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Caliper Technologies, Karolinska Institute, National Human Genome Research Institute, MWG Biotech, Bruker Daltonics, Leiden University Medical Center, Affymetrix, Arcturus Bioscience, DNA Print Genomics, Esoterix


Caliper Technologies Slashes 12 Percent of Workforce; Reorganizes Management Team

Caliper Technologies has further reduced its workforce, cutting 12 percent, or 65 people — including seven vice presidents — from its payroll as part of a restructuring following it acquisition of Zymark in July, the company said last week.

Caliper said it will also make some hires to accommodate the transfer of certain functions to the company’s Hopkinton, Mass., headquarters, “and to add skill sets which will support the company’s strategic direction.”

Caliper said that this round of layoffs and reconfiguration focuses on rationalizing R&D resources. The company hopes to reach cash-flow breakeven by the end of 2005, it said.

Karolinska Institute, NCI to Validate Non-synonymous Coding SNPs

DynaMetrix, the Karolinska Institute Cancer Genome Anatomy Project, and the US National Cancer Institute will validate probable causal SNPs from among public-domain SNPs that underlie differences in protein sequences between individuals, the groups said this week.

These non-synonymous coding sequence differences, or ns-cSNPs “probably cause much of the variation between individuals” from the perspective of disease risk and drug response, “but in practice many of the [more than] 25,000 predicted ns-cSNPs in public databases are not real or not usefully abundant in typical human populations,” the groups said.

To make this SNP class accessible to researchers, DynaMetrix will use its DASH-2 genotyping and diagnostic systems to validate ns-cSNPs in sets of 12, using African-American and Caucasian individuals [read about the DASH technology in 1/24/03 SNPtech Reporter.] After that, DASH will be used to determine allele frequency distributions in a large range of global populations in order “to detect evidence of possible evolutionary selection, indicative of functional importance.”

The project will be overseen by Anthony Brookes, who is also a co-founder of DynaMetrix. He said data from this project, which “is already well under way,” will be placed in the public-domain on the CGAP website (readers may access it here).

TGen, Mayo, Scottsdale To Build $25M Facility

The Translational Genomics Research Institute, the Mayo Clinic, and the city of Scottsdale, Ariz., will launch a $25 million research facility as part of Arizona’s push to pull in the biotech industry, the groups said last week.

The Scottsdale city council has just decided to award Tgen $3 million from the city to help start the plant, which would open at the end of 2004, according to a local report Wedesday from the Arizona Republic. This award will allow Tgen to house its Center for Translational Drug Development in the new building. Mayo and other leasing companies would use the other parts of the building.

NHGRI Forms New Social and Behavioral Research Branch

The National Human Genome Research Institute has created a new branch within its Division of Intramural Research that will translate genomics into interventions for health promotion and disease prevention, and will counsel patients with genetic disorders and their families.

The new branch, which will be called the Social and Behavioral Research Branch and be part of a new trans-NIH center called the Social and Behavioral Science Center, will also house staff from the National Institute of Mental Health and the Office of Behavioral and Social Sciences Research, in addition to the entire NHGRI branch. Heading the new branch and the inter-institute center will be Colleen McBride, director of the cancer prevention, detection and control research program at Duke University.

McBride listed four “conceptual domains” that the new division will cover: testing communications strategies aimed at relaying an individual’s risk for developing a genetic condition; developing and evaluating interventions aimed at reducing genetically susceptible individuals’ risk of acquiring a disease; translating genomic discoveries to clinical practice; and understanding the social, ethical, and policy implications of genomic research.

The inter-institute center is slated to open in January 2005, according to NHGRI director Francis Collins.

Irish Research Center Taps MWG Biotech to Outfit New Microarray Lab

Munich-based MWG Biotech will help the Alimentary Pharmabiotic Centre at University College Cork, a new Science Foundation Ireland research center based in Teagasc, Ireland, to help it create a microarray facility, the groups said last week.

Terms of the deal call for MWG to supply the APC with “the full range of its products and services,” namely its instrumentation, microarray, and bioinformatics expertise. MWG will also provide the bioinformatic design, oligonucleotides, microarrays, and support.

