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With CLIA Applications Filed, Affymetrix’s Clinical Labs Division May Open this Quarter

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 services laboratories, according to company officials.
Affy CEO Steve Fodor told analysts and investors during a third-quarter earnings call in late October 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 operation, it expects to begin processing its first clients this quarter.
Following FDA approval, the company plans to offer services on the AmpliChip Cytochrome P450 system that it co-developed with Roche, Fodor said. He added that Affy 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.
“The FDA recommendations will affect all 2D6 testing, not just AmpliChip,” he told BioArray News this week. Other companies that offer 2D6 testing include Tm Bioscience and Gentris.
Fodor said that Affy anticipates the AmpliChip assay will be available in Affy’s 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. Greg Schiffman, Affy chief financial officer, added that the company hopes to start processing “a couple of items this quarter” in its clinical labs and that it sees the clinical labs 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 Affy 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 (see BAN 1/24/2006).
Affy has not provided a target date for opening ACL, but the firm has consistently eyed the window between the end of 2006 and beginning of 2007 as a good estimate. Doug Farrell, the company's head of investor relations, wrote BioArray News in an e-mail in January that Affy intended to begin ACL operations in “the second half of 2006."
Farrell said at the time that ACL will offer a range of CLIA-regulated clinical assays, and that "available services will include current Affymetrix commercial catalogue and custom assays such as gene expression monitoring assays, DNA analysis assays, and chromosomal copy number."
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 (see BAN 3/7/2006).

“The FDA recommendations will affect all 2D6 testing, not just AmpliChip.”

Other partners include PathWork Diagnostics, which has developed a test for cancer-of-unknown primary, Epigenomics, which is working on assays for breast and prostate cancer, and bioMérieux, which is also developing a breast cancer diagnostic. In total, Fodor last month said that the company has eight diagnostic partners with 20 assays in development., which is also developing a breast cancer diagnostic. In total, Fodor last month said that the company has eight diagnostic partners with 20 assays in development. 
96-Well Plates
During the earnings call, Fodor also provided an update on the status of the firm’s 96-well plate format — one that the company believes will appeal to its pharmaceutical customers. In 2005, the company launched its ArrayStation — a man-sized high-throughput system designed for industrial purposes with a 96-well format, enabling customers to run 96 different samples on Affy arrays at the same time.
According to Fodor, Affy has retooled its high-throughput offering to include a less bulky system more attractive to industrial users. The company will also begin reintroducing protocols for the 96-well format, starting with its expression products.
The fact of the matter is we are shipping it, and we've just been pushing it out a little bit more gently into the marketplace,” Fodor said. “This quarter [we are introducing] a new 96-plate scanner that now will replace ...  a bulky system that was out in the field with … a model that is very similar to our regular GeneChip scanner,” he said.
The first products that we are delivering on it are the expression-based products,” Fodor added. He said that the system is “really targeted to more of the high-throughput application areas. “Pharma has been one customer that's been looking at this for quite a while. They look at either predictive toxicology experiments, clinical trials, or other areas,” Fodor said.
Affymetrix could not be reached for further comment on its clinical labs or the new 96-well product.

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