Document:

Exhibit

First Amendment to Pooled Patents Agreement
This First Amendment to the Pooled Patents Agreement (the “First Amendment”) is effective as of the date of last signature found below between Illumina, Inc., a Delaware corporation having a place of business at 5200 Illumina Way, San Diego, CA  92122 ("Illumina") and Sequenom, Inc., a Delaware corporation, having a place of business at 3595 John Hopkins Court, San Diego CA 92121 (“Sequenom”).  Sequenom and Illumina may be referred to herein as “Party” or “Parties.”
WHEREAS, the Parties entered into the Pooled Patents Agreement, dated December 2, 2014 (“Agreement”); 
WHEREAS, the Parties have been discussing a lowering of Test Fees in accordance with Section 3.2(c)(iii), and on March 25, 2016 the Parties reached agreement in accordance with Sections 3.2(c)(iii)(1) and (3) (such date referred to as the “Lowering Date”);
WHEREAS, the Parties desire to amend the Agreement to implement their agreement reached on the Lowering Date; and
WHEREAS, for good and valuable consideration, the Parties agree to amend the Agreement as follows:
		
	1.
	Schedule 1 is deleted in its entirety and replaced with the attached new Schedule 1.

		
	2.
	Section 7.1(b)(xi) is hereby deleted in its entirety and replaced with the following:

“(xi)    any agreement entered into by Sequenom or any Affiliate of Sequenom prior to the Effective Date granting rights under any Sequenom Patent (prior to assignment and novation of the CUHK Licenses (2008/2011)) includes an obligation for the grantee to pay Test Fees to Sequenom or such Affiliate that are in an amount that is materially consistent with (or higher than) the Test Fee amounts (based on currency exchange rates in effect on the Effective Date) set forth on Schedule 1 (excluding Section 5 and the additional $20 fee pursuant to Section 3 of Schedule 1);”
		
	3.
	Section 7.1(c)(v) is hereby deleted in its entirety and replaced with the following:

“(v)    it intends to continue prosecuting the ongoing disputes it has with Existing Illumina Litigants in a manner that, if successful, would lead to an obligation, on each such Existing Illumina Litigant that intends to perform on a going forward basis an NIPT LDT Test that is covered by a Valid Issued Claim under the Illumina Patents (excluding the CUHK Patents), to take a license under such Illumina Patents in exchange for consideration payable to Illumina that is consistent with the Test Fee amounts set forth on Schedule 1 (excluding Section 5 and the additional $20 fee pursuant to Section 3 of Schedule 1);”
		
	4.
	Section 7.1(c)(ix) is hereby deleted in its entirety and replaced with the following:

“(ix)    except as set forth on Schedule 7.1(c)(ix), any agreement entered into by Illumina or any Affiliate of Illumina prior to the Effective Date granting rights under any Illumina Patent (excluding the CUHK Patents) includes an obligation for the grantee to pay Test Fees to Illumina or such Affiliate that are materially consistent with (or higher than) the Test Fee amounts (based on currency exchange rates in effect on the Effective Date) set forth on Schedule 1 (excluding Section 5 and the additional $20 fee pursuant to Section 3 of Schedule 1);”
		
	5.
	Schedule 7.1(c)(ix) is hereby deleted in its entirety and replaced with the following:

“Two Existing Illumina Licensees (each an Illumina Technology Partner) are currently paying volume-based Test Fees to Illumina that are at or higher than the volume-based Test Fee amounts set forth on Schedule 1 (excluding Section 5 and the additional $20 fee pursuant to Section 3 of Schedule 1), however, as of the Effective Date, each such licensee is subject to a volume-based Test Fee schedule that would permit that licensee to pay Test Fees in an amount that is below the Test Fee amount on Schedule 1 (excluding Section 5) 

at such time (if ever) it achieves a certain cumulative volume and thereafter until (1) December, 2016, for one licensee or (2) January 2017, for the other licensee. 
Except as expressly modified herein, the Agreement shall remain in full force and effect in accordance with its terms.  All capitalized terms not defined in this First Amendment shall have the meaning ascribed to them in the Agreement.
IN WITNESS WHEREOF, the Parties have signed this First Amendment as of the dates indicated below.
    
