Document:

Award Agreements between the Registrant and David S. Snyder

 Exhibit 10.27 
 NIMBLEGEN SYSTEMS INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of February 9, 2006 (the date of grant), is between NimbleGen Systems Inc., a Delaware corporation (the
“Company”), and David S. Snyder (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 any of
its Subsidiaries, 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. Options; 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 60,000 shares of the Company’s Common Stock (individually, a
“Share” and jointly, the “Shares” or “Common Shares”) at the purchase price of $0.024 per Share of Common Stock (as to such Shares, the “Option Price”) and all or any part of an aggregate of 150,000 shares of
the Company’s Series E Preferred Stock (also, individually, a “Share” and jointly, the “Shares” or “Preferred Shares”) at the purchase price of $0.456 per Share of Series E Preferred Stock (as to such
Shares, the “Option Price”) any time before the tenth anniversary of the date of this Award Agreement. If the Participant exercises the Option prior to February 1, 2010, the Shares received from the exercise of the Option and, if such
Shares are Series E Preferred Stock, any shares of Common Stock received upon conversion of such Series E Preferred Stock (which also shall be “Preferred Shares”) that are unvested shares according to the schedule set forth in
Section 1.2 are hereafter referred to as “Restricted Shares” and Shares, including any such Preferred 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 after February 1, 2010, 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 be vested and/or will vest as to 1/48th of the Common Shares and 1/48th of the Preferred Shares on the first day of each calendar month commencing on March 1, 2006; provided that the Participant is still in the employ of the Company and/or any of its Subsidiaries on each vesting date.
Notwithstanding the 

 
foregoing, the Option will become fully vested upon the first to occur of the following: (a) the Participant’s death or Disability while in the
employ of the Company, or (b) the termination of the Participant’s employment with the Company and its Subsidiaries (other than a Termination for Cause), or the Participant’s termination of his employment for Good Reason (but not
otherwise), within the period commencing on the one hundred eightieth (180th) day prior to the occurrence of a Change in Control and ending on the two year anniversary of the occurrence of the Change in Control. Shares vest according to this
schedule, whether or not the Option has been exercised. For purposes hereof, “Good Reason” means, without the Participant’s consent, the occurrence of any one or more of the following during the Participant’s employment with the
Company: (i) any reduction by the Company of the Participant’s duties or responsibilities which reduction is material based on the Participant’s overall duties and responsibilities (ignoring incidental duties and responsibilities)
prior to and after such reduction which remains uncured, if cure thereof is necessary, ten (10) business days after the Participant has given written notice to the Company which specifies such reduction and the Participant’s objection
thereto; (ii) any job requirement imposed by the Company that the Participant change the Participant’s principal residence to a location more than seventy five (75) miles from Dane County, Wisconsin; or (iii) any material
breach of any obligation of the Company for the payment or provision of compensation or other benefits to the Participant set forth in that certain letter agreement between the Company and the Participant executed and delivered contemporaneously
with the execution and delivery hereof and describing terms and conditions of the Participant’s employment, which remains uncured ten (10) business days after the Participant has given written notice to the Company which specifies the
breach. 
 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) Except
as otherwise provided in paragraphs (c) through (e), if the employment of the Participant terminates or service to the Company and/or its Subsidiaries by a non-employee terminates, the Option, to the extent not exercised, shall terminate three
(3) months after termination of employment or service with the Company and/or its Subsidiaries, as the case may be. In the event that the Participant changes his employment status with the Company and/or its Subsidiaries, but continues to
render services to the Company and/or any of its Subsidiaries (e.g. changes from consultant status to employee status), such change in status does not constitute a termination of employment or service. 
 (c) If the Participant’s termination of employment with the Company and/or any of its Subsidiaries is a Termination for Cause, the
Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
  

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 (d) If termination of employment results from the Disability of the Participant, this
Option may be exercised at any time within one (1) year after such termination of employment. 
 (e) If termination of
employment results from the death of the Participant, the personal representative of the Participant’s estate, or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the
Option, may exercise any Option at any time within one (1) year after the death of the Participant. 
 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 (a) the completion of such registration or qualification of such Shares under federal, state or foreign law, ruling or
regulation as the Company shall deem to be necessary or advisable, and (b) 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. 
 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall
qualify as an incentive stock option pursuant to Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code. 
 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 

  

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outstanding shares of Series E Preferred 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 employment with the Company
and/or its Subsidiaries 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 the termination of the Participant’s employment with the Company and/or its Subsidiaries 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. 
  

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 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 employment. 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 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. 
 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. 
  

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 3.6. No Employment Rights. This Award Agreement shall not confer upon the Participant any right
with respect to continuation of employment by the Company and/or any of its Subsidiaries, nor shall it interfere in any way with the right of the Company and/or any of its Subsidiaries to terminate the Participant’s employment at any time,
except as otherwise provided in any written employment agreement between the Participant and the Company and/or any of its Subsidiaries. 
 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,
		 	Chairman of the Compensation Committee of the Board

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

	
	 /s/ David S. Snyder

	David S. Snyder

  

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 EXHIBIT A 
 NIMBLEGEN SYSTEMS INC. 2000 STOCK OPTION 
 AND RESTRICTED STOCK PLAN, 
 as amended and restated as of September 25, 2001 and as further amended 
 EXERCISE NOTICE 
 1. Exercise of Option. Effective as of today,
[exercise date], the undersigned (the “Participant”) hereby elects to exercise the Participant’s option to purchase [exercise number and class of stock: shares of the Common Stock and/or shares of the Series E Preferred
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 February 9, 2006 (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 understood 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 or her 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. 
  

