Document:

Amendment to Loan Documents

 Exhibit 10.6 
 AMENDMENT TO LOAN DOCUMENTS  
 THIS AMENDMENT TO LOAN DOCUMENTS (this
“Amendment”) is made as of this 26th day of January, 2007, by and among NIMBLEGEN SYSTEMS, INC., a Delaware corporation (“NimbleGen”), and NIMBLEGEN SYSTEMS OF ICELAND, LLC, a Delaware limited
liability company (“NimbleGen Iceland”; and together with NimbleGen, individually and collectively, “Borrower”), and GENERAL ELECTRIC CAPITAL CORPORATION, a Delaware corporation (together with its successors
and assigns, collectively, “Lender”). 
 RECITALS 
 A. Pursuant to the Amended and Restated Loan and Security Agreement, dated as of December 29, 2006 (as amended, restated, supplemented or
otherwise modified from time to time, the “Loan Agreement”), by and among Borrower and Lender, the parties have established certain financing arrangements that allow Borrower to borrow funds from Lender in accordance with the terms
and conditions set forth in the Loan Agreement. 
 B. Borrower has requested that Lender agree to make certain amendments to the Loan
Documents, and Lender is willing to agree to such requests, in accordance with the terms and conditions set forth below. 
 NOW,
THEREFORE, in consideration of the premises set forth above, the terms and conditions contained in this Amendment, and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, Lender and Borrower
hereby agree as follows: 
 1. Recitals; Definitions. The foregoing recitals, including all terms defined therein, are
incorporated herein and made a part hereof. All capitalized terms used herein (including, without limitation, in the foregoing recitals) and not defined herein shall have the meanings given to them in the Loan Agreement. 
 2. Amendments to Loan Documents. 
 (a) The following provision is hereby added to the Loan Agreement as Section 9.16(b): 
 “ (b) Any information from
time to time delivered to Lender by Borrower that is identified as confidential and that is not in the public domain shall be held by Lender as confidential, shall be used solely in connection with the Obligations (as they may be increased, amended,
refinanced, renewed or otherwise modified from time to time), the Loan Documents (including without limitation, the Warrant) and services related thereto and the transactions contemplated thereby, and shall not be disclosed by Lender to any other
Person; provided, that Lender may make disclosure of confidential information (i) to its independent accountants and legal counsel (which Persons shall be likewise bound by the provisions of this Section 9.16(b)),
(ii) pursuant to statutory and regulatory requirements or demand by any Governmental Authority, (iii) pursuant to any mandatory court order or subpoena or in connection with any legal process, (iv) pursuant to any written agreement
hereafter made between Lender and Borrower to which such information relates, which agreement permits such disclosure, (v) as necessary or advisable in connection with the exercise of any remedy by Lender under the Loan Documents, (vi) in
accordance with Section 6.11 (vii) consisting of general portfolio information that does not identify Borrower, (vii) that has heretofore been made generally available to the public or is otherwise available to Lender on a
non-confidential basis from a source that is not, to its knowledge, subject to a confidentiality agreement with Borrower, (ix) to any assignee of or participant in any of the Obligations, or to any prospective assignee or participant in any of
the Obligations, provided, that such prospective assignee or participant is subject to an agreement containing provisions substantially the same as those set forth in this Section 9.16(b), and (x) in connection with any
litigation to which Lender or its Affiliates is a party. All financial statements and reports furnished by Borrower to Lender under Section 5.1 hereof shall be deemed confidential and shall not be disclosed by Lender to any other Person
except as provided in this Section 9.16(b). In the event of any conflict between the terms of this Section 9.16(b) and those of any other contractual obligation between Lender and Borrower (whether or not a Loan Document),
the terms of this Section 9.16(b) shall govern. “ 

 (b) Exhibit G-4 of the Loan Agreement is hereby deleted in its entirety and replaced with the Exhibit G-4
attached hereto as Exhibit A. 
 (c) Each of Schedule B-11, Schedule E-25 and Schedule F-34 of the Information Certificate is hereby
deleted in its entirety and replaced with the Schedule B-11, the Schedule E-25 and the Schedule F-34 attached hereto as Exhibit B, Exhibit C and Exhibit D, respectively. 
 3. No Other Amendments. Except for the amendments expressly set forth and referred to in Section 2 above, the Loan Agreement
and all other Loan Documents shall remain unchanged and in full force and effect, and this Amendment shall be limited precisely and expressly as drafted and shall not be construed as a consent to the amendment, restatement, modification,
supplementation or waiver of any other terms or provisions of the Loan Agreement or any other Loan Document. Nothing in this Amendment is intended, or shall be construed, to constitute a novation or an accord and satisfaction of any of
Borrower’s indebtedness under or in connection with the Loan Agreement or any other indebtedness to Lender. 
 4. Confirmation of
Representations and Warranties. 
 Borrower hereby confirms that all of the representations and warranties set forth in Article IV of
the Loan Agreement continue to be true and correct as of the date hereof, except to the extent such representations and warranties by their terms expressly relate only to a prior date (in which case such representations and warranties shall be true
and correct as of such prior date). 
 5. Costs and Expenses. 
 Borrower shall be responsible for the payment of all fees, costs and expenses incurred by Lender in connection with the preparation and negotiation of
this Amendment, including, without limitation, any and all fees and expenses of Lender’s in-house and outside counsel. All fees, costs and expenses shall be due and payable upon demand of Lender, and if not paid promptly upon such demand, all
such fees, costs and expenses shall become part of the Obligations in accordance with Section 2.4 of the Loan Agreement. 
 6.
Reference to the Effect on the Loan Agreement. 
 (a) Upon the effectiveness of this Amendment, each reference in the Loan
Agreement to “this Agreement,” “hereunder,” “hereof,” “herein” or words of similar import shall mean and be a reference to the Loan Agreement as modified by this Amendment. 
 (b) Except as specifically modified above, the Loan Agreement and all other Loan Documents, shall remain in full force and effect, and are hereby
ratified and confirmed. 
 (c) The execution, delivery and effectiveness of this Amendment shall not, except as expressly provided in this
Amendment, operate as a waiver of any right, power or remedy of Lender, nor constitute a waiver of any provision of the Loan Agreement or any other documents, instruments and agreements executed or delivered in connection with the Loan Agreement.

 7. Governing Law. This Amendment shall be governed by and construed in accordance with the laws of the State of New York.

 8. Headings. Section headings in this Amendment are included for convenience of reference only and shall not constitute a
part of this Amendment for any other purpose. 
 9. Counterparts. This Amendment may be executed in counterparts, and such
counterparts taken together shall be deemed to constitute one and the same instrument. Delivery of an executed counterpart of this Amendment by telefacsimile or other electronic method of transmission shall be equally as effective as delivery of an
original executed counterpart of this Amendment. Any party delivering an executed counterpart of this Amendment by telefacsimile or other electronic method of transmission also shall deliver an original executed counterpart of this Amendment but the
failure to deliver an original executed counterpart shall not affect the validity, enforceability or binding effect of this Amendment. 
  

 2 

 [SIGNATURES FOLLOW] 
  

 3 

 IN WITNESS WHEREOF, intending to be legally bound, each party has caused this Amendment to be
executed by its duly authorized officer as of the date first written above. 
  

					
	LENDER:
	
	GENERAL ELECTRIC CAPITAL CORPORATION,
	a Delaware corporation
		
	By:	 	 /s/ Danijela Gjenero

	Name:	 	Danijela Gjenero
	Title:	 	Duly Authorized Signatory
		
	By:	 	 /s/ Scott R. Towers

	Name:	 	Scott R. Towers
	Title:	 	Duly Authorized Signatory
	
	BORROWER:
	
	NIMBLEGEN SYSTEMS INC.,
	a Delaware corporation
		
	By:	 	 /s/ David S. Snyder

	Name:	 	David S. Snyder
	Title:	 	Vice President and Chief Financial Officer
	
	NIMBLEGEN SYSTEMS OF ICELAND, LLC,
	a Delaware limited liability company
		
	By:	 	NIMBLEGEN SYSTEMS INC., its sole member
		
	By:	 	 /s/ David S. Snyder

	Name:	 	David S. Snyder
	Title:	 	Vice President and Chief Financial Officer

  

 S-1 

 EXHIBIT G-4 
 Payment Schedule for Term C Loan 
  

																			
	 Period
	  	 Starting
 Balance
	  	Takedowns	  	Payment	  	Interest	  	Principal	  	 Remaining
 Balance

