provide for the grant of deferred stock upon the completion of a specified performance period. The
provisions of deferred stock AWARDS need not be the same with respect to each recipient. 
  
 (b)            Terms and Conditions.    Deferred stock AWARDS made pursuant to this Section 8 shall be subject to the following terms and
conditions: 
  
 (i)      Subject to the provisions of the Plan, the shares
to be issued pursuant to a deferred stock AWARD may not be sold, assigned, transferred, pledged or otherwise 

 
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 encumbered during the Deferral Period or Elective Deferral Period (defined
below), where applicable, and may be subject to a risk of forfeiture during all or such portion of the Deferral Period as shall be specified by the Committee. At the expiration of the Deferral Period and Elective Deferral Period, share certificates
shall be delivered to the participant, or the participant’s legal representative, in a number equal to the number of shares covered by the deferred stock AWARD. 
  
 (ii)    Amounts equal to any dividends declared during the Deferral Period with respect to the number of shares covered by a deferred
stock AWARD will be paid to the participant currently, or deferred and deemed to be reinvested in additional deferred stock or otherwise reinvested, as determined at the time of the AWARD by the Committee, in its sole discretion. 

 
 (iii)    Subject to the provisions of paragraph (b)(iv) of this Section 8, upon termination
of the relationship with or employment by the Corporation for any reason during the Deferral Period for a given deferred stock AWARD, the deferred stock in question shall be forfeited by the participant. 
  
 (iv)    In the event of the participant’s retirement, permanent disability or death during the
Deferral Period (or Elective Deferral Period, where applicable), or in cases of special circumstances, the Committee may, in its sole discretion, when it finds that a waiver would be in the best interests of the Corporation, waive in whole or in
part any or all of the remaining deferral limitations imposed hereunder with respect to any or all of the participant’s deferred stock. Anything in the Plan to the contrary notwithstanding, upon the occurrence of a Change of Control, the
Deferral Period and the Elective Deferral Period with respect to each deferred stock AWARD shall expire immediately and all share certificates relating to such deferred stock AWARDS shall be delivered to each participant or the participant’s
legal representative. 
  
 (v)    Prior to completion of the Deferral Period, a
participant may elect to defer further the receipt of the deferred stock AWARD for a specified period or until a specified event (the “Elective Deferred Period”), provided that the Committee may, in its sole discretion, disallow any such
action. 
  
 (vi)    Each deferred stock AWARD shall be confirmed by a deferred
stock agreement or other instrument executed by the Committee and by the participant. 
  
 Section
9.    Other Stock-Based Awards.  (a)  Stock and Administration.  Other AWARDS of the Stock and other AWARDS that are valued in whole or in part by reference to, or are otherwise based
on the Stock (“Other Stock-based AWARDS”), including (without limitation) performance shares and convertible debentures, may be granted either alone or in addition to other AWARDS granted under the Plan. Subject to the provisions of the
Plan, the Committee shall have sole and complete authority to determine the employees of the Corporation and/or any of its subsidiaries to whom and the time or times 

 
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 at which such Other Stock-based AWARDS shall be made, the number of shares of the Stock to be awarded
pursuant to such Other Stock-based AWARDS and all other conditions of the Other Stock-based AWARDS. The Committee may also provide for the grant of the Stock upon the completion of a specified performance period. The provisions of Other Stock-based
AWARDS need not be the same with respect to each recipient. 
  
 (b)    Terms and
Conditions.  Other Stock-based AWARDS made pursuant to this Section 9 shall be subject to the following terms and conditions: 
  
 (i)    Subject to the provisions of this Plan, shares or interests in shares subject to Other Stock-based AWARDS made under this Section 9 may not be sold, assigned, transferred,
pledged or otherwise encumbered prior to the date on which the shares are issued, or, if later, the date on which any applicable restriction, performance or deferral period lapses. 
  
 (ii)    Subject to the provisions of this Plan and the Other Stock-based AWARD agreement, the recipients of Other Stock-based AWARDS
under this Section 9 shall be entitled to receive, currently or on a deferred basis, interest or dividends or interest or dividend equivalents with respect to the number of shares or interests therein covered by the Other Stock-based AWARDS, as
determined at the time of the Other Stock-based AWARDS by the Committee, in its sole discretion, and the Committee may provide that such amounts (if any) shall be deemed to have been reinvested in additional Stock or otherwise reinvested.

  
 (iii)    Any Other Stock-based AWARDS under this Section 9 and any Stock
covered by any such Other Stock-based AWARD may be forfeited to the extent so provided in the Other Stock-based AWARD agreement, as determined by the Committee, in its sole discretion. 
  
 (iv)    In the event of the participant’s retirement, permanent disability or death, or in cases of special circumstances, the
Committee may, in its sole discretion, when it finds that a waiver would be in the best interests of the Corporation, waive in whole or in part any or all of the remaining limitations imposed hereunder (if any) with respect to any or all Other
Stock-based AWARDS under this Section 9. Anything in the Plan to the contrary notwithstanding, any limitations imposed with respect to any Other Stock-based AWARD under this Section 9, including any provision providing for the forfeiture of any
Other Stock-based AWARD under any circumstance, shall terminate immediately upon a Change of Control and the number of shares of or interests in the Stock subject to such Other Stock-based AWARD shall be delivered to the participant (or, in the case
of an Other Stock-based AWARD with respect to which such number is not determinable, such number of shares of or interests in the Stock as is determined by the Committee and set forth in the terms of such Other Stock-based AWARD). 

 
 -12- 

  
 (v)     Each Other Stock-based AWARD under
this Section 9 shall be confirmed by an agreement or other instrument executed by the Corporation and by the participant. 
  
 (vi)     The Stock or interests therein (including securities convertible into the Stock) paid or awarded on a bonus basis under this Section 9 shall be issued for no cash consideration; the Stock or
interests therein (including securities convertible into the Stock) purchased pursuant to a purchase right awarded under this Section 9 shall be priced at least 50% of the fair market value of the Stock on the date of grant. 
  
 (vii)     The Committee, in its sole discretion, may impose such restrictions on the transferability
of Other Stock-based Awards as it deems appropriate. Any such restrictions shall be set forth in the written agreement between the Corporation and the optionee with respect to such Award. 
  
 (viii)     Each Other Stock-based AWARD to an Insider under this Section 9 shall be subject to all of the limitations and
qualifications that may be required by Section 16 of the Exchange Act and all of the rules and regulations promulgated thereunder. 
  
 Section 10.    Transfer, Leave of Absence, etc.    For purposes of the Plan: (a) a transfer of an employee from the Corporation to a subsidiary, or vice versa, or from one
subsidiary to another; (b) a leave of absence, duly authorized in writing by the Corporation, for military service or sickness, or for any other purposes approved by the Corporation if the period of such leave does not exceed 90 days; and (c) a
leave of absence in excess of 90 days, duly authorized in writing by the Corporation, shall not be deemed a termination of employment. 
  
 Section 11.    Amendments and Termination.    The Board may amend, alter, or discontinue the Plan, but no amendment, alteration, or discontinuation shall be made which would
impair the rights of an optionee or participant under any AWARD theretofore granted, without the optionee’s or participant’s consent, or which without the approval of the shareholders would: 
  
 (a)     except as is provided in Section 3 of the Plan, increase the total number of shares available
for the purpose of the Plan; 
  
 (b)     subsequent to the date of grant
decrease the option price of any stock option to less than 100% of the fair market value on the date of the granting of the option; 
  
 (c)     extend the maximum option period under Section 5(b) of the Plan; or 
  
 (d)     otherwise materially increase the benefits accruing to participants under, or materially modify the requirements as to eligibility for participation in, the Plan.

  
 The Committee may amend the terms of any AWARD theretofore granted, prospectively or retroactively, but no such
amendment shall impair the rights of any holder without such holder’s 

 
 -13- 

  
 consent. Notwithstanding the foregoing, the Board or the Committee may, in its discretion, amend the
Plan or terms of any outstanding AWARD held by a person then subject to Section 16 of the Exchange Act without the consent of any holder in order to preserve exemptions under said Section 16 which are or become available from time to time under
rules of the Securities and Exchange Commission. The Committee may also substitute new stock options for previously granted options, including previously granted options having higher option prices. 
  
 Section 12.    Unfunded Status of the Plan.    The Plan is intended to constitute an
“unfunded” plan for incentive and deferred compensation. With respect to any payments not yet made to a participant or optionee by the Corporation, nothing contained herein shall give any such participant or optionee any rights that are
greater than those of a general creditor of the Corporation. In its sole discretion, the Committee may authorize the creation of trusts or other arrangements to meet the obligations created under the Plan to deliver the Stock; provided, however,
that the existence of such trusts or other arrangements is consistent with the unfunded status of the Plan. 
  
 Section 13.    Employment at Will.    Nothing contained in the Plan, or in any option granted pursuant to the Plan, nor in any agreement made pursuant to the Plan, shall confer upon any
optionee any right with respect to continuance of employment by the Company or its subsidiaries, nor interfere in any way with the right of the Company or its subsidiaries to terminate the optionee’s employment at will or change the
optionee’s compensation at any time. 
  
 Section 14.    General
Provisions.    (a) The Committee may require each participant purchasing shares pursuant to an AWARD under the Plan to represent to and agree with the Corporation in writing that such participant is acquiring the shares
without a view to distribution thereof. The certificates for such shares may include any legend which the Committee deems appropriate to reflect any restrictions on transfer. 
  
             (b)        All certificates for shares of the Stock
delivered under the Plan pursuant to any AWARD shall be subject to such stock-transfer orders and other restrictions as the Committee may deem advisable under the rules, regulations, and other requirements of the Securities and Exchange Commission,
any stock exchange upon which the Stock is then listed, and any applicable Federal or state securities law, and the Committee may cause a legend or legends to be put on any such certificates to make appropriate reference to such restrictions.

  
             (c)        Recipients of shares of restricted stock, deferred stock and other Stock-based awards under the Plan (other
than options) shall not be required to make any payment or provide consideration other than the rendering of services. 
  
             (d)        AWARDS granted under the Plan may, in the discretion of the Committee, be granted either alone or in addition
to, in tandem with, or in substitution for, any other AWARDS granted under the Plan. If AWARDS are granted in substitution for other AWARDS, the Committee shall require the surrender of such other AWARDS in consideration for the grant of the new
AWARDS. AWARDS granted in addition to or in tandem with other AWARDS may be granted either at the same 

 
 -14- 

  
 time as or at a different time from the grant of such other AWARDS. The exercise price of any option or
the purchase price of any Other Stock-based AWARD in the nature of a purchase right shall be determined by the Committee: 
  
             (e)     Nothing contained in this Plan shall prevent the Board of Directors from adopting other or additional compensation arrangements,
subject to shareholder approval if such approval is required; and such arrangements may be either generally applicable or applicable only in specific cases. 
  
 Section 15.    Taxes.    Participants shall make arrangements satisfactory to the Committee regarding payment of any Federal, state, or local taxes of any
kind required by law to be withheld with respect to any income which the participant is required, or elects, to include in his gross income and the Corporation and its subsidiaries shall, to the extent permitted by law, have the right to deduct any
such taxes from any payment of any kind otherwise due to the participant. Anything contained herein to the contrary notwithstanding, the Committee may, in its sole discretion, authorize acceptance of Stock received in connection with the grant or
exercise of an AWARD or otherwise previously acquired in satisfaction of withholding requirements. 
  
 Section
16.    Effective Date of the Plan.    The Effective Date of the Plan is as of July 23, 2002, the date the Plan was approved by the vote of a majority of the Board of Directors. 
  
 Section 17.    Term of the Plan.    No AWARD shall be granted pursuant to the Plan after
July 23, 2012, but AWARDS theretofore granted may extend beyond that date. 
  

 
 -15-exv10w50

 

Certain confidential information contained in this document, marked by brackets, has been omitted and filed separately with the Securities
and Exchange Commission pursuant to Rule 24b-2 of the Securities Exchange Act of 1934, as Amended.

Amended and Restated Agreement

Gene Logic Inc.

Affymetrix, Inc.

-1-

 

CONTENTS

	 	 	 	 	 
	1        Introduction
	 	 	-3-	 
	

	 	 	 	 
	2        Definitions
	 	 	-3-	 
	

	 	 	 	 
	3        Probe Array Supply
	 	 	-6-	 
	

	 	 	 	 
	4        Affymetrix Proprietary Rights
	 	 	-11-	 
	

	 	 	 	 
	5        Compensation
	 	 	-12-	 
	

	 	 	 	 
	6        Intellectual Property
	 	 	-16-	 
	

	 	 	 	 
	7        Project Coordination
	 	 	-18-	 
	

	 	 	 	 
	8        Confidentiality
	 	 	-18-	 
	

	 	 	 	 
	9        Warranty
	 	 	-19-	 
	

	 	 	 	 
	10      Indemnity
	 	 	-20-	 
	

	 	 	 	 
	11      Term and Termination
	 	 	-20-	 
	

	 	 	 	 
	12      Dispute Resolution
	 	 	-21-	 
	

	 	 	 	 
	13      Miscellaneous
	 	 	-21-	 
	

	 	 	 	 
	Exhibit A
	 	 	-27-	 
	Exhibit B
	 	 	-28-	 
	Exhibit C
	 	 	-29-	 
	Exhibit D
	 	 	-30-	 
	Exhibit E
	 	 	-31-	 
	Exhibit F
	 	 	-33-	 
	Exhibit G
	 	 	-35-	 
	Exhibit H
	 	 	-36-	 
	Exhibit I
	 	 	-37-	 

-2-

 

AGREEMENT

This agreement (“Agreement”) is effective as of January 1, 2002 (“Effective
Date”) between Affymetrix, Inc. (“Affymetrix”) a Delaware corporation having
its principal place of business at 3380 Central Expressway, Santa Clara,
California 95051, and Gene Logic Inc., a Delaware corporation having its
principal place of business at 708 Quince Orchard Road, Gaithersburg, Maryland,
20878 (“Gene Logic”).

	 	 	 
	1.	 	
Introduction
	1.1	 	
Affymetrix has research, development, and manufacturing capabilities and
facilities, and has developed certain rights relevant to DNA probe array
based technology.
	1.2	 	
Gene Logic has research and development capabilities, and facilities to
conduct research and development activities for the generation of
databases useful in life sciences research.
	1.3	 	
Affymetrix and Gene Logic desire to enter into an agreement whereby
Affymetrix will supply Gene Logic and/or its Subsidiaries with DNA probe
arrays for use in Gene Logic’s and/or its Subsidiaries’ development of
database products and services.
	1.4	 	
In consideration of the mutual covenants and promises contained in this
Agreement, Affymetrix and Gene Logic agree as follows:
	
	 	 
	2.	 	
Definitions
	2.1	 	
“Affiliate” shall mean any corporation, company, partnership, joint
venture and/or firm which is controlled by or controls a Party or is under
common control with a Party, but only for so long as such Affiliate
remains an Affiliate of a Party, and only if such Affiliate is bound by
the terms of this Agreement. For purposes of this Section, “control”
shall mean, in the case of corporations (or equivalents of corporations),
direct or indirect ownership of more than 50% of the stock having the
right to vote for directors of such corporation or, in the case of
partnerships, more than 50% of the ownership interest in such partnership.
The Parties agree that MetriGenix, Inc. shall not be considered an
Affiliate of Gene Logic for the purposes of this Agreement.
	2.2	 	
“Affiliate’s Area of Interest” shall mean the use of Probe Arrays or data
therefrom as a research tool to generate gene expression data for
Affiliate’s internal research and development activities.
	2.3	 	
“Chip Improvement Inventions” shall mean all inventions for which patent
applications are filed that are conceived or first reduced to practice by
an employee or contractor of a Party or its Affiliates resulting from
design or use of the Probe Arrays supplied hereunder, and specifically
those relating to probe array manufacturing techniques, probe array
layouts, probe array packaging techniques, probe array assay techniques
([...***...]), and probe array software analysis techniques relating to
the extraction of data from probe arrays and storing such data in a
computer file, but not including software analysis techniques for later
processing of such data. It is to be understood that inventions made
independently of design or use of Probe Arrays (such as those inventions
made in the course of design or use of Gene Logic’s proprietary
technologies or other non-Affymetrix technologies) are not Chip
Improvement Inventions within the meaning of this Agreement. Chip
Improvement Inventions shall further not include any other inventions that
are conceived of or reduced to practice by an employee or contractor of a
Party or its Affiliates including, for example, expression data or
discoveries resulting

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therefrom, targets identified through the use of the Probe Arrays, or
correlations between genetic sequences and function.
	2.4	 	
“Committee” shall mean the individuals designated by Gene Logic and
Affymetrix to serve on a coordinating committee as outlined in Section 7.
	2.5	 	
“Confidential Information” shall mean all information and materials,
patentable or otherwise, of a Party disclosed by or on behalf of such
Party to the other Party and which derive value to a Party from not being
generally known, including, but not limited to DNA sequences, vectors,
cells, substances, formulations, techniques, methodology, equipment, data,
reports, know-how, trade secrets, preclinical and clinical trials and the
results thereof, sources of supply, patent positioning, and business
plans, including any negative developments. Without limiting the
foregoing, the Parties confirm their understanding that Chip Improvement
Inventions are deemed by the Parties to be the Confidential Information of
Affymetrix and that Gene Logic may not publish, disclose, divulge or
otherwise communicate to third parties Chip Improvement Inventions without
the prior written approval of Affymetrix which must be obtained.
	2.6	 	
“Custom Probe Array” means, except where otherwise set forth herein, a
custom Probe Array, based on Target Sequences submitted by Gene Logic,
sold by Affymetrix only to Gene Logic and/or its Affiliates hereunder.
	2.7	 	
“Database” shall mean a collection of Datapoints derived from a Probe
Array which is made available for license broadly in whole or in part for
use to derive additional information.
	2.8	 	
“Datapoint” shall mean a Gene represented on a Probe Array and comprises
all probe pairs on the array that represent the Gene.
	2.9	 	
“Demonstration Database” shall refer to a database of gene expression
data that contains no more than the applicable maximum number of
Datapoints. During the Term, the applicable maximum number of Datapoints
shall be [...***...] million.
	2.10	 	
“Fabrication Verification Criteria” shall mean Affymetrix’ then current
quality control criteria for the applicable Probe Arrays.
	2.11	 	
“Gene” shall refer to a nucleic acid sequence encoding a distinct RNA. A
Gene may be represented by a partial nucleic acid sequence representing an
expressed sequence tag (EST). Multiple ESTs from the same Gene are
considered a single Gene. Polymorphic variants of a nucleic acid sequence
are considered a single Gene, provided that such polymorphic variants must
have at least [...***...] % homology with the underlying Gene. If a
nucleic acid sequence encodes multiple distinct RNAs due to alternative
splicing, each alternative internal splice variant is considered a
distinct Gene.
	2.12	 	
“Gene Logic’s Area Of Interest” shall mean the use of Probe Arrays as a
research tool to generate gene expression data for a) generating databases
for license to third parties for value; and b) performing Services; and c)
performing Tox Services; and d) Gene Logic’s internal research and
development activities.
	2.13	 	
“Genetic Inventions” shall mean all genetic sequence (including related
protein) and function inventions discovered by Gene Logic through the use
of an Probe Array data including, without limitation, any invention which
is covered by an issued patent that contains data from the Probe Array
data or was supported during patent prosecution by data obtained from the
Probe Array data.
	2.14	 	
“Lot” shall refer to the standard minimum quantities Probe Arrays are
made available to third parties, as set forth in Affymetrix’ price list
and specifications.