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 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 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. 
  

					
	Submitted by:	  	Accepted by:
	PARTICIPANT:	  	NIMBLEGEN SYSTEMS INC.
			
	  
	  	By:	 	  

	David S. Snyder	  	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 [exercise date], is by and between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and the person whose name
appears on the signature page hereof (“Participant”). 
 RECITALS 
 The Company granted Participant an option (the “Option”) to purchase shares of the Company’s Common Stock and shares of the Company’s
Series E Preferred 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 Participant entered into that certain Award Agreement dated as of
February 9, 2006 (the “Award Agreement”) setting out the terms of such option grant. Participant has purchased [exercise number and class of stock: shares of the Common Stock and/or shares of the Series E Preferred Stock]
pursuant to the Award Agreement, which, together with all other such shares from time to time purchased by Participant pursuant to the Award Agreement, including those shares purchased after the date of this Agreement, are the “Shares”
hereunder. (For the avoidance of doubt, such purchased shares and therefore the “Shares” shall include shares of Common Stock into which are converted any shares of Series E Preferred Stock received from the exercise of the Option.)

 The Company made its grant of the Option on certain terms and conditions including the requirement that 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: 
  

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 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. 
 “Disability” has the meaning given in Section 2(i) of the Plan. 
 “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. 
  

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 ARTICLE II 
 RESTRICTIONS ON TRANSFER 
 2.1. General Restriction. No Transfer of the Shares may be
made by Participant (including, without limitation, an executor or personal representative, guardian, or conservator of 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
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 Participant retains the right to vote any Shares so transferred; (ii) upon 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 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 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 Participant desires to accept that offer (except for a Permitted Transfer), 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 Participant during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and Participant to sell the Shares of Participant identified in the Exercise Notice on
the terms provided in this Article III. 
  

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 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, 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 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 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 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 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, 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 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 Participant in order to consummate such Sale Transaction. 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 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 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 Participant to that effect. The Controlling Stockholder shall also cause to be remitted to Participant the proceeds attributable to the
sale of Participant’s Shares not later than three (3) business days after the closing of the Sale Transaction. If any Sale 

  

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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 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 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 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 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 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 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. 
  

 B-5 

 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.

 ARTICLE V 
 MARKET
STAND-OFF AGREEMENT 
 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, 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 Participant or beneficially owned by 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. 
  

 B-6 

 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: the Shares in which such an interest is created or exists are and continue to be (a) held of record in the name of such Stockholder and (b) managed and controlled by such Stockholder. 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. 
 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 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 

  

 B-7 

 
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 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. 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. 
 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. 
  

 B-8 

 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
	
	  

	David S. Snyder

  

 B-9 

 EXHIBIT C 
 INVESTMENT REPRESENTATION STATEMENT 
  

			
	PARTICIPANT:	  	DAVID S. SNYDER
		
	COMPANY:	  	NIMBLEGEN SYSTEMS INC.
		
	SECURITY:	  	[COMMON STOCK AND/OR SERIES E PREFERRED STOCK]
		
	AMOUNT:	  	
		
	DATE:	  	

 In connection with the purchase of the above-listed shares of [Common Stock and/or
Series E Preferred Stock] (the “Securities”), the undersigned employee, director or advisor (“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 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:

	
	  

	 David S. Snyder

	
	 Date:                     ,
20    

  

 C-2 

 NIMBLEGEN SYSTEMS, INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of December 26,
2006 (the date of grant), is between NimbleGen Systems, Inc., a Delaware corporation (the “Company”), and David S. Snyder (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 any of its Subsidiaries, 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 70,000 shares of the Company’s Common Stock (individually, a “Share” and jointly, the “Shares”) at the purchase price of $1.15 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 fourth 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 one-fourth of the Shares on the first anniversary of the
date of this Award Agreement, and an additional one-fourth of the Shares will vest as of each of the three (3) subsequent anniversaries of such date, provided that the Participant is still in the employ of the Company on each vesting date.
Notwithstanding the foregoing, the Option will become fully vested upon the first to occur of the following: (a) the Participant’s death or Disability while in the employ of the Company, or (b) the termination of the
Participant’s employment with the Company and its Subsidiaries (other than a Termination for Cause), or the Participant’s termination of his employment for Good Reason (but not otherwise), within the period commencing on the one hundred
eightieth (180th) day prior to the occurrence of a Change in Control 

 
and ending on the two year anniversary of the occurrence of the Change in Control. Shares vest according to this schedule, whether or not the Option has been
exercised. For purposes hereof, “Good Reason” means, without the Participant’s consent, the occurrence of any one or more of the following during the Participant’s employment with the Company: (i) any reduction by the
Company of the Participant’s duties or responsibilities which reduction is material based on the Participant’s overall duties and responsibilities (ignoring incidental duties and responsibilities) prior to and after such reduction which
remains uncured, if cure thereof is necessary, ten (10) business days after the Participant has given written notice to the Company which specifies such reduction and the Participant’s objection thereto; (ii) any job requirement
imposed by the Company that the Participant change the Participant’s principal residence to a location more than seventy five (75) miles from Dane County, Wisconsin; or (iii) any material breach of any obligation of the Company
for the payment or provision of compensation or other benefits to the Participant set forth in that certain letter agreement between the Company and the Participant dated as of September 18, 2006 and describing terms and conditions of the
Participant’s employment, which remains uncured ten (10) business days after the Participant has given written notice to the Company which specifies the breach. 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) Except
as otherwise provided in paragraphs (c) through (e), if the employment of the Participant terminates or service to the Company by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after
termination of employment or service with the Company, as the case may be. In the event that the Participant changes his employment status with the Company, but continues to render services to the Company (e.g. changes from consultant status to
employee status), such change in status does not constitute a termination of employment or service. 
 (c) If the
Participant’s termination of employment with the Company is a Termination for Cause, the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one
(1) year after such termination of employment. 
 (e) If termination of employment results from the death of the
Participant, the personal representative of the Participant’s estate, or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time
within one (1) year after the death of the Participant. 
  