	
					
	ILLUMINA
	 
	SEQUENOM

	By:
	/s/ Jeff Eidel
	 
	By:
	/s/ Dereck Tatman

	Name:
	Jeffrey Eidel
	 
	Name:
	Dereck Tatman

	Title:
	VP Corporate Development
	 
	Title:
	SR VP Business Development

	Date:
	April 20, 2016
	 
	Date:
	April 21, 2016Exhibit

Second Amendment to Pooled Patents Agreement
This Second Amendment to the Pooled Patents Agreement (the “Second Amendment”) is effective as of the date of last signature found below (“Second Amendment Effective Date”) between Illumina, Inc., a Delaware corporation having a place of business at 5200 Illumina Way, San Diego, CA  92122 ("Illumina") and Sequenom, Inc., a Delaware corporation, having a place of business at 3595 John Hopkins Court, San Diego CA 92121 (“Sequenom”).  Sequenom and Illumina may be referred to herein as “Party” or “Parties.”
WHEREAS, the Parties entered into the Pooled Patents Agreement, dated December 2, 2014, as amended via a First Amendment dated April 21, 2016 (“Agreement”); 
WHEREAS, the Parties have been discussing a lowering of Test Fees in accordance with Section 3.2(c)(iii), and have now reached agreement in accordance with Sections 3.2(c)(iii)(1) and (3);
WHEREAS, the Parties desire to amend the Agreement to permit lower Test Fees to be paid by certain companies, as identified herein; and
WHEREAS, for good and valuable consideration, the Parties agree to amend the Agreement as follows:
		
	1.
	Section 3.5(b)(i) is deleted in its entirety and replaced with:

(i)     Adjustment Due to Average Test Fee Collected. The Minimum Payments set forth in Section 3.5(a) are based on an average annual Test Fee collected by Illumina and Sequenom in the amount of $72 per NIPT Test. If the average Test Fee collected for a calendar year is lower than $72 per NIPT Test by 5% or more, then the Minimum Payment for the calendar year shall be adjusted downward by multiplying the then current Minimum Payment amount by the quotient of the average Test Fee actually collected and subject to sharing between Illumina and Sequenom during that calendar year divided by seventy-two dollars ({minimum payment amount}×{average Test Fee for immediately preceding calendar year}/$72).

		
	2.
	Schedule 1 is deleted in its entirety and replaced with the attached new Schedule 1.

		
	3.
	Schedules 1A and 1B are added to the Agreement after Schedule 1 and before Schedule 2.

Except as expressly modified herein, the Agreement shall remain in full force and effect in accordance with its terms.  All capitalized terms not defined in this Second Amendment shall have the meaning ascribed to them in the Agreement.

[Remainder of Page Intentionally Left Blank. Signature Page to Follow]

IN WITNESS WHEREOF, the Parties have signed this Second Amendment as of the dates indicated below.
    
	
					
	ILLUMINA
	 
	SEQUENOM

	By:
	/s/ Jeff Eidel
	 
	By:
	/s/ Eric Lindblom

	Name:
	Jeff Eidel
	 
	Name:
	Eric Lindblom

	Title:
	VP, Corporate & Business Development
	 
	Title:
	SVP

	Date:
	April 14, 2017
	 
	Date:
	April 17, 2017Exhibit

CONFIDENTIAL TREATMENT REQUESTED
CERTAIN INFORMATION OMITTED AND FILED SEPARATELY WITH THE SEC

Third Amendment to Pooled Patents Agreement
This Third Amendment to the Pooled Patents Agreement (the “Third Amendment”) is effective as of the date of last signature found below (“Third Amendment Effective Date”) between Illumina, Inc., a Delaware corporation having a place of business at 5200 Illumina Way, San Diego, CA  92122 ("Illumina") and Sequenom, Inc., a Delaware corporation, having a place of business at 3595 John Hopkins Court, San Diego CA 92121 (“Sequenom”).  Sequenom and Illumina may be referred to herein as “Party” or “Parties.”
WHEREAS, the Parties entered into the Pooled Patents Agreement, dated December 2, 2014, as amended via a First Amendment dated April 21, 2016 and via a Second Amendment dated April 17, 2017 (“Agreement”); 
WHEREAS, the Parties desire to amend Schedule 1A of the Agreement to permit lower Test Fees to be paid by certain additional companies, as identified herein; and
WHEREAS, for good and valuable consideration, the Parties agree to amend the Agreement as follows:
		
	1.
	Schedule 1A is amended to add the following entities:

[...***...]
Except as expressly modified herein, the Agreement shall remain in full force and effect in accordance with its terms.  All capitalized terms not defined in this Third Amendment shall have the meaning ascribed to them in the Agreement.

IN WITNESS WHEREOF, the Parties have signed this Third Amendment as of the dates indicated below.
    
	
					
	ILLUMINA
	 
	SEQUENOM

	By:
	/s/ Jeff Eidel
	 
	By:
	/s/ Eric Lindblom

	Name:
	Jeff Eidel
	 
	Name:
	Eric Lindblom

	Title:
	VP, Corporate & Business Development
	 
	Title:
	SVP, LabCorp.