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	2.15	 	
“Net Sales” shall mean the aggregate United States Dollar equivalent of
gross revenues derived by or payable to Gene Logic or its Subsidiaries for
or on account of the license of Databases, including Databases sold or
licensed as part of a system, package, or combination product, to third
parties including Subsidiaries where such Databases are not for re-license
or resale, less a) credits or allowances, if any, actually granted on
account of price adjustments, recalls, rejections, or return of items
previously sold, b) prompt payment or actual trade or quantity discounts
actually allowed and taken, c) excises, sales taxes, value added taxes,
consumption taxes, duties, foreign withholding tax actually withheld, or
other taxes imposed upon and paid with respect to such sales (excluding
income or franchise taxes of any kind) and d) insurance and delivery costs
actually incurred. No deduction shall be made for any item of cost
incurred by Gene Logic or its Subsidiaries in preparing, manufacturing,
shipping, or selling Databases except as permitted pursuant to a), b), c)
and d) above. Net Sales shall not include any transfer between Gene Logic
and any of its Subsidiaries for re-license or resale. If Gene Logic or a
Subsidiary licenses or sells to or through a distributor (which is not an
Affiliate or Subsidiary of Gene Logic), Net Sales shall be the gross
revenues received by Gene Logic and/or the applicable Subsidiary from the
license of the Database to such distributor. Any such distributor
arrangement must be under reasonably conventional distributor terms. In
the event that Gene Logic or any of its Subsidiaries licenses a Database
to third parties for other than monetary value (including without
limitation an equity transaction) in whole or in part, such transfer shall
be considered a license hereunder for accounting and royalty purposes.
Net Sales for any such transfers shall be determined on a
country-by-country basis and shall be equal to the higher of the fair
market value of such non-monetary consideration, or the average price of
arms length licenses by Gene Logic or its Subsidiaries for similar
products in such country during the royalty reporting period in which such
transfer occurs, or if no such arms length licensing occurred in such
country during such period, during the last period in which such arms
length sales occurred. If no such arms length licenses have occurred in a
particular country, Net Sales for such transfer shall be the average price
of arms length licenses for similar products in all countries. Gene Logic
and its Subsidiaries shall at all times act in commercially reasonable
good faith (including, without limitation, the use of generally accepted
accounting principles, consistently applied) and shall not intentionally
or knowingly inappropriately or inaccurately apportion amounts invoiced
for the purpose or effect of circumventing or depriving Affymetrix of any
benefit due under this Agreement.
	2.16	 	
“Party” shall mean Affymetrix or Gene Logic. “Parties” shall mean
Affymetrix and Gene Logic.
	2.17	 	
“Physical Defects” shall mean defects resulting from the manufacture or
handling of Probe Arrays by Affymetrix prior to shipment, such that
Affymetrix reasonably agrees that such defects are the [...***...] of
[...***...] of [...***...] to [...***...] for a [...***...]. Such
determination must be made by Affymetrix Technical Support pursuant to the
Affymetrix Replacement Policy as set forth in Exhibit F hereto.
	2.18	 	
“Probe Arrays” shall mean a solid support having an array of
polynucleotides with known location and sequence fabricated by Affymetrix
pursuant to this Agreement for use in expression analysis and shall
include Proprietary Probe Arrays and Custom Probe Arrays.

* Confidential Treatment Requested

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	2.19	 	
“Proprietary Probe Arrays” shall refer to Probe Arrays which contain
substantial proprietary genetic information of a third party for which
incremental fees are due by Affymetrix to such third party associated with
the use of such proprietary genetic information.
	2.20	 	
“Sample Supplier” shall mean a not-for-profit third party supplier of
biological samples to Gene Logic that exchanges such samples for a Sample
Supplier Database.
	2.21	 	
“Sample Supplier Database” shall mean a Database of no more than
[...***...] ([...***...]) Datapoints of the then current version of Probe
Arrays that is provided to a Sample Supplier in exchange for the samples
from which such Datapoints are derived.
	2.22	 	
“Services” shall mean the use of Probe Arrays in generation of data that
will be provided to only one third party. Services shall include
databases developed by Gene Logic and/or its Subsidiaries exclusively for
a third party customer solely for such third party customer’s internal
use. In the event that data are provided on a service basis and later
released for commercial distribution as a database, such collection of
data shall be considered a “Service” at the time delivered to a single
customer. The Parties agree that in the rollout of a Database update to
Gene Logic customers, this Service definition shall not be triggered if no
more than [...***...] elapsed between the first and last receipt of such
Database update by Gene Logic customers (excluding [...***...]).
	2.23	 	
“Significant Physical Defects” shall refer to Physical Defects in Probe
Arrays which meet Affymetrix’ [...***...] criteria for significant
physical defects as determined by Affymetrix Technical Support. It is
understood that the criteria for Significant Physical Defects are [...***...] than Affymetrix’ [...***...] replacement criteria. The list
in Exhibit D may be reasonably updated by the Committee from time-to-time.
	2.24	 	
“Subsidiary” shall mean any Affiliate which is wholly-owned by Gene Logic
and which is controlled by Gene Logic including day-to-day management
operations, but only for so long as such Subsidiary remains a Subsidiary
of Gene Logic, and only if such Subsidiary is bound by the terms of this
Agreement. For purposes of this Section, “control” shall mean, in the
case of corporations (or equivalents of corporations), direct or indirect
ownership of 100% of the stock having the right to vote for directors of
such corporation or, in the case of partnerships, 100% of the ownership
interest in such partnership.
	2.25	 	
“Subsidiary’s Area Of Interest” shall be the same as Gene Logic’s Area of
Interest.
	2.26	 	
“System(s)” shall mean fluidics station(s), work station(s),
hybridization oven(s), probe array reader(s), and associated software,
such software licensed to Gene Logic, and such fluidicsstation(s), work
station(s) and probe array reader(s) sold to Gene Logic.
	2.27	 	
“Term” shall mean the period beginning on the Effective Date and ending
on a date two (2) years thereafter, unless extended for an additional two
(2) year period at Gene Logic’s election; notice of such election to be
provided to Affymetrix in writing no less than six (6) months in advance
of the expiration of the initial Term.
	2.28	 	
“Tox Services” shall mean the use of Probe Arrays in generation of
toxicity screening data that will be provided to only one third party
solely for such third party customer’s internal use.

	 	 	 
	3.	 	
Probe Array Supply
	3.1	 	
Custom Probe Arrays may be ordered only in full Lots.
	3.2	 	
Beginning on the Effective Date, Affymetrix will deliver such quantities
of the appropriate Probe Arrays which have passed the Fabrication
Verification Criteria at or before the time specified in a properly
rendered forecast made pursuant to Section 3.3, or,

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for the first 3 months of the Term, according to a forecast previously
supplied by Gene Logic and/or its Subsidiaries and attached as Exhibit C.
	3.3	 	
Beginning on the Effective Date and on the first business day of each
month during the Term of this Agreement, Gene Logic and its Affiliates
will provide a reasonable, good faith forecast of Probe Arrays to be
supplied by Affymetrix during the following [...***...] period or the
period until the end of the Term if less than [...***...] (such forecasts
to be supplied by number of Probe Arrays and part number) to Gene Logic
and its Affiliates. The forecast will be provided according to a
mechanism and on forms to be agreed upon in good faith by the Parties.
The first and second month of such forecast (part number and individual
quantity) shall constitute a firm order. The subsequent months of such
forecast will be for capacity planning purposes only, and shall not
constitute a firm commitment. If the number of ordered Probe Arrays
forecast for a month increases by more than [...***...] from the
immediately preceding firm forecast for such month then the number of such
Probe Arrays above the [...***...] increase shall be supplied in a
reasonable time, but shall not be subject to penalty or breach on account
of late supply thereof.
	3.4	 	
Probe Arrays will be packed in Affymetrix’ standard shipping packages and
shipped to the address specified by Gene Logic and/or its Affiliates.
Deliveries will be F.C.A. Affymetrix’ facility or the facility of its
sales representative. Affymetrix will ship via a carrier selected by Gene
Logic or, if none is specified by Gene Logic, Affymetrix will select the
carrier. Title and risk of loss of damage for deliveries will pass to
Gene Logic and/or its Affiliates upon Affymetrix’ actual delivery of the
Probe Arrays to the carrier for shipment to Gene Logic and/or its
Affiliates. Gene Logic and/or its Affiliates will pay all shipping costs,
duties, and sales taxes. Gene Logic and/or its Affiliates will advise
Affymetrix if insurance is desired on any shipments of Probe Arrays, and
will reimburse Affymetrix for all such insurance charges. Affymetrix will
ship new orders of Probe Arrays within [...***...] days of receipt of
purchase order for such new orders (excluding Custom Probe Arrays which
will be provided pursuant to Section 3.6.1 and replacement Probe Arrays
pursuant to Exhibit F which will be shipped pursuant to Section 3.14).
	3.5	 	
Affymetrix will provide Gene Logic with [...***...] qualified
instructor-days of training in use of Probe Arrays and Systems at
Affymetrix’ expense and in schedules to be mutually and reasonably agreed.
In cases where Gene Logic elects to have training at Affymetrix’
facility, travel and expenses of Gene Logic personnel will be paid by Gene
Logic. Additional training will be reasonably provided by Affymetrix to
Gene Logic at the request of Gene Logic at the then current commercial
terms.

	 	 	 	 	 	 	 
	3.6	 	 	
3.6.1
	 	 	Gene Logic and/or its Affiliates are entitled to purchase
Custom Probe Array designs from Affymetrix for $[...***...] per custom
design. This pricing permits specifications for arrays of up to
[...***...] probes per Probe Array, up to [...***...] bases, and up to
[...***...] synthesis steps. Designs for a Custom Probe Array
representing eukaryotic organism genes and containing Probe Sets of [...***...]
probe pairs per gene with [...***...] μm feature sizes may contain probes
distributed across the surface of the array. When ordering Custom Probe
Arrays, Gene Logic and/or its Affiliates will identify Target Sequences
for each Custom Probe Array as set forth in the applicable documentation
provided by Affymetrix, a current version of which is attached as Exhibit
H hereto. If the

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	 	 	information received by Affymetrix does not include the information
required, Affymetrix will advise Gene Logic and/or its Affiliates
of any additional needed information. Upon Affymetrix confirming
receipt of complete Target Sequences and related information for
each Custom Probe Array design, Affymetrix will use reasonable
efforts to design, lay out, produce masks, and manufacture one Lot
of Custom Probe Arrays for each such custom design as follows: (i)
within [...***...] if Gene Logic orders [...***...]; (ii)
within [...***...] for up to [...***...] custom designs; and (iii)
for more than [...***...] custom designed, according to the schedule
quoted to Gene Logic and/or its Affiliates at the time they order
such Custom Probe Array designs. Where Gene Logic and/or its
Affiliates have ordered more than [...***...] Affymetrix reserves the right to provide the initial Lots of Custom
Probe Arrays for each such design at separate times, at Affymetrix’
sole discretion, subject to the maximum time periods described in
the previous sentence; in such case, the order that the initial
Lots of each such design will be provided relative to such other
designs and will be determined by a priority list submitted by Gene
Logic at the time it orders the designs or, if no such list is
submitted, in Affymetrix’ discretion. In no event shall Affymetrix
be obligated to supply more than [...***...] custom designs per
year. Delivery times for all additional Lots of Custom Probe
Arrays ordered pursuant to this letter will be quoted at the time
Affymetrix receives a firm order for such products and shall not
exceed [...***...] from the date of such order. Potential
deviations from the standard custom design specifications as
described above that Affymetrix may consider are outlined in
Exhibit G hereto. Gene Logic acknowledges that implementation of
any or all deviations listed in Exhibit G for a particular custom
design may increase the time period between order placement and
delivery of Custom Probe Arrays based on any such design, provided
however that any such implementation will in no event cause the
schedule to increase more than [...***...]. All such time
extensions for a particular custom design will be discussed with
Gene Logic prior to start of such design. All Custom Probe Arrays
must be ordered and purchased in whole Lot increments, where a
“Lot” is [...***...] Custom Probe Arrays, and the Lot size and/or
range may be modified by Affymetrix upon reasonable notice to Gene
Logic. The term “Target Sequences” refers to a set of Gene
sequences for which Gene Logic and/or its Affiliates will have
Affymetrix make Custom Probe Arrays pursuant to this Agreement.
Gene Logic shall be fully responsible for the Target Sequences,
and, except to the extent arising from Affymetrix’
commercialization of a particular Custom Probe Array design, Gene
Logic will settle or defend any legal proceeding brought against
Affymetrix in connection with the Target Sequences in accordance
with Section 10.1.

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3.6.2
	 	 	Standard Custom Probe Arrays are currently available
in the following formats and lot sizes:

	 	 	 	 	 
	

	Format	 	
Arrays/Wafer
	 	Minimum

Order
	

	Standard
	Midi
	Mini	 	[...***...]	 	[...***...]
	Maxi

	 	 	 	 	All Standard Custom Probe Arrays must be ordered and purchased in
whole lot increments, which may be changed upon reasonable notice
from Affymetrix. The Standard Custom Probe Array per unit list
prices are based upon Custom Probe Array format and organism.
	 	 	
3.6.3
	 	In the event Gene Logic, upon request and in its sole
discretion, elects to permit Affymetrix, in its sole discretion, to
commercialize particular Custom Probe Array designs ordered
hereunder by distributing probe arrays based on such design
(“Branded Arrays”) to third parties, the Parties agree to negotiate
in good faith for each such design the grant of a license by Gene
Logic to Affymetrix under Gene Logic’s relevant intellectual
property rights, if any, to distribute Branded Arrays based on such
design; each such license may include [...***...], if any, or
[...***...], taking into account, among other things, the
[...***...] and [...***...] based on such [...***...]