 2 

 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.

 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall qualify as an incentive stock option pursuant to
Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code. 
 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. 
 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. 

  

 3 

 
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 employment with 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 the termination of the Participant’s employment with the Company 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 employment. 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. 
  

 4 

 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 Employment Rights. This Award
Agreement shall not confer upon the Participant any right with respect to continuation of employment by the Company, nor shall it interfere in any way with the right of the Company to terminate the Participant’s employment at any time, except
as otherwise provided in any written employment agreement between the Participant and the Company. 
 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. 
  

 5 

 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,
		 	Chairman of the Compensation Committee of the Board

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

	
	 Participant:

	
	 /s/ David S. Snyder

	David S. Snyder

  

 6 

 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
December 26, 2006 (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 and 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 December 26, 2006 (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. 
 “Disability” has the meaning given in Section 2(i) of the Plan. 
 “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 

  

 B-2 

 
Company; (iv) any exchange of existing Shares for other shares of the same or a different class or series in the Company, whether through 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. 
  

 B-3 

 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 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 

  

 B-4 

 
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 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 

  

 B-5 

 
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. 
 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 

  

 B-6 

 
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. 
 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. 
  

 B-7 

 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. 
 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 employee,
director or advisor (“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-2Award Agreements between the Registrant and Emile Nuwaysir

 Exhibit 10.28 
 NIMBLEGEN SYSTEMS INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of November 22, 2000, is between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and
Emile Nuwaysir (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 (the “Plan”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors
of the Company (the “Board”) desires to induce the Participant to provide services to the Company, to provide the Participant with a stronger incentive to strive for the continued success and growth of the Company 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 5,000 shares of the Company’s Common Stock (individually, a “Share” and jointly, the “Shares”) at the purchase price of $0.30 per Share (the “Option Price”) any time on or before
November 21, 2010. If the Participant exercises the Option prior to November 22, 2004, 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 after November 21, 2004, 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 1,250 Shares on November 22, 2001, and an additional 1,250 Shares will vest as of each of the three (3) subsequent anniversaries of such date,
provided that the Participant is still in the employ of the Company on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the Participant’s death or Disability while in the employ of the Company. Shares
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, no later than November 21, 2010. 

 (b) Except as otherwise provided in paragraphs (c) through (e), if the employment of
the Participant terminates or service to the Company by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after termination of employment or service with the Company, as the case may be. In the
event that the Participant changes his employment status with the Company, but continues to render services to the Company (e.g. changes from consultant status to employee status), such change in status does not constitute a termination of
employment or service. 
 (c) If the Participant’s termination of employment with the Company is a Termination for Cause,
the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one (1) year after such termination of employment. 
 (e) If termination of employment results from the death of the Participant, the personal representative of the Participant’s estate,
or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time within one (1) year after the death of the Participant. 

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 (a) the
completion of such registration or qualification of such Shares under federal, state or foreign law, ruling or regulation as the Company shall deem to be necessary or advisable, and (b) 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. 
  

 2 

 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall qualify as an
incentive stock option pursuant to Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code, and provided that stockholders of the Company
approve the Plan on or before November 21, 2001. 
 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. 
 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 employment with 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 the termination of the Participant’s employment with the Company 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 

  

 3 

 
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 employment. 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. 
  

 4 

 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 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. 
 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 Employment Rights. This Award Agreement shall not confer upon the Participant any right with respect to continuation of
employment by the Company, nor shall it interfere in any way with the right of the Company to terminate the Participant’s employment at any time, except as otherwise provided in any written employment agreement between the Participant and the
Company. 
  

 5 

 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/ Michael J. Treble
	 	
		 	Michael J. Treble	 	
		 	President and Chief Executive Officer	 	

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

			
	 /s/ Emile F. Nuwaysir                        10/19/01
	 	
	Emile Nuwaysir	 	

  

 6 

 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,                     , 200  , 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 (the “Plan”) and the Award Agreement dated November 22, 2000 (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 understood 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 or her 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. 
  

 A-1 

 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 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. 
  

													
	Submitted by:	 		  	Accepted by:	  	
	PARTICIPANT:	 		  	NIMBLEGEN SYSTEMS INC.	  	
					
	  
	 		  	By:	  	  
	  	
	(Signature)	 		  	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 employee of the Company whose name appears on the signature page hereof (“Employee”). 
 RECITALS 
 The Company granted Employee an option (the “Option”) to purchase shares of the Company’s Common
Stock pursuant to its 2000 Stock Option and Restricted Stock Plan. The Company and Employee entered into that certain Award Agreement dated November 22, 2000 (the “Award Agreement”) setting out the terms of such option grant. The
Employee 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 Employee 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 Employee 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 

  

 B-1 

 
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. 
 “Disability” has the meaning given in
Section 2(i) of the Plan. 
 “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 Employee (including, without limitation, an
executor or personal representative, guardian, or conservator of the Employee), 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 Employee’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
Employee retains the right to vote any 

  

 B-2 

 
Shares so transferred; (ii) upon the Employee’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 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 Employee 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 Employee desires to accept that offer (except for a Permitted Transfer), the Employee 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 Employee during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and the Employee to sell the Shares of the Employee 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 Employee 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 Employee 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
Employee 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. 
  

