Award Agreements between the Registrant and Leroy Hood



 Exhibit 10.34 
 NIMBLEGEN SYSTEMS, INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of January 30, 2007 (the date of grant), is between NimbleGen Systems, Inc., a Delaware corporation
(the “Company”), and Leroy E. Hood (the “Participant”). All terms used herein and not otherwise defined shall have the same meaning as set forth in the Company’s 2000 Stock Option and Restricted Stock Plan, as amended
and restated as of September 25, 2001 and as further amended (the “Plan”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors of the Company (the “Board”) desires to induce the Participant to provide services to the Company as one
of its directors, to provide the Participant with a stronger incentive to strive for the continued success and growth of the Company and its Subsidiaries and to further align the Participant’s interests with those of the Company’s
stockholders. 
 NOW THEREFORE, in consideration of the benefits that the Company expects to be derived in connection with the
services to be hereafter rendered by the Participant, the Company and the Participant hereby agree as follows: 
 ARTICLE I

 Award of Option for Restricted Stock 
 1.1. Option; Number of Shares; Option Price. The Participant is granted the right and option to purchase (the “Option”) all or any part of an aggregate of 25,000 shares of the Company’s Common
Stock (individually, a “Share” and jointly, the “Shares”) at the purchase price of $1.74 per Share (the “Option Price”) any time before the tenth anniversary of the date of this Award Agreement. If the Participant
exercises the Option prior to the third anniversary of the date of this Award Agreement, the shares of Common Stock received from the exercise of the Option that are unvested shares according to the schedule set forth in Section 1.2 are
hereafter referred to as “Restricted Shares” and Shares that have vested are referred to as “Vested Shares.” The period during which there are Restricted Shares outstanding is referred to herein as the “Restricted
Period.” If the Option remains outstanding and is exercised on or after the fourth anniversary of the date of this Award Agreement, all of the Shares will be Vested Shares and none of the Shares will be Restricted Shares. 
 1.2. Vesting of Restricted Shares. The vesting schedule for the Shares governed by this Option is as follows. Except as otherwise provided in the
Plan and this Section 1.2, and subject to Section 1.4, the Option will vest as to 1/12th of the Shares on April 1, 2007, and an additional 1/12th of the Shares will vest as of each July 1, October 1, January 1 and
April 1 thereafter, provided that the Participant is still serving as a director of the Company on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the occurrence of a Change in Control while the
Participant is still serving as a director of the Company. Shares governed by this Option vest according to this schedule, whether or not the Option has been exercised. 







 1.3. Exercisability of Option. 
 (a) This Option is immediately exercisable and shall expire in accordance with this Section 1.3 and the Plan, but in all events, and
notwithstanding anything herein to the contrary, on the tenth anniversary of the date of this Award Agreement. 
 (b) If the
Participant’s service as a director of the Company terminates, the Option, to the extent not exercised, shall terminate three (3) months after termination of such service with the Company. 
 1.4. Method of Exercising Option. The Option may be exercised in whole or in part by delivery to the Company, at its offices in Madison,
Wisconsin, of (a) written notice identifying the Option and stating the number of Shares with respect to which it is being exercised, in the form attached hereto as Exhibit A, (b) payment in full of the Option Price of the
Shares then being acquired in the form permitted by Section 8 of the Plan, (c) execution of a stockholder agreement substantially in the form attached hereto as Exhibit B (“Stockholder Agreement”), (d) execution
of an Investment Representation Statement in the form attached hereto as Exhibit C if the Shares covered by the Option have not been registered under the Securities Act of 1933, as amended, at the time of the exercise and (e) if the
Option is exercised during the Restricted Period as defined in Section 1.1, a blank stock power for the Restricted Shares. The Company shall have the right to delay the issue or delivery of any Shares to be delivered hereunder until
(i) the completion of such registration or qualification of such Shares under any federal, state or foreign law, ruling or regulation as the Company shall deem to be necessary or advisable, and (ii) receipt from the Participant of such
documents and information as the Company may deem necessary or appropriate in connection with such registration or qualification or the issuance of Shares hereunder. 
 1.5. Prohibitions Against Transfer. The Option, and the rights and privileges conferred hereby, may not be transferred, assigned, pledged or hypothecated in any way (whether by operation of law or otherwise) by
the Participant, or be subject to execution, attachment or similar process, and shall be exercisable only by the Participant, except as provided in Section 12 of the Plan. 
 ARTICLE II 
 Provisions Governing Restricted Shares 
 2.1. Stockholder Status. Prior to the vesting of the Restricted Shares, the Participant shall not have the right to vote the Restricted Shares,
and instead, the Restricted Shares shall be voted as directed by action of the Board. The Participant agrees to execute a proxy upon request of the Board at any time during the Restricted Period appointing an agent designated by the Board to vote
the Restricted Shares. The Participant shall have the right to receive and retain all regular cash dividends paid or distributed in respect of the Restricted Shares, if any, and except as expressly provided otherwise herein, shall have all other
rights as a holder of outstanding shares of Common Stock. Until all of the Restricted Shares vest pursuant to Section 1.2, the Company shall retain custody of the stock certificates representing the Shares unless the Participant requests in
writing that the Company issue a certificate for any portion that represents Vested Shares to the Participant. As soon as practicable after the lapse of the restrictions, the Company shall issue or release or cause to be issued or released
certificate(s) representing the Shares. 
  

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 2.2. Prohibition Against Transfer. Restricted Shares may not be transferred, assigned, pledged or
hypothecated in any way (whether by operation of law or otherwise) by the Participant, or be subject to execution, attachment or similar process. Notwithstanding the foregoing, Restricted Shares may be transferred as the result of any merger,
consolidation, or share exchange involving the Company, in which event the shares received in exchange for the Shares will remain subject to this Award Agreement and treated as “Restricted Shares” hereunder. Any transfer in violation of
this Section 2.2 shall be void and of no further effect. After the Restricted Shares vest, they shall continue to be subject to the limitations on transfer contained in the Stockholder Agreement. 
 2.3. Repurchase of Restricted Shares. If the Participant’s service as a director of the Company terminates for any reason, the Company
shall have the right, but not the obligation, to purchase all or any portion of the Restricted Shares owned by the Participant. Such option shall be exercisable by the Company within six (6) months following the date of such termination of such
service by the Participant by delivery of a written notice to the Participant. The Company may assign its rights under this Section 2.3 to the stockholders of the Company (other than the Participant), at any time, on a pro rata basis. The
purchase price per share of all purchases under this Section 2.3 of Restricted Shares shall be the Option Price. 
 2.4. Payment of
Purchase Price. In the event of the purchase by the Company of Shares under Section 2.3, above, the Company, shall, within thirty (30) days of the delivery to the Participant of the notice that the Company is exercising the option to
purchase Shares, pay the purchase price in cash and shall have the option to evidence that amount of the purchase price that exceeds $10,000 by a promissory note of the Company, dated the day of purchase by the Company (the “Promissory
Note”). The Promissory Note shall be payable in four (4) equal annual installments, commencing on the Closing Date, as defined in Section 2.5, below, with each subsequent installment to be due on the anniversary date of the Closing
Date each year thereafter. Interest on the deferred balance of the purchase price shall accrue from the Closing Date at the Annual Mid-Term Federal Rate published by the Internal Revenue Service as of the end of the month preceding or coincident
with the purchase and shall be payable with each installment of principal. The Company shall have the right to prepay the deferred balance at any time, without penalty. All payments shall be applied first to interest which is accrued and unpaid and
then to principal. Any promissory note issued hereunder shall provide that all sums not yet due and payable thereunder shall be and become immediately due and payable upon any Change in Control. The parties may, by written agreement, alter or modify
the payment schedule provided herein. 
 2.5. Closing Date. The closing date (the “Closing Date”) for the purchase of any
Shares pursuant to Section 2.3, above, shall be the date the Shares are endorsed and delivered to the Company and the Company has tendered to the Participant the consideration required by this Award Agreement, including, without limitation, any
cash then due and any Promissory Note evidencing the obligations of the Company to the Participant. The Closing Date shall occur on the business day designated by the Company, but not later than seven (7) months after the Participant’s
termination of service as a director of the Company. The Participant agrees to use best efforts to cause all transactions required to be consummated hereunder to be closed as provided herein and acknowledges that time is of the essence. 

 

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 ARTICLE III 
 Miscellaneous 
 3.1. Provisions of the Plan Control. This Award Agreement shall be
governed by the provisions of the Plan, the terms and conditions of which are incorporated herein by reference. In the event that the provisions of this Award Agreement and the Plan conflict, the Plan shall control. The Plan empowers the
Administrator to make interpretations, rules and regulations thereunder, and, in general, provides that determinations of the Administrator with respect to the Plan shall be binding upon the Participant. A copy of the Plan will be delivered to the
Participant upon reasonable request. 
 3.2. Taxes. The Company may require payment or reimbursement of or may withhold any tax that
it believes is required as a result of the exercise of the Option or issuance of shares, and the Company may defer making delivery with respect to Shares for which the Option was exercised or with respect to Vested Shares which previously had been
Restricted Shares until arrangements satisfactory to the Company have been made with respect to such withholding obligations. 
 3.3. Tax
Consequences. The Participant understands that the Participant may suffer adverse tax consequences as a result of the Participant’s purchase or disposition of the Shares. The Participant represents that the Participant will consult with any
tax consultants the Participant deems advisable in connection with the purchase and disposition of the Shares. 
 3.4. Notices. Any
notice to be given to the Company under the terms of this Award Agreement shall be given in writing to the Company in care of its then principal executive officer at its then principal place of business. Any notice to be given to the Participant may
be addressed to him at his address as it appears on the payroll or other records of the Company or any affiliate thereof. Any such notice will be deemed to have been duly given: (a) upon personal delivery to the party to be notified,
(b) when sent by confirmed facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested,
postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt at the Participant’s or the Company’s address. 
 3.5. Governing Law. This Award Agreement and all questions arising hereunder or in connection herewith shall be determined in accordance with the
laws of the State of Wisconsin, without giving effect to the principles of conflicts of laws. 
 3.6. No Right to Continued Service.
This Award Agreement shall not confer upon the Participant any right with respect to continuation of service on the Board or any committee thereof, nor shall it interfere in any way with the right of the Company to terminate the Participant’s
service on the Board or any committee thereof at any time. 
  

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 3.7. Multiple Copies. One or more copies of this Award Agreement may be executed, each of which
will be deemed an original, but all of which together will constitute one and the same agreement. 
 IN WITNESS WHEREOF, the Company
has caused this Award Agreement to be executed as of the date and year first above written, which is the date of the granting of the Option evidenced hereby. 
  

			
	NIMBLEGEN SYSTEMS, INC.
		
	By:	 	 /s/ Thomas M. Palay

		 	Thomas M. Palay,
		 	Vice-Chairman of the Board of Directors and Vice President


 The undersigned Participant hereby accepts the foregoing Option and agrees to the several
terms and conditions hereof and of the Plan. 
  

