10-K 1 b414575_10k.htm FORM 10-K Prepared and filed by St Ives Financial

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549


FORM 10-K

Annual Report Pursuant to Section 13 Or 15(d) of the Securities Exchange Act of 1934
For the fiscal year ended June 30, 2006

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 1-4389


Applera Corporation

(Exact name of registrant as specified in its charter)

 

DELAWARE
(State or other jurisdiction of
incorporation or organization)
06-1534213
(I.R.S. Employer Identification No.)
 
   
301 Merritt 7, Norwalk, Connecticut
(Address of principal executive offices)
06851-1070
(Zip Code)

Registrant’s telephone number, including area code: 203-840-2000


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

 

Title of Class

 

Name of Each Exchange
on Which Registered


 


Applera Corporation-Applied Biosystems Group
Common Stock (par value $0.01 per share)

 

New York Stock Exchange

Rights to Purchase Series A Participating Junior
Preferred Stock (par value $0.01 per share)

 

New York Stock Exchange

Applera Corporation-Celera Genomics Group
Common Stock (par value $0.01 per share)

 

New York Stock Exchange

Rights to Purchase Series B Participating Junior
Preferred Stock (par value $0.01 per share)

 

New York Stock Exchange

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

Title of Class: Class G Warrants

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act.
Yes No

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.
Yes No

Note: Checking the box above will not relieve any registrant required to file reports pursuant to Section 13 or 15(d) of the Exchange Act from their obligations under those Sections

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 No

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K 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.

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

Large Accelerated Filer

Accelerated Filer

Non-accelerated filer

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes No

As of December 30, 2005, the last business day of the registrant’s most recently completed second fiscal quarter, the aggregate market value of Applera Corporation-Applied Biosystems Group Common Stock (based upon the average of the high and low price) held by non-affiliates was $4,825,162,439, and the aggregate market value of Applera Corporation-Celera Genomics Group Common Stock (based upon the average of the high and low price) held by non-affiliates was $817,324,664. As of August 16, 2006, 182,243,585 shares of Applera Corporation-Applied Biosystems Group Common Stock and 77,742,673 shares of Applera Corporation-Celera Genomics Group Common Stock were outstanding.



DOCUMENTS INCORPORATED BY REFERENCE

Annual Report to Stockholders for Fiscal Year ended June 30, 2006 - Parts I, II, and IV.

Proxy Statement for 2006 Annual Meeting of Stockholders - Part III.


 

TABLE OF CONTENTS

 

Item 1.

Business 1

 

 

Company Overview 1

 

 

Scientific Background 4

 

 

Applied Biosystems Group Business

6

 

 

Celera Genomics Group Business

28

 

 

Celera Diagnostics Restructuring

44

 

 

Marketing and Distribution Agreement

45

 

 

Applera Genomics Initiative

45

 

 

Employees

46

 

 

Financial Information About Industry Segments

46

 

 

Financial Information About Geographic Areas

47

 

 

Executive Officers of the Registrant

47

Item 1A.

Risk Factors

47

 

 

Risks Relating to Applied Biosystems

48

 

 

Risks Relating to Celera Genomics

55

 

 

Risks Relating to a Capital Structure with Two Separate Classes of Common Stock

68
Item 1B. Unresolved Staff Comments 74
Item 2. Properties 75

 

 

Applied Biosystems Group Facilities 75

 

 

Celera Genomics Group Facilities 76

 

 

Corporate Facilities 76
Item 3. Legal Proceedings 77

 

 

Commercial Litigation 77

 

 

U.S. v. Davis 80
Item 4. Submission of Matters to a Vote of Security Holders 80


 

 

Identification and Business Experience of Executive Officers

85

 

 

Family Relationships

86

 

 

Involvement in Certain Legal Proceedings

86

 

 

Audit Committee and Audit Committee Financial Expert

87

 

 

Recommendation of Nominees to our Board of Directors

87

 

 

Section 16(a) Beneficial Ownership Reporting Compliance

87

 

 

Code of Ethics

87

Item 11.

Executive Compensation

88

Item 12.

Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters

88

 

 

Securities Authorized for Issuance Under Equity Compensation Plans

88

 

 

Security Ownership of Certain Beneficial Owners

88

 

 

Security Ownership of Management

88

 

 

Changes in Control

88

Item 13.

