Document:

Secured Convertible Minimum Borrowing Note Series B

 Exhibit 10.6 
  
 THIS NOTE AND THE COMMON SHARES ISSUABLE UPON CONVERSION OF THIS NOTE HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED, OR ANY STATE SECURITIES LAWS. THIS NOTE AND THE COMMON SHARES ISSUABLE UPON CONVERSION OF THIS NOTE MAY NOT BE SOLD, OFFERED FOR SALE, PLEDGED OR HYPOTHECATED IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT AS TO THIS NOTE UNDER SAID
ACT AND ANY APPLICABLE STATES SECURITIES LAWS OR AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO TRANSGENOMIC, INC. THAT SUCH REGISTRATION IS NOT REQUIRED. 
  

SECURED CONVERTIBLE MINIMUM BORROWING NOTE SERIES B 
  
 FOR VALUE RECEIVED, TRANSGENOMIC, INC., a Delaware corporation (the “Borrower”) promises to pay to LAURUS
MASTER FUND, LTD., c/o Ironshore Corporate Services Ltd., P.O. Box 1234 G.T., Queensgate House, South Church Street, Grand Cayman, Cayman Islands, Fax: 345-949-9877 (the “Holder”) or its registered assigns, on order, the sum of
THREE MILLION DOLLARS ($3,000,000), or, if different, the aggregate principal amount of all “Loans” (as such term is defined in the Security Agreement referred to below), together with any accrued and unpaid interest hereon, on December 3,
2006 (the “Maturity Date”). 
  
 Capitalized terms
used herein without definition shall have the meanings ascribed to such terms in the Security Agreement between Borrower and the Holder dated as of December 3, 2003 (as amended, modified and supplemented from time to time, the “Security
Agreement”). 
  
 The following terms shall apply to this Secured
Convertible Minimum Borrowing Note Series B (the “Note”): 
  
 ARTICLE I 
 INTEREST 
  
 1.1. Interest Rate and Payments. Subject to Sections 5.3 and 6.7 hereof, interest payable on this Note shall accrue at a rate per annum equal to
the “prime rate” published in The Wall Street Journal from time to time, plus two percent (2.00%), but in no event less than six percent (6%) per annum (the “Contract Rate”). The Prime Rate shall be increased or
decreased as the case may be for each increase or decrease in the Prime Rate in an amount equal to such increase or decrease in the Prime Rate; each change to be effective as of the day of the change in such rate in accordance with the terms of the
Security Agreement. The Contract Rate shall be further adjusted from time to time as follows: if (i) the Borrower shall have registered the shares of the Borrower’s common stock underlying the conversion of this Note and that certain warrant
issued to Holder of even date herewith on a registration statement declared effective by the Securities Exchange Commission, and (ii) the volume weighted average price of 

 the Common Stock as reported by Bloomberg, L.P. on the Principal Market for any of the ten (10) trading days immediately
preceding a Interest Payment Date (defined below) exceeds the then applicable Fixed Conversion Price by a multiple of at least fifteen percent (15%), then the Contract Rate for the succeeding calendar month shall automatically be reduced by twenty
five basis points (25 b.p.) for such period for each such multiple of fifteen percent (15%). Interest shall be payable monthly in arrears commencing on January 1, 2004 and on the first day of each consecutive calendar month thereafter, (each, an
“Interest Payment Date”). 
  
 ARTICLE II

 ADVANCES, BORROWER CONVERSION RIGHTS, PAYMENTS UNDER NOTE 
  
 2.1. Mechanics of Advances. All Loans evidenced by this Note shall be made in accordance with the terms and
provisions of the Security Agreement. 
  
 2.2. Borrower’s
Conversion Rights. Subject to the terms hereof, the Borrower shall have the sole option to determine whether to satisfy payment of any payment of principal or interest when due either in cash or in shares of Common Stock (as defined in the
Security Agreement), or a combination of both. Each month by the tenth (10th) day of such month, the Borrower shall
deliver to the Holder a written irrevocable notice in the form of Exhibit A attached hereto electing to pay the amount specified therein payable on the first day of the next month in either cash or Common Stock, or a combination of both (each, a
“Repayment Election Notice”). Each Repayment Election Notice shall be delivered to the Holder not later than the tenth (10th) day of the month prior to the applicable payment date (the date by which such notice is required to be given being hereinafter referred to as the “Notice Date”). If, for any amount which is due on any
repayment date, a Repayment Election Notice is not delivered to the Holder by the applicable Notice Date for such repayment date, then the amount due on such repayment date shall be paid in cash. If the Borrower repays all or a portion of the amount
due on any payment date in shares of Common Stock, the number of such shares to be issued for such payment date shall be the number determined by dividing (x) the amount to be paid in shares of Common Stock, by (y) the Fixed Conversion Price. For
purposes hereof, subject to Section 3.5 hereof, the “Fixed Conversion Price” means $2.20. 
  