	
	Participant:
	
	 /s/ Leroy E. Hood

	Leroy E. Hood


  

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 Spousal Consent and Acknowledgment 
 I acknowledge that I have read the Award Agreement and the Stockholder Agreement, attached thereto as Exhibit B, and that I understand their
contents. I am aware that by their provisions my spouse agrees, among other things, to limit the transferability of and the voting rights attendant upon his or her Shares of NimbleGen Systems, Inc. which may be acquired through his or her exercise
of an Option. I am further aware that the terms and limitations set forth in such agreements shall apply to any interest I have in the Option or the Shares (including without limitation any right or interest by operation of the Wisconsin Marital
Property Law, chapter 766 of the Wisconsin Statutes, or by operation of any other law) and the interest of any of my heirs, legatees, or other transferees. I consent to and approve the provisions of the Award Agreement and the Stockholder Agreement,
and agree that the Option and the Shares and my interest in them are subject to the provisions of such Agreements, and direct the personal representative of my estate to promptly comply with all of the provisions of such Agreements. I further agree
that I will take no action at any time to hinder the operation of the Award Agreement or the Stockholder Agreement as to the Option and/or the Shares or any interest that I or my transferees have in them. 
  

											
	 Date:
	 	  
	 		 	Spouse:	 	  
	 	








 EXHIBIT A 
 NIMBLEGEN SYSTEMS INC. 2000 STOCK OPTION 
 AND RESTRICTED STOCK PLAN 
 EXERCISE NOTICE 
 1. Exercise of
Option. Effective as of today,             , 20    , the undersigned (the “Participant”) hereby elects to exercise the Participant’s
option to purchase              shares of the Common Stock (the “Shares”) of NimbleGen Systems, Inc. (the “Company”) under and pursuant to the Company’s 2000
Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further amended (the “Plan”), and the Award Agreement dated as of January 30, 2007 (the “Award Agreement”). All terms used
herein and not otherwise defined shall have the meaning set forth in the Plan, the Award Agreement, or in the form of stockholder agreement that is attached to the Award Agreement as Exhibit B (the “Stockholder Agreement”). 
 2. Representations of the Participant. The Participant acknowledges that the Participant has received, read and understands the Plan, the Award
Agreement, and the Stockholder Agreement and agrees to abide by and be bound by their terms and conditions. 
 3. Rights as
Stockholder. Until the stock certificate evidencing such Shares is issued (as evidenced by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company) and the Stockholder Agreement is executed by the
Participant, no right to vote or receive dividends or any other rights as a Stockholder shall exist with respect to the Shares, notwithstanding the exercise of the Option. The Company shall issue (or cause to be issued) such stock certificate
promptly after the Option is exercised, subject to the terms of the Award Agreement. 
 The Participant shall enjoy rights as a Stockholder,
subject to his Award Agreement and the Stockholder Agreement, until such time as the Participant disposes of the Shares or the Company and/or its assignee exercises its rights under Section 3.2 of the Stockholder Agreement or Section 2.3
of the Award Agreement. Upon such exercise, the Participant shall have no further rights as a holder of the Shares so purchased except the right to receive payment for the Shares so purchased in accordance with the provisions of the Stockholder
Agreement and/or the Award Agreement, and the Participant shall forthwith cause the certificate(s) evidencing the Shares so purchased to be surrendered to the Company for transfer or cancellation. 
 4. Delivery of Payment. The Participant delivers to the Company with this Exercise Notice payment of the Option Price for the Shares. 

5. Interpretation. Any dispute regarding the interpretation of this Exercise Notice shall be submitted by the Participant or by the Company
forthwith to the Administrator of the Plan, which shall review such dispute at its next regular meeting. The resolution of such a dispute by the Administrator shall be final and binding on all persons. 







 6. Governing Law; Severability. This Exercise Notice shall be governed by and construed in
accordance with the laws of the State of Wisconsin excluding that body of law pertaining to conflicts of law. Should any provision of this Exercise Notice be determined by a court of law to be illegal or unenforceable, the other provisions shall
nevertheless remain effective and shall remain enforceable. 
 7. Notices. Any notice to the Company permitted or required hereunder
shall be given in writing to the Company in care of its then President at its then principal place of business. Any notice to be given to the Participant may be addressed to him at his address as it appears on the payroll or other records of the
Company or any affiliate thereof. Any such notice will be deemed to have been duly given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient,
if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight
courier, specifying next day delivery, with written verification of receipt at the Participant’s or the Company’s address. 
 8.
Further Instruments. The parties agree to execute such further instruments and to take such further action as may be reasonably necessary to carry out the purposes and intent of this agreement. 
  

							
	 Participant:
	 		 	Accepted by:
		 		 	NIMBLEGEN SYSTEMS, INC.
			
	  
	 	By:	  	  

	 Print name:
	 	  
	 	Its:	  	  


  

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 EXHIBIT B 
 FORM OF 
 STOCKHOLDER AGREEMENT 
 WITH 
 NIMBLEGEN SYSTEMS, INC. 
 (Applicable to Shares Purchased By Exercise of Stock Options) 
 This Stockholder Agreement (the “Agreement”) dated as of this      day of             ,
        , is by and between NimbleGen Systems, Inc., a Delaware corporation (the “Company”), and the person whose name appears on the signature page hereof (the “Participant”).

 RECITALS 
 The Company
granted the Participant an option (the “Option”) to purchase shares of the Company’s Common Stock pursuant to its 2000 Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further
amended. The Company and the Participant entered into that certain Award Agreement dated January 30, 2007 (the “Award Agreement”) setting out the terms of such option grant. The Participant has purchased
             shares of the Company’s Common Stock pursuant to the Award Agreement, which, together with all other such shares from time to time purchased by the Participant
pursuant to the Award Agreement, including those shares purchased after the date of this Agreement, are the “Shares” hereunder. 
 The Company made its grant of the Option on certain terms and conditions including the requirement that the Participant and the Company would enter into this Agreement as a condition to the right to exercise the Option. 
 In consideration of the mutual promises herein contained and other good and valuable consideration, the receipt and sufficiency of which is hereby
acknowledged, the parties agree as follows: 
 ARTICLE I 
 DEFINITIONS 
 1.1. Certain Definitions. For purposes of this Agreement, the following
terms shall have the meanings set forth below; all other capitalized terms shall have the meanings set forth elsewhere in this Agreement: 
 “Affiliate” means (i) any person directly or indirectly controlled by a holder of capital stock of the Company, in control of a holder of capital stock of the Company, or under common control with a holder of capital
stock of the Company, (ii) any member, partner, subsidiary, officer, director or stockholder of a person or entity referred to in clause (i), and (iii) any other person or entity directly or indirectly in control of or under the control of
any person or entity referred to in clause (ii). “Controlled,” “controlled by,” and “under common control with” shall 








 
mean direct or indirect possession of the power to direct or cause the direction of management or policies (whether through ownership of voting securities,
by contract or otherwise) of a person; provided, that common control shall be conclusively presumed between or among an individual and members of the immediate family (spouse, siblings, ancestors, descendants or the spouse of any of the foregoing)
of such individual, an individual and a trust primarily for the benefit of such individual, or an immediate family member of such individual. 
 “Common Stock” means shares of the Company’s common stock, $.001 par value. 
 “Permitted
Transfer” has the meaning set forth in Section 2.2. 
 “Restricted Shares” has the meaning given in the Award
Agreement. 
 “Share(s)” has the meaning set forth in the Recitals. 
 “Stockholder” means any person who holds legal title to any issued and outstanding share of the Company’s Common Stock or preferred
stock, and any stock into which any such class of stock is converted or exchanged. 
 “Transfer” or
“Transfers” means, with respect to the Shares, any sale, pledge, hypothecation, gift, devise, distribution, or other disposition of Shares, including, but not limited to, any direct or indirect change in legal or beneficial
ownership effected by any voluntary or involuntary disposition of Shares or by operation of law or by legal or equitable process. 
 “Vested Shares” has the meaning given in the Award Agreement. 
 ARTICLE II 
 RESTRICTIONS ON TRANSFER 
 2.1.
General Restriction. No Transfer of the Shares may be made by the Participant (including, without limitation, an executor or personal representative, guardian, or conservator of the Participant), except pursuant to the terms of the Award
Agreement, this Agreement, and in accordance with the terms of the Bylaws of the Company. Any Transfer of Shares which violates the terms of the Award Agreement or this Agreement shall be voidable by the Company, and neither the Company nor its
transfer agent shall permit such transfer to be made on the stock records of the Company. 
 2.2. Permitted Transfers. The prohibition
of Section 2.1 shall not apply to any Transfer of any interest in the Participant’s Shares, provided however that this Section 2.2 does not apply to Restricted Shares, (i) to his/her spouse or lineal descendant (hereafter
“Immediate Family”) or a trust for the benefit of his/her Immediate Family, provided that the Participant retains the right to vote any Shares so transferred; (ii) upon the Participant’s death; (iii) as the result of any
merger, consolidation, or share exchange involving the Company; (iv) any exchange of existing Shares for other shares of the same or a different class or series in the Company, whether through 

  

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the exercise of conversion rights or otherwise; or (v) to the Company (hereinafter a “Permitted Transfer”). The foregoing notwithstanding, a
Transfer of Shares may not be made to a transferee described in clauses (i) or (ii) of the preceding sentence unless the transferee agrees to be bound by the terms of this Agreement applicable to Vested Shares, and in the case of a
Transfer described in clauses (iii) and (iv), the shares received in exchange for the Shares will remain subject to this Agreement and treated as “Shares” hereunder. 
 ARTICLE III 
 TRANSFER OF STOCK – GENERAL 
 3.1. Third Party Offers. If the Participant receives a bona fide written offer (“Offer”) from a third party to purchase some or all of
the Vested Shares registered in his name and the Participant desires to accept that offer (except for a Permitted Transfer), the Participant shall give written notice to the Company (the “Sale Notice”) of his desire to transfer such Vested
Shares and, in that event, the Company shall have the rights granted herein. 
 3.2. Company Option. The Company shall have an option
to purchase all or any portion of the Vested Shares which are the subject of a Sale Notice at the lesser of the price specified in the Offer or Fair Market Value, as determined under Section 3.5, and on the terms specified in Sections 3.6
and 3.7. The Company shall have thirty (30) days after delivery of the Sale Notice to exercise its option (the “Company Option Period”). This option may be exercised by giving written notice of exercise (the “Exercise
Notice”) to the Participant during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and the Participant to sell the Shares of the Participant identified in the Exercise Notice on the terms
provided in this Article III. 
 3.3. Sale to Third Party. If the Company, after receiving the Sale Notice, fails to exercise its
option as provided in Section 3.2, or if it declines to exercise the same, the Participant shall be entitled to transfer the Vested Shares to the third party on the terms contained in the Offer, and shall be entitled to have his Vested Shares
transferred on the books of the Company, but only if the third party purchaser agrees to be bound by the terms of this Agreement applicable to Vested Shares. If the Participant fails to close the transfer of his Vested Shares within sixty
(60) days after the option of the Company has expired or been waived, the restrictions contained in this Article III shall again apply and must be met prior to effecting any transfer of Vested Shares. Any transfer of Vested Shares by the
Participant to any unaffiliated third party shall comply with all applicable securities laws, and the Company may refuse to transfer any Vested Shares unless it receives such assurance and opinions from legal counsel acceptable to the Company that
any such transfer is in compliance with all applicable securities laws. 
 3.4. Drag-Along Rights. 
 (a) If one or more Stockholders (the “Controlling Stockholder”) wishes to sell all or part of the capital stock of the Company
owned by the Controlling Stockholder that represents fifty percent (50%) or more of all the voting power of all classes of stock of 

  

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the Company then outstanding in one transaction, or a series of related transactions, to a third-party who is not an Affiliate of such Controlling
Stockholder (a “Sale Transaction”), such Controlling Stockholder may, in its sole discretion, require the Participant to sell all or the same proportionate amount of Shares (including Restricted Shares at the Controlling Stockholder’s
option, in which case the Shares to be sold will become Vested Shares) as the Controlling Stockholder in accordance with this Section 3.4 (“Drag-Along Rights”). If the Controlling Stockholder exercises its Drag-Along Rights, the
Participant shall be required to sell his/her Shares or a portion of his/her Shares at a purchase price per Share and upon the same terms as the shares of the Controlling Stockholder. 
 (b) The Controlling Stockholder who desires to exercise its Drag-Along Rights shall deliver a notice to the Participant and the Company
setting forth the terms of the Sale Transaction (including the proposed closing date for the Sale Transaction), and provide all documents required to be executed by the Participant in order to consummate such Sale Transaction. The Participant shall
deliver to the Controlling Stockholder at least seven (7) business days prior to the proposed closing date referred to above all documents and certificates, correctly endorsed and executed, necessary to close the Sale Transaction. If the
Participant fails to deliver such documents to the Controlling Stockholder, the Company shall cause its books and records to show that the Shares held by the Participant have been transferred pursuant to the provisions of this Section 3.4.