Certain Relationships and Related Transactions

89

Item 14.

Principal Accountant Fees and Services

89

SIGNATURES

98

EXHIBITS, INCLUDING CERTIFICATIONS

 

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PART I

Item 1.

Business

Company Overview

Applied Biosystems and Celera Genomics Business Segments

Applera Corporation conducts business through two business segments, which are described below. Throughout this report, terms such as “Applera,” “we,” “us,” or “our” may be used to refer to Applera Corporation.

Applied Biosystems Group. Our Applied Biosystems Group, which we refer to as “Applied Biosystems” throughout this report, serves the life science industry and research community by developing and marketing instrument-based systems, consumables, software, and services. Its customers use these tools to analyze nucleic acids (DNA and RNA), small molecules, and proteins to make scientific discoveries and develop new pharmaceuticals. Applied Biosystems’ products also serve the needs of some markets outside of life science research, which we refer to as “applied markets,” such as the fields of: human identity testing (forensic and paternity testing); “biosecurity,” which refers to products needed in response to the threat of biological terrorism and other malicious, accidental, and natural biological dangers; and quality and safety testing, for example in food and the environment. A description of this business segment and developments during our 2006 fiscal year is set forth below in this Item 1 under the heading “Business–Applied Biosystems Group Business.”

Celera Genomics Group. Our Celera Genomics Group, which we refer to as “Celera Genomics” throughout this report, is primarily a molecular diagnostics business that is using proprietary genomics and proteomics discovery platforms to identify and validate novel diagnostic markers, and is developing diagnostic products based on these markers as well as other known markers. Celera Genomics maintains a strategic alliance with Abbott Laboratories for the development and commercialization of molecular, or nucleic acid-based, diagnostic products, and it is also developing new diagnostic products outside of this alliance. Through its genomics and proteomics research efforts, Celera Genomics is also discovering and validating therapeutic targets, and it is seeking strategic partnerships to develop therapeutic products based on these discovered targets. In January 2006, Celera Genomics announced its intention to sell or partner its small molecule drug discovery and development programs. During the fourth quarter of our 2006 fiscal year Celera Genomics transferred rights to several of these programs to other companies and terminated all other small molecule programs. A description of this business segment and developments during our 2006 fiscal year is set forth below in this Item 1 under the heading “Business–Celera Genomics Group Business.”

Information about the risk factors associated with our business segments is set forth below in Item 1A of this report under the headings “Risk Factors–Risks Relating to Applied Biosystems” and “Risk Factors–Risks Relating to Celera Genomics.”

We maintain a corporate staff to provide accounting, tax, treasury, legal, information technology, human resources, and other shared internal services for Applied Biosystems and Celera Genomics.


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Celera Diagnostics Restructuring

Through December 31, 2005, we operated a diagnostics business known as Celera Diagnostics. This business was a 50/50 joint venture between Applied Biosystems and Celera Genomics. In January 2006, we announced that our Board of Directors had approved a restructuring of Celera Diagnostics. As a result of the restructuring, effective as of January 1, 2006, Applied Biosystems’ interest in Celera Diagnostics was transferred to Celera Genomics in exchange for various considerations to Applied Biosystems. More information about this transaction is described below in this Item 1 under the heading “Business–Celera Diagnostics Restructuring.”

As a result of the reorganization described above and the manner by which our management now operates and assesses the business, Celera Diagnostics is no longer a separate segment within Applera, and we have restated prior period consolidating financial information to reflect this change. For more information, please see Notes 1 and 15 to our consolidated financial statements contained on pages 43 through 50, 73, and 74 of our Annual Report to Stockholders for our 2006 fiscal year.

Corporate History and Structure; Two Classes of Stock

Applera was incorporated in 1998 under the laws of the State of Delaware. Applera is the successor to “The Perkin-Elmer Corporation,” a corporation originally formed in 1939, as a result of a recapitalization completed in May 1999. As part of the 1999 recapitalization, Applera established the following two classes of common stock that were intended to reflect separately the relative performance of the businesses of Applied Biosystems and Celera Genomics, which are business units of Applera and are not separate legal entities:

 

Applera Corporation-Applied Biosystems Group Common Stock, which we refer to in this report as “Applera-Applied Biosystems stock”; and

 

Applera Corporation-Celera Genomics Group Common Stock, which we refer to in this report as “Applera-Celera stock.”

