NEW YORK (GenomeWeb) – Illumina said this week that it is continuing to penetrate the nascent clinical sequencing market with sales of both its MiSeq and HiSeq systems, reiterating its intentions to submit NGS-based assays in noninvasive prenatal testing and oncology to the US Food and Drug Administration for 510(k) clearance.
The FDA clearance of its MiSeqDx system helped spur record demand for the MiSeq, including for both the cleared and research-use-only version, in the first quarter of 2014, Illumina CEO Jay Flatley said during a conference call this week discussing the firm's first quarter results.
While he did not specify how many units were ordered, he said that approximately two-thirds of MiSeq orders were from government, translational, clinical, and commercial customers, including an order of 13 systems by the US Department of Defense to be used in a biosurveillance program to do whole-genome sequencing of bacteria and viruses.
In addition, it received "follow-on multi-unit orders from existing customers building capacity in production facilities," for example from Histogenetics, which will use the platform to do "high-resolution sequence-based HLA typing," Flatley said. HistoGenetics, which now has the largest fleet of MiSeqs of any Illumina customer, initially ordered 20 systems last year that it planned to incorporate into its HLA typing workflow.
HiSeq orders also trended toward clinical customers, as purchases shifted toward the HiSeq 2500 from the HiSeq 2000. Around 70 percent of HiSeq orders were from new customers, the majority of which were clinical, commercial, and hospital customers, and many of which are "in the early stages of assay validation, creating the potential for follow-on orders as the methods enter production," Flatley said.
Of Illumina's newly launched sequencing systems — the NextSeq 500 and the HiSeq X Ten — the NextSeq 500 is the one most likely to be adopted for clinical purposes in the near future.
Illumina shipped 65 NextSeq 500 systems, the vast majority (about 85 percent), to existing customers. Half of orders were from non-academic customers that are using the system for applications such as targeted RNA sequencing, exome sequencing, and NIPT.
In addition, the firm has generated over 2,500 new leads, and new customers account for about "one-third of the pipeline, and clinical accounts are prominent," Flatley said.
"Sequencing uptake in oncology is gaining significant traction," Flatley said. Feedback from recent conferences, including the American Association for Cancer Research conference in San Diego earlier this month, "points to standards as being a critical factor for driving adoption," he said. And as such, Illumina is collaborating with "oncology thought leaders to drive standards for the use of NGS in a clinical setting." Overall, Illumina estimates the oncology market to be around $11 billion, which will only be able to be tapped if there are standards, Flatley said.
In addition, the firm is working to develop FDA-cleared onco panels. Flatley said that it is in the process of defining the content as well as working with regulatory bodies about how to do clinical trials around such products. By end of year, he expects Illumina will have made progress in defining what the products will look like, and by 2015 the firm will be "in the midst" of developing content and assay methods and submitting regulatory filings.
Pharmaceutical companies are also increasingly interested in using sequencing for oncology, Flatley said. Initially, pharma used sequencing primarily for discovery, and mostly outsourced the sequencing to contract research organizations. Increasingly, though, "pharma is becoming a large base for us, particularly around companion diagnostics, which is moving toward sequencing," Flatley said.
For example, Amgen signed an agreement with Illumina to develop an NGS-based companion diagnostic test for its colorectal cancer drug Vectibix (panitumumab).
Illumina is also planning clinical assays in the area of reproductive health. As it has previously said, it plans to submit Verinata Health's Verifi test to the FDA for in vitro diagnostic clearance on the HiSeq 2500 by the end of the year.
Currently, Illumina offers the Verifi test as a laboratory-developed test through the CLIA-certified, CAP-accredited laboratory it gained when it acquired Verinata Health. Flatley said that Verifi revenues and volumes were at "record levels" this quarter. Previously, the firm discussed its plans to begin a technology transfer program, where it will offer clinical labs in other countries a turnkey solution for NIPT. On this week's call, Flatley said that it successfully completed such programs in France, Germany, and Italy, and that it is in discussions with two-dozen other technology transfer customers.
As a result, he said, the Verinata Health business will reach break even by the end of the year.
Additionally, he cited the New England Journal of Medicine study comparing Verifi to standard prenatal screening, as one of several studies that will demonstrate the efficacy of NIPT in average-risk women — a market six times larger than the current high-risk market, he said.
Also in the reproductive health field, Illumina plans to launch a preimplantation genetic screening assay, VeriSeq, that screens single cells for chromosomal aneuploidies. Researchers from Italy's Genoma Molecular Genetics Laboratory in Rome published a validation of the method in the journal Fertility and Sterility last month.
Flatley said that the VeriSeq assay will "launch shortly" for use on the MiSeq and will be available for use on the NextSeq 500 later this year.