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Illumina Discusses Clinical Plans, Regulatory Strategy for Oncology, Reproductive Health Markets


NEW YORK (GenomeWeb) – Illumina discussed its next steps in tapping into the clinical oncology and reproductive health next-generation sequencing markets this week, including an update to the Actionable Genome Consortium, its liquid biopsy program, and new clinical trials it has launched in the reproductive health field.

During a conference call discussing the firm's third quarter performance, CEO Jay Flatley said that despite missing Q3 revenue expectations, sales to clinical and translational customers grew by more than 40 percent compared to Q3 2014. Half of all NextSeq orders were from clinical and translational customers.

In addition, he said that the HiSeq family of sequencing instruments did especially well. For example, the Broad Institute ordered another 10 HiSeq X units specifically for its National Heart, Lung, and Blood Institute-funded project to sequence 20,000 individuals.

Looking ahead, Flatley said that opening up the HiSeq X instrument to sequencing non-human genomes — a recently announced change to the company's policy — would further boost sales. Flatley said there has been interest from agricultural customers in using the HiSeq X to sequence bovine genomes, and other potential customers have expressed interest in sequencing model organisms like rat and mouse.

On the clinical side, Flatley highlighted Illumina's advances in the oncology and reproductive health fields.


During the third quarter, Illumina launched the first product developed from its Actionable Genome Consortium, which it formed last year in collaboration with four academic cancer centers to define what constitutes an actionable cancer genome.

The research-use-only R1 OncoPanel, which has been branded as TruSight Tumor 15, is based on initial standards defined by the AGC, Flatley said, and includes 15 cancer-related genes. During the call, Flatley said that Illumina plans to launch an investigational-use-only version of the panel for pharmaceutical partners "in the next few months."

Illumina is also developing a larger RUO OncoPanel, R2, to be launched in mid-2016, which will be available to pharmaceutical partners shortly after.

Flatley said the company is still determining the best course of action for bringing one or both panels through US Food and Drug Administration clearance. "It depends on the timing and LDT guidance from the FDA," he said. "If it takes multiple years and large clinical trials to get through FDA, and LDTs are not regulated, it's hard to have a competitive regulated product," he said, since by the time the product is cleared, it will be likely be out of date.

In September, Illumina joined the Worldwide Innovative Networking (WIN) Consortium, a network of academic, industry, nonprofit, and insurance entities collaborating on personalized healthcare.

As part of the WIN consortium, Flatley said that Illumina would provide a "modified version" of its R2 OncoPanel for use in clinical trials for non-small cell lung cancer patients in mid-2016. The clinical trial will also provide Illumina with "valuable clinical utility data" on the panel, Flatley said.

Illumina has also been developing a liquid biopsy assay based on sequencing circulating tumor DNA that it plans to launch as an RUO assay.

Eventually, it plans to submit a version to the FDA, with data generated at its CLIA-certified clinical laboratory in Redwood City, Calif.

Last month, the firm said it would collaborate with Memorial Sloan Kettering Cancer Center on basic research to understand the biology of circulating tumor DNA in different cancer types. During the call, Flatley said that the two were planning a series of seven research studies over the next three years to analyze samples from around 1,000 patients.

Reproductive health

Illumina is in the final stages of recruiting patients for a clinical trial of its NGS-based preimplantation genetic screening test, VeriSeq PGS.

It is sponsoring the Single Embryo Transfer of Euploid Embryo (STAR) clinical trial and collaborating with US and UK firms Reprogenetics and Genesis Genetics, as well as other fertility centers in the US, Canada, and the UK.

Flatley said that enrollment for the STAR trial should be completed in 2016, with an analysis of interim results expected by the middle of that year. The trial will measure the impact of using VeriSeq and embryo morphology in choosing which embryo to implant on in vitro fertilization success rates.

During the quarter, sales of Illumina's VeriSeq PGS product increased 25 percent from last year's third quarter, Flatley said.

Sales of Illumina's NextSeq for noninvasive prenatal testing grew 60 percent in the quarter, Illumina President Francis deSouza said during the call, driven by China. The China NIPT market is growing particularly fast with the clearance of several assays and NGS systems by the China FDA, including a version of Illumina's NextSeq system and NIPT assay developed by Berry Genomics.

Testing services for Illumina's Verifi NIPT helped to increase year-over-year services revenue 20 percent. The company performed 50,000 tests in the quarter, the majority of them for NIPT. The company also offers genotyping and sequencing services.

Counsyl became the 36th licensee of NIPT technology this quarter as part of a supply agreement it struck with Illumina, Flatley said.

In addition, he said Illumina is making inroads on the average risk NIPT market. Illumina is "encouraged by the recent Anthem decision to reimburse for average risk and are optimistic that other top payors will follow suit," Flatley said.

Illumina's average risk test, VeriSeq NIPT, is in the "final stages of the European regulatory process for the software," he said. Early next year, Flatley said Illumina plans to have "the CE mark on the VeriSeq NIPT product for distribution as an IVD solution."

Currently, Premaitha Health is the only NIPT firm that has a CE-marked NIPT product. Unlike some IVDs, which are self-registration, NIPT is considered high risk so must go through a regulatory body in Europe to get CE marking.