 (c) The Controlling Stockholder shall have one hundred twenty (120) days from the date of the notice described in
subsection 3.4(b) above, to consummate any Sale Transaction and, promptly after such consummation, shall notify the Company and the Participant to that effect. The Controlling Stockholder shall also cause to be remitted to the Participant the
proceeds attributable to the sale of the Participant’s Shares not later than three (3) business days after the closing of the Sale Transaction. If any Sale Transaction is not consummated prior to the expiration of the one-hundred twenty
(120) day period referred to in this Section, the Controlling Stockholder may not thereafter consummate the proposed Sale Transaction (without complying again with subsection 3.4(b) above) and shall return to the Participant all documents
previously delivered to the Controlling Stockholder in connection with such Sale Transaction. 
 3.5. Fair Market Value. For purposes
of this Agreement, fair market value shall be determined in good faith by the Board of Directors (the “Fair Market Value”). 
 3.6.
Payment of Purchase Price. In the event of the purchase by the Company of Shares under Section 3.2 of this Agreement, the Company, shall, within thirty (30) days of the delivery to the Participant of the notice that the Company is
exercising the option to purchase Shares, pay the purchase price in cash and shall have the option to evidence that amount of the purchase price that exceeds $10,000 by a promissory note of the Company, dated the day of purchase by the Company (the
“Promissory Note”). The Promissory Note shall be payable in four (4) equal annual installments, commencing on the Closing Date, as defined in Section 3.7, below, with each subsequent installment to be due on the anniversary date
of the Closing Date each year 

  

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thereafter. Interest on the deferred balance of the purchase price shall accrue from the Closing Date at the Annual Mid-Term Federal Rate published by the
Internal Revenue Service as of the end of the month preceding or coincident with the purchase and shall be payable with each installment of principal. The Company shall have the right to prepay the deferred balance at any time, without penalty. All
payments shall be applied first to interest which is accrued and unpaid and then to principal. Any promissory note issued hereunder shall provide that all sums not yet due and payable thereunder shall be and become immediately due and payable upon
any Change in Control (as defined in Section 2(e) of the Plan) of the Company. The parties may, by written agreement, alter or modify the payment schedule provided herein. 
 3.7. Closing. 
 (a)
The closing date (the “Closing Date”) for the purchase of any Shares pursuant to this Article III shall be the date the Shares are endorsed and delivered to the purchaser and the purchaser has tendered to the Participant the consideration
required by this Agreement, including, without limitation, any cash then due and any Promissory Note evidencing the obligations of the purchaser to the Participant. 
 (b) The Closing Date shall occur on the business day designated by the Company, but not later than sixty (60) days following the
delivery of the applicable Exercise Notice described in Section 3.2. The Company and the Participant agree to use best efforts to cause all transactions required to be consummated hereunder to be closed as provided herein and acknowledge that
time is of the essence. 
 ARTICLE IV 
 STOCK LEGEND 
 All certificates representing Shares now owned or hereafter acquired by a party
to this Agreement or their transferee(s) shall bear a legend in substantially the form set forth below: 
 (a) THE SHARES
REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN RESTRICTIONS UPON TRANSFER, MANDATORY SALE UPON THE HAPPENING OF CERTAIN EVENTS, AND VOTING RESTRICTIONS AS SET FORTH IN CERTAIN AGREEMENTS BETWEEN THE ORIGINAL HOLDER OF THE SHARES AND THE
COMPANY, COPIES OF WHICH ARE ON FILE AT THE PRINCIPAL OFFICE OF THE COMPANY. 
 (b) THE SHARES REPRESENTED BY THIS CERTIFICATE
HAVE BEEN ACQUIRED FOR INVESTMENT AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR ANY APPLICABLE STATE SECURITIES LAW. SUCH SHARES MAY NOT BE PLEDGED, SOLD, TRANSFERRED OR HYPOTHECATED IN THE ABSENCE OF SUCH REGISTRATION OR UNLESS
THE COMPANY RECEIVES AN OPINION OF COUNSEL TO THE COMPANY REASONABLY ACCEPTABLE TO IT STATING THAT SUCH PLEDGE, SALE, TRANSFER OR HYPOTHECATION IS EXEMPT FROM THE REGISTRATION REQUIREMENTS OF SAID ACT AND ANY APPLICABLE STATE SECURITIES LAW.

  

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 ARTICLE V 
 MARKET STAND-OFF AGREEMENT 
 The Participant hereby agrees, if so requested by the managing
underwriters or the Company in connection with an initial public offering of the Company’s Common Stock, that, without the prior written consent of such managing underwriters, the Participant will not offer, sell, contract to sell, grant any
option to purchase, make any short sale or otherwise dispose of, assign any legal or beneficial interest in or make a distribution of any capital stock of the Company held by or on behalf of the Participant or beneficially owned by the Participant
in accordance with the rules and regulations of the Securities and Exchange Commission for a period of up to 180 days after the date of the final prospectus relating to the Company’s initial public offering. 
 ARTICLE VI 
 CERTAIN MARITAL
TRANSFERS 
 The creation or existence of any interest in any Shares which interest is acquired or owned by the spouse or former
spouse of any Stockholder as community or marital property during marriage, as a result of property division or other award or Transfer upon dissolution of the marriage, or as a result of any allowance or assignment of property under any applicable
community or marital property law (a “Marital Transfer”) shall be permitted by, and deemed in compliance with, this Agreement; provided, however, that the following conditions are satisfied: (a) the Shares in which such an interest is
created or exists are and continue to be (1) held of record in the name of such Stockholder and (2) managed and controlled by such Stockholder, and (b) the spouse or former spouse shall have executed a spousal consent and
acknowledgement in the form attached to the Award Agreement. At the first such time when either of the conditions in the foregoing provision cease to be satisfied with respect to any Shares, an Offer shall be deemed to have been given with respect
to such Shares. This Article VI shall not apply to a Permitted Transfer of Vested Shares in accordance with Section 2.2, above. 
 ARTICLE VII 
 GENERAL PROVISIONS 
 7.1. Further Assurances. Subject to the terms and conditions herein provided, each party hereto agrees to use its reasonable efforts to take, or cause to be taken, all actions necessary, proper or
advisable, within applicable laws and regulations to consummate and make effective, as soon as practicable, the transactions contemplated by this Agreement. If at any time before or after the date of this Agreement any further action is reasonably
necessary, proper or advisable to carry out the purposes of this Agreement, as soon as reasonably practicable each party hereto shall at the expense of the requesting party take all such reasonably necessary, proper or advisable action to effectuate
such purposes. 
  

 B-6 








 7.2. Governing Law; Jurisdiction. The interpretation and construction of this Agreement and the
resolution of any disputes arising out or of in connection with this Agreement or any breach hereof, shall, unless otherwise expressly provided, be governed by and be construed in accordance with the internal law of the State of Wisconsin without
regard to the conflicts of laws principles thereof. 
 7.3. Remedies. The parties agree that any breach of this Agreement by any party
hereto will cause the other parties hereto irreparable harm and that damages will not constitute an adequate remedy. Accordingly, the parties agree that injunctive relief, including, without limitation, the issuance of a temporary, preliminary or
permanent injunction is an appropriate and proper remedy for any breach hereof, in addition to any award of damages which may be proven. 
 7.4. Notices. Any notice to be given to the Company under the terms of this Agreement shall be given in writing to the Company in care of its President at its then principal place of business. Any notice to be given to the
Participant may be addressed to him at his address as it appears on the payroll or other records of the Company or any affiliate thereof. Any such notice will be deemed to have been duly given: (a) upon personal delivery to the party to be
notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt
requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt at the Participant’s or the Company’s address.

 7.5. Entire Agreement; Amendments. This Agreement, the Award Agreement and the Exercise Notice constitute a complete
statement of all of the arrangements between the parties as of the date hereof with respect to the transactions contemplated hereby, and thereby supersedes all prior agreements and understandings between them with respect thereto and cannot be
changed or terminated orally. 
 7.6. Termination. Sections 2.1, 3.1, 3.2, 3.3, and 3.4 of this Agreement shall terminate and be
of no further force or effect upon the earlier of (a) merger of the Company pursuant to which Stockholders of the Company receive securities of a buyer whose securities are publicly traded; or (b) consummation by the Company of a public
offering of its equity securities pursuant to a registration statement filed with the Securities and Exchange Commission under the Securities Act of 1933. Upon termination of Sections 2.1, 3.1, 3.2, 3.3, and 3.4 of this Agreement, as herein
provided, each Stockholder may deliver the certificates of his or her Shares to the secretary of the Company and have the certificates reissued, without the legend required under this Agreement appropriately modified. 
 7.7. Headings and Defined Terms. The headings in this Agreement are intended solely for convenience of reference and shall be given no effect in
the construction or interpretation of this Agreement. 
  

 B-7 








 7.8. Recitals. The recitals, first stated above, are an integral part of this Agreement and are
incorporated herein. 
 7.9. Successors. This Agreement shall inure to the benefit of, and be binding upon, the parties hereto, their
heirs, successors and assigns. 
 7.10. No Waiver. The failure of a party to insist upon strict adherence to any term of this
Agreement on any occasion shall not be considered a wavier or deprive that party of the right thereafter to insist upon strict adherence to that term or any other term of this Agreement. Any waiver must be in writing. 
 7.11. Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be considered an original, but all of which
together shall constitute the same instrument. 
 7.12. Severability. The invalidity of any provision in this Agreement shall not
affect the validity of any other provision. 
 IN WITNESS WHEREOF, the parties have executed this Agreement on the day and year first
above written. 
  

			
	NIMBLEGEN SYSTEMS, INC.,
	a Delaware corporation (the “Company”)
		
	By:	 	  

	Its:	 	  



  

			
	Participant:
	
	  

	Print name:	 	  



  

 B-8 








 EXHIBIT C 
 INVESTMENT REPRESENTATION STATEMENT 
 PARTICIPANT: 
  

	COMPANY:	NIMBLEGEN SYSTEMS, INC. 