 2.3. No Effective Registration. Notwithstanding anything to the contrary herein, the Borrower shall be prohibited from exercising its right to
repay any amount hereunder in shares of Common Stock if at any time from the Call Date (defined below) for such payment through the date upon which such payment is made by delivery of certificates for shares of Common Stock (i) there fails to exist
an effective current Registration Statement (as defined in the Registration Rights Agreement) on Form S-3 covering the resale of shares of Common Stock to be issued, or (ii) an Event of Default hereunder exists and is continuing, unless such
requirement is otherwise waived in writing by the Holder in whole or in part at the Holder’s option. 
  
 2.4. Common Stock Payment Guidelines. Notwithstanding anything to the contrary herein, if the Borrower has elected to make a payment hereunder in
shares of Common Stock and the closing price of the Common Stock as reported by Bloomberg, L.P. on the Principal Market for any of the eleven (11) trading days preceding the scheduled payment date 
  

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 was less than 110% of the Fixed Conversion Price, then the Holder shall have the option to refuse to accept any portion
of such payment in shares of Common Stock. 
  
 2.5. Optional
Payments in Common Stock. Subject to Section 2.2 hereof, if the Borrower elects to pay interest or prepay principal and the average closing price of the Common Stock on the Principal Market is greater than 110% of the Fixed Conversion Price for
a period of at least five (5) consecutive trading days, then the Borrower may, at its sole option, provide the Holder written notice (a “Call Notice”) requiring the conversion at the Fixed Conversion Price of (a) in the case
of interest, all interest due and payable for the current calendar month and (b) in the case of principal, all or a portion of the outstanding principal of this Note (subject to compliance with Section 2.3 and 3.2), together with accrued interest on
the principal amount being prepaid, in each case, as of the date set forth in such Call Notice (the “Call Date”). The Call Date shall be (a) in the case of interest, at least eleven (11) trading days prior to the first day of the
immediately succeeding calendar month and (b) in the case of principal, at least eleven (11) trading days following the date of the Call Notice. On the Call Date the Borrower shall deliver to the Holder certificates evidencing the shares of Common
Stock issued in satisfaction of the principal and/or interest being retired. Notwithstanding the foregoing, the Borrower’s right to issue shares of Common Stock in payment of obligations under this Note shall be subject to the limitation that
the number of shares of Common Stock issued at the Fixed Conversion Price in connection with any Call Notice shall not exceed 25% of the aggregate dollar trading volume of the Common Stock for the ten (10) trading days immediately preceding the Call
Date (as such volume is reported by Bloomberg, L.P. If the closing price of the Common Stock is below 110% of the Fixed Conversion Price during the ten (10) trading day period immediately preceding the Call Date, then the Holder will then be
required to convert only such amount of the Note as shall equal twenty five percent (25%) of the aggregate dollar trading volume (as such volume is reported by Bloomberg L.P.) for each day that the closing price of the Common Stock exceeded 110% of
the then applicable Fixed Conversion Price. The Borrower shall not be permitted to give the Holder more than one Call Notice under this Note during any 22-day period. 
  
 2.6. Optional Prepayment in Cash. The Borrower will have the option of prepaying this Note in full or in part at any
time in an amount equal to 103% of the amount being prepaid subject to the prepayment fees under Section 16 of the Security Agreement in the event this Note is paid in full. 
  
 ARTICLE III 
 HOLDER’S CONVERSION RIGHTS 
  
 3.1.
Optional Conversion. Subject to the terms of this Article III, the Holder shall have the right, but not the obligation, at any time until the Maturity Date, or thereafter during an Event of Default (as defined in Article V), and, subject to
the limitations set forth in Section 3.2 hereof, to convert all or any portion of the outstanding Principal Amount and/or accrued interest and fees due and payable into fully paid and nonassessable shares of the Common Stock at the Fixed Conversion
Price. The shares of Common Stock to be issued upon such conversion are herein referred to as the “Conversion Shares.” 
  

 3 

 3.2. Conversion Limitation. Notwithstanding anything contained herein to the contrary, the Holder
shall not be entitled to convert pursuant to the terms of this Note an amount that would be convertible into that number of Conversion Shares which, when added to the number of shares of Common Stock otherwise beneficially owned by such Holder
including those issuable upon exercise of warrants held by such Holder would exceed 4.99% of the outstanding shares of Common Stock of the Borrower at the time of conversion. For the purposes of the immediately preceding sentence, beneficial
ownership shall be determined in accordance with Section 13(d) of the Exchange Act and Regulation 13d-3 thereunder. The Conversion Shares limitation described in this Section 3.2 shall automatically become null and void without any notice to
Borrower upon the occurrence and during the continuance beyond any applicable grace period of an Event of Default, or upon 75 days prior notice to the Borrower. 
  