	3.7	 	
Except as explicitly permitted in Exhibit E, or otherwise set forth in
Section 5.3 below, neither Gene Logic, nor its Subsidiaries nor Affiliates
may:

	 	 	 	
1)
	 	 	transfer the Probe Arrays provided by Affymetrix
pursuant to this Agreement to third parties; or
	 	 	 	
2)
	 	 	transfer data generated therewith to any third
party except that Gene Logic and Subsidiaries may transfer
data to:

	 	 	
i)
	 	each other for use in such
Subsidiaries’ or Gene Logic’s Area of Interest or
	 	 	
ii)
	 	subscribers to a Database
	 	 	
iii)
	 	Sample Suppliers or
	 	 	
iv)
	 	in the case of Services or
Tox Services, to a single third party; or

	 	 	 	
3)
	 	 	provide services to any third party, using the
Probe Arrays provided by Affymetrix pursuant to the Agreement
except Gene Logic and/or its Subsidiaries may provide Services
or Tox Services:

	 	 	
(a)
	 	as to those Probe Arrays, excluding Custom Probe Arrays, where:

	 	 	i)	 	the Service or
Tox Service recipient agrees to limit further
distribution of the data to other third
parties consistent with Affymetrix’ normal
probe array supply terms as set forth in
Exhibit A and updated from time to time with
advance notice to Gene Logic (it being
understood that the service terms in Exhibit A
may be reasonably modified with mutual
agreement of Affymetrix and Gene Logic
consistent with the terms of this Agreement),
and

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ii)
	 	the fee for Probe
Arrays used in Services or Tox Services is
paid pursuant to Section 5.3; and

	 	 	(b)	 	as to those Custom Probe Arrays where:

	 	 	i)	 	the Service or
Tox Service recipient is a Database subscriber
(or Gene Logic has a bona fide, reasonable
belief that such recipient will become a
Database subscriber within the then-following
[...***...] month period, in which case no
more than [...***...] Custom Probe Arrays
shall be used by Gene Logic for Services or
Tox Services to such recipient prior to such
recipient becoming a Database subscriber
(however, upon such recipient’s request, Gene
Logic may replicate the Custom Probe
Array-based experiment(s) performed for such
recipient by using no more than [...***...] Custom Probe Array per each Custom
Probe Array (up to the [...***...] Custom
Probe Array maximum described above) actually
used in such experiment(s) for such recipient)
up to a maximum of [...***...] recipients per
year; Affymetrix will consider proposals made
by Gene Logic in good faith to increase the
permitted maximum number of such recipients
per year provided that Affymetrix shall have
no obligation hereunder with respect to any
such proposal); and
	 	 	
ii)
	 	the Service or
Tox Service recipient agrees to limit further
distribution of the data to other third
parties consistent with Affymetrix’ normal
probe array supply terms as set forth in
Exhibit A and updated from time to time with
advance notice to Gene Logic (it being
understood that the service terms in Exhibit A
may be reasonably modified with mutual
agreement of Affymetrix and Gene Logic
consistent with the terms of this Agreement),
and
	 	 	
iii)
	 	the fee for
Custom Probe Arrays used in Services or Tox
Services is paid as set forth in Section 5.3;
or

	 	 	 	4)	 	 	allow any third party to use the Probe Arrays
supplied by Affymetrix to Gene Logic and/or its Affiliates and
Subsidiaries under this Agreement; or
	 	 	 	
5)
	 	 	otherwise use the Probe Arrays delivered
hereunder outside of Gene Logic’s, its Affiliates’ or
Subsidiaries’ Area of Interest as applicable; or
	 	 	 	
6)
	 	 	reuse the Probe Arrays; or
	 	 	 	
7)
	 	 	use such Probe Arrays in diagnostic or other
settings requiring FDA or other regulatory agency approval
unless Gene Logic or Affiliates obtains such approval and such
Probe Arrays are to be used in a clinical trial (and such
Probe Arrays are not for microbial or pathogenic organisms).
	Gene Logic and/or its Affiliates and Subsidiaries will allow Affymetrix
reasonable, periodic (but not more often than quarterly) access to the Systems
during regular business hours and with advance written notice to ensure
compliance with the prohibition against reuse.

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	3.8	 	
All Databases transferred to a third party by Gene Logic or a Subsidiary
pursuant to this Agreement must be compliant with a community supported
standard data exchange format for gene expression data, if and when such
format is established. Gene Logic will bear its costs of such compliance.
	3.9	 	
Gene Logic and/or its Subsidiaries may not sell or license the Databases
through a distributor or agent that is involved directly or indirectly in
legal proceedings with Affymetrix or its Affiliate, or holds patent
interests adverse to Affymetrix or its Affiliates related to probe arrays,
unless such distributor or agent is approved in advance in writing by
Affymetrix. In order to enforce this provision Affymetrix must provide
Gene Logic reasonable and prompt written notice of such indirect
involvement in legal proceedings, or such adverse patent interests, upon
Affymetrix becoming aware of such indirect involvement, or such adverse
patent interests, with which counsel for Gene Logic reasonably concurs.
	3.10	 	
Affymetrix will provide sufficient genetic information to identify the
Genes on a Probe Array. If Affymetrix updates its Probe Arrays to include
additional or different genetic sequence information, Affymetrix will
provide information to the best of its ability to allow for Gene Logic to
compare its data with prior results.
	3.11	 	
Unless otherwise stated herein, Affymetrix agrees that all Probe Arrays
delivered hereunder will have an expiration date as indicated on each
Probe Array at least [...***...] from the date of delivery of such Probe
Array to Gene Logic.
	3.12	 	
The Parties agree that the following is a complete satisfaction and
accord for the replacement of Probe Arrays for NITs ([...***...] Probe Arrays) and
Human Probe Array credits ([...***...] Probe Arrays) under the Prior Agreement.
Replacement Probe Arrays shall be provided in 2002, [...***...] in the
[...***...] and [...***...] in the [...***...], in accordance with the
following:

	 	 	 	 	 	 	 
	1.	 	
[...***...] rat Probe Arrays A, B or C in any combination; and
	2.	 	
[...***...] human Probe Arrays from Affymetrix’ then-current product catalog.

	 	 	 
	 	 	
Additionally, Affymetrix will provide Gene Logic with [...***...] human
Probe Arrays free of charge to satisfy such replacement Probe Arrays
noted above.
	3.13	 	
In no event will Affymetrix be obligated to provide more than [...***...]
Probe Arrays in any one month.
	3.14	 	
All Probe Arrays supplied by Affymetrix pursuant to this Agreement shall
be subject to Affymetrix’ Replacement Policy as set forth in Exhibit F
hereto (“Replacement Policy”) and, once determined to be defective in
accordance with the Replacement Policy, replaced within [...***...]
business days of such determination.
	
	 	 
	4.	 	
Affymetrix Proprietary Rights
	4.1	 	
Until the end of the Term, Gene Logic will not buy arrays of diverse
nucleic acids on solid supports from a third party when such third party
arrays materially infringe or would materially infringe the patent or
copyright rights of Affymetrix or its Affiliates. In order to enforce
this provision Affymetrix must provide Gene Logic a) reasonable and prompt
written notice of such infringement upon Affymetrix becoming aware of such
infringement, and b) reasonable evidence of such infringement, with which
counsel for

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Gene Logic reasonably concurs. This paragraph shall not confer on Gene
Logic or any third party any rights under the patent rights of
Affymetrix.
	
	 	 
	5.	 	
Compensation
	5.1	 	
During the Term of this Agreement, in consideration for the [...***...],
the Database license, and services and other support available hereunder,
Gene Logic shall pay to Affymetrix a fee of $[...***...] annually
according to the following payment schedule: $[...***...] three months
from the Effective Date and $[...***...] at the end of every three month
period thereafter during the Term.

	5.2	 	 	5.2.1	 	 	Gene Logic agrees to purchase a minimum of $[...***...] in
HU133 Probe Arrays in the [...***...] of [...***...]. Affymetrix agrees
that the foregoing HU133 Probe Arrays delivered in accordance with the previous sentence
and all HU133 Probe Arrays purchased in [...***...] will have
an expiration date as indicated on each Probe Array at least [...***...]
from the date of delivery of such Probe Array to Gene Logic and/or its
Subsidiaries. Gene Logic commits to purchase a minimum of [...***...]
Probe Arrays during the [...***...] which includes up to [...***...] HU133
Probe Arrays ([...***...] to be shipped in [...***...]) to be used for
Upgrades in accordance with Section 5.2.3 below. If Gene Logic does not
order [...***...] Probe Arrays during the period [...***...] through
[...***...], Affymetrix reserves the right to invoice Gene Logic for, and
Gene Logic agrees to pay, the difference between [...***...] and the
number of Probe Arrays actually ordered by Gene Logic in [...***...]
multiplied by $[...***...]. If Affymetrix raises prices for the products
attached hereto in Exhibit I to Gene Logic and its Affiliates during the
period [...***...] through [...***...], the Parties agree to cancel the
above purchase commitment of [...***...] Probe Arrays and the Parties
agree to renegotiate such purchase commitment.
	 	 	 	
5.2.2
	 	 	For each expression Probe Array (excluding those Probe
Arrays for use in Services and Tox Services) delivered to Gene Logic
or its Affiliates that meets the Fabrication Verification Criteria,
Gene Logic and or its Affiliates will pay a fixed fee of the greater
of: [...***...] % of Affymetrix’ then current U.S. list price as
published in its catalog; or, $[...***...]. The foregoing
notwithstanding, for each HU133 Probe Array (excluding those HU133
Probe Arrays for use in Services or Tox Services) delivered to Gene
Logic or its Affiliates that meets the Fabrication Verification
Criteria, Gene Logic or its Affiliates will pay the lesser of: [...***...]% of Affymetrix’ then current U.S. list price (which is
currently $2,500 per array pursuant to Exhibit I) which may be
updated from time-to-time; or $[...***...]. Proprietary Probe
Arrays will be discounted equivalently provided that genetic
information access fees actually paid by Affymetrix to a third party
are not discounted and only to the extent that the genetic
information access fees are not reflected in the list price of
standard equivalently sized probe arrays.
	 	 	 	
5.2.3
	 	 	Gene Logic commits to purchase a minimum of [...***...]
HU133 Probe Arrays ([...***...] sets) to be used for the purpose of
upgrading samples previously run on Affymetrix arrays and the data
of which is included in Gene Logic’s current human database
(“Upgrade”), therefore for each HU133 Probe Array purchased solely
for the Upgrade, Gene Logic will pay the greater of: [...***...] %
of the discounted price set forth in Section 5.2.2; or,
$[...***...]. Such discount only

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	 	 	applies to HU133 Probe Arrays that are being used in the Upgrade.
Gene Logic shall [...***...] HU133 Probe Arrays [...***...] solely
for the Upgrade.
	 	 	 	
5.2.4
	 	 	The per unit Custom Probe Array pricing is based on the
[...***...] of [...***...] represented on [...***...] that varies
with both (i) [...***...] and (ii) the [...***...]of [...***...].
The current maximum list prices (which are based on a maximum
feature size of [...***...] μm) for specific species are:
$[...***...] per human Probe Pair, $[...***...] per rat Probe Pair,
$[...***...] per murine Probe Pair, $[...***...] per [...***...]
Probe Pair, $[...***...] per plant species Probe Pair and $0.01 per
yeast Probe Pair. The term “Probe Pair” as used herein shall mean
[...***...] of [...***...] and [...***...]. Without limiting the
foregoing, the current list prices by specific species for a Custom
Probe Array representing eukaryotic organism genes with [...***...]
μm feature sizes are: $[...***...] per human Probe Pair,
$[...***...] per rat Probe Pair, $[...***...] per murine Probe Pair,
$[...***...] per [...***...] Probe Pair, $[...***...] per yeast
Probe Pair and [...***...] per plant species Probe Pair.
	5.3	 	 	
5.3.1
	 	 	For those Probe Arrays used in Services, Gene Logic and/or its
Subsidiaries will pay [...***...]% of Affymetrix’ then current U.S. list price as
published in its catalog for such Probe Arrays (excluding Probe Arrays
used in providing Tox Services) (“Service Array Price”); or Gene Logic
and/or its Subsidiaries may provide Services for third parties with a
pricing agreement in effect with Affymetrix and such customers may
purchase probe arrays directly from Affymetrix, have such probe arrays
shipped directly to Gene Logic and/or its Subsidiaries for use in Services
for such Affymetrix customer, and Affymetrix will directly invoice its
customer for such probe arrays. Neither Gene Logic nor its Subsidiaries
may receive probe arrays directly from an Affymetrix customer. Gene Logic
and/or its Subsidiaries agree to use the probe arrays received under the
arrangement described in this paragraph only for the purpose of providing
Services to the particular Affymetrix customer that has directed
Affymetrix to ship such probe arrays to Gene Logic and/or its Subsidiaries
and which will receive the resulting data. Affymetrix will release use
restriction in such third parties solely to permit performance of
Services.
	 	 	 	
5.3.2
	 	 	For those Probe Arrays used in Tox Services for the
period beginning on the Effective Date and ending [...***...]
thereafter (which period may be extended by mutual agreement of the
Parties), Gene Logic and/or its Subsidiaries will pay [...***...] %
of Affymetrix’ then current U.S. list price as published in its
catalog for such Probe Arrays (“Tox Service Array Price”); or Gene
Logic and/or its Subsidiaries may provide Tox Services for
[...***...] and such customers may purchase probe arrays directly
from Affymetrix, have such probe arrays shipped directly to Gene
Logic and/or its Subsidiaries for use in Tox Services for such
Affymetrix customer, and Affymetrix will directly invoice its
customer for such probe arrays. Neither Gene Logic nor its
Subsidiaries may receive probe arrays directly from an Affymetrix
customer. Gene Logic and/or its Subsidiaries agree to use the probe
arrays received under the arrangement described in this paragraph
only for the purpose of providing Tox Services to the particular
Affymetrix customer that has directed Affymetrix to ship such probe
arrays to Gene Logic and which will receive the resulting data.
Affymetrix will release use restriction

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	 	 	in such third parties solely to permit performance of Tox Services.
The Parties agree that any Tox Service agreements signed, or bona
fide term sheets under negotiation, between Gene Logic and/or its
Subsidiaries and any third party during such [...***...] period
shall be honored by the Parties through the Term. If the period
for Tox Services is not extended, Probe Arrays for use in Tox
Services shall be subject to the prices for Probe Arrays to be used
in Services set forth in Section 5.3.1.
	 	 	 	
5.3.3
	 	 	The provisions of Sections 5.3.1 and 5.3.2 notwithstanding,
the Parties agree that i) Probe Arrays purchased to provide any
Services or Tox Services for [...***...] and its Affiliates under an
agreement in effect between [...***...] and Gene Logic and/or its
Subsidiaries and ii) a maximum of [...***...] Probe Arrays per year for use in
proof of principle services for prospective Database subscribers
whom Gene Logic and/or its Subsidiaries reasonably believes will
become Database subscribers within [...***...] of receipt of such
data, may be purchased at the greater of: [...***...] % of
Affymetrix’ then current U.S. list price as published in its
catalog; or, $[...***...]
	 	 	 	
5.3.4
	 	 	As part of the written quarterly reports provided in
accordance with Section 5.7, Gene Logic and/or its Subsidiaries
shall also indicate the number of Probe Arrays used for the
provision of Services, Tox Services and proof of principle studies
pursuant to Section 5.3.3, on a country by country basis, including
the names of such service recipients. If Probe Arrays used in
Services or Tox Services were not purchased at the price for
Services or Tox Services, Gene Logic and/or its Subsidiaries agrees
to pay the difference between the [...***...] and [...***...] price
applicable [...***...]. Such payment will be due to Affymetrix
within [...***...] after the end of each calendar quarter during the
Term.

	5.4	 	
The basis for royalties on Databases shall be equal to [...***...] percent
([...***...]%) of Net Sales to allow for value added by Gene Logic and/or its
Subsidiaries on any system, package, or combination product sold or
licensed in conjunction with a Database; such value added percentage to be
reviewed by the Parties annually. At the time and in the manner
hereinafter provided, Gene Logic and its Subsidiaries shall pay to
Affymetrix an annual royalty of [...***...]% of [...***...]% of Net Sales.

	 	 	 	5.4.1	 	 	Sample Supplier Databases will incur [...***...].
Incremental Datapoints provided to Sample Suppliers in excess of
[...***...] will be subject to royalties pursuant to Section 5.4
above.