 B-3 

 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 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 Employee 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 Employee 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 Employee 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 Employee in order to consummate such Sale Transaction. The Employee 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
Employee 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 Employee 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 Employee to that effect. The Controlling Stockholder shall also cause to be remitted to the Employee the proceeds
attributable to the sale of the Employee’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 Employee 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 Employee 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 

  

 B-4 

 
$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 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 Employee 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 Employee. 
 (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 Employee 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 

  

 B-5 

 
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. 
 ARTICLE V

 MARKET STAND-OFF AGREEMENT 
 The Employee 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 Employee 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 Employee or beneficially owned by the Employee 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 

  

 B-6 

 
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. 
 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 Employee 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 Employee’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. 
  

 B-7 

 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. 
 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:
	 	  

  

			
	 Employee
	 	
	
	  

  

			
	 Print name:
	 	  

  

 B-8 

 EXHIBIT C 
 INVESTMENT REPRESENTATION STATEMENT 
  

			
	EMPLOYEE:   	 	
		
	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 employee, director or advisor (“Employee”) represents to the Company the following: 
 (a) Employee 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.
Employee is acquiring these Securities for investment for Employee’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) Employee 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 Employee’s investment
intent as expressed herein. In this connection, Employee understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Employee’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. Employee 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. Employee further
acknowledges and understands that the Company is under no obligation to register the Securities. Employee 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-1 

 (c) Employee 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 Employee, 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) Employee 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. Employee understands that no assurances can be given that any such other
registration exemption will be available in such event. 
  

			
	Signature of Employee:	 	
		
	  
	 	
		
	Date:                     , 200  	 	

  

 C-2 

 NIMBLEGEN SYSTEMS INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of January 23, 2001 (the date of grant), is
between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and Emile Nuwaysir (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 (the “Plan”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors of the Company (the “Board”) desires to induce the Participant to provide services to the Company, to provide
the Participant with a stronger incentive to strive for the continued success and growth of the Company 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 2,500 shares of the Company’s Common Stock (individually, a “Share” and jointly, the
“Shares”) at the purchase price of 0.30 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 fourth 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 one-fourth of the Shares on the first anniversary of the date of this Award Agreement, and an additional one-fourth of the Shares will vest as of each of the three (3) subsequent anniversaries of such date, provided
that the Participant is still in the employ of the Company on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the Participant’s death or Disability while in the employ of the Company. Shares 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) Except
as otherwise provided in paragraphs (c) through (e), if the employment of the Participant terminates or service to the Company by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after
termination of employment or service with the Company, as the case may be. In the event that the Participant changes his employment status with the Company, but continues to render services to the Company (e.g. changes from consultant status to
employee status), such change in status does not constitute a termination of employment or service. 
 (c) If the
Participant’s termination of employment with the Company is a Termination for Cause, the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one
(1) year after such termination of employment. 
 (e) If termination of employment results from the death of the
Participant, the personal representative of the Participant’s estate, or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time
within one (1) year after the death of the Participant. 
 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 (a) the completion of such registration or qualification of such Shares under federal, state or foreign law, ruling or regulation as the Company shall deem to be
necessary or advisable, and (b) 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.

  

 2 

 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. 
 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall
qualify as an incentive stock option pursuant to Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code, and provided that stockholders of
the Company approve the Plan on or before November 21, 2001. 
 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. 
 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 employment with 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 the termination of the Participant’s employment with the Company 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. 
  

 3 

 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 employment. 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. 
  

 4 

 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 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. 
 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 Employment Rights. This Award Agreement shall not confer upon the Participant any right with respect to continuation of
employment by the Company, nor shall it interfere in any way with the right of the Company to terminate the Participant’s employment at any time, except as otherwise provided in any written employment agreement between the Participant and the
Company. 
 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. 
  

 5 

 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/ Michael J. Treble
	 	
		 	Michael J. Treble	 	
		 	President and Chief Executive Officer	 	

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

			
	Participant:	 	
		
	 /s/ Emile F. Nuwaysir                         10/19/01
	 	

  

 6 

 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,                     , 200  , 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 (the “Plan”) and the Award Agreement dated
                    , 200   (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 understood 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 or her 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. 
  

 A-1 

 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 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 (“Employee”). 
 RECITALS

 The Company granted Employee an option (the “Option”) to purchase shares of the Company’s Common Stock pursuant to its
2000 Stock Option and Restricted Stock Plan. The Company and Employee entered into that certain Award Agreement dated                     
(the “Award Agreement”) setting out the terms of such option grant. The Employee 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 Employee 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 Employee 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,” 

  

 B-1 

 
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. 
 “Disability” has the meaning given in Section 2(i) of the Plan. 
 “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 Employee (including, without limitation, an
executor or personal representative, guardian, or conservator of the Employee), 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 Employee’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
Employee retains the right to vote any 

  

 B-2 

 
Shares so transferred; (ii) upon the Employee’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 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 Employee 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 Employee desires to accept that offer (except for a Permitted Transfer), the Employee 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 Employee during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and the Employee to sell the Shares of the Employee 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 Employee 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 Employee 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
Employee 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. 
  

