UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549



FORM 10-K/A

(Amendment No. 2)

(Mark One)



|ý | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ------------------------------------------------------------------------------------



For the fiscal year ended December 31,
2014

OR



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------



For the transition period from 
to

Commission File Number 000-30975



TRANSGENOMIC, INC.

(Exact Name of Registrant as Specified
in its Charter)



|Delaware                                                               |  | 91-1789357                                     
|---------------------------------------------------------------------- |  | -----------------------------------------------
|(State or Other Jurisdiction of
        Incorporation or Organization) |  | (I.R.S. Employer
        Identification Number)
|                                                                       | 
|12325 Emmet Street
        Omaha, NE                                   |  | 68164                                          
|(Address of Principal Executive Offices)                               |  | (Zip Code)                                     



(402) 452-5400

(Registrant’s Telephone Number,
Including Area Code)



Securities registered pursuant to Section 12(b)
of the Act:



|Title of Each Class                     |  | Name of Each Exchange On Which Registered
|--------------------------------------- |  | -----------------------------------------
|Common Stock, par value $0.01 per share |  | The NASDAQ Capital Market                



Securities registered pursuant to Section 12(g)
of the Act:



None

(Title of Class)



Indicate by check
mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.

Yes  ̈    
No x



Indicate by check mark
if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Exchange Act.

Yes  ̈    
No x



Indicate by check mark
whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange
Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports),
and (2) has been subject to such filing requirements for the past 90 days.

Yes x    
No  ̈



Indicate by check mark
whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required
to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months
(or for such shorter period that the registrant was required to submit and post such files).

Yes  ̈No x



Indicate by check mark
if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K (§229.405 of this chapter) is not contained
herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K x



Indicate by check mark whether the registrant
is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See the definitions
of “large accelerated filer”, “accelerated filer” and “smaller reporting company” in Rule 12b-2
of the Exchange Act. (Check one):



|Large Accelerated Filer  ̈                     | Accelerated Filer  ̈        
|--------------------------------------------- | ---------------------------
|Non-Accelerated Filer  ̈                       | Smaller Reporting Company x
|(Do not check if a smaller reporting company) |                            



Indicate by check mark
whether the registrant is a shell company (as defined in Rule 12b-2 of the Act).

Yes  ̈    
No x



The aggregate market
value of the voting and non-voting common equity held by non-affiliates of the registrant based on the last reported closing price
per share of Common Stock as reported on the NASDAQ Capital Market on the last business day of the registrant’s most recently
completed second quarter was approximately $24.6 million.



At March 31, 2015, the
registrant had 11,857,078 shares of common stock outstanding.













EXPLANATORY NOTE



This Amendment No. 2 to Annual Report on
Form 10-K/A (this “Second Amendment”) is being filed by Transgenomic, Inc. (the “Company”) to amend the
Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2014, which was originally filed with the Securities
and Exchange Commission (the “SEC”) on April 15, 2015 (the “Original Form 10-K”), as amended by the Company’s
Amendment No. 1 to Annual Report on Form 10-K/A, which was filed with the SEC on August 14, 2015 (the “First Amendment”).



The Company is filing this Second Amendment
for the purpose of updating the biographical information for Paul Kinnon that was included under the heading “Executive Officers
of the Registrant” under Part I, “Item 1. Our Business” of the Original Form 10-K. The Company is also filing
this Second Amendment for the purpose of updating the biographical information for Paul Kinnon that was included under Part III,
“Item 10. Directors, Executive Officers and Corporate Governance” of the Original Form 10-K through the incorporation
by reference of information in the Company’s definitive proxy statement on Schedule 14A filed with the SEC on April 30, 2015.



In addition, as required by Rule 12b-15
promulgated under the Securities Exchange Act of 1934, as amended (“Rule 12b-15”), a new certification by the Company’s
principal executive officer and principal financial officer is filed herewith as an exhibit to this Second Amendment.



The information under Part I, “Item
1. Our Business” of the Original Form10-K is hereby amended and restated in its entirety to read as follows:



|“Item 1. | Our Business
|-------- | ------------



Transgenomic, Inc.
(“we”, “us”, “our”, the “Company” or “Transgenomic”) is a global biotechnology
company advancing personalized medicine for the detection and treatment of cancer and inherited diseases through its proprietary
molecular technologies and world-class clinical and research services. A key goal is to bring our Multiplexed ICE COLD-PCR (“MX-ICP”)
product to the clinical market rapidly through strategic licensing agreements, enabling the use of blood and other bodily fluids
for more effective and patient-friendly diagnosis, monitoring and treatment of cancer.



MX-ICP is a simple,
proprietary chemistry that amplifies the ability to detect genetic mutations by 100 - 400 fold. This chemistry has been validated
internally on all currently available sequencing platforms, including Sanger, Next Gen Sequencing and Digital PCR. By enhancing
the level of detection of genetic mutations and suppressing the normal, “wild-type” DNA, several benefits are provided.
It is generally understood that most current technologies are unable to consistently identify mutations that occur in less than
approximately 5% of a sample. However, many mutations found at much lower levels, even down to 0.01% are known to be clinically
relevant and can have significant consequences to a patient: both in terms of how they will respond to a given drug or treatment
and how a given tumor is likely to change over time. More importantly, in our view, significantly improving the level of detection
while using blood, saliva and even urine as a source for DNA, rather than depending on painful, expensive and potentially dangerous
tumor biopsies, is an important advancement in patient care with respect to cancer detection, treatment and monitoring of the disease
and can result in significant cost savings for the healthcare system by replacing invasive procedures with the simple collection
of blood or other bodily fluid. By broadening the types of samples that can be used for testing and allowing all sequencing platforms
to provide improved identification of low level mutations, MX-ICP has the potential to make testing much more patient friendly,
enable genetic monitoring of disease progression and more effectively guide treatment protocols, and reduce the overall cost of
diagnosis and monitoring while also improving patient outcomes.





2









Currently, our operations are organized
and reviewed by management along major product lines and presented in the following two business segments:



| | · | Laboratory Services. Our laboratories specialize in genetic testing for cardiology, neurology and
mitochondrial disorders, and for oncology. Our Patient Testing laboratories located in New Haven, Connecticut and Omaha, Nebraska
are certified under the Clinical Laboratory Improvement Amendment (“CLIA”) as high complexity laboratories and our
Omaha facility is accredited by the College of American Pathologists. Our Biomarker Identification laboratory located in Omaha
provides pharmacogenomics research services supporting Phase II and Phase III clinical trials conducted by pharmaceutical and biotechnology
companies. Our laboratories employ a variety of genomic testing service technologies, including our new, high performance MX-ICP
technology. ICE COLD-PCR is a proprietary ultra-high sensitivity platform technology with breakthrough potential to enable wide
adoption of personalized, precision medicine in cancer and other diseases. It can be run in any laboratory that contains standard
PCR systems. MX-ICP enables detection of multiple known and unknown mutations from virtually any sample type, including tissue
biopsies, blood, urine, saliva, cell-free DNA (“cfDNA”) and circulating tumor cells (“CTCs”) at levels
greater than 1,000-fold higher than standard DNA sequencing techniques. It is easy to implement and use within existing workflows.
| | - | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | · | Genetic Assays and Platforms. Our proprietary
product in this business segment is the WAVE® System, which has broad applicability to genetic variation detection in both
molecular genetic research and molecular diagnostics. We also distribute bio-instruments produced by other manufacturers (“OEM
Equipment”) through our sales and distribution network. Service contracts to maintain installed systems are sold and supported
by our technical support personnel. The installed WAVE base and some OEM Equipment platforms generate a demand for consumables
that are required for the continued operation of the bio-instruments. We develop, manufacture and sell these consumable products.
In addition, we manufacture and sell consumable products that can be used on multiple, independent platforms. These products include
a range of chromatography columns.
| | - | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



Segment information
related to revenues, a performance measure of profit, capital expenditures, and total assets is contained in Footnote 15 - “Operating
Segment and Geographic Information”, to our accompanying consolidated financial statements.



