Skip to main content
Premium Trial:

Request an Annual Quote

Affymetrix, Nanogen Court FDA in Effort to Drive Array Platforms Toward Molecular Dx

Building on a trend among microarray vendors to extend their market reach beyond discovery research and into the clinic, Affymetrix and Nanogen recently outlined plans to have their respective microarray platforms approved for molecular diagnostic applications.
Affymetrix officials said that the firm has recently filed applications with the state of California and the US Food and Drug Administration to enable it to perform homebrew tests in its newly developed clinical services laboratories, while Nanogen said it plans to seek 510(k) approval in 2007 for its array-based NanoChip 400 instrument and three companion diagnostic assays.
Although the market for array-based molecular diagnostics is still unproven, both firms view FDA approval as a key driver for future success.
“I believe that FDA approval will both expand our potential market and provide a stamp of acceptance for any new customers that are currently sitting on the fence about entering genetic testing themselves,” said David Ludvigson, president and chief operating officer of Nanogen, in a conference call to discuss the firm’s third-quarter earnings.
Ludvigson said that 510(k) clearance would represent a “key milestone” in the firm’s agenda for next year.
Affymetrix, meanwhile, said that its clinical lab business can profit from a recent FDA panel recommendation 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 the AmpliChip.
“Studies have suggested tamoxifen is not as effective in breast cancer patients carrying a specific version of cytochrome P450 2D6,” said Affy CEO Steve Fodor in the company’s third-quarter conference call. “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.
“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 added.
Affy: Filing the Paperwork
Fodor said that Affy filed applications in September with the state of California and with the FDA to ensure that its labs comply with the FDA’s Clinical Laboratory Improvement Amendments. If the company receives approval to begin operation, it expects to begin processing tests for its first clients this quarter.
Following FDA approval, the company plans to offer services on the AmpliChip system, Fodor said.
Affy anticipates the AmpliChip assay will be available in its CLIA lab “before the [tamoxifen] labeling changes are in effect,” Fodor said.
Affy said it believes tamoxifen’s updated label will foment demand from physicians who had been reluctant to adopt the AmpliChip. But Paul Billings, vice-president and national director of genetics and genomics at AmpliChip provider Lab Corp, was less optimistic.
“The FDA recommendations will affect all 2D6 testing, not just AmpliChip,” he told Pharmacogenomics Reporter’s sister publication BioArray News this week. Other companies that offer 2D6 testing include Tm Bioscience and Gentris.
Greg Schiffman, Affy chief financial officer, said 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.
Schiffman added 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.” Fodor had previously said that Affy Clinical Labs could be a consumables sales driver for the company as well.
 Roche had once trumpeted that the AmpliChip would drive $100 million in annual sales by 2008 [see 11/6/2003 PGx Reporter]. AmpliChip has not seen strong sales in the end-user market since its launch [see 9-6/06 PGx Reporter], so the product’s use in Affy’s CLIA-approved lab may be the key to the commercial success of the product.
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.
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.
Nanogen: Three Assays in 2007
Nanogen’s Ludvigson said the company expects to submit its NC 400 and three tests — for cystic fibrosis carrier detection, warfarin resistance, and factor V and factor II clotting mutation detection — to the FDA for 510(k) clearance in 2007.
The first of those, the cystic fibrosis test, will be submitted by the end of the first quarter. “That will be the most visible and most important milestone in 2007,” he added.
Nanogen rolled out the NC 400 in the third quarter of 2005. It has not disclosed how many of the systems it has placed so far.
During last week’s call, Ludvigson acknowledged that the NC 400 has been slow to take off in the market, and voiced hope that FDA clearance could shorten the lead time for adoption.

“I believe that FDA approval will both expand our potential market and provide a stamp of acceptance for any new customers that are currently sitting on the fence about entering genetic testing themselves.”

“The sale of this product requires long lead times, but I am pleased with the results the system is receiving,” Ludvigson said. “Most of our sales continue to be into clinical research laboratories and to our non-US distributors and most of the customers are developing their own assays using the open platform capabilities of this system,” he said.
Nanogen spokeswoman Suzanne Clancy told BioArray News this week that the CF test contains a panel of 23 mutations associated with cystic fibrosis as outlined by the American College of Obstetricians and Gynecologists in a 2004 recommendation.
Nanogen’s CF test will compete directly with a test from Osmetech Molecular Diagnostics, which won approval for its array-based eSensor cystic fibrosis carrier-detection test earlier this year. Another rival will also include Tm Bioscience, whose Tag-It CF carrier detection test was cleared by the FDA in May 2005.
However, it is not known how well these tests are actually selling, indicating that the promise of return on investment for the NC 400 is not guaranteed.
The second assay Nanogen is preparing for FDA submission is a test for Factor V Leiden, the most common mutation associated with predisposition to excessive blood clotting, and Factor II prothrombin, an enzyme that is associated with hemophilia. 
The company is also planning a test for resistance to warfarin, based on mutations in CYP2C9. Potential competitors in this area include Genelex and Clinical Data, which both recently launched tests in this area, as well as the AmpliChip, which identifies CYP2D6 and CYP2C19 genotypes [10-18-06 PGx Reporter].
Clancy said that the company may have other diagnostics in the pipeline for the NC 400, pointing to an agreement that was expanded in August between Nanogen and Fisher Scientific.
Under that agreement, Fisher agreed to provide Nanogen up to $10 million during 2007 and 2008 to research and develop infectious disease and molecular diagnostic tests.
Furthermore, Fisher and Nanogen reaffirmed their decision to explore using biomarkers from Fisher subsidiary Athena Diagnostics, which has an extensive portfolio of markers in the fields of neurology and endocrinology.

Filed under

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.