3.3. Mechanics of Holder’s Conversion. In the event that the Holder elects to convert this Note into Common Stock, the Holder shall give
notice of such election by delivering an executed and completed notice of conversion (“Notice of Conversion”) to the Borrower and such Notice of Conversion shall provide a breakdown in reasonable detail of the Principal Amount,
accrued interest and fees that are being converted. Each date on which a Notice of Conversion is delivered or telecopied to the Borrower in accordance with the provisions hereof shall be deemed a Conversion Date (the “Conversion
Date”). On each Conversion Date and in accordance with its Notice of Conversion, the Holder shall make the appropriate reduction to the Principal Amount, accrued interest and fees as entered in its records and shall provide written notice
thereof to the Borrower within two (2) Business Days after the Conversion Date. A form of Notice of Conversion to be employed by the Holder is annexed hereto as Exhibit A. Pursuant to the terms of the Notice of Conversion, the Borrower will issue
instructions to the transfer agent accompanied by an opinion of counsel within two (1) Business Days of the date of the delivery to Borrower of the Notice of Conversion and shall cause the transfer agent to transmit the certificates representing the
Conversion Shares to the Holder by crediting the account of the Holder’s designated broker with the Depository Trust Corporation (“DTC”) through its Deposit Withdrawal Agent Commission (“DWAC”) system within
three (3) Business Days after receipt by the Borrower of the Notice of Conversion (the “Delivery Date”). In the case of the exercise of the conversion rights set forth herein the conversion privilege shall be deemed to have been
exercised and the Conversion Shares issuable upon such conversion shall be deemed to have been issued upon the date of receipt by the Borrower of the Notice of Conversion. The Holder shall be treated for all purposes as the record holder of such
Common Stock, unless the Holder provides the Borrower written instructions to the contrary. 
  
 3.4. Late Payments. The Borrower understands that a delay in the delivery of the shares of Common Stock in the form required pursuant to this Article beyond the Delivery Date could result in economic loss to
the Holder. As compensation to the Holder for such loss, the Borrower agrees to pay late payments to the Holder for late issuance of such shares in the form required pursuant to this Article III upon conversion of the Note, in the amount equal to
$500 per business day after the Delivery Date. The Borrower shall pay any payments incurred under this Section in immediately available funds upon demand. 
  
 3.5. Adjustment Provisions. The Fixed Conversion Price and number and kind of shares or other securities to be issued upon conversion determined
pursuant to Section 2.2 
  

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 shall be subject to adjustment from time to time upon the happening of certain events while this conversion right remains
outstanding, as follows: 
  
 A. Reclassification, etc. If
the Borrower at any time shall, by reclassification or otherwise, change the Common Stock into the same or a different number of securities of any class or classes, this Note, as to the unpaid Principal Amount and accrued interest thereon, shall
thereafter be deemed to evidence the right to purchase an adjusted number of such securities and kind of securities as would have been issuable as the result of such change with respect to the Common Stock immediately prior to such reclassification
or other change. 
  
 B. Stock Splits, Combinations and
Dividends. If the shares of Common Stock are subdivided or combined into a greater or smaller number of shares of Common Stock, or if a dividend is paid on the Common Stock in shares of Common Stock, the Fixed Conversion Price shall be
proportionately reduced in case of subdivision of shares or stock dividend or proportionately increased in the case of combination of shares, in each such case by the ratio which the total number of shares of Common Stock outstanding immediately
after such event bears to the total number of shares of Common Stock outstanding immediately prior to such event. 
  
 C. Share Issuances. Subject to the provisions of this Section 3.5, if the Borrower shall at any time prior to the conversion or repayment in full
of the Principal Amount issue any shares of Common Stock to a person other than the Holder (except (i) pursuant to Subsections A or B above; (ii) pursuant to options, warrants, or other obligations to issue shares outstanding on the date hereof as
disclosed to Holder in writing; or (iii) pursuant to options that may be issued under any employee incentive stock option and/or any qualified stock option plan adopted by the Borrower) for a consideration per share (the “Offer Price”)
less than the Fixed Conversion Price in effect at the time of such issuance, then the Fixed Conversion Price shall be immediately reset pursuant to the formula below. For purposes hereof, the issuance of any security of the Borrower convertible into
or exercisable or exchangeable for Common Stock shall result in an adjustment to the Fixed Conversion Price at the time of issuance of such securities. If the Borrower issues any additional shares pursuant to this Subsection then, and thereafter
successively upon each such issue, the Fixed Conversion Price shall be adjusted by multiplying the then applicable Fixed Conversion Price by the following fraction: 
  
 A + B 
 (A + B) +
[((C - D) x B) / C] 
  
 A = Actual shares outstanding prior to such
offering 
 B = Actual shares sold in the offering 
 C = Fixed Conversion Price 
 D = Offer Price 
  
 D. Computation of Consideration. For purposes of any computation respecting consideration received pursuant to
Subsection C above, the following shall apply: 
  
