8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C.  20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

Date of Report (Date of earliest event reported):

November 8, 2011

TRANSGENOMIC, INC.

(Exact name of registrant as specified in its charter)

Delaware	000-30975	911789357
(State of Incorporation)	(Commission File Number)	(IRS Employer Identification Number)

12325 Emmet Street, Omaha, Nebraska	68164
(Address of principal executive offices)	(Zip Code)

(402) 452-5400
(Registrant’s telephone number, including area code)

Not applicable
(Former name or former address, if changed since last report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

o Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

o Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

o Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

o Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Item 1.01 Entry into a Material Definitive Agreement

Series A Convertible Preferred Stock:

On November 8, 2011,Transgenomic, Inc. (the “Company”) entered into an Agreement Regarding Preferred Stock (the “Preferred Stock Agreement”) with Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC, and Third Security Incentive 2010 LLC (collectively the “Holders” and each individually a “Holder”), which are the holders of all of the outstanding shares of the Company’s Series A Convertible Preferred Stock (the “Preferred Stock”). Pursuant to the Preferred Stock Agreement, the Holders and the Company agreed to amend the Certificate of Designation of the Preferred Stock to eliminate certain features of the Preferred Stock relating to (i) an anti-dilution adjustment to the conversion rate upon which the Preferred Stock is convertible into the Company’s Common Stock and (ii) an optional redemption of the Preferred Stock by the Holders (the “Certificate Amendment”); subject to the requisite stockholder approval of the Certificate Amendment at the Company’s next annual meeting of its stockholders. Pursuant to the Preferred Stock Agreement, the Holders agreed to vote the Preferred Stock and their Common Stock in favor of the Certificate Amendment and agreed to waive their rights to the features of the Preferred Stock being eliminated by the Certificate Amendment.  In exchange for the Holders entering into the Preferred Stock Agreement, the Company agreed to issue to the Holders an aggregate of $300,000 market value of Common Stock or 245,903 shares of Common Stock (the “Issued Shares”).

The purpose of adopting the Certificate Amendment is to eliminate liability accounting treatment of the Preferred Stock, which drives the significant non-cash expense that results from an increase in the Company’s stock price, and change the presentation location of the Preferred Stock and warrants held by the Holders to purchase the Preferred Stock (the “Warrants”) from their current classifications to Shareholders’ Equity. This modification will have a significant positive impact on the Company’s balance sheet and future financial results. The proforma effect of the Certificate Amendment as of September 30, 2011 is to increase Shareholders’ Equity by $12,996,000 from a reported deficit of $1,505,000 to a positive $11,491,000.

As a result of the Preferred Stock Agreement, the value of the Preferred Stock and Warrants, including the Preferred Stock conversion feature and Preferred Stock warrant liability, will be reclassified into shareholders equity as of the date of the Preferred Stock Agreement.  The following table sets forth a summary of the balance sheet as reported and pro-forma as if the Preferred Stock Agreement had been effective on September 30, 2011.

	As reported			Pro-Forma
	Dollars in Thousands
	September 30, 2011			September 30, 2011
Total Assets	$	29,974		$	29,974
Total Liabilities		29,683			18,483
Redeemable Series A convertible preferred stock		1,796			—
Total Stockholders' Equity (Deficit)		(1,505	)		11,491
	$	29,974			29,974

The foregoing descriptions of the Preferred Stock Agreement and the Certificate Amendment do not purport to be complete and are qualified in their entireties by reference to the full text of the Preferred Stock Agreement, which is filed as Exhibit 10.1 to this Current Report on Form 8-K and incorporated herein by reference.

Amendment of Registration Rights Agreement:

The Holders and the Company previously entered into that certain Registration Rights Agreement dated December 29, 2010 (the "Registration Rights Agreement"), pursuant to which the Company agreed to provide certain registration rights to the Holders with respect to the  Preferred Stock and the Preferred Stock to be acquired pursuant to the Warrants issued to the Holders.

As required by the Preferred Stock Agreement, the Holders and the Company entered into that certain First Amendment to Registration Rights Agreement dated November 8, 2011, pursuant to which the Issued Shares are added as registrable securities under the Registration Rights Agreement.

The foregoing description of the First Amendment to Registration Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the First Amendment to Registration Rights Agreement, which is filed as Exhibit 4.2 to this Current Report on Form 8-K and incorporated herein by reference.

Item 9.01.  Financial Statements and Exhibits.

(d)           Exhibits.

