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Qiagen Buys PrimeraDx to Better Enable Multiplex CDx Development, with Lilly as First Partner

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NEW YORK (GenomeWeb) — As part of its quest to become a catch-all provider of tools and technologies for molecular diagnostic and especially companion diagnostic development, Qiagen has added another molecular analysis platform to its portfolio.

Late last week Qiagen announced that it has initiated a new collaboration with Eli Lilly to co-develop companion diagnostics that simultaneously analyze DNA and RNA biomarkers in common cancers — not particularly unexpected news, considering the partners have had a fruitful relationship spanning the past several years.

However, as part of its announcement Qiagen also disclosed that it has recently acquired PrimeraDx, a Boston-area molecular diagnostics startup that has developed a multi-modal, multi-analyte testing system that will serve as the linchpin in the new Lilly agreement and gives Qiagen a platform that it believes addresses needs that its current bevy of molecular technologies does not.

"We see platforms, as well as content and biomarker IP, as enablers for our business, which is molecular diagnostics, and in my particular case it is companion diagnostics," Rainer Metzger, vice president and head of business development for pharma at Qiagen, told PCR Insider this week. "Everything that helps us to work more closely together with our customers … and enables us to get closer to the patient … is of interest to us. And this platform has that ability."

Qiagen has not disclosed details of the PrimeraDx acquisition, except that it has acquired all assets of the company, which is headquartered in Mansfield, Mass.

PrimeraDx was founded in 2005, and its primary platform — formerly called ICEPlex but now named Modaplex by Qiagen — runs an assay technology called scalable target amplification routine, or STAR, which integrates standard endpoint PCR with capillary electrophoresis to simultaneously quantitatively measure multiple target nucleic acids.

The platform continuously samples PCR reactions containing fluorescently labeled primers during sequential cycles of amplification. The amplified products are then detected by size using capillary electrophoresis, and the amplification kinetics can be reconstructed using real-time PCR algorithms to quantify the amount of material in the initial sample.

According to the company, this enables a much higher level of multiplexing than is possible with real-time PCR techniques that use fluorescent probes. As such, the system can simultaneous quantify multiple gene targets — a few dozen for practical purposes but a few hundred, theoretically — from a single reaction.

It is this level of multiplexing that interested Qiagen, which already had a real-time PCR-based molecular testing system — the QIAsymphony RGQ (Rotor-Gene Q) — and is also currently developing a next-generation sequencing system. These products, however, still fall short when it comes to the type of multi-gene panels that Qiagen is envisioning developing in oncology companion diagnostics collaborations like the one announced last week.

"The advantage of the Modaplex platform is certainly toward the multiplexing, multi-analyte type of testing," Metzger said. "You can manage way more biomarkers in real-time mode. And this also addresses some of the existing limitations with NGS, like exact and accurate quantification of RNA expression."

In addition, Modaplex has a faster turnaround time compared to NGS and a similar turnaround to real-time PCR, but "uses way less sample material, which is incredibly important for the patient," Metzger said. For example, in diseases like non-small cell lung cancer, the biopsy material is typically scant, and "you very quickly reach a limitation level with some of the sequencing technologies," Metzger said. "This is the part that is convincing for pharma, but is also the piece that is exciting for end users like central labs [and] clinical labs."

Modaplex may also eventually yield cost savings to the end user, Metzger said, noting, however, that it is still too early to quantify this. "It looks like if it comes to a final product to be launched into the market that this has also a quite attractive cost component as compared to … [NGS]. The cost for NGS … might change over time, but this is another attractive component [of Modaplex]. For these kinds of products, reimbursement is an important piece, and availability to the patient is another important component."

And finally, Qiagen saw in the PrimeraDx platform a technology that has matured to the point where it is ready to use in companion diagnostic development — particularly when considering both DNA and RNA biomarkers.

"It addresses some of the existing limitations with NGS, like exact and accurate quantification of RNA expression," Metzger said. "From pharma's perspective … they see the limitations with existing NGS [technology], especially as they look forward to moving ahead with companion diagnostic development. Pharma partners currently are concerned that NGS technology might not provide [the necessary] accuracy at this point in time. It may change … but currently pharma needs a system that is reliable, approved for [in vitro diagnostic] use … and does allow for multiplexing and multi-analyte testing."

Modaplex received 510(k) clearance from the US Food and Drug Administration in December (as ICEPlex) along with its first assay, a test for Clostridium difficile. Although PrimeraDx had said that it was pursuing infectious disease diagnostics, the C. diff clearance appeared to be more of a "gateway" to easier clearance of assays for the types of diseases that benefit from examining multiple biomarkers — in other words, cancer.

In fact, PrimeraDx had also been developing ICEPlex for oncology and CDx development, and already had its own diagnostics development partnership in place with Lilly since 2012.

Qiagen did not disclose whether it would continue PrimeraDx's existing partnership with Lilly, or whether there was overlap between that project and the new agreement signed between Qiagen and Lilly. Metzger noted that the new agreement is a continuation of Qiagen's ongoing collaboration with Lilly, but with an eye toward highly multiplexed assays. The companies, however, did not disclose what specific oncology areas they would be pursuing for CDx development.

Overall, this marks Qiagen's fourth CDx development project with Lilly. Qiagen's Therascreen KRAS RGQ PCR Kit was approved by the FDA in 2012 as a companion diagnostic to detect KRAS gene mutations in metastatic colorectal cancer patients and to indicate which patients would benefit from a tailored oncology therapy marketed by Lilly and Bristol-Myers Squibb. In 2011, Qiagen and Lilly partnered to develop a companion diagnostic that evaluates a gene mutation that plays a role in some blood cancers. And in 2013, Qiagen announced a third project, building on a master collaboration agreement, to create a companion diagnostic to guide use of an undisclosed Lilly oncology compound.

As for using Modaplex in infectious disease diagnostics, Metzger said that the possibility exists, but that is a "separate discussion" and is not part of Qiagen's short-term plans for the platform. Qiagen has already developed several infectious disease diagnostics on the QIAsymphony RGQ MDx, and in May it also received 510(k) clearance for that platform and an accompanying C. diff assay.

"What's important is that [Modaplex] is an enabling technology that we may use simultaneously with other technologies," Metzger said. "It may well be that this technology in the future will be sitting in labs next to NGS, QiaSymphony RGQ, and possibly other technologies out there in the market. It is not either-or. It is just in addition to what is already in place ... to address ... the gaps that we do have ... in order to be closer to the patient and pharma partner."

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