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Genzyme, JMF, NHGRI, Affy, EIF, Wellcome Trust, Sanger, Perlegen, GlaxoSmithKline, Stratagene, Innogenetics, Third Wave, ABI


Genzyme Launches EGFR Mutation Diagnostic

Genzyme said last week in a statement that it had launched a laboratory test to help identify patients likely to respond to some non-small cell lung cancer therapies targeted to the epidermal growth factor receptor.

Some studies have linked EGFR mutations to response to drugs like Iressa and Tarceva, but the link has not been widely accepted, and the US Food and Drug Administration has not changed the label of either drug to recommend testing.

JMF, NHGRI to Develop Newborn Screening Tests on Affy Platform

The Jeffrey Modell Foundation, a nonprofit devoted to researching pediatric immunodeficiency disorders, and the National Human Genome Research Institute intend to co-develop a post-natal screen for primary immunodeficiency based on Affymetrix's microarray platform, the three partners said this week.

NHGRI will take the lead in developing the test, which will look for a form of DNA that is found in children with healthy immune systems. If the test results are unusual, a second test based on Affy's platform will screen for specific biomarkers associated with immunodeficiency.

JMF will fund the project. A time table for when the tests would become available was not discussed.

EIF to Fund Breast Cancer Biomarker-Discovery Project

Seven biomedical-research institutions will use a three-year, $9 million award from the Entertainment Industry Foundation's Women's Cancer Research Fund to discover biomarkers associated with early stage breast cancer, the EIF said this week.

According to the EIF, the philanthropic arm of the entertainment industry, the seven partners have joined together to form the EIF/WCRF Breast Cancer Biomarker Discovery Project.

The project will be led by researchers at the Fred Hutchinson Cancer Research Center, and will also include the Pacific Northwest Research Laboratory, Dana Farber Cancer Institute, the University of Southern California's Norris Comprehensive Cancer Center and Hospital, the Institute for Systems Biology, the Broad Institute, and the University of Texas' M D Anderson Cancer Center, the EIF said.

Wellcome Trust, Sanger, Perlegen, and Affy to Genotype 15K Samples in Search of Complex Disease Genes

The Wellcome Trust Case Control Consortium, the Wellcome Trust Sanger Institute, Perlegen Sciences, and Affymetrix will jointly search for genes associated with 10 complex diseases, the partners said this week.

The consortium plans to study 11,000 samples to find genes associated with coronary heart disease, hypertension, types 1 and 2 diabetes, bipolar disorder, Crohn's disease, rheumatoid arthritis, and tuberculosis. The Wellcome Trust Sanger Institute will analyze an additional 4,000 samples to find the genetic origins of diseases such as types 1 and 2 diabetes, obesity, and malaria.

Perlegen will genotype the 15,000 individuals, producing more than 10 billion genotypes, using Affmetryx's microarray technology, including the Human Mapping 500K array set.

The WTCCC is a team of 24 human geneticists at a number of UK institutions, including the Wellcome Trust Sanger Institute, Leicester University, Cambridge University and Oxford Unviersity.

Perlegen, Using Affy Arrays, to Assay SNPs for Merck

Perlegen will provide genotyping services to Merck to find DNA variations with relevance to drug discovery, the company said this week.

Under the agreement, Perlegen scientists will assay up to 675,000 SNPs in more than 1,000 DNA samples from individuals "with important clinical characteristics" provided by Merck.

Perlegen will use Affymetrix microarrays, including the GeneChip Human Mapping 500K array set. Merck will integrate the results with in-house data from molecular profiling of tissue samples.

The companies did not disclose the terms of the agreement.

GlaxoSmithKline to Use Affy Arrays in Whole Genome-Association Studies

GlaxoSmithKline will use Affymetrix microarrays to find genetic variations associated with diseases, Affymetrix said this week.

Under the agreement, GSK will use Affy's GeneChip Human Mapping 500K array set to perform whole-genome association studies across tens of thousands of samples.

Court Permanently Bars Stratagene from Selling FullVelocity Products; Company Vows to Appeal

A US district court has permanently barred Stratagene from selling its FullVelocity QPCR and QRT-PCR products, which the court said infringe two patents held by Third Wave Technologies, Third Wave said last week.

The injunction, issued by the US District Court for the Western District of Wisconsin, prohibits Stratagene from manufacturing, selling, and offering these or any other products that violate Third Wave's US patents Nos. 6,090,543 and 6,348,314. Stratagene must also notify its customers and collaborators about the infringement.

Earlier this month, a jury found that Stratagene willfully infringed Third Wave's patents and awarded Third Wave $5.29 million in damages. Third Wave, which filed the suit last September, said it is seeking additional damages and expects a decision by the court by the end of the year.

Stratagene said today in a response that it intends to file an appeal in the Court of Appeals for the Federal Circuit in Washington, DC, "as soon as practicable." The company will seek to have the injunction lifted and the damages reduced or eliminated.

