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Following Merck and Roche's Lead, Glaxo Upgrades To Whole-Genome Genotyping With New Service Deals

Two back-to-back genotyping deals last week with Illumina and an Affymetrix service provider show that GlaxoSmithKline is expanding its existing SNP-genotyping service pacts to include more whole-genome genotyping.
Illumina and Affy service provider Expression Analysis announced their separate deals with GSK on Aug. 2. Under the terms of GSK’s agreement with Illumina, the San Diego firm will use its Sentrix HumanHap550 BeadChips for a series of whole-genome association studies for Glaxo.
The first study will involve genotyping 2,000 case and control DNA samples provided by GSK for a specific undisclosed disease, Illumina said.
At the same time, Expression Analysis said in a statement that its GSK contract will rely on Affy’s 500K mapping array set and will advance EA’s “goal of supporting pharmacogenomic studies in clinical trials."
Though both companies told BioArray News this week that the deals are extensions of previous agreements with GlaxoSmithKline, it’s the first time the drug giant will use the companies’ highest-density chips.
The deals come at a time when other large pharmaceutical companies, including Roche and Merck, are investing more in companies like Affy and Illumina for whole-genome genotyping needs. They also highlight Glaxo’s strategy of outsourcing more of its genotyping studies rather than bringing the technology in-house; apart from an October 2005 agreement with Affymetrix, all of GSK’s publicly announced genotyping projects have been service contracts.
The agreements also shows that some pharmas appear to favor using Affy and Illumina’s platforms simultaneously rather than choosing one technology over the other.
For example, Alan Sachs, vice president of molecular profiling at Merck, told BioArray News in July that the company decided to invest in its own genotyping capabilities and has set up its own genotyping facility at Merck Research Laboratories near Seattle that will use both Affy and Illumina systems (see BAN 7/5/2006).
And in May Mitch Martin, head of genomic research at Roche's Nutley, NJ-based R&D center, said there has been a “greater willingness” among pharmas “to consider whole-genome genotyping in applications." He said Roche favors mixing the platforms in their projects rather than choosing one over the other.
"Previously, Roche used [genotyping] mainly in research applications in doing screening of the genome and of candidate genes to look for associations to disease susceptibility," Martin told BioArray News at the time.
Craumer said this week that although Illumina has a 5-year relationship with Glaxo, the drug maker does not own a BeadLab for in-house genotyping experiments. “We perform the service in San Diego,” Craumer told BioArray News.
GSK was also an original adopter of Affy’s whole-genome genotyping technology when its 500K set was launched last October. The company signed a multi-year agreement with Affy to use the 500K set to perform whole-genome association studies. However, Affy has never publicly discussed the sale of its instrumentation to GlaxoSmithKline.
Pharma Bellweather?
GSK has had a lengthy relationship with Illumina, dating back to a June 2001 SNP-scoring deal. Since that time the companies have inked a number of agreements that aim to further GSK’s pharmacogenomic and whole-genome association studies, including a 2002 deal to develop SNP assays for a whole-genome linkage disequilibrium mapping product, and a more general genotyping deal in 2005.

“The agreements reveal that, rather than favoring one platform over the other, pharma has decided to use both Affy and Illumina’s respective platforms for its projects.”

Glaxo’s interest in genotyping has been a boon for Affy as well as for Affy subsidiary Perlegen, which signed three genotyping deals with GSK since 2002, most recently in September 2005 (see BAN 9/7/2005).
The willingness of Roche, Merck, and now Glaxo to adopt the high-density chips could herald greater implementation industry wide. At least that’s what Illumina CEO Jay Flatley is hoping.
Flatley said in a statement last week that the GSK agreement “underscores the increasing rate at which pharmaceutical and biotech firms are adopting genotyping technology for discovery and pharmacogenomic applications."
Flatley has been pushing that message since the company launched the HumanHap550 chip in April. Illumina signed a deal with Johnson & Johnson’s Pharmaceutical Research & Development last month to develop custom SNP content for a multi-sample Sentrix BeadChip.
Craumer said this week that the company has other undisclosed pharma customers and that, in general, Illumina doesn’t announce individual system deals “unless they are material and/or there is a strategic angle to the sale.”
Expression Analysis said this week that an increased interest from pharmaceutical companies in using Affy’s 500K chip was helping to increase its revenues.
“Genotyping, primarily using the Affymetrix 500K Mapping Array Set, has grown to be an exciting new segment of [EA’s] business in the first half of 2006,” EA said in a statement providing limited financial results for the first half of 2006.
Altogether the company said that for the first half of 2006, Expression Analysis has increased its overall revenue by just over 83 percent when compared to first half 2005 revenue.
“Expression Analysis has multiple service agreements in place to provide genotyping services, and has processed the 500K Mapping Array Set for major pharmaceutical companies, as well as universities and research hospitals,” EA said.
GSK could not be reached for comment.

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