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PathWork to Submit Affy-Based CUP Diagnostic For FDA Approval in 2006; Two More on the Way

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Fresh from inking a pact to use Affymetrix's GeneChip platform for its diagnostics, a PathWork Informatics official told BioArray News last week that the San Jose, Calif.-based molecular diagnostics company is planning to submit a test for tumors of unknown origin to the US Food and Drug Administration for approval in 2006.

If successful, PathWork's test could become the second FDA-approved in vitro diagnostic test based on the Affymetrix microarray platform. A similar collaboration between Affy and Roche yielded the AmpliChip CYP450 test that the agency approved nearly one year ago (see BAN 1/5/2005).

According to CEO Glenda Anderson, PathWork is "actively engaged with the FDA now and we do plan to take each of our products to the FDA for clearance." She added that the company plans to launch its first product in 2006.

Anderson said that the rationale behind PathWork's decision to release a test for identifying tissue of origin in cancer sufferers, also known as cancer of unknown primary, was "very strategic."

"It requires a large number of genes to do well, so it really lends itself to a microarray platform," she said, adding that CUP is "a difficult problem." Anderson said that nearly 30,000 patients a year are diagnosed with CUP and face a "costly, frustrating, and time-consuming series" of diagnostic procedures that are "successful just 25 percent of the time."

Anderson said that the test may become available in some CLIA-approved laboratories in advance of FDA approval but that the company's "primary path is to take this through the FDA."


"The fundamental technology that we've developed and that we use to discover these multiplexed tests is inherently platform independent."

After receiving approval, PathWork plans to "sell this kit to clinical labs to identify the tissue of origin for metastatic cancers."

"That will help clinicians to better match their patients to treatment-specific guidelines and its likely to improve outcome," she said.

The Deal with Affy

In addition to the tests for cancer of unknown primary, Anderson said that PathWork has developed two more diagnostic tests for colon and prostate cancer that will run on the Affymetrix platform, although these tests remain in "feasibility testing."

Affy will manufacture the chip for the first diagnostic, called the PathChip, for PathWork.

"We've chosen to launch our first product on a microarray that is OEM manufactured by Affy for some important strategic reasons," Anderson explained. The most important of these, she said, is that "Affymetrix is one of the only manufacturers that is currently capable of producing a microarray in compliance with FDA [and] good manufacturing processes."

"The tests in our pipeline will all share the PathChip microarray technology that Affy manufactures for us," she said.

However, that's not to say that PathWork couldn't launch its tests on another array platform. "The fundamental technology that we've developed and that we use to discover these multiplexed tests is inherently platform independent," Anderson said.

Anderson said it was "not unlikely" that PathWork could partner with a different array manufacturer and that it "expects to move forward with additional partners over time."

Still, for the time being, PathWork will be used as an example of Affymetrix's newly found flexibility in partnering with smaller diagnostic companies, after a year of partnering with larger ones like Roche, Veridex, and BioMeríeux.

Affy inked its deal with Veridex in January, and so far the J&J unit has been quiet with regards to when it plans to roll out a test on the Gene Chip platform (see BAN 1/5/2005).

A BioMérieux spokesperson did not mention any plans to release a diagnostic test in the near future during an interview with BioArray News last month (see BAN 10/19/2005).

During Affy's third-quarter conference call last month, CEO Stephen Fodor said the agreement with PathWork, as well as UK-based ArraDx, to develop tests on the company's platform expanded the "breadth" of the Powered by Affymetrix program "from large enterprises to more focused diagnostic ventures" (see BAN 10/26/2005).

A representative from ArraDx declined to discuss the company's relationship with Affymetrix or possible diagnostics, citing the fact that ArraDx has "recently been acquired by a larger organization and will change its name as a result." A formal statement from the firm regarding the acquisition is expected in several weeks, the representative said.

While it may have broadened its reach, Affy appears to still be fairly selective about who it permits to use its platform under the Powered by Affymetrix program. To date, five partners have been announced. According to Thomas Schlumpberger, director of molecular diagnostics at Affy, "Affymetrix has been selective because we are focused on partnering with companies that share our vision and are dedicated to improving healthcare along with us."

Schlumpberger pointed out via e-mail that Affy has partnered with "three out of the top 10" industry-leading molecular diagnostic companies, but that it has "also partnered with other emerging molecular diagnostic companies that are highly interested in and capable of developing microarray-based molecular diagnostic tests for smaller, specific disease areas, such as oncology."

"Our collaboration with PathWork Informatics would be an example of this type of relationship," Schlumberger said.

— Justin Petrone ([email protected])

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