 (a) in the
case of the issuance of shares of Common Stock for cash, the consideration shall be the amount of such cash, provided that in no case shall any deduction be made for any commissions, discounts or other expenses incurred by the Borrower for any
underwriting of the issue or otherwise in connection therewith; 
  

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 (b) in the case of the issuance of shares of Common Stock for a consideration in whole or in part other
than cash, the consideration other than cash shall be deemed to be the fair market value thereof as determined in good faith by the Board of Directors of the Borrower (irrespective of the accounting treatment thereof); and 
  
 (c) Upon any such exercise, the aggregate consideration received for such
securities shall be deemed to be the consideration received by the Borrower for the issuance of such securities plus the additional minimum consideration, if any, to be received by the Borrower upon the conversion or exchange thereof (the
consideration in each case to be determined in the same manner as provided in clauses (a) and (b) of this Subsection (D)). 
  
 3.6. Reservation of Shares. During the period the conversion right exists, the Borrower will reserve from its authorized and unissued Common Stock
a sufficient number of shares to provide for the issuance of Common Stock upon the full conversion of this Note. The Borrower represents that upon issuance, such shares will be duly and validly issued, fully paid and non-assessable. The Borrower
agrees that its issuance of this Note shall constitute full authority to its officers, agents, and transfer agents who are charged with the duty of executing and issuing stock certificates to execute and issue the necessary certificates for shares
of Common Stock upon the conversion of this Note. 
  
 3.7.
Registration Rights. The Holder has been granted registration rights with respect to the shares of Common Stock issuable upon conversion of this Note as more fully set forth in a Registration Rights Agreement dated the date hereof.

  
 ARTICLE IV 
 EVENTS OF DEFAULT 
  
 The occurrence of any of the following events is an Event of Default (“Event of Default”): 
  
 4.1. Failure to Pay Principal, Interest or other Fees. The Borrower
fails to pay when due any installment of principal, interest or other fees hereon or on any other promissory note issued pursuant to the Security Agreement, when due in accordance with the terms of such note. 
  
 4.2. Breach of Covenant. The Borrower breaches any covenant or other
term or condition of this Note in any material respect and such breach, if subject to cure, continues for a period of thirty (30) days after the occurrence thereof. 
  
 4.3. Breach of Representations and Warranties. Any material representation or warranty of the Borrower made herein,
or the Security Agreement, or in any Ancillary Agreement shall be materially false or misleading. 
  

 6 

 4.4. Stop Trade. An SEC stop trade order or Principal Market trading suspension of the Common
Stock shall be in effect for 5 consecutive days or 5 days during a period of 10 consecutive days, excluding in all cases a suspension of all trading on a Principal Market, provided that the Borrower shall not have been able to cure such trading
suspension within 30 days of the notice thereof or list the Common Stock on another Principal Market within 60 days of such notice. The “Principal Market” for the Common Stock shall include the NASD OTC Bulletin Board, NASDAQ SmallCap
Market, NASDAQ National Market System, American Stock Exchange, or New York Stock Exchange (whichever of the foregoing is at the time the principal trading exchange or market for the Common Stock), or any securities exchange or other securities
market on which the Common Stock is then being listed or traded. 
  
 4.5. Default Under Related Agreement. The occurrence of an Event of Default under and as defined in the Security Agreement. 
  
 4.6. Failure to Deliver Common Stock or Replacement Note. The Borrower’s failure to timely deliver Common Stock to the Holder pursuant to and
in the form required by this Note, and Section 9 of the Security Agreement, or if required, a replacement Note if such failure to timely deliver Common Stock shall not be cured within two (2) Business Days or such failure to deliver a replacement
Note is not cured within seven (7) Business Days. 
  
 4.7.
Payment Grace Period. The Borrower shall have a three (3) business day grace period to pay any monetary amounts due under this Note or the Security Agreement or any Related Document, after which grace period the Default Rate shall apply to
the monetary amounts due. 
  
 ARTICLE V 
 DEFAULT PAYMENTS 
  
 5.1. Default Payment. If an Event of Default occurs, the Holder, at its option, may elect, in addition to all rights and remedies of Holder under
the Security Agreement and all obligations of Borrower under the Security Agreement, to require the Borrower to make a Default Payment (“Default Payment”). The Default Payment shall be the outstanding principal amount of the Note,
plus accrued but unpaid interest, all other fees then remaining unpaid, and all other amounts payable hereunder. 
  
 5.2. Default Payment Date and Default Notice Period. The Default Payment shall be due and payable on the fifth business day after an Event of
Default as defined in Article IV (“Default Payment Date”) has occurred and is continuing beyond any applicable grace period. The period between the date upon which of an Event of Default has occurred and is continuing beyond any
applicable grace period and the Default Payment Date shall be the “Default Period.” If during the Default Period, the Borrower cures the Event of Default, the Event of Default will no longer exist and any additional rights the
Holder had triggered by the occurrence and continuance of an Event of Default will no longer exist. If the Event of Default is not cured during the Default Notice Period, all amounts payable hereunder shall be due and payable on the Default Payment
Date, all without further demand, presentment or notice, or grace period, all of which hereby are expressly waived. 
  

