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Posted: October 27, 2008

Applied Biosystems Announces Grant Program for Genomic, Epigenomic and Transcriptome Studies

(Nanowerk News) As part of its commitment to promote basic research in the life sciences, Applied Biosystems Inc. today announced the creation of a grant program for genomic, epigenomic and transcriptome studies. The $10K Genome Grant Program is based on the concept of sequencing an entire genome for $10,000. Applied Biosystems is launching this program to inspire new genomic sequencing studies on next-generation sequencing technology. By extending the SOLiD™ System into other critical applications, such as RNA and epigenetic analysis, researchers will be able to advance the use of genomic data for clinical research and personalized medicine. Grant submissions are due by December 31, 2008. Results will be announced in February 2009.
Applied Biosystems recently announced the development of its SOLiD 3 System, which is the only commercially available platform in the life science industry to provide a path to a $10,000 genome. This new ultra-high- throughput genomic sequencing platform includes significant productivity enhancements and cost-reduction, enabling researchers to dramatically drive down the cost of genomic sequencing projects for all organisms. The $10K Genome Grant Program, as well as the new SOLiD 3 System, will be introduced through an Applied Biosystems SOLiD Roadshow which began last week, and will travel through 19 cities throughout the United States and Europe.
The grant program will award the first-place winner up to 60 gigabases or 750 million tags of sequencing data to an individual representing an academic institution or laboratory. Applied Biosystems will perform all sequencing, primary data generation, and analysis using the SOLiD 3 System. Ten second-place winners will be selected with each being awarded one (2-slide) run, which will be conducted on a SOLiD 3 platform by either Applied Biosystems or a member of the SOLiD System Service Provider Program, such as SeqWright DNA Technology Services (www.seqwright.com), or other global members to be determined.
Grant program entries will be reviewed by a panel of renowned scientists and industry thought leaders. This distinguished panel includes:
  • Sean Grimmond, Ph.D., group leader in the genomics and computational group at the Institute of Molecular Bioscience at the University of Queensland
  • Yoshihide Hayashizaki M.D., Ph.D, director of the Omics Science Center at the Institute for Physical and Chemical Research (RIKEN)
  • John McPherson, Ph.D., cancer genomics director at the Ontario Institute of Cancer Research
  • Stanley F. Nelson, M.D., professor and vice-chair of human genetics and professor of psychiatry within the David Geffen School of Medicine at the University of California at Los Angeles (UCLA)
  • Stefan Schreiber, M.D., professor of medicine and gastroenterology at the Christian-Albrechts University in Kiel
  • Chung-I Wu, Ph.D., professor in the department of ecology and evolution at the University of Chicago and the director of Beijing Institute of Genomics
  • Francisco de la Vega, Ph.D., distinguished scientific fellow and vice president of SOLiD Applications and Bioinformatics at Applied Biosystems
  • Kevin McKernan, senior director of SOLiD scientific operations at Applied Biosystems
  • Michael Rhodes, Ph.D., $10K Genome Grant Program chairman and senior manager of SOLiD product applications at Applied Biosystems
  • Bob Setterquist, Ph.D., director, scientific operations transcriptome analysis at Applied Biosystems
  • High-throughput genomic technology, such as the SOLiD 3 System, is expected to allow clinical researchers to find new and better ways to understand, detect, control and treat illness. Scientific visionaries, such as Dr. Schreiber, are using the SOLiD technology to find answers to difficult scientific and health questions. His clinical research interests include chronic inflammatory bowel disease, such as Crohn’s disease, ulcerative colitis, as well as human healthy aging. Recently, he and his team used Applied Biosystems technologies to identify several disease genes for complex inflammatory disorders. These include ATG16L1, a gene coding for a variant protein that leads to a defect in autophagy in Crohn’s disease, and ANXA11, a disease gene in srcoidosis probably involved in T cell-apoptosis. The results of his team’s work resulted in the first systemic genome wide association scan in ulcerative colitis. At the Institute of Clinical Molecular Biology at Christian-Albrechts University, he is also responsible for designing and organizing clinical trials of novel drugs for inflammatory bowel disease and the functional disorders of the gastrointestinal tract.
    “The technical enhancements made to the SOLiD 3 System are integral to enabling a path for molecular epidemiology studies, and to accelerate the knowledge provided by genome-wide association studies to a full understanding of sequence based risk factors,” said Dr. Schreiber. “The power of Applied Biosystems’ $10,000 genome sequencing technology will promote a paradigm shift in our approach to comparative sequence analysis for complex disease research. By lowering the cost of sequencing, researchers will be afforded more opportunities to explore the role of rare genetic variations and examine how they contribute to common ailments.”
    Another thought leader who is part of the $10K Grant Program judging panel is Dr. Nelson whose Nelson Lab at UCLA uses genomic approaches to further the study of cancers, including glioblastoma, which is the most common and lethal form of primary brain cancer. His research team is using large-scale gene expression analysis, alternative splicing analysis, chromosomal loss information, and now whole-genome sequence data to paint refined portraits of the mutational landscape of individual brain cancers. The researchers are also developing bioinformatic approaches to use this information to identify and prioritize novel therapeutic targets.
    “Dramatically lowering the cost of whole genome sequencing permits the investigation of many more genomes than were previously possible,” said Dr. Nelson. “This will ultimately allow scientists to identify individual genes that are frequent mutational targets in the process of cancer formation. The human genome community is poised to sequence thousands of genomes that are necessary to get a clearer picture of sequence variation and haplotype structure in human populations that are the underpinnings of identifying allele associations with all human diseases.”
    Researchers interested in the $10K Genome Grant Program are encouraged to submit a proposal that includes a statement of the underlying project goals, the type and status of the project samples, and availability of bioinformatics resources. For more detailed information about the grant program, please visit http://info.appliedbiosystems.com/SOLiD10K For additional information about the SOLiD Roadshows, please visit http://info.appliedbiosystems.com/SOLID2008
    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 including whole genome sequencing and targeted resequencing, transcriptome analysis, small RNA discovery, gene expression profiling, chromatin immunoprecipitation (ChIP), microbial and eukaryotic resequencing, digital karyotyping, medical sequencing, and genotyping, among others. 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.
    With unsurpassed sensitivity, the SOLiD 3 System allows researchers to adopt a systems-biology approach to studying simple and complex organisms. Systems biology is the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions. On a single platform, researchers can use a global, hypothesis-neutral approach to survey the contents of genomes, transcriptomes, and epigenomes, or the collection of chemical modifications to DNA. The superior accuracy of the system, greater than 99.94% with 2-base encoding, provides researchers performing studies of genetic variation with the highest data quality compared to other sequencing platforms.
    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. The SOLiD 3 System is available as an upgrade to an existing platform, or as a stand-alone instrument. It is expected to be globally available in early 2009. Further information about the SOLiD 3 System is available at http://solid.appliedbiosystems.com.
    Source: Applied Biosystems (press release)
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