	Date:
	August 21, 2017
	 
	Date:
	August 28, 2017EX-4.2

 Exhibit 4.2 

SUCAMPO PHARMACEUTICALS, INC. 

AND 
 U.S. BANK NATIONAL
ASSOCIATION, 
 as Trustee 

FIRST SUPPLEMENTAL INDENTURE 

Dated as of February 13, 2018 

3.25% Convertible Senior Notes due 2021 

 FIRST SUPPLEMENTAL INDENTURE, dated as of February 13, 2018 (this “Supplemental
Indenture”), among Sucampo Pharmaceuticals, Inc., a Delaware corporation (the “Company”), as issuer, and U.S. Bank National Association, a national banking association organized under the laws of the United States of
America, as trustee (the “Trustee”), to the Indenture, dated as of December 27, 2016 (as supplemented or otherwise modified prior to the date hereof, the “Indenture”), between the Company and the Trustee. 

WHEREAS, the Company has heretofore executed and delivered the Indenture, pursuant to which the Company issued its 3.25% Convertible Senior
Notes due 2021 (the “Notes”) in the original aggregate principal amount of $300,000,000; 
 WHEREAS, the Company has
entered into an Agreement and Plan of Merger, dated as of December 23, 2017 (as amended, supplemented, restated or otherwise modified, the “Merger Agreement”), by and among the Company, Mallinckrodt plc, an Irish public limited
company (the “Parent”), and Sun Acquisition Co., a Delaware corporation and wholly-owned subsidiary of Parent (“Merger Sub”); 

WHEREAS, pursuant to the terms of the Merger Agreement, Merger Sub will merge with and into the Company (the “Merger”) on the
date hereof with the Company, as the surviving entity in the Merger, becoming a wholly owned subsidiary of Parent as of the date hereof; 

WHEREAS, the Merger constitutes a Merger Event under the Indenture; 

WHEREAS, Section 14.07(a) of the Indenture provides that, prior to or at the effective time of any Merger Event, the Company or the
successor or purchasing Person, as the case may be, shall execute with the Trustee a supplemental indenture permitted under Section 10.01(g) of the Indenture providing that, at and after the effective time of such Merger Event, the right to
convert each $1,000 principal amount of Notes shall be changed into a right to convert such principal amount of Notes into the kind and amount of shares of stock, other securities or other property or assets (including cash or any combination
thereof) that a holder of a number of shares of Common Stock equal to the Conversion Rate immediately prior to such Merger Event would have owned or been entitled to receive upon such Merger Event; 

WHEREAS, in connection with the Merger, each outstanding share of Common Stock prior to the effective time (other than certain shares of
Common Stock as set forth in the Merger Agreement) shall be converted into the right to receive an amount in cash equal to $18.00, without interest and subject to any applicable withholding taxes, in accordance with the terms of the Merger
Agreement; 
 WHEREAS, Section 10.01 of the Indenture provides that the Company, when authorized by resolutions of the Board of
Directors of the Company (the “Board of Directors”) and the Trustee may enter into an indenture or indentures supplemental to the Indenture to, among other things, (i) make any change that does not adversely affect the rights
of any Holder or (ii) in connection with any Merger Event, provide that the Notes are convertible into Reference Property, subject to the provisions of Section 14.02 of the Indenture, and make such related changes to the terms of the Notes
to the extent expressly required by Section 14.07 of the Indenture; 
 WHEREAS, the Board of Directors, by resolutions adopted on
December 22, 2017, has duly authorized the Company’s entry into and delivery of this Supplemental Indenture, and the entry into this Supplemental Indenture by the parties hereto is permitted or authorized by the provisions of the
Indenture; 

  
 2 

 WHEREAS, in connection with the execution and delivery of this Supplemental Indenture, the
Trustee has received an Officer’s Certificate and an Opinion of Counsel as contemplated by Sections 10.05 and 17.05 of the Indenture; and 

WHEREAS, the Company has requested that the Trustee execute and deliver this Supplemental Indenture and have satisfied all requirements
necessary to make this Supplemental Indenture a valid instrument in accordance with its terms. 
 WITNESSETH: 

NOW THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the receipt of which is hereby acknowledged,
the Company covenants and agrees with the Trustee as follows for the equal and ratable benefit of the Holders: 
 ARTICLE 1 

DEFINITIONS 
 Section 1.01.
Definitions in the Supplemental Indenture. Unless otherwise specified herein or the context otherwise requires: 
 (a) a term
defined in the Indenture has the same meaning when used in this Supplemental Indenture unless the definition of such term is amended or supplemented pursuant to this Supplemental Indenture; 

(b) the terms defined in this Article and in this Supplemental Indenture include the plural as well as the singular; and 

(c) unless otherwise stated, a reference to a Section or Article is to a Section or Article of this Supplemental Indenture. 