	 1/26/2007
	  			  	$	2,500,000.00	  			  			  			  	$	2,500,000.00
	 2/1/2007
	  	$	2,500,000.00	  			  	$	4,156.25	  	$	4,156.25	  			  	$	2,500,000.00
	 3/1/2007
	  	$	2,500,000.00	  			  	$	82,999.96	  	$	24,937.50	  	$	58,062.46	  	$	2,441,937.54
	 4/1/2007
	  	$	2,441,937.54	  			  	$	82,999.96	  	$	24,358.33	  	$	58,641.63	  	$	2,383,295.91
	 5/1/2007
	  	$	2,383,295.91	  			  	$	82,999.96	  	$	23,773.37	  	$	59,226.59	  	$	2,324,069.32
	 6/1/2007
	  	$	2,324,069.32	  			  	$	82,999.96	  	$	23,182.60	  	$	59,817.36	  	$	2,264,251.96
	 7/1/2007
	  	$	2,264,251.96	  			  	$	82,999.96	  	$	22,585.91	  	$	60,414.05	  	$	2,203,837.91
	 8/1/2007
	  	$	2,203,837.91	  			  	$	82,999.96	  	$	21,983.28	  	$	61,016.68	  	$	2,142,821.23
	 9/1/2007
	  	$	2,142,821.23	  			  	$	82,999.96	  	$	21,374.64	  	$	61,625.32	  	$	2,081,195.91
	 10/1/2007
	  	$	2,081,195.91	  			  	$	82,999.96	  	$	20,759.93	  	$	62,240.03	  	$	2,018,955.88
	 11/1/2007
	  	$	2,018,955.88	  			  	$	82,999.96	  	$	20,139.09	  	$	62,860.87	  	$	1,956,095.01
	 12/1/2007
	  	$	1,956,095.01	  			  	$	82,999.96	  	$	19,512.05	  	$	63,487.91	  	$	1,892,607.10
	 1/1/2008
	  	$	1,892,607.10	  			  	$	82,999.96	  	$	18,878.75	  	$	64,121.21	  	$	1,828,485.89
	 2/1/2008
	  	$	1,828,485.89	  			  	$	82,999.96	  	$	18,239.15	  	$	64,760.81	  	$	1,763,725.08
	 3/1/2008
	  	$	1,763,725.08	  			  	$	82,999.96	  	$	17,593.16	  	$	65,406.80	  	$	1,698,318.28
	 4/1/2008
	  	$	1,698,318.28	  			  	$	82,999.96	  	$	16,940.72	  	$	66,059.24	  	$	1,632,259.04
	 5/1/2008
	  	$	1,632,259.04	  			  	$	82,999.96	  	$	16,281.79	  	$	66,718.17	  	$	1,565,540.87
	 6/1/2008
	  	$	1,565,540.87	  			  	$	82,999.96	  	$	15,616.27	  	$	67,383.69	  	$	1,498,157.18
	 7/1/2008
	  	$	1,498,157.18	  			  	$	82,999.96	  	$	14,944.12	  	$	68,055.84	  	$	1,430,101.34
	 8/1/2008
	  	$	1,430,101.34	  			  	$	82,999.96	  	$	14,265.26	  	$	68,734.70	  	$	1,361,366.64
	 9/1/2008
	  	$	1,361,366.64	  			  	$	82,999.96	  	$	13,579.63	  	$	69,420.33	  	$	1,291,946.31
	 10/1/2008
	  	$	1,291,946.31	  			  	$	82,999.96	  	$	12,887.16	  	$	70,112.80	  	$	1,221,833.51
	 11/1/2008
	  	$	1,221,833.51	  			  	$	82,999.96	  	$	12,187.79	  	$	70,812.17	  	$	1,151,021.34
	 12/1/2008
	  	$	1,151,021.34	  			  	$	82,999.96	  	$	11,481.44	  	$	71,518.52	  	$	1,079,502.82
	 1/1/2009
	  	$	1,079,502.82	  			  	$	82,999.96	  	$	10,768.04	  	$	72,231.92	  	$	1,007,270.90
	 2/1/2009
	  	$	1,007,270.90	  			  	$	82,999.96	  	$	10,047.53	  	$	72,952.43	  	$	934,318.47
	 3/1/2009
	  	$	934,318.47	  			  	$	82,999.96	  	$	9,319.83	  	$	73,680.13	  	$	860,638.34
	 4/1/2009
	  	$	860,638.34	  			  	$	82,999.96	  	$	8,584.87	  	$	74,415.09	  	$	786,223.25
	 5/1/2009
	  	$	786,223.25	  			  	$	82,999.96	  	$	7,842.57	  	$	75,157.39	  	$	711,065.86
	 6/1/2009
	  	$	711,065.86	  			  	$	82,999.96	  	$	7,092.89	  	$	75,907.07	  	$	635,158.79
	 7/1/2009
	  	$	635,158.79	  			  	$	82,999.96	  	$	6,335.71	  	$	76,664.25	  	$	558,494.54
	 8/1/2009
	  	$	558,494.54	  			  	$	82,999.96	  	$	5,570.98	  	$	77,428.98	  	$	481,065.56
	 9/1/2009
	  	$	481,065.56	  			  	$	82,999.96	  	$	4,798.63	  	$	78,201.33	  	$	402,864.23
	 10/1/2009
	  	$	402,864.23	  			  	$	82,999.96	  	$	4,018.57	  	$	78,981.39	  	$	323,882.84
	 11/1/2009
	  	$	323,882.84	  			  	$	82,999.96	  	$	3,230.73	  	$	79,769.23	  	$	244,113.61
	 12/1/2009
	  	$	244,113.61	  			  	$	82,999.96	  	$	2,435.04	  	$	80,564.92	  	$	163,548.69
	 1/1/2010
	  	$	163,548.69	  			  	$	82,999.96	  	$	1,631.40	  	$	81,368.56	  	$	82,180.13
	 1/25/2010
	  	$	82,180.13	  			  	$	82,999.88	  	$	819.75	  	$	82,180.13	  	$	 —  

	*	A portion of the Term Facility Commitment Fee in an amount equal to $12,500 shall be applied to the Period 1 payment in accordance with Section 2.3(f) of the Loan Agreement.

 Exhibit A 
  

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860 

 Exhibit B 
 SCHEDULE B-11 
 Material Contracts 
  

	 	1.	License Agreement, Sigma Aldrich Co. 

  

	 	2.	License Agreement, Oxford Gene Technology IP Limited 

  

	 	3.	License Agreement, WARF 

  

	 	4.	Lease Agreement, Madison 

  

	 	5.	Lease Agreement, Iceland 

  

	 	6.	Supply Agreement, Affymetrix 

  

	 	7.	Distributor Agreement, Bucher Biotech AG 

  

	 	8.	Distributor Agreement, RZPD 

  

	 	9.	Distributor Agreement, Central European Biosystems 

  

	 	10.	Distributor Agreement, IFOM-IEO Campus for Oncogenomics 

  

	 	11.	Distributor Agreement, Genetic Research Instrumentation 

  

	 	12.	Distributor Agreement, Ecogen S.A. 

  

	 	13.	Distributor Agreement, Westburg 

  

	 	14.	Distributor Agreement, GeneChannel Biotech 

  

	 	15.	Distributor Agreement, GeneFrontier 

  

	 	16.	Distributor Agreement, Research Biolabs PTE LTD 

  

	 	17.	Distributor Agreement, Macrogen 

  

	 	18.	Distributor Agreement, PCL Lab 

  

	 	19.	Distributor Agreement, Cold Spring Biotech Corp. 

  

	 	20.	Distributor Agreement, Fen Jih Biomedical & Instrument Co., Ltd. 

  

	 	21.	Government Grant, R21 CA116365-01 

  

	 	22.	Government Grant, 5 R01 HG003129-03 

  

	 	23.	Government Grant, 5 R01 HG003107-03 

 Exhibit B 

 

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860 

	 	24.	Consulting Agreement, Dirk van den Broek 

  

	 	25.	Consulting Agreement, Christian C. Oste 

  

	 	26.	Consulting Agreement, David C. Sneider 

  

	 	27.	Amended and Restated Supply Agreement, LindGen EHF 

  

	 	28.	Supply Agreement, Proligo Products LLC 

  

	 	29.	Exclusive Technology License Agreement, University of Texas System* 

  

	 	30.	Agreement (granting a license to), Texas Instruments Incorporated 

  

	 	31.	Commercial Use License Agreement, Affymetrix, Inc.* 

  

	 	32.	Supply and Licence Agreement, Oxford Gene Technology (Operations) Limited 

  

	 	33.	Licence Agreement, Oxford Gene Technology IP Limited* 

  

	 	34.	Agreement (relating to license), Wolfgang Pfleidlerer** 

  

	 	35.	Employment Agreements (various forms), all employees 

  

	 	36.	Agreement, Robert Palay and Thomas Palay 

  

	 	37.	Transaction Bonus Agreements, various employees 

  

	 	38.	Award (stock option) Agreements, various employees and consultants 

  

	 	39.	Letter Agreement (relating to stock option), Gregory P. McGuiness 

  

	 	40.	License Agreement, Invitrogen Corporation* 

  

	 	41.	Sub-License Agreement, Invitrogen IP Holdings, Inc.* 

  

	 	42.	License Agreement, Spotfire Inc. 

	*	Agreement contains confidentiality restrictions such that Borrower will deliver a copy thereof if an appropriate confidentiality agreement is in effect; with Lender’s
permission, a copy is not being delivered herewith for purposes of item (c) on Exhibit D to the Loan Agreement. 

	**	Agreement may contain confidentiality restrictions such that Borrower will deliver a copy thereof if an appropriate confidentiality agreement is in effect; with Lender’s
permission, a copy is not being delivered herewith for purposes of item (c) on Exhibit D to the Loan Agreement. 

  

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860 

 Exhibit C 
 SCHEDULE E-25 
  

	1.	Consulting Agreement, Dirk van den Broek 

  

	2.	Consulting Agreement, Christian C. Oste 

  

	3.	Consulting Agreement, David C. Sneider 

  

	4.	Agreement, Robert Palay and Thomas Palay 

  

	5.	Consulting Agreements from time to time with members of the Company’s Scientific Advisory Board. The current members of the Company’s Scientific Advisory Board are Michael
Sussman, Franco Cerrina, Fred Blattner and Harold “Skip” Garner. 

 Exhibit B 
  

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860 

 Exhibit D 
 NIMBLEGEN SYSTEMS, INC. 
 PATENT STATUS January 26, 2007 
 WARF PATENT APPLICATIONS 
  

	 	1.	Method and Apparatus for Synthesis of Arrays of DNA Probes 

 S. N. 09/253,460 2/22/99 
 Issued as U. S. Patent No. 6,375,903 April 23, 2002

  

	 	2.	CIP of Method and Apparatus for Synthesis etc (CIP) 

 Pending/Materials to provoke Interference have been filed. 
  

	 	3.	Method and Apparatus for Synthesis of Arrays of DNA Probes (Continuation of basic case) Pending. 

  

	 	4.	Apparatus for Synthesis of Arrays of DNA Probes (Divisional or continuation of 09/637,891) 

 Pending application S.N. 11/524,082, filed September 20, 2006. 
  

	 	5.	Flow Cell for Synthesis of Arrays of DNA Probes and the Like (Mechanics of flow cell) 

 S. N. 09/473,369 11/10/99 
 Issued as U.S. Patent No. 6,315,958. 
  

	 	6.	Flow Cell for Synthesis of Arrays of DNA probes and the Like (continuation of flow cell case) 

 S. N. 10/053,368 11/9/01 (Continuation) 
 Issues as U.S. Patent No. 6,444,175. 
 NIMBLEGEN CASES 
  

	 	1.	Q&B 90068 Gray Scale Idea 

 Pending. S.
N. 10/061,577 filed Jan 31, 2002. 
 PCT US03/02526 filed Jan 28, 2003 
  

	 	2.	Q&B 90084 Coherent Light Optical System for MAS 

 Provisional application S. N. 60/353,491 filed Jan. 31, 2002. 
 Pending as S. N. 10/277,530
filed Oct. 21, 2002. 
 PCT US03/02524 filed Jan 28, 2003 
  

	 	3.	Q&B 90106 Volatile Buffer Hybridization Wash for Array Analysis 

 Provisional application S. N. 60/353,841 filed Feb 1, 2002. 
 Pending S. N. 10/355,784 filed
Jan 31, 2003 
  

	 	4.	Q&B 90114 High Contrast Flow Cell 

 Pending S. N. 10/062,918 filed Feb 1, 2002. 
 PCT US03/02541 filed Jan. 28, 2003 
 Australia 2003210720 filed Jan 28, 2003 
 Canada 2474623 filed Jan 28, 2003 
 Europe 03737558 filed Jan 28, 2003 
 Iceland 7369 filed Jan 28, 2003 
 Japan 2003-565630 filed Jan 28, 2003 
 Exhibit B 
  

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860 

	 	5.	Q&B 90131 Reduced Numerical Aperture Optics for MAS 

 Pending S. N. 10/062,967 filed Jan 31, 2002. 
 PCT US03/02568 filed Jan 28, 2003 

Canada 2474488 filed Jan 28, 2003 
 Europe 03735055 filed Jan 28, 2003 
 Iceland 7368 filed Jan 28, 2003 
 Japan 2003-564288 filed Jan 28, 2003 
  

	 	6.	Q&B 90149 Direct Detection of RNA Hybridization 

 Provisional application S. N. 60/335,377 filed Nov. 2, 2001. 
 Pending S. N. 10/062,918 filed
Nov. 1, 2002 
 PCT US02/35379 filed November 11, 2002. 
  