More information about Applera-Applied Biosystems stock and Applera-Celera stock is set forth below in Item 5 of this report under the heading “Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of Equity Securities.” Also, information about the risk factors associated with our capital structure and our two classes of common stock is set forth below in Item 1A of this report under the heading “Risk Factors–Risks Relating to a Capital Structure with Two Separate Classes of Common Stock.”

Available Information

Websites. We maintain Internet websites for Applera, Applied Biosystems, and Celera Genomics. All interested persons can access the following information on these websites free of charge:

 

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 with or furnished to the Securities and Exchange Commission;

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Section 16 “insider transaction” reports, which include Forms 3, 4, and 5, filed by our officers and directors with the SEC; and

 

information relating to our corporate governance, including: our Corporate Governance Guidelines; our Code of Business Conduct and Ethics, which is applicable to our officers, directors, and employees; the charters for the Audit/Finance Committee, the Management Resources Committee, and the Nominating/Corporate Governance Committee of our Board of Directors; information on how to communicate with our Board of Directors, including our non-management directors; and information on how to report valid complaints to the Company regarding accounting and related matters.

We make our SEC reports and the insider transaction reports available on our websites as soon as reasonably practicable after they are electronically filed with, or furnished to, the SEC.

The following table indicates how to access the documents described above on our Applera, Applied Biosystems, and Celera Genomics websites. In addition, you can obtain copies of these materials by calling our corporate Secretary at 203-840-2000 or by making a request in writing mailed to: Attention: Secretary, Applera Corporation, 301 Merritt 7, P.O. Box 5435, Norwalk, CT 06856-5435.

 

Website Addresses:

 

www.applera.com
www.appliedbiosystems.com
www.celera.com

SEC Filings:

 

Click on the link to “SEC Filings” in the “Investors & Media” section of the website, and then click again on the link to “SEC Filings.”

“Insider Transaction” Reports:

 

Click on the link to “SEC Filings” in the “Investors & Media” section of the website and then click again on the link to “SEC Insider Filings.”

Corporate Governance Information:

 

Click on the link to “Corporate Governance” in the “Corporate” section of the Applera website. Click on the link to “Corporate Governance” in the “Investors & Media” section of the Applied Biosystems or Celera Genomics websites.

Except for any documents on our websites that are expressly incorporated by reference into this report, the information contained on our websites is not incorporated by reference into this report and should not be considered to be a part of this report. All of these website addresses are included in this document as inactive textual references only.

Information Incorporated by Reference. The SEC allows us to “incorporate by reference” some information from parts of other documents filed with the SEC, including:

 

our Annual Report to Stockholders for our 2006 fiscal year, which we refer to in this report as our “2006 Annual Report”; and

 

our Proxy Statement relating to our Annual Meeting of Stockholders to be held on October 19, 2006, which we refer to in this report as our “2006 Proxy Statement.”

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When we “incorporate by reference,” that means that we are referring you to important information in other documents that have been filed with the SEC rather than repeating that information in this report. We recommend that you refer to the information that we indicate is contained in the other documents and which is incorporated by reference into this report. The portions of our 2006 Annual Report that are incorporated by reference into this report are included as Exhibit 13 to this report.

Scientific Background

All living organisms contain biological molecules. The most numerous are in the categories of: nucleic acids, which include DNA and RNA; proteins; carbohydrates; and lipids. Biological molecules are typically much larger and more complex than common molecules, and there is a wide diversity in the types of biological molecules present in living organisms. These characteristics make the analysis of biological molecules significantly more complex than the analysis of smaller compounds. Key advances in therapeutics have often come from an understanding of either proteins or DNA.

DNA molecules provide instructions that ultimately control the synthesis of proteins within a cell, a process referred to as gene expression. DNA molecules consist of chemical subunits, called nucleotides, bound in two long strands formed by a chemical “backbone” made up of sugar and phosphate molecules. There are four nucleotides – adenine, cytosine, guanine, and thymine – often abbreviated with their first letters A, C, G, and T and often referred to as bases. In a DNA molecule, the nucleotides in the two strands are bound together in pairs to form a structure that resembles a twisted ladder, which is often referred to as a double helix. The bound pairs of nucleotides, which form the rungs of the ladder, are often referred to as base pairs.

