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Pharma Partnering Wanes for Sequenom; Clinical Lab Collaboration May Develop Cancer Diagnostic

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Announcing the discovery of another gene linked to breast cancer, Sequenom is looking for a reference-lab partner to help it develop a new diagnostic — but it still isn’t holding its breath for a pharma partner.

The gene, nuclear mitotic apparatus protein, or NuMA, has polymorphisms that “occur fairly frequently in the population that significantly increase the risk to develop breast cancer,” said Toni Schuh, Sequenom CEO. Along with the ICAM gene and two more “high-confidence” genes the company is currently working on, it hopes NuMA will become a diagnostic useful for population screening, he said.

The well-known BRCA1 and BRCA2 genes confer a six- to eight-fold increase in breast cancer risk in families with a cancer history, but a very small role in breast cancer risk for the population as a whole, said Schuh. “ICAM has an impact on the entire population — you see about a 40 percent risk increase,” while families with a history of cancer show an increase of “more than three-fold,” he said. With NuMA, individuals with a cancer history show a four-fold increase in cancer risk, while the population shows about a two-fold risk increase.

Sequenom, which identified the gene using its flagship MassArray platform, has not evaluated the market potential of the NuMA-ICAM test, said Schuh. Myriad Genetics sells more than $40 million of the BRCA test per year, according to a Myriad spokesperson.

“We are confident that we can do the additional clinical validation work that is required for these genes during this year,” said Schuh. He was unwilling to disclose how and when Sequenom would commercialize the tests, but he said the company would “start a dialogue with major diagnostic companies” and laboratories.

In a July interview with Pharmacogenomics Reporter soon after Sequenom announced it would scuttle its internal drug-discovery business, Schuh said the company’s genetic assets, including disease-associated genes and mutations in breast cancer and 10 other diseases, were “of very high strategic value for organizations that are considering to make investments in these disease fields.” [see Pharmacogenomics Reporter, 8/5/2004] However, he added, “the market for target deals is not very attractive.”

Asked this week whether the market had changed since then, Schuh said, “That [statement was] related to target deals for pharmaceutical development, and I think it’s fair to say that the interest of pharmaceutical companies to obtain access to new targets is, at this point in time, moderate at best.”

But Schuh did not express the same measured expectations for collaborations outside of pharma deals. “If you look at the diagnostic space, you see a very strong momentum as far as it relates to genomic and genetic research into clinical use,” he told Pharmacogenomics Reporter this week. This momentum includes increasing interest by service laboratories and diagnostic companies in obtaining “access to content,” he said.

Also indicative of this momentum are new and non-traditional players, including: “medical systems suppliers,” such as GE Healthcare, which is expanding into diagnostics from its position as a medical imagining player; companies in the “medical device business”; and “IT companies who have identified this as a major growth area,” such as Sun Microsystems, which is developing a virtual pharmaceutical development lab, said Schuh.

“When you characterize the opportunity of targets for the marketplace of molecular medicine in the broadest sense … there the interest is increasing,” Schuh said.

If there is increasing interest in diagnostics from medical system and device companies, it may be embodied by the moves of goliaths such as Siemens and GE Healthcare. Indeed, as Pharmacogenomics Reporter wrote in October, Siemens Medical Solutions division bought four of Sequenom’s Compact MassArray platforms, placing them in four diagnostic and clinical labs in the United States and Europe to study their potential use as clinical diagnostics platforms [see Pharmacogenomics Reporter, 10/28/2004].

In addition, GE Healthcare bought and absorbed Amersham about one year ago, later announcing its intention to produce DNA- and protein-based clinical diagnostics [see Pharmacogenomics Reporter, 9/2/2004].

In its genome-wide scans, Sequenom identified genes in the 11 disease areas that the company considered “significant” contributors to disease risk, said Schuh this week. “The primary reason to do that was to have diagnostic intellectual property that could converge with our platform, in order to enter the diagnostic space,” he said.

“To the extent that these genes were also appropriate pharmaceutical targets, we also wanted to capture the therapeutic value” through collaborations, Schuh said.

In the arena of pharmaceutical collaborations, Sequenom signed one agreement related to its osteoporosis targets with Procter & Gamble. The company also has target validation collaborations with Bristol Myers and Pfizer, said Schuh. But in assessing the uptake of the targets, Schuh said the company would have expected a stronger response.

Companies working on innovative targets can check whether they are genetically valid using Sequenom’s “database-type” licensing program, a service that “seems to get some nice traction,” Schuh said.

An eventual genetic test would also have prognostic value, said Schuh. Carriers of the cancer-linked ICAM allele carry not only a higher risk of breast cancer, but a “significantly higher” rate of organ metastasis, he said.

The company has not developed a diagnostic of the sort envisaged for the NuMA, ICAM, and other genes before. The company’s genome-scan studies, underway since 1998, were intended to build a catalog of genetic associations that could be correlated to clinical outcomes.

The ICAM study, which appeared in the Dec. 15 issue of the journal Cancer Research, was the first published research to result from Sequenom’s genome scan efforts.

— CW

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