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Eager for Entry to Diagnostics Arena, Sequenom Publishes the First of Its Genome-Scan Studies

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In the first published study from its genome-scan genetic association strategy, Sequenom is looking to change its luck.

The company hopes its research, which reports the discovery of polymorphisms in intercellular adhesion molecule genes linked to a greater risk of breast or prostate cancer, will help it attract a compatible suitor capable of helping it develop a prognostic or diagnostic test based on its work.

“We are looking now specifically for collaborators from diagnostic laboratories, [with whom] we can conduct large-scale validation studies, particularly focusing on disease outcome and treatment outcome,” said Andy Braun, an author of the recent paper and Sequenom’s chief medical officer.

Ultimately, a collaboration would result in a test that would establish an income stream separate from Sequenom’s genotyping business, and unrelated to its now-defunct drug-discovery efforts. The company plans to validate biomarkers to help clinicians decide how aggressive cancer therapy should be, said Braun. The company also hopes that such a marker will forecast five-year survival, he added.

Braun would not disclose which or how many companies Sequenom is discussing its collaboration plans with, but the partner must be a “big, clinical laboratory with access to samples” capable of conducting retrospective studies and prospective studies.

After a year of work in collaboration with a partner, Sequenom should be able to produce a prognostic diagnostic based on the ICAM study, said Braun.

The company has not developed this sort of diagnostic before, and the 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, published in in the Dec. 15 issue of the journal Cancer Research, is the first paper to be published from Sequenom’s genome scan efforts. “What took us four years to really commence the first genome scan was the establishment of an infrastructure that allows us to combine a tremendous amount of samples, and technology, as well as reagent sets,” said Braun.

Additional genome scans the company has carried out include osteoporosis, osteoarthritis, Type 2 diabetes, and “other types of common disorders,” said Braun. It plans to follow the article with “about 10” more publications that are currently in the pipeline, he said.

In a press release, Sequenom touted the study as “among the most important findings in cancer genetics since the discovery of BRCA1 and BRCA2.”

The researchers identified the ICAM gene region on chromosome 19 during a genome-wide association study using approximately 28,000 SNPs targeting 16,000 known and predicted genes, said Braun. “We had 1,200 cases and 1,200 controls approximately,” with about 700 breast cancer and about 500 prostate samples, said Braun.

Independently, the researchers discovered an association between the same region of chromosome 19 and prostate cancer, said Braun. “We didn’t take the prostate sample and ask whether this [region] was associated with prostate cancer,” he said. Rather, the two parallel genome scans, with four independent cohorts — three breast cancer cohorts and one prostate — revealed the same associated region.

Individuals having a particular version of the ICAM region have a “40 percent higher risk” of developing breast or prostate cancer, and “34 percent of individuals carry two copies” of this version, according to a Sequenom statement.

The ICAM proteins may also prove to be valuable drug targets, the statement added.

After further database analysis, the group identified an association of the same gene region to organ metastasis in breast cancer, “which is pretty exciting, since it gives us a tool where we can predict the aggressiveness of the disease,” Braun said. The group does not have the data to associate any gene regions with prostate metastasis, although it is working with “another group” that will collaborate in another large-scale association study to find that association, he added.

Sequenom wants to continue to expand upon the ICAM results with more extensive tests. The company is preparing to study in more depth four other chromosome regions associated with breast cancer clinical outcomes, said Braun. “Those four we can also combine to do a diagnostic analysis for predictive medicine, which allows us to calculate the likelihood that somebody will suffer from breast cancer,” he said.

The company needs a “much larger” cohort to pursue the more ambitious diagnostic, Braun said.

Investor reaction to the ICAM study was fairly strong — shares closed at $1.39 on Dec. 22, a rise of 25 percent since Dec. 11. The stock has traded near or below $1 for most of the past four months. It twice narrowly missed by one day being sent a delisting warning letter from the Nasdaq exchange for failing to keep its stock closing price above $1 for 30 consecutive trading days (see Pharmacogenomics Reporter’s sister publication GenomeWeb News, 12/6/2004).

— CW

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