3.1 Certificate of Designation of Series A Convertible Preferred Stock dated as of December 28, 2010 (incorporated by reference to Exhibit 3.1 to Registrant’s Report on Form 8-K (Registration No. 000-30975) filed on January 4, 2011.)

4.1 Registration Rights Agreement dated December 29, 2010, by and among Transgenomic, Inc., Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC, and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.3 to Registrant’s Report on Form 8-K (Registration No. 000-30975) filed on January 4, 2011.)

4.2 First Amendment to Registration Rights Agreement dated November 8, 2011.

10.1 Agreement Regarding Preferred Stock dated November 8, 2011.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

	TRANSGENOMIC, INC.
Dated:  November 14, 2011	By:	/s/ Brett L. Frevert
		Brett L. Frevert
		Chief Financial Officer

EX-4.2

FIRST AMENDMENT TO REGISTRATION RIGHTS AGREEMENT

THIS FIRST AMENDMENT TO REGISTRATION RIGHTS AGREEMENT ("Amendment") is made and entered into as of November 8, 2011, by and among Third Security Senior Staff 2008 LLC, a Virginia limited liability company, Third Security Staff 2010 LLC, a Virginia limited liability company, and Third Security Incentive 2010 LLC, a Virginia limited liability company (collectively the “Holders” and each individually a “Holder”), and Transgenomic, Inc., a Delaware corporation (the “Company”).

WITNESSETH:

WHEREAS, the Holders and the Company entered into that certain Registration Rights Agreement dated December 29, 2010 (the "Registration Rights Agreement"), pursuant to which the Company agreed to provide certain registration rights to the Holders with respect to the securities issuable upon conversion of the Series A Convertible Preferred Stock of the Company (the “Series A Preferred”) acquired or to be acquired by the Holders pursuant to that certain Series A Convertible Preferred Stock Purchase Agreement dated as of December 29, 2010 and certain warrants issued to the Holders by the Company.

WHEREAS, the Holders and the Company entered into that certain Agreement Regarding Preferred Stock dated the same date as the date of this Amendment, pursuant to which the Company agreed to issue to each Holder, in proportion to their respective ownership of the Series A Preferred, shares of Common Stock of the Company (the “Issued Shares”) in exchange for the Holders agreement to approve amendments to the terms of the Series A Preferred deleting certain rights of the holders of Series A Preferred and the waiver by the Holders to assert such rights.

WHEREAS, the Agreement Regarding Preferred Stock requires the Company to amend the Registration Rights Agreement as provided in this Amendment.

NOW THEREFORE, in consideration of the recitals to this Amendment which are incorporated herein by this reference, the mutual covenants contained herein, and other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties do hereby agree as follows:

1.           Capitalized terms used in this Amendment without definition shall have the meanings given to such defined terms in the Registration Rights Agreement.

2.           The Registration Rights Agreement is amended to include the Issued Shares in the definition of “Registrable Securities.”

3.           Except as altered, modified and amended by this Amendment, the Registration Rights Agreement is in all respects, ratified, approved and confirmed and the terms, covenants and conditions therefore shall remain in full force and effect.  All references in the Registration Rights Agreement to "this Agreement" shall be deemed references to the Registration Rights Agreement as modified by this Amendment.

4.           This Amendment may be executed in any number of counterparts, each of which shall be an original, but all of which shall constitute one and the same instrument.

IN WITNESS WHEREOF, the parties have executed this Amendment as of the date first above written.

[Signature page follows]

Third Security Senior Staff 2008 LLC,
a Virginia limited liability company
By:	/s/ Randal J. Kirk
	Name:  Randal J. Kirk
	Title:   Manager, Third Security, LLC,
	which is the Manager of
	Third Security Senior Staff 2008 LLC
Third Security Staff 2010 LLC,
a Virginia limited liability company
By:	/s/ Randal J. Kirk
	Name: Randal J. Kirk
	Title:   Manager, Third Security, LLC,
	which is the Manager of
	Third Security Staff 2010 LLC
Third Security Incentive 2010 LLC,
a Virginia limited liability company
By:	/s/ Randal J. Kirk
	Name: Randal J. Kirk
	Title:   Manager, Third Security, LLC,
	which is the Manager of
	Third Security Incentive 2010 LLC
Transgenomic, Inc.,
a Delaware corporation
By:	/s/ Craig J. Tuttle
	Name: Craig J. Tuttle
	Title:   President

EX-10.1

AGREEMENT REGARDING PREFERRED STOCK

This Agreement Regarding Preferred Stock is made and entered into as of November 8, 2011, by and among Third Security Senior Staff 2008 LLC, a Virginia limited liability company, Third Security Staff 2010 LLC, a Virginia limited liability company, and Third Security Incentive 2010 LLC, a Virginia limited liability company (collectively the “Holders” and each individually a “Holder”), and Transgenomic, Inc., a Delaware corporation (the “Company”).