 B-3 

 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 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 Employee 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 Employee 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 Employee 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 Employee in order to consummate such Sale Transaction. The Employee 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
Employee 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 Employee 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 Employee to that effect. The Controlling Stockholder shall also cause to be remitted to the Employee the proceeds
attributable to the sale of the Employee’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 Employee 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 Employee 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 

  

 B-4 

 
$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 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 Employee 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 Employee. 
 (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 Employee 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 

  

 B-5 

 
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. 
 ARTICLE V

 MARKET STAND-OFF AGREEMENT 
 The Employee 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 Employee 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 Employee or beneficially owned by the Employee 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 

  

 B-6 

 
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. 
 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 Employee 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 Employee’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. 
  

 B-7 

 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. 
 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:	 	  

  

			
	Employee:	 	
	
	  

  

			
	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 employee, director or advisor (“Employee”) represents to the Company the following: 
 (a) Employee 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.
Employee is acquiring these Securities for investment for Employee’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) Employee 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 Employee’s investment
intent as expressed herein. In this connection, Employee understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Employee’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. Employee 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. Employee further
acknowledges and understands that the Company is under no obligation to register the Securities. Employee 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-1 

 (c) Employee 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 Employee, 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) Employee 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. Employee understands that no assurances can be given that any such other
registration exemption will be available in such event. 
  

			
	Signature of Employee:	 	
		
	  
	 	
		
	Date:                     , 200  	 	

  

 C-2 

 NIMBLEGEN SYSTEMS INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of May 31, 2001 (the date of grant), is between
NimbleGen Systems Inc., a Delaware corporation (the “Company”), and Emile Nuwaysir (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 (the “Plan”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors of the Company (the “Board”) desires to induce the Participant to provide services to the Company, to provide
the Participant with a stronger incentive to strive for the continued success and growth of the Company 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 1,000 shares of the Company’s Common Stock (individually, a “Share” and jointly, the
“Shares”) at the purchase price of $0.75 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 fourth 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 one-fourth of the Shares on the first anniversary of the date of this Award Agreement, and an additional one-fourth of the Shares will vest as of each of the three (3) subsequent anniversaries of such date, provided
that the Participant is still in the employ of the Company on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the Participant’s death or Disability while in the employ of the Company. Shares 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) Except
as otherwise provided in paragraphs (c) through (e), if the employment of the Participant terminates or service to the Company by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after
termination of employment or service with the Company, as the case may be. In the event that the Participant changes his employment status with the Company, but continues to render services to the Company (e.g. changes from consultant status to
employee status), such change in status does not constitute a termination of employment or service. 
 (c) If the
Participant’s termination of employment with the Company is a Termination for Cause, the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one
(1) year after such termination of employment. 
 (e) If termination of employment results from the death of the
Participant, the personal representative of the Participant’s estate, or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time
within one (1) year after the death of the Participant. 
 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 (a) the completion of such registration or qualification of such Shares under federal, state or foreign law, ruling or regulation as the Company shall deem to be
necessary or advisable, and (b) 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.

  

 2 

 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. 
 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall
qualify as an incentive stock option pursuant to Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code, and provided that stockholders of
the Company approve the Plan on or before November 21, 2001. 
 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. 
 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 employment with 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 the termination of the Participant’s employment with the Company 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. 
  

 3 

 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 employment. 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. 
  

 4 

 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 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. 
 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 Employment Rights. This Award Agreement shall not confer upon the Participant any right with respect to continuation of
employment by the Company, nor shall it interfere in any way with the right of the Company to terminate the Participant’s employment at any time, except as otherwise provided in any written employment agreement between the Participant and the
Company. 
 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. 
  

 5 

 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/ Michael J. Treble
	 	
		 	Michael J. Treble	 	
		 	President and Chief Executive Officer	 	

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

			
	Participant:	 	
		
	 /s/ Emile F. Nuwaysir                        10/19/01
	 	

  

 6 

 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,                     , 200  , 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 (the “Plan”) and the Award Agreement dated
                    , 200   (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 understood 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 or her 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. 
  

 A-1 

 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 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 (“Employee”). 
 RECITALS

 The Company granted Employee an option (the “Option”) to purchase shares of the Company’s Common Stock pursuant to its
2000 Stock Option and Restricted Stock Plan. The Company and Employee entered into that certain Award Agreement dated                     
(the “Award Agreement”) setting out the terms of such option grant. The Employee 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 Employee 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 Employee 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,” 

  

 B-1 

 
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. 
 “Disability” has the meaning given in Section 2(i) of the Plan. 
 “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 Employee (including, without limitation, an
executor or personal representative, guardian, or conservator of the Employee), 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 Employee’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
Employee retains the right to vote any 

  

 B-2 

 
Shares so transferred; (ii) upon the Employee’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 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 Employee 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 Employee desires to accept that offer (except for a Permitted Transfer), the Employee 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 Employee during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and the Employee to sell the Shares of the Employee 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 Employee 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 Employee 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
Employee 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. 
  

 B-3 

 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 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 Employee 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 Employee 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 Employee 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 Employee in order to consummate such Sale Transaction. The Employee 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
Employee 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 Employee 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 Employee to that effect. The Controlling Stockholder shall also cause to be remitted to the Participant the proceeds
attributable to the sale of the Employee’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 Employee 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 Employee 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 

  

 B-4 

 
$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 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 Employee 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 Employee. 
 (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 Employee 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 

  

 B-5 

 
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. 
 ARTICLE V

 MARKET STAND-OFF AGREEMENT 
 The Employee 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 Employee 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 Employee or beneficially owned by the Employee 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 

  

 B-6 

 
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. 
 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 Employee 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 Employee’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. 
  