ARTICLE 2 
 EFFECT OF MERGER ON
CONVERSION 
 Section 2.01. Conversion Right. In accordance with and subject to Section 14.07 of the Indenture, as a result
of the Merger, each $1,000 in principal amount of Notes is, at and after the effective time of the Merger, convertible in accordance with the terms of the Indenture into the right to receive the amount of cash that a holder of a number of shares of
Common Stock equal to the Conversion Rate immediately prior to the consummation of the Merger would have owned or been entitled to receive upon the consummation of the Merger. For all conversions that occur at or after the effective time of the
Merger in accordance with and subject to Article 14 of the Indenture, (i) the consideration due upon conversion of each $1,000 principal amount of Notes shall be solely cash in an amount equal to the Conversion Rate in effect on the applicable
Conversion Date (as may be increased by any Additional Shares pursuant to Section 14.03 of the Indenture), multiplied by the price paid per share of Common Stock in the Merger, and (ii) the Company shall satisfy the conversion obligation
by paying cash to converting Holders on the third Business Day immediately following the relevant Conversion Date. 

  
 3 

 ARTICLE 3 

MISCELLANEOUS 

Section 3.01. Ratification of Indenture. The Indenture, as supplemented by this Supplemental Indenture, is in all respects
ratified and confirmed, and this Supplemental Indenture shall be deemed part of the Indenture in the manner and to the extent herein and therein provided. 

Section 3.02. Trustee Not Responsible for Recitals. The recitals herein contained are made by the Company and not by the Trustee,
and the Trustee assumes no responsibility for the correctness thereof. The Trustee makes no representation as to the validity or sufficiency of this Supplemental Indenture. All of the provisions contained in the Indenture in respect of the rights,
privileges, immunities, powers, and duties of the Trustee shall be applicable in respect of the Supplemental Indenture as fully and with like force and effect as though set forth in full herein. 

Section 3.03 Successors. All agreements of the Company and the Trustee in this Supplemental Indenture will bind their respective
successors. 
 Section 3.04. Governing Law. THIS SUPPLEMENTAL INDENTURE AND ANY CLAIM, CONTROVERSY OR DISPUTE ARISING UNDER OR
RELATED TO THIS SUPPLEMENTAL INDENTURE SHALL BE GOVERNED BY, AND CONSTRUED IN ACCORDANCE WITH, THE LAWS OF THE STATE OF NEW YORK. 

Section 3.05. Headings, Etc. The titles and headings of the articles and sections of this Supplemental Indenture have been
inserted for convenience of reference only, are not to be considered a part hereof, and shall in no way modify or restrict any of the terms or provisions hereof. 

Section 3.06. Execution in Counterparts. This Supplemental Indenture may be executed in any number of counterparts, each of which
shall be an original, but such counterparts shall together constitute but one and the same instrument. The exchange of copies of this Supplemental Indenture and of signature pages by facsimile or PDF transmission shall constitute effective execution
and delivery of this Supplemental Indenture as to the parties hereto and may be used in lieu of the original Supplemental Indenture for all purposes. Signatures of the parties hereto transmitted by facsimile or PDF shall be deemed to be their
original signatures for all purposes. 
 Section 3.07. Severability. In the event any provision of this Supplemental Indenture
shall be invalid, illegal or unenforceable, then (to the extent permitted by law) the validity, legality or enforceability of the remaining provisions shall not in any way be affected or impaired. 

Section 3.08. Waiver of Jury Trial. EACH OF THE COMPANY AND THE TRUSTEE HEREBY IRREVOCABLY WAIVES, TO THE FULLEST EXTENT PERMITTED
BY APPLICABLE LAW, ANY AND ALL RIGHT TO TRIAL BY JURY IN ANY LEGAL PROCEEDING ARISING OUT OF OR RELATING TO THIS SUPPLEMENTAL INDENTURE OR THE TRANSACTIONS CONTEMPLATED HEREBY. 

Section 3.09. Effectiveness. This Supplemental Indenture shall become effective upon, without further action by the parties
hereto, the effective time of the Merger. 
 [Signature Page Follows] 

  
 4 

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

					
	SUCAMPO PHARMACEUTICALS, INC.
		
	By:	 	/s/ Peter Greenleaf
		 	Name:	 	Peter Greenleaf
		 	Title:	 	 Chief Executive Officer,
 Chairman of the
Board of Directors

  

					
	 U.S. BANK NATIONAL
 ASSOCIATION, as
Trustee

		
	By:	 	/s/ Raymond S. Haverstock
		 	Name:	 	Raymond S. Haverstock
		 	Title:	 	Vice President

 SIGNATURE PAGE TO SUPPLEMENTAL INDENTURE

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