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 5.3. Default Interest Rate. Following the occurrence and during the continuance of an Event of
Default, interest on this Note shall automatically be increased to the Default Rate, and all outstanding Obligations, including unpaid interest, shall continue to accrue interest from the date of such Event of Default at such interest rate
applicable to such Obligations until such Event of Default is cured or waived. 
  
 5.4. Cumulative Remedies. The remedies under this Note shall be cumulative. 
  
 ARTICLE VI 
 MISCELLANEOUS 
  
 6.1. Failure or Indulgence Not Waiver. No failure or delay on the part
of the Holder hereof in the exercise of any power, right or privilege hereunder shall operate as a waiver thereof, nor shall any single or partial exercise of any such power, right or privilege preclude other or further exercise thereof or of any
other right, power or privilege. All rights and remedies existing hereunder are cumulative to, and not exclusive of, any rights or remedies otherwise available. 
  

6.2. Notices. Any notice herein required or permitted to be given shall be in writing and provided in accordance with the terms of the Security
Agreement. 
  
 6.3. Amendment Provision. The term
“Note” and all reference thereto, as used throughout this instrument, shall mean this instrument as originally executed, or if later amended or supplemented, then as so amended or supplemented, and any successor instrument as it may be
amended or supplemented. 
  
 6.4. Assignability. This Note
shall be binding upon the Borrower and its successors and assigns, and shall inure to the benefit of the Holder and its successors and assigns, and may be assigned by the Holder in accordance with the requirements of the Security Agreement.

  
 6.5. Cost of Collection. If default is made in the
payment of this Note, the Borrower shall pay the Holder hereof reasonable costs of collection, including reasonable attorneys’ fees. 
  
 6.6. Governing Law. This Note shall be governed by and construed in accordance with the laws of the State of New York, without regard to principles
of conflicts of laws. Any action brought by either party against the other concerning the transactions contemplated by this Agreement shall be brought only in the state courts of New York or in the federal courts located in the state of New York.
Both parties and the individual signing this Note on behalf of the Borrower agree to submit to the jurisdiction of such courts. The prevailing party shall be entitled to recover from the other party its reasonable attorney’s fees and costs. In
the event that any provision of this Note is invalid or unenforceable under any applicable statute or rule of law, then such provision shall be deemed inoperative to the extent that it may conflict therewith and shall be deemed modified to conform
with such statute or rule of law. Any such provision which may prove invalid or unenforceable under any law shall not affect the validity or unenforceability of any other provision of this Note. Nothing contained herein shall be deemed or operate to
preclude the Holder from bringing suit or taking other legal action against the 
  

 8 

 Borrower in any other jurisdiction to collect on the Borrower’s obligations to Holder, to realize on any collateral
or any other security for such obligations, or to enforce a judgment or other court order in favor of Holder. 
  
 6.7. Maximum Payments. Nothing contained herein shall be deemed to establish or require the payment of a rate of interest or other charges in
excess of the maximum permitted by applicable law. In the event that the rate of interest required to be paid or other charges hereunder exceed the maximum permitted by such law, any payments in excess of such maximum shall be credited against
amounts owed by the Borrower to the Holder and thus refunded to the Borrower. 
  
 6.8. Security Interest. The Holder of this Note has been granted a security interest in certain assets of the Borrower more fully described in the Security Agreement. 
  
 6.9. Construction. Each party acknowledges that its legal counsel
participated in the preparation of this Note and, therefore, stipulates that the rule of construction that ambiguities are to be resolved against the drafting party shall not be applied in the interpretation of this Note to favor any party against
the other. 
  
 [Balance of page intentionally left blank; signature
page follows.] 
  

 9 

 IN WITNESS WHEREOF, the Borrower has caused this Secured Convertible Minimum Borrowing Note to be
signed in its name effective as of this 3rd day of December, 2003. 
  

			
	 TRANSGENOMIC, INC.

		
	 By:
	 	 /s/ Michael J. Draper

	 	 	 Name: Michael J. Draper

	 	 	 Title: CFO

  

	
	 WITNESS:

	
	 /s/ Jerry Pearson

  

 10 

 NOTICE OF CONVERSION 
  
 (To be executed by the Holder in order to convert the Note) 
  
 The undersigned hereby elects to convert $             of
the principal and $             of the interest due on the Secured Convertible Minimum Borrowing Note issued by Transgenomic, Inc. (the “Borrower”) on December 3, 2003 into
Shares of Common Stock of the Borrower according to the conditions set forth in such Note, as of the date written below 
  

			
	 Date of Conversion: 
	 	  

		
	Conversion Price: 	 	  

		
	Shares To Be Delivered: 	 	  

		
	Signature: 	 	  

		
	Print Name: 	 	  

		
	Address: 	 	  

		
	Holder DWAC instructions 	 	  

  

 11 

 AMENDMENT NO. 1 TO SECURED CONVERTIBLE MINIMUM BORROWING NOTE 
 SERIES B 
 OF 
 TRANSGENOMIC, INC. 
  