 B-7 

 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. 
 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:
	 	  

  

			
	 Employee:
	 	
	
	  

  

			
	 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 employee, director or advisor (“Employee”) represents to the Company the following: 
 (a) Employee 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.
Employee is acquiring these Securities for investment for Employee’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) Employee 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 Employee’s investment
intent as expressed herein. In this connection, Employee understands that, in the view of the Securities and Exchange Commission, the statutory basis for such exemption may be unavailable if Employee’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. Employee 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. Employee further
acknowledges and understands that the Company is under no obligation to register the Securities. Employee 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-1 

 (c) Employee 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 Employee, 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) Employee 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. Employee understands that no assurances can be given that any such other
registration exemption will be available in such event. 
  

			
	Signature of Employee:	 	
		
	  
	 	
		
	Date:                     , 200  	 	

  

 C-2 

 NIMBLEGEN SYSTEMS INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of May 10, 2003 (the date of grant), is between
NimbleGen Systems Inc., a Delaware corporation (the “Company”), and Emile Nuwaysir (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 (the “Plan”). 
 WITNESSETH: 
 WHEREAS, the Board of Directors of the Company (the “Board”) desires to induce the Participant to provide services to the Company, to provide
the Participant with a stronger incentive to strive for the continued success and growth of the Company 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 20,000 shares of the Company’s Common Stock (individually, a “Share” and jointly, the
“Shares”) at the purchase price of $1.28 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 fourth 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 one-fourth of the Shares on the first anniversary of the date of this Award Agreement, and an additional one-fourth of the Shares will vest as of each of the three (3) subsequent anniversaries of such date, provided
that the Participant is still in the employ of the Company on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the first to occur of the following: (a) the Participant’s death or Disability while
in the employ of the Company or (b) the termination of the Participant’s employment by the Company (other than a Termination for Cause) within ninety (90) days after the occurrence of a Change in Control or within ninety
(90) days after a new chief executive officer is hired by the Company. However, the immediate vesting provided for in clause (b) of the foregoing sentence will be contingent upon the Participant providing the Company with a release of
claims against the Company, in form and substance 

 
reasonably satisfactory to the Company, and taking such other cooperative actions as the Company may request. Shares 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) Except
as otherwise provided in paragraphs (c) through (e), if the employment of the Participant terminates or service to the Company by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after
termination of employment or service with the Company, as the case may be. In the event that the Participant changes his employment status with the Company, but continues to render services to the Company (e.g. changes from consultant status to
employee status), such change in status does not constitute a termination of employment or service. 
 (c) If the
Participant’s termination of employment with the Company is a Termination for Cause, the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one
(1) year after such termination of employment. 
 (e) If termination of employment results from the death of the
Participant, the personal representative of the Participant’s estate, or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time
within one (1) year after the death of the Participant. 
 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 (a) the completion of such registration or qualification of such Shares under federal, state or foreign law, ruling or regulation as the Company shall deem to be
necessary or advisable, and (b) 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.

  

 2 

 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. 
 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall
qualify as an incentive stock option pursuant to Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code, and provided that stockholders of
the Company approve the Plan on or before November 21, 2001. 
 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. 
 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 employment with 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 the termination of the Participant’s employment with the Company by delivery of a written notice to the Participant. The Company may assign its rights under this 

  

 3 

 
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 employment. 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. 
  

 4 

 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 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. 
 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 Employment Rights. This Award Agreement shall not confer upon the Participant any right with respect to continuation of
employment by the Company, nor shall it interfere in any way with the right of the Company to terminate the Participant’s employment at any time, except as otherwise provided in any written employment agreement between the Participant and the
Company. 
 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. 
  

 5 

 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/ Robert J. Palay
	 	
		 	Robert J. Palay	 	
		 	President and Chief Executive Officer	 	

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

			
	Participant:	 	
		
	 /s/ Emile F. Nuwaysir
	 	

  

 6 

 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,                     , 200  , 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 (the “Plan”) and the Award Agreement dated
                    , 200   (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 understood 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 or her 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. 
  

 A-1 

 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 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 (“Participant”). 
 RECITALS 
 The Company granted Participant an option (the “Option”) to purchase shares of the Company’s
Common Stock pursuant to its 2000 Stock Option and Restricted Stock Plan. The Company and Participant entered into that certain Award Agreement dated
                     (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 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 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,” 

  

 B-1 

 
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. 
 “Disability” has the meaning given in Section 2(i) of the Plan. 
 “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 

  

 B-2 

 
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 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. 
  

 B-3 

 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 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 

  

 B-4 

 
$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 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 

  

 B-5 

 
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. 
 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 

  

 B-6 

 
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. 
 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. 
  

