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Qiagen to Relaunch GeneReader NGS System in US, Sidestepping IP Dispute With Illumina

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NEW YORK (GenomeWeb) — Qiagen said this week that it plans to relaunch its GeneReader next-generation sequencing system in the US after developing a new sequencing chemistry that it believes circumnavigates intellectual property constraints placed on the current chemistry by a legal dispute with Illumina.

In addition, Qiagen said that the new chemistry provides "enhanced sequencing performance characteristics," though it did not provide additional details. Company representatives are expected to provide further information on the chemistry's performance in a presentation this week at the Association for Molecular Pathology annual meeting in Charlotte, North Carolina.

"This is a testament to the technology that we have amassed over the last five years," Qiagen CEO Peer Schatz told GenomeWeb in an interview. "We actually were able to come up with alternative … approaches, and different molecules. We obviously can't go into great detail at this moment, but we're taking a very different approach than what is described in the very narrow claim that remains in the rubble, basically, of the Illumina IP estate."

The full commercialization of the GeneReader sequencer, which is part of a workflow by the same name that consists of several instruments and products, has progressed in fits and starts, with the first limited early-access systems placed in customers' hands about three years ago and a goal to commercialize the system in 2014. The sequencing system is based on technology Qiagen acquired in 2012 from Intelligent Bio-Systems, a startup that had been developing an NGS platform with sequencing technology developed by Columbia University's Jingyue Ju.

In 2014, Qiagen delayed full commercialization another year, citing the need to tweak certain chemistry and workflow components. Meanwhile, early users continued to test other components Qiagen developed as part of a complete sequencing workflow. At the AMP meeting later in 2014, for example, Weill Cornell Medical College's Helen Fernandes shared some early feedback with conference-goers, noting that the workflow, which used a Qiagen cancer mutation panel and Thermo Fisher Scientific's Ion PGM, demonstrated a high analytical performance with particular promise for calling low-level mutations.

Then at last year's AMP meeting, Qiagen unveiled a new iteration of the workflow, complete with the GeneReader sequencing instrument, along with a 12-gene cancer panel and some early results from an evaluation study by researchers at the Broad Institute.

Qiagen finally began full commercialization of GeneReader earlier this year in the US, after having already started selling the complete suite in other parts of the world. Schatz told GenomeWeb this week that the company had already placed the sequencer with several US customers when, after about six weeks of commercial availability, a federal court in September issued a preliminary injunction halting sales of GeneReader instruments in the US as part of a legal battle concering the sequencing chemistry that had begun in 2012 between Columbia University, Intelligent Bio-Systems, and Illumina.

In a statement this week, Schatz noted that the company remains convinced of its IP positions on the legacy GeneReader chemistry; nevertheless, the relaunch in the US was made possible because Qiagen accelerated the development of the new sequencing chemistry, including "a replacement of the very chemical group that is under dispute."

Elaborating on this point, Schatz told GenomeWeb that "we still have a very difficult time comprehending how this decision came about in September … but we're now in early November, eight weeks later, and we have a pathway to making the [new] chemistries available to customers early in December. We were actually also able to continue to supply existing customers over the last few weeks and no customer had to discontinue their work."

Qiagen said that the new chemistry will also be made available to select customers in the US as part of an early-access phase beginning in December, followed by a broad commercial launch in the US in the first quarter of 2017 and in other regions of the world in Q2 2017.

The current components of the GeneReader workflow include the QiaCube for automated DNA extraction and library preparation; the GeneReader sequencing instrument; and Qiagen Clinical Insight (QCI), a platform for sequence data analysis and variant interpretation that consists of two tools, QCI-Analyze and QCI-Interpret.

In addition, through a partnership announced this week with lab informatics company Genohm, Qiagen will offer GeneRead Link, a middleware co-developed by the two companies to ensure complete chain of custody from sample processing to final reports with full connectivity to laboratory information management systems. As part of the partnership with Genohm, GeneReader customers who do not already have a LIMS solution can connect to Genohm’s proprietary SLims solution, Qiagen said.

Furthermore, Qiagen currently offers the QIAact Actionable Insights Tumor Panel for GeneReader, which consists of 12 clinically actionable genes involved in breast, ovarian, colorectal, and lung cancer, as well as melanoma. The company also has additional panels in development, such as the QIAact Breast Panel, QIAact Lung Panel, QIAact Onco-Heme Panel, and Gene Expression Signatures Panel, and will offer a customization option.

Finally, in a conference call last week recapping Qiagen's third quarter earnings, Schatz noted two other technology enhancements for the GeneReader workflow. First, the company launched protocols for using its QIAsymphony system as a high-throughput, integrated, and automated option for nucleic acid sample processing in front of GeneReader. In addition, in June Qiagen announced the expansion of GeneReader for use with liquid biopsy samples, adding to its current capabilities with FFPE samples.

With the US launch, Qiagen will be targeting the same demographic it has outside the US so far: oncologists who are typically conducting tumor classification experiments across the five tumor types represented in the Actionable Insights panel.

This includes "laboratories that are very versed in NGS, and have large NGS infrastructure, but simply want to take the pain out of having to manage complex workflows and high volumes of samples … and put them on GeneReader [to] flex up into very high sample throughput, up to a few thousand samples a year," Schatz told GenomeWeb. "But it can also do very economical sample throughput in the dozens of samples per year. So there is a high degree of versatility … [down to] labs that are maybe only doing 500 panels a year."

Qiagen has always maintained that the actual GeneReader sequencing instrument is not as important as the entire sequencing workflow for obtaining actionable results, a concept it calls "sample to insight." Accordingly, the company's pricing model uses a "price-per-insight" fee structure wherein customers do not pay for the hardware but for each clinical report the system generates.

In addition, the company has not disclosed many specifications about the sequencing instrument's technical performance. Instead, it trumpets the platform's high level of concordance with existing gold-standard assays.

One Friday at AMP, Qiagen and its collaborators are expected to present data showing that results obtained using the GeneReader with the new tumor panel on 42 previously tested FFPE colorectal cancer samples were 100 percent concordant with results from its own FDA-approved Therascreen KRAS RGQ PCR assay, its CE-marked Therascreen RAS Extension Pyro Assay, and an alternative NGS system from another undisclosed vendor.

"What we decided to do was benchmark our NGS assays off the same datasets that we have been, that we developed with the PCR assays, and it doesn't get more gold standard than that," Schatz told GenomeWeb this week. "While other companies typically benchmark off of all kinds of research studies, presenting data in different ways, we benchmark off of gold-standard FDA-approved assays, and that's a completely novel and very appreciated approach, and a high road we will continue to take."

At the same time, the company says that its new chemistry will further enhance the performance characteristics of GeneReader, but is not providing many specifics for now.

"The performance improvements we always said we are targeting are read length and output enhancements, and also workflow enhancements, some of which we've already delivered on this year," Schatz said. "People in this industry focus so much on the sequencing performance, and it is so clear at the same time that the sequencing performance is only a fraction of the error causes — it's actually in the sample preparation and informatics. That's why we spent an extraordinary amount of time on this. But the sequencer itself provides … very solid, very competitive performance data, and is a sequencing-by-synthesis instrument with a new chemistry that will provide greater accuracy."