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AMDeC, University of Michigan, IDEC Pharmaceuticals, Pfizer, Tallwood Venture Capital


AMDeC Greenlights Iobion’s GeneTraffic for Key Microarray Integration Project

AMDeC, a consortium of 39 New York medical schools and research institutions, said last week Iobion’s GeneTraffic Multi software will serve as a key building block as it integrates its microarray data.

A total of 20 GeneTraffic servers will be installed across the AMDeC network, which supports an estimated 19,000 researchers. AMDeC’s microarray resource center, based at the University of Rochester, will coordinate the project and plans to use GeneTraffic Multi to handle microarray data from both Affymetrix GeneChip brand microarrays and spotted array experiments.

Andrew Brooks, director of the Functional Genomics Center at the University of Rochester Medical Center and the head of the microarray resource center, said AMDeC’s long-term plans include developing a MIAME-compliant gene expression database, which may use the EBI’s ArrayExpress as a central repository and would be capable of contributing data to the NCBI’s Gene Expression Omnibus.

“The very first step to that was to find a central analytical tool that will be available to investigators throughout the AMDeC consortium, that will allow them to store their raw data files, in addition to having access to other data sets to expand their analysis,” said Brooks.


Researchers Use Microarrays to Discover GENE Expression pattern in Prostate Cancer

Scientists at the University of Michigan Comprehensive Cancer Center have used microarrays to identify a gene called EZH2 that appears to be highly expressed in metastatic prostate cancer.

In an article published in the Oct. 10 issue of Nature, Arul M. Chinnaiyan, an assistant professor of pathology and urology at the University of Michigan medical school, said his research team used 10,000-gene cDNA microarrays to profile gene expression in prostate cancer tissue. EZH2 expression was at “the top of the list” of 55 genes found to be more active in metastatic prostate cancer than in localized prostate cancer. This is the first study linking EZH2 to solid tumors, Chinnaiyan said.

Four hundred of these tissue samples were donated by University of Michigan Health System patients who died from hormone-refractory metastatic prostate cancer.


IDEC Pharmaceuticals extends subscription to Gene Logic’s Oncology dataBASE

Gene Logic of Gaithersburg, Md., announced last week that IDEC Pharmaceuticals has extended its subscription to the GeneExpress Oncology DataSuite.

The suite includes information derived from microarray analysis of the Gene Logics tissue repository as well as bioinformatics software, content and updates, as well as training and support.

Terms of the deal were not disclosed.


Pfizer Takes stake in Canada’s ChondroGene In Osteoarthritis Discovery Collaboration

ChondroGene and Pfizer announced a collaboration for the identification of novel therapeutic targets and biomarkers for the treatment and diagnosis of osteoarthritis, the Toronto, Canada-based company said last week.

ChondroGene has created a human cartilage-specific microarray that it uses to research gene expression of the human cartilage cell.

Pfizer will access ChondroGene’s database of cartilage-specific clinical and gene expression information to search for potential novel therapeutic targets for osteoarthritis.

With this agreement, ChondroGene said it will accelerate its biomarker research program. The two-year collaboration is valued at up to $4.7 million -- without milestones and royalties. As part of the collaboration, Pfizer will buy 1.2 million shares of ChondroGene at $0.33 a share.


Tallwood Venture Capital Closes $180M Fund For Semiconductors, Related Technology

Tallwood Venture Capital of Palo Alto, Calif., announced Monday the closing of a $180 million venture capital fund focusing on investments in semiconductors and related technology.

The fund is notable here because of the presence of Reza Kasnavi, a partner with Tallwood, who formerly worked at Agilent Technologies and IBM Microelectronics, and was a researcher at the Stanford Genome Center, developing high-throughput chip technologies for DNA sequencing. Kasnavi has a PhD in electrical engineering from Stanford.


Clarification: Off by One Chromosome

Last week’s article, “Nature, Lancet Endorse MGED Data Guidelines for Microarray Experiments” contained an incorrect reference to Chris Gunter, an associate editor at Nature. “I am actually a woman,” she wrote in an e-mail message.

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.