Document:

EXHIBIT 10.1

Confidential treatment has been requested
for portions of this exhibit.  The copy
filed herewith omits the information subject to the confidentiality
request.  Omissions are designated as [***].  A complete version of this exhibit has been
filed separately with the Securities and Exchange Commission.

Amendment Agreement

December 22, 2006

This
Amendment Agreement (this “Amendment”)
dated as of the date first written above is entered into by F. Hoffmann-La Roche Ltd., a Swiss corporation (“Roche”), Roche
Molecular Systems, Inc., a Delaware corporation (“RMS”), and Affymetrix,
Inc., a Delaware corporation (“Affymetrix”).  RMS is a wholly-owned direct subsidiary of
Roche.  Roche, RMS and Affymetrix are
each a “Party” and collectively the “Parties.”

Roche
and Affymetrix have entered into the following agreements (collectively,
together with this Amendment, the “Collaboration Agreements”)
on January 29, 2003:  (i) the Common
Terms Agreement, (ii) the License Agreement, (iii) the Supply Agreement, (iv) the
Affymetrix Instrument Agency Agreement, (v) the Diagnostic Product Agency
Agreement, (vi) the Standstill Agreement and (vii) the R&D Agreement.  The Collaboration Agreements also include the
P450 Addendum Agreement among the Parties dated June 24, 2003, the
Amendment Agreement among the Parties dated February 17, 2004, and the
Amendment Agreement among the Parties dated December 8, 2004.  All capitalized terms not otherwise defined
herein shall have the meanings set forth in the Common Terms Agreement.

The
Parties now desire to amend and supplement the Collaboration Agreements on the
terms set forth herein.

The
Parties therefore agree as follows:

1.               Installment Payments. Roche is
hereby relieved of its obligations to pay License Installment Payments under
Section III(b) of the License Agreement (as amended), and such section is
hereby deleted in its entirety.

2.               Most Favorable Terms and
Conditions. Affymetrix is hereby relieved of its obligations
under Section IV(k)(i), IV(k)(ii) and IV(k)(iii) of the License Agreement (as
amended), and such sections are hereby deleted in their entirety. In addition,
Affymetrix’ notice obligations under Section IV(k)(v) of the License Agreement
(as amended) shall apply only with respect to the running royalty rate in a Third
Party license and, if the Third Party license was entered into in conjunction
with a chip supply arrangement, the Chip transfer or sales price.

3.               Milestone
Payments.

(a)                                  Section III(d)(i) of the License Agreement (as amended) is hereby further
amended to read in full as follows:

(i) Upon the earlier to occur of (A) initial
Regulatory Approval for a particular Diagnostic Product in any of the United
States, Japan or Germany, or (B) commercial aggregate gross sales for a
particular Diagnostic Product in the United States of at least $[***] over four
consecutive calendar quarters, then for such Diagnostic Product:

(1)                                  US$[***] if Affymetrix has contributed substantially to the Content of
such Diagnostic Product; or

 

(2)                                  US$[***] if Affymetrix has not contributed substantially to the Content
of such Diagnostic Product; and

(b)                                 The US$[***] aggregate maximum on Milestone Payments payable under
Section III(d) of the License Agreement (as amended) is removed, but the
Parties hereby agree that, notwithstanding clauses (i) and (ii) (as amended) in
such Section III(d),

(i) if the aggregate amount of all prior Milestone
Payments does not exceed US$[***] but an additional Milestone Payment will
bring the aggregate amount of all Milestone Payments above $[***], then the
portion of the additional Milestone Payment which causes such amount to be
exceeded shall be the lesser of (x) the amount otherwise due without regard to
this clause (ii) and (y) an amount to be negotiated by the Parties that shall
in no event be less than US$[***] nor more than US$[***], and

(ii) if the aggregate amount of all prior Milestone
Payments exceeds US$[***] then the amount of each additional Milestone Payment
shall be an amount to be negotiated by the Parties that shall in no event be
less than US$[***] nor more than US$[***], and

(iii) if the aggregate amount of all prior Milestone
Payments exceeds US$[***], then any additional Milestone Payment shall only be
achieved and payable if and when initial Regulatory Approval for the relevant
Diagnostic Product has been achieved in the United States and Germany, and
commercial aggregate gross sales for such Diagnostic Product have reached at
least $[***] worldwide.

(c)                                  The Milestone Payments defined in Section III(d)(i) (as amended) already
reflect the [***]% reduction described in Section 3(a) of the December 08, 2004
Amendment Agreement. Accordingly, no portion of such Milestone Payments shall
be deleted or creditable against future royalties payable under Section III(c)
of the License Agreement.

