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Applied Biosystems Announces Software Development Initiative for Next-Generation Sequencing.


Software Development Community Expected to Facilitate the Advancement of Bioinformatics Applications for the SOLiD[TM] System and Other Next-Generation Sequencing Platforms

FOSTER CITY, Calif. -- Applied Biosystems Applied Biosystems, Inc. (formerly NASDAQ: ABIO) is the original name of a pioneer biotechnology company founded in 1981 in Foster City, California, among the Silicon Valley cities of the southern San Francisco Bay Area.  (NYSE NYSE

See: New York Stock Exchange
:ABI Abi (ā`bī) [short for Abijah], in the Bible, King Hezekiah's mother.


(Application Binary Interface) A specification for a specific hardware platform combined with the operating system.
), an Applera Corporation business, today announced an initiative to support life scientists and independent software vendors (ISVs) in the development and potential commercialization of bioinformatics applications for next-generation DNA sequencing platforms. As part of this initiative, the company is expanding its Software Development Community to include sample data sets, data file formats and data conversion tools for its SOLiD[TM] System, one of the life-science industry's most advanced ultra-high-throughput, next-generation sequencing platforms. Applied Biosystems is the first manufacturer of next-generation instrument systems to make these tools available to the bioinformatics community. It is doing so to directly address the industry-wide challenges associated with analyzing and managing the vast amounts of research data generated by this ultra-high-throughput technology.

Applied Biosystems expects this initiative to drive innovation and speed the development of new tools that will enable researchers to find more answers faster and more cost effectively, thereby helping life scientists to realize the full potential of next-generation sequencing. The promise of next-generation sequencing technology is to broaden the applications of genomic information in medical research and health care, reduce the cost of DNA sequencing without sacrificing quality, and enable discoveries that may revolutionize the practice of medicine.

Recently, more than 40 researchers from 30 leading academic and commercial institutions convened at Applied Biosystems' headquarters in Foster City, Calif. to provide input and share best practices with each other on their respective next-generation sequencing software development initiatives. Among the participants were scientists from the Christian-Albrechts-University in Kiel, Germany, who expressed interest in developing software applications to better understand genetic variations that may correlate with chronic inflammatory diseases, including Crohn's disease Crohn's disease: see colitis. , ulcerative colitis ulcerative colitis

Inflammation of the colon, especially of its mucous membranes. The inflamed membranes develop patches of tiny ulcers, and the diarrhea contains blood and mucus.
, atopic dermatitis Atopic Dermatitis Definition

Eczema is a general term used to describe a variety of conditions that cause an itchy, inflamed skin rash. Atopic dermatitis, a form of eczema, is a non-contagious disorder characterized by chronically inflamed skin and
, and sarcoidosis Sarcoidosis Definition

Sarcoidosis is a disease which can affect many organs within the body. It causes the development of granulomas. Granulomas are masses resembling little tumors. They are made up of clumps of cells from the immune system.
.

"The promise that next-generation, genetic-analysis technologies will generate better data, faster, and at a lower cost will only be realized when there are sufficient software applications that allow researchers to analyze this data," said Michael Wittig, a bioinformatician at the Institute for Clinical Molecular Biology molecular biology, scientific study of the molecular basis of life processes, including cellular respiration, excretion, and reproduction. The term molecular biology was coined in 1938 by Warren Weaver, then director of the natural sciences program at the Rockefeller  in Kiel. "Applied Biosystems' willingness to provide access to tools and reference data sets is helping us to more rapidly develop the software applications that are necessary to advance our work in understanding genetic variation."

The Joint Genome Institute The DOE Joint Genome Institute (JGI) was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory (LBNL), Lawrence Livermore  (JGI JGI Joint Genome Institute
JGI Jane Goodall Institute
JGI Just Got It (chat)
JGI Just Google It
) is an Applied Biosystems early-access collaborator that provides contract sequencing services and develops computational and bioinformatic tools for data management and mining. JGI serves approximately 500 scientists working on a broad range of sequencing projects and provides many of the software applications that they rely on to analyze the data JGI generates on their behalf.

"We are not only interested in the quality of the data each platform generates; but equally as important is how willing each vendor is to collaborate with the research community to provide the necessary tools and resources for developing the required software applications," said Dr. Darren Platt, Ph.D., head of informatics at JGI. "Applied Biosystems has been very forthcoming in sharing information about the SOLiD system platform. We anticipate that this level of assistance will enable us to rapidly develop the software applications our laboratories need to accelerate next-generation research projects."

As part of this program, Applied Biosystems has dedicated resources to create and support a community of bioinformatics experts that it expects will advance application development in the many research areas supported by the SOLiD system platform. These include but are not limited to whole genome sequencing; chromatin immunoprecipitation (ChIP); microbial microbial

pertaining to or emanating from a microbe.


microbial digestion
the breakdown of organic material, especially feedstuffs, by microbial organisms.
 sequencing; gene expression; microRNA discovery; digital karyotyping Karyotyping
A laboratory test used to study an individual's chromosome make-up. Chromosomes are separated from cells, stained, and arranged in order from largest to smallest so that their number and structure can be studied under a microscope.
; epigenetic epigenetic /epi·ge·net·ic/ (-je-net´ik)
1. pertaining to epigenesis.

