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In Genome Quebec s Grand Plan for Illumina s Genotyping System, HapMap Is Half the Story

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By selling its newly released SNP-genotyping platform to Genome Quebec earlier this month, Illumina has ensured that its technology will produce fully one-fourth of the data for the International HapMap Project.

Illumina also hopes the deal will derive longer-term revenue through backdoor channels: This spring, as Genome Quebec installs Illumina’s platform and begins cranking out hundreds of thousands of SNPs per day for the HapMap, Genome Quebec will market its remaining cap-acity to industry and academia.

“We’re very excited about having this platform in Genome Quebec,” said Paul L’Archeveque, president of the regional group. “I think that being in Quebec and trying to build genomic strength in the province is an indication that we’re making some important progress.”

Genome Quebec became the first customer of Illumina’s SNP-genotyping unit Jan. 9. The platform, which Illumina says is more like a full-blown lab than a traditional genotyping instrument, will reside at the Genome Quebec Innovation Centre, located on the top three floors of a building completed this month on the McGill University campus.

Meantime, Illumina’s HapMap effort, led by co-founder Mark Chee, will use the company’s instrument alone to absorb half of the workload for the project — almost 250,000 assays — it shares with partners David Altshuler, of the Whitehead Institute for Biomedical Research; Richard Gibbs, of Baylor College of Medicine; Pui-Yan Kwok, of UCSF; and Aravinda Chakravarti, of Johns Hopkins.

Thomas Hudson, the PI and head of the Canadian HapMap effort, was instrumental in selection the Illumina patform. The researcher, who knew Chee “through previous collaborations” when the Genome Quebec researcher was assistant director at the Whitehead Center for Genome Research, said he has “been following the development of the Illumina bead-array platform for several years” and “was quite impressed” by it.

Proving Ground

“My group was already evaluating [high-throughput genotyping platforms] for the haplotype-map project … and we decided to go to Illumina to visit the operations,” he said. After evaluating “most of the high-throughput platforms on the market,” Hudson said he was hooked on Illumina.

According to Illumina, the unit, which is at the heart of a legal skirmish with Applied Biosystems, costs between $1.5 million and $2 million and can produce up to 1 million genotypes per day. Still unnamed, the product comprises Sherlock scanning equipment, GoldenGate assay protocols, LIMS and analytical software, fluid-handling robotics, and access to Sentrix array matrices and reagents.

Hudson said what drew him to the platform was its “1,000-fold multiplex, which [means] much reduced genotype costs.” Also at the top of the list was the fact that “the redundancy and controls that are built in provide confidence scores that are very useful.”

To make the most of this platform, Hudson, L’Archeveque, and Illumina decided Genome Quebec would be able turn some of its existing customers into users of Illumina’s platform. Half of Genome Quebec’s 50 researchers will use half of the unit’s capacity. The balance will be reserved for “other in-house projects, collaborations, and genotyping services to the research community” — and likely opening royalty streams for Illumina in the process.

Currently, Genome Quebec offers genomics services to Canadian academic and private-sector labs, said Hudson, who named as examples Affymetrix’s GeneChip platform, microsatellite genome scans, and SNPs based on Applied Biosystems’ TaqMan chemistry.

“We have a larger and larger number of products in Canada that are large-scale disease-association studies, for which the haplotype map will be used,” said Hudson. “So we anticipate that … our customers are going to want to start doing genome-wide haplotype mapping in a couple of years.”

Existing pharma companies include SNP Consortium member Bristol-Myers Squibb, for whom GW has performed genome scans “for a number of years,” and a collection of small biotech shops in Canada, according to Hudson.

“Immediately, the Illumina technology is for the HapMap, but down the road most of the work will be applications for disease-association pharmacogenetics,” he explained.

To be sure, Genome Quebec has not yet used the Illumina platform to lasso any additional pharma customers. “But I don’t want to line up customers before we have begun our production for the HapMap,” Hudson said. The platform, he added, will be operational in April producing hundreds of thousands of SNPs each day.”

“As soon as we’re up and running this huge amount of extra capacity is when we’ll start lining up” customers,” Hudson said.

— KL

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