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Two Affy Partners Launch Tests in Europe, Intensify Talks with FDA to Bring Dxs to US

Two European molecular-diagnostics companies that have developed tests on Affymetrix’s microarray platform are commercializing the assays in Europe while simultaneously engaging the US Food and Drug Administration with the hope selling the tests in the US sometime next year.
Last week, Marseille, France-based Ipsogen launched in Europe its MapQuant Dx HER2 test, which measures a set of HER2-amplified genes that correlate with HER2 protein expression. HER2 over-expression is linked to aggressive forms of breast cancer.
In May, Ipsogen launched MapQuant Dx Genomic Grade, which uses a 97-gene signature taken from biopsies to measure tumor grade — a consensus indicator of tumor proliferation, risk of metastasis, and response to chemotherapy (see BAN 6/3/2008).
Meantime, Skyline Diagnostics, based in Rotterdam, the Netherlands, is gearing up to launch next month an Affy-based assay that uses a gene-expression signature to classify patients according to their subtype of acute myeloid leukemia. The test will be Skyline’s first entry to the molecular diagnostics market.
As Ipsogen and Skyline focus on selling their GeneChip-based tests to European customers in coming months, they are also preparing to engage the FDA with the goal of launching the tests in the US sometime in 2009, according to company officials.
Skyline Diagnostics CEO Henk Vietor told BioArray News recently that the company will launch its first product for European customers in January. The AML test, called AML Profiler, will first be offered as a service from Skyline’s headquarters in Rotterdam, where it will receive and analyze bone marrow samples.
Vietor said that the market for Skyline’s AML test is “relatively small.” According to the National Cancer Institute, 9,000 cases are diagnosed in the US annually. However, he said that this will allow Skyline to enter a market with virtually no competition from other array-based diagnostic firms. Tests for multiple myeloma, acute lymphatic leukemia, and brain cancer are also in the pipeline, he added.
To support the launch of AML Profiler, Vietor said that Skyline has also partnered with several “opinion leaders” in Europe that Skyline will train with the goal of offering the test in their labs next year.
“They will have the same infrastructure to perform the analysis. We are quite confident that they can run the test independently from Skyline,” Vietor said. “They are familiar with gene expression and they can run samples and analysis.”
Once Skyline’s partners have the CEL files, Vietor said the information will be shared on a server with Skyline, which will perform the analysis and return the results to the client. Vietor said that Skyline will start with three labs and then expand its services to include other labs.
He declined to name Skyline’s partners, but said that they were labs in Germany and the UK that specialize in hematology and gene-expression profiling.
US Landing
While Skyline lays the foundation for its European launch, it has begun discussing a route to regulatory clearance in the US with the FDA. Vietor said that the company in October had a pre-investigational device-exemption meeting with the FDA after which it decided to pursue pre-market approval.He estimated it would take approximately 12 to 18 months for Skyline to complete the PMA process.
If Skyline wins FDA clearance next year, it will have made good on a plan, disclosed in April, to have a test sold in the US in 2009. At the time, Vietor said the US launch strategy would be similar to Skyline’s European efforts. The company’s test is tentatively priced at around €2,000 ($2,500) (see BAN 4/22/2008).

“If we are approved [in the US] it will make it easier to get reimbursement, and acceptance of our test will be higher.”