	 	7.	Q&B 90157 Prepatterned substrate 

 Provisional application S. N. 60/353,219 filed Jan. 31, 2002. 
 Pending S. N. 10/279.200 filed October 23,
2002. 
 Issued as US Patent No. 7157229 January 2, 2007. 
 PCT US03/02525 filed January 28, 2003. 
 Australia 2003214924 filed Jan 28, 2003. 
 Canada 2474601 filed Jan 28, 2003. 
 Europe 03710770 filed Jan 28, 2003. 
 Iceland 7367 filed Jan 28, 2003. 
 Japan 2003-563707 filed Jan 28, 2003. 
  

	 	8.	Q&B 90165 Array of arrays 

 Provisional
application S. N. 60/383,559 filed May 24, 2002. 
 Pending S. N. 10/444,307 filed May 23, 2003. 
 PCT US03/16429 filed May 23, 2003. 
 Australia 2003124607 filed May 23, 2003. 
 Canada 2487093 filed May 23, 2003.

 Europe              filed May 23, 2003. 
 Iceland 7611 filed May 23, 2003. 
 Japan 2004-508254 filed May 23, 2003. 
  

	 	9.	Q&B 90181 Array of Arrays with visible alignment marks 

 Provisional application S. N. 60/415,119 filed Sept. 30, 2002. 
 Pending S. N. 10/675,329
filed Sept. 30, 2003. 
  

	 	10.	Q&B 90190 Sandwich Hybridization Method 

 Provisional application S. N. 60/415,118 filed Sept. 30, 2002. 
 Combined with 90238 for conventional filing.

  

	 	11.	Q&B 90203 Maskless Microarray with Hydrophobic barriers 

 Provisional patent S. N. 60/414,777 filed Sept. 27, 2002. 
 Pending S. N. 10/673,760 filed
Sept. 29, 2003 
 Pending (divisional) S.N. 11/604,582 filed Nov. 27, 2006. 
  

	 	12.	Q&B 90211 Synthesis of multiple oligos per feature 

 Provisional application S. N. 60/415,046 filed Oct 1, 2002. 
 Pending S. N. 10/674,766 filed
Sept. 30, 2003. 
 PCT US03/30725 filed Sept. 30, 2003. 
  

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860 

	 	13.	Q&B 90220 Hybridization Wheel 

 Provisional application S. N. 60/500,142 abandoned 
  

	 	14.	Q&B 90238 Parallel loading of arrays 

 Provisional application S. N. 60/415,090 filed Oct. 1, 2002. 
 Pending S. N. 10/674,768 filed Sept. 30, 2003.

 PCT US03/30841 filed Sept. 30, 2003. 
  

	 	15.	Q&B 00010 PCR on a chip 

 Provisional
application 60/535,982 filed January 12, 2004. 
 Pending S. N. 11/034,374 filed Jan 12, 2005 
 PCT US05/00935 filed Jan 12, 2005 
  

	 	16.	Q&B 00013 AI Base Calling Algorithm 

 Provisional application 60/539,220 filed January 26, 2004. 
 Pending S. N. 11/043,294 filed Jan. 26, 2005

 PCT US05/02429 filed Jan 26, 2005 
  

	 	17.	Q&B 00012 Comparative Genomic Resequencing 

 Provisional application S. N. 60/560,447 filed April 8, 2004 
 Pending S.N. 11/101,841 filed April 8, 2005

  

	 	18.	Q&B 00019 Variable Probe Length Selection 

 Provisional application 60/581,121 filed June 18, 2004 
 Pending S.N. 11/156,439 filed June 20, 2005

 PCT US05/22153 filed June 20, 2005 
  

	 	19.	Q&B 00021 Probe Optimization Methods 

 Provisional application 60/650,265 filed Feb. 4, 2005 
 Pending S.N. 11/157,629 filed June 21, 2005 

PCT US05/21971 filed June 21, 2005 
  

	 	20.	Q&B 00026 Optimized Probe Selection Method 

 Pending S.N. 11/346,927 filed Feb. 3, 2006 
 WO US06/04017 filed Feb. 3, 2006 
  

	 	21.	Q&B 00025 Method for Identification and Monitoring of Epigenetic Modifications 

 Pending WO US06/047513 filed Dec. 13, 2006 
  

	 	22.	Q&B 00027 Use of Microarrays for Genomic Representation Selection 

 Provisional application S.N. US 60/794,560 filed April 24, 2006 
  

	 	23.	Q&B 00029 Method and Composition for Enrichment of Genomic Regions 

 Provisional application: US 60/832,719 filed July 21, 2006 
 Cases acquired from Light Biology:

  

	 	24.	U. S. Patent No. 6,295,153 to Garner 

  

	 	25.	U.S. Ser. No. 09/998,341 filed Nov. 29, 2001 Digital Optical Chemistry Micromirror Imager (Garner) 

 Interference 105,455 (JL) terminated by Bd. Pat. App. Int.; appeal possible 
  

	 	26.	U.S. Ser. No. 09/999,239 filed Nov. 29, 2001 Digital Chemistry Micromirror Imager (Garner) 

 Interference 105,455 (JL) terminated by Bd. Pat. App. Int.; appeal possible 
  

 Amd to Loan Doc & Waiver to A&R LSA 
 DC - 026625/0005 - 2422860Office Lease by and among the Registrant

 Exhibit 10.10 
 1 SCIENCE COURT 
 OFFICE LEASE 
 BETWEEN 
 WARZYN BUILDING ASSOCIATES, LANDLORD 
 AND 
 NIMBLEGEN SYSTEMS, INC. 
 AND NIMBLEGEN SYSTEMS, LLC, TENANT 
 TABLE OF CONTENTS 
  

					
	Section	  	Page
	1.	  	Leased Premises	  	1
	2.	  	Term of Lease	  	1
	3.	  	Security Deposit	  	1
	4.	  	Rental	  	2
	5.	  	Services Provided	  	2
	6.	  	Repairs and Maintenance	  	4
	7.	  	Fire or Casualty	  	4
	8.	  	Construction	  	5
	9.	  	Use of Leased Premises	  	6
	10.	  	Janitorial Services	  	6
	11.	  	Rights of Parties	  	6
	12.	  	Assignments and Subleases	  	6
	13.	  	Injury and Loss	  	7
	14.	  	Eminent Domain	  	7
	15.	  	Entry of Landlord	  	7
	16.	  	Subordination of Mortgages	  	7
	17.	  	Building Rules and Regulations	  	7
	18.	  	Signs	  	8
	19.	  	Surrender	  	8
	20.	  	No Waiver; Separability and Miscellaneous	  	8
	21.	  	Notices	  	8
	22.	  	Default	  	9
	23.	  	Estoppel Certificate	  	10
	24.	  	Alterations and Additions	  	10
	25.	  	Recording	  	11
	26.	  	Building Manager	  	11
	27.	  	Brokerage	  	11
	28.	  	Waiver of Trial by Jury and Counterclaims	  	11
	29.	  	Limitation of Landlord’s Liability	  	11
	30.	  	Environmental Compliance	  	11
	31.	  	Parking	  	13
	32.	  	Financial Information	  	13

 Addendum 
 Exhibits A and
B—Floor Plans 
 Exhibit C—Building Rules and Regulations 
  

 ii 

 1 SCIENCE COURT 
 OFFICE LEASE 
 THIS LEASE, made this 14th day of November, 2000, by and between WARZYN BUILDING ASSOCIATES,
hereinafter referred to as the “Landlord”, and NIMBLEGEN SYSTEMS, INC. and NIMBLEGEN SYSTEMS, LLC, hereinafter collectively referred to as the “Tenant.” 
 WITNESSETH: 
 1. Leased Premises. Landlord hereby leases to Tenant, and Tenant
hereby leases from Landlord, on the terms, covenants, and conditions herein stated the premises on the bottom and first floors of 1 Science Court in Madison, Wisconsin (the “building”) as outlined on the floor plans attached hereto as
Exhibits A and B and hereby incorporated and made a part hereof (the “Leased Premises”), together with the non-exclusive right of use of the common areas of the building, reserving to Landlord the right to use the roof and exterior walls.
Exhibits A and B also indicate shared areas leased by one of the two tenants in the building but which can be used by the other party (the “Shared Area”). 
 2. Term of Lease. This Lease is for a term of thirty (30) months, commencing January 11, 2001, and terminating at 11:59 p.m. on July 10, 2003. Such period together with any options to extend as
provided in the attached Addendum as to which Tenant has properly exercised its option to extend shall hereinafter collectively be referred to as the “term.” If possession of the Leased Premises is not delivered to Tenant by
January 11, 2001, this Lease shall commence on the first day of the calendar month following the delivery of the Leased Premises to Tenant. To the extent Tenant suffers out-of-pocket expenses resulting from Landlord’s failure to deliver
the Leased Premises to Tenant on or before January 11, 2001, Landlord shall, after Tenant has begun to occupy the Leased Premises, assign to Tenant, without cost or expense to Landlord, any rights Landlord has to collect damages from its
previous tenant for its previous tenant’s failure to timely vacate. Tenant shall not have any further rights or remedies against Landlord for such delayed occupancy. If the Leased Premises are delivered and Tenant accepts possession on any day
earlier than the first day of the calendar month, rental for the interim shall be paid by Tenant on a pro rata basis. Such earlier or later taking of possession shall not change the termination date of this Lease. If possession of the Leased
Premises is not delivered to Tenant by March 11,2001, time being of the essence, Tenant shall have the right to terminate this Lease by giving Landlord written notice of termination on or after March 11, 2001 and prior to delivery of
possession of the Leased Premises to Tenant. 
 3. Security Deposit. Tenant has paid Landlord at the execution hereof the amount of
Seventy-Two Thousand Nine Hundred Thirty-Six Dollars ($72,936) as security (the “Security Deposit”) for the performance of the terms hereof by Tenant, which shall be returned to Tenant within thirty (30) days after the termination of
the Lease if it has discharged its obligations to Landlord in full, although Fifty-Four Thousand Seven Hundred Dollars ($54,700) of the Security Deposit may be returned earlier as provided in the last sentence of this section. In the event of
Tenant’s default, Landlord may, at its option, apply all or part of the deposit to cure such default in whole or in part. Landlord may, in its sole discretion, resort to any or all rights and remedies against Tenant before applying such
deposit. Use of such deposit shall not prevent Landlord from exercising other rights or remedies provided by this Lease or at law 

 
or in equity. Throughout the term of this Lease, Tenant shall replenish any portion of the deposit used, applied or retained within ten (10) days of
written demand therefor by Landlord. Landlord may commingle and invest the deposit without obligation to pay interest on or account for the deposit. Landlord may assign the deposit to any successor in interest, thereby releasing Landlord from
liability therefor. Tenant may not assign the deposit without Landlord’s prior written consent. At such time as Tenant provides Landlord with a true and complete balance sheet, certified for accuracy and completeness by Tenant’s chief
financial officer, which fairly depicts Tenant’s net worth (defined as Tenant’s tangible net assets, reasonably valued, less its liabilities) as depicted on Tenant’s balance sheet exceeds Nine Million Dollars ($9,000,000) and provided
Tenant is not otherwise in default under this Lease (and would not be in default with the passage of time or the giving of notice or both), then Landlord shall return to Tenant Fifty-Four Thousand Seven Hundred Dollars ($54,700) of the Security
Deposit. Tenant may from time to time substitute a standby letter of credit for all or a portion of the Security Deposit, in form and from a financial institution reasonably satisfactory to Landlord. 
 4. Rental Tenant shall pay Landlord Eighteen Thousand Two Hundred Thirty-Six Dollars ($18,236) per month as gross rent for the first lease year. A
lease year shall be from February 1 through January 31 of the next succeeding year. Rent for any partial month at the beginning and end of the term shall be based on the then monthly rent multiplied by a fraction, the numerator of which is
the number of days the Lease continues during such partial month and the denominator of which is the number of days in such month. 
 Each
succeeding lease year, the Tenant shall pay the Landlord in equal monthly installments an amount equal to the annualized gross rent for the preceding lease year plus the product obtained by multiplying that rent by four percent (4%). By way of
example, the annualized gross rent shall increase by four percent (4%) commencing February 1, 2002. The gross rent required by this Lease shall be paid to Landlord without notice or demand and without abatement, deduction, setoff or
recoupment in advance by the first day of each month. 
 The rent payable hereunder is intended to be a gross rent and Landlord shall be
responsible for and shall pay as and when due all ground lease rent, its mortgage payments, real estate taxes, property insurance and maintenance and operating costs of the real property except as otherwise expressly set forth herein to the
contrary. 
 5. Services Provided. 
 a. Subject to the remaining provisions of this Paragraph 5, Landlord shall at Landlord’s sole cost, provide utilities, including water, gas, electrical, heating and air conditioning costs and snow removal.