	5.5	 	
The Parties agree that the value of royalties due to Affymetrix under the
Agreement between Gene Logic and Affymetrix dated January 1, 1999 is
$[...***...] and not subject to audit, royalties accruing pursuant to Section
5.4 from the Effective Date forward shall be subject to a one-time
$[...***...] credit applicable to royalties incurred in aggregate, by Gene
Logic, its Subsidiaries and between such parties, during the Term of this
Agreement so that notwithstanding the foregoing provisions, Gene Logic
shall not be liable to pay Affymetrix for any royalty until such time as
the aggregate royalties accrued pursuant to this Section 5.4 exceed
$[...***...], at which time Gene Logic shall commence paying Affymetrix for all
royalties accruing hereunder in excess of the credit in accordance with
the terms of the Agreement. Notwithstanding any provision to the contrary
in this Agreement, Gene Logic will be responsible for any and all
royalties [...***...] due to third parties for Probe Arrays supplied to
Gene Logic hereunder, and

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the Probe Array fees and Database royalties described in this Agreement
shall be exclusive of any such royalty.
	5.6	 	
Except as to royalty payments, all amounts referred to in this Section 5
will be invoiced by Affymetrix when due. Royalty payments will be due as
specified in Section 5.7. All Probe Arrays will be deemed accepted unless
they are returned to Affymetrix within [...***...] of delivery to Gene
Logic, with written explanation of the basis on which such Probe Arrays
have been returned on Affymetrix’ standard “Return Materials
Authorization” according to the procedures provided for in such Return
Materials Authorization. All payments will be made to Affymetrix
[...***...] from the date of invoicing by Affymetrix. Late payments shall
bear interest at the rate of [...***...] per month. All payments in this
Agreement will be made in the form of a check or wire transfer to
Affymetrix in U.S. Dollars.
	5.7	 	
Gene Logic shall deliver to Affymetrix within [...***...] after the end
of each calendar quarter during the Term, a written report showing its
computation of payments due under Section 5 of this Agreement including
any Net Sales of licenses of Databases by Gene Logic or its Subsidiaries
during such calendar quarter. All Net Sales shall be segmented in each
such report according to licenses by Gene Logic and each Subsidiary on a
country by country basis, including the rates of exchange used to convert
such royalties to U.S. Dollars from the currency in which the licenses
were made. For the purposes of this Agreement, the rates of exchange to
be used for converting royalties to U.S. Dollars shall be those published
for the purchase of U.S. Dollars in the Wall Street Journal for the last
business day of the calendar quarter for which payment is due.
Simultaneously with the delivery of each such report Gene Logic shall
tender payment in U.S. Dollars of all royalties shown to be due therein.
Where royalties are due for licenses of Databases in a country where, by
reason of currency regulations it is impossible or illegal for Gene Logic
or its Subsidiaries to transfer royalty payments to Affymetrix, such
royalties shall be deposited in whatever currency is allowable in a bank
in that country that is reasonably acceptable to Affymetrix. Any and all
income or similar taxes imposed or levied on account of the receipt of
royalties payable under this Agreement which are required to be withheld
by Gene Logic shall be paid by Gene Logic on behalf of Affymetrix and
shall be paid to the proper taxing authority. Proof of payment shall be
secured and sent to Affymetrix as evidence of such payment in such form as
required by the tax authorities having jurisdiction over Gene Logic or its
Subsidiaries. Such taxes shall be deducted from the royalty that would
otherwise be remitted by Gene Logic or its Subsidiaries.
	5.8	 	
Systems may be acquired/licensed by Gene Logic and its Subsidiaries at
[...***...] percent ([...***...] %) [...***...] Affymetrix’ list prices
and under otherwise standard terms. If during the Term Gene Logic decides
to replace [...***...] or more of its Systems, Affymetrix agrees to
discuss in good faith [...***...] for such System replacements.
	5.9	 	
As to transactions with [...***...] Affymetrix customers expressly
licensed by Affymetrix to use Affymetrix’ current DNA probe array products
for the commercialization of gene expression databases, and [...***...]
under this Section 5.9 any [...***...] (including without limitation
[...***...] and [...***...] has [...***...], and [...***...] or
[...***...] or other [...***...] with [...***...]), Affymetrix has not,
and will not make such products commercially available to such for-profit
customers on terms

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more favorable, taken as a whole, than those offered to Gene Logic in
this Agreement without offering such terms to Gene Logic. For the
purposes of this section, a “database” shall mean a collection of gene
expression datapoints derived from a probe array provided to a third
party by Affymetrix or its authorized representative, [...***...] the
[...***...] in a [...***...], and made available by such third party for
license broadly in whole or in part for use to derive additional
information; the term “database” shall exclude without limitation (i)
[...***...], (ii) [...***...], (iii) [...***...], or (iv) [...***...].
Such terms shall be offered only for the overlapping period of Probe
Array supply in situations where Probe Arrays are made available at
prices/royalties lower than those provided herein. It is understood that
if one of the following term(s) is more favorable to any such [...***...]
customer, Gene Logic shall be offered such more favorable terms, provided
that if Gene Logic accepts such term(s), Gene Logic shall [...***...]
under which [...***...] has [...***...] of such [...***...]: a)
[...***...]; b) [...***...]; and c) [...***...].
	5.10	 	
Affymetrix will maintain a running record of the average variance from
the delivery times specified in Section 3.4. In the event that the
average delivery time in any calendar quarter for Probe Arrays delivered
to Gene Logic is more than [...***...] greater than the times specified in
Section 3.4, the price of all Probe Arrays scheduled to be delivered
during the next quarter shall be decreased by [...***...] % for each
business day that such average is more than [...***...] late. In the
event that more than [...***...] % of the Probe Arrays delivered to Gene
Logic in a [...***...] during the Term are replaced for Significant
Physical Defects pursuant to Exhibits D, all such Probe Arrays that are
replaced by Affymetrix for Significant Physical Defects will be considered
to be delivered [...***...] late in the above calculation. It is
understood that commercial standards and commercial incentives regarding
replacement for Significant Physical Defects will be no less favorable to
Gene Logic than those in this Section 5.10.
	5.11	 	
Affymetrix will provide early access to new product releases to Gene
Logic in a manner similar to its Easy Access “Gold” customers.
	5.12	 	
Affymetrix will use commercially reasonable efforts to advise Gene Logic
at least thirty (30) days before Affymetrix’ first commercial sale and
license of a specific mammalian gene expression Database to third parties,
and shall use reasonable efforts to advise Gene Logic of the development
of such mammalian gene expression Databases where Affymetrix has the legal
right to do so, provided that nothing herein shall be construed as
conferring upon Gene Logic any right to veto any such sale, license or
development of a mammalian gene expression Database. Gene Logic
acknowledges and agrees that any such advisement and the circumstances to
which it relates are deemed to be the Confidential Information of
Affymetrix.
	
	 	 
	6.	 	
Intellectual Property
	6.1	 	
Any invention made during the course of and as part of this Agreement
shall be owned according to inventorship of the relevant applications,
provided that Gene Logic (and its Subsidiaries and Affiliates) agree to
assign to Affymetrix at Affymetrix’ cost all Chip Improvement Inventions.
Gene Logic agrees to communicate periodically technology improvements and
developments relating to probe array technology to the Committee,
excluding those improvements made independently of the use of Probe Arrays
(such as those made in the course of the design or use of Gene Logic’s
proprietary technologies or other non-Affymetrix technologies).

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	6.2	 	
If Gene Logic and/or its Affiliates elects, at its sole discretion, to
commercialize a [...***...], then Gene Logic and/or its Affiliates as
applicable agrees to negotiate in good faith with Affymetrix for at least
a non-exclusive license, but only for the commercialization or development
of probe arrays. Such license will be negotiated to include [...***...],
and need only be provided if a third party has not already been granted a
conflicting license (or an option to obtain such a license) at the time
the [...***...] is made. Gene Logic and/or its Affiliates need not
disclose [...***...] to Affymetrix until such time as corresponding
patents are published disclosing such Genetic Inventions. For purposes of
clarity, it is understood that this Section shall not be applicable to
inventions made by Database customers of Gene Logic.
	6.3	 	
Affymetrix grants to Gene Logic a non-exclusive, [...***...] right and license to use
the GeneChip operating system software in association with the Probe
Arrays and Systems delivered hereunder. Such license will be for use of
the GeneChip operating system software on the workstations provided with
the Systems during the Term of this Agreement. Additional copies and
software may be purchased at a discount of [...***...] % from then
standard list prices. Such discount not to be applied to software
maintenance fees. Bug fixes will be provided at [...***...] to Gene
Logic for a period of [...***...]. Support delivered with the Systems will
be provided to Gene Logic through a single Gene Logic individual
designated by Gene Logic at each of such facilities. Software will be
licensed subject to Affymetrix standard software license terms and
conditions (written or click-through license).
	6.4	 	
To the extent that Affymetrix owns with the right to sublicense without
any obligation or accounting to any un-Affiliated third party, as of the
Effective Date or during the Term, patent rights (“Database Patent
Rights”) that are [...***...] by Gene Logic as otherwise expressly
permitted by this Agreement (the “Database Field”), Affymetrix hereby
grants to Gene Logic and/or its Subsidiaries, and Gene Logic and/or its
Subsidiaries accepts from Affymetrix, a worldwide, royalty-bearing as
agreed upon herein, non-exclusive license, without the right to
sublicense, under any such patent rights to make, but not have made, use,
sell, offer for sale, import and distribute (including through
distributors as otherwise expressly permitted by this Agreement) solely
for the purpose of carrying out those activities expressly contemplated by
this Agreement within the Database Field. For purposes of clarification,
this limited license is only intended to give Gene Logic [...***...]
created by Gene Logic using Probe Arrays supplied hereunder, and shall not
be interpreted as a license to any specific gene or protein content or
application, nor shall it be interpreted to mean that Affymetrix shall
provide any information, data, know-how, trade secrets, materials or
assistance to Gene Logic for use in developing or commercializing such
Databases or any other database of genomic or proteomic information. For
further clarification, Gene Logic’s Databases licensees are only licensed
under the Database Patent Rights to the extent they use such Databases
with Datapoints generated by Gene Logic using Probe Arrays supplied
hereunder and provided to such licensees in connection with the license of
such Databases.
	6.5	 	
The Parties acknowledge and agree that, to the extent that Affymetrix
makes SIF and/or probe pair sequence information generally available to
its probe array customers, Gene Logic shall also have the right to
disclose such SIF and/or probe pair sequence information, as applicable,
to third parties for the purpose of Gene Logic licensing or developing
Databases or selling Services and Tox Services to such third parties as

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otherwise expressly permitted by this Agreement, provided that each such
third party agrees in writing to be bound by confidentiality obligations
consistent with those set forth in Section 8 hereof provided that Gene
Logic shall not commercialize SIF sequences as a stand alone product
without mutual agreement of the Parties. In the event Affymetrix decides
to generally charge a fee to its customers for access to SIP and/or probe
pair sequences, Affymetrix shall notify Gene Logic and the Parties shall
negotiate a commercial access arrangement within [...***...] of such
notification.
	6.6	 	
Gene Logic will reasonably provide recognition of Affymetrix by way of
display of its trademarks in its database products generated pursuant to
this Agreement. Such products will be maintained at reasonable quality,
and Affymetrix grants a non-exclusive right to use its trademarks on such
products. Gene Logic will allow Affymetrix reasonable review and approval
of the use of such trademarks.
	6.7	 	
The Parties also hereby agree that, in the event Gene Logic has a web
site containing the logos of, and/or hyperlinks to, un-Affiliated third
parties, Gene Logic will include Affymetrix’ GeneChip logo and hyperlink
to Affymetrix’ website in the same or more favorable manner (to be
reasonably determined by the Parties) on such Gene Logic website under the
same or more favorable terms and conditions.
	
	 	 
	7.	 	
Project Coordination
	7.1	 	
The parties will form the Committee to aid in coordinating such
activities under this Agreement as may be mutually agreed by the Parties.
The Committee shall be composed of an equal number of representatives of
Affymetrix and Gene Logic as each shall respectively appoint and be
reasonably acceptable to the other Party. The decisions of the Committee
shall be unanimous. A quorum shall consist of at least one Committee
representative from each Party. The Committee shall act only with the
concurring votes of both Parties. A Party’s representatives shall serve
at the discretion of such Party and may be substituted for or replaced at
any time by such Party. The Committee shall meet at least three times
during the Term, except at such times as the Parties mutually believe
there are no significant agenda items. The Committee will be responsible
for establishing other appropriate operational requirements for the
Committee.
	7.2	 	
In addition, the Committee will participate in development of appropriate
standards for Significant Physical Defects. Affymetrix will communicate
potential standards for Significant Physical Defects and commercially
reasonable standards so reviewed will be adopted in the first calendar
year of the Term.
	
	 	 
	8.	 	
Confidentiality
	8.1	 	
For a period of 5 years from disclosure to the other Party, each Party
shall maintain the Confidential Information of the other Party in
confidence (including the terms of this Agreement), and shall not
disclose, divulge, or otherwise communicate such Confidential Information
of the other, or use it for any purpose, except as permitted or
contemplated by this Agreement, and in order to carry out the terms and
objectives of this Agreement. The Parties will use reasonable precautions
to prevent and restrain the unauthorized disclosure of such Confidential
Information of the other Party. The provisions of this paragraph shall
not apply to Confidential Information which:

	 	 	 	8.1.1	 	 	was known or used by the receiving Party or its Affiliates
without any restriction on disclosure, prior to its date of
disclosure to the receiving Party, as evidenced by the prior written
records of the receiving Party or its Affiliates; or

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8.1.2
	 	 	either before or after the date of the disclosure to the
receiving Party is lawfully disclosed without restriction on
disclosure to the receiving Party or its Affiliates by an
independent, unaffiliated third party rightfully in possession of
the Confidential Information, provided that if such Confidential
Information is provided to the receiving Party by a third party
rightfully in possession of the Confidential Information, but with
restrictions on disclosure, the receiving Party may use such
Confidential Information in accordance with such restrictions of the
third party;
	 	 	 	
8.1.3
	 	 	either before or after the date of the disclosure to the
receiving Party becomes published or generally known to the public
through no fault or omission of the receiving Party or its
Affiliates;
	 	 	 	
8.1.4
	 	 	is required to be disclosed by the receiving Party or its
Affiliates to comply with applicable laws, to comply with a court
order, or to comply with governmental regulations, provided that the
receiving Party provides prior written notice of such disclosure to
the other Party and takes reasonable and lawful actions to avoid
and/or minimize the degree of such disclosure;
	 	 	 	
8.1.5
	 	 	is independently developed by the receiving Party or its
Affiliates without reference to the Confidential Information.

	8.2	 	
Affymetrix may not publish the results of Gene Logic’s or its Affiliates’
use of the Probe Arrays without approval of Gene Logic or its Affiliates
respectively. Gene Logic may at its option publish results of the use of
the Probe Arrays. Subject to the limitations of Section 3 above Gene
Logic may publish the results of its research at its sole discretion. In
the event that Gene Logic chooses to publish such results, if Affymetrix
scientists have contributed to such work, authorship will be according to
scientific input and Affymetrix will cooperate in such publications. If
it is decided that publications will be made pursuant to this Section,
Affymetrix and Gene Logic will provide the other Party draft versions of
all publications reporting results of the use of the Probe Arrays, and
will provide at least 60 days for technical review thereof, and will allow
for removal of Confidential Information. For purposes of this Section
“publication” shall refer to conventional scientific publications and not
to the license of database products.
	
	 	 
	9.	 	
Warranty
	9.1	 	
Both Parties to this Agreement represent and warrant that they have the
full right and authority to enter into and perform this Agreement.
	9.2	 	
Affymetrix warrants that the Probe Arrays delivered hereunder do not
incorporate the trade secret or copyright rights of a third party.
Affymetrix DISCLAIMS ALL OTHER REPRESENTATIONS AND WARRANTIES, EXPRESS OR
IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES RELATING TO
INTELLECTUAL PROPERTY, MERCHANTABILITY, AND FITNESS FOR A PARTICULAR
PURPOSE. Affymetrix shall have no liability under any theory of strict
liability, negligence, whether active or passive, or products liability.
Affymetrix’ entire liability shall in no event exceed the compensation
hereunder. Affymetrix shall have no liability for any consequential,
incidental, or special damages. Gene Logic understands that the risks of
loss herein are reflected in the price of the Probe Arrays and access fees
and that the terms would have been different if there had been a different
allocation of risk.

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	9.3	 	
All Chip Improvement Inventions made available to Affymetrix hereunder
shall be on an as-is basis. Gene Logic DISCLAIMS ALL OTHER
REPRESENTATIONS AND WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES RELATING TO INTELLECTUAL PROPERTY,
MERCHANTABILITY, AND FITNESS FOR A PARTICULAR PURPOSE. Gene Logic makes
no warranty that it will ever develop any Database or that it will be able
to license any Database, if developed. Gene Logic shall have no liability
under any theory of strict liability, negligence, whether active or
passive, or products liability on account of the license of Database or
the sale of Chip Improvement Inventions. Gene Logic shall have no
liability for consequential, incidental, or special damages.
	
	 	 
	10.	 	
Indemnity
	10.1	 	
Affymetrix will indemnify Gene Logic and its Affiliates against liability
and will settle or defend any suit or proceeding brought against Gene
Logic and its Affiliates to the extent based on a claim that the Probe
Arrays delivered hereunder directly infringe an issued patent in the
United States of America, [...***...]. Affymetrix will indemnify Gene
Logic and its Affiliates against liability and will settle or defend any
suit or proceeding brought against Gene Logic and its Affiliates to the
extent based on a claim that the Probe Arrays delivered hereunder
indirectly (i.e. through contributory infringement or inducement) infringe
an issued patent in the United States of America, [...***...] if a) a
hybridization method using probe arrays, or probe arrays themselves, or
equivalent hybridization devices are specifically identified as an element
of the claims of such patent in a device claim, or use of these is
specifically identified as an element of the claims of such patent in a
method claim, and b) the patentability of such device or method claims was
materially related to the recitation of the hybridization method or the
probe arrays or equivalent hybridization device, or their use. Affymetrix
shall have no liability under this paragraph to the extent that the
alleged infringement arises out of any addition or modification to the
Probe Arrays or their use by Gene Logic and its Affiliates not specified
by Affymetrix, or Gene Logic’s and its Affiliates’ combination of the
Probe Arrays with other devices not specified by Affymetrix. The
indemnifying Party shall pay [...***...]. For this paragraph to apply the
indemnified Party must inform the indemnifying Party within 14 days of
notice of any claim or suit being made or brought, and give the
indemnifying Party the full authority, information, and assistance
necessary to settle or defend such suit or proceeding. The indemnifying
Party shall not be bound in any manner by any settlement made without its
prior written consent. Any liability hereunder shall be [...***...]. In
the event that the Probe Arrays are held to infringe and their use is
enjoined as a result of infringement for which it has indemnified Gene
Logic and its Affiliates, Affymetrix may obtain for Gene Logic and its
Affiliates the right to continue using such Probe Arrays, modify them to
become noninfringing, or grant Gene Logic and its Affiliates a credit for
the cost of unused Probe Arrays, and accept the return of unused Probe
Arrays. This paragraph states the entire liability for infringement of
intellectual property rights and is in lieu of all other warranties,
express or implied except as stated in Section 9.
	