Business Strategy



Our primary objective
is to commercialize MX-ICP for the clinical diagnostics market through strategic licensing agreements. MX-ICP facilitates the use
of blood and other bodily fluids for the effective and efficient diagnosis and treatment of cancer. It does this by enhancing the
level of detection of mutant DNA by 100 - 400 fold. In tumors, mutations can often be found occurring with a frequency of around
5%, which current technologies can readily identify. However, other mutations can be present at much lower frequencies. MX-ICP
makes possible 0.1% and even 0.01% levels of detection of mutant DNA. We believe that MX-ICP can help dramatically improve the
diagnosis and treatment/monitoring of cancer patients. Using MC-ICP-based tests, clinicians can effectively and economically monitor
a patient’s therapy and progress on an ongoing basis. We plan to commercialize this product directly, but more importantly
and more immediately, expect to partner with a significant number of life sciences companies to accelerate the adoption and use
of the technology.



Our next set of objectives
focuses on strengthening a number of our existing businesses. We continue to provide products and services to biomedical researchers,
physicians, medical institutions and diagnostic and pharmaceutical companies that are tied to identifying and understanding genetic
mutations and variations and their roles in disease. Our products and services help scientists and physicians understand and predict
disease and drug response. As medical practitioners learn to correlate specific mutations and patterns of mutation with specific
disease states, drug responses and patient outcomes, it becomes possible to optimize a treatment regimen to a specific patient.
This is known as personalized or precision medicine.





3







Our internal estimates
for the size of the cancer diagnostics market, based on multiple industry sources, suggests a rapidly growing market with a current
annual value of $2.5 billion, built on only tissue biopsies and not accounting for growth due to the potential for liquid biopsies
or increased testing to monitoring cancer patients. Growth in this market has been in part fueled by the rapid adoption of Next-Generation
Sequencing (“NGS”) and Digital PCR, along with an emphasis by the U.S. Food & Drug Administration (“FDA”)
for better and more uniform compliance regarding Laboratory Designed Test assays. In spite of these changes in the market, there
is still a need for more informative data to help guide treatment. We believe that this will only occur when there is a move to
blood and liquid testing of cancer patients earlier and more regularly (monitoring) to ensure more accurate diagnoses and more
targeted and effective treatments. We believe that MX-ICP is at the forefront of technologies designed to accomplish this transition
away from traditional biopsies, analysis and monitoring and will help allow for precision medicine to become a reality.



Transgenomic does not
intend to build the extensive infrastructure necessary to fully commercialize MX-ICP. While there are applications of the technology
that we will sell directly, we anticipate that the majority of revenues will be generated through a combination of exclusive, non-exclusive
or semi-exclusive licenses to partners and collaborators. Our goal is to establish the fastest time to market possible for our
product and to leverage already existing infrastructure rather than depend on making significant capital expenditures or other
investments of our own. Our potential partners generally fall into one of three categories:



| | · | Laboratory instrumentation and reagents
suppliers (such as: Thermo Fisher Scientific, Inc., Illumina, Inc., Bio-Rad Laboratories, Inc., Qiagen N.V. and Affymetrix,
Inc.). The usefulness of MX-ICP across all platforms and its ability to detect tumor mutations in a wide range of samples make
such companies natural partners for Transgenomic. We believe that MX-ICP has the potential to greatly expand the market for cancer
monitoring as a complement, not as a competitor, to existing products.
| | - | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | · | Pharmaceutical and Biotechnology companies
(such as: Amgen, Inc., Novartis AG, Clovis Oncology, Inc., AstraZeneca plc, GlaxoSmithKline plc and Bristol-Myers Squibb Company).
For companies developing new cancer drugs, MX-ICP has the potential to reduce the risk of clinical trials, as well as support the
development of companion diagnostics to match drugs with patients.
| | - | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



| | · | Clinical Laboratories (such as:
Laboratory Corporation of America Holdings, Quest Diagnostics Incorporated and the many CLIA-certified laboratories throughout
the United States). MX-ICP would allow clinical laboratory firms to effectively compete with more specialized providers and to
become full service providers as personalized, precision medicine becomes more widely adopted.
| | - | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



The markets in which
we compete require a wide variety of technologies, products and capabilities. The combination of technological complexity and rapid
change within our markets makes it difficult for a single company to develop all of the solutions that it desires to offer as part
of its family of products and services. We work to broaden the range of products and services we deliver to customers in target
markets through acquisitions, investments and alliances. We employ the following strategies to address the need for new or enhanced
products and services:



| | · | Developing new technologies and products
internally;
| | - | ----------------------------------------------------

| | · | Acquiring all or parts of other companies;
| | - | ------------------------------------------

| | · | Entering into joint-development efforts
with other companies; and
| | - | -----------------------------------------------------------------

| | · | Reselling other companies’ products.
| | - | ------------------------------------





4







Our strategy is to
leverage the discoveries in our Research and Development (R&D) and Biomarker Identification laboratories to create “kits”
or assays to distribute through our Genetic Assays and Platforms segment, as well as tests to conduct in our Patient Testing laboratories.



We will continue to
develop new applications for, and enhancements of, MX-ICP and capitalize on our expertise and intellectual properties to develop
unique new applications of the MX-ICP technology for potential partnerships. We will focus on growth in our core markets via direct
sales and business development activities with industry leaders across the globe.



Products



MX-ICP is our proprietary
technology product with industry transforming potential. It is exclusively licensed by Transgenomic from Dana-Faber Cancer Institute.
MX-ICP is a unique amplification technology that suppresses wild-type (normal) DNA and thereby enables the selective amplification
of all mutations (genetic alterations) present in that region of the genome. As a result of its ultra-high sensitivity (1000 times
more sensitive than standard DNA sequencing alone), it works on almost all sample types that contain DNA, including tissue, blood,
urine and saliva or sputum; it can be used on all sequencing platforms; and it is easily implemented into standard laboratory processes
without significant investment of time or resources. MX-ICP has applications in all therapeutic areas, but the first and major
focus at this time is the estimated $2.5 billion market for cancer testing. The Company also believes that the current market for
clinical diagnostic (MDx) use of PCR, which is estimated to be in excess of $10 billion in 2015 based on external reports, will
continue to grow and is a validation of the size of market for this type of technology and product. Importantly, MX-ICP is platform
agnostic and can therefore be integrated and implemented into any clinical testing, basic research or biopharmaceutical laboratory.
In addition, the MX-ICP product is a simple chemical reagent that is able to be mass-produced and supplied efficiently to any end
user.



Our highly specialized
genetics analytical services and expertise are utilized by our Biomarker Identification laboratory in Omaha, Nebraska and in our
CLIA-certified Patient Testing laboratories in Omaha, Nebraska and New Haven, Connecticut. Our Biomarker Identification laboratory
supports pharmaceutical companies in their clinical trials, primarily Phase II and Phase III trials. Our Patient Testing laboratories
support medical professionals in the diagnosis and treatment of patients, primarily in the specialties of Cardiology and Neurology,
with a range of tests within each medical specialty.



