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Questions Remain for Array Molecular Diagnostics

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The US Food and Drug Administration’s recent clearance of the first microarray-based test and instrument platform for in vitro diagnostic uses marked a major advance for microarray makers, and while the industry is optimistic about the prospects of selling products to this field, there are some very real reasons why a dose of caution should counter the exuberance.

A chance to compete in the estimated $20 billion molecular diagnostics market and move beyond traditional gene expression research applications has been a key goal of microarray manufacturers for several years. The FDA — and previous to that European regulatory authorities — made that goal attainable with the Dec. 23 clearance of Affymetrix’s GeneChip 3000Dx instrument platform and half of Roche Molecular Diagnostics’ CYP450 AmpliChip.

Michael McNulty, senior director of molecular diagnostics for Agilent, a microarray competitor to Affymetrix that is currently evaluating the diagnostics space and a potential entry, cites cancer and cardiovascular disease as two areas where microarray-based diagnostics are likely to have a significant impact. But he also urges caution over how payors might respond to the new technologies, and says that educating the codemakers at the American Medical Association would be a key to the potential growth of microarray-based diagnostics.

The other question hanging over the industry is whether physicians will use the microarray-based tests, particularly the CYP450 test. Thus far, there hasn’t been great demand for CYP450 tests that are already on the market, says Paul Billings, a senior geneticist and vice president for biotechnology and healthcare strategy at LabCorp.

— Ed Winnick

PATENT WATCH

US Patent No. 6,846,635. Microarrays and their manufacture. Inventors: Norman Anderson, Leigh Anderson, James Braatz. Assignee: Large Scale Proteomics. Issued: January 25, 2005.

The invention relates to microarrays containing bioreactive molecules that are prepared by using a separate fiber for each compound in the array. The arrays are constructed by sectioning bundles of tubules or rods, each containing unique reactants to produce large numbers of identical arrays. The arrays have applications in performing a variety of different quantitative biochemical analyses based on, for example, enzymatic activities, immunochemical activities, nucleic acid hybridization and small molecule binding.

 

US Patent No. 6,844,151. Methods for production of arrays with modified oligonucleotide and polynucleotide compositions. Inventor: Roderic Dale. Assignee: Oligos Etc. Issued: January 18, 2005.

The patent describes methods for producing arrays having associated modified nucleic acid structures, such as acid stable and/or end-blocked nucleic acids such as 2’-O--R oligonucleotides. In one embodiment of the invention, the arrays exhibit an increased binding affinity with complementary nucleic acids, and in particular with complementary RNA. In another use, the associated nucleic acids of the array exhibit substantial acid resistance, allowing the arrays to be treated with low pH solutions. Also, the modified associated nucleic acids of the array exhibit substantial resistance to nuclease degradation.

Datapoint

63

Percentage of scientists favoring a universal database of microarray studies, from a survey of 313 scientists who published or reviewed microarray studies in the journal Physiological Genomics.

 

The Immune Tolerance Network has chosen Expression Analysis to serve as its microarray core facility. Using Affymetrix GeneChips, EA will help support clinical trials for the ITN, an international collaborative research project studying kidney and liver transplantation.

 

Lumera has acquired exclusive rights to heterodimer protein technology from Helix Biopharma to further its development of a protein microarray.

 

Under the terms of a deal to settle the patent infringement litigation between Mergen and Oxford Gene Technology, Mergen has acquired a license from OGT to manufacture and sell microarrays for investigating gene expression.

 

BioSource International and Whatman Schleicher & Schuell are set to launch the first commercially available planar phosphoarray later this year. The array, called the Mercatur Phosphoarray, contains 10 analytes — each specific for a different phosphorylated protein.

 

Agilent has launched its comparative genomic hybridization microarray product, which examines chromosomal changes related to cancer. The CGH array uses total genomic DNA to detect chromosomal changes across the entire genome.

 

Illumina has released a platform for gene expression profiling of formalin-fixed paraffin-embedded samples, as well as the first product for the assay, a cancer panel.

 

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