	 	 
	11.	 	
Term and Termination
	11.1	 	
This Agreement shall extend until the end of the Term, unless terminated
earlier as set forth below.

* Confidential Treatment Requested

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	11.2	 	
If either Party should fail to perform any obligations under this
Agreement, the other Party may give written notice to the defaulting Party
calling attention to the default. In the event of a material breach or
default, said other Party shall have the right to terminate this Agreement
upon sixty (60) days prior written notice to said defaulting Party calling
attention to the default unless said breach or default is corrected within
sixty (60) days after such notice. Such notice shall specifically state
that the nonbreaching Party intends to terminate this Agreement. Said
right to terminate for default shall be in addition to, and without
prejudice to the exercise of, any other remedies available in law or
equity.
	11.3	 	
Upon termination of this Agreement due to expiration of the Term Gene
Logic and its Affiliates may continue to use the Probe Arrays previously
purchased by Gene Logic and its Affiliates [...***...] and subject to the
warranty and return provisions provided in this Agreement. Gene Logic and
its Affiliates understands that no license is conveyed or implied for use
of the Systems herein for Probe Arrays other than those manufactured or
licensed by Affymetrix.
	11.4	 	
Upon termination of this Agreement, the following provisions will
survive: Sections 2, 3.7, 3.8, 3.9, 5.4, 5.5, 5.7, 6, 8, 9, 10, 11.3,
11.4, 12, 13.
	
	 	 
	12.	 	
Dispute Resolution
	12.1	 	
No termination for breach or default hereof shall arise, nor shall any
action, claim or setoff be permitted, until the following procedures have
been satisfied. A designated representative of each of Affymetrix and
Gene Logic shall meet in person or by teleconference within seven (7) days
as reasonably requested by either Party to review any dispute with respect
to the interpretation of any provision of this Agreement or with respect
to the performance of either Party under this Agreement. If the
disagreement is not resolved by the designated representatives by mutual
agreement within fourteen (14) days after a meeting to discuss the
disagreement, either Party may at any time thereafter provide the other
written notice specifying the terms of such disagreement in reasonable
detail. Within seven (7) days of receipt of such notice, the chief
executive officers of Affymetrix and Gene Logic, or their executive
officer designees, shall meet at a mutually agreed upon time and location
or by teleconference for the purpose of resolving such disagreement. They
will discuss the problems and/or negotiate for a period of up to twenty
(20) days in an effort to resolve the disagreement or negotiate an
acceptable interpretation or revision of the applicable portion of this
Agreement mutually agreeable to both Parties, without the necessity of
formal procedures relating thereto.
	
	 	 
	13.	 	
Miscellaneous
	13.1	 	
Gene Logic shall keep, and shall cause its Affiliates to keep, for a
period of at least three (3) years following the expiration of the
Agreement fully adequate, accurate, and true books of accounts and other
records containing all information and data which may be necessary to
ascertain and verify the fees and royalties payable hereunder and usages
of Probes Arrays provided hereunder, including, but not limited to, books,
records and electronic files showing each Database License transaction and
the net invoice price for said transaction, as appropriate. During the
Term of this Agreement and for a period of three (3) years following the
time at which the relevant fee or payment is due, Affymetrix shall have
the right, upon commercially reasonable notice, but not to exceed once per
contract year, during regular business hours and upon ten (10) days
notice, to have an auditing firm acceptable to all Parties make such
examination as Affymetrix deems

* Confidential Treatment Requested

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necessary to verify said records and books of account. In the event that
such examination reveals a discrepancy between the royalties or amounts
payable hereunder and the royalties or amounts actually paid, all such
additional royalties or amounts, together with interest from the date
when such additional royalties or amounts would have been due, shall be
paid to Affymetrix within thirty (30) days of written notice from
Affymetrix of such discrepancy. Any such audit shall be at Affymetrix’
sole expense and performed by a nationally recognized accounting firm.
In the event that a deficiency of more than [...***...] is discovered,
the audit shall be at Gene Logic’s expense. The auditing firm conducting
the examination shall be under appropriate obligations of confidentiality
to all Parties hereto such that, 1) if no discrepancy is found between
royalties and amounts payable and actually paid for a given contract
year, the auditing firm shall report that and nothing else to the
Parties, 2) if a discrepancy in favor of Affymetrix is found between
royalties and fees payable and actually paid, the auditing firm shall
report the amount of the discrepancy and only those particulars necessary
for the understanding of the Parties of the nature of the overpayment and
Gene Logic shall pay such discrepancy to Affymetrix within forty-five
(45) days of the date of the audit report, if a discrepancy in favor of
Gene Logic is found between royalties or amounts payable and actually
paid, the auditing firm shall report the amount of the discrepancy and
only those particulars necessary for the understanding of the Parties of
the nature of the overpayment, and Affymetrix shall reimburse Gene Logic
within forty five (45) days of the date of the audit report, and 3) any
given contract year may only be audited once, and 4) in no event shall
the auditing firm reveal to any Party hereto any information it may gain
during the course of the examination other than as previously stated, and
5) in no event shall the auditing firm reveal to any third party any
information it may gain during the course of the examination. The
Parties agree that auditors chosen to perform audits pursuant to this
Section 12.1 and Section 12.2 below will not be compensated on a
commission for findings basis.
	13.2	 	
Affymetrix shall keep, and shall cause its Affiliates to keep, for a
period of at least three (3) years following the expiration of the
Agreement fully adequate, accurate, and true books of accounts and other
records containing all information and data which may be necessary to
ascertain and verify the fees and royalties receivable hereunder,
including, but not limited to, books, records and electronic files, as
appropriate. During the Term of this Agreement and for a period of three
(3) years following the time at which the relevant fee or payment is due,
Gene Logic shall have the right, upon commercially reasonable notice, but
not to exceed once per contract year, during regular business hours and
upon ten (10) days notice, to have an auditing firm acceptable to all
Parties make such examination as Gene Logic deems necessary to verify said
records and books of account. In the event that such examination reveals
a discrepancy between the royalties or amounts payable hereunder and the
royalties or amounts actually paid, all such additional royalties or
amounts, together with interest from the date when such additional
royalties or amounts would have been due, shall be paid to Gene Logic
within thirty (30) days of written notice from Gene Logic of such
discrepancy. Any such audit shall be at Gene Logic’s sole expense and
performed by a nationally recognized accounting firm. In the event that a
deficiency of more than [...***...] is discovered, the audit shall be at
Affymetrix’ expense. The auditing firm conducting the examination shall
be under appropriate obligations of confidentiality to all Parties hereto
such that, 1)

* Confidential Treatment Requested

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if no discrepancy is found between royalties and amounts payable and
actually paid for a given contract year, the auditing firm shall report
that and nothing else to the Parties, 2) if a discrepancy in favor of
Gene Logic is found between royalties and fees receivable and actually
received, the auditing firm shall report the amount of the discrepancy
and only those particulars necessary for the understanding of the Parties
of the nature of the overpayment and Affymetrix shall pay such
discrepancy to Gene Logic within forty-five (45) days of the date of the
audit report, if a discrepancy in favor of Affymetrix is found between
royalties or amounts payable and actually paid, the auditing firm shall
report the amount of the discrepancy and only those particulars necessary
for the understanding of the Parties of the nature of the overpayment,
and Gene Logic shall reimburse Affymetrix within forty five (45) days of
the date of the audit report, and 3) any given contract year may only be
audited once, and 4) in no event shall the auditing firm reveal to any
Party hereto any information it may gain during the course of the
examination other than as previously stated, and 5) in no event shall the
auditing firm reveal to any third party any information it may gain
during the course of the examination.
	13.3	 	
GENE LOGIC UNDERSTANDS THAT THE PROBE ARRAYS DELIVERED HEREUNDER ARE NOT
FDA APPROVED. GENE LOGIC AGREES NOT TO USE THE PROBE ARRAYS DELIVERED
HEREUNDER IN ANY CLINICAL OR OTHER SETTING REQUIRING FDA REVIEW OR
APPROVAL EXCEPT THAT GENE LOGIC MAY USE THE PROBE ARRAYS IN CLINICAL
TRIALS WHEN IT OBTAINS ALL REQUIRED FDA OR OTHER REGULATORY APPROVALS
REQUIRED FOR USE IN SUCH TRIALS. GENE LOGIC WILL INDEMNIFY AFFYMETRIX FOR
ANY CLAIMS MADE BY A PATIENT ARISING FROM THE USE OF THE PROBE ARRAYS.
THE PROBE ARRAYS AND SYSTEMS ARE NOT LICENSED EXCEPT AS SPECIFICALLY
RECITED HEREIN UNDER ANY INTELLECTUAL PROPERTY RIGHTS OF AFFYMETRIX.
	13.4	 	
Neither Party nor any of its Affiliates shall originate any news relating
to this Agreement without the prior written approval of the other Party,
which approval shall not be unreasonably withheld, or except as otherwise
required by law.
	13.5	 	
Either Party may assign any rights or obligations of this Agreement to a
party who acquires all or substantially all of the relevant assets of the
assigning Party by merger or sale of assets or otherwise. In the case
where the Agreement is to be assigned or transferred by merger or sale of
assets or otherwise of Gene Logic to a third party listed in Exhibit B, or
its Affiliate, the written consent of Affymetrix must be obtained.
	13.6	 	
This Agreement shall be construed according to the laws of California
without regard to conflict of law provisions.
	13.7	 	
In the event of any controversy or claim relating to, arising out of or
in any way connected to any provision of this Agreement (“Dispute”), the
Parties shall seek to settle their differences amicably between
themselves. Any unresolved Dispute shall be finally resolved by final and
binding arbitration. Whenever a Party shall decide to institute
arbitration proceedings, it shall give written notice to that effect to
the other Party. The Party giving such notice shall refrain from
instituting the arbitration proceedings for a period of ten (10) days
following such notice to allow the Parties to attempt to resolve the
Dispute between themselves. If the Parties are still unable to resolve
the dispute, the Party giving notice may institute the arbitration
proceeding under the rules of JAMS. Arbitration shall be held in the city
of the defendant’s home office and, if the plaintiff

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prevails in such arbitration, the reasonable travel expenses of the
plaintiff will be paid by the defendant. The arbitration shall be
conducted before a single arbitrator mutually chosen by the Parties, but
if the parties have not agreed upon a single arbitrator within fifteen
(15) days after notice of the institution of the arbitration proceeding,
then a single arbitrator shall be chosen under JAMS rules. All
arbitrator(s) eligible to conduct the arbitration must undertake in
writing as a condition of service to render their opinion(s) promptly
after the final arbitration hearing. No arbitrator shall have the power
to award punitive damages or any award of multiple damages under this
Agreement and such awards are expressly prohibited. Decisions of the
arbitrator shall be final and binding on the Parties. Judgment on the
award of the arbitrator may be entered in any court having jurisdiction
thereof. Except to the extent entry of judgment and any subsequent
enforcement may require disclosure, all matters relating to the
arbitration, including the award, shall be held in confidence by the
Parties.
	13.8	 	
The waiver by either Party of a breach or a default of any provision of
this Agreement by the other Party shall not be construed as a waiver of
any succeeding breach of the same or any other provision, nor shall any
delay or omission on the part of either Party to exercise or avail itself
of any right power or privilege that it has or may have hereunder operate
as a waiver of any right, power or privilege by such Party.
	13.9	 	
This Agreement and the documents referred to herein are the full
understanding of the Parties with respect to the subject matter hereof and
supersede all prior understandings and writings relating to the subject
matter herein. No waiver alteration or modification of any of the
provisions herein shall be binding unless in writing and signed by the
Parties by their duly authorized representatives. This Agreement shall
replace and supercede in their entirety the agreement effective as of
January 1, 1999 between Gene Logic and Affymetrix and all amendments
thereto (collectively, the “Prior Agreement”). Notwithstanding the
foregoing, where this Agreement adds, deletes or modifies a term from the
Prior Agreement, the applicability and effect of such addition, deletion
or modification shall be prospective from the Effective Date of this
Agreement only (i.e. not retroactive) and the Prior Agreement shall govern
all circumstances prior to the Effective Date of this Agreement unless
otherwise expressly and unambiguously stated herein. No waiver alteration
or modification of any of the provisions herein shall be binding unless in
writing and signed by the Parties by their authorized representatives.
	13.10	 	
The headings in this Agreement are for convenience only and shall not be
considered in construing this Agreement.
	13.11	 	
In the event that any provision of this Agreement is held by a court of
competent jurisdiction to be unenforceable because it is invalid or in
conflict with any law of any relevant jurisdiction, the validity of the
remaining provisions shall not be affected, and the rights and obligations
of the Parties shall be construed and enforced as if the Agreement did not
contain the particular provision(s) held to be unenforceable.
	13.12	 	
This Agreement shall be binding on and inure to the benefit of the
Parties and their successors and permitted assigns.
	13.13	 	
None of the provisions of this Agreement shall be for the benefit of or
enforceable by any third party.
	13.14	 	
Any notice required under this Agreement shall be made by overnight mail
or courier to the addresses below.

-24-

 

	 	If to Gene Logic:

Gene Logic Inc.

708 Quince Orchard Road

Gaithersberg, MD 20878

Attn: Chief Financial Officer

	 	If to Affymetrix:

Affymetrix, Inc.

3380 Central Expressway

Santa Clara, California 95051

Attn: President

	 	 	 
	13.15	 	
The Parties shall not be liable for delay or nonperformance if
performance is rendered impracticable by the occurrence of any condition
beyond the reasonable control of a Party, if such Party has used
reasonable efforts to avoid such occurrence. Such Party shall give notice
to the other Party in writing promptly, and thereupon the affected Party’s
performance shall be excused and the time for performance shall be
extended for the period of delay or inability to perform due to the
occurrence.
	13.16	 	
This Agreement may be executed in any number of counterparts, each of
which shall be deemed an original but all of which together shall
constitute one and the same instrument.

-25-

 

IN WITNESS WHEREOF, the Parties hereto have caused this Agreement to be
executed by their properly and duly authorized officers or representatives as
set forth below.

	 
	Affymetrix, Inc.
	 
	/s/ Susan E. Siegal

	 
	By: Susan E. Siegal

	 
	Date: 12/20/01

	 
	Gene Logic Inc.
	 
	/s/ Mark D. Gessler

	 
	By: Mark D. Gessler

	 
	Date: 12/20/01

-26-

 

Exhibit A

Service Recipient terms

Expression Service Addendum

This Addendum contains terms and conditions in addition to the general Terms
and Conditions of Affymetrix, Inc. (AAFX”) relevant to Buyer.

“Expression Probe Array Data” shall mean data from expression probe arrays.

“Genetic Inventions” shall mean all genetic sequence (including related
protein) and function inventions discovered by Buyer through the use of an
Expression Probe Array Data including, without limitation, any invention which
is covered by an issued patent that contains data from the Expression Probe
Array Data or was supported during patent prosecution by data obtained from the
Expression Probe Array Data.

Restricted Use Rights. Buyer may only use the Expression Probe Array
Data provided hereunder to investigate the presence and/or levels of expressed
nucleic acid sequences in the ordinary course of Buyer’s normal internal
pharmaceutical and diagnostic research and development activities including
clinical trials. In addition, Buyer agrees not to (a) transfer an Expression
Probe Array Data to any third party; or (b) provide services to or on behalf of
any third party that relate to an Expression Probe Array Data; or (c)
distribute, transfer, license or otherwise make available to a third party any
data or database that is obtained from the use of an Expression Probe Array
Data, except i) Buyer may license data obtained from the Expression Probe Array
Data to a third party licensee specifically related to a particular drug or
target that has been discovered through use of the Expression Probe Array Data
when such third party licensee will distribute such drug or target, ii) Buyer
may transfer data within a bona fide collaboration in which Buyer’s
collaborator has provided substantial scientific input to experimental design
and such relationship is set forth in an agreement signed by all parties prior
to the use of any Expression Probe Array Data to generate such data (bona fide
collaborations do not include arrangements whose primary purpose is to give a third party access to data or databases or
provide nucleic acid hybridization services), iii) Buyer may transfer data to a
third party so long as Buyer receives no consideration or other quid-pro-quo
for such transfer (e.g. such transfer cannot be contingent on the third party
and Buyer exchanging other goods, services or intellectual property), or iv)
Buyer may publish data as part of a normal, peer reviewed scientific
publication or public scientific presentation; or (d) use an Expression Probe
Array Data or data therefrom in a clinical diagnostic setting. Buyer agrees
that third parties may only receive data from Expression Probe Array Data under
(c)(i)-(iii) hereof pursuant to written agreements containing obligations
explicitly benefitting AFX that are no less restrictive than those in this
Agreement and which require such third party recipients not to sublicense or
further distribute or transfer such data.