The “long term” deal will have APC buying a “substantial volume” of products from MWG “in the forecoming months,” the groups said. Financial details were not disclosed.

The APC employs 50 scientists and clinicians who investigate the means by which bacterial flora in the gastrointestinal tract influence health and disease.

The research interests of the APC include host and bacterial gene expression in pathogenesis, bacteria or virus-host interactions, and immunological interactions, according to the center.

Bruker Daltonics, Leiden University Medical Center, Pen Protein Biomarker Alliance

Bruker Daltonics and the Leiden University Medical Center will collaborate to discover proteomic bio- markers, the groups said last week.

For the agreement, which extends a previous collaboration between the two groups, the LUMC bought from Bruker four mass spectrometry systems and certain clinical proteomics sample preparation tools and bioinformatics platforms.

LUMC said it will “provide feedback” to Bruker Daltonics on the instrumentation, methods, and software development for clinical research.

Specifically, LUMC’s glycoproteomics group has bought from Bruker an Esquire HCT ion trap mass spectrometer for glycan analysis. Additionally, another HCT ion trap will be used for “proteomics work in general,” LUMC said.

“We have had a high degree of success with our Ultraflex TOF/TOF mass spectrometer, and are now adding a second one,” the lab said in a statement. It will be installing an Apex-Q 9.4 Tesla hybrid Q-q-FTMS system with the ESI/MALDI Combisource, and an ECD/IRMPD accessory for post-translational modifi-cation studies. The lab said it will use the APEX-Q and the second Ultraflex TOF/TOF for clinical proteomics and glycoprotein research.

Rob Tollenaar, principal investigator in LUMC’s department of surgery’s translational research project, said his team will use the mass-spec tools “within the framework of our ... diagnostic and prognostic biomarker research program for the analysis of serum and tissue samples.” His lab’s research is focused on the improvement of surgical cancer treatment, especially for colorectal, breast, and gastric cancer, as well as cancer diagnosis.

Affy, Arcturus to Co-develop Gene Expression Tools for Paraffin-Embedded Samples

Affymetrix and Arcturus Bioscience plan to co-develop new tools to enable researchers to analyze gene-expression data on paraffin-embedded clinical biopsy samples, the firms said last week.

Terms of the deal call for Arcturus Paradise reagents, which the company developed to extract and amplify RNA from paraffin-embedded tissues, to be adapted for use in gene expression analysis with Affy’s new GeneChip human genome X3P array.

In recent decades, hospitals have been collecting millions of clinical tissue samples. The current procedure for preserving these samples involves immersing tissue in formalin and embedding it in paraffin wax. “Until now, researchers thought that this formalin-fixed, paraffin-embedded preservation process destroyed, modified, or degraded the nucleic acids, specifically the DNA and RNA, in biopsy samples, precluding gene expression analysis,” the companies said.

Through this collaboration, Affy’s X3P array will enable researchers to study approximately 44,000 human gene transcripts in paraffin-embedded biopsy samples, according to Alan Dance, senior vice president of Affymetrix’ applications business unit. He added that the X3P array “is specifically designed to detect shorter RNAs, which are common in these types of samples.”

DNA Print Secures $8M In Debt Financing

DNA Print Genomics said today that La Jolla Cove Investors has committed to invest up to $8 million in the company over the next two years.

The transaction, which is subject to regulatory approval, involves a commitment of $400,000 per month over twenty months, and is a debenture convertible into common stock and warrants to purchase common stock.

DNA Print, of Sarasota, Fla., said it will use the financing to hire personnel, expand its operations including its clinical pharmacogenomics program, and pursue business in pharmacogenomics, forensic, and consumer products.

Esoterix Opens New Molecular Diagnostic Facility in California

Esoterix has completed a new molecular diagnostic-testing center in California. The facility, Calabasas Hills, will offer a range of molecular-based diagnostic assays. It will create expanded testing capabilities for Esoterix, and will also deliver improvements in assay performance, sample handling, and turnaround times, the company said.


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The Scan

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Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.