In cardiology, our
FAMILION® family of tests focuses on detecting mutations that can cause cardiac
channelopathies, cardiomyopathies and other rare, potentially lethal heart conditions. The specific diseases include Long QT Syndrome
(“LQTS”), Familial Atrial Fibrillation (“FAF”), Hypertrophic Cardiomyopathy (“HCM”) and Dilated
Cardiomyopathy (“DCM”). By reducing uncertainty and finding the specific genetic causes of cardiac channelopathies
and cardiomyopathies, the FAMILION tests can:



| | · | Help diagnose a patient’s disease;
| | - | ----------------------------------

| | · | Guide treatment options; and
| | - | ----------------------------

| | · | Determine whether family members are at
risk.
| | - | ---------------------------------------------



In neurology, we focus
on mitochondrial disorders, epilepsy and epilepsy-like diseases. We employ a wide variety of technologies, including industry standards
such as Sanger sequencing and NGS. In 2013, we introduced whole exome sequencing, which is based on NGS, and which specialists
use to diagnose and treat exceptionally difficult to identify neurological disorders in patients.



Our expanding oncology
tests are focused heavily on genetic mutations commonly associated with the major cancer types - lung, colorectal, breast and prostate.
We primarily test for mutations in the KRAS, NRAS, BRAF and PIK3CA genes, all associated with the most common types of cancers.
The presence or absence of these mutations increasingly influences oncologists’ treatment choices for their patients. We
have been focused on testing for low level mutations in colorectal cancer tissue biopsies that are targets for new therapies, and
we intend to continue this and improve on it as we incorporate our MX-ICP technology products into our oncology testing menu. We
also offer tests for hereditary cancer-predisposing syndromes.





5







Our laboratory expertise
is leveraged in our Genetic Assays and Platforms segment, which focuses on assembly and delivery of highly-sensitive mutation detection
equipment, primarily our WAVE platform. We also sell WAVE MCE and Hanabi instruments, as well as the bioconsumables, including
test kits used with these instruments for molecular testing and cytogenetics. Our equipment systems offer discovery and detection
of genetic variations at close to 100% sensitivity, making them among the most sensitive and accurate technologies for detection
of known and unknown mutations and single nucleotide polymorphisms (SNPs). These equipment systems are used throughout the world
to screen for a large variety of diseases. More than 350 human genes have been screened entirely or partly using Direct High Pressure
Liquid Chromatography (DHPLC), the underlying technology used by our equipment systems. A multitude of other applications are being
used with WAVE Systems in such diverse areas as plant genomics, microbial analysis and drug sensitivity.



We continue to leverage
the synergies of our two segments, capitalizing on discoveries in our R&D and Biomarker Identification laboratories to create
“kits” or test assays to distribute through our Genetic Assays and Platforms segment, as well as tests to conduct in
our Patient Testing laboratories.



Sales and Marketing



Our strategy for commercializing
MX-ICP is to focus on enabling strategic licensing technology agreements with established partners in the fields of: instrumentation
and reagent suppliers, biotechnology and pharmaceutical companies, and clinical laboratories. In order to optimize this we are
focusing on these business to business activities and using external consultants with significant market and domain expertise to
accelerate this strategy. We anticipate announcing the first such transaction[s] in 2015. Additionally MX-ICP will be offered as
a part of our services to our pharmaceutical and biotechnology clients by our dedicated services team, in order to enable clinical
studies and patient stratification work currently underway or in development with our current clients. Our core Sales and Support
team consists of regionally-based sales people, service engineers and applications scientists to support our sales and marketing
activities worldwide. We have sold our legacy products and services to customers in over 50 countries. We use a direct sales
and support staff for sales in the U.S. and Europe. For the rest of the world, we sell our products through dealers and distributors
within local markets. We currently have over 35 dealers and distributors.



Customers



We expect to expand
our customer base in 2015 and onwards through licensing and partnership agreements for MX-ICP with instrumentation and reagents
suppliers, pharmaceutical and biotechnology companies and clinical laboratories.



Currently, physicians
requesting genetic tests for their patients are our primary source of current revenues for laboratory services. Fees for laboratory
testing services rendered for these physicians are billed either to the physician, the patient or the patient’s third-party
payer such as an insurance company or Medicare. Billings are typically on a fee-for-service basis. The patient or third-party payer
is billed at our patient fee schedule. Commercial insurance providers are billed at contracted rates or other generally-accepted
market reimbursement rates. Revenues received from Medicare billings are based on government-established fee schedules and reimbursement
rules.



Our customers include
a number of large, established pharmaceutical, biotech and commercial companies as well as leading academic and medical institutions
in the U.S. and abroad. No customer accounted for more than 10% of our consolidated net sales for the years ended December 31,
2014, 2013 or 2012. Information regarding the revenues attributable to U.S. and international markets is set forth in Footnote
15 - “Operating Segment and Geographic Information”, to our accompanying consolidated financial statements.





6







Research and Development



We continue to invest
in research and development in order to remain competitive and to take advantage of new business opportunities as they arise. We
maintain a program of research and development with respect to platform technologies, such as ICE COLD-PCR, instruments, test kits
and services, engaging existing and new technologies to create scientific and medical applications that will add value to patient
care as well as significant commercial value. Major areas of focus include the (i) development of ICE COLD-PCR applications
for ultra-high sensitivity mutation detection in any liquid (including blood, sputum and urine) and tissue samples (fresh, frozen,
FNA, FFPE, etc.); (ii) development of a new strategy for mutation detection and sequence confirmation using micro-capillary electrophoresis;
(iii) use of commercially-available assays and the development of custom assays for detection of somatic mutations in cancer samples
using NGS and digital PCR or droplet PCR; and (iv) development of biomarker assays for the marketplace. For the years ended December 31,
2014, 2013 and 2012, our research and development expenses were $2.9 million, $3.2 million and $2.5 million, respectively.



Manufacturing



We manufacture bioconsumable
products including our test kits, separation columns, liquid reagents and enzymes. The major components of our WAVE Systems are
manufactured for us by a third party. We integrate our hardware and software with these third party manufactured components. Our
manufacturing facilities for WAVE Systems and bioconsumables are located in Omaha, Nebraska and San Jose, California.



Intellectual Property



To establish and protect
our proprietary technologies and products, we rely on a combination of patent, copyright, trademark and trade secret laws, license
agreements’ contractual confidentiality provisions and confidentiality agreements. Our WAVE Systems and related consumables
are protected by patents and in-licensed technologies that expire in various periods through 2030. Our ICE COLD-PCR platform technology
is protected by in-licensed patents that expire in various periods through 2031. As part of the FAMILION acquisition in 2010, we
acquired exclusive rights to the FAMILION family of genetic tests for inherited disease, including the patents protecting this
technology. As we expand our product offerings, we also are extending our patent development efforts to protect such product offerings.
Established competitors, as well as companies that purchase and enforce patents and other intellectual property, may already have
patents covering similar products. There is no assurance that we will be able to obtain patents covering our products, or that
we will be able to obtain licenses from such companies on favorable terms or at all. However, while patents are an important element
of our success, our business as a whole is not significantly dependent on any one patent.



We will continue to
file patent applications, seek new licenses, take advantage of available copyright and trademark protections and implement appropriate
trade secret protocols to protect our intellectual property. Despite these precautions, there can be no assurance that misappropriation
of our products and proprietary technologies will not occur.



In addition to our
own products, we distribute or act as a sales agent for OEM Equipment developed by third parties. Our rights to those third party
products and the associated intellectual property rights are limited by the terms of the contractual agreement between us and the
respective third party.



Although we believe
that our developed and licensed intellectual property rights do not infringe upon the proprietary rights of third parties, there
can be no assurance that third parties will not assert infringement claims against us. Further, there can be no assurance that
intellectual property protection will be available for our products in the U.S. or foreign countries.





7







Like many companies
in the biotechnology and other high-tech industries, third parties have in the past and may in the future assert claims or initiate
litigation related to patent, copyright, trademark or other intellectual property rights to business processes, technologies and
related standards that are relevant to us and our customers. These assertions have increased over time as a result of the general
increase in patent claims assertions, particularly in the United States. Third parties may also claim that their intellectual property
rights are being infringed by our customers’ use of a business process method that utilizes products in conjunction with
other products, which could result in indemnification claims against us by our customers. Any claim against us, with or without
merit, could be time-consuming and a distraction to management, result in costly litigation, cause product delivery delays, require
us to enter into royalty or licensing agreements or pay damages or amounts in settlement, prohibit us from selling certain products
or require us to develop alternative non-infringing technology. We could also be required to defend or indemnify our customers
against such claims.