Intellectual Property. If Buyer elects, at its sole discretion, to
commercialize a Genetic Invention, then Buyer agrees to negotiate in good faith
with AFX for at least a non-exclusive license, but only in the field of probe
arrays. Such license will be negotiated to include commercially reasonable
royalty payments, and need only be provided if a third party has not already
been granted a conflicting license (or an option to obtain such a license) at
the time the Genetic Invention is made. Buyer need not disclose Genetic
Inventions to AFX until such time as corresponding patents are published
disclosing such Inventions.

Confidentiality. Buyer agrees not to disclose any or all of the
contents of this Agreement to any third party except: with the prior written
consent of AFX; if required to do so by a final order of a court of competent
jurisdiction; or, as is otherwise required by applicable law following notice
of not less than thirty (30) days to the other parties hereto.

	 
	INSTITUTION NAME (Please print):
	 
	

	 
	By:
	

	 
	Name:
	

	 
	Title:
	

	 
	Date:
	

Signature of Buyer Officer or Designee. By signing the above, the signatory is
representing and warranting that they are authorized to enter into this
Agreement on behalf of Buyer.

-27-

 

Exhibit B

Third Party List

[...***...]

[...***...]

[...***...]

[...***...]

[...***...]

[...***...]

* Confidential Treatment Requested

-28-

 

Exhibit C

Initial Forecast

	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	Part #	 	Part name
	 	Description
	 	Chips/unit
	 	Month

[...***...]
	 	[...***...]
	 	[...***...]
	 
	 	 	 	 	 	 	 	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	[...***...]	 	[...***...]
	 	[...***...]
	 	[...***...]	 	 	 	 	 	 	 
	 	 	 	 	TOTALS
	 	 	 	[...***...]
	 	[...***...]
	 	[...***...]
	 
	 	 	 	 	[...***...]
	 	 	 	[...***...]
	 	[...***...]	 	 	 
	

* Confidential Treatment Requested

-29-

 

Exhibit D

ExemplarySignificant Physical Defects1

I. Examples of Items That Are Significant Physical Defects

1) [...***...] that are reproducibly found on Probe Arrays. [...***...] is
[...***...]. Physical evidence of [...***...].

2) Damage to [...***...] of probe pairs on [...***...]
such that a [...***...] in any of a set of replicate experiments which occurs on
[...***...] of the Probe Arrays in [...***...] of Probe Arrays.

3) Physical defects that Affymetrix reasonably agrees compromise the ability of any single array
to provide data from [...***...] of [...***...].

	 	 	 
	II	 	
Examples of Items That Are Not Significant Physical Defects
	
	 	 
	1)	 	
Physical Defects that do not compromise [...***...] of
probe sets and do allow accurate Datapoints to be obtained.
	
	 	 
	2)	 	
Random Physical Defects that do not compromise the ability of that array
to provide Datapoints, even though they may be [...***...]

	 	 	1 The [...***...] that [...***...] are not [...***...] to be [...***...] of [...***...].

* Confidential Treatment Requested

-30-

 

Exhibit E

Amendment dated January 9, 2001 to the agreement between Gene Logic and

Affymetrix dated January 1, 1999 (“Prior Agreement”)

We understand from our recent meeting with you that Gene Logic has a
collaboration with [...***...] and that Gene Logic and [...***...] desire for
Gene Logic to purchase a [...***...] Custom Probe Array design from Affymetrix
under the Prior Agreement; the Target Sequences for such Custom Probe Array
design will be generated by Gene Logic and submitted by Gene Logic to
Affymetrix. Gene Logic will be entitled to purchase such Custom Probe Arrays
from Affymetrix pursuant to the terms and conditions, including price terms, of
the Prior Agreement, and [...***...] will be entitled to purchase such Custom
Probe Arrays from Affymetrix pursuant to the terms and conditions, including
price terms, of the current probe array supply agreement in effect between
[...***...] and Affymetrix.

We also understand from you that [...***...] has authorized Gene Logic to
permit Affymetrix to manufacture and sell such [...***...] Custom Probe Arrays
to other Gene Logic ToxExpress subscribers subject in each case to the probe
array supply terms and conditions, including price terms, in effect between the
respective ToxExpress subscriber and Affymetrix; provided that such ToxExpress
subscribers (other than [...***...]) may only use such Custom Probe Arrays for
expression analysis in the field of toxicology research and not for any other
research and development purpose. In addition to accepting Affymetrix’ probe
array supply terms and conditions, Affymetrix acknowledges that purchasers
other than [...***...] or Gene Logic of such [...***...] Custom Probe Arrays
will be required under their respective agreements with Gene Logic to provide
notice within 15 days of filing a patent application and provide a copy of said
filed application and to grant nonexclusive, fully paid-up, royalty-free
licenses back to Gene Logic and other ToxExpress subscribers for any toxicity
markers that are discovered using such Custom Probe Arrays; Gene Logic shall be
responsible for imposing, monitoring and enforcing this requirement.

Subject to Gene Logic’s payment of the applicable fees as described in the
Prior Agreement, Affymetrix agrees to design, manufacture and make available
for sale such [...***...] Custom Probe Arrays and to limit the distribution of
such Custom Probe Arrays to Gene Logic, [...***...] and other Gene Logic
ToxExpress subscribers; Gene Logic will submit a complete written list of
current ToxExpress subscribers to Affymetrix when it submits the [...***...]
Target Sequences and will make periodic updates to such list as changes in its
subscription base occur. For the avoidance of doubt, the design fee(s) will be
paid to Affymetrix by Gene Logic as described in the Prior Agreement and the
price charged by Affymetrix for such Custom Probe Arrays will be in accordance
with then-current price terms and conditions in effect between Affymetrix and
each individual purchaser; except for their respective agreements already in
effect with Affymetrix, neither [...***...] nor Gene Logic will have any input
into the price charged by Affymetrix for such Custom Probe Arrays. Also for
clarity, neither Gene Logic nor [...***...] shall have any intermediary role in
the purchase of Custom Probe Arrays by, or delivery of Custom Probe Arrays to,
other parties.

Gene Logic represents and warrants that the foregoing information is accurate,
that Affymetrix has the fully paid-up, royalty-free worldwide right and license
under Gene Logic’s and [...***...] ‘s intellectual property rights (including
any toxicity markers discovered using the

* Confidential Treatment Requested

-31-

 

Custom Probe Arrays) to make, have made, use, sell, offer to sell, import,
reproduce, modify, prepare derivative works and distribute Custom Probe Arrays
(including through multiple tiers of distribution), as contemplated herein, and
that Gene Logic has the capacity and authority to enter into and fully perform
under this Second Amendment to the Prior Agreement. Without limiting the
foregoing, Gene Logic shall be fully responsible for the Target Sequences, and
Gene Logic will settle or defend any legal proceeding brought against
Affymetrix, its Affiliates, or customers or suppliers of either, in connection
with the Target Sequences in accordance with Section 10.1 of the Prior
Agreement.

-32-

 

Exhibit F

Affymetrix Replacement Policy

Affymetrix will replace any Probe Array found to be physically defective (per
definition of Physical Defects established by this agreement) with an array of
the same type, unless the Probe Array in question is no longer commercially
available, in which case a mutually agreed upon alternative may be substituted.
Except as provided in Section 5.10, in kind replacement by like Probe Array(s)
will be the sole remedy available in response to physical defect or other
replacement claims. Also Probe Arrays will be replaced if through no fault of
the user an Affymetrix System, previously in good working order, and covered
under a valid Affymetrix service contract (or, in the [...***...] of a
[...***...] in [...***...] with the [...***...] with regards to
[...***...]), malfunctions causing Probe Array(s) to be rendered un-analyzable.
In cases where [...***...] causes such malfunction, no liability to replace
the affected Probe Array(s) will be incurred by Affymetrix. In no case will
Affymetrix be liable to replacement claims where the [...***...] and
[...***...] as [...***...] are not [...***...].

Requests for replacement of defective Probe Arrays shall consist of an itemized
list of the Probe Arrays, including Probe Array type, array lot number,
[...***...] and any other information reasonably deemed pertinent to an
investigation. [...***...] will conform to standards of nomenclature
established by Affymetrix as enumerated in the table below. Note that table
below is intended as an [...***...] and it is understood that the
replacement decision is an independent determination, to be made by Affymetrix
representative separate from this [...***...]. The [...***...] defined in
table below may be amended from time to time as deemed necessary by the
Committee to adequately document array performance issues. Affymetrix reserves
the right to request and review any relevant data or procedures it reasonably
considers necessary to diligently investigate the source of the problem prior
to authorizing replacement of arrays in question. In the interest of
[...***...] the [...***...] of [...***...] and in [...***...] and [...***...],
the Committee will review quarterly the [...***...] as a [...***...] of
[...***...] during the [...***...].

* Confidential Treatment Requested

-33-

 

[...***...]

	 	 	 
	[...***...];	 	[...***...]
	[...***...]	 	
[...***...]
	 	 	 
	 	 	 
	 	 	 

* Confidential Treatment Requested

-34-

 

Exhibit G

Proposed deviations from Custom Probe Array design specifications:

	 	 	 
	1.	 	
[...***...] of specific [...***...]. [...***...] may choose to
[...***...] themselves for the [...***...] of [...***...]. [...***...]
would be [...***...] from a [...***...] by [...***...] to be [...***...]
for [...***...] on [...***...] and [...***...]. [...***...] does not
[...***...] the [...***...] of [...***...] by [...***...] Logic.
Estimated [...***...]
	2.	 	
[...***...] may [...***...] that have [...***...]. [...***...] does not
[...***...] the [...***...] of [...***...] with [...***...] the
[...***...] of [...***...]. No additional [...***...] is [...***...] to
be [...***...]
	3.	 	
[...***...] may [...***...] that [...***...] from [...***...] be
[...***...] on [...***...]. [...***...] information from [...***...]
would not be [...***...] to [...***...]. Estimated [...***...]
	4.	 	
[...***...] may [...***...] to [...***...] from [...***...] in a
[...***...]. Estimated [...***...]
	5.	 	
[...***...] may [...***...] the [...***...] which the [...***...] will be
[...***...]. If this [...***...] is provided [...***...] as an
[...***...], there is no [...***...] for [...***...]. If [...***...]
requires [...***...] to [...***...] the [...***...] of [...***...] or
other [...***...] will be added to [...***...]

For the avoidance of doubt, the Parties agree that (i) all information relating
to probe sequence and/or selection thereof is acknowledged by Gene Logic to be
the Confidential Information of Affymetrix and any improvement based thereupon
shall be deemed by the Parties to be a Chip Improvement Invention and subject
to Section 6 of the Collaboration Agreement; and (ii) all information relating
to Target Sequence and/or selection thereof is acknowledged by Affymetrix to be
the Confidential Information of Gene Logic and any improvement based thereupon
shall be subject to Section 6 of the Collaboration Agreement.

* Confidential Treatment Requested

-35-

 

Exhibit H

Affymetrix Custom Probe Array Design Guide

(See attached)

-36-

 

 

 

Genechip® Custom Array Design Guide

A Guide for Ordering Genechip® Custom Arrays

For Research Use Only

Not For Use In Diagnostic Procedures

700506 Rev. 1

 

 

AFFYMETRIX, INC.

3380 Central Expressway

Santa Clara, CA 95051 USA

Tel: 1-888-362-2447 (1-888 DNA- CHIP)

Fax: 1-408-731-5441

AFFYMETRIX UK Ltd.

91 Milton Park

Abingdon

Oxon OX14 4RY

United Kingdom

Tel: +44 (0)7000 785 803

Fax: +44 (0)7000 785 804

sales@affymetrix.com

www.affymetrix.com

For research use only

Not for use in diagnostic procedures

	 	 
	Part No. 700506

Copyright 2000 Affymetrix, Inc. All right reserved. Affymetrix®,
GeneChip®, 
HuSNPTM, GenFlexTM, 417TM, 418TM, 428TM, Pin-and
RingTM, Flying ObjectiveTM, ,
, Genetic Analysis Technology
ConsortiumTM, and  are trademarks used by
Affymetrix, Inc.

Products may be covered by one or more of the following patents and/or sold
under license from Oxford Gene Technology: U.S. Patent Nos. 5,445,934;
5,744,305; 5,700,637; 5,945,334 and EP 619 321; 373 203 and other foreign or
U.S. patents.

	

 

 

Table of Contents

	 	 	 	 	 	 	 
	GENECHIP CUSTOM ARRAY DESIGN PROCESS OVERVIEW
	 	 	4	 
	 	The Genechip® Probe Array Design Process
	 	 	5	 
	 	Preliminary Design Approval
	 	 	6	 
	 	Design Request
	 	 	6	 
	 	Array Design
	 	 	6	 
	 	Post Array Design
	 	 	7	 
	 	Purchase Order
	 	 	7	 
	 	Design Information
	 	 	7	 
	 	 	Standard Custom Expression Array Design
	 	 	7	 
	 	 	Number of Probe Sets on an Array
	 	 	8	 
	 	 	Minimum Order Per Array Format
	 	 	9	 
	 	 	Design Request Form
	 	 	9	 
	 	 	Example of a Design Request Form
	 	 	11	 
	 	 	Sequence File
	 	 	12	 
	 	 	Instruction File
	 	 	13	 
	 	 	Pruning Sequence File
	 	 	19	 
	 	 	Pruning Instruction File
	 	 	19	 
	UNDERSTANDING THE DESIGN PROPOSAL
	 	 	20	 
	 	Information
	 	 	20	 
	 	Probe Selection Rules
	 	 	21	 
	 	Actions Required
	 	 	22	 
	CONTACT INFORMATION
	 	 	24	 
	 	Sales
	 	 	24	 
	 	Customer Service
	 	 	24	 
	 	Chip Design
	 	 	24	 
	 	Technical Support
	 	 	25	 
	 	Trademarks
	 	 	25	 
	 	Limited License
	 	 	25	 
	 	Copyright
	 	 	26	 

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	3	 

 

GeneChip Custom Array Design Process Overview

This section provides you with a step by step overview of the process for
designing your custom GeneChip® probe array. The four major steps which
comprise the design process are:

	 	1.	 	Preliminary design approval
	 
	 	2.	 	Design request
	 
	 	3.	 	Array design
	 
	 	4.	 	Post array design

Note:

	•	 	The terms “you,”
“your” and “yourself” refer to the requestor from the customer side.
	 
	•	 	The terms “we,” “us” and “our” refer to Affymetrix, Inc.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	4	 

 

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	5	 

 

Preliminary Design Approval

The first step in the design process is to contact an Affymetrix Sales
Representative and request to have a custom GeneChip® probe array designed to
your specifications (for contact information, see page 24).

Affymetrix Sales staff will work with you on the Purchase Order, while Technical Support will
work on planning the technical specifications of the design. If your design is
approved, you will be contacted by your Sales Representative. If your design is
not approved, you will also be contacted by your Sales Representative, and you
will need to submit a modified design to Technical Support. This initial
approval process ensures that we deliver a high quality customized probe array
that meets with your satisfaction.

Design Request

After your design has been approved, the next step is to submit a Purchase
Order to our Customer Service Department and to forward the associated design
information to the Affymetrix Chip Design Group (see page 7 for details).

Affymetrix Customer Service personnel reviews the purchase order and verifies
that it is complete. Your Purchasing Agent will be contacted for any necessary
clarifications. When everything is complete, the Affymetrix Chip Design Group
is notified, and a confirmation message is sent to your Purchasing Agent.

As soon as the design information is received, the Affymetrix Chip Design Group
sends you a “Design Received” message1, regardless of the Purchase Order
status.

When we have both the complete Purchase Order and the design
information, the Affymetrix Chip Design Group sends you a “Design Request
Accepted” message. This message signifies that work can begin on your
customized probe array.

Array Design

We start the array design process by assigning a Chip Designer to your project.
This individual acts as your contact person during the design process. If the
designer has questions regarding your specifications, he/she will send you a
“Design Clarification” message. Likewise, if you have questions for the
designer, you can send us a “Design Clarification” message presenting your
questions.

It may be necessary to send additional sequences. If this occurs, we request
that you send the complete updated sequence and/or instruction files. This
prevents confusion and ensures that we design the array representing all of
your sequences of interest.

Upon completion of the design of your array, you
will receive a “Design Proposal” describing the results. Please thoroughly
review the proposal and let us know how to proceed with your design (see page
20 for details). Once you accept the proposal, we then begin working on
designing the mask for your custom array.