 b. Landlord shall at all times maintain the building as normally provided in an office facility located in the area in which the building
is located. Provided Tenant is not in default hereunder, Landlord shall, at Landlord’s expense, provide the following services: (i) heat and air conditioning Monday through Friday from 7 a.m. to 6 p.m.; Saturdays from 8 a.m. to 2 p.m.,
excluding holidays, as is reasonably necessary for the comfortable occupancy and use of the Leased Premises under normal business operations and in the absence of the use of machines or equipment which affect the temperature otherwise maintained in
the Leased Premises; (ii) hot and 

  

 2 

 
cold water from the regular building outlets for drinking, lavatory and toilet purposes only; (iii) electricity as provided by the local electric
utility company through the building’s normal electric distribution system; (iv) window washing of the exterior of all windows in the Leased Premises, weather permitting at intervals to be reasonably determined by Landlord; and
(v) such additional services on such terms and conditions as Landlord may from time to time reasonably determine. 
 c. Whenever heat
generating machines or equipment, including, but not limited to, telephone equipment and computers, are selected by Tenant for use in the Leased Premises and such machinery or equipment adversely affects the seasonal temperature otherwise maintained
by the building’s air conditioning system, Landlord reserves the right to install supplementary air conditioning units in the Leased Premises, or elsewhere in the building and the cost thereof, including, but not limited to, the cost of
installation, operation and maintenance thereof, shall be paid by Tenant to Landlord upon demand by Landlord as additional rent thereunder. 
 d. If, in Landlord’s reasonable opinion, Tenant is using electricity or electrical services of the building in an amount in excess of the amount normally used by tenants of the building for normal office use, Landlord may, at its
option (i) charge Tenant directly an amount equal to Landlord’s estimate of Tenant’s use of electricity at the Leased Premises (based upon the rate of electricity then being charged to Landlord by the provider of electricity of the
building), or (ii) install an electric meter to meter the use of electricity by Tenant at the Leased Premises, and bill Tenant for such excess electricity (i.e., amounts in excess of the amount normally used by tenants of the building for
normal office use) based upon actual use, which Tenant shall pay, along with the cost of installing such meter, as additional rent hereunder. 
 e. Tenant agrees that Landlord shall not be liable, by abatement of rent, for damages, or otherwise, for failure to furnish or delay in furnishing any service, which failure or delay is caused, in whole or in part, by war, insurrection,
civil disturbance, riots, acts of God, governmental action, repairs, improvements, alterations, strikes, lockouts or picketing (whether legal or illegal) inability to obtain electricity, fuel or supplies, accidents, casualties, acts caused directly
or indirectly by Tenant (or Tenant’s agents, representatives, employees, licensees or invitees) or any other act or cause beyond the reasonable control of Landlord (collectively, “force majeure”). Any such failure or delay in
furnishing any service shall be without any liability of Landlord to Tenant and shall not be deemed to be an eviction or disturbance in any manner of Tenant’s use and possession of the Leased Premises or relieve Tenant from its obligation to
pay all rent when due or from any other obligation hereunder. Notwithstanding the foregoing, if the furnishing of any such service is interrupted for more than fifteen (15) consecutive days other than because of force majeure and such
interruption materially impairs Tenant’s ability to conduct its business within the Leased Premises. Tenant shall have the right to terminate this Lease by giving Landlord written notice of termination at any time after the expiration of such
fifteen (15) day period and prior to the resumption of service. 
 f. Tenant shall have twenty-four (24) hour, seven (7) days
per week access to the Leased Premises. Tenant acknowledges and agrees, however, that access shall be subject to such safety protections as, by way of example but not limitation, use of access cards, as Landlord deems necessary or appropriate and
that services shall be limited as provided in Subparagraph 5(b), above. 
  

 3 

 g. Tenant shall not waste power, heat, cooling or water, and shall comply with all applicable
governmental regulations. Electricity shall only be used for illumination and operation of standard office and laboratory computers and equipment. If any nonstandard equipment is utilized, Landlord’s prior written consent shall be required and
such equipment must be separately metered and such costs both for the metering and for the service itself shall be directly borne and paid for by Tenant. Landlord shall not be liable or responsible for interruptions in utility supplies regardless of
the cause for such interruption except to the extent it results from Landlord’s intentional failure to pay its bills for such services when due or the gross negligence or willful misconduct of Landlord or Landlord’s employees, agents or
contractors. 
 h. Tenant shall make arrangements directly with the telephone company for telephone service in the Leased Premises desired by
Tenant. Tenant shall pay the entire cost of all telephone charges with respect to the Leased Premises and for the maintenance and replacement of light fixtures, lamps, bulbs, tubes, ballasts and starters located within the Leased Premises, as well
as exit sign bulbs. 
 6. Repairs and Maintenance. Landlord agrees to make all necessary repairs to the exterior walls, exterior
doors, windows, corridors and parking lots of the building and to keep the building housing the Leased Premises and the exterior grounds in good repair and condition. Landlord agrees to keep all building equipment, such as elevators, plumbing,
heating, air conditioning, and similar equipment in good repair, but shall not be liable or responsible for breakdowns or temporary interruptions in service where reasonable efforts are used to restore service. No compensation or claim or diminution
of rent will be allowed or paid by Landlord by reason of inconvenience, annoyance or injury to business, arising from the necessity of repairing the Leased Premises or any portion of the building, however the necessity may occur. 
 Tenant agrees that it will make all interior, nonstructural repairs to the Leased Premises not required above to be made by Landlord and to do all
redecorating, including carpeting, remodeling, alteration and painting required by it during the term. Notwithstanding anything contained in the first sentence of this Paragraph 6, Tenant will also pay for any other repairs to the Leased Premises or
the building resulting from its negligence or wrongful intentional acts or that of its agents, employees or invitees and Tenant will also maintain the Leased Premises in a safe, clean, neat, and sanitary condition. All repairs and work by Tenant
shall be done in a good and workmanlike manner and comply with insurance and governmental regulations. 
 7. Fire or Casualty. In the
event the Leased Premises are wholly or partially destroyed by fire or other casualty covered by the usual form of fire and extended coverage insurance rendering them untenantable, Landlord shall, except as otherwise provided in the last sentence of
this paragraph, rebuild, repair, or restore the Leased Premises to substantially the same condition as when the same were furnished to Tenant, and the Lease shall remain in effect during such period. Tenant shall bear the cost of any moving expenses
incurred in moving its property and fixtures as a result of any casualty. In the event of total destruction, gross rent shall abate during the period of reconstruction, and in the event of partial destruction, such rent shall abate pro rata during
the period of reconstruction. In the event, however, that the building containing the Leased Premises is damaged or destroyed to the extent of more than one-third of its replacement cost, Landlord may elect to terminate this Lease by notice to
Tenant within sixty (60) days of the casualty. 
  

 4 

 If thirty-three percent (33%) or more of the square footage of the Leased Premises is damaged or
destroyed by fire or other casualty, Landlord shall provide Tenant with written notice of the estimated time to repair such damage, such notice to be given within thirty (30) days after the date of such casualty. If Landlord reasonably
estimates that the time to repair will be more than one hundred fifty (150) days, or if in any event Landlord fails to repair the damage within one hundred fifty (150) days of the date of such casualty (subject to force majeure), then in
either event Tenant shall have the right to terminate this Lease by giving Landlord written notice of termination within thirty (30) days after receipt of Landlord’s estimate, or within thirty (30) days after the expiration of the one
hundred fifty (150) day period, as applicable. 
 Tenant agrees to be responsible for its own property and any fire insurance policy
carried by Tenant insuring its property located in or upon the Leased Premises shall contain a provision whereby the insurance carrier waives any right of subrogation against Landlord. 
 Each party hereby mutually releases and waives any and all rights of subrogation against the other party which, in the absence of this release and
waiver, would arise in favor of any insurance company insuring either party against loss by fire, extended coverage, casualty and loss of any other type, resulting from damage to or destruction of the building of which the Leased Premises form a
part. 
 Tenant agrees to comply with all rules and regulations of the Board of Fire Underwriters and the rules and regulations of the city,
county, and state; provided that Tenant shall not be required to make any exterior or structural alteration or addition to the building. 
 8. Construction. Tenant has inspected the Leased Premises and knows its condition, acknowledges that no express or implied warranties have been made, and agrees to accept the Leased Premises in “AS IS” condition. Landlord
is not required to perform any work in or about the Leased Premises to ready them for Tenant’s occupancy. Tenant may, however, reduce its first month’s base rent by Ten Thousand Dollars ($10,000) which Tenant covenants and agrees it will
use to ready the Leased Premises for its occupancy. 
 Tenant shall pay for all other work required to make the Leased Premises ready for
Tenant’s occupancy, but before doing its work, Tenant shall furnish Landlord with written plans and specifications for Tenant’s work and obtain Landlord’s written approval, which approval shall not constitute an agreement subjecting
Landlord’s interest in the Leased Premises to liens nor otherwise create any principal-agent relationship between the parties. All Tenant’s work shall be done in a good and workmanlike manner, using first class materials. Prior to
performing any such work, Tenant shall procure and deliver builder’s risk and liability insurance naming Landlord, its mortgagee, its ground lessor and its Building Manager as additional insureds. Tenant shall pay for such work when due and
payable, and indemnify, defend and hold Landlord harmless therefrom, obtaining lien waivers therefor from all contractors, subcontractors, materialmen and laborers and delivering all such lien waivers to Landlord. However, should any claim for lien
be filed against the Leased Premises, Tenant shall procure its discharge within thirty (30) days by payment or bonding. If Tenant fails to so 

  

