GeneCalling

GeneCalling is a mRNA profiling technology finding increased use in the field of genomics and invented by Dr. Jonathan M. Rothberg and developed by "CuraGen" Corporation [www.curagen.com] . This genomics technique rapidly identifies candidate genes for use in drug discovery and development. Differences between gene expression in healthy tissues and disease or drug responsive tissues are examined and compared in this technology. Known as well as novel genes in any organism - most commonly humans, animals, plants and pathogens - can be detected by this open expression system.

History

On February 17, 1999 "CuraGen" was granted a patent covering its open architecture system of gene expression technology. The patent was entitled "Method and Apparatus for Identifying, Classifying, or Qualifying DNA Sequences in a Sample Without Sequencing," and covered the newly developed GeneCalling process [SeedQuest Press Release, 1999] . While most methods of analyzing gene expression to this point were closed systems such as ChIP, the open nature of this system was groundbreaking in its provision of greater flexibility through analysis of gene expression without prior sequence information as well as the ability to compare these results to a sequence database.

Methodology of GeneCalling

The steps and methodology involved in GeneCalling are illustrated in figure 1. First, mRNAs are isolated from a given sample and processed into fragments for analysis. This usually involves the synthesis and subdivision of double-stranded cDNAs from polyA RNA. Distinct sets of restriction enzymes can then be used to digest sets of the divided cDNAs and resulting fragments ligated to labelled adapters to be amplified by PCR. PCR products are then purified and subjected to gel electrophoresis on a mounted platform employing stationary laser excitation and a multi-colour charge-coupled device imaging system [Klein, Sharon et al. α5β1 Integrin Activates an NF-KB-dependent Program of Gene Expression Important for Angiogenesis and Inflammation. Molecular and Cellular Biology 22, 5912-5922: 2002] . A fluorescent label at the 5' end of one of the PCR primers allows for visualization of the PCR fragments, and the cDNAs are subjected to several isolated and identical restriction digests to generate a merged profile based on peak height and variance [Shimkets, R.A. et al Gene Expression Analysis by Transcript Profiling Coupled to a Gene Database Query. "Nat. Biotechnology" 17, 798-803: 1999] . The merged digestion profiles from the cDNA preparations are then compared to locate differentially expressed fragments (such as between normal tissue and diseased or drug responsive tissue); these profiles are compared by means of various internet-ready databases such as GeneScape [Internet database of "CuraGen" Corporation] .

Advantages and Benefits

The GeneCalling process is robust and efficient. It is well validated and requires only minimal sized samples. Furthermore, it is widespread in its scope, identifying nearly all genes in a given area of research. Beyond this, it identifies subtle changes in gene expression while maintaining reproducibility. Because it is an open expression system, no prior knowledge of sequence information is required, and the ability to share information obtained through databases allows for a complete analysis of gene and protein function [Crasta, O R. Open Architecture expression profiling of plant transcriptomes and gene discovery using GeneCalling Technology. "Methods Mol Biol". 236, 381-394: 2003] .

Means of Discovery

According to "CuraGen", GeneCalling permits scientists and researchers to make advances and breakthroughs by the following means:

• Systematically identify new and infrequently expressed genes - In the development of new therapies, such genes may serve as potential targets.

• Identify genes important in disease and drug response - With the identification of novel genes, measurement of gene activity in the context of disease or drug response can be performed and compared.

• Comparison of newly identified genes across a number of species by use of comparative genomics - A better understanding of gene function can be obtained through a comparison across model organisms and other species.

• Clarification of gene pathways - Newly identified genes are associated with specific proteins and biological pathways.

• Differentiate small changes in gene expression - A biological response to drug treatment involves critical early stage genes that can be identified.

• Information sharing - GeneCalling data can link to various databases and allow for the updating of gene lists [CuraGen Corporation. GeneCalling. 2002. http://portal.curagen.com/genecalling_portal/index.htm] .

Relevance/Function

Several peer reviewed journals have published articles with results from GeneCalling applications in human cells as well as other systems [Gene Expression Analysis by Transcript Profiling Coupled to a Gene Database Query. "Nature Biotechnology" 17, 798-803: 1999] [Expression Profiling of the Maize Flavonoid Pathway Genes Controlled by Estradiol-Inducible Transcription Factors CRC and P. "The Plant Cell" 12, 65-79: 2000] . This technique is also finding relevant application in several emerging fields of genomics including pharmacogenomics, toxicogenomics, and pharmacogenetics [Integrating Expression-Based Drug Response and SNP-Based Pharmacogenetic Strategies Into a Single Comprehensive Pharmacogenomics program. "Drug Development Research" 49, 54-64: 2000] . GeneCalling applications have led to: identification of markers of efficacy and toxicity for pharmaceutical compounds, the location of human versions of differentially expressed genes, identification of genetic variations (cSNPs), evaluation of numerous drug candidates, and discovery of potential novel therapeutics [CuraGen Corporation. GeneCalling. 2002. http://portal.curagen.com/genecalling_portal/index.htm] .

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