Applied Biosystems Offers Commentary About Discovery of Increased Genetic Variation in Human Genome
At the Genome, Medicine and the Environment meeting, a three-day gathering of many of the world's leading genomics researchers, Kevin McKernan, Ph.D., one of the inventors of the SOLiD(TM) System, Applied Biosystems' next-generation DNA sequencing platform, today said that this discovery will fundamentally change the way people approach and conduct genomics-related research. As a result, life scientists using next-generation sequencing technologies to pursue the study of complex genomes will require systems capable of addressing this increased genetic variation.
The majority of genetic differences between individuals are represented by single base changes, or SNPs (single nucleotide polymorphisms), which are scattered throughout the approximately 3 billion bases of the human genome. In the PLoS Biology study, researchers identified more than 1.2 million previously unknown genetic variants, including SNPs and structural variants. McKernan believes that high throughput, scalability, and accuracy of emerging genetic analysis technologies will be the ultimate success factors for associating this increased genetic variation with how individuals respond to treatments for disease.
"This finding is a calling for us to raise the bar, to usher in the next-generation life sciences era, in which highly sophisticated technologies will be required to fulfill the promise of next-generation sequencing," said McKernan, a senior director for Applied Biosystems' molecular and cell biology division. "To unlock the hidden knowledge in complex genomes, researchers will need ultra-high-throughput platforms capable of producing highly accurate sequence data and the ability to scale those systems to support future studies of increasing complexity."
Next-generation sequencing platforms capable of ultra-high-throughput will become more common for the study of complex genomes because as the technologies mature, the cost of analysis will continue to decrease. As part of its continued development of next-generation sequencing technology, Applied Biosystems (NYSE:ABI), an Applera Corporation business, today announced that the SOLiD System is currently the industry's highest throughput next-generation sequencing platform. In Applied Biosystems' development laboratories, the SOLiD System has generated sequence data that has exceeded 4 gigabases (GB). This sequence data has been shared with some of the company's early access customers and collaborators. This output of sequence per run surpasses the number of bases that comprise the entire human genome, which makes this system effective for carrying out whole human genome studies.
Applied Biosystems achieved this advanced throughput by enriching the beads on the system. Beads are an integral part of the SOLiD System's open-slide format architecture, enabling the platform to be scaled to support a higher density of sequence per slide. 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 platform's current hardware or software. Applied Biosystems' development team reports that over the past 15 months, the SOLiD System has doubled its throughput every 3 months. McKernan and the development team believe the system's architecture may support even higher levels of throughput that will facilitate the study of complex genomes.
Along with the scalable bead technology, mate-paired library preparation is a method that enables highly accurate mapping and sequence assembly. This combination, which is unique to the SOLiD System, helps researchers to cost effectively identify specific genomic regions where structural variations are located. This is significant because a key finding of the individual human genome study revealed that structural variation accounts for almost 74% of the variant DNA sequence in the human genome.
A key to understanding structural variation is the ability to visualize structural rearrangements, such as gene copy number variations, single-base duplications, inversions, insertions, and deletions. The SOLiD System is currently generating read lengths of 35 base pairs - a 30% increase from 6 months ago - which increases the accuracy of locating where both single base and structural variation occurs.
Increased read lengths provide researchers using the SOLiD System a raw base accuracy greater than 99.94% due to 2-base encoding, a mechanism that discriminates random or systematic errors from true SNPs. This represents a 5-fold better performance than any data currently published to date on alternative next-generation platforms. Applied Biosystems believes that in order to understand the role of genetics in health and disease, researchers will need a robust next-generation sequencing system that can identify the location of structural variation in genomes.
"We recognize the paradigm shift created by the PLoS Biology study and believe that technical advancements made to the SOLiD platform uniquely position it to address the increased genetic variation in the human genome," said McKernan. "We expect that the advancements to the throughput, accuracy, and scalability of the SOLiD System will enable researchers to make more meaningful associations between genetic variation and medical conditions. This is expected to be crucial in the emerging era of personalized medicine."
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.
In the study that reported the first sequencing of an individual's diploid genome, researchers used Applied Biosystems' 3730xl DNA Analyzers and BigDye(R) Terminator chemistry to sequence the DNA. By having a diploid genome, the researchers were able to compare DNA from both sets of chromosomes, which revealed the amount of genetic variation. This was the same DNA sequencing platform that helped scientists to sequence the first human genome, a composite genome of several individuals.
In developing the SOLiD System, Applied Biosystems continues its leadership in DNA sequencing by commercializing a technology that helps scientists to better understand and treat disease based on genomic information. Applied Biosystems will officially announce the commercial availability of the SOLiD System later this month. Further information about the SOLiD System is available at http://solid.appliedbiosystems.com.
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. Its customers use these tools to analyze nucleic acids (DNA and RNA), small molecules, and proteins to make scientific discoveries and develop new pharmaceuticals. The Applied Biosystems' products also serve the needs of some markets outside of life science research, which we refer to as "applied markets." These include 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, such as testing required for food and pharmaceutical manufacturing. 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 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 the development and customer acceptance of new products; (2) the risk of unanticipated difficulties associated with the further development of the SOLiD(TM) System; (3) sales dependent on customers' capital spending policies and government-sponsored research; and (4) 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.
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(C)Copyright 2007. Applied Biosystems. All rights reserved. Applera, Applied Biosystems, AB (Design) and BigDye are registered trademarks and SOLiD is a trademark of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries.
Contact
Applied Biosystems
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Posted: October 2007