(d)                                 Nothing in this Section 3(b) of this Amendment shall alter the provisions
of Section 3(b) of the December 08, 2004 Amendment Agreement with regards to
the maximum quarterly Milestone Payments.

4.               Roche Discretion.  By entering into this Amendment, Roche has
elected not to give an Early Termination Notice with respect to the optional
termination effective date of December 31, 2007. Accordingly, Roche hereby
waives its early termination rights (including full termination and Partial
Termination) as provided in Section VI(b) of the License Agreement (as
supplemented and amended) with respect to such date. For clarity, nothing in
this Amendment shall in any way limit Roche’s complete discretion to give an
Early Termination Notice (whether relating to a full termination or a Partial
Termination) with respect to any subsequent optional termination effective
dates in accordance with the Collaboration Agreements (as amended) for any or
no reason.

5.               General Provisions.

(a)          Collaboration
Agreement.  For all purposes of
the Collaboration Agreements, this Amendment shall constitute a Collaboration
Agreement, and the definition of the term “Collaboration Agreements” in the
Common Terms Agreement is hereby amended accordingly.  Without limiting the generality of the foregoing,
Section VI (General) of the Common Terms Agreement shall apply to this
Amendment and is incorporated by reference as if fully set forth herein.

(b)         Relation to
Other Collaboration Agreements. 
As amended by this Amendment, the Collaboration Agreements remain in
full force and effect.

 

IN WITNESS WHEREOF the Parties have
executed this Amendment.

	
  AFFYMETRIX, INC.

  	
   

  	
  F. HOFFMANN-LA ROCHE LTD.

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By:

  	
  /s/ Noel Doheny

  	
   

  	
  By:

  	
   
  /s/ Florian Zabel

  
	
   

  	
  Name:

  	
  Noel Doheny

  	
   

  	
   

  	
  Name:

  	
  Florian Zabel

  
	
   

  	
  Title:

  	
  Senior Vice President,

  Molecular Diagnostics

  	
   

  	
   

  	
  Title:

  	
  Legal Counsel

  
	
   

  	
   

  	
   

  	
   

  	
  By:

  	
   
  /s/ Robert Yates

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
  Name:

  	
  Robert Yates

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
  Title:

  	
  Head of Business Development

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  ROCHE MOLECULAR SYSTEMS, INC.

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
  By:

  	
  /s/ Daniel P. O’Day

  
	
   

  	
   

  	
   

  	
  Name:  Daniel P. O’Day

  
	
   

  	
   

  	
   

  	
  Title:Exhibit 4.1

FOURTH
SUPPLEMENTAL INDENTURE

THIS FOURTH
SUPPLEMENTAL INDENTURE (this “Supplemental Indenture”) dated as of
December 26, 2006 by and among Great Lakes Dredge & Dock Corporation, a
Delaware corporation (the “Issuer”), NASDI Holdings Corporation, a Delaware
corporation, Great Lakes Dredge & Dock Company, a New Jersey corporation,
Great Lakes Caribbean Dredging, Inc., a Delaware corporation, Dawson Marine
Services Company, a Delaware corporation, North American Site Developers, Inc.,
a Massachusetts corporation, Fifty-Three Dredging Corporation, a New Jersey
corporation, JDC Soil Management & Development Inc., a Massachusetts
corporation and Great Lakes Dredge & Dock Company, LLC, a Delaware limited
liability company (collectively, the “Guarantors”), Great Lakes
Dredge & Dock Holdings Corp., a Delaware corporation (“Holdings”)
and BNY Midwest Trust Company, an Illinois trust company, as trustee under the
indenture referred to below (the “Trustee”).

RECITALS

WHEREAS, the
Issuer and the Guarantors have previously executed and delivered to the Trustee
an indenture, dated as of December 22, 2003, as supplemented and amended from
time to time (the “Indenture”), providing for the issuance of an
aggregate principal amount of up to $175,000,000 of 73⁄4% Senior Subordinated
Notes due 2013 (the “Notes”);

WHEREAS, pursuant
to that certain Merger Agreement dated as of the date hereof by and among the
Issuer and Holdings, the Issuer shall merge with and into Holdings and Holdings
shall be the surviving corporation;

WHEREAS, Holdings,
as the surviving corporation, is required under Section 5.01 of the Indenture
to execute and deliver to the Trustee a supplemental indenture pursuant to
which Holdings shall assume all of the obligations of the Issuer under the
Indenture, the Registration Rights Agreement and the Notes; and

WHEREAS, pursuant
to Section 9.01 of the Indenture, the Issuer, the Guarantors, Holdings and the
Trustee are authorized to execute and deliver this Supplemental Indenture.