 5 

 
discharge such lien, Landlord at its option may discharge the lien and treat the cost as rental payable with the next installment and without Landlord being
deemed to waive or release Tenant’s default resulting from its failure to discharge the lien. 
 9. Use of Leased Premises. The
Leased Premises described above are leased to Tenant for the sole purpose of conducting a business specializing in research and development in the fields of applied electronics and biotechnology, and Tenant agrees that it will use the Leased
Premises in such manner as to not interfere with or infringe on the rights of other tenants in the building. Tenant agrees to comply with all applicable laws, ordinances, and regulations in connection with its use of the Leased Premises. Tenant
shall not abandon the Leased Premises during the term, shall not commit or suffer waste or cause any nuisance or other act or thing to occur which disturbs the quiet enjoyment of any other tenant or which increases the insurance risk or would
prevent the obtaining of insurance. Tenant acknowledges that the building is subject to an underlying ground lease with University Research Park, Inc. and a mortgage (together with other loan documents) to First Bank, N.A., and Tenant covenants and
agrees not to take any actions or fail to take any actions that would cause Landlord to be in default under any such documents (or any successor, replacement or amended documents). 
 10. Janitorial Services. Tenant shall provide all janitorial services within the Tenant’s suite and common areas of the building using the
cleaning service designated by the Building Manager. To the extent there is joint billing for such service with the tenants in the building, Tenant shall pay to Landlord within ten (10) days of billing, as additional rent, its proportionate
share of such billing as reasonably determined by the Building Manager. Tenant shall use its good faith efforts to keep the common areas and its own space reasonably neat and clean. 
 11. Right of Parties. Landlord warrants Tenant shall have the right of peaceful possession of the Leased Premises during the term and so long as
Tenant shall not be in default. 
 12. Assignments and Subleases. Tenant may not assign this Lease nor sublet the Leased Premises
without the prior written consent of Landlord, which consent shall not be unreasonably withheld, so long as (a) Landlord’s ground lessor and mortgagee consent and Tenant pays all costs associated with such consent; (b) the proposed
user’s use of the Leased Premises will not adversely impact on other uses of the building and shall not result in increased wear and tear to the building or increased costs to Landlord; (c) the proposed user’s financial condition is
equivalent to or better than that of Tenant at the time of entering into this Lease, as reasonably determined by Landlord; and (d) Tenant remains bound by all provisions of this Lease. This provision applies to both assignments by operation of
law and voluntary assignments. Any sale or other transfer of a controlling interest in Tenant in one or more transactions shall, for purposes of this paragraph, be deemed an assignment of this Lease unless the transferee or purchaser continues the
business in substantially the same manner. Landlord’s consent to any assignment or sublease shall not be deemed a consent to any subsequent assignment or sublease, nor shall it constitute a waiver or release of Tenant from any Lease covenants
or conditions, and Landlord may collect rent and other payments direct from an assignee or subtenant without releasing Tenant from primary responsibility hereunder. Tenant shall pay Landlord all rent or other payments under any permitted assignment
or sublease should such rent or payments exceed, on a per square foot basis, the rent or other payments payable under this Lease. 
  

 6 

 13. Injury and Loss. Tenant agrees to carry public liability insurance in an amount not less than
Two Million Dollars ($2,000,000) for anyone person and Two Million Dollars ($2,000,000) for anyone accident, and Five Hundred Thousand Dollars ($500,000) property damage insuring Tenant, and shall name Landlord and its Building Manager, ground
lessor and mortgagee, if any, as additional insureds and shall furnish a certificate evidencing such insurance coverage to Landlord. 
 Tenant shall maintain on all of its personal property in, on or about the Premises, an “all risk” property policy containing an agreed amount endorsement in an amount not less than one hundred percent (100%) of the full
replacement cost valuation. The proceeds from any such policy shall be used by Tenant for the replacement of such personal property. 
 14.
Eminent Domain. In the event any portion of the Leased Premises is taken from Tenant under eminent domain proceedings, Tenant shall have no right, title, or interest in any award made for such taking, except for any separate award made
directly to Tenant for fixtures and improvements installed by Tenant or relocation costs. If all or a substantial portion (over one-third of the floor area) of the Leased Premises is taken under eminent domain, this Lease shall terminate when title
vests in such condemning authority. Base rent shall abate, proportionately or in full as the case may be, from and after such date of taking. 
 15. Entry of Landlord. Landlord reserves the right to enter upon the Leased Premises at reasonable times for the inspection of the same, for showing to prospective purchasers and lenders and for maintenance and repairs, retaining an
easement therefor including the installation of utility lines, and reserves the right, during the last six (6) months of the term, to show the Leased Premises at reasonable times, upon at least twenty-four (24) hours’ notice (either
verbal or written) to Tenant, to prospective tenants. 
 16. Subordination of Mortgages. This Lease shall be subject and subordinate
to the lien of any mortgage and/or ground lease provided the mortgagee and/or ground lessor shall recognize this Lease and agree not to disturb Tenant’s possession in the event of foreclosure if Tenant is not in default beyond any applicable
notice and grace period. Tenant shall execute and deliver documents evidencing this subordination as may be required by any mortgagee or ground lessor within ten (10) days of Landlord’s request therefor. 
 17. Building Rules and Regulations. Tenant agrees to abide by all rules and regulations of the building reasonably imposed by Landlord from time
to time for the cleanliness, good appearance, proper maintenance, good order, and reasonable use of the Leased Premises and the building and as may be necessary for the proper enjoyment of the building by all tenants and their clients, customers and
employees. Any and all such building rules and regulations shall be commercially reasonable and uniformly applied to all tenants within the building. The building rules and regulations currently in force are set forth in Exhibit C attached hereto
and made a part hereof. 
  

 7 

 18. Signs. Tenant shall not install any signs in or about the Leased Premises visible from the
exterior of the building without the prior written consent of Landlord, with Landlord’s consent not to be unreasonably withheld so long as such signs comply with all applicable governmental laws, rules and orders; any other covenants or
restrictions governing the Research Park; and the rights of any other tenants in the building. Landlord agrees to provide suitable directory signage to facilitate public identification of Tenant. 
 19. Surrender. At the expiration of the term, Tenant shall surrender the Leased Premises to Landlord, broom clean and in as good condition as they
were in at the beginning of the term, ordinary wear and tear only excepted. Tenant shall remove all of its property and repair any damage caused by such removal. If Tenant holds over after the expiration or termination of this Lease, such holdover
at Landlord’s option shall constitute a month-to-month tenancy at one and one-half (1.5) times the base rent, all without prejudice to such other rights and remedies as are available to Landlord under this Lease or at law or in equity.

 20. No Waiver; Separability and Miscellaneous. The consent of Landlord in any instance to any variation of the terms of this Lease,
or the receipt of rent with knowledge of any breach, shall not be deemed to be a waiver as to any breach of any covenant or condition herein contained, nor shall any waiver be claimed as to any provision of this Lease unless the same be in writing,
signed by Landlord or Landlord’s authorized agent. No payment by Tenant or receipt by Landlord of a lesser amount than the rent or other payment herein stipulated shall be deemed to be other than on account of the earliest stipulated rent or
other payment, nor shall any endorsement or statement on any check or any accompanying letter be deemed an accord and satisfaction, and Landlord may accept and collect on any such check or payment without prejudice to Landlord’s right to
recover the balance thereof, or to pursue any other remedy. This Lease contains the entire agreement between the parties and shall be binding upon and inure to the benefit of the parties hereto and their successors and assigns (subject to the
limitations on assignment contained herein). The submission of this Lease for review or approval shall not constitute an offer to lease or otherwise entitle Tenant to any rights hereunder, and only a fully executed Lease shall be binding upon the
parties. This Lease shall be governed by and construed under the laws of the State of Wisconsin. 
 If any term or provision of this Lease or
any application thereof shall be invalid or unenforceable, then the remaining terms and provisions of this Lease and any other application of such term or provision shall not be affected thereby. 
 21. Notices. Each provision of this Lease or any applicable laws or other requirements with reference to the sending, mailing, or delivery of any
notice or the making of any payment shall be deemed to be complied with when and if the following steps are taken: 
 a. All rent and other
payments required to be made by Tenant to Landlord hereunder shall be payable to Warzyn Building Associates and mailed to: 
 Warzyn Building Associates 
 c/o Oakbrook Commercial Real Estate, Inc. 
 P.O. Box 45530 
 Madison, WI 53744-5530 
  

 8 

 or to such other address as Landlord may specify from time to time by written notice delivered in accordance herewith.

 b. Any notice or other document required or permitted to be delivered hereunder shall be given by personal delivery, by facsimile
transmission, Federal Express or its equivalent, or by certified or registered mail postage prepaid, and deemed to be delivered when received at the respective addresses set out below, or at such other address as they have theretofore specified by
written notice delivered in accordance herewith: 
  

			
	 LANDLORD:
	  	 TENANT:

	Warzyn Building Associates	  	Nimblegen Systems, Inc.
	 c/o Oakbrook Commercial Real
 Estate,
Inc.
	  	 1 Science Court
 Madison, WI 53711

	(For mail delivery)	  	Attn: President
	P.O. Box 45530	  	
	Madison, WI 53744-5530	  	
	(For other deliveries:)	  	
	2 Science Court	  	
	Madison, WI 53711	  	

 22. Default. In the event Tenant fails to pay any rent or other payments due hereunder or
fails to keep and perform any of the other terms or conditions hereof, time being of the essence, or if Tenant shall be adjudicated bankrupt or insolvent, or if a receiver or trustee should be appointed by reason of Tenant’s inability to pay
its debts, or if any assignment shall be made of Tenant’s property for the benefit of creditors, then five (5) days after written notice of default from Landlord (unless the character of the default is such as to require more time and
Tenant is exercising diligence in curing same), Landlord may, if such default has not been corrected, resort to any and all legal and equitable remedies or combination of remedies which Landlord may desire to assert, including, but not limited to,
one or more of the following: (1) lock the doors to the Leased Premises and exclude Tenant therefrom; (2) enter the Leased Premises and remove all persons or property therefrom; (3) declare this Lease at an end and terminated;
(4) sue for the rent due and to become due under the Lease; (5) declare all rent and other payments to Landlord for the unexpired remaining term to be immediately due and payable and recover as liquidated damages an amount equal to the
difference between the base rent for the unexpired term of this Lease and the then rental value of the Leased Premises (discounted to present value at eight percent (8%)); (6) sue for any damages sustained by Landlord; and (7) continue the
Lease in effect but terminating Tenant’s right of possession and relet the Leased Premises on such terms and conditions as Landlord may deem advisable with Tenant remaining liable for the monthly rent plus the reasonable cost of obtaining
possession of the Leased Premises and of any repair or alterations necessary to prepare the Leased Premises for reletting, less the rentals received from such reletting, if any. No action of Landlord shall be construed as an election to terminate
this Lease unless written notice of such intention be given to Tenant. Tenant agrees to pay as additional rental, all attorneys’ fees and other costs and expenses incurred by the Landlord in enforcing any of Tenant’s obligations under this
Lease. All rights and remedies enumerated above shall be cumulative and none shall exclude any other right and remedy allowed by law or equity, which may be exercised and enforced concurrently or as occasion therefor arises, and Landlord’s
failure to enforce same shall not be deemed a wavier of such default or a consent to its continuation. 
  

