Applied Biosystems SOLiD(TM) System Used to Survey RNA Landscape of Mouse Stem Cells; Study Expected to Help Scientists Better Understand Genetic Basis of Complex Diseases

FOSTER CITY, Calif.–Scientists from the University of Queensland, Australia and Applied Biosystems Inc. (NYSE:ABI – News) have teamed together to conduct the most comprehensive analysis to date of a mammalian transcriptome, the vast collection of RNAs transcribed from a mouse genome. RNA expression analysis data from this study represents the highest-resolution view of mammalian transcriptomes derived from both differentiated cells and stem cells. Results of this study are expected to help researchers to more fully understand the complexity of the genomic landscape of mammals. The study, published in this month’s issue of the journal Nature Methods, was also discussed at the International Congress of Genetics (ICG) meeting taking place this week.

According to the authors of this paper, results of this study are significant because their findings will help researchers to identify distinguishing features in the genetic makeup of stem cells, and better understand how breakdowns in molecular pathways can lead to complex diseases such as cancer. For example, having a reliable method for detecting RNA splice variants will be essential for understanding gene fusion events, which are molecular characteristics of cancers such as leukemia. Screening human cell samples for these kinds of RNA signatures has the potential to be developed into a diagnostic approach for identifying cancer at the molecular level.

Almost all of the DNA in the mammalian genome is transcribed into either RNA molecules from genes that encode proteins, or non-coding RNAs that regulate the activity of genes. By profiling the totality of RNA transcripts generated from the genomes of mouse embryoid body (EB) cells and embryoid stem cells (ESC), researchers in this study generated more than 10 billion bases of sequence from all RNA transcripts. This in-depth level of coverage of mouse cell line transcriptomes revealed thousands of previously unknown RNA transcripts, and allowed researchers to discern between RNAs transcribed from the coding or sense strand, and non-coding RNAs that reside on the anti-sense strand of double-stranded DNA.

By also identifying an unexpectedly large number of variant transcripts derived from genomic loci of stem cells, researchers shed light on the complexity of biological pathways involved in regulating the pluripotency of stem cells, a key to understanding how stem cells differentiate into specific cell types.

Applied Biosystems’ SOLiD™ System was an essential technology used by scientists to profile the mammalian transcriptomes with an unprecedented depth of coverage. Researchers used the SOLiD System to perform a sequencing-based transcriptome profiling technique, using methodology developed at the University of Queensland to construct short quantitative random RNA libraries (SQRL).

Using the SQRL method, researchers created random cDNA libraries that gave them 25-35 base-pair length sequence tags, each tag representing a particular RNA transcript generated from the mouse genome. The ability of the SOLiD System to both accurately detect even minute quantities of RNA transcripts and generate up to 240 million sequence tags per run enabled the researchers to rapidly perform a digital RNA expression analysis application and obtain an exact count of the number of RNA sequence tags generated from the genome of the different cell lines.

“For the first time we are starting to accumulate data sets that allow us to look at that entire complexity of all of the RNA present in a mammalian cell, said Dr. Sean Grimmond Ph.D., an associate professor at the Institute of Molecular Bioscience, University of Queensland, and senior author of the study. “This finding demonstrates that a digital gene expression methodology performed with the SOLiD System is far superior to array profiling approaches in terms of having a higher sensitivity and being able to see more RNAs in a transcriptome.”

By counting the number of sequence tags, and finding tags that map to previously discovered genes in archived data bases, the researchers were able to calculate the number of variant RNA transcripts that originate from specific regions or loci of the genome. From these short sequence tags, they were able to characterize RNAs as splice variants, multiple RNA transcripts that result from transcription of a single region of the genome; identify single base changes, or SNPs within transcripts; and detect other kinds of variants.

According to the authors of this study, the SQRL technique, which benefits from the tag throughput levels of the SOLiD System, effectively profiled transcriptomes by detecting RNA expression events that occur below the level of detection of traditional transcriptome analysis technologies such as microarrays.

Current array hybridization technologies are insufficient to address the complexities of the mammalian transcriptome, as they do not have the sensitivity to detect RNAs expressed at very low levels. Moreover, array profiling requires hybridization of transcripts to a known complementary sequence that has been fixed on a slide or chip. Alternatively, the SQRL method allows researchers to use a hypothesis-neutral approach to RNA expression analysis that identifies the low levels of novel non-coding RNAs expressed as splice variants, anti-sense strands, as well as repeat genetic elements, which make up a large portion of the transcriptome.

