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Qiagen to Focus Nascent NGS Business on Sample Prep and Clinical Market

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This article has been updated from a version posted Nov. 6 to include additional comments from Qiagen.

Qiagen this week launched four new next-gen sequencing related products, all of which will focus on sample prep, and one of which will be geared specifically toward the clinical sequencing market.

The products are part of a next-gen sequencing initiative that the company kicked off in June. As part of that initiative it purchased private sequencing firm Intelligent Bio-Systems and said that it would incorporate elements of IBS' Mini-20 sequencing system with its own extraction methods, sample prep, and bioinformatics (CSN 6/27/2012).

As its first clinical sequencing products, Qiagen is launching GeneRead DNASeq Gene Panel kits. It is offering a comprehensive cancer panel that will target 124 genes related to cancer and eight subpanels that will target genes relevant for breast, liver, lung, prostate, colon, gastric, and ovarian cancers, as well as leukemia. Customers will also be able to design their own cancer panels, combining a breast and lung panel, for instance.

One element that sets Qiagen's cancer sequencing panels apart from others, said Dirk Loeffert, director of research and development for Qiagen, is that they have built-in quality control, which assesses the quality of the starting material and the performance of the enrichment so that precious sequencing capacity and reagents are not wasted. Additionally, customers will also have access to online software and cloud-based bioinformatics, so that they will not have to do any data trimming or other data analysis after the sequencing step.

"The customer doesn't have to interact with the bioinformatics pipeline," Loeffert told CSN at the American Society of Human Genetics conference this week. He said that the pipeline will send data straight to the cloud and a report will be generated.

While these initial panels are for research use only, Qiagen would ultimately like to validate them for diagnostic purposes, said Peter Urbitsch, head of global business applications in DNA. He declined to provide a specific timeline for the launch of diagnostic panels, but noted that it's "a future path" for the company.

Additionally, the company plans to expand to other disease areas like autism or other multi-gene phenotypes, Urbitsch told CSN at ASHG.

The cancer panels are based on the company's GeneGlobe portfolio of "biologically and clinically characterized and annotated molecular content," CEO Peer Schatz said during the call. GeneGlobe already contains more than 60,000 well defined and characterized molecular assays, he said, and those are the ones that will be used for next-gen sequencing applications.

Schatz said the company decided to focus on targeted sequencing because "cancer researchers, or clinical researchers in a broader sense, prefer to do targeted sequencing, which saves time and money."

He added that clinical sequencing customers have "been telling us that the current competitive offerings, which are focused on life sciences, do not meet their needs, and this is delaying the uptake" of sequencing in the clinical market.

The targeted sequencing panels will rely on the company's QIAcube and QIAsymphony platforms for automating the sample prep process, Schatz said.

Schatz added that the sequencing platform itself —for which the company has not yet disclosed its launch timeline — will "have a very competitive profile against alternatives."

Among its features will be the ability to process 20 individual samples in parallel, the ability to load flow cells and reagents continuously and while in operation. Additionally up to 20 different assay types can be processed at the same time, he said.

Schatz said that he would provide more details on the system in 2013. He has previously said that it will make use of sequencing-by-synthesis technology that was being developed as part of IBS's Mini-20 system.

In terms of making the system and sequencing assays compliant with regulatory bodies, Schatz said that Qiagen was prepared for a number of options, including developing a system and assays that would be compatible within a CLIA-certified laboratory, for assays that could play a "strong role in secondary or third-line testing," or for bringing a system and assays through US Food and Drug Administration 510(k) clearance.

With regards to FDA clearance, he said that there are currently "a lot of moving parts," and that it is difficult to know how the FDA will regulate sequencing.

He added that clinical sequencing could take on a different form in Europe and Asia, where there has been a "faster adoption in certain areas."

"We have all our chips in place" and solutions for all segments of the clinical market, he added.

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