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Sequenom Aims to Corner SNP-ermarket

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Sequenom recently completed the largest known SNP validation study to date, adding 3,148 novel SNPs to the public domain. “The whole study was designed and confirmed in three and a half weeks,” says Toni Schuh, president and CEO.

Sequenom worked in collaboration with the National Cancer Institute, but the SNPs studied and validated were not specifically cancer-related. NCI funded assays and Sequenom paid for validation of the near-million-dollar project. “The advantage for us,” Schuh says, “is that we now have the assays for all these SNPs. These are all very high-value SNPs.”

Sequenom simultaneously developed its automated assay design engine, which was essential to designing more than 9,000 assays for the study and will be used in an upcoming 100,000-SNP project with Incyte.

The expense and effort involved in making the assays is a stumbling block for other companies, Schuh contends. “That’s something that people who want to play in large-scale genotyping easily forget about. It’s in fact very quickly a multimillion-dollar game,” he says.

Sequenom’s mass spectrometer technology is capable, with multiplexing, of processing 250,000 mass arrays each day, or even more by pooling DNA samples. “The bottleneck is not the detection anymore,” Schuh says — it’s doing the PCRs.

Based on its current technology advantage, Sequenom sees itself dominating the industry. Schuh predicts that when another study comes out and tops these numbers, “it’ll still be Sequenom.”

— Meredith Salisbury

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