	1	 	All e-mail messages described in this document shall have the following
information in the Subject line: <Array description> - <Array
name>: <e-mail
description>. The array name is an 11-character code for
your design. The array description is provided by you in the Design Request
Form. For example, a “Design Request Accepted” message will have something like
“Rat Discovery-abRATDISCla: Design Request Accepted” as the subject of the message.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	6	 

 

Post Array Design

After the mask design is completed and we verify that all the submitted
sequences are acceptable, you are sent a “Design Complete” message. Based on
the date of this message, Affymetrix Customer Service will confirm the delivery
date of your arrays. From this point on, technical questions regarding your
arrays should be addressed to your Technical Support Representative.

Submitting a Design Request

A design request consists of two items:

	1.	 	A Purchase Order (PO)
	 
	2.	 	Information related to your design.

Both items must be complete before The Affymetrix Chip Design Group may begin
work on your custom array.

Purchase Order

A PO is a commitment to buy our products and services. The PO for a custom
expression array consists of the following:

	1.	 	The design fee2
	 
	2.	 	An initial order for the first lot(s) of arrays. A Purchase Order must
include both items in order to be considered complete. The PO number for the
Design Fee must be the same as that in the Design Request Form (see Minimum
Order Per Array Format on page 9) and must be sent to the Affymetrix Customer
Service Group.

Design Information

Standard Custom Expression Array Design

Below are the standard design options available for your custom array.
Deviations from these parameters are not considered a Standard Custom Design
and shall be subject to additional fees.

	•	 	Sequence information: from a single eukaryotic species
	 
	•	 	Target strandedness: antisense
	 
	•	 	Feature size: 20,24 or 50 micron
	 
	•	 	Number of probe pairs per sequence: 16 or more
	 
	•	 	Probe length: 25

	2	 	The design fee and lot size may be specified in your contract. Contact your
Sales Representative if you have any questions.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	7	 

 

	•	 	Probe set format: distributed probe sets
	 
	•	 	Design: single array or multi-array set3
	 
	•	 	Array format: Standard (49 arrays/wafer), Midi (100 arrays/wafer) and Mini (169
arrays/wafer) are available.

In addition, the following standard Affymetrix controls are also included in every design:

	•	 	Edge controls
	 
	•	 	Corner checkerboards
	 
	•	 	Cycle fidelity
	 
	•	 	Cycle fidelity sense
	 
	•	 	QC controls
	 
	•	 	Spaced normalization
	 
	•	 	Center cross
	 
	•	 	Controls on all arrays: bioB, bioC, bioD, CRE, TRP, LYS, PHE, THR, DAP, 4 murine
genes, 4 yeast genes
	 
	•	 	Controls for Human, Murine,
Rat, Yeast, or Arabidopsis depending on your design

The completed custom array is tested using predetermined QC controls.

Number of Probe Sets on an Array

The following matrix calculates the approximate number of probe sets that will
fit on a Standard size custom array (this is in addition to the Affymetrix
controls).

	 	 	 	 	 	 	 	 	 
	 	 	16 probe-pair design	 	20 probe-pair design
	 	 	
	 	

	20 μm
	 	 	12,574	 	 	 	10,059	 
	24 μm
	 	 	8,665	 	 	 	6,932	 
	50 μm
	 	 	1,870	 	 	 	1,496	 

The following matrix calculates the approximate
number of probes that can be
accommodated on an array based on the feature size and array format.

	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	Standard	 	Midi	 	Mini
	 	 	
	 	
	 	

	 	 	(49 arrays)	 	(100 arrays)	 	(169 arrays)
	20 μm
	 	 	402,386	 	 	 	156,143	 	 	 	62,942	 

	3	 	A multi-array set design means that you have submitted enough sequences that
require the design of two or more arrays. However, since you will be submitting
one set of design information, the probe selection will be done as for a single
design. If the design requires two or more arrays, the arrays will be
manufactured as separate designs with costs for each additional design and
array.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	8	 

 

	 	 	 	 	 	 	 	 	 	 	 	 	 
	24 μm
	 	 	277,303	 	 	 	106,231	 	 	 	41,998	 
	50 μm
	 	 	59,858	 	 	 	20,623	 	 	 	5,951	 

16 or 20 probe pairs are used on our commercial arrays. The number of
sequences that can be represented on an array can be calculated by using the
following formula.

(number of probes for a particular feature size & array format) / (2 x [number
of probe pairs])

We recommend that you submit 10-15% more sequences than can actually fit on an
array, since some sequences may be lost in the pruning process.

Minimum Order Per Array Format

The array format that is used is determined by the number of genes you want to
interrogate. The various formats yield a varying number of arrays per wafer.
The chart below outlines the number of arrays that need to be ordered for the
corresponding formats.

	 	 	 	 	 
	Format	 	Minimum Order
	
	 	

	Standard
	 	 	80 +/- 10	 
	Midi
	 	 	90 +/- 10	 
	Mini
	 	 	160 +/- 10	 

Design Request Form

An example of the Design Request Form can be found on Page 11. The form can be
obtained via email from Technical Support at support@affymetrix.com or by
telephone at 1-888-DNA- CHIP (1-888-362-2447). Customers in Europe can call +44
(0) 7000 785 803 (Europe). The Design Request Form will be sent to you via
email in Microsoft® Word format.

The following information must be included in your Design Request Form:

	•	 	PO number and date of request
	 
	•	 	Contact information
	 
	•	 	Specific information on your design (e.g., array description, feature
size, sequence file name, instruction file name, etc).

We have created selection lists, with or without defaults, for each field
requiring a specific option. This feature may not be initially apparent upon
reviewing the document. You must click a field (gray area) to view the
available options. All other fields in the document are text fields.

The following fields always require information:

	•	 	All fields in the Requestor Information section

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	9	 

 

	•	 	Array name4
	 
	•	 	Array description
	 
	•	 	Sequence file name
	 
	•	 	Instruction file name
	 
	•	 	Species
	 
	•	 	Number of sequences per probe array
	 
	•	 	Number of probe pairs per sequence
	 
	•	 	Feature size
	 
	•	 	Minimum number of acceptable probes per sequence (see details on page 21)
	 
	•	 	Array format

All other selection list fields: if no selection is made, the defaults will be
used

The following fields require information under the conditions specified:

	 	 	 
	Pruning sequence file name:	 	
when you want to prune, or exclude,
certain sequences in addition to the ones
used to select probes
	 	 	 
	Constitutively expressed genes:	 	
when the species specified is not a
commercially available product.
	 	 	 
	rRNA sequence:	 	
when the species specified is not a
commercially available product.

If you are unsure of the information required in any of the required text
fields, please write “don’t know.” We will work with you to determine the
applicable information. If the information has been supplied elsewhere]it is
acceptable to reference that field. Every mandatory field must be filled out.

If you have array design instructions that are not captured in the Instruction
File, please include them in the Special Instructions section.

	4	 	The “Array name” you
provide us can be up to 8 characters in length. It can be
a combination of any alphanumeric characters and underscores. We will then add
a 2-character pretix to represent your company/institution, and a 1-character
suffix to represent the target strandedness of your design. For example, if ABC
Company is requesting an antisense Rat design, they might specify the Chip Name
to be “RATDISCl”, and the final Array Name will look like
“abRATDISCla”

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	10	 

 

Example of a Design Request Form

The following is an example of a completed design request form:

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	11	 

 

Sequence File

The “Sequence File” should contain all the sequences from which probes will be
selected. Sequences to be used for pruning purposes only (i.e. no probes will
be represented) must be included in the “Pruning Sequence File” and not the
“Sequence file” (see Pruning Sequence File on page 19 for more detail).

The “Sequence File” must be in a FastA format. The FastA format is a text file
containing a sequence name on one line, followed by one or more lines of
sequence. The “Sequence File” has the following additional characteristics:

	•	 	The sequence name must correspond to the value in the “name” column in the “Instruction File” (see Instruction File on page
13 for more information on the Instruction File)
	 
	•	 	All names defined in the “Instruction File” must exist in the “Sequence File”, and vice versa.
	 
	•	 	A “>” precedes the sequence name.
	 
	•	 	The sequence name must be unique.
	 
	•	 	No blank lines should exist between sequences.
	 
	•	 	A comment may follow the sequence name. It is important to note that comments
will be ignored during chip design.

Example: contents of file “gene.txt” in FastA format

>AA618977 [insert comment here]

gttttgtctttggttaaagtaccttttgcatcatgattctttgagatgtttagattatttctagttcccgctggcttatg
attttcattgattcatagcaagtttgtgcatagataagttgttgtgtaaaataactggtttatagcttgattcttattgt
tgatgaaaaaa

>AA618981

agatcttacggactatctgatgaagatcttgactgagagaggttacagttttacgacgacagcggaacgtgagatagtcc
gagac
atcaaggagaaactgtgttgttgccttggatttcgcaggagatgggtacggcagcttcgagttcggcgttggagaagagt
tatgagcttcctgatggtcaag
tgattactattggtaacgagcggtraattctattatgaagctgtacccaacacagtattgtc

>ABCD

agatcttacggactatctgatgaagatcttgactgagagaggttacagttttacgacgacagcgg~cgtgagatagtccg
agac atcaaggagaaactgtgttatgttg

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	12	 

 

instruction File5

Description of Columns

The “Instruction File” is a text file containing the following tab delimited
columns. The name and database columns are required in the instructions. All
other columns are optional.

name

The Accession Number in GenBank or the ID referring to a sequence in the public
domain databases. If this is not applicable, then indicate a proprietary ID, up
to 20 characters in length. This ID must not end with an underscore followed by a single alphanumeric
character (e.g. _i, _3); nor can it end with _at, _st, or_bt. In addition, the following
special characters are not allowed anywhere in the “name”:

# (pound sign)

* (asterisk)

? (question mark)

; (semi-colon)

: (colon)

| (pipe)

~ (tilda)

` (tick mark)

, (comma)

\ (back slash)

/ (forward slash)

’ (apostrophe)

‘’ (single quotation marks)

“” (double quotation marks)

<> (angle brackets)

{} (curly brackets)

[ ] (square brackets)

If you want to give the probe sets that represent your submitted sequences
unique names for use in data analysis, you may do so by providing an alias (See
“alias” column description). If no alias is provided, then the contents of the
“name” column will also be used as the probe set name.

	5	 	Some examples can be found on Page 18.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	13	 

 

database

The biological database from which the sequence names are derived. This field
can be up to 50 characters in length. If the sequences are NOT from a public
database, please use “Proprietary” as the value for this column.

alias

The “alias” is the designation used for the probe set names. It is a
descriptive name made of up to 20 characters. The alias must not end with an
underscore followed by a single alphanumeric character (e.g. _i, _3); nor can
it end with _at, _st, or _bt . In addition, the following special characters
are not allowed anywhere in the “alias”:

# (pound sign)

* (asterisk)

? (question mark)

; (semi-colon)

: (colon)

| (pipe)

~ (tilda)

` (tick mark)

, (comma)

\ (back slash)

/ (forward slash)

’ (apostrophe)

‘’ (single quotation marks)

“” (double quotation marks)

<> (angle brackets)

{} (curly brackets)

[ ] (square brackets)

Please refer to page 18 for examples that illustrate different
relationships between “name” and “alias”.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	14	 

 

hyperlink

Provide the identifier in the public databases from which the sequences were
derived, preferably the GenBank version number when possible. An example of the
version number can be seen in the figure below.

hyperlinkDatabase

The name of the public database for the hyperlink. If “hyperlink” and
“hyperlinkDatabase” are provided, then you will be able to click the hyperlink
within the Microarray Suite software and view the sequence information through
your web navigation software. This is possible only if the public database
supports links.

species

The name of the species from which the sequence is isolated. This column can be
up to 80 characters. It should correspond to what is listed in the Design
Request Form.

start

Within the sequence, the numeric (1-based) position of the start of the region
of interest. This column is required if “end” is specified. Normally, probes
are selected from the last 600 bases from the 3’ end (the
3’ end is the 30th base
from the end of the sequence). This means that the probe selection region will
be from the 630th base to the 30th base from the 3’ end of the sequence. For
example, if a sequence is 1,000 bases long, the probe selection region will be
from base 371 to base 970 (600 bases) e.g.,

If this is not desirable, then the “start” and “end” columns should be used.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	15	 

 

end

Within the sequence, the numeric (1-based) position of the end of the region of
interest. This column is required if “start” is specified.

startSeq

A sequence used for checking purposes. It includes the base at “start” and the
next few bases up to a total of 8 bases. This column is required if “start” is
specified.

endSeq

A sequence used for checking purposes. It includes the base at “end” and the
previous few bases up to a total of 8 bases. This column is required if “end”
is specified.

reverseSeq

Should we reverse complement the sequences before using them? “Y” to reverse
complement or “N” to use as is. If this column is not provided, we will assume that
“reverseSeq” is “N” for all sequences.

For “Y”, the “start”/
“end” and “startSeq”/ “endSeq” refer to the sequence
before it is reversed.

When no “start”/“end” values
are specified)the sequence with “reverseSeq”=“Y”
will be reverse-complemented first, and then the probe selection region will be
set on the reverse-complemented sequence, using the default values (last 600
bases from the 3’ end).

When “start”/ “end” values are specified, the probe selection region set will
correspond to the range set by the “start”/“end” values.

During the design, we add the suffix “_RC” to your original names (not the
alias) for any sequences in which “reverseSeq” is “Y”. If you do choose this
option, it is advised that you provide an alias for your sequence so that you
can distinguish which sequence(s) have been reverse-complemented.

Typically, this field is used if you are providing a sequence from the
non-coding strand, (e.g. most 3’ EST sequences from GenBank) or a sequence that
you do not know which direction is

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	16	 

 

coding. In the second case, you would typically specify the sequence twice
in the instruction file, and say “Y” the first time, and “N” the second time.

description

An optional description of the sequence up to 4000 characters. This serves as
the annotation for your sequences.

copies

The number of times the same probe set representing the same sequence is to be
tiled on the array. If not provided, all probe sets will only be tiled once.
However, if it is desirable for some of the probe sets representing specific
sequences to be tiled more than once, then this column can be used.

Example (instruction file):

	 	 	 	 	 
	name	 	
alias
	 	copies
	AB000l	 	
seqAB
	 	3

These replicate probe sets will be designated on the array as “seqAB_at” (the
original set) and “seqAB_copyl_at” and “seqAB_copy2_at” (two copies of the
original set).

Additional Information

Finally, you may include up to 10 classification columns of additional
data for your sequences. These columns can have any headings other than the
ones mentioned above, are limited to 256 characters each, and are for
descriptive purposes only.

Additional characteristics of the Instruction File:

	•	 	All alphanumeric and character fields are case insensitive.
	 
	•	 	Duplicate columns are not allowed.
	 
	•	 	If there is a value for an optional column (i.e. alias) in one row, then there
must be values for that optional column in ALL rows, except for the following
columns:

species

description

hyperlink and hyperlink database

classification columns

The values you provide in the following columns directly affect the array
design:

	•	 	alias
	 
	•	 	species
	 
	•	 	start
	 
	•	 	end
	 
	•	 	reverseSeq
	 
	•	 	copies

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	17	 

 

The values you provide for the other columns will have no effect on the array
design. However, providing these values will give you more information about
your final array design, especially if you want to analyze the data gathered
from different arrays.

Examples6

	1.	 	An example of the simplest design is shown below. It selects probes from the
last 600 bases from the 3’ end (where the 3’ end is the 30th base from the end
of the sequence) and names the probe sets using the same name as the sequences:

	 	 	 
	name	 	
database
	A	 	
Proprietary
	B	 	
Proprietary

	2.	 	To specify the probe set names different from the sequence names, you can
add an “alias” column to your instruction file:

	 	 	 	 	 
	name	 	
database
	 	alias
	A	 	
Proprietary
	 	C
	B	 	
Proprietary
	 	D

	 	 	In terms of probes, the above instruction specifying an alias gives you exactly
the same probe sets as the instructions used in Example 1. However, the probe
set names will be different. The probe set for sequence A will be called C
(C_at), and D for sequence B.
	 
	3.	 	To select probes from a specific region of interest, add the “start”, “end”,
“startSeq” and “endSeq” columns:

	 	 	 	 	 	 	 	 	 	 	 
	name	 	
database
	 	start
	 	end
	 	startSeq
	 	endSeq
	A	 	
Proprietary
	 	1
	 	70
	 	ACCG
	 	CCGT
	B	 	
Proprietary
	 	100
	 	200
	 	GGGA
	 	TAAA

	 	 	Probes for sequence A will be selected from the first 70 bases of the sequence.
Probes for sequence B will be selected from the 100th base to the
200th base of
the sequence.
	 
	4.	 	To select probes from only certain regions within a sequence, specify the
instruction file as follows:

	 	 	 	 	 	 	 	 	 	 	 	 	 
	name	 	
database
	 	alias
	 	start
	 	end
	 	startSeq
	 	endSeq
	A	 	
Proprietary
	 	C
	 	1
	 	70
	 	ACCG
	 	CCGT
	A	 	
Proprietary
	 	C
	 	80
	 	200
	 	TTTA
	 	TAAA

	 	 	Bases 1 through 70 will be concatenated to bases 80 through 200 of sequence
A. Probes will then be selected from this concatenated region. The probe set
generated will be called C, to distinguish it from the original sequence since
it is not the entire sequence that we are using to select probes. This can be a
good way to avoid selecting probes from certain intronic regions within your
sequence.
	 