  

	SECURITY:	COMMON STOCK 

 AMOUNT: 
 DATE: 
 In connection with the purchase of the above-listed
shares of Common Stock (the “Securities”), the undersigned director (“Participant”) represents to the Company the following: 
 (a) Participant is aware of the Company’s business affairs and financial condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision to acquire the
Securities. Participant is acquiring these Securities for investment for Participant’s own account only and not with a view to, or for resale in connection with, any “distribution” thereof within the meaning of the Securities Act of
1933, as amended (the “Securities Act”). 
 (b) Participant acknowledges and understands that the Securities
constitute “restricted securities” under the Securities Act and have not been registered under the Securities Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of
Participant’s investment intent as expressed herein. In this connection, Participant understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Participant’s
representation was predicated solely upon a present intention to hold these Securities for the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the
Securities, or for a period of one year or any other fixed period in the future. Participant further understands that the Securities must be held indefinitely unless they are subsequently registered under the Securities Act or an exemption from such
registration is available. Participant further acknowledges and understands that the Company is under no obligation to register the Securities. Participant understands that the certificate evidencing the Securities will be imprinted with a legend
which prohibits the transfer of the Securities unless they are registered or such registration is not required in the opinion of counsel satisfactory to the Company, and any other legend required under applicable state securities laws. 







 (c) Participant is familiar with the provisions of Rule 701 and Rule 144, each
promulgated under the Securities Act, which, in substance, permit limited public resale of “restricted securities” acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to the satisfaction of certain
conditions. Rule 701 provides that if the issuer qualifies under Rule 701 at the time of the grant of the Option to the Participant, the exercise will be exempt from registration under the Securities Act. In the event the Company becomes subject to
the reporting requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, ninety (90) days thereafter (or such longer period as any market stand-off agreement may require) the Securities exempt under Rule 701 may be resold,
subject to the satisfaction of certain of the conditions specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited “broker’s transaction” or in transactions directly with a market maker (as
said term is defined under the Securities Exchange Act of 1934); and, in the case of an affiliate, (2) the availability of certain public information about the Company, (3) the amount of Securities being sold during any three month period
not exceeding the limitations specified in Rule 144(e), and (4) the timely filing of a Form 144, if applicable. 
 In the
event that the Company does not qualify under Rule 701 at the time of grant of the Option, then the Securities may be resold in certain limited circumstances subject to the provisions of Rule 144, which requires the resale to occur not less than one
year after the later of the date the Securities were sold by the Company or the date the Securities were sold by an affiliate of the Company, within the meaning of Rule 144; and, in the case of acquisition of the Securities by an affiliate, or by a
non-affiliate who subsequently holds the Securities less than two years, the satisfaction of the conditions set forth in sections (1), (2), (3) and (4) of the paragraph immediately above. 
 (d) Participant further understands that in the event all of the applicable requirements of Rule 701 or 144 are not satisfied,
registration under the Securities Act, compliance with Regulation A, or some other registration exemption will be required; and that, notwithstanding the fact that Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange
Commission has expressed its opinion that persons proposing to sell private placement securities other than in a registered offering and otherwise than pursuant to Rules 144 or 701 will have a substantial burden of proof in establishing that an
exemption from registration is available for such offers or sales, and that such persons and their respective brokers who participate in such transactions do so at their own risk. Participant understands that no assurances can be given that any such
other registration exemption will be available in such event. 
  

	
	Signature of Participant:
	
	  

	Date:
                                        ,
20    


  

 C-2 








 NIMBLEGEN SYSTEMS, INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of January 30, 2007
(the date of grant), is between NimbleGen Systems, Inc., a Delaware corporation (the “Company”), and Leroy E. Hood (the “Participant”). All terms used herein and not otherwise defined shall have the same meaning as
set forth in the Company’s 2000 Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further amended (the “Plan”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors of the Company (the
“Board”) desires to induce the Participant to provide services to the Company and/or its Subsidiaries as the Chairman of the “Scientific Advisory Committee” of the Board (the “Committee”), to provide the Participant
with a stronger incentive to strive for the continued success and growth of the Company and its Subsidiaries and to further align the Participant’s interests with those of the Company’s stockholders. 
 NOW THEREFORE, in consideration of the benefits that the Company expects to be derived in connection with the services to be hereafter rendered by
the Participant, the Company and the Participant hereby agree as follows: 
 ARTICLE I 
 Award of Option for Restricted Stock 
 1.1. Option; Number of Shares; Option Price. The Participant is granted the right and option to purchase (the “Option”) all or any part of an aggregate of 10,000 shares of the Company’s Common Stock (individually, a
“Share” and jointly, the “Shares”) at the purchase price of $1.74 per Share (the “Option Price”) any time before the tenth anniversary of the date of this Award Agreement. If the Participant exercises the Option prior
to the third anniversary of the date of this Award Agreement, the shares of Common Stock received from the exercise of the Option that are unvested shares according to the schedule set forth in Section 1.2 are hereafter referred to as
“Restricted Shares” and Shares that have vested are referred to as “Vested Shares.” The period during which there are Restricted Shares outstanding is referred to herein as the “Restricted Period.” If the Option remains
outstanding and is exercised on or after the fourth anniversary of the date of this Award Agreement, all of the Shares will be Vested Shares and none of the Shares will be Restricted Shares. 
 1.2. Vesting of Restricted Shares. The vesting schedule for the Shares governed by this Option is as follows. Except as otherwise provided in the
Plan and this Section 1.2, and subject to Section 1.4, the Option will vest as to 1/12th of the Shares on April 1, 2007, and an additional 1/12th of the Shares will vest as of each July 1, October 1, January 1 and
April 1 thereafter, provided that the Participant is still serving as the Chairman of the Committee on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the occurrence of a Change in Control while the
Participant is still serving as the Chairman of the Committee. Shares governed by this Option vest according to this schedule, whether or not the Option has been exercised. 







 1.3. Exercisability of Option. 
 (a) This Option is immediately exercisable and shall expire in accordance with this Section 1.3 and the Plan, but in all events, and
notwithstanding anything herein to the contrary, on the tenth anniversary of the date of this Award Agreement. 
 (b) If the
Participant’s service as the Chairman of the Committee terminates, the Option, to the extent not exercised, shall terminate three (3) months after termination of such service with the Company. 
 1.4. Method of Exercising Option. The Option may be exercised in whole or in part by delivery to the Company, at its offices in Madison,
Wisconsin, of (a) written notice identifying the Option and stating the number of Shares with respect to which it is being exercised, in the form attached hereto as Exhibit A, (b) payment in full of the Option Price of the
Shares then being acquired in the form permitted by Section 8 of the Plan, (c) execution of a stockholder agreement substantially in the form attached hereto as Exhibit B (“Stockholder Agreement”), (d) execution
of an Investment Representation Statement in the form attached hereto as Exhibit C if the Shares covered by the Option have not been registered under the Securities Act of 1933, as amended, at the time of the exercise and (e) if the
Option is exercised during the Restricted Period as defined in Section 1.1, a blank stock power for the Restricted Shares. The Company shall have the right to delay the issue or delivery of any Shares to be delivered hereunder until
(i) the completion of such registration or qualification of such Shares under any federal, state or foreign law, ruling or regulation as the Company shall deem to be necessary or advisable, and (ii) receipt from the Participant of such
documents and information as the Company may deem necessary or appropriate in connection with such registration or qualification or the issuance of Shares hereunder. 
 1.5. Prohibitions Against Transfer. The Option, and the rights and privileges conferred hereby, may not be transferred, assigned, pledged or hypothecated in any way (whether by operation of law or otherwise) by
the Participant, or be subject to execution, attachment or similar process, and shall be exercisable only by the Participant, except as provided in Section 12 of the Plan. 
 ARTICLE II 
 Provisions Governing Restricted Shares 
 2.1. Stockholder Status. Prior to the vesting of the Restricted Shares, the Participant shall not have the right to vote the Restricted Shares,
and instead, the Restricted Shares shall be voted as directed by action of the Board. The Participant agrees to execute a proxy upon request of the Board at any time during the Restricted Period appointing an agent designated by the Board to vote
the Restricted Shares. The Participant shall have the right to receive and retain all regular cash dividends paid or distributed in respect of the Restricted Shares, if any, and except as expressly provided otherwise herein, shall have all other
rights as a holder of outstanding 

  

 2 








 
shares of Common Stock. Until all of the Restricted Shares vest pursuant to Section 1.2, the Company shall retain custody of the stock certificates
representing the Shares unless the Participant requests in writing that the Company issue a certificate for any portion that represents Vested Shares to the Participant. As soon as practicable after the lapse of the restrictions, the Company shall
issue or release or cause to be issued or released certificate(s) representing the Shares. 
 2.2. Prohibition Against Transfer.
Restricted Shares may not be transferred, assigned, pledged or hypothecated in any way (whether by operation of law or otherwise) by the Participant, or be subject to execution, attachment or similar process. Notwithstanding the foregoing,
Restricted Shares may be transferred as the result of any merger, consolidation, or share exchange involving the Company, in which event the shares received in exchange for the Shares will remain subject to this Award Agreement and treated as
“Restricted Shares” hereunder. Any transfer in violation of this Section 2.2 shall be void and of no further effect. After the Restricted Shares vest, they shall continue to be subject to the limitations on transfer contained in the
Stockholder Agreement. 
 2.3. Repurchase of Restricted Shares. If the Participant’s service as a director of the Company
terminates for any reason, the Company shall have the right, but not the obligation, to purchase all or any portion of the Restricted Shares owned by the Participant. Such option shall be exercisable by the Company within six (6) months
following the date of such termination of such service by the Participant by delivery of a written notice to the Participant. The Company may assign its rights under this Section 2.3 to the stockholders of the Company (other than the
Participant), at any time, on a pro rata basis. The purchase price per share of all purchases under this Section 2.3 of Restricted Shares shall be the Option Price. 
 2.4. Payment of Purchase Price. In the event of the purchase by the Company of Shares under Section 2.3, above, the Company, shall, within thirty (30) days of the delivery to the Participant of the
notice that the Company is exercising the option to purchase Shares, pay the purchase price in cash and shall have the option to evidence that amount of the purchase price that exceeds $10,000 by a promissory note of the Company, dated the day of
purchase by the Company (the “Promissory Note”). The Promissory Note shall be payable in four (4) equal annual installments, commencing on the Closing Date, as defined in Section 2.5, below, with each subsequent installment to be
due on the anniversary date of the Closing Date each year thereafter. Interest on the deferred balance of the purchase price shall accrue from the Closing Date at the Annual Mid-Term Federal Rate published by the Internal Revenue Service as of the
end of the month preceding or coincident with the purchase and shall be payable with each installment of principal. The Company shall have the right to prepay the deferred balance at any time, without penalty. All payments shall be applied first to
interest which is accrued and unpaid and then to principal. Any promissory note issued hereunder shall provide that all sums not yet due and payable thereunder shall be and become immediately due and payable upon any Change in Control. The parties
may, by written agreement, alter or modify the payment schedule provided herein. 
 2.5. Closing Date. The closing date (the
“Closing Date”) for the purchase of any Shares pursuant to Section 2.3, above, shall be the date the Shares are endorsed and delivered to 

  

 3 








 
the Company and the Company has tendered to the Participant the consideration required by this Award Agreement, including, without limitation, any cash then
due and any Promissory Note evidencing the obligations of the Company to the Participant. The Closing Date shall occur on the business day designated by the Company, but not later than seven (7) months after the Participant’s termination
of service as a director of the Company. The Participant agrees to use best efforts to cause all transactions required to be consummated hereunder to be closed as provided herein and acknowledges that time is of the essence. 
 ARTICLE III 
 Miscellaneous

 3.1. Provisions of the Plan Control. This Award Agreement shall be governed by the provisions of the Plan, the terms and
conditions of which are incorporated herein by reference. In the event that the provisions of this Award Agreement and the Plan conflict, the Plan shall control. The Plan empowers the Administrator to make interpretations, rules and regulations
thereunder, and, in general, provides that determinations of the Administrator with respect to the Plan shall be binding upon the Participant. A copy of the Plan will be delivered to the Participant upon reasonable request. 
 3.2. Taxes. The Company may require payment or reimbursement of or may withhold any tax that it believes is required as a result of the exercise
of the Option or issuance of shares, and the Company may defer making delivery with respect to Shares for which the Option was exercised or with respect to Vested Shares which previously had been Restricted Shares until arrangements satisfactory to
the Company have been made with respect to such withholding obligations. 
 3.3. Tax Consequences. The Participant understands that
the Participant may suffer adverse tax consequences as a result of the Participant’s purchase or disposition of the Shares. The Participant represents that the Participant will consult with any tax consultants the Participant deems advisable in
connection with the purchase and disposition of the Shares. 
 3.4. Notices. Any notice to be given to the Company under the terms of
this Award Agreement shall be given in writing to the Company in care of its then principal executive officer at its then principal place of business. Any notice to be given to the Participant may be addressed to him at his address as it appears on
the payroll or other records of the Company or any affiliate thereof. Any such notice will be deemed to have been duly given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during
normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit
with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt at the Participant’s or the Company’s address. 
 3.5. Governing Law. This Award Agreement and all questions arising hereunder or in connection herewith shall be determined in accordance with the
laws of the State of Wisconsin, without giving effect to the principles of conflicts of laws. 
  