Government Regulation



We are subject to a
variety of federal, state and municipal environmental and safety laws based on our use of hazardous materials in both manufacturing
and research and development operations. We believe that we are in material compliance with applicable environmental laws and regulations.
However, if we cause contamination to the environment, intentionally or unintentionally, we could be responsible for damages related
to the clean-up of such contamination or individual injury caused by such contamination. We cannot predict how changes in laws
and regulations will impact how we conduct our business operations in the future or whether the costs of compliance will increase
in the future.



Regulation by governmental
authorities in the United States and other countries is not expected to be a significant factor in the manufacturing, labeling,
distribution and marketing of our products and systems. However, we continue to monitor and engage in dialog with the FDA and other
regulatory bodies. Please see the section of this Annual Report entitled “Risk Factors” for other risks associated
with regulatory requirements.



Competition



The markets in which
we operate are highly competitive and characterized by rapidly changing technological advances. Many of our competitors possess
greater resources than us and may be able to develop and offer a greater breadth of products and/or services, coupled with significant
marketing and distribution capabilities. We compete principally on the basis of uniquely enabling scientific technical advantages
in specific but significant market segments.



Our Laboratory Services
segment faces competition from a number of companies offering contract DNA sequencing and other genomic analysis services, including
SeqWright and others. In addition, several clinical diagnostics service providers, such as LabCorp, Quest Diagnostics, Foundation
Medicine, GeneDx and Baylor College of Medicine, also offer related laboratory services. Finally, additional competition arises
from academic core laboratory facilities. Competition for our WAVE System arises primarily from DNA sequencing and genotyping technologies.
Competitors in these areas include, among others, Thermo Fisher, Qiagen N.V., F. Hoffman-La Roche, Ltd., Sequenom, Inc and Illumina,
Inc. Competition for some of our non-WAVE consumable products comes from numerous well-diversified life sciences reagents providers,
including, among others, Thermo Fisher, Qiagen N.V., Roche, Agilent Technologies, Inc. and Promega Corporation.



Employees



As of December 31,
2014 and 2013, we had employees focused in the following areas of operation:





8







|                                    |  | December 31, |    
|----------------------------------- |  | ------------ | ---
|                                    |  | 2014         |    
|Manufacturing and Laboratory        |  |              | 84 
|Sales, Marketing and Administration |  |              | 60 
|Research and Development            |  |              | 8  
|                                    |  |              | 152



Of our 152 total employees as of December
31, 2014, a total of 150 were full-time employees.



Our
employees were employed in the following geographical locations:



|                                       |  | December 31, |    
|-------------------------------------- |  | ------------ | ---
|                                       |  | 2014         |    
|United States                          |  |              | 131
|Europe (other than the United Kingdom) |  |              | 11 
|United Kingdom                         |  |              | 10 
|                                       |  |              | 152



General Information



We were incorporated
in Delaware on March 6, 1997. Our principal office is located at 12325 Emmet Street, Omaha, Nebraska 68164 (telephone: 402-452-5400).
This facility houses certain administrative staff and laboratories. We maintain manufacturing facilities in Omaha, Nebraska and
San Jose, California. We maintain research and development offices in Omaha, Nebraska. We maintain laboratories in Omaha, Nebraska
and New Haven, Connecticut that have been certified under the CLIA. Our New Haven facility also houses certain administrative operations.



Our Internet website
is located at http://www.transgenomic.com. The information on our website is not a part of this Annual Report. We make available
free of charge on our website our Annual Reports on Form 10-K, Quarterly Reports on Form 10-Q, Current Reports on Form 8-K and
amendments to those reports filed or furnished pursuant to Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as amended
(the “Exchange Act”), as soon as reasonably practicable after we electronically file such material with, or furnish
it to, the SEC. Our SEC reports can be accessed through the investor relations section of our Internet website.



The public may also
read and copy any materials we file with the SEC at the SEC’s Public Reference Room at 100 F Street, N.E., Room 1580, Washington,
DC 20549. The public may obtain information on the operation of the Public Reference Room by calling the SEC at 1-800-SEC-0330.
The SEC also maintains an Internet website that contains reports, proxy and information statements and other information regarding
issuers that file electronically with the SEC. The SEC’s Internet website is located at http://www.sec.gov.



Executive Officers of the Registrant



Paul Kinnon.
Mr. Kinnon, age 51, has served as our President and Chief Executive Officer and a Director since September 2013 and as our Interim
Chief Financial Officer since October 2014. Mr. Kinnon has more than 20 years of global leadership experience in innovative life
science and diagnostics companies. From January through August 2013, he provided consulting services to the life science sector
as a Partner at Arch Global Research. During a portion of this time, Mr. Kinnon provided consulting services to us. From January
2007 to December 2012, Mr. Kinnon was President, Chief Executive Officer and a Director of ZyGEM Corporation Limited, a biotechnology
company, where he transformed the company from a regional enzyme provider into a leader in integrated microfluidic technologies
for forensic and clinical diagnostic applications. From May 2006 to June 2007, Mr. Kinnon was Vice President & General Manager
Environmental Diagnostics (later expanded to Applied Markets) at Invitrogen Corporation (now Life Technologies), a high growth
life sciences and diagnostics firm, and from October 2004 until April 2006, he was Vice President, Global Strategic Alliances at
Invitrogen. Previously, Mr. Kinnon also held business, sales and marketing roles of increasing responsibility at Guava Technologies,
Inc., Cellomics, Inc. and other life science companies. Mr. Kinnon earned his Bachelor of Sciences degree in Applied Chemistry
at Coventry University in the United Kingdom and holds a Diploma of Marketing. A petition in bankruptcy was filed against ZyGEM
Corporation Limited in April 2013.





9







Leon F. Richards.
Mr. Richards, age 58, was appointed our Chief Accounting Officer by our Board of Directors in October 2014. Mr. Richards is
an experienced corporate finance executive and certified public accountant with more than 30 years of experience building and leading
financial organizations. Mr. Richards has served as our Controller since November 2012. He most recently served as Controller and
Chief Accounting Officer of Baldwin Technology Company, Inc., a leading global supplier of process automation equipment for the
printing and publishing industry, from May 2004 to September 2012. Mr. Richards earned his Bachelor of Business Administration
and Accounting from Iona College.”



The information under Part III, “Item
10. Directors, Executive Officers and Corporate Governance” of the Original Form10-K is hereby amended and restated in its
entirety to read as follows:



“Board of Directors and Committees



Our Board consists
of five directors. The Board is divided into three classes with directors in each class serving for a term of three years. The
terms of office of the current Class I, Class II and Class III directors will expire in 2016, 2017 and 2015, respectively.
The Preferred Stockholders are entitled, as a separate voting group, to elect two of the five directors (the “Preferred Stock
Directors”). The Common Stockholders are entitled, as a separate voting group, to elect the three remaining directors (the
“Common Stock Directors”). There is one Common Stock Director in each class. There is one Preferred Stock Director
in each of Class I and Class II, but not a Preferred Stock Director in Class III.



Robert M. Patzig is
the current Preferred Stock Director in Class I, Paul Kinnon is the current Common Stock Director in Class I, Doit L. Koppler,
II is the current Preferred Stock Director in Class II, John D. Thompson is the current Common Stock Director in Class II and Michael
A. Luther, Ph.D. is the current Common Stock Director in Class III.



