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Will FDA require EA microarray proficiency tests?

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Expression Analysis is preparing to begin a second round of its proficiency testing program for microarray facilities, in which it compares variability in Affymetrix gene expression experiment outcomes within and among different labs.

But while experts agree that standardization will be important to the industry, whether or not the US Food and Drug Administration will require proficiency testing as a basis for approving diagnostic products remains a big question.

Expression Analysis recently completed phase 1 of the program, which is not intended to grade facilities on a pass/fail basis, but rather to provide a basis for developing performance standards. The company believes that these performance standards are likely to be crucial to firms that eventually seek FDA approval of microarray-based diagnostic products.

“In clinical diagnostics, proficiency testing is done in all CLIA-certified laboratories,” says Steve McPhail, president and CEO of the Durham, North Carolina-based microarray services firm. “So we felt as microarray testing progressed into clinical trials and use in clinical diagnostics, proficiency testing would become a requirement.”

The FDA, however, has not yet said that proficiency testing will be necessary for approval of microarray-based diagnostic products for clinical or non-clinical use. John Leighton, a supervisory pharmacologist within FDA’s Division of Oncology Drug Products who has extensive experience with microarray technology, says that it is entirely possible the FDA won’t require such testing as a basis for approval, at least not when it comes to a specific test.

“Probably what we’ll say in the end is, from the non-clinical perspective, that what you need to do is demonstrate certain characteristics of your assay,” Leighton says. “So we’ll take a step back and define what you need to do, and how you go about that will be up to you.” But, he adds, that could change: “The field is rapidly evolving, and it may turn out that one standard is appropriate for all tests.”

— Edward Winnick

PATENT WATCH

US Patent No. 6,773,676. Devices for performing array hybridization assays and methods of using the same. Inventor: Carol Schembri. Assignee: Agilent Technologies. Issued: August 10, 2004.

Covers array hybridization devices and methods for their use. The subject devices are characterized by having a substantially planar bottom surface, a cover, at least one fluid port, and at least one adjustable spacing element for adjusting the spacing between an array and the bottom surface. The inventions find use in a variety of array-based applications, including nucleic acid array hybridizations.

US Patent No. 6,773,886. Binary encoded sequence tags. Inventors: Joseph Kaufman, Matthew Roth, Paul Lizardi, Li Feng, Darin Latimer. Assignees: Agilix, Yale University. Issued: August 10, 2004.

Covers a method for the comprehensive analysis of nucleic acid samples and a detector composition. The method, referred to as Binary Encoded Sequence Tags, involves the generation of a set of nucleic acid fragments; adding an adaptor to the ends containing a recognition site for cleavage at a site offset from the recognition site; cleaving the fragment to generate fragments having a plurality of sticky ends; and indexing of the fragments into sets based on the sequence of sticky ends.

Datapoint

34,000
Approximate number of gene targets on newly released Rat Whole Genome Bioarray from GE Healthcare — formerly Amersham Biosciences — for use on the company’s CodeLink microarray platform.

Affymetrix files suit against Illumina for alleged infringement of six patents. The suit claims that Illumina’s BeadArray and Sentrix instruments incorporate inventions covered by Affymetrix’s patents.

CombiMatrix enters into a multi-year strategic alliance with Furuno Electric to design, engineer, and build a bench-top DNA microarray synthesizer for custom microarrays that utilizes CombiMatrix’s semiconductor-based electrochemical synthesis technology.

The US government expands its contract with Nanosphere to develop a tool to detect DNA sequences of biological warfare agents. The expansion allows Nanosphere to optimize the Verigene platform into a field-deployable system.

BioTrove acquires an exclusive license from Stanford University for patent applications covering the use of a through-hole structured microarray to perform PCR.

Bothell, Wash.-based Lumera raises $41.7 million in its initial public offering of 6 million shares priced at $6.95 per share. The spinoff from Microvision makes wireless antennas, disposable biochips for DNA identification, and electro-optic devices.

Two Japanese firms, DNA Chip Research and Bio Matrix Research, form a partnership to market gene expression profiling analysis using DNA Chip Research’s AceGene microarray, a technology jointly developed by DNA Chip Research and HitachiSoft.