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By Malorye A. Branca

May 7, 2002 | The market for validated SNPs is heating up, and Sequenom Inc. wants to be at the head of the pack. In April the company launched its portal, which provides subscribers with a neat package of resources for SNP (Single Nucleotide Polymorphisms) research. Clients can confirm whether specific SNPs are known to be "real" (they occur commonly enough to be potentially useful genetic markers), look up SNP assays, and order Sequenom's confirmed assays from the site.

Later this summer Applied Biosystems (ABI) plans to offer more than 200,000 validated SNP sets. Orchid Biosciences has about 70,000 available, and Third Wave Technologies has more than 100,000 validated SNPs. Each company uses its own platform to identify the SNPs, and there are other distinctions between their offerings. For example, ABI's SNP sets are developed using the Celera human genome sequence data. According to Orchid spokesperson Barbara Lindheim, "Our SNP sets contain a higher proportion of medically relevant SNPs."

SNPs are common genetic markers that are useful for pharmacogenomics and other types of genetic studies. "The frequency of the SNPs is very important," explains Charles Cantor, Sequenom chief science officer. "If you are doing a full genome scan, or doing genetics on any large region, you don't want to be using rare SNPs."

"We've been compiling the data for this site for more than two-and-a-half years," says Sequenom product manager Meghan Lane. "We have tried to take the best of the public SNP data and combine it with our proprietary information in such a way that provides the greatest use to researchers."

Sequenom claims to have more confirmed SNPs than any other supplier.  "We have designed more than two million SNP assays, and validated about 400,000 of these," says Cantor.  Some of these SNPs were confirmed in collaboration with Incyte Genomics or GlaxoSmithKline. Sequenom has genotyping collaborations with both of these companies. Sequenom's SNP assays are not new, but they hope more people will use them now that they are on the Web.

Sequenom thought carefully about their business model. "The only model we have seen for a database is where people say 'You give us $4 million and we give you our data,'" explains project leader Steven Cox. "We decided to do something new."  Subscribers to will pay an upfront licensing fee between $20,000 to $100,000 (depending on their other contracts with the company), and then pay only for the parts of the database they use. "We wanted to make it so just about anyone could afford it," says Cox., says Cantor, "is a natural fit for the Web." Researchers don't have to send any of their valuable data out to the site to make use of it. Rather, they will go there to do searches and order assays.

Besides generating its own revenue, one goal of the site is to encourage more groups to buy Sequenom's MassARRAY genotyping platform, which is already one of the most popular with high-volume users. More than 65 of the systems have been sold to date. 

"We sell the MassARRAY platform, but we are also the biggest user," says Lane.  Sequenom recently began doing its own drug discovery.  "We are now two companies," explains Cantor. "We provide technology to do high-throughput genetic drug discovery, and we do our own." 

For reprints and/or copyright permission, please contact  Jay Mulhern, (781) 972-1359,