Sequenom Inc. said it has identified genetic markers related to breast cancer in four genes, with each gene having forms that either increase or decrease the risk of developing breast tumors.

The expectation is that the markers will be used to develop both diagnostics and therapeutics, if possible, said Sequenom CEO Toni Schuh.

"The objective at this point in time clearly is to partner with companies and entities that have a position in the market, or servicing and product companies to partner these out," Schuh said. "Of course, in the long run we also want to offer diagnostic genetic and predisposition panels on our own platform."

At the moment, San Diego-based Sequenom's platform is mass-spectrometry based, which he said is "a high-end platform and not necessarily a platform for the broadest market penetration at this point in time."

Schuh said the company is in "a number" of partnering conversations related to the discoveries, although he expects that it will be anywhere between three months and 12 months to negotiate a deal, given the time it takes to negotiate term sheets and draw up contracts.

Sequenom said its data indicate that common combinations of its breast cancer markers "increase the average risk of developing breast cancer by a factor of two, and are present in about 11 percent of the female population." In certain rare combinations, it said, the risk of breast cancer is increased by up to a factor of five.

"The protective forms of the genes are present in approximately 13 percent of the female population and are associated with a five-fold decreased risk of developing breast cancer compared to the general population," the company said.

The marker panel was identified in Sequenom's genetics program using unrelated patient and control subjects of European descent, although it said it has replicated the initial association of the markers in an independent Australian cohort.

"These discoveries have triggered on a fairly broad-scale, fairly vivid conversations with major diagnostic service and major diagnostic product companies," Schuh said.

Schuh also said that the "gene itself shows a very, very strong association to cancer," explaining that it carries a 50 percent risk increase to develop the disease.

"It's a very frequent mutation, so that's not a mutation that one in 100 have, it's something you see, say, in one of about eight women," he said.

Developing diagnostics to determine a woman's risk to develop breast cancer based on these markers is more certain than developing therapeutics to treat the resulting disease.

"For the therapeutic value of these genes, it is then essential to assess first whether there is biology in place that suggests that you are indeed talking about a druggable target," Schuh said.

As an example of an identified gene not always resulting in a drug, Schuh pointed to the fact that researchers know the gene that seems to cause cystic fibrosis, but the disease is not cured. They know the role that Braca plays in breast cancer, without knowing how to drug it.

To aid in finding out if a gene is druggable, Sequenom acquired Axiom Biotechnologies, also based in San Diego, in September 2002. Founded in 1995, Axiom came with a fully equipped cellular biology laboratory and biological research capabilities, such as target validation and assay development, as well as capabilities in medicinal chemistry.

Three of the four genes that are in the panel show very specific inhibition of human breast cancer cell proliferation when you knock them down in a small interference RNA experiment in human cell lines, which Schuh called "a highly specific result."

"So we can, with very high specificity, stop the cell proliferation of breast cancer cells while we do not see any biological response in normal breast tissue cells and while we do not see any effect in any other cancer cells," Schuh said. "That's a fairly beautiful result. If you have a gene that says in a human clinical genetics experiment [there is] very high risk association to breast cancer, you replicate that in an entirely independent population, so you could say the gene causes breast cancer."

With the fourth gene, Sequenom has discovered that it can "selectively in human breast cancer cells shut of the ability to form metastasis," Schuh said.

"What that would mean is that you could develop a drug that would [form] a protection shield for a woman immediately after the primary diagnosis [of breast cancer]," Schuh said, adding, "That would be huge."