Certain biographical
information regarding our director nominee and directors continuing in office after the Annual Meeting, including their ages as
of April 21, 2015 and the dates that they were first elected to our Board, is set forth below. In each individual’s biography
we have highlighted specific experience, qualifications, and skills that have led the Board to conclude that such individual is
a valued member of our Board. In addition to these specific attributes, all of our directors have significant expertise in one
or more areas of importance to our business and have high-level managerial experience in relatively complex organizations or are
accustomed to dealing with complex problems. We believe all of our directors are individuals of high character and integrity, are
able to work well with others, and have sufficient time to devote to the affairs of our company.





10









|Name                                            |  | Age |  | Principal Occupation                                                                         |  | Director Since |  | Term to Expire
|----------------------------------------------- |  | --- |  | -------------------------------------------------------------------------------------------- |  | -------------- |  | --------------
|                                                |  |     |  |                                                                                              |  |                |  |               
|CLASS III DIRECTOR NOMINEE                     
|                                               
|Michael A. Luther, Ph.D., Common Stock Director |  | 58  |  | Senior Vice President, Discovery and Development Services, Albany Molecular Research, Inc.   |  | 2014           |  | 2015          
|                                                |  |     |  |                                                                                              |  |                |  |               
|CLASS I DIRECTORS CONTINUING IN OFFICE         
|                                               
|Robert M. Patzig, Preferred Stock Director      |  | 46  |  | Chairperson of the Board, Transgenomic, Inc.                                                 |  | 2010           |  | 2016          
|                                                |  |     |  |                                                                                              |  |                |  |               
|Paul Kinnon, Common Stock Director              |  | 52  |  | President, Chief Executive Officer and Interim Chief Financial Officer of Transgenomic, Inc. |  | 2013           |  | 2016          
|                                                |  |     |  |                                                                                              |  |                |  |               
|CLASS II DIRECTORS CONTINUING IN OFFICE        
|                                               
|Doit L. Koppler, II, Preferred Stock Director   |  | 51  |  | Managing Director and Treasurer, Third Security, LLC                                         |  | 2010           |  | 2017          
|                                                |  |     |  |                                                                                              |  |                |  |               
|John D. Thompson, Common Stock Director         |  | 66  |  | Retired Senior Vice President, Strategy & Corporate Development, Invitrogen Corporation      |  | 2014           |  | 2017          



Michael A. Luther,
Ph.D. Dr. Luther has served as Senior Vice President, Discovery and Development Services, at Albany Molecular Research,
Inc. (NASDAQ: AMRI), a global contract research and manufacturing organization offering drug discovery, development and manufacturing
services, since October 2013, where he is responsible for the strategic, operational and business development activities for Albany
Molecular Research, Inc.’s global discovery and development divisions. From August 2012 to September 2013, Dr. Luther was
Corporate Vice President of Global Discovery Research Services at Charles River Laboratories (NYSE: CRL), a global provider of
products and services to pharmaceutical and biotechnology companies, government agencies and academic institutions, where he served
as the general manager of the firm’s discovery business unit, including developing and implementing strategic and operating
plans. Prior to his role at Charles River, from March 2009 to August 2012, he was President and a member of the Board of Directors
of the David H. Murdock Research Institute, a non-profit contract research organization located in Kannapolis, North Carolina,
where he led and directed all activities of the institute, including applied research and development activities. From November
2006 to March 2009, Dr. Luther held the position of Vice President and Site Head at Merck Frosst, a pharmaceutical company in Montreal,
Canada, focused on the delivery of Phase I product candidates from target to clinic for novel therapeutics in respiratory and metabolic
disorders. Prior to Merck Frosst, from 1991 to 2006, he held positions of increasing responsibilities at GlaxoSmithKline, a global
healthcare company that researches and develops a broad range of innovative medicines and brands, culminating in his appointment
as Vice President, High Throughput Biology. Dr. Luther holds a Bachelor of Science degree in Biology and Chemistry from North Carolina
State University, a Master in Business Administration from Duke University, Fuqua School of Business, and a Ph.D. in Biophysical
Chemistry from Saint Louis University School of Medicine. He has served as a member of the board of directors of Islet Sciences,
Inc., a biopharmaceutical company (OTC: ISLT), since March 2014. The Board selected Dr. Luther to serve as a director because
it believes he possesses valuable experience in the healthcare and pharmaceutical industries and extensive strategic, scientific
and business experience in such industries, which brings a unique and valuable perspective to the Board.



Robert M. Patzig.
On February 12, 2015, Mr. Patzig was appointed Chairperson of the Board. He had been standing Chairperson since January 1, 2015
and has been a Board member since December 2010. Since June 2014, Mr. Patzig has also served as Board Chair of Ligmincha International,
a non-profit organization focused on the preservation and dissemination of Tibetan Bon Buddhism. Until December 31, 2014, Mr. Patzig
was Senior Managing Director and the Chief Investment Officer for Third Security, LLC, an investment firm with a concentration
in life science. Mr. Patzig joined Third Security upon its inception in 1999. Mr. Patzig’s responsibilities included identifying
and evaluating investment opportunities for Third Security and its funds as well as general portfolio oversight and portfolio management.
Prior to the formation of Third Security, Mr. Patzig served as Director of Market Research and Analysis at GIV Holding, Inc. and
Director of Research Services at General Injectables & Vaccines, Inc. He served as a member of the Board of Directors of Cyntellect,
Inc. from February 2011 until June 2012 and previously as Chairman of the Board from July 2007 to September 2008. Mr. Patzig was
a Director of the Virginia Biotechnology Association, a non-profit industry advocacy group from 2006 until 2011. Mr. Patzig served
as a member of the Board of Directors of Intrexon Corporation from May 2005 to February 2008 and was Chairman from February 2007
to February 2008. He served as a member of the Board of Directors of Synchrony, Inc. from February 2006 to April 2008. Mr. Patzig
also served as the head of the Investment Committee for Howe and Rusling, Inc. a registered investment advisor from 2001 until
its sale in 2006. Mr. Patzig received a B.A. in Philosophy and an M.A. in English from Virginia Tech. The Board appointed Mr. Patzig
as its Chairperson because of his substantial biotechnology industry experience as well has his securities and investment expertise.





11







Paul Kinnon.
Mr. Kinnon has served as our President and Chief Executive Officer and a Director since September 2013. On October 31, 2014, Mr.
Kinnon was appointed Interim Chief Financial Officer. Mr. Kinnon has more than 20 years of global leadership experience in innovative
life science and diagnostics companies. From January through August 2013, he provided consulting services to the life science sector
as a Partner at Arch Global Research. During a portion of this time, Mr. Kinnon provided consulting services to us. From January
2007 to December 2012, Mr. Kinnon was President, Chief Executive Officer and a Director of ZyGEM Corporation Limited, a biotechnology
company, where he transformed the company from a regional enzyme provider into a leader in integrated microfluidic technologies
for forensic and clinical diagnostic applications. From May 2006 to June 2007, Mr. Kinnon was Vice President & General Manager
Environmental Diagnostics (later expanded to Applied Markets) at Invitrogen Corporation (now Life Technologies), a high growth
life sciences and diagnostics firm, and from October 2004 until April 2006, he was Vice President, Global Strategic Alliances at
Invitrogen. Previously, Mr. Kinnon also held business, sales and marketing roles of increasing responsibility at Guava Technologies,
Inc., Cellomics, Inc. and other life science companies. Mr. Kinnon earned his Bachelor of Sciences degree in Applied Chemistry
at Coventry University in the United Kingdom and holds a Diploma of Marketing. A petition in bankruptcy was filed against ZyGEM
Corporation Limited in April 2013. The Board selected Mr. Kinnon to serve as a director because he is our Chief Executive Officer
and because of his expansive knowledge and experience in the life science industry, as well as his past executive management roles
at both life science and biotechnology companies.



