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Illumina Mulls FDA Clearance of HiSeq 2000; Sees Strong Demand for Whole-Genome Sequencing


By Julia Karow

This story was originally published Sept. 16.

As clinically oriented whole-genome sequencing projects are gaining traction, Illumina is considering whether to apply for 510(k) approval for its HiSeq 2000 platform, according to a company official.

Illumina launched the HiSeq 2000, its highest-throughput sequencing platform, earlier this year and has seen stronger-than-expected demand for the instrument (IS 8/3/2010).

At the Morgan Stanley Global Healthcare conference in New York this week, Christian Henry, Illumina's CFO and general manager of its life sciences business, said that the HiSeq has already lowered the cost of human genome sequencing to $10,000 or less, "and over the near term, or near-mid term, we should be able to get to the $1,000 genome with this kind of technology."

With that falling cost has come an "incredible demand" for human whole-genome sequencing, he said, as scientists are thinking of ever bigger projects. "Whereas last year, a 25-sample project would be a monster project, this year, a 50-to-100-sample project is a big project, and at some of the bigger centers, folks are thinking about, 'How can I do a 500-sample project or a 1,000-sample project?'" Henry said.

What these groups sometimes fail to mention, he added, is that these projects will often not happen immediately but over a period of time, because getting access to and preparing suitable samples "is always going to be a challenge."

Illumina has also witnessed a growing interest in clinical sequencing, he said, and is currently evaluating whether to submit the HiSeq system for 510(k) approval by the FDA. Clinical sequencing "is going to be a very significant market opportunity," according to Henry, particularly in oncology.

He said that doctors have already ordered whole-genome sequencing of tumor/normal pairs for their patients through Ilumina's individual genome sequencing service. "It's definitely not a routine thing happening, but you're starting to see physicians do that here and there, and also starting to see in the research community a lot of excitement about the analysis … so we have to prepare our instrumentation to be regulated and approved, so customers can, in fact, go in that direction," he explained. Earlier this year, Illumina was granted 510(k) clearance for its BeadXpress system and is currently seeking the same approval for its iScan array reader.

But while demand for human whole-genome sequencing has been growing, Henry doubted that researchers will contract much of it out to service providers. Illumina recently started offering human whole-genome sequencing services for researchers through its Illumina Genome Network. Complete Genomics is pursuing that market exclusively under its business model, a potential threat to Illumina's instrument and reagent sales, and Illumina recently filed a patent infringement suit against Complete Genomics, shortly after the firm filed for an IPO.

"For the vast majority, scientists like to have control over their samples, and scientists like to have control of the instrumentation," Henry said, adding that "probably about 10 percent of the market or so is available to us and to others as a service-based business."

Henry claimed that "the vast majority of people," given sufficient funding, will purchase a HiSeq system rather than use Illumina's service. "That way, they have much more flexibility in the applications that they can do, they have much more control over their own samples, and they have much more control over the data analysis side of it, too, because they can look at all the information, not just what a provider would provide them with."

He said Illumina has been surprised by how many of its customers have been able to come up with funding to purchase a HiSeq, which has a list price of $690,000. "Customers have been able to combine budgets, put funds together, and the funding hasn't been a constraint on purchasing the equipment," he said. Overall, "more and more funding is moving into sequencing, giving folks bigger capital budgets," not only in the US, but also in other parts of the world, including Europe and Asia.

High demand for HiSeq has required Illumina to scale up manufacturing of both the instrument and consumables. During the second quarter, the company scaled up its HiSeq production capacity by five-fold, and the goal during the current quarter is to double it again. Henry said that some parts for the HiSeq have a lead time of three to six months, but that the company has "aggressively managed the supply chain," has hired additional personnel, and has added space for manufacturing. While customers may still have to wait for their HiSeq to ship, the time for installing it has fallen from 10 days to five, he said.

A recent hiccup in the manufacture of HiSeq flow cells has been "immaterial" to Illumina's growth margin and top line, Henry said. The flow cell manufacturer had "some issue with their bonding process," he explained, forcing Illumina to put additional quality-control measures in place, which lowered the flow cell yield and their supply to the market. He added that the issue "was a little bit overblown" by others.

Henry said Illumina expects that "well over half" of its current Genome Analyzer customers will acquire a HiSeq instrument "at some point in time," though this might take on the order of two years. Illumina also continues to sell GAs, he added, in line with its strategy to offer different types of sequencing platforms at varying price points to different users.

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