 April 15, 2004 
  
 Reference is made to that certain Secured Convertible Minimum Borrowing Note Series B dated as of December 3, 2003 made by TRANSGENOMIC, INC., a Delaware Borrower (the “Borrower”) in favor LAURUS MASTER FUND, LTD., c/o
Ironshore Corporate Services Ltd., P.O. Box 1234 G.T., Queensgate House, South Church Street, Grand Cayman, Cayman Islands (the “Laurus”“) in the original principal amount of Three Million Dollars ($3,000,000), (the “MB
Note”). Capitalized terms used herein without definition shall have the meanings ascribed to such terms in the MB Note. 
  
 WHEREAS, each of the Borrower and Laurus desires to make certain changes to the MB Note to address the comments made by the National Association of
Securities Dealer Automated Quotation System market where the common stock of the Borrower is listed for trading. 
  
 NOW, THEREFORE, in consideration of the above, and for other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged,
the parties hereto agree as follows: 
  

	 	1.	 	Section 3.2 of the MB Note is hereby deleted in its entirety and replaced with the following: 

  
 “3.2 Conversion Limitation. Notwithstanding anything contained herein to the contrary, the
Holder shall not be entitled to convert pursuant to the terms of this Note an amount that would be convertible into that number of Conversion Shares which, when added to the number of shares of Common Stock otherwise beneficially owned by such
Holder including those issuable upon exercise of warrants held by such Holder would exceed 4.99% of the outstanding shares of Common Stock of the Borrower at the time of conversion. For the purposes of the immediately preceding sentence, beneficial
ownership shall be determined in accordance with Section 13(d) of the Exchange Act and Regulation 13d-3 thereunder. The Conversion Shares limitation described in this Section 3.2 shall automatically become null and void without any notice to
Borrower upon the occurrence and during the continuance beyond any applicable grace period of an Event of Default, or upon 75 days prior notice to the Borrower. Notwithstanding anything contained herein to the contrary, the number of shares of
Common Stock issuable by the Borrower and acquirable by the Holder at a price below $1.80 per share pursuant to the terms of the Secured Convertible Minimum Borrowing Notes, Secured Revolving Note and/or Warrants issued by the Borrower to the Holder
pursuant to that certain Security Agreement dated December 3, 2003 (the “December Transaction Documents”), shall not exceed an aggregate of 5,595,705 shares of the Borrower’s Common Stock, (subject to appropriate adjustment for stock
splits, stock dividends, or other similar recapitalizations 
  

 12 

 affecting the Common Stock) (the “Maximum Common Stock Issuance”), unless the issuance
of shares hereunder in excess of the Maximum Common Stock Issuance shall first be approved by the Borrower’s shareholders. If at any point in time and from time to time the number of shares of Common Stock issued pursuant to the terms of the
December Transaction Documents, together with the number of shares of Common Stock that would then be issuable by the Borrower to the Holder in the event of a conversion or exercise pursuant to the terms of the December Transaction Documents, would
exceed the Maximum Common Stock Issuance but for this Section, the Borrower shall promptly call a shareholders meeting to solicit shareholder approval for the issuance of the shares of Common Stock hereunder in excess of the Maximum Common Stock
Issuance. 
  

	 	2.	 	The foregoing amendment shall be effective as of the date hereof. 

  

	 	3.	 	There are no other amendments to the MB Note. 

  

	 	4.	 	The Borrower hereby represents and warrants to Laurus that as of the date hereof all representations, warranties and covenants made by Borrower in connection with the MB Note are
true correct and complete and all of Borrower’s covenants requirements have been met. As of the date hereof, no Event of Default under any Ancillary Agreements (as defined in the Security Agreement) has occurred or is continuing.

  
 IN WITNESS WHEREOF, each of the Borrower
and Laurus has caused this Amendment No. 1 to Secured Convertible Minimum Borrowing Note Series B to be signed in its name this 15 th day of April, 2004. 
  

			
	TRANSGENOMIC, INC.
		
	 By:
	 	 /s/ Mitchell L. Murphy

	 	 	 Name: Mitchell L. Murphy

	 	 	 Title: VP, Secretary & Treasurer

	
	LAURUS MASTER FUND, LTD.
		
	 By:
	 	 /s/ David Grin

	 Name: David Grain

	 Title:

  

 13EXHIBIT 4.1

 AMENDMENT NO. 2 
 TO 
 RIGHTS AGREEMENT 
  
 THIS AMENDMENT NO. 2 TO RIGHTS AGREEMENT (this “Amendment”) is effective as of March 25, 2004, between XM
SATELLITE RADIO HOLDINGS INC., a Delaware corporation (the “Company”), and EQUISERVE TRUST COMPANY, N.A. (the “Rights Agent”). 
  