 9 

 Any amount due from Tenant to Landlord herein which is not paid when due shall bear interest at the
lesser of twelve percent (12%) per annum or the highest interest rate allowed by law from the due date until paid; but the payment of such interest shall not excuse or cure any default by Tenant under this Lease. 
 If Tenant defaults in the doing of any act herein required to be made or done by Tenant, then Landlord may, but shall not be required to, do such act,
and if Landlord shall incur any charge or expense on behalf of Tenant under the terms of this Lease, the amount of the expense thereof shall be paid by Tenant to Landlord as additional rent together with the next monthly installment of base rent;
provided, however, that the making of such payment or the doing of such act by Landlord shall not operate to cure such default by Tenant, or to estop Landlord from the pursuit of any remedy to which Landlord would otherwise be entitled. 

If Landlord fails to perform or observe any of the obligations on Landlord’s part to be performed or observed pursuant to this Lease, and such
failure continues for thirty (30) days after written notice thereof is sent by Tenant to Landlord informing Landlord of such failure, then Landlord shall be deemed to be in default under this Lease; provided, however, that if the failure set
forth in Tenant’s notice is such that it requires more than thirty (30) days to correct, Landlord shall not be deemed to be in default hereunder if Landlord: (i) promptly and diligently commences curing the failure within thirty
(30) days after written notice is sent by Tenant to Landlord informing Landlord of such failure; and (ii) diligently prosecutes the cure to completion following the expiration of the original thirty (30) day period set forth herein.
Upon such default by Landlord, Tenant may, as its sole remedy, perform the same for and on behalf of Landlord, the cost of which performance, upon the proper payment thereof, together with all interest and penalties necessarily paid in connection
therewith and any and all other damages incurred by Tenant as a result of any such default, shall be paid to Tenant by Landlord upon demand, with interest thereon at the lesser of (i) twelve percent (12%); or (ii) the maximum rate then
permitted by law, from the date of each expenditure and/or incidence. If the default involves the failure of Landlord to pay monies due to Tenant under this Lease, interest shall accrue on such past due sums from and after the expiration of the
thirty (30) day cure period set forth above at the interest rate set forth above. 
 23. Estoppel Certificate. Promptly upon
request, but in no event more than twenty (20) days after request, therefor from Landlord, Tenant agrees to execute and deliver to Landlord or its proposed purchaser or mortgagee a statement certifying (if such be the case) that this Lease is
in full force and effect, the date to which rent and other amounts have been paid, that there are no offsets or defenses thereto, and that the Landlord is not in default, or stating those claimed by Tenant, and certifying as to such other matters as
Landlord may reasonably request. 
 24. Alterations and Additions. Tenant will not make any alterations or additions to the Leased
Premises without first obtaining Landlord’s prior written consent, which consent will not be unreasonably withheld. Any such work shall be performed by Tenant pursuant to the requirements of Section 8 hereof governing Tenant’s work,
including plans and specifications, insurance, quality, 
  

 10 

 
payment and indemnification against liens. All such items and work shall become the property of Landlord unless, at the time Landlord consents to such
alteration, Landlord requests that Tenant remove them and restore the Leased Premises to its current condition, ordinary wear and tear excepted, upon expiration of the term for whatever reason. 
 25. Recording. Tenant shall not record this Lease without Landlord’s prior written consent and such recordation shall, at the option of
Landlord, constitute a non-curable default of Tenant hereunder. Either party shall, upon request of the other, execute, acknowledge, and deliver to the other a “short form” memorandum of this Lease for recording purposes. 
 26. Building Manager. The Building Manager is authorized to act for, and in the name of, Landlord for any and all purposes under this Lease except
the execution of leases and amendments, renewals, extensions and modifications thereof, and Tenant shall direct any and all notices and inquiries regarding this Lease to the Building Manager. The Landlord reserves the right to substitute any other
person, firm or corporation for the Building Manager, upon written notice thereof by Landlord to Tenant. 
 27. Brokerage. Landlord
and Tenant each represent that they have had no dealings with any real estate broker, finder or other persons, with respect to this Lease in any manner, except Oakbrook Commercial Real Estate, Inc., and Landlord will be responsible for the
commission to such party. Tenant agrees to indemnify and hold harmless Landlord against and from any claim for any brokerage commission or other fees and all costs, expenses, and attorneys fees in connection therewith, arising out of arty dealings
had by Tenant with any broker other than Oak brook Commercial Real Estate, Inc. 
 28. Waiver of Trial by Jury and Counterclaims. The
parties hereto shall, and they hereby do, waive trial by jury in any action, proceeding or allowable counterclaim brought by either of the parties hereto against the other on any matters whatsoever arising out of or in any way connected with this
Lease, the relationship of Landlord and Tenant, Tenant’s use and occupancy of the Leased Premises and/or any claim of injury or damage. 
 29. Limitation of Landlord’s Liability. Tenant shall look only to Landlord’s interest in the building and the lot on which it is located for satisfaction of Tenant’s remedies for the collection of a judgment (or other
judicial process) requiring the payment of money by Landlord in the event of any default by Landlord hereunder, and no other property or assets of Landlord or its partners or principals, disclosed or undisclosed, shall be subject to levy, execution
or other enforcement for the satisfaction of Tenant’s remedies under or with respect to this Lease, the relationship of Landlord and Tenant hereunder or Tenant’s use or occupancy of the Leased Premises. 
 30. Environmental Compliance. During the term of this Lease, Tenant shall: 
 a. Timely comply with all applicable Environmental Laws relating to Tenant’s possession of the Leased Premises and the conduct of Tenant’s
business; 
 b. Provide Landlord, immediately upon receipt thereof, with copies of any correspondence, notice, pleading, citation,
indictment, complaint, order, decree or other document from any source asserting or alleging violation upon the Leased Premises of any Environmental Laws, or asserting or alleging a circumstance or condition upon the Leased Premises which may
require a financial contribution by Tenant or a cleanup, remedial action or other response by or on the part of Tenant under any Environmental Laws. 
  

 11 

 c. Permit Landlord, in the event Landlord has reasonable cause to believe that there exists a condition
or circumstance created by Tenant, its employees or invitees during the term warranting an environmental inspection or audit, at Tenant’s expense to retain a qualified environmental engineer selected by Landlord to perform an environmental
inspection and/or audit of the Leased Premises to evaluate Tenant’s compliance with Environmental Laws, and to test for Hazardous Substances on the Leased Premises, and for risks associated with exposure to Hazardous Substances. Tenant shall
permit Landlord and its employees and agents access to the Leased Premises and the books and records of Tenant as necessary for the performance of the environmental inspection and/or audit; 
 d. At its expense, remove or contain any Hazardous Substances on the Leased Premises that were brought onto the Leased Premises by Tenant, its employees
or invitees during the term, or perform other corrective action as required by applicable law or by Landlord, acting reasonably, if at anytime it is determined that such Hazardous Substances present a health hazard on the Leased Premises or are
required to be removed or contained or other corrective action is required by any Environmental Laws. 
 e. Definitions 
 i. As used herein, “Environmental Laws” shall mean any federal, state and local laws including statutes, regulations, rulings,
orders, administrative interpretations and other governmental restrictions and requirements relating to the discharge of air pollutants, water pollutants or process waste water or otherwise relating to the environment or Hazardous Substances (as
defined herein) including, but not limited to, Chapters 280 through 299 of the Wisconsin Statutes, the Federal Toxic Substances Control Act, the Federal Disposal Act, the Federal Clean Air Act, the Federal Clean Water Act, the Federal Resource
Conservation and Recovery Act of 1976, the Federal Comprehensive Environmental Response, Compensation and Liability Act of 1980, regulations of the Regulatory Agency, and regulations of any state department of natural resources or state
environmental protection agency now or at any time hereafter in effect. 
 ii. As used herein, “Hazardous
Substances” shall mean any hazardous waste or substance, asbestos or asbestos-containing material, pollutant, solid, liquid, gaseous, or thermal irritant or contaminant (such as smoke, vapor, soot, fumes, acids, alkalis, chemicals or waste,
including materials to be recycled in the future, reconditioned or reclaimed), petroleum or petroleum-based product, polychlorinated biphenyl (in the form of electrical transformers, fluorescent light fixtures with ballasts, cooling oils or any
other device or form), urea-formaldehyde foamed-in-place insulation, or any other hazardous or toxic waste or substance as defined or included under Environmental Laws. 
 Landlord warrants and represents that, to the best of Landlord’s actual knowledge, the Leased Premises comply with all applicable Environmental Laws. Landlord represents and covenants to Tenant that, to the best
of Landlord’s actual knowledge, the 

  

 12 

 
Leased Premises do not contain any Hazardous Substances in amounts in excess of applicable standards. Landlord is not aware of any underground storage tanks.
In the event it is determined that there are Hazardous Substances on, upon or within the Leased Premises or any other environmental conditions not caused by Tenant in violation of any Environmental Laws or which result in action by either local,
state or federal environmental agencies, then if, in the opinion of any environmental engineer reasonably chosen by Tenant and approved by Landlord (which consent will not be unreasonably withheld) such violation and/or action materially impairs
Tenant’s ability to conduct business upon the Leased Premises and Tenant ceases to operate from the Leased Premises as a direct result thereof, all rent, payable by Tenant hereunder shall, in lieu of all other rights and remedies, abate during
such period as Tenant’s ability to so operate is materially impaired, and if such condition continues for in excess of ninety (90) days, either party shall have the right to terminate this Lease and all rights and obligations hereunder by
giving written notice to the other party at any time after the expiration of such ninety (90) day period and so long as such condition continues. 
 The obligations of the parties hereunder shall survive the termination of this Lease. 
 31. Parking.
Tenant and its employees and visitors shall have the non-exclusive right to use fifty-three (53) parking spaces, at no cost to Tenant, located in the parking area on the property. The parking area shall be used in common with other tenants of
the building, their employees and visitors. The use of the parking area is subject to such reasonable rules and regulations as may be imposed by Landlord from time to time, including but not limited to a requirement that Tenant furnish Landlord with
the automobile license numbers of the vehicles customarily used by Tenant and its employees. Landlord shall have the right to conduct inspections of the parking area to assure compliance with this Paragraph 31. Tenant’s failure to comply with
the terms of this Paragraph 31 shall constitute a default under the terms of this lease. 
 32. Financial Information. Tenant
covenants and agrees to provide to Landlord within sixty (60) days after the end of each fiscal quarter of Tenant’s, a balance sheet showing Tenant’s financial condition as of the end of the immediately preceding fiscal quarter, which
balance sheet shall comply with generally accepted accounting principles and be certified for accuracy and completeness by the Tenant’s chief financial officer. Any failure to timely provide such financial statements shall constitute a default
under this Lease. Such financial information shall be provided on a consolidated basis for Nimblegen Systems, Inc. and Nimblegen Systems, LLC. 
 IN WITNESS WHEREOF, the parties have hereunto set their hands (or caused this Lease to be executed by their authorized agents) on the date hereinbefore set forth. 
  

