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Children's National Medical Center, BioTrove, DNAVision, Luminex, UCSF, Affymetrix, Genzyme, Moffitt Cancer Center, Third Wave Technologies, Qiagen, Primera Biosystems

Children's National Medical Center to Use BioTrove Genotyping Platform in Studies
Researchers at the Children’s National Medical Center in Washington, DC, will use BioTrove’s OpenArray SNP genotyping system to investigate genes associated with diseases such as diabetes and skeletal muscle hypertrophy, the company announced this week.
The center anticipates that the OpenArray system, which generates hundreds of thousands of SNP and qPCR data points each day, will expedite its determination of the genes influencing disease states in young patients.
“The high-throughput OpenArray system enables us to process samples in weeks instead of years, and its high accuracy helps conduct in-depth research without depleting our precious DNA samples,” said Eric Hoffman, director of Children’s National Research Center for Genetic Medicine.
The technology will be applied to several NIH-funded projects, including a collaboration with Howard University researchers aimed at assessing pre-symptomatic risk factors for early onset type 2 diabetes in African-American children.

DNAVision to Offer Genotyping Services on Luminex Platform
Brussels-based DNAVision said this week that it is now offering DNA genotyping services using the Luminex xMAP platform.
The firm said that the xMAP technology expands its current offerings and enables it to provide custom SNP genotyping for medium- to large-scale studies.
DNAVision did not disclose any financial terms associated with use of the Luminex platform.

UCSF Team Identifies 18 SNPs Linked to MS Therapy Response
Researchers have identified a set of 18 SNPs that may explain why some individuals respond better to a widely used multiple sclerosis treatment than others.
Researchers from the University of California, San Francisco, used Affymetrix 100K SNP arrays to identify specific mutations associated with better responses to interferon beta therapy for MS. Their findings appeared this week in the online version of Archives of Neurology.
According to the National Institute of Neurological Disorders and Stroke, approximately 250,000 to 300,000 Americans suffer from multiple sclerosis, a degenerative disease caused by a progressive loss in the coating surrounding the nerves that leads to muscle weakness and, sometimes, paralysis. To date, there is no cure for MS and around 80 percent of individuals with the disease eventually end up disabled.
While treatment with interferon beta has been shown to slow disease progression, the treatment is not effective for all patients — roughly half of those who receive interferon beta therapy relapse or continue deteriorating. In addition, the risk of adverse side effects for the treatment, ranging from flu-like symptoms to depression, is high.
In an effort to solve this problem, the researchers followed for two years a group of individuals with the most common form of MS, known as relapsing-remitting MS, as they received interferon beta therapy. Then researchers conducted genomic comparisons between treatment responders and non-responders to try to get an “unbiased detection of DNA variants associated with interferon beta therapy response.”
Of the 206 Southern European individuals tested, 99 responded well to the therapy, and 107 didn’t. By pooling and comparing DNA that had been hybridized to Affymetrix 100K GeneChips, the team identified dozens of candidate small nucleotide polymorphisms that were associated with a positive response to the interferon beta treatment.
After narrowing down the field to the most likely 35 candidate SNPs, the team added more than 80 individuals to the study, looking patient-by-patient to determine whether those SNPs continued to correspond to better outcomes following interferon beta therapy. The researchers found that 18 of the 35 SNPs were significantly associated with positive interferon beta treatment response.
Of these 18 mutations, seven lie within genes and the remainder are in non-coding regions. The researchers found that the top-ranked SNPs that differed between responders and non-responders were related to glutamate and gamma-aminobutyric acid receptors — a “provocative” finding that suggests a link between neuronal excitation and the effect of interferon beta therapy, but one that requires further study, the authors said.
While the authors note that additional research needs to be done to further validate the study and understand the functional role of interferon beta, the work has the potential to change the approach to MS treatment from a game of hit-and-miss to a more systematic, personalized plan of attack.
“The identification of pharmacogenetic polymorphisms provides important new insights into the mechanism of interferon beta action,” the authors noted, “bringing the paradigms of rational drug design and personalized medicine one step further.”