WITNESSETH:

WHEREAS, the Company and the Holders previously entered into that certain Series A Convertible Preferred Stock Purchase Agreement dated as of December 29, 2010 (the “Purchase Agreement”) pursuant to which the Holders purchased 2,586,205 shares of Series A Convertible Preferred Stock of the Company (the “Series A Preferred”) and received warrants (“Warrants”) to purchase an aggregate of 1,293,102 shares of Series A Preferred;

WHEREAS, in connection with entering into the Purchase Agreement, the Holders and the Company entered into a Registration Rights Agreement, dated December 29, 2010 (the “Registration Rights Agreement”), pursuant to which the Company agreed to provide certain registration rights to the Holders with respect to the securities issuable upon conversion of the Series A Preferred, including any Series A Preferred issued in connection with the exercise of any Warrants;

WHEREAS, the Holders presently own all of the outstanding Series A Preferred and all of the Warrants;

WHEREAS, the Board of Directors of the Company has adopted Resolutions setting forth (i) a proposed amendment of the Certificate of Incorporation of the Company, attached hereto as Exhibit A, changing the Certificate of Designation of the Series A Preferred by deleting in its entirety: (a) Section 4(e)(v) thereof captioned: Adjustment of Conversion Rate after a “Diluting Issue” and (b) Section 5 thereof captioned: Optional Redemption, declaring the advisability of the amendment, and directing that the proposed Amendment be considered at the next annual meeting of the stockholders of the Company (the “Certificate Amendment”); and (ii) a proposed Amendment to the Registration Rights Agreement, attached hereto as Exhibit B, to amend the definition of “Registrable Securities” to include the shares of Common Stock issued to the Holders in connection with the transaction contemplated hereby (the “Rights Amendment,” and, together with the Certificate Amendment, the “Amendments”);

WHEREAS, the parties to this Agreement desire to agree upon certain matters relating to the Amendments and the terms of the Series A Preferred;

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NOW, THEREFORE, in consideration of the premises and the mutual covenants set forth in this Agreement, the parties to this Agreement agree as follows:

1.  Definitions.  As used in this Agreement, unless the context otherwise requires:

(a) “Agreement” means this Agreement Regarding Preferred Stock as the same may be amended, supplemented or modified in accordance with the terms hereof.

(b) “Amendments” has the meaning assigned to such term in the recitals to this Agreement.

(c) “Annual Meeting” means the next annual meeting of the stockholders of the Company after the date of this Agreement at which the proposed Certificate Amendment is voted upon.

(d) “Certificate Amendment” has the meaning assigned to such term in the recitals to this Agreement.

(e) “Common Stock” means the Company’s Common Stock.

(f) “Company” has the meaning assigned to such term in the recitals to this Agreement.

(g) “Holder” and “Holders” have the meanings assigned to such terms in the recitals to this Agreement.

(h) “Person” means any individual, corporation, limited liability company, partnership, trust, incorporated or unincorporated association, joint venture, joint stock company, government (or agency or political subdivision thereof) or other entity of any kind.

(i) “Purchase Agreement” has the meaning assigned to such term in the recitals to this Agreement.

(j) “Registration Rights Agreement” has the meaning assigned to such term in the recitals to this Agreement.

(k) “Rights Amendment” has the meaning assigned to such term in the recitals to this Agreement.

(l) “Series A Preferred" means the Company’s Series A Convertible Preferred Stock.

(m) “Transferee” means any Person who becomes an owner, by issuance, assignment, sale or otherwise, of (i) Series A Preferred originally held by a Holder or (ii) any Warrants or Warrant Shares, other than a Holder.

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(n) “Warrant Shares” means the shares of Series A Preferred issuable upon exercise of the Warrants.

(o) “Warrants” has the meaning assigned to such term in the recitals to this Agreement.