			
	Landlord:
	
	WARZYN BUILDING ASSOCIATES
		
	By:	 	 /s/ Charles A. Stoll

  

 13 

							
	Tenant:
		
	NIMBLEGEN SYSTEMS, INC.	 	NlMBLEGEN SYSTEMS, LLC
				
	By:	 	 /s/ David C. Sneider
	 	By:	 	 /s/ David C. Sneider

		 	David C. Sneider	 		 	David C. Sneider
		 	Vice President and Chief Financial Officer	 		 	

  

 14 

 ADDENDUM 
 TO BE ATTACHED TO AND MADE A PART OF 
 LEASE AGREEMENT, DATED NOVEMBER 14, 2000, 
 BETWEEN WARZYN BUILDING ASSOCIATES, LANDLORD 
 AND NIMBLEGEN SYSTEMS, INC. 
 AND NIMBLEGEN SYSTEMS, LLC, TENANT 
 Extension Option. Provided Tenant is not then in default with respect to any material term of this Lease (with the parties agreeing that any
monetary default, whether in the payment of rent or otherwise, shall irrebutably be deemed material) at the time this option is exercised and does not default at any time through commencement of the extension term, and provided this Lease continues
in full force and effect, Tenant, at its option, may have two (2) consecutive one (1) year options to extend the term of this Lease subject to the Tenant giving written notice of exercise of this option upon the Landlord which Landlord
must receive at least one hundred eighty (180) days before the expiration of the original lease term, or the first extended term, as the case may be, upon the terms and provisions of this Lease, except for this option, and subject to the
rentals and other payments as set forth in Sections 4 and 5 of this Lease, including annual adjustments for each year of such extension term. Time is of the essence with respect to the exercise of this option. 

 FIRST AMENDMENT AND RENEWAL OF LEASE 
 THIS FIRST AMENDMENT AND RENEWAL OF LEASE, made this      day of January 2004, by and between PERRY ARMSTRONG AND DAVID
WALSH, (hereinafter referred to as “Landlord”), and NIMBLEGEN SYSTEM, LLC, (hereinafter referred to as “Tenant”). 
 WITNESSETH: 
 WHEREAS, Landlord and Tenant have entered into a Lease, dated November 14, 2000, (hereinafter referred to as
“said Lease”), whereby Tenant is presently leasing office space at 1 Science Court, Madison, Wisconsin (hereinafter referred to as the “Leased Premises”); and, 
 WHEREAS, Landlord and Tenant desire to further modify and amend said Lease. 
 NOW, THEREFORE, in consideration of mutual covenants and agreements and good and valuable consideration, the delivery and receipt of which is hereby
acknowledged by and between Tenant and Landlord, the parties do hereby agree to renew and amend said Lease as follows: 
 1. Leased
Premises. Tenant currently leases on the bottom and first floors as outlined on Exhibit A and Exhibit B attached hereto. 
 2.
Term. The term of said Lease will be extended for one year effective July 11, 2004 and terminating on July 10, 2005. 
 3.
Base Rent. The monthly base rental rate will be as follows: 
 2/1/04 to
6/30/05         $19,724.06/per month 
 7/1/05 to 7/10/05
         $6,362.60 
 4. No Other Changes. All other provisions of said Lease shall remain the
same and shall continue in full force and effect. 
 5. Incorporation Into Lease. Landlord and Tenant agree that executed counterparts
of this First Amendment and Renewal of Lease shall be attached to, and become a part of, the respective copies of said Lease now in the possession of each party hereto. 
 IN WITNESS WHEREOF, Landlord and Tenant have duly executed this First Amendment and Renewal of Lease on the day and year first above written. 
  

							
	 NIMBLEGEN SYSTEM, LLC
 Tenant
	 	 PERRY ARMSTRONG AND DAVID WALSH,
 Landlord

				
	 By:
	 	 /s/ David Sneider
	 	By:	 	 /s/ Perry Armstrong

		 	David Sneider,	 		 	
		 	Vice President and Chief Financial Officer	 		 	

 EXHIBIT A 
 [Floor map goes here] 
  

 EXHIBIT B 
 [Floor map goes here] 

 SECOND AMENDMENT AND RENEWAL OF LEASE 
 THIS SECOND AMENDMENT AND RENEWAL OF LEASE, made this 10th day of May, 2005, by and between PERRY ARMSTRONG AND DAVID WALSH, (hereinafter referred to as
“Landlord”), and NIMBLEGEN SYSTEMS, INC., (hereinafter referred to as “Tenant”). 
 WITNESSETH: 
 WHEREAS, Landlord and Tenant have entered into a Lease, dated November 14, 2000, (hereinafter referred to as “said Lease”), and a First
Amendment and Renewal of Lease, dated January 1, 2004, whereby Tenant is presently leasing office and lab space at 1 Science Court, Madison, Wisconsin (hereinafter referred to as the “Leased Premises”); and, 
 WHEREAS, Landlord and Tenant desire to further modify and amend said Lease. 
 NOW, THEREFORE, in consideration of mutual covenants and agreements and good and valuable consideration, the delivery and receipt of which is hereby
acknowledged by and between Tenant and Landlord, the parties do hereby agree to renew and amend said Lease as follows: 
  

	 	1.	Leased Premises. Tenant’s Leased Premises shall be 11,441 useable square feet and 12,242 rentable square feet as shown as “NimbleGen Leased Premises” on
Exhibit A attached hereto. The Leased Premises include 887 useable square feet on the first floor that Tenant previously subleased from MWH Americas, Inc. (“MWH”), and 224 useable square feet of 1st floor storage space (labeled
“crating room” on Exhibit A). 

  

	 	2.	Term. The term (“Term”) of said Lease will be extended for two years effective July 11, 2005 and terminating on July 10, 2007. 

 

	 	3.	Base Rent. The annual base rental rate will be $19.25 per rentable square foot for the initial term of this Second Amendment. 

  

	 	4.	Renewal Options. Pursuant to all other conditions contained in the Lease Addendum to said Lease, Tenant, at its option, may have four (4) consecutive 15-month options to
extend the Term of Said Lease (“Option to Extend”). To exercise the Option to Extend, Tenant must give Landlord notice of exercise at least 180 days before the expiration of the existing Term. Upon exercising the Option to Extend, the
annual base rental rate shall increase by 3.0% per year during the first two renewal options and 2.0% during the second two renewal options. 

  

	 	5.	 Shared Area. The lunchroom, large conference room, and small conference room near the front entrance, together constituting 1,580 square feet and as more
specifically depicted on Exhibit A, shall be shared area for the use of all building tenants (“Shared Area”). Tenant shall have the sole right to convert the Shared Area into Tenant’s Leased Premises at any time during the Term of
this Lease (“Conversion Right”). If Tenant should exercise the Conversion Right, the Tenant’s 

	 	 
Leased Premises shall consist of 13,021 (the sum of the original useable square feet, 11,441, and the square feet in the Shared Area, 1,580) rentable square
feet and rent payments shall be calculated based on 13,021 square feet. 

  

	 	6.	First Right of Refusal. Landlord grants Tenant an ongoing First Right of Refusal for any space that becomes vacant in the building during the terms. Upon availability of
space, Landlord shall notify Tenant in writing. Tenant shall have twenty business days to exercise its Right to expand into said space. If exercised, the lease rate and other business terms for the expansion space will be identical to those
contained in Tenant’s Lease at the time of expansion, including the termination date. The tenant improvement allowance for the expansion space will be $5.00 per usable square foot times the number of years (or fraction thereof) until
termination of this Second Amendment or extension thereof. Tenant may not exercise this Right on 2nd floor space prior to converting the Shared Area space to leased office space as provided in Paragraph 5 of this Second Amendment.

  

	 	7.	Janitorial Service. During the term of the Second Amendment and any extensions thereof, Base Rent will include Tenant janitorial. The attached Exhibit C outlines the service
specifications. 

  

	 	8.	Continuation of Utility Bill back. Landlord and Tenant acknowledge and agree that Tenant’s electrical, gas, and water usage exceeds the amount normally used by office
tenants. Pursuant to Paragraph 5(d) of said Lease and in accordance with past practices, Tenant will continue to pay for the electrical, gas and water costs in excess of a base year amount ($63,088 in 2004), which amount changes periodically based
on changes in rates and actual usage. Landlord reserves the right to install a submeter on the electrical service that feeds the rooftop HVAC unit that serves the lower level lab space, in which case Tenant shall be billed back its actual share of
the electrical usage for that rooftop HVAC unit. 

  

	 	9.	Repairs and Maintenance. The following language shall be added to Paragraph 6 of said Lease: “In the event Landlord does not provide timely maintenance and repair to the
Premises, Tenant may, after notifying Landlord thirty (30) days in advance and allowing Landlord the right to cure the problem, contract out the services to remedy the problem and deduct the expenses from rent payment.”

  

	 	10.	Refurbishment Allowance. Provided Tenant is not then in default with respect to any material term of this Second Amendment or extension thereof, and upon occupying the
Premises for five years from the commencement date of this Second Amendment, Tenant shall be entitled to a Refurbishment Allowance in the amount of $5.00 times the number useable square feet occupied, under the following conditions:

  

	 	a.	Tenant must use the funds for Premises remodeling and not for personal property or equipment purchases. 

	 	b.	Refurbishment plan to be approved in writing by Property Manager, such approval not to be unreasonably withheld. 

  

	 	c.	Work to be performed by a contractor of owner’s choice that is familiar with the building’s HVAC system. 

  

	 	11.	Premises Renovations and Building Capital Improvements. Landlord shall have the work performed as outlined on the attached Exhibit B. 

  

	 	12.	Prohibition of Building Addition. Landlord shall not, while Tenant remains an occupant in the building, allow a new building or building addition to be constructed on site,
except as provided for in Exhibit B. 

  

	 	13.	Outdoor Storage. Beginning no later than December 1, 2005, Tenant shall be entitled to the use of one-half of the outside storage enclosure at no extra cost. Tenant
shall use good faith efforts to keep the outside storage enclosure reasonably neat and clean. 

  

	 	14.	MWH Amendment Required. The Tenant’s right to the portions of this Second Amendment that pertain to space that MWH currently occupies is subject to MWH’s agreement
to terminate its rights to said spaces. A copy of the lease amendment that formally terminates MWH’s rights to said spaces shall be attached to this Second Amendment. If no such agreement is reached, Tenant shall not be entitled to occupy said
spaces and Tenant’s square footage and rent shall be adjusted ratably until Tenant is entitled to occupy said spaces. 

  

	 	15.	No Other Changes. All other provisions of said Lease shall remain the same and shall continue in full force and effect. 

  

	 	16.	Incorporation Into Lease. Landlord and Tenant agree that executed counterparts of this Second Amendment and Renewal of Lease shall be attached to, and become a part of, the
respective copies of said Lease now in the possession of each party hereto. 

 IN WITNESS WHEREOF, Landlord and Tenant have
duly executed this First Amendment and Renewal of Lease on the day and year first above written. 
  

							
	 NIMBLEGEN SYSTEMS, INC.
 Tenant
	    	 PERRY ARMSTRONG AND DAVID WALSH
 as
successors to Warzyn Building Associates, Landlord

				
	By:	 	 /s/ David Sneider
	    	By:	 	 /s/ Perry Armstrong

		 	David Sneider,	    		 	
		 	Vice President and Chief Financial Officer	    		 	

 EXHIBIT A 
 [Floor map goes here] 
  

 EXHIBIT B 
 Premises Renovations & Building Capital Improvements 
 Renovations: (to be completed by July 10,
2005 or as noted below) 
  

	1.	Remove locks on doors leading to hallway/bathrooms adjacent to lower lever lab and manufacturing area. This area to be available for all building tenants’ use.