“Using the SQRL approach allowed us to discover RNA molecules that could not have been discovered using alternative methods such as array profiling,” said Kevin McKernan, Applied Biosystems’ senior director of scientific operations, and one of the co-authors of the study. “For example, this method allowed us to discover thousands of new splice variants. Also, being able to capture information about which DNA strand—sense, or anti-sense—contains specific RNA transcripts provides us with an important detail for gaining a better understanding of anti-sense regulation and how non-coding RNAs function.”

Researchers also used the SOLiD system to detect SNPs in both coding and non-coding RNAs, making it possible for them to explore mutation status and RNA editing events on a genome-wide scale, furthering their understanding of how variant non-coding RNA transcripts influence regulation of gene expression.

About the SOLiD System

The SOLiD System is an end-to-end genomic analysis solution comprised of a sequencing unit, a computing cluster, and data storage. The platform is based on sequencing by oligonucleotide ligation and detection. Unlike polymerase sequencing approaches, the SOLiD System utilizes a proprietary technology called stepwise ligation, which generates high-quality data for applications including: whole genome sequencing, chromatin immunoprecipitation (ChIP), microbial sequencing, digital karyotyping, medical sequencing, genotyping, gene expression, and small RNA discovery, among others.

Unparalleled throughput, scalability and accuracy distinguish the SOLiD™ System from other next generation sequencing platforms. The system can be scaled to support a higher density of sequence per slide through bead enrichment. Beads are an integral part of the SOLiD System’s open-slide format architecture, which enables the system to generate greater than 6 gigabases of sequence data per run. The SOLiD System has demonstrated runs greater than 13 billion bases of mappable sequence data per run in customer laboratories, and up to 17 billion bases of mappable sequence data at Applied Biosystems’ research and development facilities. The combination of the open-slide format, bead enrichment, and software algorithms provide the infrastructure for allowing it to scale to even higher throughput, without significant changes to the system’s current hardware or software. The SOLiD System’s unique 2-base encoding provides built-in error checking capability that distinguishes random or systematic errors from true single base changes, or single nucleotide polymorphisms (SNPs). This capability helps researchers to detect SNPs with greater than 99.94 percent sequencing accuracy.

About Applied Biosystems Inc.

Applied Biosystems Inc. (formerly known as Applera Corporation) is a global leader in the development and marketing of instrument-based systems, consumables, software, and services for academic research, the life science industry and commercial markets. Driven by its employees’ belief in the power of science to improve the human condition, the company commercializes innovative technology solutions for DNA, RNA, protein and small molecule analysis. Customers across the disciplines of academic and clinical research, pharmaceutical research and manufacturing, forensic DNA analysis, and agricultural biotechnology use the company’s tools and services to accelerate scientific discovery, improve processes related to drug discovery and development, detect potentially pathogenic microorganisms, and identify individuals based on DNA sources. Applied Biosystems has a comprehensive service and field applications support team for a global installed base of high-performance genetic and protein analysis solutions. On June 12, 2008, Applera Corporation and Invitrogen Corporation (NASDAQ: IVGN – News) announced that their Boards of Directors had approved a definitive merger agreement under which Invitrogen will acquire all of the outstanding shares of Applied Biosystems stock. The merger is subject to customary closing conditions and is targeted to close in the fall of 2008. Further information regarding the merger will be provided in a joint proxy statement/prospectus to be mailed to stockholders of the company and Invitrogen. Investors and security holders are urged to read this document when it becomes available because it will contain important information. Applied Biosystems Inc. is headquartered in Norwalk, CT, and reported sales of approximately $2.1 billion during fiscal 2007. Information about Applied Biosystems, including reports and other information filed by the company with the Securities and Exchange Commission, is available at http://www.appliedbiosystems.com. All information in this news release is as of the date of the release, and Applied Biosystems does not undertake any duty to update this information unless required by law.

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 of 1995 provides a “safe harbor” 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 customer acceptance of the SOLiD System; (2) the risk of unanticipated difficulties associated with the further development of the SOLiD™ System; 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.