WHEREAS, the Company and the Rights Agent are party to a Rights Agreement, dated as of August 2, 2002, as amended (the “Rights
Agreement”); 
  
 WHEREAS, in accordance with Section 27
of the Rights Agreement, the Company and the Rights Agent desire to amend the Rights Agreement on the terms and conditions hereinafter set forth; and 
  
 WHEREAS, for purposes of this Amendment, capitalized terms not otherwise defined herein shall have the respective meanings set forth in the Rights
Agreement, as amended by this Amendment. 
  
 NOW, THEREFORE, in
consideration of the premises and the mutual agreements herein set forth, the parties hereby agree as follows: 
  
 1.    Amendments to Section 1. 
  
 (a) Section 1(a) of the Rights Agreement, relating to the definition of the term “Acquiring Person,” is amended to read in its entirety as
follows: 
  
 “Acquiring Person” shall mean any Person
(as such term is hereinafter defined) who or which, together with all Affiliates and Associates (as such terms are hereinafter defined) of such Person, shall be the Beneficial Owner (as such term is hereinafter defined) of 15% or more of the shares
of Class A Common Stock then outstanding, but shall not include (i) the Company, (ii) any Subsidiary of the Company, or (iii) any employee benefit plan of the Company or any Subsidiary of the Company, or any Person holding shares of Class A Common
Stock for or pursuant to the terms of any such plan to the extent, and only to the extent, of such shares so held. Notwithstanding the foregoing, neither of American Honda Motor Co., Inc. (together with its Affiliates and Associates,
“Honda”) or General Motors Corporation (together with its Affiliates and Associates, including OnStar Corporation, “GM;” GM and Honda, together with their respective Affiliates and Associates, are each referred to sometimes
hereinafter as a “Qualified Exempt 

 
Person”), shall be deemed an “Acquiring Person;” provided however, that if after the Debt Refinancing Date, any Qualified Exempt Person shall
at any time beneficially own a number of shares of Class A Common Stock equal to or greater than (x) the number of shares of Class A Common Stock beneficially owned by such Qualified Exempt Person as of the Debt Refinancing Date, plus (y) two
percent (2%) of the total number of shares of Class A Common Stock then outstanding, then such Qualified Exempt Person shall be deemed an “Acquiring Person” hereunder as to all of the shares of Class A Common Stock then beneficially owned
by it and its Affiliates and Associates. For purposes of the above calculations, in determining whether GM constitutes an “Acquiring Person,” it shall be understood that shares of Class A Common Stock issued or issuable to GM (i) as
payment of interest accrued on the New GM Notes, (ii) as payment of interest accrued under the GM Credit Facility, (iii) upon conversion of the New GM Notes, (iv) upon exercise of the GM Warrant, (v) as payment of subscriber acquisition payments
under the GM Distribution Agreement or in satisfaction of the Company’s obligations under any other contract with GM, (vi) in connection with the issuance and sale on or prior to the Debt Refinancing Date to General Motors Corporation or any of
its Affiliates and Associates of additional shares of Class A Common Stock or securities convertible into or exercisable for Class A Common Stock, or (vii) in connection with any agreement prepared to document any of the issuances or potential
issuances described in clauses (i) through (vi) above and the transactions and arrangements contemplated thereby, regardless of when such interest accrues, such New GM Notes are converted, such GM Warrant is exercised, such subscriber acquisition
payments or other contractual obligations become payable, such shares of Class A Common Stock are sold, or the securities convertible or exercisable for shares of Class A Common Stock are converted into or exercised for shares of Class A Common
Stock, shall be deemed to have been outstanding and beneficially owned by GM as of the Debt Refinancing Date. For purposes of the above calculations, in determining whether Honda constitutes an “Acquiring Person,” it shall be understood
that shares of Class A Common Stock issued or issuable to Honda upon conversion of the New Investor Notes, regardless of when such New Investor Notes are converted, shall be deemed to have been outstanding and beneficially owned by Honda as of the
Debt Refinancing Date. Notwithstanding the foregoing, The TCW Group, Inc. (together with its Affiliates and Associates, “TCW”) shall not be deemed an “Acquiring Person” unless TCW becomes the Beneficial Owner of more than 19.9%
of the shares of Class A Common Stock then outstanding. Notwithstanding the foregoing, no Person shall become an “Acquiring 

  