Doit L. Koppler,
II.Mr. Koppler joined Third Security as Managing Director and Treasurer in 2001 and manages the finance function of Third
Security and is involved with several portfolio companies of Third Security’s managed investment funds. Mr. Koppler
served as Vice President, Treasurer and a member of the Board of Directors of Vital Diagnostics Holding Corp., a global supplier
of products and services for the clinical laboratory in the traditional in vitro diagnostics market with a focus on the physician’s
office, hospital and small-to-medium sized laboratory segments from its inception in 2006 through 2012. Mr. Koppler served
as Chairman and Chief Executive Officer of New River Funds, a family of no-load mutual funds, from its inception in 2003 through
2008 and as the Chief Investment Officer of New River Advisers, LLC, the investment adviser to New River Small Cap Fund, predecessor
to Southern Sun Small Cap Fund. Mr. Koppler served as a member of the Board of Directors of IntelliMat, Inc. from November
2006 to July 2008. Prior to joining Third Security, Mr. Koppler served as Vice President and Controller of General Injectables &
Vaccines, Inc., a $120 million distributor of injectable biologics and vaccines primarily to outpatient physician offices, from
1992 to 2000. From 1987 to 1992, he was a Manager in the audit practice of Ernst & Young LLP. Mr. Koppler is a Certified
Public Accountant, Chartered Global Management Accountant and a Member of the American Institute of Certified Public Accountants.
He has also held Series 7 and Series 66 securities registrations. Mr. Koppler received a B.S. in Accounting from Salem International
University. The Board selected Mr. Koppler to serve as a director because of his valuable financial expertise, including his
public accounting and financial reporting experience.



John D. Thompson.Mr. Thompson has served as a consultant and board member to a number of life sciences enterprises. He was Senior Vice President,
Strategy and Corporate Development at Invitrogen Corporation, where he completed over 20 transactions with an aggregate value in
excess of $2 billion, in-licensed more than 200 compounds, and charted the company’s ambitious growth plans. Previously Mr.
Thompson was Senior Vice President, Strategic and Business Development at Dexter Corporation, where he led restructuring activities
involving more than a dozen acquisitions and divestitures. Earlier he was Vice President, Financial Services and Treasurer, where
he negotiated financings totaling $100 million, and refinanced multicurrency debt and credit agreements. Mr. Thompson also worked
at Dexter subsidiary, Life Technologies. As Senior Vice President and General Manager, Americas Research Products Division, he
helped achieve annual double-digit sales and earnings growth while divesting less promising businesses. As Vice President Finance,
Secretary and Treasurer, he helped focus the business on high technology products, oversaw the merger that resulted in the formation
of Life Technologies and helped ensure the success of its IPO. Mr. Thompson began his career in public accounting at Ernst &
Young. Mr. Thompson received a BBA degree from Cleveland State University. The Board selected Mr. Thompson to serve as a director
because it believes he brings extensive experience in life sciences business development, corporate strategy and mergers and acquisitions
at top tier firms to our Board. He was selected the Chairperson of the Audit Committee in February 2015.





12







Section 16(a) Beneficial Ownership
Reporting Compliance



Section 16(a)
of the Exchange Act and the rules of the SEC require our directors, certain officers and beneficial owners of more than 10% of
our outstanding common stock to file reports of their ownership and changes in ownership of our common stock with the SEC. We believe
all Section 16 reports were filed in a timely manner during 2014, except for one Form 4 to report the grant of a stock option
made on March 13, 2014 that was inadvertently filed late by Dr. Luther.



Code of Business Conduct and Ethics



Our Board has adopted
a code of ethical conduct that applies to our principal executive officer, principal financial officer and senior financial management.
This code of ethical conduct is embodied within our Code of Business Conduct and Ethics, which applies to all persons associated
with our Company, including our directors, officers and employees (including our principal executive officer, principal financial
officer, principal accounting officer and controller). The Code of Business Conduct and Ethics is available in the Investor Relations
section of our website at www.transgenomic.com. In order to satisfy our disclosure
requirements under Item 5.05 of Form 8-K, we will disclose amendments to, or waivers of, certain provisions of our Code of Business
Conduct and Ethics relating to our chief executive officer, chief financial officer, chief accounting officer, controller or persons
performing similar functions on our website promptly following the adoption of any such amendment or waiver.



Corporate Governance



Committees of our Board of Directors



Our Board has established
and delegated certain responsibilities to its standing Audit Committee, Compensation Committee and Nominating and Corporate Governance
Committee.



Audit Committee



We have a separately
designated standing Audit Committee established in accordance with Section 3(a)(58)(A) of the Securities Exchange Act of 1934,
as amended (the “Exchange Act”). The Audit Committee’s primary duties and responsibilities include monitoring
the integrity of our financial statements, monitoring the independence and performance of our external auditors, and monitoring
our compliance with applicable legal and regulatory requirements. The functions of the Audit Committee also include reviewing periodically
with our independent registered public accounting firm the performance of the services for which they are engaged, including reviewing
the scope of the annual audit and its results, reviewing with management and the auditors the adequacy of our internal accounting
controls, reviewing with management and the auditors the financial results prior to the filing of quarterly and annual reports,
reviewing fees charged by our independent registered public accounting firm and reviewing any transactions between our Company
and related parties. Our independent registered public accounting firm reports directly and is accountable solely to the Audit
Committee. The Audit Committee has the sole authority to hire and fire the independent registered public accounting firm and is
responsible for the oversight of the performance of their duties, including ensuring the independence of the independent registered
public accounting firm. The Audit Committee also approves in advance the retention of, and all fees to be paid to, the independent
registered public accounting firm. The rendering of any auditing services and all non-auditing services by the independent registered
public accounting firm is subject to prior approval of the Audit Committee.





13







The Audit Committee
operates under a written charter which is available in the Investor Relations section of our website at www.transgenomic.com.
The Audit Committee is required to be composed of directors who are independent under the rules of the SEC and the listing standards
of The Nasdaq Stock Market LLC (“NASDAQ”).



The current members
of the Audit Committee are directors Mr. Patzig, Dr. Luther and Mr. Thompson, the Chairperson of the Audit Committee, all of whom
have been determined by the Board to be independent under the NASDAQ listing standards and rules adopted by the SEC applicable
to audit committee members. The Board has determined that each of Mr. Patzig, Dr. Luther and Mr. Thompson qualifies as an “audit
committee financial expert” under the rules adopted by the SEC and the Sarbanes Oxley Act of 2002. The Audit Committee met
eight times during 2014 and did not take any actions by written consent.



Executive Officers of the Registrant



Paul Kinnon.
Mr. Kinnon, age 51, has served as our President and Chief Executive Officer and a Director since September 2013 and as our Interim
Chief Financial Officer since October 2014. Mr. Kinnon has more than 20 years of global leadership experience in innovative life
science and diagnostics companies. From January through August 2013, he provided consulting services to the life science sector
as a Partner at Arch Global Research. During a portion of this time, Mr. Kinnon provided consulting services to us. From January
2007 to December 2012, Mr. Kinnon was President, Chief Executive Officer and a Director of ZyGEM Corporation Limited, a biotechnology
company, where he transformed the company from a regional enzyme provider into a leader in integrated microfluidic technologies
for forensic and clinical diagnostic applications. From May 2006 to June 2007, Mr. Kinnon was Vice President & General Manager
Environmental Diagnostics (later expanded to Applied Markets) at Invitrogen Corporation (now Life Technologies), a high growth
life sciences and diagnostics firm, and from October 2004 until April 2006, he was Vice President, Global Strategic Alliances at
Invitrogen. Previously, Mr. Kinnon also held business, sales and marketing roles of increasing responsibility at Guava Technologies,
Inc., Cellomics, Inc. and other life science companies. Mr. Kinnon earned his Bachelor of Sciences degree in Applied Chemistry
at Coventry University in the United Kingdom and holds a Diploma of Marketing. A petition in bankruptcy was filed against ZyGEM
Corporation Limited in April 2013.



