SAGE: A new tool for the discovery of improved cancer treatments The accuracy and sensitivity of our gene expression technology make it possible to identify genes expressed at very low levels, which is often the case with genes that control crucial biological processes and therefore represent potential drug targets. SAGE has identified many genes that were previously unknown.
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SAGE is a patented, high-efficiency method of simultaneously detecting and measuring the levels of virtually all genes expressed in a cell at a given time. It can be used in a wide variety of applications to identify disease-related genes, analyze the effects of drugs on tissues, and provide insight into disease pathways.
Genomics has the potential to revolutionize the life science development and discovery process by providing a wealth of new genes that help us understand disease pathways and by providing new targets for health and nutrition products. The critical question, however, is how to harness this wealth of information and synthesize it into a select group of relevant, prioritized targets. Gene expression analysis is a critical tool in this prioritization and selection process.
Recognizing that, Genzyme Molecular Oncology (GMO) has recently acquired commercial rights to an extremely powerful expression analysis tool known as SAGE™ (Serial Analysis of Gene Expression). Not only has GMO positioned SAGE as the cornerstone of its own genomics and drug discovery efforts, but it is now providing interested companies with access to this remarkable technology.
THE SAGE METHOD
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SAGE is a patented proprietary sequence-based technology for gene identification and quantitation developed by Bert Vogelstein, Ken Kinzler, and Victor Velculescu at the Johns Hopkins University Oncology Center. (Patent No. 5,695,937)
In order to use SAGE for transcript identification and quantitation, messenger RNA (mRNA) is first prepared from the desired cell or tissue sample. Complementary DNA (cDNA) is then synthesized from the mRNA using standard techniques. At this point, the entire population of cDNA molecules is treated using proprietary techniques to create a single unique "tag" from each cDNA. The sequence of the tags serves to identify each transcript. The number of times each tag occurs measures the number of copies of the mRNA originally present in the biological sample. GMO has developed proprietary software to perform tag identification and quantitation and uses its bioinformatics tools to create a relational database of the expression profile.
THREE PRINCIPLES UNDERLIE THE SAGE TECHNOLOGY:
• One short oligonucleotide sequence from a defined location within a transcript ("tag") allows accurate quantitation.
• Tag size (10-14bp) is optimal for high throughput while maintaining accurate gene identification and quantitation.
• The combined power of serial and parallel processing increases data throughput by orders of magnitude when compared to conventional approaches.
These attributes combine to enable rapid, accurate analysis of gene expression patterns.1
THE SAGE ADVANTAGE
SAGE is highly efficient, able to detect low abundance genes, very accurate, and extremely sensitive.
The SAGE method avoids bias inherent in PCR-based transcript amplification processes. The serial analysis of short oligonucleotide tags enables approximately 50 fold more SAGE tags than ESTs to be sequenced using comparable sequencing effort. This allows greater depth of analysis which results in quantitation at high confidence levels and significantly increases the probability of detecting low abundance genes. The data from each tissue is immortalized in an electronic database which allows multiple comparisons with other tissues without repetitive wet lab procedures.
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SAGE Compares Favorably to Other Gene Expression Methods
SAGE provides expression information directly as sequence - the gold standard for genetic research. The key attributes of SAGE derive from the short tags offering high efficiency sequencing and therefore dramatically improved productivity and considerably reduced research costs over non-tag methods.
Compared to Oligo Arrays (gene chips):
SAGE is more efficient. Oligo arrays must hybridize many oligomers to assure an interpretable sequence. This limits the number of sequences that can be arrayed on any one chip. With short tags and parallel processing, SAGE is able to achieve a greater depth of tags, avoiding that problem. Furthermore, oligo arrays are incapable of discovering novel genes and are not yet readily available.
Compared to cDNA arrays (DNA chips):
SAGE is much less biased since SAGE avoids numerous PCR amplification and hybridization steps which may introduce and compound errors. Furthermore, SAGE is able to quantitate expression level differences in multiple experiments over time without requiring additional wet lab procedures. This is not true of cDNA arrays.
Compared to Transcript Imaging (EST's):
SAGE unequivocally offers a much more in-depth, comprehensive analysis where the interpretation of the results (differential expression) is backed-up with statistical significance, thereby essentially giving results that are more believable and "confirmable" by other means.
Compared to Differential Display (DD or reverse transcriptase PCR):
SAGE provides immortal data that can be queried as many times as one wishes. The big drawback with DD is non-quantitative results and a high frequency of false leads, both of which are overcome when performing a SAGE analysis.
For confirmation of these wonderful attributes you may refer to recent publications which document and demonstrate SAGE's capabilities.
SAGE allows you to work smart by saving valuable time and effort. |
