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Illumina's Flatley Discusses Future Diagnostics Path, Array Roadmap at Goldman Sachs Conference

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By Justin Petrone

Illumina believes its arrays will be used "routinely for medical management" in coming years and has seen "very significant uptake" for its next generation of Omni BeadChips, according to its highest official.

CEO Jay Flatley said last week that the San Diego vendor is working with the US Food and Drug Administration to determine the best regulatory path for array-based tests, though it recognizes that the line between research, diagnostics, and consumer genetics is becoming increasingly blurred.

According to Flatley, Illumina has been discussing with the agency "how you begin to think about doing approvals of products that have hundreds of tests on them without running clinical trials," noting that to "approve one array just isn't practical."

Illumina believes that "traditional notions of validation aren't going to be possible," and that the "right answer is not going to be how to run 100 million clinical trials" to validate an array-based test, he said.

Flatley made his comments during the Goldman Sachs Global Healthcare Conference, which was webcast from Los Angeles last week.

Illumina has stated previously that it believes its chips will be used in diagnostics. Earlier this year, the firm said it submitted a cytogenetics package to the FDA as part of its preliminary investigational device exception process. The submission includes the company's iScan system plus its HumanCytoSNP-12 and HumanOmni1-Quad chips (BAN 1/26/2010).

Flatley said last week that the company is a "leader in the consumer genomics market," and "provides arrays to most consumer genotyping companies." Illumina recently received a letter from the FDA requesting information on why it believes its platforms does not need to be cleared by the agency. The agency noted that 23andMe and Decode Genetics use Illumina's research-use-only Infinium HumanHap550 array in their direct-to-consumer genetic-testing service (BAN 6/15/2010). Illumina was the only platform vendor contacted by the FDA.

Flatley predicted that it will become increasingly difficult to separate research from diagnostics over time. "It's our view that roughly in a five-year time frame the lines between the research, consumer, and diagnostics markets are going to get hazy," Flatley said. "You will see convergence of these markets," he said.

According to Flatley, regulation of the molecular diagnostics space is still focused on "single-analyte tests either prescribed sequentially or in a small group." With the increased use of both arrays and high-throughput sequencing, though, it has become more difficult to apply this model to the regulation of tests based on these platforms. He said that both technologies are generating content that can be used in new diagnostics.

"We are now in the era of rich genome-wide association studies, and we think a lot of content will come from these programs; sequencing human genomes is becoming routine, and sequencing of cancer biopsies is becoming economical," Flatley said.

Because of this, Flatley predicted that "arrays will be used routinely for medical management, price per sample will be well under $100 per array, and we'll be able to put all relevant markers on those arrays."

'Resurgence of Revenue'

During his talk at Goldman Sachs, Flatley said that the firm is beginning to see a "resurgence of revenue" in its array business; making up for a slowdown in the market for genome-wide association tools that Illumina has continued to insist will rebound once more rare-variant content becomes available. He cited sequential growth in array sales over the past two quarters as proof of this revival.

"There has been a lot of talk about the GWAS market and whether it was a dead market," Flatley said. "And we have stood by our conviction that last year there was a lull in the GWAS market because of the need to get richer content onto the chips," he said.

Illumina earlier this month began shipping its HumanOmni2.5-Quad DNA Analysis BeadChip. The array includes newly discovered genome-wide common and rare variants from the 1000 Genomes Project selected to maximize its ability to detect new associations, the firm said. The new chip is available in a four-sample format composed of approximately 10 million markers per array (BAN 6/8/2010).

Illumina also began shipping its HumanOmni1S-8 BeadChip, which allows current or former users of Illumina's Omni1-Quad or OmniExpress BeadChips to access new 1000 Genomes Project-derived content without having to purchase the Omni2.5. The 8-sample array contains the majority of new content present on the Omni2.5, and is part of a number of arrays the company will introduce to smooth the transition of current users to Illumina's anticipated HumanOmni5 BeadChip, which is scheduled to be launched later this year.

Flatley said that Illumina is seeing "very significant uptake" of the Omni2.5 from "customers beginning to do these next-generation GWAS studies," and that the new chips "fit right into the roadmap" Illumina has put forward of delivering the technology. "We are very pleased with what we believe is a resurgence of revenue in GWAS," he said.

Flatley did not discuss a launch date for the Omni5, but the company has said previously that it will become available during the second half of this year. Flatley said that Omni5 product development is "currently constrained" by the 1000 Genomes Project, which is still generating new content. Once Illumina has access to that "last bit of content," the firm will be able to "get it into production and get it to the market quickly."

The 1000 Genomes Project last week released data for its pilot phase. The two-year production phase of the effort, which ultimately aims to analyze the genomes of as many as 2,500 people, will end in early 2011.

Central to Illumina's business plan is its so-called roadmap, which calls for the introduction of supplementary chips to give customers access to all the content that will eventually be available on the Omni5. "We have created the ability for customers to start at different positions in this roadmap," Flatley said. "You could start with the Omni2.5 or the OmniExpress and then very economically get up to the Omni2.5 or the Omni5," he said. Illumina has also launched a multi-sample preparation kit so that customers can prepare one sample for use on multiple chips over time.

While Flatley noted that around 450 associations have been discovered using whole-genome genotyping arrays in GWA studies, the firm now believes its first generation of chips lacked the power to explain most of the heritability of human disease. For instance, the company’s Omni1-Quad BeadChip, launched last year, had 92 percent coverage of common variants available in the International HapMap Project, which concluded in 2005.

With the data generated by 1000 Genomes, though, the number of known variants has grown from about 10 million to 30 million. "The power of those original chips isn't what we thought as human variation is greater than we originally assumed," Flatley said. With the Omni2.5, Illumina now provides coverage of 80 percent of variants found up to a frequency of 2.5 percent in the population, and the Omni5 chip will provide "greater" coverage. "That's all fertile ground for new discovery," Flatley said.

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