 -2- 

 
Person” as the result of an acquisition of shares of Class A Common Stock by the Company which, by reducing the number of shares of Class A Common Stock
outstanding, increases the proportionate number of shares of Class A Common Stock beneficially owned by such Person to 15% or more of the shares of Class A Common Stock then outstanding (or in the case of a Qualified Exempt Person, increases the
proportionate number of shares of Class A Common Stock beneficially owned as of the date hereof by an additional 2%); provided, however, that if a Person shall become the Beneficial Owner of 15% or more of the Class A Common Stock then outstanding
(or in the case of a Qualified Exempt Person, increases the proportionate number of shares of Class A Common Stock beneficially owned as of the date hereof by an additional 2%) by reason of share purchases by the Company and shall, after such share
purchases by the Company, become the Beneficial Owner of any additional shares of Class A Common Stock, then such Person shall be deemed to be an “Acquiring Person” if such Person is then the Beneficial Owner of 15% or more of the Class A
Common Stock then outstanding. Notwithstanding the foregoing, if the Board of Directors of the Company determines in good faith that a Person who would otherwise be an “Acquiring Person,” as defined pursuant to the foregoing provisions of
this paragraph (a), has become such inadvertently, without any intention of changing or influencing control of the Company, and such Person divests as promptly as practicable a sufficient number of shares of Class A Common Stock so that such Person
would no longer be an “Acquiring Person,” then such Person shall not be deemed an “Acquiring Person” for any purposes of this Agreement unless and until such Person shall again become an “Acquiring Person;” provided,
that, to the extent the parties (the “Members”) to either the Shareholders’ Agreement (as defined herein) or the Director Agreement (as defined herein) could be deemed a “group” (as such term is used in Rule 13d-5 of the
general Rules and Regulations under the Exchange Act (as defined herein)), no Member shall be deemed an “Acquiring Person” for any purpose of this Agreement unless and until such Member becomes the Beneficial Owner of 15% or more of the
shares of Class A Common Stock then outstanding without including the number of shares Beneficially Owned by the other Members. 
  
 2.     Benefits. Nothing in the Rights Agreement, as amended by this Amendment, shall be construed to give to any Person other
than the Company, the Rights Agent and the registered holders of the Rights Certificates (and, prior to the Distribution Date, the registered holders of the Common Stock) any legal or equitable right, remedy or claim under the Rights Agreement, as
amended by this 

  

 -3- 

 
Amendment; but the Rights Agreement, as amended by this Amendment, shall be for the sole and exclusive benefit of the Company, the Rights Agent and the
registered holders of the Rights Certificates (and, prior to the Distribution Date, registered holders of the Common Stock). 
  
 3.    Descriptive Headings. Descriptive headings of the several Sections of this Amendment are inserted for convenience only
and shall not control or affect the meaning or construction of any of the provisions hereof. 
  
 4.    Governing Law. This Amendment shall be deemed to be a contract made under the laws of the State of Delaware and for all purposes shall be governed by and construed in accordance with
the laws of such State. 
  
 5.    Other
Terms Unchanged. The Rights Agreement, as amended by this Amendment, shall remain and continue in full force and effect and is in all respects agreed to, ratified and confirmed hereby. Any reference to the Rights Agreement after the date first
set forth above shall be deemed to be a reference to the Rights Agreement, as amended by this Amendment. 
  
 6.    Counterparts. This Amendment may be executed in any number of counterparts. It shall not be necessary that the signature
of or on behalf of each party appears on each counterpart, but it shall be sufficient that the signature of or on behalf of each party appears on one or more of the counterparts. All counterparts shall collectively constitute a single agreement. It
shall not be necessary in any proof of this Amendment to produce or account for more than a number of counterparts containing the respective signatures of or on behalf of all of the parties. 
  
 7.    Severability. If any term, provision,
covenant or restriction of this Amendment is held by a court of competent jurisdiction or other authority to be invalid, void or unenforceable, the remainder of the terms, provisions, covenants and restrictions of this Amendment shall remain in full
force and effect and shall in no way be affected, impaired or invalidated. 
  
 [Signature Pages Follow] 
  

 -4- 

 IN WITNESS WHEREOF, the parties hereto have caused this Amendment to be duly executed and attested by the
appropriate authorized persons. 
  

									
	 Attest:
	 	 	 	 XM SATELLITE RADIO HOLDINGS INC.

					
	By:	 	     /s/ Joseph M. Titlebaum
	 	 	 	By:	 	     /s/ Hugh Panero

	 	 	
	 	 	 	 	 	

	 	 	 Name:     Joseph M. Titlebaum
 Title:       Executive Vice President
	 	 	 	 	 	 Name:     Hugh Panero
 Title:       President and CEO

  
  

									
	 Attest:
	 	 	 	 EQUISERVE TRUST COMPANY, N.A.

					
	By:	 	     /s/ Paula Gill
	 	 	 	By:	 	     /s/ James P. Mitchell

	 	 	
	 	 	 	 	 	

	 	 	 Name:     Paula Gill
 Title:       Account Manager
	 	 	 	 	 	 Name:     James P. Mitchell
 Title:       Senior Account Manager

  

 -5-

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