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Can Dxs Thin Down Microarrays for the Clinics?

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“This is the counterrevolution against systems biology, and it’s thin slicing,” Francis Barany, keynote speaker at the Feb. 17 Clinical Genomics meeting, said.

By that comment, Barany, a professor of Microbiology and Immunology at Cornell University’s Weill College of Medicine, summarized what he sees as a step critical to getting molecular diagnostics for tumors into the clinic and the minds of doctors. The term “thin slicing,” popularized by author Malcolm Gladwell, and which Gladwell credits to the field of psychology, refers to the ability of humans to grasp their environment using a tiny amount of information. In the context of Barany’s comments, it refers to the paring down of microarray expression data to its barest essentials. Just as importantly, physicians need a reliable and cheap mutation-detection platform, Barany said.

A key part of the argument is that doctors really have little use for the deluge of information that arrays provide. That extra data can even work to prevent molecular diagnostics from entering the clinic, said Barany. “People complain that physicians are too conservative. It’s not true. They won’t allow new information into the clinic that doesn’t help the patient — you can’t treat a 30,000-gene expression profile,” he said. The cost of microarrays is another major barrier, he added.

To be sure, Barany has an interest in promoting a simplified approach. He is the director of an international colon cancer research consortium that has been developing mathematical approaches to separate useful expression data from the chaff. A novel universal DNA array he and collaborators developed — featuring PCR-ligase detection reaction and endonuclease V-ligase mutation scanning — should “allow clinicians to use simpler and more cost-effective techniques … to verify the clinical significance of various markers,” he said.

Ultimately, the plan is to develop sensitive, point-of-care devices for physicians to identify tumor-related mutations on site, said Barany.

— Chris Womack

 

PATENT WATCH

 

US Patent 6,861,256. Therapeutic and diagnostic tools for impaired glucose tolerance conditions. Assignee: The General Hospital Corporation. Inventors: Gary Ruvkun, Scott Ogg. Issued: March 1, 2005.

This patent covers novel genes and methods for the screening of therapeutics found to be useful in the treatment of impaired glucose tolerance conditions, according to the abstract, in addition to diagnostics and therapeutics for identifying or treating those conditions.

 

US Patent 6,861,220. Genetic screening methods. Assignee: Ramot University Authority for Applied Research & Industrial Development. Inventors: Dan Canaani, Arnold Simons, Naomi Dafni, Iris Dotan. Issued: March 1, 2005.

This patent covers a method for screening molecules to identify any which would have a synthetic lethal property when combined with a particular gene carrying a non-lethal mutation, according to the abstract. The method covers steps beginning with transfecting a reporter gene into mammalian cells through to growing cells and screening for molecules with lethal properties.

 

Datapoint

$74 million

Series D financing round raised by Perlegen Sciences with new and previous investors. The money will go toward the company’s pipeline of late-stage drugs, according to Perlegen.

 

The long-awaited guidelines for voluntarily submitted pharmacogenomics data were expected to be made public by FDA in mid-March, the agency announced earlier the same month. The original document was released as a draft in November 2003, and the formal document has been anticipated for several months.

 

In other FDA news, a recently issued genotyping guidance could stand to ease the process for molecular diagnostics companies to design and get approval for array-based tests to predict drug metabolism.

 

The Translational Genomics Research Institute has teamed up with Kronos Science Laboratories for a joint Alzheimer’s research study, an 18-month effort to examine some 570,000 SNPs from people with and without the disease. The program is expected to cost $6 million.

 

Sequenom announced that a team of researchers using its MassArray genotyping tool had uncovered a gene mutation linked to age-related macular degeneration. Researchers hailed from Boston University and the University of Texas Southwestern Medical Center.

 

Perlegen was awarded a grant from the National Institute of Arthritis and Musculoskeletal and Skin Diseases to conduct a whole-genome study of rheumatoid arthritis. DNA samples will be provided by the North American Rheumatoid Arthritis Consortium and the National Arthritis Foundation.

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