Leon F. Richards.
Mr. Richards, age 58, was appointed our Chief Accounting Officer by our Board of Directors in October 2014. Mr. Richards is
an experienced corporate finance executive and certified public accountant with more than 30 years of experience building and leading
financial organizations. Mr. Richards has served as our Controller since November 2012. He most recently served as Controller and
Chief Accounting Officer of Baldwin Technology Company, Inc., a leading global supplier of process automation equipment for the
printing and publishing industry, from May 2004 to September 2012. Mr. Richards earned his Bachelor of Business Administration
and Accounting from Iona College.



There are no family
relationships between or among any of our executive officers or directors.”





14







Part IV



|Item 15. | Exhibits, Financial Statement Schedules.
|-------- | ----------------------------------------



| | (a) | The following documents are filed as part of the Company’s Annual Report on Form 10-K for the year ended December 31,
2014:
| | --- | ---------------------------------------------------------------------------------------------------------------------------



|1 | Financial Statements. The following financial statements of the Registrant are included in response to Item 8 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2014:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
|- | -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
|  | Report of Independent Registered
Public Accounting Firm.
                                             

Consolidated Balance Sheets of
the Registrant and Subsidiary as of December 31, 2014 and 2013.


Consolidated Statements of Operations
of the Registrant and Subsidiary for the years ended December 31, 2014, 2013 and 2012.


Consolidated Statements of Comprehensive
Loss of the Registrant and Subsidiary for the years ended December 31, 2014, 2013 and 2012.


Consolidated Statements of Stockholders’
Equity of the Registrant and Subsidiary for the years ended December 31, 2014, 2013 and 2012.


Consolidated Statements of Cash
Flows of the Registrant and Subsidiary for the years ended December 31, 2014, 2013 and 2012.


Notes to Consolidated Financial
Statements of the Registrant and Subsidiary.







|2 | Financial Statement Schedules.                                                                                                              
|- | --------------------------------------------------------------------------------------------------------------------------------------------
|  |                                                                                                                                             
|  | All financial statement schedules
are omitted because the information is inapplicable or presented in the notes to the financial statements.





|3 | Exhibits. The following exhibits are filed as required by Item 15(a)(3) of the Company’s Annual Report on Form 10-K for the year ended December 31, 2014. Exhibit numbers refer to the paragraph numbers under Item 601 of Regulation S-K:
|- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------



|†2.1 |  | Asset Purchase Agreement among the Registrant, Scoli Acquisition Sub, Inc. and Axial Biotech, Inc. dated August 27, 2012 (incorporated by reference to Exhibit 2.1 to the Registrant's Quarterly Report on Form 10-Q filed on November 8, 2012).
|---- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|     |  |                                                                                                                                                                                                                                                 
|3.1  |  |                                                                                                                                                                                                                                                 
|     |  |                                                                                                                                                                                                                                                 
|3.2  |  |                                                                                                                                                                                                                                                 
|     |  |                                                                                                                                                                                                                                                 
|3.3  |  |                                                                                                                                                                                                                                                 
|     |  |                                                                                                                                                                                                                                                 
|3.4  |  |                                                                                                                                                                                                                                                 
|     |  |                                                                                                                                                                                                                                                 
|3.5  |  |                                                                                                                                                                                                                                                 
|     |  |                                                                                                                                                                                                                                                 
|3.6  |  |                                                                                                                                                                                                                                                 
|     |  |                                                                                                                                                                                                                                                 
|4.1  |  |                                                                                                                                                                                                                                                 





15









|4.2  |  |                                                                                                                                                                                                                                                                                                                        | Form of Series A Convertible Preferred Stock Warrant issued to Third Security Senior Staff 2008 LLC, Third Security Staff 2010 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on January 4, 2011).
|---- |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.3  |  | Registration Rights Agreement, dated December 29, 2010, by and among the Registrant, 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 the Registrant’s Current Report on Form 8-K filed on January 4, 2011).    
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.4  |  | First Amendment to Registration Rights Agreement dated November 8, 2011 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on November 14, 2011).                                                                                                                         
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.5  |  | Form of Warrant issued by the Registrant to the Third Security Entities on February 7, 2012 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).                                                                                                     
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.6  |  | Form of Warrant issued by the Registrant to the Investors on February 7, 2012 (incorporated by reference to Exhibit 10.3 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).                                                                                                                   
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.7  |  | Form of Registration Rights Agreement entered into by and among the Registrant, the Third Security Entities and the Investors dated February 2, 2012 (incorporated by reference to Exhibit 10.4 to the Registrant’s Current Report on Form 8-K filed on February 7, 2012).                                            
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.8  |  | Registration Rights Agreement, entered into by and among the Registrant and the Investors, dated January 24, 2013 (incorporated by reference to Exhibit 10.3 to the Registrant’s Current Report on Form 8-K/A filed on January 31, 2013).                                                                             
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.9  |  | Form of Warrant issued by the Registrant to the Investors on January 30, 2013 (incorporated by reference to Exhibit 10.2 to the Registrant’s Current Report on Form 8-K/A filed on January 31, 2013).                                                                                                                 
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.10 |  | Registration Rights Agreement, dated as of March 5, 2014, by and among the Registrant, Third Security Senior Staff 2008 LLC, Third Security Staff 2014 LLC and Third Security Incentive 2010 LLC (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on March 6, 2014).    
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.11 |  | Form of Warrant issued by Transgenomic, Inc. to the Investors and the advisor on October 22, 2014 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).                                                                                                
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.12 |  | Form of Unsecured Convertible Promissory Note issued by Transgenomic, Inc. to the Investor pursuant to the Unsecured Convertible Promissory Note Purchase Agreement, dated as of December 31, 2014 (incorporated by reference to Exhibit 4.2 to the Registrant’s Current Report on Form 8-K filed on January 7, 2015).
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.13 |  | Form of Indenture, between the Registrant and one or more trustees to be named (incorporated by reference to Exhibit 4.15 to the Registrant’s Registration Statement on Form S-3 (Registration No. 333-201907) filed on February 6, 2015).                                                                            
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.14 |  | Form of Common Stock Warrant Agreement and Warrant Certificate (incorporated by reference to Exhibit 4.16 to the Registrant’s Registration Statement on Form S-3 (Registration No. 333-201907) filed on February 6, 2015).                                                                                            
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.15 |  | Form of Preferred Stock Warrant Agreement and Warrant Certificate (incorporated by reference to Exhibit 4.17 to the Registrant’s Registration Statement on Form S-3 (Registration No. 333-201907) filed on February 6, 2015).                                                                                         
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.16 |  | Form of Debt Securities Warrant Agreement and Warrant Certificate (incorporated by reference to Exhibit 4.18 to the Registrant’s Registration Statement on Form S-3 (Registration No. 333-201907) filed on February 6, 2015).                                                                                         
|     |  |                                                                                                                                                                                                                                                                                                                       
|4.17 |  | Form of Debt Securities (to be filed by amendment as Exhibit 4.19 to the Registrant’s Registration Statement on Form S-3 (File No. 333-201907) filed on February 6, 2015 or as an exhibit to a Current Report on Form 8-K).                                                                                           





