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Qiagen Forges Ahead with GeneReader, NGS Workflow; Expects Early-Access Placements this Year

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Qiagen is on schedule to begin shipping its GeneReader next-generation sequencing system to early-access customers this year and plans to reveal technical specifications about the platform this fall.

"The project is fully on track and has been going very successfully," CEO Peer Schatz told In Sequence during a visit to the company's headquarters in Hilden near Düsseldorf, Germany, last week.

He said it is Qiagen's goal to bring an instrument with a "very competitive profile" to market that will especially appeal to customers in clinical research as well as, later on, in molecular diagnostics and that will have the potential to develop further over the next few years.

However, the company does not want to generate hype or expectations it cannot meet, so until it has set specifications, "we have to remain a little vague" on technical details, he said.

Qiagen launched its next-gen sequencing initiative last year, when it acquired Intelligent Bio-Systems, a Waltham, Mass.-based startup that had been developing an NGS platform using sequencing-by-synthesis chemistry developed by Jingyue Ju at Columbia University (IS 6/26/2012).

Last fall, Qiagen released its first products for next-generation sequencing, a number of reagent kits that are compatible with existing NGS platforms. Among them is a single-cell DNA amplification kit, an rRNA depletion kit, a library quantification kit, and a cancer gene panel with several subpanels (IS 11/6/2012).

Earlier this year, the company revealed initial details about its own NGS platform and workflow, which will be highly automated, combining a standard QiaCube for gene panel amplification and library preparation, a dedicated QiaCube NGS instrument for bead-based library amplification in droplets, the GeneReader sequencer, and initial data analysis on a PC (IS 2/26/2013).

Software from Ingenuity Systems, which Qiagen acquired this spring, will help with data interpretation (BI 5/3/2013).

Development for the NGS platform takes place at different sites, a concept that has proven successful with Qiagen's PCR-based technology, Schatz said.

On the engineering front, the work is shared between the former IBS team in Waltham and a team at Qiagen Instruments, based in Hombrechtikon, Switzerland. The Swiss site, which also produces the company's QiaCube and QiaSymphony sample prep platforms, focuses on developing the final commercial instrument.

The sequencing reagent portfolio is developed by two closely collaborating teams at the former IBS site and at Qiagen's headquarters in Hilden, the latter being responsible for final product development and commercialization.

Finally, content for the gene panels to be run on the GeneReader is being developed by Qiagen's biological research content group in Frederick, Md., which has also been working on content for Qiagen's PCR-based panels. There will be two NGS gene panel portfolios: one that is sequencing platform-agnostic, including the already launched DNAseq Gene Panel kit for cancer, and another one that will be dedicated for the GeneReader.

Last week, a researcher in Qiagen's R&D lab in Hilden was conducting a sequencing run on a prototype of the GeneReader, named "Superman." The lab expects to receive updated versions of the instrument from the former IBS site later this month.

According to Dietrich Hauffe, senior vice president and head of Qiagen's life sciences business area, the company changed "pretty much everything" around the original sequencing platform built by IBS, including the chemistry, fluidics, and mechanics (CSN 7/17/2013). It retained the basic architecture of 20 rotating flow cells, which allow for random access and continuous loading during a run.

The company said previously that the GeneReader will be able to generate up to 2 gigabases of data per flow cell and multiplex up to 12 samples on each. It is not yet revealing the read length, whether paired-end reads will be available, or the price of the instrument and reagents.

A number of clinical research labs already have alpha systems of the GeneReader installed for testing, and a phased market entry of the commercial system will start with their installation at selected early-access customer sites later this year.

According to Peter Urbitsch, Qiagen's director of global business applications DNA, who was involved in scouting technologies prior to the acquisition of IBS, the company decided to focus on developing a benchtop sequencing system because it wanted "to help and support our clients in the market, which are more the individual labs, not so much the core [sequencing] centers."

Hauffe acknowledged that Qiagen still has a "white spot" when it comes to high-throughput sequencing, a gap that the company hopes to fill "someday," but according to Urbitsch, "right now, for us the goal is definitely to get our foot into the benchtop sequencing arena, where we also see the biggest need."

He said the company noticed that with existing sequencing platforms, users generally build a workflow around the sequencer using third-party equipment, which he said is time-consuming and cumbersome. "That's something we wanted to make easier for users — to have a workflow that starts with a primary sample and delivers at the end not a mass of data, but a result and interpretation of the results."

Thus, he said, Qiagen is focusing on developing "a modular system with a very high degree of automation."

One of the distinguishing features of Qiagen's platform will be the ability to add samples to an ongoing run, rather than having to batch samples, and to include different sequencing applications in the same run, for example RNA-seq, ChIP-seq, or gene panel sequencing.

Qiagen will continue to pursue a dual strategy of providing instruments – like the QiaCube – and reagent kits for use with other sequencing platforms, as well as offering its own sequencing system. "We are not going to discontinue helping people with third-party platforms, but we will do this in parallel to developing and marketing the GeneReader workflow," Urbitsch said.

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