 4 








 3.6. No Right to Continued Service. This Award Agreement shall not confer upon the Participant any
right with respect to continuation of service on the Board or any committee thereof, including the Committee, nor shall it interfere in any way with the right of the Company to terminate the Participant’s service on the Board or any committee
thereof, including the Committee, at any time. 
 3.7. Multiple Copies. One or more copies of this Award Agreement may be executed,
each of which will be deemed an original, but all of which together will constitute one and the same agreement. 
 IN WITNESS WHEREOF,
the Company has caused this Award Agreement to be executed as of the date and year first above written, which is the date of the granting of the Option evidenced hereby. 
  

			
	NIMBLEGEN SYSTEMS, INC.
		
	By:	 	 /s/ Thomas M. Palay

		 	Thomas M. Palay,
		 	Vice-Chairman of the Board of Directors and Vice President


 The undersigned Participant hereby accepts the foregoing Option and agrees to the several
terms and conditions hereof and of the Plan. 
  

	
	 Participant:

	
	 /s/ Leroy E. Hood

	Leroy E. Hood


  

 5 








 Spousal Consent and Acknowledgment 
 I acknowledge that I have read the Award Agreement and the Stockholder Agreement, attached thereto as Exhibit B, and that I understand their
contents. I am aware that by their provisions my spouse agrees, among other things, to limit the transferability of and the voting rights attendant upon his or her Shares of NimbleGen Systems, Inc. which may be acquired through his or her exercise
of an Option. I am further aware that the terms and limitations set forth in such agreements shall apply to any interest I have in the Option or the Shares (including without limitation any right or interest by operation of the Wisconsin Marital
Property Law, chapter 766 of the Wisconsin Statutes, or by operation of any other law) and the interest of any of my heirs, legatees, or other transferees. I consent to and approve the provisions of the Award Agreement and the Stockholder Agreement,
and agree that the Option and the Shares and my interest in them are subject to the provisions of such Agreements, and direct the personal representative of my estate to promptly comply with all of the provisions of such Agreements. I further agree
that I will take no action at any time to hinder the operation of the Award Agreement or the Stockholder Agreement as to the Option and/or the Shares or any interest that I or my transferees have in them. 
  

							
	 Date:
	 	_______________________	  	Spouse:	 	  









 EXHIBIT A 
 NIMBLEGEN SYSTEMS INC. 2000 STOCK OPTION 
 AND RESTRICTED STOCK PLAN 
 EXERCISE NOTICE 
 1. Exercise of
Option. Effective as of today,
                                        ,
20    , the undersigned (the “Participant”) hereby elects to exercise the Participant’s option to purchase
                     shares of the Common Stock (the “Shares”) of NimbleGen Systems, Inc. (the “Company”) under and
pursuant to the Company’s 2000 Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further amended (the “Plan”), and the Award Agreement dated as of January 30, 2007 (the
“Award Agreement”). All terms used herein and not otherwise defined shall have the meaning set forth in the Plan, the Award Agreement, or in the form of stockholder agreement that is attached to the Award Agreement as Exhibit B (the
“Stockholder Agreement”). 
 2. Representations of the Participant. The Participant acknowledges that the Participant has
received, read and understands the Plan, the Award Agreement, and the Stockholder Agreement and agrees to abide by and be bound by their terms and conditions. 
 3. Rights as Stockholder. Until the stock certificate evidencing such Shares is issued (as evidenced by the appropriate entry on the books of the Company or of a duly authorized transfer agent of the Company)
and the Stockholder Agreement is executed by the Participant, no right to vote or receive dividends or any other rights as a Stockholder shall exist with respect to the Shares, notwithstanding the exercise of the Option. The Company shall issue (or
cause to be issued) such stock certificate promptly after the Option is exercised, subject to the terms of the Award Agreement. 
 The
Participant shall enjoy rights as a Stockholder, subject to his Award Agreement and the Stockholder Agreement, until such time as the Participant disposes of the Shares or the Company and/or its assignee exercises its rights under Section 3.2
of the Stockholder Agreement or Section 2.3 of the Award Agreement. Upon such exercise, the Participant shall have no further rights as a holder of the Shares so purchased except the right to receive payment for the Shares so purchased in
accordance with the provisions of the Stockholder Agreement and/or the Award Agreement, and the Participant shall forthwith cause the certificate(s) evidencing the Shares so purchased to be surrendered to the Company for transfer or cancellation.

 4. Delivery of Payment. The Participant delivers to the Company with this Exercise Notice payment of the Option Price for the
Shares. 
 5. Interpretation. Any dispute regarding the interpretation of this Exercise Notice shall be submitted by the Participant
or by the Company forthwith to the Administrator of the Plan, which shall review such dispute at its next regular meeting. The resolution of such a dispute by the Administrator shall be final and binding on all persons. 







 6. Governing Law; Severability. This Exercise Notice shall be governed by and construed in
accordance with the laws of the State of Wisconsin excluding that body of law pertaining to conflicts of law. Should any provision of this Exercise Notice be determined by a court of law to be illegal or unenforceable, the other provisions shall
nevertheless remain effective and shall remain enforceable. 
 7. Notices. Any notice to the Company permitted or required hereunder
shall be given in writing to the Company in care of its then President at its then principal place of business. Any notice to be given to the Participant may be addressed to him at his address as it appears on the payroll or other records of the
Company or any affiliate thereof. Any such notice will be deemed to have been duly given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient,
if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight
courier, specifying next day delivery, with written verification of receipt at the Participant’s or the Company’s address. 
 8.
Further Instruments. The parties agree to execute such further instruments and to take such further action as may be reasonably necessary to carry out the purposes and intent of this agreement. 
  

									
	Participant:	 	 	 	 	 	Accepted by:
		 		 		 	NIMBLEGEN SYSTEMS, INC.
			
	  
	 	By:	 	  

	Print name:	 		 	  
	 	Its:	 	  


  

 A-2 








 EXHIBIT B 
 FORM OF 
 STOCKHOLDER AGREEMENT 
 WITH 
 NIMBLEGEN SYSTEMS, INC. 
 (Applicable to Shares Purchased By Exercise of Stock Options) 
 This Stockholder Agreement (the “Agreement”) dated as of this              day of
            ,             , is by and between NimbleGen Systems, Inc., a Delaware corporation (the
“Company”), and the person whose name appears on the signature page hereof (the “Participant”). 
 RECITALS

 The Company granted the Participant an option (the “Option”) to purchase shares of the Company’s Common Stock pursuant
to its 2000 Stock Option and Restricted Stock Plan, as amended and restated as of September 25, 2001 and as further amended. The Company and the Participant entered into that certain Award Agreement dated January 30, 2007 (the “Award
Agreement”) setting out the terms of such option grant. The Participant has purchased              shares of the Company’s Common Stock pursuant to the Award Agreement,
which, together with all other such shares from time to time purchased by the Participant pursuant to the Award Agreement, including those shares purchased after the date of this Agreement, are the “Shares” hereunder. 
 The Company made its grant of the Option on certain terms and conditions including the requirement that the Participant and the Company would enter into
this Agreement as a condition to the right to exercise the Option. 
 In consideration of the mutual promises herein contained and other good
and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, the parties agree as follows: 
 ARTICLE I

 DEFINITIONS 
 1.1. Certain Definitions. For purposes of this Agreement, the following terms shall have the meanings set forth below; all other capitalized terms shall have the meanings set forth elsewhere in this Agreement: 
 “Affiliate” means (i) any person directly or indirectly controlled by a holder of capital stock of the Company, in control of a
holder of capital stock of the Company, or under common control with a holder of capital stock of the Company, (ii) any member, partner, subsidiary, officer, director or stockholder of a person or entity referred to in clause (i), and
(iii) any other person or entity directly or indirectly in control of or under the control of any person or entity referred to in clause (ii). “Controlled,” “controlled by,” and “under common control with” shall









 
mean direct or indirect possession of the power to direct or cause the direction of management or policies (whether through ownership of voting securities,
by contract or otherwise) of a person; provided, that common control shall be conclusively presumed between or among an individual and members of the immediate family (spouse, siblings, ancestors, descendants or the spouse of any of the foregoing)
of such individual, an individual and a trust primarily for the benefit of such individual, or an immediate family member of such individual. 
 “Common Stock” means shares of the Company’s common stock, $.001 par value. 
 “Permitted
Transfer” has the meaning set forth in Section 2.2. 
 “Restricted Shares” has the meaning given in the Award
Agreement. 
 “Share(s)” has the meaning set forth in the Recitals. 
 “Stockholder” means any person who holds legal title to any issued and outstanding share of the Company’s Common Stock or preferred
stock, and any stock into which any such class of stock is converted or exchanged. 
 “Transfer” or
“Transfers” means, with respect to the Shares, any sale, pledge, hypothecation, gift, devise, distribution, or other disposition of Shares, including, but not limited to, any direct or indirect change in legal or beneficial
ownership effected by any voluntary or involuntary disposition of Shares or by operation of law or by legal or equitable process. 
 “Vested Shares” has the meaning given in the Award Agreement. 
 ARTICLE II 
 RESTRICTIONS ON TRANSFER 
 2.1.
General Restriction. No Transfer of the Shares may be made by the Participant (including, without limitation, an executor or personal representative, guardian, or conservator of the Participant), except pursuant to the terms of the Award
Agreement, this Agreement, and in accordance with the terms of the Bylaws of the Company. Any Transfer of Shares which violates the terms of the Award Agreement or this Agreement shall be voidable by the Company, and neither the Company nor its
transfer agent shall permit such transfer to be made on the stock records of the Company. 
 2.2. Permitted Transfers. The prohibition
of Section 2.1 shall not apply to any Transfer of any interest in the Participant’s Shares, provided however that this Section 2.2 does not apply to Restricted Shares, (i) to his/her spouse or lineal descendant (hereafter
“Immediate Family”) or a trust for the benefit of his/her Immediate Family, provided that the Participant retains the right to vote any Shares so transferred; (ii) upon the Participant’s death; (iii) as the result of any
merger, consolidation, or share exchange involving the Company; (iv) any exchange of existing Shares for other shares of the same or a different class or series in the Company, whether through 