Genes are individual segments of these DNA molecules that carry the specific information necessary to perform particular biological functions including, for example, to construct particular proteins. Genes may contain from several dozen to tens of thousands of nucleotides. The entire collection of DNA in an organism, called the genome, may contain a wide range of nucleotides, including as few as 4 million nucleotides in the case of simple bacteria and 3.1 billion base pairs of nucleotides in the case of human beings.

RNA molecules are similar to DNA in structure and are essential for biological function through a number of biochemical activities within the human body. There are different types of RNA molecules, each of which has a different function. For example, messenger RNA, the most widely understood form of RNA, acts as an intermediary between DNA and protein, transcribing the genetic code from DNA into proteins.

Principally driven by the “biotechnology revolution” and the increasing focus on DNA, researchers are developing a better understanding of DNA’s role in human disease. An increased appreciation of how DNA ultimately determines the functions of living organisms has generated a worldwide effort to identify and sequence genes of many organisms, including the genes that make up the human genome. We believe the best scientific evidence to date indicates that the number of genes in the human genome that code for proteins is between 25,000 and 30,000. The study of genes and other genetic material of organisms is now commonly referred to as genomics.

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The field of genomics research generally includes three broad categories of analysis, consisting of sequencing, genotyping, and gene expression studies:

 

Sequencing is performed to determine the exact order of the individual nucleotides in a DNA strand. Sequencing was used to identify the nucleotides in the entire human genome and other species. It has also been used to identify naturally occurring genetic variations in the human genome, which are referred to as single nucleotide polymorphisms, or SNPs. Scientists believe that SNPs can be correlated with, for example, susceptibility to disease, disease prognosis, therapeutic efficacy, and therapeutic toxicity, and therefore may have diagnostic or therapeutic utility.

 

Genotyping is performed to determine a particular sequence variant of a gene and its particular association with an individual’s DNA. Genotyping is not performed to determine the complete structure of the gene, but rather is performed to determine if the particular DNA sequence variant, typically a SNP, can be associated with, for example, susceptibility to a particular disease or response to a particular drug.

 

Gene expression is performed to determine whether a particular gene is expressed, or present, and in some cases at what levels, in a relevant biological material. This analysis can be used, for example, to measure and compare gene activity in various biological samples, such as samples from populations of healthy and diseased individuals, or from populations at different stages of disease development. These types of studies may be useful in the development of diagnostic tests and therapeutic treatments.

As researchers learn more about DNA and RNA, they are also developing a better understanding of the role of proteins in human disease through efforts in the field of proteomics, the study of proteins expressed, or coded, by genes. Proteins are the products of genes and, along with gene expression and modification, are believed to be key drivers and mediators of cellular function and biological system activity. The understanding and treatment of disease today involves the study of genes and the proteins they code for, and frequently involves the measurement of a drug’s ability to bind to specific proteins in the body.

Although DNA contains the code for proteins, scientists have discovered that the body may modify proteins after they have been made in cells. These modifications, referred to as post-translational modifications, can alter a protein’s function, leading to changes in the biological reactions that take place in cells, which researchers refer to as biological pathways. These post-translational modifications complicate the study of proteins, because scientists studying proteins and seeking to understand their role in health and disease need a more thorough characterization of proteins than simply knowing their genetic, or DNA, code.

We believe that gene and protein research will increase as companies in the pharmaceutical and biotechnology industries seek to improve their drug discovery and development efforts. We also believe that ongoing drug discovery and development efforts will increase research of cells as researchers seek to further understand how drugs work in the body.

The growth in DNA, protein, and other life science research has created the need for systems that facilitate the collection, organization, and analysis of the large amounts of data generated by this research. This demand has led to the development of the science of

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bioinformatics. The science of bioinformatics seeks to blend biology and computing to transform massive amounts of data into useful information.


