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Boreal to Offer OnTarget Tumor Mutation Detection Through Clinical Partnerships; Broaden Assay

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NEW YORK (GenomeWeb) – Boreal Genomics plans to provide its OnTarget assay for tumor mutation profiling through partnerships with clinical laboratories and diagnostic companies while its R&D team focuses on developing broader assays, GenomeWeb has learned.

Over the last two years, the Vancouver, British Columbia-based company has been offering OnTarget — which enriches DNA containing specific tumor mutations through a combination of oligo hybridization probes and specialized electrophoresis, followed by next-gen sequencing — as a service to a variety of customers, including academic research labs and pharmaceutical companies. "We take the haystack, keep the needles, and throw out the hay," the company describes OnTarget on its website.

Providing the assay through CLIA-certified partner laboratories will allow the company to expand into new markets, for example phase 3 and 4 clinical trials, and apply it at a larger scale than it could with its own laboratory.

In addition, Boreal plans to venture into new diagnostic applications of profiling mutations in circulating tumor DNA from liquid biopsies, for example for therapy selection, minimal residual disease monitoring, and ultimately, cancer screening and early detection. Those types of tests would be offered through partnerships with diagnostic firms.

Following a strategic decision last fall to offer the technology through partnerships, Boreal consolidated its operations into its original Vancouver location, closing its San Francisco Bay Area location. After an $18 million Series C financing round in 2013, the company had originally planned to expand operations in Mountain View, Calif., and to sell the OnTarget instrument to customers, but will no longer do so.

Boreal's current OnTarget assay detects a total of 96 hotspot mutations in nine cancer genes. "We focus on actionable driver mutations that have high clinical utility to the oncologist or a pharmaceutical company," David Broemeling, Boreal's vice president of marketing and business development, told GenomeWeb. At the moment, the test targets solid tumors and has been applied to a variety of cancer types, including colon cancer, lung cancer, and melanoma.

The assay starts by extracting DNA, for example from a plasma sample. After barcoding the DNA through limited-cycle PCR, mutant alleles are enriched over wildtype alleles using synchronous thermal-electrophoretic separation in a gel cartridge. This is followed by library construction and sequencing on an Illumina MiSeq. In the final analysis step, mutations are quantified and reported.

The assay can detect mutations present at a frequency of 0.01 percent or less. What is even more important, Broemeling explained, is that it can detect mutations in single molecules. "The real goal is to be single-molecule-sensitive, and being able to retain that sensitivity even in a high wild-type background," he said.

Compared to other tumor profiling assays for circulating tumor DNA, OnTarget has "equal or greater" sensitivity, Broemeling said, and it tests for more mutations in parallel than some other approaches that focus on a single gene.

The assay is also less expensive than commercial targeted sequencing panels, he said. While those assays also have high sensitivity, they require deep sequencing because they do not enrich for mutant DNA, driving up sequencing costs.

He declined to reveal the price per sample for the OnTarget assay but said the company has "put a significant effort" into lowering costs over the last year "to make this fit with the existing reimbursement landscape" for population-wide screening tests. Those tests typically run in the range of hundreds rather than thousands of dollars, he said.

In a study published in Oncotarget last December, researchers from Boreal and Stanford University School of Medicine demonstrated the potential clinical utility of the test for colorectal cancer testing. Specifically, the researchers assayed a panel of 46 mutations in plasma and tumor samples from 38 patients, including those with non-metastatic and metastatic disease.

They found the detection limit to be 0.001 percent, or 1 molecule in 100,000, for most of the mutations in the panel. The mutations they detected were concordant in tissue and plasma for 93 percent of the metastatic patients and 54 percent of the non-metastatic patients, suggesting that the plasma assay might be useful as a non-invasive surrogate for tissue biopsies in patients with metastatic disease, according to the paper.

"Using this assay we provide evidence for ctDNA as a very promising non-invasive tool for real-time tumor molecular profiling in CRC, including the setting of resectable metastatic disease, where more accurate information about residual disease, prognosis, and tumor molecular evolution should enable optimization of perioperative therapy," the authors wrote.

On the R&D side, Boreal is working on new technology to broaden the coverage of the OnTarget assay. Specifically, company researchers are developing ways to assay genes without a priori knowledge of specific mutations. This would enable them, for example, to include tumor suppressor genes, where mutations may arise in many different areas.

Boreal has already filed for intellectual property for the new methodology, which will no longer involve oligo probes targeting specific mutations, but is not revealing details yet. "We definitely have a path to broad-coverage assays while minimizing sequencing bandwidth and cost," Broemeling said.

Besides commercializing the OnTarget assay, Boreal continues to sell its Aurora platform for extracting high molecular weight DNA from soil and other difficult samples. The technology "continues to have a very passionate customer base" and the company sees "exciting new applications" for it in the context of long-read DNA sequencing, Broemeling said.

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