  

 B-2 








 
the exercise of conversion rights or otherwise; or (v) to the Company (hereinafter a “Permitted Transfer”). The foregoing notwithstanding, a
Transfer of Shares may not be made to a transferee described in clauses (i) or (ii) of the preceding sentence unless the transferee agrees to be bound by the terms of this Agreement applicable to Vested Shares, and in the case of a
Transfer described in clauses (iii) and (iv), the shares received in exchange for the Shares will remain subject to this Agreement and treated as “Shares” hereunder. 
 ARTICLE III 
 TRANSFER OF STOCK – GENERAL 
 3.1. Third Party Offers. If the Participant receives a bona fide written offer (“Offer”) from a third party to purchase some or all of
the Vested Shares registered in his name and the Participant desires to accept that offer (except for a Permitted Transfer), the Participant shall give written notice to the Company (the “Sale Notice”) of his desire to transfer such Vested
Shares and, in that event, the Company shall have the rights granted herein. 
 3.2. Company Option. The Company shall have an option
to purchase all or any portion of the Vested Shares which are the subject of a Sale Notice at the lesser of the price specified in the Offer or Fair Market Value, as determined under Section 3.5, and on the terms specified in Sections 3.6
and 3.7. The Company shall have thirty (30) days after delivery of the Sale Notice to exercise its option (the “Company Option Period”). This option may be exercised by giving written notice of exercise (the “Exercise
Notice”) to the Participant during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and the Participant to sell the Shares of the Participant identified in the Exercise Notice on the terms
provided in this Article III. 
 3.3. Sale to Third Party. If the Company, after receiving the Sale Notice, fails to exercise its
option as provided in Section 3.2, or if it declines to exercise the same, the Participant shall be entitled to transfer the Vested Shares to the third party on the terms contained in the Offer, and shall be entitled to have his Vested Shares
transferred on the books of the Company, but only if the third party purchaser agrees to be bound by the terms of this Agreement applicable to Vested Shares. If the Participant fails to close the transfer of his Vested Shares within sixty
(60) days after the option of the Company has expired or been waived, the restrictions contained in this Article III shall again apply and must be met prior to effecting any transfer of Vested Shares. Any transfer of Vested Shares by the
Participant to any unaffiliated third party shall comply with all applicable securities laws, and the Company may refuse to transfer any Vested Shares unless it receives such assurance and opinions from legal counsel acceptable to the Company that
any such transfer is in compliance with all applicable securities laws. 
 3.4. Drag-Along Rights. 
 (a) If one or more Stockholders (the “Controlling Stockholder”) wishes to sell all or part of the capital stock of the Company
owned by the Controlling Stockholder that represents fifty percent (50%) or more of all the voting power of all classes of stock of 

  

 B-3 








 
the Company then outstanding in one transaction, or a series of related transactions, to a third-party who is not an Affiliate of such Controlling
Stockholder (a “Sale Transaction”), such Controlling Stockholder may, in its sole discretion, require the Participant to sell all or the same proportionate amount of Shares (including Restricted Shares at the Controlling Stockholder’s
option, in which case the Shares to be sold will become Vested Shares) as the Controlling Stockholder in accordance with this Section 3.4 (“Drag-Along Rights”). If the Controlling Stockholder exercises its Drag-Along Rights, the
Participant shall be required to sell his/her Shares or a portion of his/her Shares at a purchase price per Share and upon the same terms as the shares of the Controlling Stockholder. 
 (b) The Controlling Stockholder who desires to exercise its Drag-Along Rights shall deliver a notice to the Participant and the Company
setting forth the terms of the Sale Transaction (including the proposed closing date for the Sale Transaction), and provide all documents required to be executed by the Participant in order to consummate such Sale Transaction. The Participant shall
deliver to the Controlling Stockholder at least seven (7) business days prior to the proposed closing date referred to above all documents and certificates, correctly endorsed and executed, necessary to close the Sale Transaction. If the
Participant fails to deliver such documents to the Controlling Stockholder, the Company shall cause its books and records to show that the Shares held by the Participant have been transferred pursuant to the provisions of this Section 3.4.

 (c) The Controlling Stockholder shall have one hundred twenty (120) days from the date of the notice described in
subsection 3.4(b) above, to consummate any Sale Transaction and, promptly after such consummation, shall notify the Company and the Participant to that effect. The Controlling Stockholder shall also cause to be remitted to the Participant the
proceeds attributable to the sale of the Participant’s Shares not later than three (3) business days after the closing of the Sale Transaction. If any Sale Transaction is not consummated prior to the expiration of the one-hundred twenty
(120) day period referred to in this Section, the Controlling Stockholder may not thereafter consummate the proposed Sale Transaction (without complying again with subsection 3.4(b) above) and shall return to the Participant all documents
previously delivered to the Controlling Stockholder in connection with such Sale Transaction. 
 3.5. Fair Market Value. For purposes
of this Agreement, fair market value shall be determined in good faith by the Board of Directors (the “Fair Market Value”). 
 3.6.
Payment of Purchase Price. In the event of the purchase by the Company of Shares under Section 3.2 of this Agreement, the Company, shall, within thirty (30) days of the delivery to the Participant of the notice that the Company is
exercising the option to purchase Shares, pay the purchase price in cash and shall have the option to evidence that amount of the purchase price that exceeds $10,000 by a promissory note of the Company, dated the day of purchase by the Company (the
“Promissory Note”). The Promissory Note shall be payable in four (4) equal annual installments, commencing on the Closing Date, as defined in Section 3.7, below, with each subsequent installment to be due on the anniversary date
of the Closing Date each year 

  

 B-4 








 
thereafter. Interest on the deferred balance of the purchase price shall accrue from the Closing Date at the Annual Mid-Term Federal Rate published by the
Internal Revenue Service as of the end of the month preceding or coincident with the purchase and shall be payable with each installment of principal. The Company shall have the right to prepay the deferred balance at any time, without penalty. All
payments shall be applied first to interest which is accrued and unpaid and then to principal. Any promissory note issued hereunder shall provide that all sums not yet due and payable thereunder shall be and become immediately due and payable upon
any Change in Control (as defined in Section 2(e) of the Plan) of the Company. The parties may, by written agreement, alter or modify the payment schedule provided herein. 
 3.7. Closing. 
 (a)
The closing date (the “Closing Date”) for the purchase of any Shares pursuant to this Article III shall be the date the Shares are endorsed and delivered to the purchaser and the purchaser has tendered to the Participant the consideration
required by this Agreement, including, without limitation, any cash then due and any Promissory Note evidencing the obligations of the purchaser to the Participant. 
 (b) The Closing Date shall occur on the business day designated by the Company, but not later than sixty (60) days following the
delivery of the applicable Exercise Notice described in Section 3.2. The Company and the Participant agree to use best efforts to cause all transactions required to be consummated hereunder to be closed as provided herein and acknowledge that
time is of the essence. 
 ARTICLE IV 
 STOCK LEGEND 
 All certificates representing Shares now owned or hereafter acquired by a party
to this Agreement or their transferee(s) shall bear a legend in substantially the form set forth below: 
 (a) THE SHARES
REPRESENTED BY THIS CERTIFICATE ARE SUBJECT TO CERTAIN RESTRICTIONS UPON TRANSFER, MANDATORY SALE UPON THE HAPPENING OF CERTAIN EVENTS, AND VOTING RESTRICTIONS AS SET FORTH IN CERTAIN AGREEMENTS BETWEEN THE ORIGINAL HOLDER OF THE SHARES AND THE
COMPANY, COPIES OF WHICH ARE ON FILE AT THE PRINCIPAL OFFICE OF THE COMPANY. 
 (b) THE SHARES REPRESENTED BY THIS CERTIFICATE
HAVE BEEN ACQUIRED FOR INVESTMENT AND HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933 OR ANY APPLICABLE STATE SECURITIES LAW. SUCH SHARES MAY NOT BE PLEDGED, SOLD, TRANSFERRED OR HYPOTHECATED IN THE ABSENCE OF SUCH REGISTRATION OR UNLESS
THE COMPANY RECEIVES AN OPINION OF COUNSEL TO THE COMPANY REASONABLY ACCEPTABLE TO IT STATING THAT SUCH PLEDGE, SALE, TRANSFER OR HYPOTHECATION IS EXEMPT FROM THE REGISTRATION REQUIREMENTS OF SAID ACT AND ANY APPLICABLE STATE SECURITIES LAW.

  

 B-5 








 ARTICLE V 
 MARKET STAND-OFF AGREEMENT 
 The Participant hereby agrees, if so requested by the managing
underwriters or the Company in connection with an initial public offering of the Company’s Common Stock, that, without the prior written consent of such managing underwriters, the Participant will not offer, sell, contract to sell, grant any
option to purchase, make any short sale or otherwise dispose of, assign any legal or beneficial interest in or make a distribution of any capital stock of the Company held by or on behalf of the Participant or beneficially owned by the Participant
in accordance with the rules and regulations of the Securities and Exchange Commission for a period of up to 180 days after the date of the final prospectus relating to the Company’s initial public offering. 
 ARTICLE VI 
 CERTAIN MARITAL
TRANSFERS 
 The creation or existence of any interest in any Shares which interest is acquired or owned by the spouse or former
spouse of any Stockholder as community or marital property during marriage, as a result of property division or other award or Transfer upon dissolution of the marriage, or as a result of any allowance or assignment of property under any applicable
community or marital property law (a “Marital Transfer”) shall be permitted by, and deemed in compliance with, this Agreement; provided, however, that the following conditions are satisfied: (a) the Shares in which such an interest is
created or exists are and continue to be (1) held of record in the name of such Stockholder and (2) managed and controlled by such Stockholder, and (b) the spouse or former spouse shall have executed a spousal consent and
acknowledgement in the form attached to the Award Agreement. At the first such time when either of the conditions in the foregoing provision cease to be satisfied with respect to any Shares, an Offer shall be deemed to have been given with respect
to such Shares. This Article VI shall not apply to a Permitted Transfer of Vested Shares in accordance with Section 2.2, above. 
 ARTICLE VII 
 GENERAL PROVISIONS 
 7.1. Further Assurances. Subject to the terms and conditions herein provided, each party hereto agrees to use its reasonable efforts to take, or cause to be taken, all actions necessary, proper or
advisable, within applicable laws and regulations to consummate and make effective, as soon as practicable, the transactions contemplated by this Agreement. If at any time before or after the date of this Agreement any further action is reasonably
necessary, proper or advisable to carry out the purposes of this Agreement, as soon as reasonably practicable each party hereto shall at the expense of the requesting party take all such reasonably necessary, proper or advisable action to effectuate
such purposes. 
  

 B-6 








 7.2. Governing Law; Jurisdiction. The interpretation and construction of this Agreement and the
resolution of any disputes arising out or of in connection with this Agreement or any breach hereof, shall, unless otherwise expressly provided, be governed by and be construed in accordance with the internal law of the State of Wisconsin without
regard to the conflicts of laws principles thereof. 
 7.3. Remedies. The parties agree that any breach of this Agreement by any party
hereto will cause the other parties hereto irreparable harm and that damages will not constitute an adequate remedy. Accordingly, the parties agree that injunctive relief, including, without limitation, the issuance of a temporary, preliminary or
permanent injunction is an appropriate and proper remedy for any breach hereof, in addition to any award of damages which may be proven. 
 7.4. Notices. Any notice to be given to the Company under the terms of this Agreement shall be given in writing to the Company in care of its President at its then principal place of business. Any notice to be given to the
Participant may be addressed to him at his address as it appears on the payroll or other records of the Company or any affiliate thereof. Any such notice will be deemed to have been duly given: (a) upon personal delivery to the party to be
notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five (5) days after having been sent by registered or certified mail, return receipt
requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written verification of receipt at the Participant’s or the Company’s address.

