Skip to main content
Premium Trial:

Request an Annual Quote

Taking Next Step in Molecular Dx Strategy, Affymetrix Seeks FDA OK for Clinical Lab

Affymetrix recently filed applications with the state of California and the US Food and Drug Administration to enable patient testing in its newly developed clinical laboratories, according to company officials.
Affymetrix CEO Steve Fodor recently told analysts and investors during a third-quarter earnings call that the company filed applications in September with California and with the FDA to review its labs to make sure they comply with the FDA’s Clinical Laboratory Improvement Amendments. If the company receives approval to begin operations, it expects to begin serving its first clients this quarter.
When Affymetrix begins running tests at its lab it will likely expand its opportunities in the molecular diagnostics market. It is not certain, however, whether microarrays are the best technology for conducting molecular diagnostics. Many industry experts believe that RT-PCR-based tests are better suited to diagnostic testing.
Nonetheless, Affymetrix, along with partner Roche Molecular Diagnostics, won US and European approval last year to sell the CYP450 AmpliChip as an in vitro diagnostic. The product is based on Affymetrix’s GeneChip platform.
Affymetrix is one of a number of molecular biology tool firms that have branched out into the rapidly growing molecular diagnostics market. Roche is the clear-cut leader in the roughly $2 billion market, which is expected to double by 2010, but there are dozens of other companies from start-ups to well-established diagnostics and research-tool firms employing a variety of technologies as they seek a share of the market.
Many of the firms that comprise the BCW Index have either entered the molecular diagnostics field or are planning on doing so in the near future. Qiagen, for example, booked around $115 million in molecular diagnostics revenue in 2005, and has been very aggressive on the acquisition front in an attempt to expand its share in the market.
Other firms, such as Stratagene, Third Wave Technologies, bioMérieux, and Digene are developing their own PCR-based assays. In addition, there are a variety of microarray technology firms, including Illumina, CombiMatrix, and Nanogen, that are sizing up their opportunities in the molecular diagnostics field. GE Healthcare and Applied Biosystems also are major competitors in the microarray space, but it remains to be seen whether these rivals employ that technology or other tools in developing molecular diagnostics.
Earlier this year, ABI sold its 50-percent stake in Celera Diagnostics to Celera Genomics in exchange for the right to sell instruments to end-user diagnostic customers (see BioCommerce Week 1/11/2006). ABI has yet to disclose which of its technologies will form the basis of its molecular diagnostic products, but the firm’s RT-PCR, mass spec, and microarray technologies are all possibilities.
While some of these other molecular diagnostic players are developing their own assays or are making OEM assays for others, most have not gone as far as Affymetrix in establishing a CLIA-approved clinical lab. CombiMatrix is the exception, having established CombiMatrix Molecular Diagnostics, which offers CLIA-approved tests.
Affy’s Lab Plans
Following FDA approval, Affymetrix plans to offer services on the AmpliChip Cytochrome P450 system that it co-developed with Roche, Fodor said. He added that the firm is hoping to capitalize on an FDA panel recommendation last month to re-label the breast cancer drug tamoxifen to include genetic-specific information for women who carry a variant of the cytochrome P450 2D6 gene, a mutation included on AmpliChip.
“Studies have suggested tamoxifen is not as effective in breast cancer patients carrying a specific version of cytochrome P450 2D6,” Fodor said. “This decision directly links to the availability of the AmpliChip system produced by Affymetrix for Roche. The AmpliChip system is the only FDA-cleared assay for the detection of cytochrome P2D6 variance,” he said.
Paul Billings, vice-president and national director of genetics and genomics at Lab Corp, which offers the AmpliChip, was less optimistic about the impact the FDA recommendations could have on adoption.

“This is a significant example of how our GeneChip technology can …migrate to FDA-approved formats and ultimately improve the safety and efficacy of widely used drugs.”

“The FDA recommendations will affect all 2D6 testing, not just AmpliChip,” he told BioCommerce Week sister publication BioArray News this week. Other companies that offer 2D6 testing include Tm Bioscience and Gentris.
Fodor said that Affymetrix anticipates the AmpliChip assay will be available in its CLIA lab “before the labeling changes are in effect.” Overall, the firm sees the FDA's recommendation as well as the imminent opening of its labs as facilitating greater downstream use of its technology at a time when clinicians have been reluctant to adopt the AmpliChip.
“This is a significant example of how our GeneChip technology can …migrate to FDA-approved formats and ultimately improve the safety and efficacy of widely used drugs,” Fodor said.
Affymetrix CFO Greg Schiffman added that the company hopes to start processing “a couple of items this quarter” in its clinical labs and that it sees the clinical lab business contributing some “revenue ramp” next year. Still, Schiffman maintained that the success of ACL will not be gauged so much by “absolute revenue” as on “a goal of accelerating the utilization of chips in a clinical environment.”
In January, Fodor said that Affymetrix Clinical Labs could be a consumables sales driver for the company as well. “While we don’t expect significant revenues from ACL in 2006, we do expect to stimulate additional growth in consumables as researchers work to validate biomarker signatures for broad diagnostic applications,” he said at the time.
Affymetrix has not discussed which assays it will initially offer at ACL beyond the AmpliChip Cytochrome P450, but the roster could grow to include other assays being developed by its molecular diagnostics partners. Roche, for example, is also planning on introducing AmpliChip assays for leukemia, lymphoma, and p53 detection over the next decade. According to Roche, the AmpliChip leukemia assay could receive FDA clearance by 2008 or 2009.

Justin Petrone contributed to this article.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.