 B-7 

 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. 
 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 employee, director or advisor (“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-1 

 (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:                     , 200  	 	

  

 C-2 

 NIMBLEGEN SYSTEMS INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of October 7, 2005 (the date of grant), is
between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and Emile Nuwaysir (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 any of its Subsidiaries, 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 150,000 shares of the Company’s Series E
Preferred Stock (individually, a “Share” and jointly, the “Shares”) at the purchase price of $0.456 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 November 1, 2008, the shares of Series E Preferred Stock received from the exercise of the Option and any shares of Common Stock received upon conversion of shares of such Series E Preferred Stock
(“Common Shares”) that are unvested shares according to the schedule set forth in Section 1.2 are hereafter referred to as “Restricted Shares” and Shares or Common 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 after October 31, 2008, 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 be vested and/or will vest as to 3,125 Shares on the first day of each calendar month
commencing on the later of November 1, 2004 and the day on which the Participant has commenced full-time employment with the Company and/or any of its Subsidiaries; provided that the Participant is still in the employ of the Company and/or any
of its Subsidiaries on each vesting date. Notwithstanding the foregoing, the Option will become fully vested upon the first to occur of the following: (a) the Participant’s death or Disability while in the employ of the Company,
(b) the occurrence of a Change in Control or a Qualified IPO, or (c) the termination of the Participant’s employment with the Company and 

 
its Subsidiaries (other than a Termination for Cause) within the one hundred eighty (180) day period ending on the occurrence of a Change in Control or
a Qualified IPO. However, the immediate vesting provided for in clause (b) of the foregoing sentence will be contingent upon the Participant providing the Company with a release of claims against the Company, in form and substance reasonably
satisfactory to the Company, and taking such other cooperative actions as the Company may request. Shares vest according to this schedule, whether or not the Option has been exercised. For purposes hereof, “Qualified IPO” means a
Series E and F Qualified IPO as defined in the Fifth Amended and Restated Certificate of Incorporation of the Company, as further amended. 
 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) Except as otherwise provided in paragraphs (c) through (e), if the employment of the Participant terminates or service to the
Company and/or its Subsidiaries by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after termination of employment or service with the Company and/or its Subsidiaries, as the case may be. In
the event that the Participant changes his employment status with the Company and/or its Subsidiaries, but continues to render services to the Company and/or any of its Subsidiaries (e.g. changes from consultant status to employee status), such
change in status does not constitute a termination of employment or service. 
 (c) If the Participant’s termination of
employment with the Company and/or any of its Subsidiaries is a Termination for Cause, the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one
(1) year after such termination of employment. 
 (e) If termination of employment results from the death of the
Participant, the personal representative of the Participant’s estate, or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time
within one (1) year after the death of the Participant. 
 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

  

 2 

 
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 (a) the completion of such registration or qualification of such
Shares under federal, state or foreign law, ruling or regulation as the Company shall deem to be necessary or advisable, and (b) 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. 
 1.6. Incentive Stock Option
Treatment. It is intended that all of the Option shall qualify as an incentive stock option pursuant to Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in
Section 422(d) of the Code. 
 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 Series E Preferred 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. 
  

 3 

 2.3. Repurchase of Restricted Shares. If the Participant’s employment with the Company
and/or its Subsidiaries 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 the termination of the Participant’s employment with the Company and/or its Subsidiaries 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 employment. 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, 

  

 4 

 
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 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. 
 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 Employment Rights. This Award
Agreement shall not confer upon the Participant any right with respect to continuation of employment by the Company and/or any of its Subsidiaries, nor shall it interfere in any way with the right of the Company and/or any of its Subsidiaries to
terminate the Participant’s employment at any time, except as otherwise provided in any written employment agreement between the Participant and the Company and/or any of its Subsidiaries. 
 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. 
  

 5 

 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,	 	
		 	 Chairman of the Compensation Committee
 of the Board
	 	

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

			
	 /s/ Emile F. Nuwaysir
	 	
	Emile Nuwaysir	 	

  

 6 

 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:	 	  
	  	
		 		  		  	Print Name:	 	  
	  	

 EXHIBIT A 
 NIMBLEGEN SYSTEMS INC. 2000 STOCK OPTION 
 AND RESTRICTED STOCK PLAN, 
 as amended and restated as of September 25, 2001 and as further amended 
 EXERCISE NOTICE 
 1. Exercise of Option. Effective as of today,
[exercise date], the undersigned (the “Participant”) hereby elects to exercise the Participant’s option to purchase [exercise number] shares of the Series E Preferred 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 October 7, 2005 (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 understood 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 or her 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. 
  

 A-1 

 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 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. 
  

											
	Submitted by:	 		  	Accepted by:	  	
	PARTICIPANT:	 		  	NIMBLEGEN SYSTEMS INC.	  	
					
	  
	 		  	By:	  	  
	  	
	Emile Nuwaysir	 		  	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 [exercise date], is by and between NimbleGen Systems Inc., a Delaware corporation (the “Company”), and the person whose name
appears on the signature page hereof (“Participant”). 
 RECITALS 
 The Company granted Participant an option (the “Option”) to purchase shares of the Company’s Series E Preferred 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 Participant entered into that certain Award Agreement dated as of October 7, 2005 (the “Award
Agreement”) setting out the terms of such option grant. Participant has purchased [exercise number] shares of the Company’s Series E Preferred Stock pursuant to the Award Agreement, which, together with all other such shares from
time to time purchased by 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 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 

  

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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. 
 “Disability” has the meaning given in
Section 2(i) of the Plan. 
 “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 Participant (including, without limitation, an
executor or personal representative, guardian, or conservator of 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 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
Participant retains the right to vote any 

  

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Shares so transferred; (ii) upon 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 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 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 Participant desires to accept that offer (except for a Permitted Transfer), 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 Participant during the Company Option Period. Delivery of the Exercise Notice shall obligate the Company to purchase and Participant to sell the Shares of 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, 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 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
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. 
  

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 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 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 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, 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 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 Participant in order to consummate such Sale Transaction. 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 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 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 Participant to that effect. The Controlling Stockholder shall also cause to be remitted to Participant the proceeds attributable to the
sale of 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 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 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 

  

 B-4 

 
$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 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 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 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 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 

  

 B-5 

 
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. 
 ARTICLE V

 MARKET STAND-OFF AGREEMENT 
 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, 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 Participant or beneficially owned by 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. 
  