 7.5. Entire Agreement; Amendments. This Agreement, the Award Agreement and the Exercise Notice constitute a complete
statement of all of the arrangements between the parties as of the date hereof with respect to the transactions contemplated hereby, and thereby supersedes all prior agreements and understandings between them with respect thereto and cannot be
changed or terminated orally. 
 7.6. Termination. Sections 2.1, 3.1, 3.2, 3.3, and 3.4 of this Agreement shall terminate and be
of no further force or effect upon the earlier of (a) merger of the Company pursuant to which Stockholders of the Company receive securities of a buyer whose securities are publicly traded; or (b) consummation by the Company of a public
offering of its equity securities pursuant to a registration statement filed with the Securities and Exchange Commission under the Securities Act of 1933. Upon termination of Sections 2.1, 3.1, 3.2, 3.3, and 3.4 of this Agreement, as herein
provided, each Stockholder may deliver the certificates of his or her Shares to the secretary of the Company and have the certificates reissued, without the legend required under this Agreement appropriately modified. 
 7.7. Headings and Defined Terms. The headings in this Agreement are intended solely for convenience of reference and shall be given no effect in
the construction or interpretation of this Agreement. 
  

 B-7 








 7.8. Recitals. The recitals, first stated above, are an integral part of this Agreement and are
incorporated herein. 
 7.9. Successors. This Agreement shall inure to the benefit of, and be binding upon, the parties hereto, their
heirs, successors and assigns. 
 7.10. No Waiver. The failure of a party to insist upon strict adherence to any term of this
Agreement on any occasion shall not be considered a wavier or deprive that party of the right thereafter to insist upon strict adherence to that term or any other term of this Agreement. Any waiver must be in writing. 
 7.11. Counterparts. This Agreement may be executed in two or more counterparts, each of which shall be considered an original, but all of which
together shall constitute the same instrument. 
 7.12. Severability. The invalidity of any provision in this Agreement shall not
affect the validity of any other provision. 
 IN WITNESS WHEREOF, the parties have executed this Agreement on the day and year first
above written. 
  

			
	 NIMBLEGEN SYSTEMS, INC.,

	 a Delaware corporation (the “Company”)

		
	By:	 	  

	Its:	 	  

	
	Participant:
	
	  

	Print name:	 	  



  

 B-8 








 EXHIBIT C 
 INVESTMENT REPRESENTATION STATEMENT 
  

			
	 PARTICIPANT:
	  	
		
	 COMPANY:
	  	NIMBLEGEN SYSTEMS, INC.
		
	 SECURITY:
	  	COMMON STOCK
		
	 AMOUNT:
	  	
		
	 DATE:
	  	

 In connection with the purchase of the above-listed shares of Common Stock (the
“Securities”), the undersigned director (“Participant”) represents to the Company the following: 
 (a)
Participant is aware of the Company’s business affairs and financial condition and has acquired sufficient information about the Company to reach an informed and knowledgeable decision to acquire the Securities. Participant is acquiring these
Securities for investment for Participant’s own account only and not with a view to, or for resale in connection with, any “distribution” thereof within the meaning of the Securities Act of 1933, as amended (the “Securities
Act”). 
 (b) Participant acknowledges and understands that the Securities constitute “restricted securities”
under the Securities Act and have not been registered under the Securities Act in reliance upon a specific exemption therefrom, which exemption depends upon, among other things, the bona fide nature of Participant’s investment intent as
expressed herein. In this connection, Participant understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Participant’s representation was predicated solely upon a
present intention to hold these Securities for the minimum capital gains period specified under tax statutes, for a deferred sale, for or until an increase or decrease in the market price of the Securities, or for a period of one year or any other
fixed period in the future. Participant further understands that the Securities must be held indefinitely unless they are subsequently registered under the Securities Act or an exemption from such registration is available. Participant further
acknowledges and understands that the Company is under no obligation to register the Securities. Participant understands that the certificate evidencing the Securities will be imprinted with a legend which prohibits the transfer of the Securities
unless they are registered or such registration is not required in the opinion of counsel satisfactory to the Company, and any other legend required under applicable state securities laws. 







 (c) Participant is familiar with the provisions of Rule 701 and Rule 144, each
promulgated under the Securities Act, which, in substance, permit limited public resale of “restricted securities” acquired, directly or indirectly from the issuer thereof, in a non-public offering subject to the satisfaction of certain
conditions. Rule 701 provides that if the issuer qualifies under Rule 701 at the time of the grant of the Option to the Participant, the exercise will be exempt from registration under the Securities Act. In the event the Company becomes subject to
the reporting requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, ninety (90) days thereafter (or such longer period as any market stand-off agreement may require) the Securities exempt under Rule 701 may be resold,
subject to the satisfaction of certain of the conditions specified by Rule 144, including: (1) the resale being made through a broker in an unsolicited “broker’s transaction” or in transactions directly with a market maker (as
said term is defined under the Securities Exchange Act of 1934); and, in the case of an affiliate, (2) the availability of certain public information about the Company, (3) the amount of Securities being sold during any three month period
not exceeding the limitations specified in Rule 144(e), and (4) the timely filing of a Form 144, if applicable. 
 In the
event that the Company does not qualify under Rule 701 at the time of grant of the Option, then the Securities may be resold in certain limited circumstances subject to the provisions of Rule 144, which requires the resale to occur not less than one
year after the later of the date the Securities were sold by the Company or the date the Securities were sold by an affiliate of the Company, within the meaning of Rule 144; and, in the case of acquisition of the Securities by an affiliate, or by a
non-affiliate who subsequently holds the Securities less than two years, the satisfaction of the conditions set forth in sections (1), (2), (3) and (4) of the paragraph immediately above. 
 (d) Participant further understands that in the event all of the applicable requirements of Rule 701 or 144 are not satisfied,
registration under the Securities Act, compliance with Regulation A, or some other registration exemption will be required; and that, notwithstanding the fact that Rules 144 and 701 are not exclusive, the Staff of the Securities and Exchange
Commission has expressed its opinion that persons proposing to sell private placement securities other than in a registered offering and otherwise than pursuant to Rules 144 or 701 will have a substantial burden of proof in establishing that an
exemption from registration is available for such offers or sales, and that such persons and their respective brokers who participate in such transactions do so at their own risk. Participant understands that no assurances can be given that any such
other registration exemption will be available in such event. 
  

	
	 Signature of Participant:

	
	  

	 Date:
                                        ,
20    



  

 C-2 








 NIMBLEGEN SYSTEMS, INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of January 30,
2007, is between NimbleGen Systems, Inc., a Delaware corporation (the “Company”), and Leroy E. Hood (“Director”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors of the Company (the “Board”)
desires to induce Director to provide services to the Company as a director of the Company and as the Chairman of the “Scientific Advisory Committee” of the Board and to provide Director with a stronger incentive to strive for the
continued success and growth of the Company and its subsidiaries. 
 NOW THEREFORE, in consideration of the benefits that the Company
expects to be derived in connection with the services to be hereafter rendered by Director, the Company and Director hereby agree as follows: 
 ARTICLE I 
 Certain Definitions 
 1.1. “Account” shall mean a bookkeeping account being administered for the benefit of Director under this Agreement, as described in
Section 2.1. 
 1.2. “Award (director)” shall mean the amount of compensation credited to a subaccount of
Director’s Account from time to time in accordance with this Award Agreement. Subject to vesting and adjustment as described in Article III, the Award shall be Fourteen Thousand Seven Hundred Fifty and 00/100 Dollars ($14,750). 
 1.3. “Award (Committee chair)” shall mean the amount of compensation credited to a subaccount of Director’s Account from time to
time in accordance with this Award Agreement. Subject to vesting and adjustment as described in Article IV, the Award shall be Five Thousand Nine Hundred and 00/100 Dollars ($5,900). 
 1.4. “Award Units (director)” shall mean the number of Twenty Five Thousand (25,000), subject to proportionate adjustment as determined
by the Board in the event of any change in the outstanding Common Stock by reason of a stock split, stock dividend, combination or reclassification of shares, recapitalization, merger, or similar event in each case occurring after the date of this
Agreement. 
 1.5. “Award Units (Committee chair)” shall mean the number of Ten Thousand (10,000), subject to proportionate
adjustment as determined by the Board in the event of any change in the outstanding Common Stock by reason of a stock split, stock dividend, combination or reclassification of shares, recapitalization, merger, or similar event in each case occurring
after the date of this Agreement. 
 1.6. “Base Amount” shall mean the amount of One Dollar and Fifteen Cents ($1.15)
subject to proportionate adjustment as determined by the Board in the event of any change in the 








 
outstanding Common Stock by reason of a stock split, stock dividend, combination or reclassification of shares, recapitalization, merger, or similar event in
each case occurring after the date of this Agreement. 
 1.7. “Change in Control” shall mean the occurrence of any of the
following events: 
 (a) Any “person” (as such term is used in Sections 13(d) and 14(d) of the Securities Exchange
Act of 1934, as amended) is or becomes the “beneficial owner” (as defined in Rule 13d-3 under said Act), directly or indirectly, of securities of the Company representing more than 50% of the total voting power represented by the
Company’s then outstanding voting securities, provided, however, no change of control shall be deemed to occur as a result of an acquisition of voting securities of the Company by any other corporation or entity where immediately following such
acquisition, more than 50% of the total voting power represented by such entity’s then outstanding voting securities is owned by the individuals and entities owning the Company’s outstanding voting securities, in substantially the same
proportions, immediately prior to such acquisition; 
 (b) a merger or consolidation of the Company with another corporation
in which the Company is not the survivor, provided, however, no change of control shall be deemed to occur if immediately following such merger or consolidation, more than 50% of the total voting power represented by such other corporation’s
then outstanding voting securities is owned by the individuals and entities owning the Company’s outstanding voting securities, in substantially the same proportions, immediately prior to such merger or consolidation; or 
 (c) the sale or disposition by the Company of all or substantially all the Company’s assets, provided, however, no change of control
will be deemed to occur if such sale or disposition is to another entity where, immediately following such transaction, more than 50% of the total voting power represented by such entity’s then outstanding voting securities is owned by the
individuals and entities owning the Company’s outstanding voting securities, in substantially the same proportions, immediately prior to such transaction. 
 Following an event described in any of the provisos to clauses (a), (b), or (c), above, the acquiring, successor, or transferee entity, as the case may be, will thereafter be treated as the Company for purposes of this definition.

 1.8. “Code” shall mean the Internal Revenue Code of 1986, as amended from time to time. 
 1.9. “Committee” shall mean the Scientific Advisory Committee of the Board. 
 1.10. “Common Stock” shall mean the $0.001 par value common stock of the Company. 
  

