Scientists from the Broad Institute of MIT and Harvard, a leading genome research institute, will use ultra-high throughput genomic analysis systems from Applied Biosystems Inc. (NYSE:ABI) to further conduct comprehensive analyses of the genetic changes that characterize cancer in humans. Applied Biosystems today announced that it will add five new SOLiD™ Systems to the Broad Institute’s existing base of genomics analysis technologies. With a total of eight SOLiD Systems, scientists from the Broad Institute plan to use these DNA sequencing platforms to expand their studies of the genetic underpinnings of cancer and other complex human diseases. The development of sophisticated genomic analysis sequencing technologies has opened the door to a new era of life-science research, enabling scientists to completely survey entire cancer genomes within individuals. By creating a catalog of both single base changes, or SNPs, and large segments of DNA rearrangements in genomes known as structural variants, researchers hope to one day identify all sources of genetic variation that contribute to cancer. This kind of portrait of the genetic underpinnings of disease will help scientists to lay the groundwork for the molecular events that occur in the generation of individual cancers. Researchers at the Broad Institute are using the SOLiD System for large-scale discovery of genetic variation in human genome samples. The primary goal of this research is to generate comprehensive catalogues of genomic abnormalities in tumors from many different cancer types that are of clinical and societal importance across the globe, accelerating research into the causes and control of cancer. Genomic analysis platforms capable of ultra-high throughput are quickly becoming established as the standard for the study of complex genomes because as the technologies mature, the cost of analysis continues to decrease. In its work with its existing SOLiD Systems, the Broad Institute has completed sequencing experiments with yields of up to 13.4 billion bases per run: more than four times the number of bases that comprise an entire human genome. “The Broad Institute recognizes that Applied Biosystems is a leader in DNA sequencing and has extensive knowledge of developing and applying new technologies that advance genomics research,” said Robert Nicol, director of sequencing operations at the Broad Institute. “We are looking forward to working with them to further our knowledge of the molecular underpinnings of cancer.” Dr. Chad Nusbaum, co-director of Broad’s genome sequencing and analysis program added, “The SOLiD System technology has scaled significantly since its commercial availability just one year ago. We are excited to further test SOLiD’s accuracy rate and throughput capabilities on these important cancer genome projects.” The SOLiD System offers two critical advantages for complex genomics and disease studies. First, the mate-pair analysis capability enables scientists to detect multiple types of structural variants which are likely to contribute to human diversity and disease susceptibility. These include insertions and deletions (indels), inversions, translocations, duplications and copy number polymorphisms. Mate-pair analysis provides detailed information about the orientation of the reads and the distance between mate-paired ends. The SOLiD System can generate millions of mappable mate-paired sequences from a wide range of DNA insert sizes, between 0.6 – 10 kilo bases (kb), to detect most structural changes and precisely define the breakpoints of particular rearrangements. Large paired-end tag libraries enable researchers to quickly cover the entire genome to identify large structural variations. Short pair-end tag libraries can then be used to identify small structural variations and precisely map the boundaries of specific large structural variations. The other advantage of the SOLiD System is the high bead density per slide. By combining a greater number of tags with large mate paired libraries, researchers will be able to obtain greater genomic and physical coverage per run. “The use of multiple SOLiD Systems by the Broad Institute for important cancer research demonstrates that the platform is well suited for analysis of complex genomes, and will play a key role in new discoveries related to understanding the molecular basis of disease,” said Shaf Yousaf, president for Applied Biosystems’ molecular and cell biology genomic analysis division. “The mate-pair analysis capabilities of SOLiD have been shown to be instrumental in helping scientists from several different institutions investigate how structural variation impacts genomics.” Applied Biosystems’ new genomic analysis platform, the SOLiD 3 System, is the only commercially available platform in the life science industry to provide a path to a $10,000 genome. Significant cost-reduction and productivity enhancements have been built into the platform, enabling researchers to dramatically drive down the cost of sequencing entire genomes of all organisms, and expand applications for DNA, RNA and epigenetic analysis. Use of this system is expected to help life science researchers move one step closer to the mainstream use of genomic data for clinical research and personalized medicine. About the SOLiD 3 System The SOLiD 3 System is the life science industry’s most comprehensive solution from sample to results. The platform is based on sequencing by oligonucleotide ligation and detection. Unlike polymerase sequencing approaches, the platform utilizes a proprietary technology called stepwise ligation, which generates the industry’s most cost-effective and accurate mappable sequence data for a variety of applications. The SOLiD 3 System is capable of generating 20 billion bases of mappable sequence data per run in customer laboratories, and has demonstrated runs of greater than 25 billion bases of mappable sequence data at Applied Biosystems’ research and development facilities. The SOLiD 3 System is supported by one of the life-science industry’s most comprehensive service and support organization of more than 2,000 dedicated field personnel worldwide, specializing in business consulting and protocol development, instrument optimization, and data and application integration. Further information about the SOLiD 3 System is available at https://solid.appliedbiosystems.com. The SOLiD 3 System is available as an upgrade to an existing platform, or as a stand-alone instrument. To receive the SOLiD 3 upgrade, contact a regional service representative, who can install components that include a new compute cluster, automation components and reagent cooling hardware, and software. The SOLiD 3 System is expected to be globally available in early 2009.