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Posted: September 16, 2008
The Genome Institute of Singapore Adds Genomic Analysis Systems for Cancer Research
(Nanowerk News) Scientists from the Genome Institute of Singapore (GIS), a leading genome research institute, will use ultra-high throughput genomic analysis systems from Applied Biosystems Inc. (NYSE:ABI) to undertake a comprehensive analysis of the genetic changes that characterize cancer in humans. Applied Biosystems announced today that GIS will add three new SOLiD™ Systems to its existing base of genomics analysis technologies. With a total of four SOLiD Systems, GIS scientists plan to use these DNA sequencing platforms to expand their study 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 working at a number of different institutions 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.
For their cancer genomics research projects, scientists at GIS are interested in using highly accurate, ultra-high throughput genomic analysis technologies to help them to more thoroughly investigate how structural variants contribute to the development of cancer. Structural variants consist of gene copy-number variations, single-base duplications, inversions, translocations, insertions and deletions. Recent studies have shown these genetic changes may occur in both normal and diseased cells. Therefore, it is important to characterize all structural changes to understand which variations may lead to abnormal function.
“By identifying all of the genetic variants present in cancer genomes, scientists will be able to better understand the disease,” said Dr. Yijun Ruan, associate director for genomic technologies at GIS. “We evaluated several technologies for this kind of research, and concluded that the SOLiD System fits very well with our paired end di-tag (PET) technology and will provide us with a platform that enables rapid, accurate and cost-effective study of a variety of types of genetic variants present in cancer genomes.”
Together with Dr. Chia-Lin Wei, senior group leader for GIS’ Genome Technology and Biology group, the researchers are responsible for the institute’s DNA sequencing programs.
“We have been using the SOLiD System since January 2007. We are happy with its performance and output. We believe that acquiring the additional platforms will help us accelerate our research,” said Dr. Wei.
The paired-end analysis capability of the SOLiD System enables scientists interested in complex genomic studies to analyze wide ranges of DNA insert sizes of up to 10,000 base pairs. Insert sizes are pairs of sequences separated by a known distance between them. 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 use of multiple SOLiD Systems by GIS 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.”
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 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.
Unparalleled throughput, inherent scalability and unmatched 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 of nearly 15 billion bases of mappable sequence data per run in customer laboratories, and has demonstrated runs of greater than 20 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. This capability helps researchers to detect SNPs with greater than 99.94 percent sequencing accuracy.