 2 








 1.11. “Determination Date (director)” shall mean the date of the first to occur of
(a) the termination of Director’s service as a director of the Company for any reason that constitutes separation from service under Section 409A of the Code or (b) January 1, 2010. 
 1.12. “Determination Date (Committee chair)” shall mean the date of the first to occur of (a) the termination of Director’s
service as the Chairman of the Committee for any reason that constitutes separation from service under Section 409A of the Code or (b) January 1, 2010. 
 1.13. “Fair Market Value” as of any applicable date, shall mean the value of a share of Common Stock determined as follows: 
 (a) If the Common Stock is listed on any established stock exchange or national market system, its Fair Market Value shall be the closing
sales price for such stock (or the mean between the high bid and low asked prices, if no sales were reported) as quoted on such exchange or system for the date in question, as reported in The Wall Street Journal or such other source as the
Administrator deems reliable; 
 (b) If the Common Stock is regularly quoted by a recognized securities dealer but selling
prices are not reported, its Fair Market Value shall be the mean between the high bid and low asked prices for the Common Stock on the date in question; or 
 (c) In the absence of an established market for the Common Stock, the Fair Market Value thereof the Fair Market Value thereof shall be determined in good faith by the Board. 
 1.14. “Maximum Appreciated Amount” shall mean the amount of One and  74/100 Dollars ($1.74), subject to proportionate adjustment as determined by the Board in the event of any change in
the outstanding Common Stock by reason of a stock split, stock dividend, combination or reclassification of shares, recapitalization, merger, or similar event in each case occurring after the date of this Agreement. 
 ARTICLE II 
 Account and
Grant of Awards 
 2.1. Establishment of Account. Effective as of the date of this Agreement, the Company shall establish on
its books a separate account in Director’s name known as the “Hood Incentive Compensation Account,” having a subaccount “Hood Incentive Compensation Account—Award (director)” and a subaccount “Hood Incentive
Compensation Account—Award (Committee chair).” The Account shall be used to determine the incentive compensation to which Director may be entitled under this Agreement. 
 2.2. Award. Effective as of the date of this Agreement, the Company shall separately record in the appropriate subaccount of Director’s
Account (a) the Award (director) and (b) the Award (Committee chair). 
  

 3 








 ARTICLE III 
 Vesting, Adjustment and Distribution of Award (director) 
 3.1. Vesting of Award
(director). 
 (a) The vesting schedule for the Award (director) is as follows: Except as otherwise provided in this
Section 3.1, the Award (director) will vest as to 1/12th of the Award (director) on April 1, 2007, and an additional 1/12th of the Award (director) will vest as of each July 1, October 1, January 1 and April 1
thereafter, provided that Director is still serving as a director of the Company on each vesting date. 
 (b) Notwithstanding
the foregoing, the Award (director) will become fully vested upon the occurrence of a Change in Control while Director is still serving as a director of the Company. 
 3.2. Adjustment of Award (director). 
 (a) On the Determination Date (director), if
the Fair Market Value as of the Determination Date (director) is less than the Maximum Appreciated Amount but is not less than the Base Amount, then the Award (director) credited to the appropriate subaccount of Director’s Account shall be
adjusted to be the amount equal to the product obtained by multiplying (i) the Award Units (director) times (ii) the net amount of such Fair Market Value less the Base Amount; if such Fair Market Value is equal to or less than the Base
Amount, the Award (director) credited to the appropriate subaccount of Director’s Account shall be adjusted to be zero. 
 (b) On the Determination Date (director), the Award (director) credited to the appropriate subaccount of Director’s Account after any adjustment thereof pursuant to Section 3.2(a) hereof shall be adjusted to be the amount equal to
the product obtained by multiplying (i) such Award (director) times (ii) the portion (expressed as a percentage) thereof that then is vested and has not been forfeited in accordance with Section 3.1. 
 3.3. Distribution of Award (director). The Award (director) credited to the appropriate subaccount of Director’s Account after adjustment
pursuant to Section 3.2 hereof shall be paid to Director in a lump sum no later than on the ninetieth (90th) day after the Determination Date (director). 
 ARTICLE IV 
 Vesting, Adjustment and Distribution of Award (Committee chair)

 4.1. Vesting of Award (Committee chair). 
 (a) The vesting schedule for the Award (Committee chair) is as follows: Except as otherwise provided in this Section 4.1, the Award
(Committee chair) will vest as to 1/12th of the Award (Committee chair) on April 1, 2007, and an additional 1/12th of the Award (Committee chair) will vest as of each July 1, October 1, January 1 and April 1 thereafter,
provided that Director is still serving as the Chairman of the Committee on each vesting date. 
  

 4 








 (b) Notwithstanding the foregoing, the Award (Committee chair) will become fully vested
upon the occurrence of a Change in Control while Director is still serving as the Chairman of the Committee. 
 4.2. Adjustment of Award
(Committee chair). 
 (a) On the Determination Date (Committee chair), if the Fair Market Value as of the Determination
Date (Committee chair) is less than the Maximum Appreciated Amount but is not less than the Base Amount, then the Award (Committee chair) credited to the appropriate subaccount of Director’s Account shall be adjusted to be the amount equal to
the product obtained by multiplying (i) the Award Units (Committee chair) times (ii) the net amount of such Fair Market Value less the Base Amount; if such Fair Market Value is equal to or less than the Base Amount, the Award (Committee
chair) credited to the appropriate subaccount of Director’s Account shall be adjusted to be zero. 
 (b) On the
Determination Date (Committee chair), the Award (Committee chair) credited to the appropriate subaccount of Director’s Account after any adjustment thereof pursuant to Section 4.2(a) hereof shall be adjusted to be the amount equal to the
product obtained by multiplying (i) such Award (Committee chair) times (ii) the portion (expressed as a percentage) thereof that then is vested and has not been forfeited in accordance with Section 4.1. 
 4.3. Distribution of Award (Committee chair). The Award (Committee chair) credited to the appropriate subaccount of Director’s Account after
adjustment pursuant to Section 4.2 hereof shall be paid to Director in a lump sum no later than on the ninetieth (90th) day after the Determination Date (Committee chair). 
 ARTICLE V 
 Miscellaneous 
 5.1. Beneficiary Designation. If Director’s death should occur prior to the payment of all amounts due hereunder, any amounts otherwise
payable to him shall be paid to such beneficiary or beneficiaries as Director may have last designated in a writing delivered to the Secretary of the Company, which shall be in the form of Exhibit A attached hereto or such other form as the
Board may from time to time adopt for such purpose. If no effective beneficiary designation has been made, or if any designated beneficiary shall predecease Director, such payments shall be made to Director’s estate. If any designated
beneficiary should survive, Director, but die before payment of all amounts due hereunder, such payment shall, unless Director shall have designated otherwise, be made to such beneficiary’s estate. The Company shall have no responsibility for
the validity of any beneficiary designation made by Director or any of his designated beneficiaries and shall be fully protected if it acts thereon in good faith. 
  

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 5.2 Withholding. The Company shall deduct from any payments made to Director or his designated
beneficiary or beneficiaries under this Agreement any federal, state, local or other taxes or charges which the Company is from time to time required to deduct under applicable law, if any. The Company shall have the right to rely upon an opinion of
legal counsel or its independent accountant as to the amount to be so deducted. 
 5.3. Nontransferability of Benefits. Except as is
specifically provided otherwise in Section 5.1 hereof and to the extent permitted by law, the right of Director, any beneficiary of Director or any other person claiming by or in his right to receive any payment hereunder shall not be subject
to alienation, sale, transfer, assignment, pledge, attachment, garnishment or encumbrance of any kind, and no payments due hereunder shall be subject in any manner to the debts or liabilities of Director or any other person. Any attempt by Director,
any beneficiary of Director or any other person to alienate, sell, transfer, assign, pledge or otherwise encumber any such payments, whether presently or thereafter payable, shall be null and void and without legal effect. 
 5.4. Notices. Any notice to be given to the Company under the terms of this Award Agreement shall be given in writing to the Company in care of
its then Chairman at its then principal place of business. Any notice to be given to Director may be addressed to him at his address as it appears on the payroll or other records of the Company or any affiliate thereof. Any such notice will be
deemed to have been duly given: (a) upon personal delivery to the party to be notified, (b) when sent by confirmed facsimile if sent during normal business hours of the recipient, if not, then on the next business day, (c) five
(5) days after having been sent by registered or certified mail, return receipt requested, postage prepaid, or (d) one (1) day after deposit with a nationally recognized overnight courier, specifying next day delivery, with written
verification of receipt at Director’s or the Company’s address. 
 5.5. Governing Law. This Award Agreement and all
questions arising hereunder or in connection herewith shall be determined in accordance with the laws of the State of Wisconsin, without giving effect to the principles of conflicts of laws. 
 5.6. No Right to Continued Service. This Award Agreement shall not confer upon Director any right with respect to continuation of service on the
Board or any committee thereof, including the Committee, nor shall it interfere in any way with the right of the Company to terminate Director’s service on the Board or any committee thereof, including the Committee, at any time. 
 5.7. Independence of Agreement. It is intended that this Agreement be construed and implemented independently of any and all other benefit or
compensation plans, contracts arrangements of the Company. Accordingly, except as otherwise determined by the Board, the benefits payable and payments made hereunder shall not be deemed a part of any regular, recurring compensation to Director for
any purposes and, except as may be expressly otherwise provided in any such plan, contract or arrangement, shall not be included in, nor shall they or this Agreement have any effect on, the determination of benefits under any other benefit plan,
contract or similar arrangement of the Company. 
  

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 5.8. Multiple Copies. One or more copies of this Award Agreement may be executed, each of which
will be deemed an original, but all of which together will constitute one and the same agreement. 
  

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 IN WITNESS WHEREOF, the Company has caused this Award Agreement to be executed as of the date and
year first above written. 
  

							
		 	NIMBLEGEN SYSTEMS, INC.	  	
				
		 	By:	  	 /s/ Thomas M. Palay
	  	
		 		  	Thomas M. Palay,	  	
		 		  	Vice-Chairman of the Board of Directors and Vice President	  	

 The undersigned Director hereby accepts the foregoing Award and agrees to the several terms and
conditions hereof. 
  

					
		 	Director:	 	
			
		 	 /s/ Leroy E. Hood
	 	
		 	Leroy E. Hood	 	

  

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 Exhibit A 
 Beneficiary Designation 
 1. I hereby revoke any and all previous beneficiary designations and
designate the following beneficiary or beneficiaries to receive any benefit which becomes payable under that certain Award Agreement dated as of January 30, 2007, between NimbleGen Systems, Inc. and me to which the form of this Beneficiary
Designation is attached (the “Agreement”) after my death. I reserve the right, at any time, to revoke, alter, or amend this designation in any manner, and I recognize that the Beneficiary Designation on file with the Company at the
time of my death will be controlling. 
 2. I hereby direct that the person(s) indicated below are to receive any benefit payable under the
Agreement after my death: 
  

			
	 Name, Address and SSN of Beneficiary
	  	 Percentage of
 Benefit Payable

		
	  
	  	  

		
	  
	  	  

		
	  
	  	  

		
	  
	  	  

		
		  	100%
		  	 

 INSTRUCTIONS: Enter the full name and current address of each beneficiary. If more than one beneficiary is
named, each will receive an equal share unless otherwise indicated above. 
 3. I understand that if no beneficiary survives me, any benefit
due to me under the Agreement will be paid to my estate. I further understand that if any person designated as a beneficiary predeceases me, any amount otherwise payable to such beneficiary will be reallocated to those persons designated as
beneficiaries who survive me. 
  

							
	  
	 		 	                                      
  
	  
	 	(Print Name)	 		 	Date