	5.	 	To have more than one probe set produced from the same sequence, specify a
different alias for each probe set you are interested in:

	 	 	6 The examples are to be used for illustrative purposes only. Only the relevant
columns are shown and they may not line up as well in a red instruction file.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	18	 

 

	 	 	 	 	 	 	 	 	 
	database
	 	start
	 	end
	 	startSeq
	 	endSeq
	Proprietary
	 	1
	 	70
	 	ACCG
	 	CCGT
	
Proprietary
	 	80
	 	200
	 	TTTA
	 	TAAA

	 	 	Probe set C will be selected
from bases 1 through 70 of sequence A. Probe Set D
will be selected from bases 80 through 200 of sequence A.
	 
	6.	 	To reverse-complement a sequence before probe selection, add the
“reverseSeq” column to the instruction file:

	 	 	 	 	 	 	 
	name	 	
database
	 	alias
	 	reverseSeq
	A	 	
Proprietary
	 	C
	 	N
	A	 	
Proprietary
	 	E_RC
	 	Y

Probe set E_RC will be selected from the last 600 bases (the last 630th base to
30th base) of the reverse-complement of sequence E.

Pruning Sequence File

By default, we prune, i.e., match and exclude, against all sequences submitted
for probe selections, including certain Affymetrix controls (bioB, bioC, etc).
If the design is for a commercially available species, we prune your sequences
against constitutively expressed genes and rRNA sequences represented on these
arrays. Additionally, if there are other sequences that you would like us to
prune against while selecting probes, they should be included in the “Pruning
Sequence File”. We will not select probes from the “Pruning Sequence File”. The
format of this file is the same as the “Sequence File” (see Sequence File on
page 12). Every sequence name in the “Pruning Sequence File” should correspond
to the “name” in the “Pruning Instruction File” (see below).

If you wish, you may also specify to prune against Affymetrix’ sequences used
to produce the latest commercially available Genechip® probe arrays.

Pruning Instruction File

The “Pruning Instruction File” is optional. However, if you do choose to
provide one, it should follow the format for the normal “Instruction File”,
excluding the following columns from the “Pruning Instruction File.”

	•	 	alias
	 
	•	 	start
	 
	•	 	end
	 
	•	 	startSeq
	 
	•	 	endSeq
	 
	•	 	copies

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	19	 

 

Understanding the Design Proposal

Information

A design proposal is sent to you when we finish selecting probes from your
sequences. The proposal lists all of the sequences you have requested be
included in the design, followed by several columns indicating how these
sequences are represented.

The columns are:

	 	 	 
	Name:	 	
The name of your sequence.
	 	 	 
	Alias:	 	
The alias provided in the Instruction File.
	 	 	 
	TotalProbeSets:	 	
The total number of probe set(s) representing the sequence.
	 	 	 
	TotalProbes:	 	
The total number of probe pairs representing the sequence.
	 	 	 
	Normal:	 	
The number of “unique” probe sets that meet the requested # of probe pairs per sequence.
	 	 	 
	Incomplete (_i):	 	
The number of “unique” probe sets that are fewer than the requested # of probe pairs per sequence.

The following 5 columns show the number of ADDITIONAL probes we could get by
dropping certain design constraints7.

	 	 	 
	Motif (_g):	 	
The number of probes we obtain by requiring that the
probes exactly match some number (> 1) of sequences
for which we were able to pick enough unique probes.
These probes are labeled as “_g”.
	 	 	 
	Identical (_s):	 	
The number of probes we obtain by requiring that the
probes exactly match some number (>1) of sequences for
which we were not able to pick enough unique probes.
These probes are labeled as “_s”.
	 	 	 
	Similar (_f):	 	
The number of probes we obtain by dropping all similarity
constraints. These probes are labeled as “_f”.
	 	 	 
	Rule (_r):	 	
The number of probes we obtain by dropping our
heuristics. These probes are labeled as “_r”.
	 	 	 
	Neural Net (_n):	 	
The number of probes we obtain by dropping the neural net
model. These probes are labeled as “_n”.

The last 3 columns explain the other sequences in _g, _s and _f columns.

	7	 	See page 21 for more detail on Probe Selection Rules.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	20	 

 

	 	 	 
	Represented By:	 	
This sequence is also represented by the probe set for the
named sequence.
	 	 	 
	IdenticalSeqs:	 	
The probes for this sequence exactly match these other sequences.
	 	 	 
	SimilarSeqs:	 	
The probes for this sequence are similar to these other sequences.

Please note: the minimum number of probes per sequence is set to the number you
define in the design request form. For example, in the “incomplete (_i)”
column, the number of probes will be zero if less than this number of probes
were selected from that sequence.

Probe Selection Rules

The ultimate outcome of the probe selection process is dependent on the quality
of the sequences submitted. A small percentage of the sequences that you submit
may not yield the desired number of probe pairs after our selection rules have
been applied. In this case, we may be able to relax some of the rules and label
the resulting probe sets with an appropriate suffix outlined below.

	 	 	 
	_s:	 	
Remove similarity constraints. We are unable to identify the desired number of unique probes for the specified set of
sequences; however, we are able to identify among that set a number of sequences that share identical probes. Only probes
representing identical regions among the sequence set are included.
	 	 	 
	_i:	 	
Incomplete probe set. It is not possible to select the full number of unique probes.
	 	 	 
	_r:	 	
Some rules dropped. By dropping some rules, we are able to select additional probes to obtain the number of probes
requested.
	 	 	 
	_f:	 	
Ignore family similarity. By relaxing this rule, we remove similarity constraints and only prune the probes based on the
number of synthesis steps, the heuristic rules, the neural net, and the maximum number of probes. Some of the selected
probes will not be identical to all members of the specified sequence family.
	 	 	 
	_g:	 	
For sequences for which we are able to identify enough unique probes, and
we can also select probes from regions that are identical among several
different sequences, we then tile the common sequences on the array in
addition to the unique part of each sequence. These additional common
sequences are useful to interrogate the expression level of a common
motif, or to provide you with cross-checking of expression levels of two
or more sequences. Typically, if you choose to include _g sequences, you
may interrogate up to 5% of your sequences twice. This choice should be
made if you want chat additional data.
	 	 	 
	_n:	 	
Relax the neural net model. This is not recommended.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	21	 

 

The following diagram is a graphical representation
of “_i”, “_s”, “_f”,“_g” and unique sets.

Legend

F: a set of related sequences

S: a sequence

PS: a probe set

P: a probe

This diagram shows some of the possible relationships between sequences and
probe sets on an individual probe array. The solid lines show how sequences or
sequence sets are represented by individual probes or probe sets. If a solid
line is connected to a box, then it applies to all of the circles in that box;
if it is connected to a circle in the box, then it applies only to that
particular circle.

For example, the line connecting the S circle to the _i Group box, indicates
that all of the probes in that set represent only the connected sequence, and
do not represent the other sequence in the same box. Whereas the line
connecting the F box to the _s Group box indicates that all of the _s probes
represent both sequences in the box.

Actions Required

Once you receive the design proposal, you need to review it and decide which of
the following action(s) you would like us to take:

	1.	 	Tile everything as recommended in the design proposal.
	 
	2.	 	Tile only certain sequences (specify which) and/or certain types (specify
which types). If you choose this option, please do the following:

	 	a.	 	Put the sequences in a priority list (if they are not already so when
submitted), i.e. the most important sequence on top to the least important
sequence at the bottom. We will tile the probe set(s) for each sequence
starting from the top and continue downward until the array is filled.
	 
	 	b.	 	Tell us the maximum number of probe sets that will be used to interrogate
each sequence. This is important since it is possible that some sequences may
be represented by more than one probe set. For example, sequence A might have
an

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	22	 

 

	 	 	 	Incomplete(_i) set and a Rule(_r) set. If you specify the maximum to be one,
then only one set will be tiled to represent sequence A. If you specify the
maximum to be two or greater, then both sets will be tiled to represent
sequence A.
	 
	 	c.	 	Tell us the order of preference for selecting the probe set(s). For
example, you might only want a maximum of one probe set to represent a
sequence, and your order of preference might be: Normal, _i, _r, _s, _f.. Using
this order, if there are Normal probes, then the Normal probe set would be
tiled to represent the sequence. If not, then we would go to the next category
to see if there are Incomplete (_i) probes. If yes, then the probe sets would
include an Incomplete(_i) set; if not, then we would move on to the _r probes,
and so on until we reach the _f Group, the last category. If there are no probes
in any of the categories listed, then the sequence will not be represented on
the array.

	3.	 	Provide additional sequences for those that cannot be well represented. When
providing these additional sequences, please resubmit the COMPLETE revised
“Sequence File” and “Instruction File”. This necessitates repeating the probe
selection process by the Affymetrix Chip Design Group, lengthening the total
design time. Therefore, we advise that you submit 10-15% more sequences than
desired at the beginning of the design process.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	23	 

 

Contact Information

Sales

Contact Sales for Genechip product information.

Email sales@affymetrk.com

	 	 	 	 	 
	Address:	 	
USA

Affymetrix, Inc.

3380 Central Expressway

Santa Clara, CA 95051

USA
	 	Europe

Affymetrix UK, Ltd.

Mercury Park

Wycombe Lane

Wooburn Green

High Wycombe

Bucks HPlO OHH

United Kingdom

	 	 	 	 	 
	Phone:

Fax:	 	
1-408-731-5503

1-408-48 1-0422

	 	+44 (0) 7000 785 803

+44 (0) 7000 785 804

Customer Service

For prompt attention to your purchase orders, please address all purchase
orders to Customer Service. Orders sent to a specific salesperson might be
delayed as most of our salespeople travel extensively.

Address:

	 	Affymetrix, Inc.

1170 Kifer Road

Sunnyvale, CA 94086

Fax: 1-800-499-7309 (United States only)

Fax: 1-408-481-9442

Chip Design

All design information should be sent to Chip Design.

Email Chip_Orders@affymetrix.com

Address:

	 	Affymetrix, Inc.

1170 Kifer Road

Sunnyvale, CA 94086

Fax: 1-408-731-5380

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	24	 

 

Technical Support

All general technical questions not related to a specific design and all
support issues should be addressed to Technical Support.

Email:

support@affymetrix.com

	 	 	 	 	 
	Address:	 	
USA
Affymetrix, Inc.

3380 Central Expressway

Santa Clara, CA 95051

USA

	 	Europe

Affymetrix UK, Ltd.

Mercury Park

Wycombe Lane

Wooburn Green

High Wycombe

Bucks HPlO OHH

United Kingdom

	Phone:	 	
1-888-DNA-CHIP

(1-888-362-2447
	 	+44(0) 7000 785 803
	Fax:	 	
1-408-481-0435
	 	+44(0) 7000 785 804

Trademarks

Affymetrix®, GeneChip®,
TM, EASITM, HuSNPTM, GenFlexTM, 417TM, 418TM, 428TM,
Pin-and-RingTM, Flying ObjectiveTM, TM,
, Genetic Analysis Technology
ConsortiumTM, and  are trademarks owned or used by Affymetrix, Inc.

Products may be covered by one or more of the following patents and/or sold
under license from Oxford Gene Technology: U.S. Patent Nos. 5,445,934;
5,744,305; 5,700,637, 5,945,334; and EP 619 321; 373 203 and other foreign or
US. patents.

Limited License

EXCEPT AS EXPRESSLY SET FORTH HEREIN, NO RIGHT TO COPY, MODIFY,
DISTRIBUTE, MAKE DERIVATIVE WORKS OF, PUBLICLY DISPLAY, MAKE, HAVE MADE, OFFER
TO SELL, SELL, USE OR IMPORT PROBE ARRAYS OR ANY OTHER PRODUCT IS CONVEYED OR
IMPLIED WITH THE PROBE ARRAYS, INSTRUMENTS, SOFTWARE, REAGENTS OR ANY OTHER
ITEMS PROVIDED HEREUNDER EXCEPT FOR CERTAIN ARRAYS AND REAGENTS DESIGNATED AS
“ANALYTE SPECIFIC REAGENTS” (SEE APPLICABLE PACKAGE INSERT) WHICH ARE LICENSED
FOR USE AS ANALYTE
SPECIFIC REAGENTS OR RESEARCH USE, ALL PRODUCTS (INCLUDING THE PROBE, ARRAYS,
INSTRUMENTS, SOFTWARE, AND REAGENTS) DELIVERED HEREUNDER ARE LICENSED TO BUYER
FOR RESEARCH USE ONLY. THIS LIMITED LICENSE PERMITS ONLY THE USE BY BUYER OF
THE PARTICULAR PRODUCT(S), IN ACCORDANCE WITH THE WRITTEN INSTRUCTIONS PROVIDED
THEREWITH, THAT BUYER PURCHASES FROM AFX OR ITS AUTHORIZED REPRESENTATIVE. THE
PURCHASE OF ANY PRODUCT(S) DOES NOT BY ITSELF CONVEY OR IMPLY THE RIGHT TO USE
SUCH PRODUCT(S) IN COMBINATION WITH ANY OTHER PRODUCT(S). IN PARTICULAR, (i) NO
RIGHT TO MAKE, HAVE MADE OR DISTRIBUTE OTHER PROBE ARRAYS IS

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	25	 

 

CONVEYED OR IMPLIED BY THE PROBE ARRAYS, (ii) NO RIGHT TO MAKE, HAVE MADE,
IMPORT, DISTRIBUTE, OR USE PROBE ARRAYS IS CONVEYED OR IMPLIED BY THE
INSTRUMENTS OR SOFTWARE, AND (iii) NO RIGHT TO USE PROBE ARRAYS IN COMBINATION
WITH INSTRUMENTS OR SOFTWARE IS CONVEYED UNLESS ALL COMPONENT PARTS HAVE BEEN
PURCHASED FROM AFX OR ITS AUTHORIZED REPRESENTATIVE. FURTHERMORE, PROBE ARRAYS
DELIVERED HEREUNDER ARE LICENSED FOR ONE (1)TIME USE ONLY AND MAY NOT BE
REUSED. THE PRODUCTS TO NOT HAVE FDA APPROVAL. NO PATENT LICENSE IS CONVEYED TO
BUYER TO USE, AND BUYER AGREES NOT TO USE, THE PRODUCTS IN ANY SETTING
REQUIRING FDA OR SIMILAR REGULATORY APPROVAL OR EXPLOIT THE PRODUCTS IN ANY
MANNER NOT EXPRESSLY AUTHORIZED IN WRITING BY AFX IN ADVANCE.

Copyright

© 2001 Affymetrix, Inc. All rights reserved.

	 	 	 	 	 
	GeneChip® Custom Array Design Request Guide	 	 	26	 

 

Exhibit I

List prices as of January 1, 2002

Standard Probe Arrays

USD

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	Part Numbers	 	 	 	Per Array Price
	

	Human Arrays	 	5 Pack	 	30 Pack	 	Name	 	 	 	 
	

	 	 	 	
900303
	 	 	 	900304
	 	 	Human Genome U95A Array
	 	 	2000	 
	

	 	 	 	
900305
	 	 	 	900306
	 	 	Human Genome U95B Array
	 	 	1000	 
	

	 	 	 	
900307
	 	 	 	900308
	 	 	Human Genome U95C Array
	 	 	1000	 
	

	 	 	 	
900309
	 	 	 	900310
	 	 	Human Genome U95D Array
	 	 	1000	 
	

	 	 	 	
900311
	 	 	 	900312
	 	 	Human Genome U95E Array
	 	 	1000	 
	

	 	 	 	
	 	 	 	
	 	 	Human Genome U133A
	 	 	2500	 
	

	 	 	 	
	 	 	 	
	 	 	Human Genome U133B
	 	 	2500	 
	

	Rat Arrays	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	 	
900249
	 	 	 	900286
	 	 	Rat Genome U34A
	 	 	1600	 
	

	 	 	 	
900250
	 	 	 	900287
	 	 	Rat Genome U34B
	 	 	1000	 
	

	 	 	 	
900251
	 	 	 	900288
	 	 	Rat Genome U34C
	 	 	1000	 
	

	Mouse Arrays	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	 	
900343
	 	 	 	900344
	 	 	Murine Genome U74A V.2 Array
	 	 	1500	 
	

	 	 	 	
900357
	 	 	 	900358
	 	 	Murine Genome U74B V.2 Array
	 	 	1000	 
	

	 	 	 	
900359
	 	 	 	900360
	 	 	Murine Genome U74C V.2 Array
	 	 	1000	 
	

	Drosophila Arrays	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	 	
900335
	 	 	 	900336
	 	 	Drosophila Genome Array
	 	 	1000	 
	

	Arabidopsis Arrays	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	 	
900292
	 	 	 	900293
	 	 	Arabidopsis Genome Array
	 	 	800	 
	

	Yeast Arrays	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	 	
900256
	 	 	 	900285
	 	 	Yeast Genome S98
	 	 	800	 
	

	E.coli Arrays	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	

	 	 	 	
900284
	 	 	 	900295
	 	 	E. coli Genome Array
	 	 	800	 
	

-37-

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