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Affy to Launch Exon Arrays in Second Half of Year

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Affymetrix plans to launch a host of new expression arrays in either the third or fourth quarter of this year, an official said at the Molecular Medicine Tri-Conference held in April in San Francisco. Affy currently offers an array for Arabidopsis, a model plant organism, that can generate expression profiles for mRNA transcripts, but the new product line will represent Affy’s first foray into the emerging exon array market.

Exon arrays enable scientists to generate expression profiles for splice variants in a genome. Alternatively spliced mRNA is of interest to researchers and drug makers, and in some cases human diseases have been associated with splice variants. John Blume, the company’s vice president of expression research, said that by analyzing the expression of the complete genome with exon arrays, researchers would have a better chance of developing drug targets to be used in diagnosing or crafting therapies for disease. “It’s the transcriptome expression, not the gene expression,” Blume said during his presentation.

According to Blume, Affymetrix has created exon arrays for the human, mouse, and rat genomes, all of which will be made available to customers before the end of the year. Arrays for these organisms will come out at the same time, he added. Software is being developed with early access customers for exon array use, and in the future Affy plans to offer splice variant analysis as well as whole transcriptome analysis as part of the offering, Blume said.

In a conference call with investors, Affymetrix CEO Stephen Fodor said the human exon array will contain around 6.5 million probes that will analyze splice variants of approximately 1 million exons. “We believe that this product will fundamentally redefine our understanding of how tens of thousands of genetic elements can code for hundreds of thousands of proteins,” said Fodor.

—Justin Petrone

 

PATENT WATCH

US Patent 6,887,665. Methods of array synthesis. Inventors: Mark Trulson, Glenn McGall, Jacqueline Fidanza. Assignee: Affymetrix. Issued: May 3, 2005.

The patent covers methods of forming high-density arrays of peptides, polynucleotides, and other polymer sequences using combinatorial solid-phase synthesis. The described method for synthesizing high-density arrays employs radiation-labile protecting groups and photolithographic masks to achieve spatially defined combinatorial polymer synthesis on a substrate surface. In those embodiments, masks are used to control the selective exposure to radiation in specific locations of a surface provided with linker molecules containing radiation-labile or chemically labile protecting groups.

 

US Patent 6,889,143. Methods and systems for estimating the melting temperature for polynucleotide molecules. Inventors: Mark Behlke, Lingyan Huang, Richard Owczarzy, Joseph Walder. Assignee: Integrated DNA Technologies. Issued: May 3, 2005.

The patent covers methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, particularly duplexes of oligonucleotides that may be used as primers or probes in PCR or hybridization assays. The invention also relates to methods and systems for designing and selecting oligonucleotide probes and primers having a predicted melting temperature which is optimized for such assays. The patent also covers algorithms and methods for predicting the melting temperature of a nucleic acid having a predetermined sequence.

 

Datapoint

47,400

System Biosciences announced in May that its GeneNet siRNA Library offers researchers access to libraries that target 47,400 human or 39,000 mouse transcripts.

 

The priority project for Trans-Big, an EU-wide breast cancer network, will be MINDACT — Microarray in Node-Negative Disease May Avoid Chemotherapy — a consortium-wide trial to use microarray technology to develop biomarkers for selecting those patients who need chemotherapy and those who can do without.

 

One year after it released an array-based in vitro diagnostic for periodontal disease, Greiner Bio-One plans to launch an in vitro diagnostic for cervical cancer called PapilloCheck, a microarray-based IVD for cancer of the cervix.

 

Asterand will include CompuCyte’s quantitative cytometric analysis of tissues and tissue microarrays as a part of its current research molecular pathology services.

 

Exiqon has signed a licensing agreement with Thermo Electron to allow the company to produce and supply locked nucleic acids, which can be used for microarray-based expression profiling, SNP detection, and genotyping.

 

NCI will evaluate Ciphergen’s ProteinChip Series 4000 platform as part of an effort to identify technology capable of detecting protein patterns that can classify cancer states, particularly with respect to ovarian cancer.

 

Gene expression assay technology firm HTG has closed a series B financing round worth $3.4 million. That brings the firm’s total VC funding to $4.6 million.

 

 

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