2.             Issuance of Common Stock to Holders.  Promptly upon the full execution of this Agreement, and in consideration for the waiver of certain rights by the Holders pursuant to paragraph 4 below, Company shall issue to each Holder, in proportion to their respective ownership of the Series A Preferred, the number of shares of Common Stock determined by dividing $300,000 by the last trading price for the Common Stock as of the date of this Agreement.  In the event such calculation results in a fractional share to be issued to any Holder, such fractional share shall be rounded up to the next whole share.

3.           Approval of Amendments and Voting Agreement.  The Company and each Holder consents to and approves the Amendments, subject to any requisite stockholder approval.  The Company agrees to recommend to its stockholders the approval of the Certificate Amendment and to submit such proposal to its stockholders at its next Annual Meeting of Stockholders, which the Company agrees it will hold no later than May 31, 2012.  Each Holder agrees to vote the shares of Series A Preferred, including the Warrant Shares, if any, and Common Stock owned of record by such Holder in favor of the Certificate Amendment at the Annual Meeting. In addition, each Holder agrees not to transfer, prior to the Annual Meeting, any of the Series A Preferred, Warrant Shares or Warrants owned by such Holder unless the Transferee agrees to and assumes the obligations of such Holder under this Agreement as they relate to the Series A Preferred, Warrant Shares and Warrants held by or transferred or issued to such Transferee or becomes a Holder as provided in Section 11 of this Agreement.

4.           Waiver of Holders’ Rights.   Without limiting the generality of the other obligations of the Holders under this Agreement, each Holder hereby waives and agrees not to assert, and agrees to cause its Transferees to waive and not to assert, any rights which such Holder or Transferee would have pursuant to Section 4(e)(v) or Section 5 of the Certificate of Designation of the Series A Preferred.

5.           Representations and Warranties of Holders. Each Holder hereby represents and warrants to the Company as follows:

(a) Organization.  Holder is duly organized, validly existing and in good standing under the laws applicable to its formation or organization.

(b) Capacity, Authorization and Enforceability.  Holder has full power and authority to enter into this Agreement and to perform all its obligations under this Agreement.  This Agreement has been duly authorized, executed and delivered by Holder and constitutes its legal, valid and binding obligations enforceable against it in accordance with its terms.

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(c) No Violation.  The execution, delivery and performance of this Agreement will not violate or cause a default under any of the documents applicable to the formation, organization or governance of Holder, or any law, rule or regulation of any governmental authority.

(d) Experience.  Holder has such knowledge and experience in financial and business matters that it is capable of evaluating the merits and risks of acquiring the Common Stock contemplated hereby.  Holder is an "accredited investor" as such term is defined in Rule 501 of Regulation D promulgated under the Securities Act of 1933, as amended (the “Securities Act”).

(e) Information Provided Respecting the Company.  Holder is a stockholder of the Company and as such has been supplied with information and materials concerning the Company and its operations, structuring and financing.  The Company has provided Holder with the opportunity to discuss with and ask questions of the Company's representatives concerning its financial and business affairs.

(f) Investment.  Holder is acquiring the Common Stock in the ordinary course of its business, for investment for its own account, not as a nominee or agent, and not with the view to, or for resale in connection with, any distribution thereof. Holder understands that the Common Stock to be issued to Holder pursuant to this Agreement has not been, and will not be, registered under the Securities Act by reason of a specific exemption from the registration provisions of the Securities Act, the availability of which depends upon, among other things, the bona fide nature of the investment intent and the accuracy of Holder's representations as expressed herein.

(g) Rule 144.  Holder acknowledges that the Common Stock must be held indefinitely unless subsequently registered under the Securities Act or unless an exemption from such registration is available.  Holder is aware of the provisions of Rule 144 promulgated under the Securities Act which permit limited resale of securities acquired in a private placement subject to the satisfaction of certain conditions.

(h) Ownership.   As of the date hereof Holder owns all of the Series A Preferred and Warrants it acquired pursuant to the Purchase Agreement, it has not exercised its Warrants to receive any Warrant Shares, and it has not transferred or agreed to transfer any of its rights or interests in the Series A Preferred, Warrant Shares or Warrants.

6.           Representations and Warranties of the Company.   The Company hereby represents and warrants to the Holders as follows:

(a) Organization.  The Company is duly organized, validly existing and in good standing under the laws applicable to its formation or organization.

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(b) Capacity, Authorization and Enforceability.  The Company has full corporate power and authority to enter into this Agreement and to perform all its obligations under this Agreement.  This Agreement has been duly authorized, executed and delivered by the Company and constitutes its legal, valid and binding obligations enforceable against it in accordance with its terms.