2. altering the activity of genes without changing their structure.
 profiling; and detection of rare genetic variants among others. Applications such as these have been identified by prospective customers as being important to driving the early adoption of next-generation sequencing.

"Collaboration with our early-access customers and bioinformatics experts has given us ample opportunity to clearly define what is required to help them to successfully develop the software applications that will ensure their success in conducting next-generation sequencing projects," said Kimberlee S. Caple, vice president and general manager for Applied Biosystems' next-generation sequencing business unit. "Application-specific software is crucial in building the bridge from the quality data generated by the SOLiD System to new insights that will advance biomedical research by broadening the use of genomic information."

The SOLiD System, based on sequencing by oligonucleotide ligation ligation /li·ga·tion/ (li-ga´shun) the application of a ligature.

tubal ligation  sterilization of the female by constricting, severing, or crushing the uterine tubes.
 and detection, is Applied Biosystems' next-generation system for ultra high-throughput DNA analysis DNA analysis Any technique used to analyze genes and DNA. See Chromosome walking, DNA fingerprinting, Footprinting, In situ hybridization, Jeffries' probe, Jumping libraries, PCR, RFLP analysis, Southern blot hybridization. . Unlike polymerase sequencing approaches, the SOLiD System utilizes a proprietary technology called stepwise stepwise

incremental; additional information is added at each step.


stepwise multiple regression
used when a large number of possible explanatory variables are available and there is difficulty interpreting the partial regression
 ligation, which generates high quality data for applications such as whole genome sequencing, medical sequencing, genotyping, gene expression and small RNA RNA: see nucleic acid.
RNA
 in full ribonucleic acid

One of the two main types of nucleic acid (the other being DNA), which functions in cellular protein synthesis in all living cells and replaces DNA as the carrier of genetic
 discovery. Currently in use by early-access customers, the SOLiD System will be commercially available beginning in October.

Applied Biosystems is a global leader in the development and commercialization of instrument-based systems, consumables, software, and services for the life-science market and is the recognized market leader in the commercialization of DNA sequencing platforms. For more information about the SOLiD System or the Software Development Community please visit: http://solid.appliedbiosystems.com or http://www.appliedbiosystems.com/support/software_community/

About Applera Corporation and Applied Biosystems

Applera Corporation consists of two operating groups. The Applied Biosystems Group serves the life science industry and research community by developing and marketing instrument-based systems, consumables, software, and services. Customers use these tools to analyze nucleic acids Nucleic acids
The cellular molecules DNA and RNA that act as coded instructions for the production of proteins and are copied for transmission of inherited traits.
 (DNA DNA: see nucleic acid.
DNA
 or deoxyribonucleic acid

One of two types of nucleic acid (the other is RNA); a complex organic compound found in all living cells and many viruses. It is the chemical substance of genes.
 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 paternity testing

see parentage 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. Applied Biosystems is headquartered in Foster City, CA, and reported sales of approximately $2.1 billion during fiscal 2007. The Celera Group 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 maintains a strategic alliance with Abbott 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 is also discovering and validating therapeutic targets, and it is seeking strategic partnerships to develop therapeutic products based on these discovered targets. Information about Applera Corporation, including reports and other information filed by the company with the Securities and Exchange Commission, is available at http://www.applera.com, or by telephoning 800.762.6923. Information about Applied Biosystems is available at http://www.appliedbiosystems.com.

Applied Biosystems Forward Looking Statements

Certain statements in this press release are forward-looking. These may be identified by the use of forward-looking words or phrases such as "should, "planned," and "expect," among others. These forward-looking statements are based on Applera Corporation's current expectations. The Private Securities Litigation Reform Act The Private Securities Litigation Reform Act of 1995 (PSLRA) implemented several significant substantive changes affecting certain cases brought under the federal securities laws, including changes related to pleading, discovery, liability, class representation and awards fees and  of 1995 provides a "safe harbor Safe Harbor

1. A legal provision to reduce or eliminate liability as long as good faith is demonstrated.

2. A form of shark repellent implemented by a target company acquiring a business that is so poorly regulated that the target itself is less attractive.
" for such forward-looking statements. In order to comply with the terms of the safe harbor, Applera Corporation notes that a variety of factors could cause actual results and experience to differ materially from the anticipated results or other expectations expressed in such forward-looking statements. These factors include but are not limited to: (1) rapidly changing technology and dependence on the development and customer acceptance of new products; (2) sales dependent on customers' capital spending capital spending

Spending for long-term assets such as factories, equipment, machinery, and buildings that permits the production of more goods and services in future years.
 policies and government-sponsored research; and (3) other factors that might be described from time to time in Applera Corporation's filings with the Securities and Exchange Commission. All information in this press release is as of the date of the release, and Applera does not undertake any duty to update this information, including any forward-looking statements, unless required by law.

For Research Use Only. Not for use in diagnostic procedures.

(c)Copyright 2007. Applied Biosystems. All rights reserved. Applera, Applied Biosystems, AB (Design), and Celera are registered trademarks and SOLiD is a trademark of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.
COPYRIGHT 2007 Business Wire
No portion of this article can be reproduced without the express written permission from the copyright holder.
Copyright 2007, Gale Group. All rights reserved.

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Date:Sep 4, 2007
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