16









|4.18   |  | Specimen Preferred Stock Certificate and Form of Certificate of Designation of Preferred Stock (to be filed by amendment as Exhibit 4.20 to the Registrant’s Registration Statement on Form S-3 (File No. 333-201907) filed on February 6, 2015 or as an exhibit to a Current Report on Form 8-K).                            
|------ |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|       |  |                                                                                                                                                                                                                                                                                                                               
|4.19   |  | Form of Warrant to Purchase Common Stock (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on February 27, 2015).                                                                                                                                                                
|       |  |                                                                                                                                                                                                                                                                                                                               
|*10.1  |  | The Registrant’s 2006 Equity Incentive Plan, as amended (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on January 28, 2014).                                                                                                                                                 
|       |  |                                                                                                                                                                                                                                                                                                                               
|*10.2  |  | 1999 UK Approved Stock Option Sub Plan of the Registrant (incorporated by reference to Exhibit 10.7 to the Registrant's Registration Statement on Form S-1 (Registration No. 333-32174) filed on March 10, 2000).                                                                                                             
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.3   |  | License Agreement, dated August 20, 1997, between the Registrant and Leland Stanford Junior University (incorporated by reference to Exhibit 10.15 to the Registrant’s Registration Statement on Form S-1 (Registration No. 333-32174) filed on March 10, 2000).                                                              
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.4   |  | License Agreement, dated December 1, 1989, between Cruachem Holdings Limited (a wholly owned subsidiary of the Registrant) and Millipore Corporation (incorporated by reference to Exhibit 10.13 to the Registrant’s Annual Report on Form 10-K filed on March 25, 2002).                                                     
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.5   |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.6   |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.7   |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.8   |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.9   |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|*10.10 |  | Employment Agreement between the Registrant and Mark P. Colonnese (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on September 17, 2012).                                                                                                                                     
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.11  |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.12  |  | Forbearance Agreement, dated February 7, 2013, by and between the Registrant and Dogwood Pharmaceuticals, Inc. (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on February 8, 2013).                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.13  |  |                                                                                                                                                                                                                                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                               
|10.14  |  | First Amendment to Loan and Security Agreement among the Registrant, Third Security Senior Staff 2008 LLC, as administrative agent and a lender, and the other lenders party thereto, dated August 2, 2013 (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on August 6, 2013).
|       |  |                                                                                                                                                                                                                                                                                                                               
|*10.15 |  | Employment Agreement between the Registrant and Paul Kinnon, effective September 30, 2013 (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on September 30, 2013).                                                                                                             





17







|*10.16 |  | Form of Incentive Stock Option Agreement between the Registrant and Paul Kinnon, effective September 30, 2013 (incorporated by reference to Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed on November 14, 2014).                                                                                                                  
|------ |  | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|*10.17 |  | Form of Stock Appreciation Rights Agreement between the Registrant and Paul Kinnon, effective September 30, 2013 (incorporated by reference to Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed on November 14, 2014).                                                                                                               
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|*10.18 |  | Form of Stock Appreciation Rights Agreement between the Registrant and Mark Colonnese, effective September 30, 2013 (incorporated by reference to Exhibit 10.5 to the Registrant’s Quarterly Report on Form 10-Q filed on November 14, 2014).                                                                                                            
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|*10.19 |  | Form of Stock Appreciation Rights Agreement under the 2006 Equity Incentive Plan (incorporated by reference to Exhibit 10.5 to the Registrant’s Current Report on Form 8-K filed on September 30, 2013).                                                                                                                                                 
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.20  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.21  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.22  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.23  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|‡10.24 |  | Collaboration Agreement, dated as of October 9, 2013, by and between the Registrant and PDI, Inc.                                                                                                                                                                                                                                                        
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|‡10.25 |  | Surveyor Kit Patent, Technology, and Inventory Purchase Agreement, dated as of July 1, 2014, by and between the Registrant and Integrated DNA Technologies, Inc. (incorporated by reference to Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed on November 12, 2014).                                                               
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.26  |  | Securities Purchase Agreement, dated as of October 22, 2014, by and among Transgenomic, Inc. and the Investors (incorporated by reference to Exhibit 4.1 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).                                                                                                                      
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.27  |  | Limited Waiver and Fifth Amendment to Loan and Security Agreement among Transgenomic, Inc., Third Security Senior Staff 2008 LLC, as administrative agent and a lender, and the other lenders party thereto, dated October 22, 2014 (incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed on October 22, 2014).
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|10.28  |  | Unsecured Convertible Promissory Note Purchase Agreement, dated
        as of December 31, 2014, by and between Transgenomic, Inc. and the Investor (incorporated by reference to Exhibit 10.1 to the Registrant’s
        Current Report on Form 8-K filed on January 7, 2015).                                                                         
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|#12.1  |  | Statement Regarding the Computation of Ratio of Earnings to Fixed Charges and Preferred Share Dividends for the Years Ended December 31, 2010, 2011, 2012, 2013 and 2014                                                                                                                                                                                 
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|#21    |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|#23.1  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|#23.2  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|#24    |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|#31.1  |  |                                                                                                                                                                                                                                                                                                                                                          
|       |  |                                                                                                                                                                                                                                                                                                                                                          
|+31.2  |  |                                                                                                                                                                                                                                                                                                                                                          





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|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                           |                                                                                                                                        
|-------- |  | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------
|31.3     |  |                                                                                                                                                                                                                                                                                                                                                                                                                           | Certification of Principal Executive Officer and Principal Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#**32.1  |  | Certification of Principal Executive Officer and Principal Financial Officer pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.                                                                                                                                                                                                                                                                                  
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#101.INS |  | XBRL Instance Document                                                                                                                                                                                                                                                                                                                                                                                                   
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#101.SCH |  | XBRL Taxonomy Extension Schema Document                                                                                                                                                                                                                                                                                                                                                                                  
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#101.CAL |  | XBRL Taxonomy Extension Calculation Linkbase Document                                                                                                                                                                                                                                                                                                                                                                    
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#101.DEF |  | XBRL Taxonomy Extension Definition Linkbase Document                                                                                                                                                                                                                                                                                                                                                                     
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#101.LAB |  | XBRL Taxonomy Extension Label Linkbase Document                                                                                                                                                                                                                                                                                                                                                                          
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#101.PRE |  | XBRL Taxonomy Extension Presentation Linkbase Document                                                                                                                                                                                                                                                                                                                                                                   
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|†        |  | Pursuant to Item 601(b)(2) of Regulation
        S-K, the schedules to this agreement have been omitted. The Registrant agrees to furnish supplementally a copy of any omitted schedule
        to the Securities and Exchange Commission upon request.                                                                                                                                                                  
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|*        |  | Denotes exhibit that constitutes a management contract, or compensatory plan or arrangement.                                                                                                                                                                                                                                                                                                                             
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|**       |  | These certifications are not deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, or otherwise subject to the liability of that section. Such certifications will not be deemed to be incorporated by reference into any filing under the Securities Act of 1933 or the Securities Exchange Act of 1934, except to the extent that the Registrant specifically incorporates it by reference.
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|‡        |  | Confidential treatment has been granted with respect to certain portions of this exhibit. Omitted portions have been filed separately with the SEC.                                                                                                                                                                                                                                                                      
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|#        |  | Included with the Registrant’s Annual Report on Form 10-K for the year ended December 31, 2014, filed with the SEC on April 15, 2015, which is being amended hereby.                                                                                                                                                                                                                                                     
|         |  |                                                                                                                                                                                                                                                                                                                                                                                                                          
|+        |  | Included with the Registrant’s Amendment No. 1 to Annual Report on Form 10-K/A for the year ended December 31, 2014, filed with the SEC on August 14, 2015.                                                                                                                                                                                                                                                              





19









SIGNATURES



Pursuant to the requirements of Section 13
or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned,
thereunto duly authorized.





|                       |     | Transgenomic, Inc.                                                                                                                                              
|---------------------- | --- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------
|                       |     |                                                                                                                                                                 
|Dated: August 21, 2015 | By: | /s/ Paul Kinnon                                                                                                                                                 
|                       |     | Paul Kinnon
        President, Chief Executive Officer and Interim Chief Financial
        Officer (Principal Executive Officer and Principal Financial Officer)





20