On May 6, Stratagene countersued Third Wave in the US District Court for the District of Delaware, which is still pending, claiming that Third Wave infringes its Full Velocity technology. Stratagene seeks monetary damages and a permanent injunction to prevent Third Wave from selling its Invader Plus products.

Stratagene reiterated today that its infringing Full Velocity products have contributed less than $400,000 in revenues since they were made available last year, and that other embodiments of the FullVelocity technology do not infringe Third Wave's patents.

Innogenetics Sues Third Wave, Abbott for Infringing Its HCV Genotyping Technology

Innogenetics is suing Third Wave Technologies and Abbott Laboratories for infringing its hepatitis C virus genotyping patents, the Gent, Belgium-based company said last week.

In the suits, filed with the US District Court for the Western District of Wisconsin, Innogenetics claims that both Abbott and Third Wave have been infringing its US Patent No. 5,846,704, which covers a process for typing HCV isolates. Both companies have refused to take a license to the technology, according to Innogenetics. The company said it expects a ruling within 12 months.

Third Wave and Innogenetics have been partners since at least April 2004, when the two companies signed a four-year marketing and distribution agreement, under which Innogenetics distributes a number of Third Wave's Invader molecular diagnostic products exclusively in Europe.

ABI, Breaking Silence, Says It Is Working on Next-Generation Sequencing Technologies

Applied Biosystems President Cathy Burzik acknowledged last week that the firm is working on next-generation DNA sequencing technologies, but said the company is not ready to provide details.

ABI has "a number of approaches under development," she said during a Q&A session following her presentation at the UBS Global Life Sciences Conference, held here this week. Burzik said a "cluster approach" was one possibility for development, but she declined to provide further details, saying that the firm is working on patent filings.

Company officials have been asked frequently over the past year about whether ABI is developing any technologies that would eventually replace its capillary electrophoresis sequencing instruments. Industry insiders also are keen to learn whether ABI plans to partner with or acquire one of the many firms developing alternative sequencing technologies. Up until now, ABI had declined to answer those questions.

At the JP Morgan Healthcare Conference in San Francisco in April, Burzik said that the firm had identified 35 companies that were developing the alternative approaches, such as single-molecule sequencing and DNA clustering efforts. 454 Life Sciences, Agencourt Bioscience, Solexa, and Helicos BioSciences have the most advanced of these new technologies, with instruments either placed or soon to be placed at major research institutions.

However, these newer technologies are still several years away from delivering on the promise of the $1,000 genome. Lee Hood, president of the Institute for Systems Biology, recentlytold GenomeWeb News, "My guess is that within 10 years there'll be new nanotechnology approaches that will ... make the human genome well under $1,000."

Burzik reiterated on last week ABI's belief that the newer technologies are not going to make an impact over the next couple of years, and the firm does not see an end to the dominance of capillary electrophoresis in the DNA sequencing market. "We're very committed to sequencing," she said, noting that the firm has more than 12,000 capillary electrophoresis instruments installed worldwide.

Affy Warns that Low Manufacturing Yields Will Lead to $10M-12M Shortfall in Q3 Revenues

Affymetrix said last week that "low initial-production yields" of its 500K Mapping Array Set will result in a revenue shortfall of $10 million to $12 million for the quarter ended Sept. 30, or as much as 13 percent below its previous guidance of $92 million in product-related revenues for the quarter.

In a conference call following the announcement, Greg Schiffman, senior vice president and CFO, said the company had a "little bit of a hiccup with our ability to ramp production and get yields to where we need to have them" during the quarter. He said that the manufacturing issue affected only the 500K chip.

"While we have recently seen improving yields, these improvements occurred late in the quarter and we now project that we will be unable to manufacture enough product to meet our revenue target," CEO Stephen Fodor said in a statement.

Affymetrix officials said during the conference call that they plan to expand the company's manufacturing plant in Sacramento, Calif., by 60 percent through 2006, and that they also plan to open a new plant in Singapore next year.


Filed under

The Scan

Wolf Howl Responses Offer Look at Vocal Behavior-Related Selection in Dogs

In dozens of domestic dogs listening to wolf vocalizations, researchers in Communication Biology see responses varying with age, sex, reproductive status, and a breed's evolutionary distance from wolves.

Facial Imaging-Based Genetic Diagnoses Appears to Get Boost With Three-Dimensional Approach

With data for more than 1,900 individuals affected by a range of genetic conditions, researchers compared facial phenotype-based diagnoses informed by 2D or 3D images in the European Journal of Human Genetics.

Survey Suggests Multigene Cancer Panel VUS Reporting May Vary Across Genetic Counselors

Investigators surveyed dozens of genetic counselors working in clinical or laboratory settings, uncovering attitudes around VUS reporting after multigene cancer panel testing in the Journal of Genetic Counseling.

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.