Genzyme Licenses Dx Rights to Moffitt Proteins for Lung Cancer Test
Genzyme has licensed the diagnostic testing rights to two proteins from the Moffitt Cancer Center that it plans to develop into tests that could help predict patients’ response to non-small cell lung cancer treatments, the company said this week.
Tampa, Fla.-based Moffitt, designated a Comprehensive Cancer Center by the National Cancer Institute, has found that the proteins RRM1 and ERCC1 may help to predict the effectiveness of NSCLC treatments, because the expression levels of the proteins correlated to responses to two common drugs.
Genzyme said it will develop and market a diagnostic test to measure the expression level of these proteins in NSCLC patients in order to help direct doctors trying to make first-line treatment decisions. Cambridge, Mass.-based Genzyme will provide Moffitt with milestone payments and royalties from the sale of any licensed products or services stemming from the research.
Genzyme’s national medical director, Bruce Horten, said the first-line treatment step for NSCLC is “a key decision point in the management of patients for whom getting the right drug as quickly as possible is critical.”

Court Dismisses Third Wave's Antitrust Case Against Qiagen; HPV Patent Litigation Still Ongoing
Qiagen said last week that a US district court has dismissed an antitrust suit that Third Wave Technologies filed against it last year as part of an ongoing legal battle over human papillomavirus testing technology.
Qiagen said that the US District Court for the Western District of Wisconsin has granted its Qiagen Gaithersburg subsidiary, formerly Digene, summary judgment on the antitrust counterclaims.
Judge Barbara B. Crabb ruled that Third Wave had "failed to show any violations" by Qiagen of antitrust laws, Qiagen said.
The ruling came on the first anniversary of the legal dispute, which began when Digene filed suit against Third Wave for infringing US Patent No. 5,643,715, entitled “Human Papillomavirus Type 52 DNA Sequences and Methods for Employing the Same.” The patent is assigned to Georgetown University and has been exclusively licensed to Digene.
In March, Third Wave countersued for “monopolistic abuse,” noting that its claims were “based on Digene’s repeated abuse of its substantial market power … and the direct and substantial antitrust injury to Third Wave and consumers resulting directly from Digene’s anti-competitive conduct.”
In July, the Wisconsin court agreed with Third Wave’s definitions for each of the disputed patent claims in its suit against Digene and denied a request by Digene to reconsider the ruling. Qiagen officials later said they planned to appeal the claims-construction ruling.
Peer Schatz, CEO of Qiagen, said in a statement Friday that the ruling regarding the antitrust counterclaims “makes clear that Qiagen's leadership in the marketplace for HPV testing is the result of the trust we have earned with our customers based on the quality and performance of our molecular diagnostic solutions for HPV, our products' overwhelming clinical validation, and the fact that we are the first and only company to have received FDA approval for our molecular HPV test."
The company cited Crabb's ruling, which stated that Qiagen "is selling a product that many customers prefer over the product defendant is selling, with the not surprising result that defendant has not captured as many customers as it wishes it had."
In response, Third Wave Technologies President and CEO Kevin Conroy said in a statement this week, "We respectfully disagree with the court's ruling Friday on our anti-trust claims and are considering our options."
He added that Third Wave had "won the most important battle in our dispute with Digene last October when Digene said it couldn't win its patent suit unless it successfully appealed the court's Markman order that constructed the patent claims at issue in Third Wave's favor."
Qiagen said it will “continue to aggressively pursue its pending patent litigation, in which Qiagen alleges that Third Wave is infringing on Qiagen intellectual property.”

Primera Raises $21M To Support Development of PCR-Based Dx System
Primera Biosystems said last week that it has raised $21 million in series B financing that it will use to develop diagnostic instruments and reagent kits for clinical research.
The funding round was led by Abingworth and included investments from Interwest Partners, Malaysian Technology Development Corporation, MPM Capital, Burrill & Company, and the Invus Group.
Primera is developing the Scalable Target Amplification Routine platform, or STAR, a bench-top quantitative real-time PCR system.
The company is also developing an assay to measure multiple viral agents to cause infections in immune comprised patients and a multiplex fungal test, both using the STAR system.

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