By choosing to take the expression-based test through the PMA process, Vietor speculated the firm could receive institutional support from the FDA. “If we decide to go this route, we have some favorable things from the FDA; they will give it priority and they will waive costs associated with application for PMA,” Vietor said.
Vietor speculated that Skyline may seek clearance in a “modular fashion” by submitting the assay, the Affymetrix platform it runs on, and the analysis software, to the FDA for review all independently. Vietor added that Skyline may perform limited US studies to supplement the data it has collected in Europe.
Skyline tested the assay on approximately 600 samples and has performed additional studies to measure chip stability, RNA stability, sample collection and handling, intermediate precision experiments, and assay reproducibility.
“If we are approved [in the US] it will make it easier to get reimbursement, and acceptance of our test will be higher,” Vietor said. “This will make it easier for market acceptance and will provide us with a lot of opportunities.”
Vietor said that Skyline has plans to eventually market its test worldwide. He did not elaborate.
On the money side, in October 2007 Skyline closed a series A financing round led by Erasmus MC Biomedical Fund and Life Sciences Partners, both of Rotterdam, for an undisclosed sum. To sustain Skyline’s efforts to sell its test in Europe and the US, Vietor said that the company will most likely seek a new round of financing.
“We will start a new round of financing in January and that will be primarily used to fund expanding marketing and sales efforts and in licensing in new signatures,” Vietor said. “We will of course seek new investors in this round of financing.”
As Skyline prepares to enter the European market, Ipsogen has added another test to its menu and has plans to add a third. The company’s MapQuant Dx HER2 assay is made to complement Genomic Grade, while an additional assay to measure endocrine response in breast cancer patients should also hit the market in coming months.
Jean-Marc Le Doussal,director of Ipsogen’s breast cancer program, told BioArray News that the firm “aims to provide, through MapQuant Dx, key predictive tests for breast cancer, and HER2 is an important one.”
Like Skyline, Ipsogen also has a service model and offers its tests to clients through its lab in Marseilles as well as via DNAVision, a genetic-services company and Affymetrix service provider based in Gosselies, Belgium. Next year, Le Doussal said that Ipsogen will consider making its test available as a service through more hospitals and private labs.
Ipsogen also has a subsidiary in New Haven, Conn., and Le Doussal said in June that the company is preparing talks with the US Food and Drug Administration to develop a roadmap to the eventual 510(k) clearance of MapQuant Dx (see BAN 6/3/2008).
“In the US, we plan a launch in 2009 and we are in the process of discussing this issue with the FDA. We have a grading test, and there is a strong precedent with histological grading,” Le Doussal said at the time. “We don’t know what the FDA will ask, but we already have a lot of data.”
This week, Le Doussal said that the firm’s plans for the US market have not changed since June, and that Ipsogen is still on schedule to begin serving US customers next year. 
To support its efforts, Ipsogen in June raised €11.8 million ($18.7 million) in its initial public offering. The company began trading on the Alternext market, a sub-market of the global NYSE Euronext market geared towards smaller to mid-sized companies, under the symbol ALIPS on June 16 (see BAN 7/22/2008).
Le Doussal declined to discuss any plans for future financing, but said that Ipsogen is on track to break even in 2010. According to Ipsogen, revenues for the first half of this year grew 42 percent to €1.5 million for the six months ended June 30. Meantime, net loss widened 78 percent to €804,000 for the same period.
If Ipsogen and Skyline win FDA clearance next year, they will join two other Affy partners that already have cleared tests in the market and may be joined by other Affy-based diagnostics on the market the next few years.
The first GeneChip-based test to be cleared for clinical use was Roche’s CYP450 AmpliChip, which launched in early 2005. In July of this year, Sunnyvale, Calif.-based Pathwork Diagnostics had its tissue of origin test cleared for clinical use, making it the second Affy partner to do so (see BAN 8/5/2008). 
According to the array vendor, it expects to see more tests on the market soon from a variety of partners including Ipsogen, Skyline, Medical Prognosis Institute, Almac Diagnostics, Veridex, BioMerieux, and others.
During the company’s third-quarter earnings call in October, President and incoming CEO Kevin King told analysts that the company expects to “see continued growth in our molecular diagnostics business, as our partners launch new diagnostic test to help personalize therapies.
“We’ve got a pipeline of other assays that are being developed by partners that include prognostic tools for breast cancer, diagnostic assays for breast cancer, prostate cancer, liver cancer, as well as a whole host of others,” he said. “I think there are 14 products overall in the pipeline.”

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