  

	2.	Based on mutually agreeable plans, create a new entrance and reception area for Tenant. Tenant shall provide preliminary design goals to Landlord and Landlord shall arrange to have
an architect create a drawing with material and color specifications for Tenant’s approval Landlord shall have the greater of 90 days from lease signing or 60 days from Tenant’s approval of plan to complete the work.

  

	3.	Perform minor wall repairs and paint as needed in Premises. Tenant and Landlord shall conduct a walk-through of the Premises and mutually agree to the scope of the work. Tenant to
be responsible for moving furniture and equipment as required to accommodate said painting. 

  

	4.	Steam clean carpet in Premises. Tenant to be responsible for moving furniture and equipment as required to accommodate said carpet cleaning. 

  

	5.	Repair office doors as needed so they will remain open when desired. 

  

	6.	Repair leaking valve in lower level, replace missing ceiling tiles as needed. 

  

	7.	Monitor temperature in the lab space and diagnose and repair if a problem is found. 

 Capital Improvements: (to be completed by October 31, 2005 or as noted below) 
  

	1.	Remodel building front entrance and lobby, complete with building directory, to be completed at the same time as #2 of Renovations. 

  

	2.	Replace two rooftop HVAC units that serve the office portions of the building. 

  

	3.	Replace Premises VAV boxes and related ductwork and computer control package. Tenant to be responsible for moving furniture and equipment as required to perform the replacements.

  

	4.	Install a new motor and compressor and convert to a double sheave system on the rooftop HVAC unit serving the lab/manufacturing area. 

  

	5.	Install a hydraulic dock lift outside the rear loading area. Specifications to be mutually agreed to and consistent with Tenant’s need to lift crates onto delivery trucks.

 EXHIBIT C 
 Premises Janitorial Service Specifications 
  

					
	Services Performed (Office Areas)	  	Daily	    	 Collect trash and recycled cardboard.
 Vacuum
carpet.
 Mop tile floors.
 Spot clean wall and carpet stains when noticed or as directed.
 Spot dust, wipe tables, spot brush
chairs.
 Spot clean entryway glass.

			
		  	2x/month	    	 Dust cleared portions of desks, window sills, etc.
 Dust blinds.
 Order supplies if needed.

			
		  	Monthly	    	 Walk through building searching for wall and carpet stains.
 Spot clean partition glass.

			
		  	4 times/year	    	Edge vacuum carpet.
			
		  	2 times/year	    	Vacuum furniture.
			
	Services Performed (Lab Areas)	  	Daily	    	Collect trash and recycled cardboard set in hallway.
			
		  	2x/week	    	Vacuum under agreed-upon tables.
			
		  	Weekly	    	Vacuum & mp lab floors in large lab area.
			
		  	2x/month	    	Vacuum & mp lab floors in small lab area.
			
	 Services Performed
 (Office Areas)
	  	N/A	    	No admittance.

 THIRD AMENDMENT OF LEASE 
 THIS THIRD AMENDMENT OF LEASE, made this 16th day of November, 2005, by and between PERRY ARMSTRONG AND DAVID WALSH, (hereinafter referred to as
“Landlord”), and NIMBLEGEN SYSTEMS, INC., (hereinafter referred to as “Tenant”). 
 WITNESSETH: 
 WHEREAS, Landlord and Tenant have entered into a Lease dated November 14, 2000, (hereinafter referred to as “said Lease”), a First
Amendment and Renewal of Lease dated January 1, 2004, and a Second Amendment and Renewal of Lease dated May 10, 2005 whereby Tenant is presently leasing office and lab space at 1 Science Court, Madison, Wisconsin (hereinafter referred to
as the “Leased Premises”); and, 
 WHEREAS, Landlord and Tenant desire to further modify and amend said Lease. 
 NOW, THEREFORE, in consideration of mutual covenants and agreements and good and valuable consideration, the delivery and receipt of which is hereby
acknowledged by and between Tenant and Landlord, the parties do hereby agree to renew and amend said Lease as follows: 
  

	 	1.	Leased Premises. Commencing November 4,2005, Tenant’s Leased Premises shall be 12,544 useable square feet and 13,422 rentable square feet. The location of the
additional Leased Premises is depicted on Exhibit A attached hereto. 

  

	 	2.	Base Rent. The annual base rental rate will be adjusted based on the revised Premises area, with the base rental rate per square foot remaining the same as outlined in the
Second Amendment and Renewal of Lease. 

  

	 	3.	No Other Changes. All other provisions of said Lease shall remain the same and shall continue in full force and effect. 

  

	 	4.	Incorporation Into Lease. Landlord and Tenant agree that executed counterparts of this Third Amendment of Lease shall be attached to, and become a part of, the respective
copies of said Lease now in the possession of each party hereto. 

 IN WITNESS WHEREOF, Landlord and Tenant have duly executed
this First Amendment and Renewal of Lease on the day and year first above written. 
  

							
	 NIMBLEGEN SYSTEMS, INC.
 Tenant
	 	 PERRY ARMSTRONG AND DAVID WALSH
 Landlord

				
	By:	 	 /s/ David Sneider
	 	By:	 	 /s/ David Walsh

		 	David Sneider,	 		 	
		 	Vice President and Chief Financial Officer	 		 	

 EXHIBIT A 
 [Floor map goes here] 

 FOURTH AMENDMENT OF LEASE 
 THIS FOURTH AMENDMENT OF LEASE, made this 10th day of August 2006, by and between PERRY ARMSTRONG AND DAVID WALSH, (hereinafter referred to as
“Landlord”), and NIMBLEGEN SYSTEMS, INC., (hereinafter referred to as “Tenant”). 
 WITNESSETH: 
 WHEREAS, Landlord and Tenant have entered into a Lease dated November 14, 2000, (hereinafter referred to as “said Lease”), a First
Amendment and Renewal of Lease dated January 1, 2004, a Second Amendment and Renewal of Lease dated May 10, 2005 and a Third Amendment of Lease dated November 16, 2005 whereby Tenant is presently leasing office and lab space at 1
Science Court, Madison, Wisconsin (hereinafter referred to as the “Leased Premises”); and, 
 WHEREAS, Landlord and Tenant desire
to further modify and amend said Lease. 
 NOW, THEREFORE, in consideration of mutual covenants and agreements and good and valuable
consideration, the delivery and receipt of which is hereby acknowledged by and between Tenant and Landlord, the parties do hereby agree to renew and amend said Lease as follows: 
  

	 	 1.
	 Leased Premises. Commencing August 9, 2006, Tenant’s Leased Premises shall be 16,301 square feet,
including the addition of manufacturing space in the lower level and the lunchroom and conference rooms on the 1st
floor. The location of the additional Leased Premises is depicted on Exhibit A attached hereto. 

  

	 	2.	Base Rent. Base rent will increase to $313,794.24 annually ($26,149.52 per month). 

  

	 	3.	Tenant Improvement Allowance. Landlord is delivering the space in an “as is” condition and Tenant hereby waives its right to receive a Tenant Improvement Allowance
for its expanded Premises in exchange for other good and valuable consideration, the receipt of which the parties acknowledge by executing this Fourth Amendment. 

  

	 	4.	Shared Area. Per paragraph five of the Second Amendment and Renewal of Lease, Tenant has exercised its Conversion Right and will now occupy the 1,580 square feet of Shared
Area on an exclusive basis. The resulting change in square footage has been incorporated into the new Leased Premises. 

  

	 	 5.
	 First Right of Refusal-2nd Floor. As a result of exercising its Conversion Right for the Shared Area, Tenant’s First Right of Refusal, as described in
Paragraph 6 of the Second Amendment and Renewal of Lease, is exercisable for the 2nd floor. Tenant acknowledges that it has been provided the opportunity to occupy the entire 2nd floor, has declined to exercise its Right of First Refusal, and waives
its twenty-day notice requirement. Paragraph 6 the Second Amendment and Renewal of Lease is hereby deleted as to Tenant’s rights on 2nd Floor but remains in place as to available space in the Lower Level. 

	 	6.	No other Changes. All other provisions of said Lease shall remain the same and shall continue in full force and effect. 

  

	 	7.	Incorporation Into Lease. Landlord and Tenant agree that executed counterparts of this Fourth Amendment of Lease shall be attached to, and become a part of, the respective
copies of said Lease now in the possession of each party hereto. 

 IN WITNESS WHEREOF, Landlord and Tenant have duly executed
this Fourth Amendment of Lease on the day and year first above written. 
  

							
	 NIMBLEGEN SYSTEMS, INC.
 Tenant
	    	 PERRY ARMSTRONG AND DAVID WALSH
 Landlord

				
	By:	 	 /s/ David S. Snyder
	    	By:	 	 /s/ Perry Armstrong

		 	David S. Snyder,	    		 	
		 	Vice President and Chief Financial Officer	    		 	

 EXHIBIT A 
 [Floor map goes here] 

 FIFTH AMENDMENT OF LEASE 
 THIS FIFTH AMENDMENT OF LEASE, made this 15th day of February, 2007, by and between FAIRVIEW RIDGE III, LLC (hereinafter referred to as
“Landlord” as successor in interest to Perry Armstrong and David Walsh, and NIMBLEGEN SYSTEMS, INC., (hereinafter referred to as “Tenant”). 
 WITNESSETH: 
 WHEREAS, Landlord and Tenant have entered into a Lease dated November 14, 2000, a First
Amendment and Renewal of Lease dated January 1, 2004, a Second Amendment and Renewal of Lease dated May 10, 2005, a Third Amendment of Lease dated November 16, 2005, and a Fourth Amendment dated August 10, 2006 (hereinafter
referred to as “said Lease”), whereby Tenant is presently leasing office and lab space at 1 Science Court, Madison, Wisconsin (hereinafter referred to as the “Leased Premises”); and, 
 WHEREAS, Landlord and Tenant desire to further modify and amend said Lease. 
 NOW, THEREFORE, in consideration of mutual covenants and agreements and good and valuable consideration, the delivery and receipt of which is hereby
acknowledged by and between Tenant and Landlord, the parties do hereby agree to renew and amend said Lease as follows: 
  

	 	1.	Term. The Term of said Lease shall end on August 31, 2007. 

  

	 	2.	No other Changes. All other provisions of said Lease shall remain the same and shall continue in full force and effect. 

  

	 	3.	Incorporation Into Lease. Landlord and Tenant agree that executed counterparts of this Fifth Amendment of Lease shall be attached to, and become a part of, the respective
copies of said Lease now in the possession of each party hereto. 

 IN WITNESS WHEREOF, Landlord and Tenant have duly executed
this Fourth Amendment of Lease on the day and year first above written. 
  

							
	 NIMBLEGEN SYSTEMS, INC.
 Tenant
	 	 FAIRVIEW RIDGE III, LLC
 (successor in interest to Perry Armstrong & David Walsh)
 Landlord

				
	 By:
	 	 /s/ David S. Snyder
	 	By:	 	 /s/ Patrick Sweeney

		 	David S. Snyder,	 		 	Patrick Sweeney, Managing Member
		 	Vice President and Chief Financial Officer

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