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Illumina, DeCode Build 1M SNP Chip; Q2 Launch to Coincide with Release of Affy's 6.0 SNP Array

Building on a previous agreement to co-develop diagnostics, Illumina last week announced that it has designed two new BeadChips for whole-genome genotyping studies with partner DeCode Genetics.
In a statement, Illumina said that the companies collaborated on selecting content for Illumina’s 450S BeadChip, a supplement to its existing HumanHap550 array for genotyping studies, as well as its Human 1M BeadChip, which the company claims will enable whole-genome and copy number variation analysis on a single chip.
Both the 450 supplement and the 1M chip are due in the second quarter, timing that will pit their release against Affymetrix, which has also announced a Q2 launch date for its 1-million SNP product, the SNP 6.0 array.
The synchronized launch dates indicate that that the market for whole-genome genotyping, which was fiercely competitive in 2006, could grow even more combative in 2007.
Sarah Shaw Murray, staff genotyping science manager at Illumina, said that the upcoming genotyping BeadChips underscore the firm’s decision to expand its content beyond the SNPs identified in the human HapMap study to include SNPs from regions of interest requested by its customers, as well as copy number variant information obtained through its partnership with DeCode Genetics.
Murray said that the content on the 450S chip plus the content of the HumanHap550 is “exactly the same” as the content that will appear on the 1M BeadChip when it is released.
Murray said Illumina has used a tag SNP approach to design its arrays since it designed the HumanHap300 chip that it launched in 2005. “We chose SNPs that are population specific and that can serve as proxies for other SNPs,” she said, noting that for the 1M chip, “we wanted to look outside tag SNPs.”
Murray said that the company considered other content strategies that could be useful for studies involving disease traits and whole-genome studies in order to create a next-generation genotyping array for its customers. The firm ultimately turned to copy number variation, a genomic phenomenon that is often surveyed by scientists using other microarray technologies, such as array comparative hybridization.
Once Illumina decided to include content for CNV analysis, it turned to partner DeCode Genetics. The two companies inked a deal last May covering the development of diagnostics on Illumina’s bead-based BeadXpress system (see BAN 5/16/2006). According to Jeff Gulcher, chief scientific officer at the Icelandic biotech, the decision to cooperate with Illumina on new genotyping products was “bilateral.”
“We were talking about what the future of Illumina and DeCode were in terms of our genetic analyses,” Gulcher told BioArray News last week. “We of course had a lot of experience looking at copy number variants. We suggested that this was extra content that would be useful for us and their customers,” he said.
The companies then worked to “try and define regions of the genome that are more likely to be unstable or more likely to have CNV across the population, and some of those changes of course we hope will correlate with some diseases,” Gulcher added.
According to Murray, DeCode had identified proprietary CNV regions that Illumina wanted to put on its new chips. “They had a number of regions that they had identified independently,” she said. “In this capacity we collaborated with DeCode because they had novel CNV regions that at some point will become public domain, but currently they are not.”
Gulcher said that the genotyping product development collaboration and the BeadXpress diagnostics project are separate. Still, he said it is possible that the projects could intersect in the future. “They are independent at the moment, but … if we find copy number variants that correlate with disease and then turn out to be useful clinically as a diagnostic, we’d certainly consider using Illumina’s diagnostic platform as a way of commercializing it,” he said.
Perfect Timing?
When Illumina launches its 1M BeadChip in the second quarter, the product will most likely compete head-to-head with a similar 1-million SNP product from its rival Affymetrix. Last week Affy CEO Stephen Fodor told investors at the JP Morgan Annual Healthcare Conference in San Francisco that the company is selecting content for the 1M SNP product from a master list of 1.6 million SNPs (see BAN 1/9/2007).
Affy said last week that it has begun initial shipments of its SNP 5.0 array, a single chip for genotyping studies that offers 500,000 SNPs and an additional 500,000 probes to measure other genetic differences, such as copy number variation (see BAN 1/9/2007).
When the 1-million SNP chips launch, it will be the first time that Affy and Illumina will release competing genotyping products at the same time. Affy originally launched its Mapping Array 500K Set in late summer 2005, while Illumina began shipping its 550 BeadChip in April 2006 (see BAN 10/5/2005, BAN 4/25/2006).

“If we find copy number variants that correlate with disease and then turn out to be useful clinically as a diagnostic, we’d certainly consider using Illumina’s diagnostic platform as a way of commercializing it.”

However, both products will launch a bit later than initially expected. Last July, Affymetrix singled out the first quarter of 2007 as the expected launch date for the 1-million SNP chip, while Illumina said in March 2005 that it would have a 1-million SNP product on the market by June 2006 (see BAN 7/25/2006, BAN 5/4/2005).
Last week, both firm addressed the delays in their launches. According to Marcus Hausch, academic marketing manager of DNA products at Affy, the firm’s 6.0 array will be in the hands of some early-access customers this quarter, allowing the company to technically meet its initial deadline.
“The full commercial launch of the SNP 5.0 will be later this quarter,” Hausch wrote in an e-mail to BioArray News. “We are on schedule to introduce the SNP 6.0 product this quarter to a limited number of customers. The full commercial launch will follow.” 
According to Illumina’s Murray, the company’s 2005 statement indicated that the company had the “capacity to go to one million.” She added that Illumina benefited in the long run by delaying the launch of a 1-million SNP product.
“If we came out [with] a one million product then, the cost would have been much higher and there wouldn’t have been as big a market demand,” she said.
She also hinted that 1 million will not be the density ceiling for the firm’s whole-genome genotyping array line. “The ultimate resolution is being able to resequence the genome and at some point people [will] probably want that. There’s always room for improvement and room for more,” she said.