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Illumina CEO Says Next Round of GWAS Will Be Done on Arrays, Not Sequencers

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This story was originally posted on Jan. 15.

By Justin Petrone

Though Illumina was "handed a number of challenges in 2009," including slowing demand for its whole-genome genotyping arrays from researchers conducting genome-wide association studies, the company's CEO last week said that he is confident the market's appetite for arrays will revive this year.

Jay Flatley also said that while there is enthusiasm for Illumina's sequencing instruments, the company believes that arrays are currently "faster," "cheaper," and "more accurate" than existing next-generation sequencers for GWAS.

Flatley, who made his remarks during a presentation at the JP Morgan Healthcare Conference in San Francisco last week, reiterated previous comments that in the past year Illumina has experienced a "slowdown in the genome-wide association market that exceeded our predictions largely because researchers held off on new projects awaiting novel content from the 1000 Genomes Project."

Illumina has pledged to make that rarer variation content available on a new generation of arrays scheduled to launch later this year (see BAN 11/3/2009).

During his talk, Flatley discussed Illumina's newly launched HiSeq 2000 sequencer, which has two flow cells instead of the one on the Genome Analyzer and can sequence 200 gigabases per run.

The company estimates that the HiSeq 2000, which has a list price of $690,000, will allow users to sequence a human genome at 30-fold coverage for around $10,000, and to analyze gene expression in up to 200 samples for $200 per sample.

But even though the throughput for sequencers is increasing and costs are decreasing, Flatley said that sequencing is still "not an applicable technology for the next round of GWAS that will happen over the next few years" as researchers look to rarer variation to explain the heritability of human diseases.

"Arrays are a hundred times cheaper, a hundred times faster, and materially more accurate than sequencing will be over the next couple of years," Flatley said.

He also said that the money will be there to finance such studies. "The GWAS budget from [the National Institutes of Health] in '09 grew about 30 percent over '08, and if you add the [American Recovery and Reinvestment Act] stimulus on top of that [it grew by] about 90 percent," Flatley said.

According to an analysis by BioArray News, as much as $42 million, or 55 percent, of the $76 million in stimulus grants awarded to array-related projects went to GWAS (see BAN 10/13/2009).

Flatley noted that during the fourth quarter of 2009, Illumina "saw a rebound in our GWAS business" compared with first-quarter levels. "Our GWAS business also grew sequentially," he added.

Flatley also announced unaudited fourth-quarter revenues of $176 million, above the roughly $168 million predicted by analysts. Illumina has decided to stop providing quarterly guidance, Flatley said. But he said that the firm expects 2010 revenue growth of at least 20 percent.

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