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 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 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 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. 
  

 B-7 

 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. 
 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
	 	
	
	  

	 Emile Nuwaysir

  

 B-8 

 EXHIBIT C 
 INVESTMENT REPRESENTATION STATEMENT 
  

			
	PARTICIPANT:	 	EMILE NUWAYSIR
		
	COMPANY:	 	NIMBLEGEN SYSTEMS INC.
		
	SECURITY:	 	SERIES E PREFERRED STOCK
		
	AMOUNT:	 	
		
	DATE:	 	

 In connection with the purchase of the above-listed shares of Series E Preferred Stock (the
“Securities”), the undersigned employee, director or advisor (“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-1 

 (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 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:	 	
		
	  
	 	
	Emile Nuwaysir	 	
		
	Date:                     , 20    	 	

  

 C-2 

 NIMBLEGEN SYSTEMS, INC. 
 AWARD AGREEMENT 
 This Award Agreement, entered into as of December 26,
2006 (the date of grant), is between NimbleGen Systems, Inc., a Delaware corporation (the “Company”), and Emile Nuwaysir (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 any of its Subsidiaries, 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 60,000 shares of the Company’s Common Stock (individually, a “Share” and jointly, the “Shares”) at the purchase price of $1.15 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 fourth 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 one-fourth of the Shares on the first anniversary of the
date of this Award Agreement, and an additional one-fourth of the Shares will vest as of each of the three (3) subsequent anniversaries of such date, provided that the Participant is still in the employ of the Company on each vesting date.
Notwithstanding the foregoing, the Option will become fully vested upon the first to occur of the following: (a) the Participant’s death or Disability while in the employ of the Company, or (b) the termination of the
Participant’s employment with the Company and its Subsidiaries (other than a Termination for Cause), or the Participant’s termination of his employment for Good Reason (but not otherwise), within the period commencing on the one hundred
eightieth (180th) day prior to the occurrence of a Change in Control 

 
and ending on the two year anniversary of the occurrence of the Change in Control. Shares vest according to this schedule, whether or not the Option has been
exercised. For purposes hereof, “Good Reason” means, without the Participant’s consent, the occurrence of any one or more of the following during the Participant’s employment with the Company: (i) any reduction by the
Company of the Participant’s duties or responsibilities which reduction is material based on the Participant’s overall duties and responsibilities (ignoring incidental duties and responsibilities) prior to and after such reduction which
remains uncured, if cure thereof is necessary, ten (10) business days after the Participant has given written notice to the Company which specifies such reduction and the Participant’s objection thereto; (ii) any job requirement
imposed by the Company that the Participant change the Participant’s principal residence to a location more than seventy five (75) miles from Dane County, Wisconsin; or (iii) any material breach of any obligation of the Company
for the payment or provision of compensation or other benefits to the Participant set forth in any written agreement between the Company and the Participant then in effect and describing terms and conditions of the Participant’s employment,
which remains uncured ten (10) business days after the Participant has given written notice to the Company which specifies the breach. 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) Except as otherwise provided in paragraphs (c) through (e), if the employment of
the Participant terminates or service to the Company by a non-employee terminates, the Option, to the extent not exercised, shall terminate three (3) months after termination of employment or service with the Company, as the case may be. In the
event that the Participant changes his employment status with the Company, but continues to render services to the Company (e.g. changes from consultant status to employee status), such change in status does not constitute a termination of
employment or service. 
 (c) If the Participant’s termination of employment with the Company is a Termination for Cause,
the Option may not be exercised and all of the Participant’s rights in the Option shall be forfeited upon such termination of employment. 
 (d) If termination of employment results from the Disability of the Participant, this Option may be exercised at any time within one (1) year after such termination of employment. 
 (e) If termination of employment results from the death of the Participant, the personal representative of the Participant’s estate,
or a person who by bequest, inheritance, or otherwise by reason of the Participant’s death acquired the right to exercise the Option, may exercise any Option at any time within one (1) year after the death of the Participant. 

 

 2 

 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.

 1.6. Incentive Stock Option Treatment. It is intended that all of the Option shall qualify as an incentive stock option pursuant to
Section 422 of the Code to the extent it meets the requirements thereof, including the $100,000 per year limitation contained in Section 422(d) of the Code. 
 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. 
 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. 

  

 3 

 
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 employment with 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 the termination of the Participant’s employment with the Company 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 employment. 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. 
  

 4 

 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 Employment Rights. This Award
Agreement shall not confer upon the Participant any right with respect to continuation of employment by the Company, nor shall it interfere in any way with the right of the Company to terminate the Participant’s employment at any time, except
as otherwise provided in any written employment agreement between the Participant and the Company. 
 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. 
  

 5 

 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/ David S. Snyder
	 	
		 	David S. Snyder,	 	
		 	Vice President and Chief Financial Officer	 	

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

			
	Participant:	 	
		
	 /s/ Emile Nuwaysir
	 	
	Emile Nuwaysir	 	

  

 6 

 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
December 26, 2006 (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 and 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 December 26,
2006 (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. 
 “Disability” has the meaning given in Section 2(i) of the Plan. 
 “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 

  

 B-2 

 
Company; (iv) any exchange of existing Shares for other shares of the same or a different class or series in the Company, whether through 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. 
  

 B-3 

 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 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 

  

 B-4 

 
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 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 

  

 B-5 

 
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. 
 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. 
  

 B-7 

 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. 
 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 employee, director or advisor (“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

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