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Illumina CEO Sheds More Light on Consumer Genotyping Market, Future Product Strategy

Declaring Illumina’s product architecture sturdy enough to support whatever the market demands, CEO Jay Flatley last week painted a sunny picture of the genotyping market at Leerink Swann’s Life Science Tools Roundtable Conference in New York.
Specifically, Flatley said that the firm’s assays and existing products are flexible enough to handle higher-density arrays should the market call for them, as well as some of the potential consumer genotyping services that Illumina is beginning to explore.
Illumina first disclosed its plans to enter the consumer genotyping market last month, when it announced that it is working with 23andMe, a Mountain View, Calif.-based personal genetics testing start-up. Last week, Flatley fleshed out how an arrangement between 23andMe might work, with Illumina augmenting an existing array with customized content and then offering the resulting chip through a service (see BAN 8/7/2007).
“We are very excited about a new opportunity in consumer genotyping and we see this as a very exciting market in the next couple of years,” Flatley said at Leerink Swann. According to Flatley, the arrays that Illumina could offer 23andMe “will use [Illumina’s] existing architecture but they will have different SNPs on them.
“So if your target is to do consumer genotyping with SNPs that are medically relevant, you may want to trawl through the literature and discover every SNP that is known to have an association and make sure that is on your chip,” Flatley said.
He added that for Illumina, “that is easy to do because we have the architecture in our product line so you could take a [HumanCNV370-Duo DNA Analysis BeadChip] and augment it with an additional 60,000 SNPs that you have gleaned from the literature, or you could do that on the HumanHap550 as well,” he said. “That’s very likely the kind of chip you will see used in consumer genotyping.”
Illumina’s CNV370-Duo chip is a multi-sample whole-genome array that genotypes two samples simultaneously using more than 370,000 markers each. It provides both copy number variant and SNP content. The HumanHap550 is Illumina’s best selling product and contains more than 550,000 SNPs from the International HapMap Project. Whichever chip eventually makes it to the consumer genotyping market, Flatley said that it will most likely be available through a service.
“We really think this is going to be a service-oriented business and that customers will come to Illumina or other providers and the genotyping will be done separately,” he said. In an e-mail to BioArray News last week, Flatley defined this new personalized market as one where there is no clinician standing in between a test provider and an individual.
“If an individual submits their sample to be genotyped, signs the appropriate consents, pays for the work and gets the data, that is consumer genotyping,” he wrote (see BAN 8/7/2007).
Illumina so far has not disclosed any other partners in the nascent consumer genotyping market. A spokesperson for 23andMe confirmed last week that the companies are working together, but declined to answer more detailed questions. According to 23andMe’s website, the firm is planning an official launch by the end of the year.
The 2-Million SNP Question
During the Leerink Swann conference, Flatley also addressed Illumina’s plans for the SNP genotyping market, which continues to be the primary pillar of the firm’s business even as it continues to successfully place its digital microbead-based BeadXpress and next-gen sequencing Genome Analyzer instrument with customers.
Over the past two years Illumina’s SNP genotyping offering has diversified to offer population-specific products for association studies, like the HumanHap650Y BeadChip for African population studies, or to offer more multi-sample possibilities, like the recently launched Infinium HumanHap550-Duo BeadChip, which provides the same content as the HumanHap550 BeadChip in a dual-sample format to increase throughput and reduce price.

“If the market wants 2 million SNPs instead of 1 million SNPs, we’ll have the ability to go there.”

Flatley said that of all the firm’s products, he expects the HumanHap550-Duo and Human 1M BeadChip — launched last month — to meet customer demand over the next year. He specifically said that the firm believes that its multi-sample format will remain a key factor in attracting customers.
“For us multi-sample is core to our strategy and we have done that across several different product lines right now,” he said. “If I had to predict a year out from today I would say that 40 percent [of sales] would be for the the 1M, and maybe 40 percent would be in a 550-Duo type of configuration,” he said.
“There are still customers using our 370 product in a duo configuration that believe that that is all they need in a Caucasian population because the coverage is so good ... there is no reason to move to a 550 or 1M,” he said.
Flatley’s comments echoed those of John Blume, Affymetrix’s vice president of RNA products, who said during the Leerink Swann conference that many of Affy’s customers see no current need for the firm to introduce higher-density chips (see related story, this issue).
Still, Flatley said that the firm has the capabilities in place to introduce a 2-million-feature SNP genotyping product for whole-genome genotyping studies in the future, should the market request it.
“If you look at genomic coverage, we have very even coverage across the entire genome and the way our assay works gives us access to virtually any SNP,” Flatley explained. “The [Infinium] Assay is very robust and very scalable and if the market wants 2 million SNPs instead of 1 million SNPs we’ll have the ability to go there,” he said.
According to Flatley, the proliferation of new SNP genotyping arrays in the marketplace will continue to feed the large whole-genome association studies that demand large quantities of the arrays. This will in turn buoy the whole-genome genotyping market even as newer markets, like consumer genotyping, take off.
“As far out as we can look we see [whole-genome association studies] continuing; as the chip capabilities increase we see people going back and doing larger studies with the new chips, in some cases augmenting the chips they’ve been using with some of our newer chips,” Flatley said.

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