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Cofactor Genomics Launches First RNA-Seq Clinical Assay

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NEW YORK (GenomeWeb) – Cofactor Genomics earlier this month launched its first product since deciding to refocus its efforts exclusively on RNA sequencing and software development.

The Pinnacle assay, which has been through what the company considers a robust validation process, looks at gene fusions and gene expression in patient tumor samples to provide physicians with potential treatment targets for cancer patients.

The test is available through the company's laboratory in St. Louis, which holds a CLIA certificate of accreditation from CAP. "CAP is considered to have a higher regulatory stringency than CLIA, and therefore CAP-accredited laboratories also meet CLIA regulatory requirements," Natalie LaFranzo, director of scientific projects and market development at Cofactor, said in an interview.

The company also expects a commercial launch of its immuno-oncology-focused assay, Paragon, later this year. It is currently available in beta.

"Cofactor is a biotechnology and software company that uses RNA as a foundation for assay and diagnostic development," Jon Armstrong, co-founder and CSO, said in an interview.

Cofactor started out eight years ago as a next-generation sequencing company. Armstrong and co-founders Jarret Glasscock and David Messia all worked together on the Human Genome Project and were among the first researchers to see sequencing technology come online in research labs.

About three years ago, the company decided that DNA sequencing was becoming a commodity market and while it believed there was still potential in developing novel DNA sequencing research tools it wanted to focus efforts to develop tools in other arenas. Through its NGS roots, Cofactor had begun to accumulate expertise in RNA sequencing and decided it held greater potential for research to transition to focus exclusively on RNA-seq. "We realized there was a gap in applying clinical RNA sequencing in the market," LaFranzo said.

Ultimately, the company wants to take RNA-sequencing based diagnostics to the clinic in the same way that DNA-sequencing transitioned to the clinic. To start, it has spent the last 18 months working to address the diverse needs of its consumers. One critical issue it recognized was that sample type was often a limiting factor. Researchers working with a fresh frozen sample often have different needs than those working with older samples with limited material amounts or high levels of degradation. "There aren't a lot labs that were really comfortable processing those samples," LaFranzo said. "We tried to consider all the different types of samples that a researcher might encounter and develop protocols that would accommodate each of those."

Developing software designed to better process diverse sample types and reduce the complexity of genomic data has been at the core of the company's RNA-seq assay development efforts, Armstrong said. "We prefer not to think about software and molecular as not being two separate pieces anymore in genomics. These are actually two pieces that actually have to be together for [clinical RNA] assay development as we move forward and try to have some effect on human disease," he added.

The Pinnacle assay offers consumers flexibility to ask different questions of clinical interests since it can not only be used to look at different sample types, including formalin-fixed, paraffin-embedded or fresh tumor tissue, but it can also provide both gene fusion and gene expression data about the tumor. The assay takes the expression data generated from the sample and compares it to gene expression profiles of the cancer type of interest from the company's internal database, LaFranzo said. The internal database builds on the National Institute of Health's Cancer Genome Atlas, and includes data on 28 cancer types, she added.  

Cofactor has launched the Pinnacle assay at a list price of $2,250 per sample, "competitively priced relative to DNA assays currently on the market," LaFranzo said.

The Paragon assay, which is scheduled to launch later this year, has an even stronger software component to not only "deconvolute" the complexity of gene expression information for clinical use in immuno-oncology, but also to help run the assay on the sequencing platform. One of the primary uses for the assay would be to provide researchers with insight into biomarkers that could predict a patient's outcome to treatment, LaFranzo said.

"Historically, it could be problematic [to get genetic immuno-oncology data]," Armstrong said. "A tumor might get cut up and sent to ten different places for different assays. It might be flow cytometry, it could be microarray, it could be DNA profiling. With our Paragon assay, we try to combine all of that into one single RNA extraction."

While the Paragon assay is still in beta, early user FLX Bio, a South San Francisco, California-based biotechnology company focused on immuno-oncology therapy development, has been pleased with the "high quality experimental output" of the product, Gene Cutler, director of computational biology for FLX Bio, said in an email. The company announced its plan to work with Cofactor in December of last year to help develop a novel RNA-based immuno-oncology analysis platform. Cutler added that he "was impressed with [Cofactor's] expertise in the field and the quality of the data from our pilot experiment."

Cofactor is one of several companies commercializing RNA-based diagnostics, including Personalis and NanoString. "The NanoString sequence model is a little different. Their goal is to sell you a NanoString platform and have you commercialize or develop the assay in your own laboratory," LaFranzo said. "We are an LDT service provider lab so our goal is for clinicians [or pharmaceuticals companies] to ship their samples to us and we would process them in our CAP lab."

When asked about whether a platform-based model would be more economically feasible, FLX Bio's Cutler said "It doesn't make sense for a young therapeutics company like FLX to focus resources on developing RNA sequencing capabilities in house. Operationally for us to remain nimble and lean, as well as to get the best possible results, it makes sense for us to partner with Cofactor Genomics."

Armstrong mentioned that Cofactor has other assays in its product pipeline, but declined to disclose further details. "These will not be the only two [assays] that we release," he said. "My hope is that within 18 months we would have anywhere between four to six assay products."

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