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Illumina Gains 'Early Penetration' into Clinical Markets as It Eyes More FDA Submissions

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Illumina said this week that sales of its MiSeq system — including the US Food and Drug Administration-cleared MiSeqDx — its TruSight targeted panels, genomes ordered through its Fast Track services, and HiSeq 2500, are driving its sequencing technology into clinical markets.

"Our results clearly demonstrate the early penetration of NGS into reproductive health, oncology, and other clinical markets, and our improving competitive position," CEO Jay Flatley said during a conference call discussing the firm's 2013 fourth quarter results.

During the call Flatley said that the firm received orders in Q4 for eight MiSeqDx systems, which received FDA clearance in late November, including some from "molecular pathology labs looking to transition [cystic fibrosis] testing to NGS."

Additionally, MiSeq customers showed interest in the company's TruSight panels, which are disease-specific content panels designed to be run on the MiSeq and interpreted with the CLIA- and HIPAA-compliant GeneInsight Suite software.

In particular, customers were especially interested in TruSight One — a panel launched last October that targets 4,813 genes with known associated clinical phenotypes. Nearly 70 customers placed orders for TruSight One, Flatley said, the "best initial market reaction" the company has ever received for a new product. In total, 200 customers ordered TruSight kits, and "many are in the early stages of validation" for laboratory-developed tests, he added.

Illumina's services business, which includes Fast Track whole genomes, genotyping, and the Verinata Health NIPT business, grew 70 percent in the fourth quarter to $51 million compared to $30 million in the fourth quarter of 2012. The firm shipped 5,000 whole genomes through its Fast Track service, a record number and more than twice the number of genomes sequenced in the year ago quarter, which was enabled by reducing its turnaround time to eight weeks.

Illumina also received orders for more than 12,000 whole genomes, including 10,000 from the University of Cambridge and Genomics England for a population sequencing project. Flatley said that project will be "critical to accelerating the discovery of new associations of human variation and disease."

While Illumina does not break out revenues from sales of Verinata Health's Verifi test because it supplies the other US-based NIPT firms with sequencing instruments and reagents, Flatley said that the firm believes the NIPT market in total continues to be a growing market.

"The next big milestone to think about is the extent to which this moves into the average risk categories," he said. "That will significantly broaden out the market for all our customers."

Flatley also reiterated the firm's intention to submit the Verifi test on the HiSeq 2500 to the FDA for in vitro diagnostic clearance this year.

Illumina is also making headway into the commercial and hospital markets with its HiSeq 2500. In the fourth quarter, 90 percent of HiSeq orders were for the 2500, Flatley said. Of those, 60 percent were from existing customers that remain capacity constrained, but of the new customers, 40 percent were from commercial and hospital markets.

Earlier this month, Illumina provided details about its strategy for the clinical market, including its intention to tap into the estimated $12 billion oncology market by developing NGS-based Onco Panels.

During this week's call, Flatley elaborated on the different ways in which the firm plans to capture that market. He said that there will be "multiple sub-segments of the oncology market."

One would be reached with a "low-complexity panel," or the "actionable genome panel," Flatley said. That would include only genes with specific therapeutic decisions — those that are currently reimbursed for single-gene testing. That panel, "we'd get approved through the FDA," he said.

Separately, Illumina intends to develop a panel that would be used for companion diagnostic testing for pharmaceutical companies to use in clinical trials.

Then there is the middle part of the market, which is the market Foundation Medicine currently occupies, Flatley said. That market includes "higher complexity panels," including "everything our panels will have plus a whole lot more." That panel will also be able to "deal with rare cases where you don't know exactly what you're looking for," he said. Finally, on the higher end, there will be customers that sequence exomes and whole genomes of cancer patients.

Looking ahead, Flatley said that the two new sequencing instruments Illumina unveiled at the JP Morgan Healthcare Conference in San Francisco earlier this month will also eventually expand Illumina's presence in the clinical market.

The HiSeq X Ten is a $10 million system that is sold as a set of 10 units, each of which will have the capability to sequence five whole human genomes in one day, or generate 1.8 terabases of data in under three days. The system will not have immediate clinical applications, but because it is expected to drive down the cost of human genome sequencing to $1,000, Flatley said that it will open up clinical sequencing by "improving the clinical utility of the genome."

Today, "we've only scratched the surface about what the genome means," he said.

Additionally, Flatley said during the call that the firm received its fifth customer order, from Decode Genetics, which is owned by Amgen. Whether this is a sign that pharmaceutical companies in general will be interested in the HiSeq X Ten still remains to be seen, Flatley said, but "at $1,000 [per genome], this has catalyzed the imagination of many of our customer types."

The NextSeq 500, on the other hand, will target the clinical market more directly. The benchtop system uses a two-channel design and new optics and will be especially suited for the NIPT market. The firm also previously said that it would submit the NextSeq 500 to the FDA, although it has not provided a timeline.

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