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BIOARRAY BRIEFS: Dec 14, 2001

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Epoch Biosciences Gets ‘Groovy’ SBIR Grant for Probe Development

Epoch Biosciences, a Bothell, Wash., startup that is developing reagents and chemistries for genomics, was awarded an $872,000 Small Business Innovation Research grant from the National Institutes of Health to develop its DNA fingerprinting probes.

The two-year Phase II research grant, entitled “Rapid Genotyping with Minor-Groove-Binder-Containing Probes,” covers the development of the company’s Minor Groove Binder technology, which includes modified bases and new dyes. The technology is designed to increase the ability of oligonucleotides to detect single nucleotide polymorphisms. The grant also covers the development of multi-colored probes.

 

Rosetta Licenses Resolver to Aventis Pharmaceuticals

Adding another pharmaceutical company to its roster of customers, Rosetta Biosoftware has licensed its Resolver Gene Expression Data Analysis System to Aventis Pharmaceuticals.

The Kirkland, Wash., company released Rosetta Resolver Version 3.0, the latest version of its enterprise-wide data analysis system for microarrays. The company is a division of Merck, but functions as a separate organization, allowing it to license Resolver to a number of other pharmaceutical companies, including Bristol-Myers Squibb and GlaxoSmithKline.

 

Agilent Adds New Mouse cDNA Microarray to Portfolio of Offerings

Agilent Technologies has introduced an 8,500-gene mouse cDNA microarray kit to its portfolio of array offerings this week. This new rodent array strengthens the Palo Alto, Calif., company’s efforts to provide a product range that could eventually rival that of Affymetrix.

The mouse microarray includes Incyte clones that are sequence-verified and spotted down on glass slides using Agilent’s proprietary SurePrint inkject non-contact deposition process. The arrays use two-color labeling formats, and come in a kit of four with a hybridization buffer, a protocol, and a CD that thoroughly lists the features on the arrays.

This kit is the third microarray kit the company has rolled out since July. Agilent also offers the Human 1 cDNA and Human 2 cDNA microarray kits, which are arrays of 10,000 genes each and also use Incyte’s gene content.

In November, Agilent gained license to Incyte’s full range of gene content. This licensure occurred just after Incyte exited from the array manufacturing business, making Agilent the apparent heir to Incyte’s microarray legacy — although Motorola and others have also licensed Incyte’s gene content.

 

PerkinElmer Opens European Technical Center in Cambridge, UK

Less than a month after completing its acquisition of Packard Biosciences, PerkinElmer Life Sciences announced it was opening a centralized European Technical Center in Cambridge, UK.

Given that PerkinElmer and Packard both have facilities in the UK and a number of European countries, this announcement can be seen as an initial step toward consolidation of these offices.

Packard, however, has not yet closed down its UK facility. The new facility will offer sales and support, expanded genomics and proteomics research capabilities, and training of field engineers as well as demonstrations of instruments.

 

Molecular Staging Publishes Paper on Microarray Applications of Rolling Circle Amplification

Molecular Staging, of New Haven, CT, has published an article detailing the way that rolling circle amplification (RCA) technology can be used to detect nucleic acids in microarrays. The article, which appears in the November issue of Nucleic Acids Research, describes how RCA can be used to amplify signals on the chip without interfering between the various amplification products.

“There is a need for compatible signal amplification procedures to increase sensitivity without loss of multiplexing,” stated Girish Nallur, lead author of the paper. “The unique features of RCA make it a suitable technology for the direct measurement of nucleic acids on microarrays without the need for a biasing pre-amplification step.”

The researchers reported in this article that as few as 150 molecules bound to the microarray surface could be detected if RCA was used.

Molecular Staging has licensed RCA technology from Yale, where Yale School of Medicine associate professor of pathology Paul Lizardi developed it.

Ciphergen Packages Software with Protein Chips

Ciphergen Biosystems has rolled out its ProteinChip Biomarker System, which combines its ProteinChips and its Biomarker Patterns software for pattern recognition-based statistical analysis of protein expression levels. By packaging the software and chips together into a system, the company hopes to offer it as a solution for researchers, enabling them to query protein samples from tissues, urine, and serum.

“There wasn’t a complete package before now” said Ciphergen spokesperson Dick Rubin. Ciphergen had only started distributing this new software module for multivariate statistical analysis and for correlating biomarkers with disease condition in the past quarter.

Rubin said the new package also includes biochips with “improved performance,” meaning better reproducibility from chip to chip.

 

Canadian Candida Arrays Anyone?

The microarray lab at Canada’s National Research Council has produced a new updated version of its Candida albicans microarrays. The arrays, which include 6,100 Candida ORFs, can be orderd through the lab’s website, http://dirac.bri.nrc.ca/microarraylab/micro/products_e.html.

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.