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PrimeraDx Readying ICEPlex, C. Diff Assay for FDA; Developing Follow-on Infectious Disease Panels

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PrimeraDx, a Mansfield, Mass.-based molecular diagnostics firm, is on track to submit its highly multiplexed PCR-based testing system and associated assay for Clostridium difficile to the US Food and Drug Administration this quarter, CEO Matt McManus said recently.

Assuming the assay and system, called ICEplex, are approved by FDA, it will enable PrimeraDx to quickly move forward with commercialization in the US of a number of other assays — for both infectious disease and oncology — intended to take advantage of the platform's multiplexing capabilities more so than the C. difficile assay does.

"That will be a big event for the company, because instead of being just CE IVD marked, the … entire system and assay will be FDA cleared," McManus told PCR Insider last week. ICEPlex and the C. difficile assay received the CE IVD mark in the EU in September (PCR Insider, 9/13/2012).

"But in more complicated testing in this space, we have a number of panels [in development]," he added. "Our technology lends itself to panelizing infectious disease workups, and as much as the multi-modal aspects are important in oncology … on the infectious disease side, being able to multiplex and quantitate has really opened up some interesting panels."

PrimeraDx's benchtop ICEPlex platform 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 STAR technology and ICEPlex platform work by continuously sampling PCR reactions containing fluorescently labeled primers during sequential cycles of amplification. The amplified products can then be 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 PrimeraDx, this enables a much higher level of multiplexing than is possible with real-time PCR techniques that use fluorescent probes, such as TaqMan-based methods. The upshot is that the system can simultaneous quantify multiple gene targets — a few dozen for practical purposes but a few hundred, theoretically — from a single reaction.

In 2011, PrimeraDx opened up the ICEPlex platform for laboratories to develop their own tests (PCR Insider, 7/14/2011). And although the platform was originally designed for infectious disease assays, the company has been making great strides in also developing oncology and companion diagnostic assays for ICEPlex.

For instance, last June the company entered into a multi-year agreement with Eli Lilly to develop ICEPlex assays in support of multiple therapeutic development programs (PCR Insider, 6/28/2012); and in March PrimeraDx and Quest Diagnostics revealed their plans to co-develop and commercialize molecular diagnostic products and services in support of targeted therapeutics (PCR Insider, 3/28/2013). Also, in September the company won a grant from the National Cancer Institute to develop a gene expression profiling assay that can rapidly detect diffuse large B-cell lymphoma subgroups.

In the midst of all this, however, the company has still not lost sight of its infectious disease test development. Although PrimeraDx last year delayed a planned FDA submission of ICEPlex and the C. difficile assay in order to develop a more complete submission reflecting the highly quantitative and multiplexed nature of its technology, the submission is back on track, as is the development of several new infectious disease panels.

To gear up for the anticipated approval, PrimeraDx has been busy partnering with various academic institutions and clinical laboratories to validate these infectious disease panels.

For instance, McManus told PCR Insider that PrimeraDx very recently completed an evaluation of an ICEPlex transplant virus panel in collaboration with "a major reference lab" that the company cannot yet disclose due to confidentiality concerns. This assay is intended to detect and quantify multiple viral loads for many of the common viruses — such as cytomegalovirus, Epstein-Barr virus, BK virus, and human herpesviruses — that are problematic for transplant patients.

"We did 300 clinical samples [and] validated the targets," McManus said. "One of the interesting things is by being able to multiplex and quantitate, we picked up co-infections that would have otherwise been missed."

McManus said that labs typically test for a first pathogen of interest, and if that target is positive, it may not test for another infectious agent. "For instance, the first thing you usually test for is BK [virus], and we found that it comes up as a low positive in a number of patients that were, for example, EBV-positive, that you would not have picked up if you had just tested for BK and stopped. Not only that, those were often the majority infections, and that's where quantitation becomes important. From a clinical standpoint, it's a much better way to test and manage patients, being able to multiplex and quantitate."

McManus said that PrimeraDx is currently working with its laboratory partner to prepare a manuscript for publication in a peer-reviewed journal.

The company also last year worked with the Henry M. Jackson Foundation for the Advancement of Military Medicine, under a grant from the US Department of Defense, to validate a highly multiplexed fungal panel for testing directly from whole blood. "We tested about 120 clinical isolates and compared those with incumbent methods," McManus said. "And ours [compared favorably]. This is a highly sensitive, highly specific molecular test for a fairly wide range of pathogens."

Company scientists are also planning to present a poster entitled "Simultaneous Detection and Differentiation of Medically Important Fungal Pathogens — Candida, Aspergillus, and Cryptococcus spp. — on ICEPlex System" at the American Society of Microbiology general meeting in Denver next month.

McManus said that PrimeraDx is also working on a bacterial infection panel, a 13-target respiratory viral panel, and a sexually transmitted infection panel.

"We have a fairly broad infectious disease pipeline," he said. "For instance our STI panel detects the usual suspects — viral, fungal, bacterial, and protozoans. As much noise is made about [Trichomonas] and [chlamydia and gonorrhea] testing, we actually put all of those into a single, easy-to-use reaction. Whatever the patient comes in with, and the ordering physician ticks off on the list, the lab would have one workflow and they get all the answers they need."

"These are actually productizeable assays — we haven't launched them yet — but we're not just doing experiments, [we're doing] clinical validation and such," McManus added.

In the meantime, PrimeraDx is selling ICEPlex and the C. difficile test for clinical use in Europe and is working to place its systems in US laboratories to enable research-use-only test development.

"In addition to the instrument and the consumables for it — which are not analyte-specific — we have a software package that helps users develop multiplex assays," McManus said. "This is one area where we add a lot of value."

Lastly, PrimeraDx plans to launch a number of its own RUO test kits, primarily in the oncology space, by the end of the year. The company will also likely pursue CE IVD marking for many of those assays.

"We validate the test fully for research use, and really that level of validation is equivalent to a CE mark," McManus said. "As we launch these RUO kits, we'll also be doing the CE marking on them."

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