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Illumina Focuses on Bringing NGS Tests to Market in Second Half of 2015


NEW YORK (GenomeWeb) – As clinical and translational customers make up an increasing percentage of Illumina's customer base, the firm is looking to launch a number of next-generation sequencing-based tests this year in the oncology and reproductive health space.

In addition, the company continues to make improvements to its fleet of NGS systems, including the recently launched SeqLab solution for HiSeq X customers and the full commercial launch of automated sample prep system NeoPrep.

The firm also has launched a MiSeq promotion for customers that are new to NGS, which is essentially a "starter bundle" that includes the MiSeq system, training, sample prep, core consumables, and a service plan to "get a new sequencing lab up and running," Illumina President Francis de Souza said during a conference call discussing the firm's second quarter performance.

During the second quarter, Illumina's revenues climbed 21 percent to $539.4 million, driven by record sequencing consumable sales, demand for HiSeq — particularly the HiSeq 4000 — and NextSeq instruments, and its services business — which includes noninvasive prenatal testing services, products, and license fees. Illumina's array business, by contrast, saw falling revenues despite an increase in volumes, due to pricing pressure.

GenomeWeb's coverage of the full Q2 financial results is available here.


During the third quarter, Illumina plans to launch the first version its planned cancer panel as a research-use-only product. The 15-gene OncoPanel will set "the groundwork for our OncoPanel products that will be CE-IVD marked and FDA approved," Illumina CEO Jay Flatley said during the conference call. 

In addition, Illumina is developing an expanded 170-gene panel that it plans to launch early next year to "address the needs of the research market" and to be used by the company's pharmaceutical partners in conjunction with clinical trials, Flatley said.

The oncology market continues to be a growing segment of Illumina's customer base, and this quarter saw a 35 percent year-over-year increase in shipments to both research and clinical oncology customers, Flatley said. The NextSeq 500 instrument is particularly popular in the oncology segment, with orders for that instrument growing 50 percent year over year from oncology customers, including a "large order" from a liquid biopsy company.

Flatley predicted that the oncology market would hit an "inflection point" and "explode" when guidelines recommend, and it becomes standard of care, to sequence every tumor when it is biopsied.

The company is also working on a liquid biopsy assay. Flatley said that effort would likely "begin with targeted panels, from us and from others, that have specific knowledge of the variants that are known in particular cancer types." Previously, Flatley said that the company would provide clinical utility data on the assay by the end of the year and would first launch an RUO assay before ultimately developing a product for US Food and Drug Administration submission.

Reproductive health

Illumina is also looking to launch a CE-IVD marked NIPT on the NextSeq instrument. Flatley said the test, dubbed VeriSeq NIPT, was in the "final stages of the European regulatory process for the software," and the firm hopes to have the CE mark shortly. That would be followed by a CE mark on the VeriSeq NIPT product as an IVD solution.

Illumina also offers the noninvasive test Verifi as a service and has a patent pool with Sequenom through which it licenses technology for labs to develop their own version of the test. Flatley said that total NIPT revenue, including products, services, and test fees, grew more than 50 percent in Q2 2015 compared to Q2 2014.

During the second quarter, Flatley said that the company signed five new partnerships outside the US to develop and run the VeriSeq NIPT protocol and now has 19 such partners that will eventually run the test from their respective labs.

Sales to in vitro fertilization reference laboratories grew 25 percent in the quarter, due to demand for Illumina's NGS-based preimplantation genetic screening test, VeriSeq PGS, he added.

HiSeq 4000 and HiSeq X

Illumina recently launched its SeqLab product for its HiSeq X customers, a product it designed in collaboration with GenoLogics and Hamilton Robotics to standardize and optimize the whole-genome sequencing workflow. The product includes "LIMS system, liquid handling robotics, and data analysis, and the consulting services a lab would require to get up and running," de Souza said.

Flatley said the SeqLab product would help boost system utilization among customers. Currently, he said, there is a large discrepancy between system usage among its customers, with a few customers running the machines consistently, but a large number of customers who are not. According to de Souza, customers said that the HiSeq X's required IT and informatics were "daunting" and that as a result, it took them a long time to get their labs up and running.

Flatley added that the company has "debate[d] the future of the HiSeq X," including potentially enabling other applications aside from whole-genome sequencing and enabling non-human genomes to be sequenced. "At some point, it's likely we'll make some changes, but have nothing to report today," he said.

With regards to the HiSeq 4000 instrument, Flatley said that it is "now the leading HiSeq platform." A number of genome centers and commercial customers placed multi-unit orders for the system this quarter.

Flatley predicted that over the next several years, customers would migrate from the HiSeq 2500 to the HiSeq 4000. However, because customers like the Rapid Run mode on the HiSeq 2500, the firm would consider introducing that feature on the HiSeq 4000, although it is "not actively working on it yet."