(c) No Violation.  The execution, delivery and performance of this Agreement will not violate or cause a default under any of the documents applicable to the formation, organization or governance of the Company, or any law, rule or regulation of any governmental authority.

7.             Notices.  All notices required or permitted to be given under this Agreement shall be in writing, addressed as hereinafter indicated, and shall be deemed to have been duly given when received if personally delivered or on the next business day if sent by an overnight express delivery service or on the third business day after mailing if sent by United States certified mail, postage prepaid.  Whenever notice is to be given to a Transferee, the notice shall be addressed to such Transferee's address as it appears in the records of the Company.

If to the Company:   Transgenomic, Inc.

12325 Emmet Street

Omaha, Nebraska 68164

Attention: Craig J. Tuttle

If to Holders:             c/o Third Security, LLC

1881 Grove Avenue

Radford, Virginia 24141

Attention: Tad Fisher

A party may change its address for notice by giving notice of such change as provided in this Paragraph 7.

8.              Binding Effect and Benefits.  The terms of this Agreement shall be binding upon and inure to the benefit of the parties to this Agreement and their respective Transferees, successors, and assigns.

9.             Term of Agreement.  This Agreement shall become effective on the date of this Agreement and shall remain in full force and effect until the first to occur of any of the following events:

(a)           The agreement in writing by all parties to this Agreement that this Agreement shall terminate, which termination shall occur at the time set forth in such written agreement; or

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(b)           The Certificate Amendment has been duly approved by the stockholders of the Company at the Annual Meeting in compliance with the Delaware General Corporation Law.

10.             Entire Agreement and Amendments.  This Agreement contains the entire understanding and agreement among the parties with respect to the subject matter of this Agreement and supersedes any prior agreements among the parties pertaining to the matters covered by this Agreement.  There are no representations, warranties, promises, covenants, or understandings with respect to the subject matter of this Agreement other than those expressly set forth in this document.  No change, modification, or amendment of this Agreement shall be valid unless in writing and signed by all of the parties to this Agreement, except as provided in Paragraph 11 in connection with the addition of a Holder.

11.             Additional Holders.  Any Person who is not now a Holder but hereafter becomes a Transferee and, with the consent of the Company, becomes a party to this Agreement shall be included in the terms "Holders" and "Holder" so long as such Person holds the Series A Preferred, Warrants or Warrant Shares. Such additional Holder shall agree in writing to be bound by the terms and conditions of this Agreement, and such written agreement must be accepted by the Company in writing.

12.             Severability.  Whenever possible, each provision of this Agreement shall be interpreted in such manner as to be effective and valid under applicable law; but if any provision of this Agreement is held to be invalid, illegal, or unenforceable in any respect under any applicable law or rule in any jurisdiction, then such invalidity, illegality, or unenforceability shall not affect any other provision or any other jurisdiction, but this Agreement shall be reformed, construed, and enforced in such jurisdiction as if such invalid, illegal, or unenforceable provision had never been contained in this Agreement.

13.             Headings.  The headings of the several paragraphs of this Agreement are for reference purposes only and shall not affect the meaning or interpretation of this Agreement.

14.             Counterparts.  This Agreement may be executed in one or more counterparts, each of which shall be deemed to be an original and all of which together shall constitute one and the same instrument.

15.             Governing Law.  This Agreement shall be governed by the laws of the State of Delaware applicable to contracts made and to be performed entirely in such state.

IN WITNESS WHEREOF, the parties have executed this Agreement as of the date first above written.

[Signature page follows]

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Third Security Senior Staff 2008 LLC,
a Virginia limited liability company
By:	/s/ Randal J. Kirk
	Name: Randal J. Kirk
	Title:   Manager, Third Security, LLC,
	which is the Manager of
	Third Security Senior Staff 2008 LLC
Third Security Staff 2010 LLC,
a Virginia limited liability company
By:	/s/ Randal J. Kirk
	Name:  Randal J. Kirk
	Title:   Manager, Third Security, LLC,
	which is the Manager of
	Third Security Staff 2010 LLC
Third Security Incentive 2010 LLC,
a Virginia limited liability company
By:	/s/ Randal J. Kirk
	Name:  Randal J. Kirk
	Title:   Manager, Third Security, LLC,
	which is the Manager of
	Third Security Incentive 2010 LLC
Transgenomic, Inc.,
a Delaware corporation
By:	/s/ Craig J. Tuttle
	Name:  Craig J. Tuttle
	Title:    President

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