Applied Biosystems Group Business

Overview

Applied Biosystems serves the life science industry and research community by developing and marketing instrument-based systems, consumables, software, and services. Its customers use these tools to analyze nucleic acids (DNA and RNA), small molecules, and proteins to make scientific discoveries and develop new pharmaceuticals. Applied Biosystems’ products and services are designed to address the demand for increased automation and efficiency in pharmaceutical and biotechnology laboratories by combining the detection capabilities of analytical instruments with advances in automation and laboratory work-flow design. The markets for Applied Biosystems’ products and services span the spectrum of the life sciences industry and research community, including: basic human disease research and genetic analysis performed by universities, government agencies, and other non-profit organizations; pharmaceutical drug discovery, development, and manufacturing; and agriculture research. Applied Biosystems’ products also serve the needs of some markets outside of life science research, which we refer to as “applied markets,” such as the fields of: human identity testing (forensic and paternity testing); “biosecurity,” which refers to products needed in response to the threat of biological terrorism and other malicious, accidental, and natural biological dangers; and quality and safety testing, for example in food and the environment.

In March 2006, Applied Biosystems announced that it completed the acquisition of the Research Products Division of Ambion, Inc., for approximately $279 million in cash, including transaction costs. The acquired business, based in Austin, Texas, develops and supplies products used by researchers to study RNA and its role in disease development and progression. Applied Biosystems pursued this acquisition as part of a strategy of expanding its consumables products. More information about this acquisition is set forth below in this description of Applied Biosystems’ business under the heading “Products for the Molecular Biology Market–Ambion Acquisition; RNA Consumables.”

For information on revenues from instruments and consumables for our 2006, 2005, and 2004 fiscal years, refer to pages 27, 28 and 30 of Management’s Discussion and Analysis in our 2006 Annual Report, which pages are incorporated herein by reference.

Products for the Molecular Biology Market

Customers in the molecular biology market use systems for the analysis of nucleic acids including DNA and RNA. DNA molecules provide instructions that ultimately control the synthesis of proteins within a cell, a process referred to as gene expression. RNA molecules are similar to DNA in structure and are essential for biological function through a number of biochemical activities within the human body. There are different types of RNA molecules, each of which has a different function. For example, messenger RNA, the most widely understood

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form of RNA, acts as an intermediary between DNA and protein, transcribing the genetic code from DNA into proteins.

Applied Biosystems has developed technologies, instrument systems, and consumables products that address the needs of a wide array applications within this market, including for example: basic research; pharmaceutical and diagnostic discovery and development; biosecurity testing, including infectious disease analysis; human identity testing, including forensic and paternity testing; and food and environment quality and safety testing. These technologies, systems, and consumable products support key methods of analysis, including DNA sequencing, genotyping, and gene expression studies, which are described in further detail above in Item 1 of this report under the heading “Scientific Background.”

PCR and Real-Time PCR Systems and Related Consumables. Polymerase chain reaction, commonly referred to as PCR, is a process in which a short strand of DNA is copied multiple times, or amplified, so that it can be more readily detected and analyzed. Applied Biosystems’ PCR product line includes amplification instruments, known as thermal cyclers, several combination thermal cyclers and PCR detection systems, known as real-time PCR systems, and reagents, disposables, and software necessary for the PCR amplification and detection process.

The following table lists the thermal cyclers offered by Applied Biosystems:

 

Instrument

 

Capacity


 

9800 Fast PCR System

 

96 well

GeneAmp® PCR System 9700 Thermal Cyclers

 

60, 96, Dual 96, and Dual 384 well

Applied Biosystems 2720 Thermal Cycler

 

96 well

Technologically, these instruments are distinguished among each other primarily based on: their capacity for simultaneously processing multiple samples, determined based on the number of consumable “wells” that can be accommodated; and the speed at which the thermal cycling process is completed. The model 9800 instrument is the most advanced thermal cycler offered by Applied Biosystems, and can complete the thermal cycling process substantially faster than other instruments offered by Applied Biosystems.

Applied Biosystems’ real-time PCR systems, which it previously referred to as “sequence detection systems,” include the following instruments:

 

Instrument

 

Capacity/Speed


 

Applied Biosystems 7900HT Real-Time PCR System

 

96 or 384 well/Available as Fast

Applied Biosystems 7500 Real-Time PCR System