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WaferGen, Qiagen Japan Pact to Focus on High-Throughput Biomarker Validation, Eventually NGS

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WaferGen Biosystems said this week that it has inked a co-marketing agreement with Qiagen KK, Qiagen's Japanese subsidiary, to jointly promote WaferGen's SmartChip Real-Time PCR system and consumable chips with Qiagen's PCR assays and, eventually, sequencing products.

For WaferGen, the agreement is a "big milestone" in that it is its first agreement with a "bona fide" commercial partner, and provides the company with access to a geographic market it previously did not inhabit, CEO Ivan Trifunovich told PCR Insider this week.

Further, the agreement may feed into WaferGen's recently rejiggered strategy to position its flagship SmartChip platform as a supplemental tool both up- and downstream of next-generation sequencing, Trifunovich said.

Under the agreement, Qiagen and WaferGen will market each other's products in Japan with the purpose of helping life science researchers more quickly develop and validate biomarkers that are potential candidates for molecular diagnostics by using the SmartChip system, the companies said.

"We envision the use of our technology [for] whatever application is of use to Japanese customers," Trifunovich said. "That includes all the applications that we have to offer now, and that we are going to offer in the future."

WaferGen has a sales presence in the US and Europe, making the entrée into Japan a crucial aspect of the Qiagen agreement.

"We are pretty excited about Japan, because it's the third largest market [worldwide], and Qiagen has a strong presence there and we did not," Trifunovich said. "I would also venture to say it's the first deal we've done with a bona fide commercial player. All of the [partnerships] we have announced so far are with universities.

The SmartChip system consists of the SmartChip cycler, which runs microscale qPCR reactions in 5,184-well consumable chips that the company preloads with target-specific primers, or that customers design using the SmartChip nanodispenser module. The system enables highly parallel gene expression studies and biomarker validation, among other applications.

Qiagen said in a statement that prior to inking the partnership, it successfully validated the SmartChip platform and now believes that it can play "an important part" of a comprehensive product offering.

"There is a substantial customer need to ramp up discovery efforts through targeted screening and confirmation, and our integrated approach will provide one-stop shopping for a variety of academic and industrial clients," Stephane Perrey, president of Qiagen KK, said in a statement. "We will be able to guide customers through the series of steps necessary for an effective biomarker discovery and validation program, by providing both the instrumentation and assays necessary for the accomplishment of their scientific goals."

A Qiagen spokesperson elaborated in an email that the agreement with WaferGen focused on Japan "because of certain customer needs that we saw there;" and that "Wafergen has the platform [and] we have the content — the PCR arrays from our SABio portfolio."

The spokesperson was referring to Qiagen's RT2 Profiler PCR arrays, which the company acquired along with SABio in 2009 (PCR Insider, 12/17/2009), and have traditionally comprised sets of optimized real-time PCR primer assays for 96-well plates, 384-well plates, or 100-well discs for pathway- or disease-focused genes and appropriate RNA quality controls, according to the company's website.

According to Qiagen's website, the company offers dozens of these PCR panels, which can be categorized by pathways such as apoptosis, cell cycle, cytokine and inflammation, signal transduction, stem cell and development, and toxicology; or disease categories, including cancer, cardiovascular disease, CNS disorders, immune disorders, infectious diseases, and metabolic diseases. Qiagen also offers custom arrays for gene or miRNA expression, genomic DNA analysis, or epigenetic analysis, among other applications.

By porting these assays to WaferGen's SmartChip platform, Qiagen will enable customers to essentially decrease their volume and increase their throughput.

"The only thing that's remaining is to put their content onto our chips," Trifunovich said. "We are somewhat chemistry-agnostic. If someone wants to put TaqMan or something like that on SmartChip, we can give them an empty chip. We do have a strategic partnership with [Integrated DNA Technologies as our] preferred supplier in the US (PCR Insider, 7/12/2012). But we are offering multiple chemistries on our chip, and in Japan, Qiagen will bundle their PCR assays with our chip."

Another key component to the new partnership is the potential to pair SmartChip with Qiagen's fledgling NGS business.

Last June, Qiagen acquired US-based NGS firm Intelligent Bio-Systems, noting at the time that it planned to develop the company's sequencing technology for the molecular diagnostics and clinical research markets.

Qiagen said this week that the forthcoming sequencing platform is one element of an initiative to create "integrated NGS workflows that combine innovative instrumentation and consumables into a sample-to-result offering" planned for launch later this year.

Also this week, the company announced the availability of a new "sample-to-result" sequencing workflow consisting of the QiaCube module for automated nucleic acid isolation and purification and library preparation; GeneRead DNAseq target enrichment gene panels; QiaCube NGS instrument for automated sequencing template preparation; and GeneReader benchtop sequencer (the former IBS system) and associated software.

It is unclear how the SmartChip system might complement this workflow, but WaferGen has recently noted that it believes that the platform could be a useful tool for PCR-based target enrichment ahead of NGS (PCR Insider, 1/10/2013); and biomarker validation downstream of NGS (PCR Insider, 2/7/2013). The company has been exploring these applications with renewed vigor in recent months since it has had difficulty selling SmartChip as a basic gene expression analysis platform.

"It is a PCR-based platform, and you can do all sorts of things with PCR," Trifunovich said. "We're now combining that target enrichment together with the downstream marker validation, genotyping and gene expression, in a high-throughput fashion. And we are planning additional applications. But the focus right now is really providing everything auxiliary to NGS."

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