NOW THEREFORE, in
consideration of the foregoing and mutual covenants herein contained and
intending to be legally bound, the parties hereto mutually covenant and agree
for the equal and ratable benefit of the holders of the Notes as follows:

1.             DEFINED TERMS. As used in this
Supplemental Indenture, terms defined in the Indenture or in the preamble or
recital hereto are used herein as therein defined, except that the term “holders”
in this Supplemental Indenture shall refer to the term “Holders” as defined in
the Indenture and the Trustee acting on behalf of and for the benefit of such
Holders. The words “herein,” “hereof” and hereby and other words of similar
import used in this Supplemental Indenture refer to this Supplemental Indenture
as a whole and not to any particular section hereof.

2.             ASSIGNMENT AND ASSUMPTION.

 

(a)           As of the date hereof, the Issuer
hereby transfers and assigns to Holdings, and Holdings hereby assumes and
undertakes from the Issuer, all rights, powers, commitments, obligations and
liabilities of the Issuer under the Indenture, the Registration Rights
Agreement and the Notes (collectively, the “Assigned Instruments”) and
agrees to be bound by all other applicable provisions of the Assigned
Instruments.

(b)           With effect on and after the date
hereof, the Issuer shall be released from its obligations and covenants under
the Assigned Instruments.

3.             NOTICES. All notices or other
communications to Holdings shall be given as provided for the Company in 13.02
of the Indenture.

4.             RATIFICATION OF INDENTURE;
SUPPLEMENTAL INDENTURES PART OF INDENTURE. Except as expressly amended hereby,
the Indenture is in all respects ratified and confirmed and all the terms,
conditions and provisions thereof shall remain in full force and effect. This
Supplemental Indenture shall form a part of the Indenture for all purposes, and
every holder of Notes heretofore or hereafter authenticated and delivered shall
be bound hereby.

5.             GOVERNING LAW. THIS SUPPLEMENTAL
INDENTURE SHALL BE GOVERNED BY, AND CONSTRUED IN ACCORDANCE WITH, THE LAWS OF
THE STATE OF NEW YORK.

6.             TRUSTEE MAKES NO REPRESENTATION.
The Trustee makes no representation as to the validity or sufficiency of this
Supplemental Indenture. The recitals and statements herein are deemed to be
those of the Issuer and the Guarantors and not of the Trustee.

7.             COUNTERPARTS. The parties may sign
any number of copies of this Supplemental Indenture. Each signed copy shall be
an original, but all of them together represent the same agreement.

8.             EFFECT OF HEADINGS. The Section
headings herein are for convenience only and shall not affect the construction
thereof.

[REMAINDER OF PAGE
INTENTIONALLY LEFT BLANK]

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IN WITNESS
WHEREOF, the parties hereto have caused this Supplemental Indenture to be duly
executed as of the date first above written.

	
  

  	
  ISSUER:

  
	
   

  	
  GREAT LAKES DREDGE & DOCK CORPORATION

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  
	
   

  	
   

  
	
   

  	
  GUARANTORS:

  
	
   

  	
  GREAT LAKES DREDGE & DOCK COMPANY, LLC

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  
	
   

  	
   

  
	
   

  	
  GREAT LAKES DREDGE & DOCK COMPANY

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  

 

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  GREAT LAKES CARIBBEAN DREDGING, INC.

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  
	
   

  	
   

  
	
   

  	
  DAWSON MARINE SERVICES COMPANY

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  
	
   

  	
   

  
	
   

  	
  NORTH AMERICAN SITE DEVELOPERS, INC.

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  

 

 4
 

 

 

	
  

  	
  FIFTY-THREE DREDGING CORPORATION

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Paul Dinquel

  
	
   

  	
  Name:

  	
  Paul Dinquel

  
	
   

  	
  Title:

  	
  VP

  
	
   

  	
   

  
	
   

  	
  JDC SOIL MANAGEMENT & DEVELOPMENT INC.

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  
	
   

  	
   

  
	
   

  	
  NASDI HOLDINGS CORPORATION

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  
	
   

  	
   

  
	
   

  	
  HOLDINGS:

  
	
   

  	
  GREAT LAKES DREDGE & DOCK HOLDINGS CORP.

  
	
   

  	
   

  
	
   

  	
  By:

  	
  /s/ Deborah A. Wensel

  
	
   

  	
  Name:

  	
  Deborah A. Wensel

  
	
   

  	
  Title:

  	
  Sr. VP & CFO

  

 

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  TRUSTEE:

  
	
   

  	
  BNY MIDWEST TRUST COMPANY, As Trustee

  
	
   

  	
   

  
	
   

  	
  By: 

  	
  M. Callahan

  
	
   

  	
  Name: 

  	
  M. Callahan

  
	
   

  	
  Title:

  	
  Vice President

  

 

 6

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