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IIlumina and UCSD Partner for Study, Modified Oligo Anchoring Technology, Third Wave Cuts Oligo Supply Operations

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Hairpins or Straight Pins?

 

In the April 15 issue of Nucleic Acids Research, Gianluca De Bellis and colleagues from Segrate, Italy, describe a modified method for anchoring oligonucleotides on a glass slide and using the resulting microarray for enzyme-based mutation detection.

The original method, published in NAR by scientists at Amersham Pharmacia Biotech last year, involves oligonucleotide hairpins with multiple phosphorothioates along the loop that are coupled to glass slides pre-activated by bromoacetylation.

Using a ligation reaction instead of minisequencing as the readout, the Italian scientists tested the influence of several variables on the strength of the fluorescent signal. These included the number of phosphorothioate anchoring points on the oligo and the usage of hairpin versus linear oligonucleotides. They found that more anchoring points increased the signal intensity, and that hairpin oligos were not superior to linear probes. Phosphorothioate-modified oligos, they wrote, are “simple to obtain and cheaper” than the more common aminolinkers, and bromoacetylated surfaces are “stable, do not require particular storage conditions and react quickly with phosphorothioates.”

 

Sweet Home Alabama

 

Invitrogen’s decision last week to close its Huntsville, Ala. facility will disrupt life as usual not only for the workers at that facility who were laid off, but also for IntegriDerm, a small specialty microarray company that occupies space in the facility.

As of press time, IntegriDerm founder and CEO Thomas Dooley was “in discussions” with Invitrogen on this matter.

IntegriDerm manufactures the DermArray, a 5,500-spot microarray with a subset of genes related to skin disease, and PharmArray, a microarray focused on target genes for pharmaceutical development.

Dooley said he thought that the planned closing of the Huntsville plant would not affect the availability of DermArray and PharmArray sales and service projects.

 

Spectral Seeks Material

 

Spectral Genomics of Houston is looking for $12 million in additional financing, in a round that is due to close this summer.

The company develops genomic microarrays in which a patented chemistry of BAC clones with linkers forms a tight covalent bond to the naked glass. The core technology underpinning these arrays was developed by Allen Bradley and Wei-wen Cai, two researchers at Baylor College of Medicine who serve as scientific advisors to the company.

Spectral closed its initial fundraising round in early 2001 with an undisclosed sum from Burrill & Company, BMCT, and Baylor College of Medicine.

 

Illumina Snags Neighbor UCSD for SNP Deal

 

Bead array maker Illumina has teamed up with neighbor University of California San Diego to provide the university’s laboratory of psychiatric genomics with SNP genotyping services.

Illumina will use its fiber optic BeadArray technology to genotype specified samples provided by the laboratory. The company will look at specified SNPs, identify additional potential SNPs and design functional assays for the SNP loci. Many of these SNPs are located on chromosome 22, which is believed to be associated with bipolar disorders and schizophrenia, according to Illumina.

The study is funded by the Department of Veteran Affairs.

 

CombiMatrix Sells System in Japan

 

CombiMatrix KK, the Japanese subsidiary of CombiMatrix, has sold its gene chip synthesizer to the Computational Biology Research Center, a division of the Japanese National Institute of Advanced Industrial Science and Technology.

CombiMatrix, a subsidiary of Squolamie, Wash.-based Acacia Research, makes semiconductor-based microarrays with spots called “virtual flasks.”

Under the agreement, the center also has access to CombiMatrix’s informatics tools.

“We investigated several technologies currently on the market and found that the CombiMatrix system best suited our needs from the flexibility, customization and cost standpoint,” said Yutaka Akiyama, Director of the CBRC, in a statement. “The CombiMatrix technology will help us to quickly verify many of our predictions and to make fast changes to our programs as well as quickly reiterate experimental design.”

CombiMatrix KK, a joint venture between CombiMatrix and Marubeni, is the subsidiary and exclusive supplier of CombiMatrix products in Japan.

 

Licenses, Licenses

 

Swiss bioinformatics company GeneData’s US subsidiary has licensed its enterprise microarray analysis software, GeneData Expressionist, to Stanford University School of Medicine.

Stanford researcher Thomas Quertermous plans to use the system in data analysis of vascular disease microarray studies with 45,000-gene mouse chips. ”The ability of Expressionist to handle data from different microarray formats is critical for our analysis of the data emerging from parallel studies we are conducting in mouse and human,” said Quertermous.

Meanwhile, the Rosetta Biosoftware division of Merck has licensed the Rosetta Resolver gene expression analysis system to Japan’s National Institute of Radiological Sciences.

NIRS will use the Rosetta software for research into radiation therapy of malignancies and radiation-based disease diagnostics.

This is Rosetta Biosoftware’s first license in Asia Pacific.

 

Wave Goodbye

 

Third Wave of Madison, Wis., said this week it will focus its 25 percent staff cut on its oligonucleotide supply operations.

The company “is currently exploring several probe-supply alternatives, such as spinning off, outsourcing and/or otherwise divesting portions of its lower-margin probe manufacturing operations …,“ a company spokesman told BioArray News’ sister publication GenomeWeb.

Third Wave, which announced the staff reductions last week, had a headcount of roughly 300 people at the end of 2001. A spokesman said that while the layoffs were “across the board,” they do not forecast a departure from genomics research and that all of its product development activities will continue.

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