This article has been updated to correct that cell-free DNA, not plasma, is injected into the cartridge.
Boreal Genomics has developed a platform to enrich mutant DNA over wildtype DNA and is commercializing it for profiling tumor mutations in cell-free DNA from patient plasma samples.
The company, which has locations in Vancouver and Los Altos in the San Francisco Bay area, is about to start selling an instrument, called OnTarget, and associated reagent kits to customers, and currently offers a mutation profiling service that couples OnTarget with next-generation sequencing.
Longer term, the firm is working on non-invasive clinical diagnostic tests, for example to monitor drug resistance based on mutation profiles, which it plans to offer as laboratory-developed tests through a partnership with a CLIA facility.
In 2010, Boreal raised $6.9 million in funding in a Series B round that was led by venture capital firms Arch Venture Partners, Kearny Venture Partners, and GrowthWorks Capital and also included InQTel.
Nitin Sood, Boreal's CEO, noted that monitoring tumor mutations throughout treatment in a non-invasive fashion is becoming increasingly important as the number of targeted cancer therapies that rely on specific mutations rises, so doctors can react swiftly when resistance mutations appear, for example.
A fundamental challenge is that during treatment, the overwhelming majority of free plasma DNA tends to be normal DNA, and only a small percentage is mutant cancer DNA. Existing target enrichment methods – based on PCR or hybridization, for example – do not distinguish between the normal and mutant DNA, so during the analysis, real cancer mutations get lost in the background of sequencing errors.
OnTarget, on the other hand, enriches only mutant DNA, leaving wildtype DNA behind, Sood explained, even if the difference is only a single base pair.
The platform uses DNA probes directed against specific mutations in cancer genes. After the sample — cell-free DNA extracted from plasma — is injected into a cartridge containing the probes, a rotating electric field is applied, along with various temperature changes. This leads to transient hybridizations between the sample and the probes, resulting in a mobility difference between mutated and normal DNA, which separates the two.
Underlying the approach is Boreal's Synchronous Coefficient of Drag Alteration or SCODA technology, a patent-protected electrophoresis method developed by Andre Marziali's group at the University of British Columbia. Boreal sells another instrument platform, called Aurora, that uses SCODA to concentrate nucleic acids from environmental samples in a small volume (In Sequence 1/27/2009).
Sood said that OnTarget has been able to enrich mutant DNA more than a millionfold over wildtype DNA, with a yield of more than 50 percent of the input DNA. A year ago, UBC researchers affiliated with the company published a paper in PLOS One describing the technology, which has since been significantly improved, he said. That paper also described the separation of differentially methylated DNA, another possible use of the technology.
In collaboration with researchers at Memorial Sloan-Kettering Cancer Center, Boreal has tested its technology on FFPE samples from a small number of cancer patients and was able to detect resistance mutations in EGFR with higher sensitivity than a LNA PCR-based assay. It is now planning to expand the size of the study and to move from FFPE to plasma samples, Sood said.
While the enriched DNA can be analyzed by a variety of methods, including PCR-based approaches and Sanger sequencing, Boreal recommends next-gen sequencing. For NGS-based assays, OnTarget enrichment increases the mutation detection sensitivity about 100-fold, Sood said.
So far, the company has placed OnTarget instruments with a number of early-access customers, including academic researchers, service providers, and pharmaceutical companies.
Ryan Morin, an assistant professor at Simon Fraser University, has had the instrument since last November and has used it in conjunction with sequencing to detect mutations in several genes in a plasma sample from a non-Hodgkin lymphoma patient.
The OnTarget system was able to enrich the mutant DNA significantly, so instead of 1 percent of sequence reads, 90 percent matched the mutation of interest. This allowed the researchers "to be confident in the data instead of just wondering whether the low level of reads matching our mutant were just sequencing errors or actual signal," Morin told CSN. The system, he added, "seems to be working quite well in our hands, and fairly consistently so far."
Morin said that digital PCR is another way of picking up rare mutations in a background of wildtype DNA, but it is difficult to multiplex to high levels and requires a new assay to be designed for each mutation. "With OnTarget, you can multiplex the capture, as long as you know all of the mutations you want to capture, and then detect them all at the end with sequencing," he said.
One current limitation of the technology, he said, is that it requires prior knowledge of the mutations of interest. "Just like with digital PCR, you need to have an idea of what mutations you want to go after. You can't capture and detect something if you don't know what mutation to design probes for," he said.
Following validation, Morin, who is also affiliated with the BC Cancer Agency's Genome Sciences Centre, plans to apply OnTarget to several different cancer types, especially those with very low levels of circulating tumor DNA.
Boreal plans to start selling the system in May for approximately $90,000, along with reagent kits for catalog and custom panels of cancer mutations that will cost about $300 per sample.
According to its website, Boreal offers a panel with 46 mutations in four cancer genes – BRAF, EGFR, KRAS, and PI3K – as well as a panel covering 100 mutations in a total of eight cancer genes.
The company also provides a research service for cancer mutation detection that uses OnTarget and sequencing on Ilumina's MiSeq and includes DNA extraction and data analysis. While the cost of the service varies significantly, depending on sample volume and other factors, it is in the range of $2,500 per sample, Sood said.
Boreal is marketing its instrument and services to pharmaceutical companies interested in monitoring cancer patients with certain mutations in clinical trials or in monitoring drug response in animal models, as well as to academic researchers.
Currently, the company's assay can analyze up to 100 mutations simultaneously, but Boreal is working on a new product – to be released within the next six months to early-access customers – that will allow researchers to detect any mutation, including unknown ones.
Sood said this technology, which will no longer require probes, will work on the existing OnTarget platform and use the same basic technology to create a mobility shift between mutant and wildtype DNA, but will use new reagent kits. He declined to provide further details as the company is in the process of filing patents.
In addition to offering instruments and services, Boreal is developing clinical diagnostic assays to monitor cancer mutations, which it plans to offer as LDTs in partnership with a CLIA laboratory. It hopes to start generating revenue from clinical diagnostics in mid-2015, Sood said.
One example for such a diagnostic would be an assay to monitor the occurrence of resistance mutations in EGFR in lung cancer patients being treated with erlotinib, marketed by Roche's Genentech as Tarceva.
Another potential assay would monitor mutation profiles in patients with pre-cancerous lung nodules in order to detect early when these nodules turn into cancer.
Boreal analyzes cell-free DNA, but the company is also interested in working with others that focus on circulating tumor cells and is in discussions with a potential partner. Boreal's technology could help enrich DNA from circulating tumor cells over DNA from white blood cells, Sood explained, and it could complement assays based on circulating tumor cells with its own assays of cell-free DNA.
Selling instruments first "will generate the data and the market awareness for these clinical diagnostics," Sood said. "If we jump in today, it's too early."