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Illumina Lays Out Plans for Dx Sequencing as 454 also Considers Diagnostic Apps for Its Technology

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This article has been updated to include additional information from Illumina.

Sequencing will play a prominent role in Illumina's three-pronged strategy to develop diagnostic tests and services, according to the company's chief executive.

Separately, Roche's 454 Life Sciences has disclosed it is considering ways to make its sequencing technology available for diagnostic applications.

Illumina does not currently sell any products in the molecular diagnostic space, which it estimates to be worth $3 billion today, and $5 billion by 2011, but it has come up with a three-part strategy to enter the market, all of which involve sequencing, according to President and CEO Jay Flatley, who spoke at the JPMorgan Healthcare Conference in San Francisco last week.

The first part is a "platform partnering" program under which Illumina will work with customers to develop diagnostic applications. The plan involves both Illumina's existing BeadXpress genotyping platform and its Avantome sequencing technology, which it acquired last summer but has not yet commercialized.

At the moment, the BeadXpress platform is "at the forefront" of this program, and Illumina is "already working with customers" to develop genotyping assays for blood typing, prenatal testing, and certain pharmacogenomics applications, according to Flatley. He said that the company hopes to obtain FDA approval for the BeadXpress platform in the second half of the year.

He did not elaborate on the nature of the diagnostic tests that Illumina wants to develop on the Avantome platform, or the partners involved in developing these sequencing-based tests.

The second leg of Illumina's strategy is a plan to open a CLIA-certified diagnostic laboratory that will "introduce services using DNA sequencing." Flatley said this lab will enable the company to enter the diagnostic market earlier than its other programs.

He said the company plans to apply for CLIA certification during the first half of this year and hopes to start generating revenue from diagnostic services in the second half of 2009.

Flatley said the CLIA lab will offer services that are based on proprietary content from Illumina's licensing and discovery program, but it will also offer sequencing services for "traditional targets" to "begin to generate revenue," such as carrier testing for Rett syndrome; drug-resistance testing for HIV and Mycobacterium; mutation detection in the genes P53, KRAS, BRAF, EGFR; and HLA testing.

According to an Illumina spokeswoman, the company's primary interest for the CLIA lab is to provide sequencing services on its Genome Analyzer.

The third part of Illumina's diagnostic strategy is a large-scale internal oncology discovery research project, under which Illumina will study ovarian and gastric cancer.

This year, the company plans to sequence approximately 50 cancer genomes and their normal controls — about 20 in the first half and 30 in the second half of the year, according to Flatley. It will also conduct whole-transcriptome and methylation-profiling analyses of these samples.

He said the company is embarking on this research project at this time because "we can sequence now so rapidly, and at such great cost points."

After validating the results in a larger number of samples, Illumina plans to develop diagnostic tests using these results on its array platform. For ovarian cancer in particular, the goal of the project is to "identify very early markers for diagnosis" and to "begin to look at the genetics of therapy resistance, in particular resistance to platinum therapy," according to Flatley.

Illumina is not the only company that is considering its sequencing platform for diagnostic applications. Researchers have already been using Roche's 454 sequencing technology in related areas, for example to study drug resistance of HIV, HCV, and HBV, or to look for mutations in cancer genes that cause drug resistance. Now, 454 Life Sciences itself is looking into how to make its instrument applicable to diagnostics.

"The system's high accuracy and quick run time make 454 sequencing ideal for medical applications," Christopher McLeod, 454's president and CEO, told In Sequence in an e-mail message. "We are discussing with regulatory authorities the best path to make 454 sequencing technology available for diagnostic use."

"We are sure that 454 sequencing is the best technology for future use in healthcare," said Manfred Baier, head of Roche Applied Science, via e-mail.

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