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TwinStrand Targets Toxicity Testing, Cancer Diagnostics for Sequencing Error Correction Tech

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NEW YORK (GenomeWeb) – TwinStrand Biosciences is preparing to launch its first products, based on its proprietary technology for sequencing error correction and rare variant detection, as the company shifts from R&D to commercial activities.

The move towards commercialization follows a year of partnerships, during which the University of Washington spinout, which raised $3.5 million in seed funding last year, developed its duplex sequencing technology for a number of applications. Over the last year, the company doubled its headcount to 14 employees, and earlier this month, it hired Chris Benoit, a former executive of Enzymatics (now owned by Qiagen), as CEO.

TwinStrand's duplex sequencing technology was first described by a team at UW in 2012 in a paper in the Proceedings of the National Academy of Sciences. It involves the use of unique adaptors to tag each strand of a DNA duplex prior to amplification and sequencing. This allows users to distinguish between PCR or sequencing errors and true mutations — the latter are present in reads derived from both the upper and the lower strand — and reduces the sequencing error rate to under one in 10 million, according to the company. Thus, even extremely rare mutations can be detected.

TwinStrand licensed the foundational US patent, which issued last year, exclusively from UW and has filed close to 30 patent applications worldwide, according to Jesse Salk, the company's co-founder and CSO. "In the last year, we went from a fairly small group of an R&D team and have taken what we originally developed at the University of Washington and made it robust and practical for widespread commercial use," he said.

This involved optimizing the biochemistry and analysis tools to make the method more efficient and cost effective, and applying it to problems that could result in commercial products. To do so, TwinStrand offered the method as a service to partners interested in specific applications.

According to Benoit, the first product, to be launched within the next few months, will be a general-purpose reagent kit that will allow researchers who have been toying with the method as described in the original UW publication to run it in a more streamlined and cost-efficient manner. Following that, TwinStrand will release a series of follow-on products with application-specific content.

For those, the company has focused on early detection of ovarian cancer, residual disease detection in leukemia patients, early detection of resistance to targeted cancer drugs, and genotoxicity testing. "In each one of those areas, we are building out kitted solutions," Salk said. "We've been listening to and working with [our partners] very closely to build these products to the exact needs that they have," he added, and the firm plans to begin shipping the first kits in the second half of this year.

Other applications that TwinStrand previously considered, for example in forensics, remain "in the queue" but will not be among the first products, Salk said.

The company and its partners are also preparing publications on ovarian cancer early detection and genotoxicity testing, he said, that they plan to put out on a preprint server within the next couple of months.

Genotoxicity testing in particular — assessing whether a substance is mutagenic — is a promising use of the technology, he said, because duplex sequencing can directly measure mutations within days or weeks of exposure and "provide much more rapid and complete information about the likely mechanism of a mutagen to drug and chemical companies in the preclinical field." TwinStrand has presented work on this, conducted in partnership with MilliporeSigma and Amgen, at several conferences, Salk noted, and will present this and other data at several upcoming conferences this year.

Bob Young, program consultant and study director for in vivo mutations, toxicology, at MilliporeSigma's BioReliance Testing Services, said in an email that his company started working with TwinStrand in the fall of 2016 and has been using duplex sequencing to measure the frequency of ultra-rare mutations in response to various mutagens, with the goal of using the data as an enhanced biomarker of cancer risk in repeat-dose rodent toxicology studies. "The benefit will be earlier and improved identification of cancer risk and potential reduction in the time, cost, and number of animals used in drug and chemical development," he said.

So far, the duplex sequencing data "meets the needs for mutant frequency and mutant spectrum analysis in repeat-dose rodent toxicology studies," he said, and is able to measure mutation frequencies, functional classes, and spectra in a similar way as a traditional assay. "The added benefits are that duplex sequencing can be used in any species with any gene and provides additional information, such as functional classes of mutants formed, mutant spectra, and insight into early clonal amplification of cancer driver genes," he said.

Duplex sequencing is not the only error correction method in existence, though, and Salk and his UW colleagues surveyed a number of others in a recent Nature Reviews Genetics article, including the Safe-SeqS method developed by researchers at Johns Hopkins University and an approach described by another UW group that uses single-molecule molecular inversion probes.

However, duplex sequencing is the most accurate method, according to Salk, because it compares information from both DNA strands in a way that other approaches cannot. "For some applications, it's overkill, it's far more accurate than you need. For other applications, it's critical," he said. "What we as a company are doing is, rather than pretending these other technologies are not useful for certain applications, we are really focused on the places where solutions don't exist, where those other technologies are not accurate enough."

For genotoxicity testing, for example, mutations occurring at a frequency of 1 in 10 million need to be detected, and "there is simply no way that any of these [other] tools could ever work," he said. "It doesn't mean they're not useful … but we are focused on where we are truly enabling."

According to Young, duplex sequencing is the only technology he is aware of that has an error rate below the spontaneous background mutation level of mammalian DNA. "This is an essential attribute for measuring any treatment-related increase over the background mutant frequency," he said.

To support its first commercial products, TwinStrand plans to grow its headcount by about 30 percent over the next six to nine months, Benoit said, and to build out capabilities in marketing and sales, finance, and production and testing.

It is also seeking to raise a small amount of funding, largely from existing investors, he said, and is pursuing a number of strategic partnerships in additional markets.

Longer term, TwinStrand also plans to launch in vitro diagnostics products. "As we get [a research-use product] into the market and understand as a company what it takes to build such a product, we will also be putting the pieces in place to support an IVD filing," Benoit said, for example for an early-stage ovarian cancer diagnostic. Last year, the company won a $2.3 million SBIR Fast Track grant from the National Institutes of Health to develop such a test. A diagnostic for this indication could be ready in three to five years, he estimated, "but we have to walk before we run — we have a number of steps to accomplish before we are in a position that we would be a player in the diagnostic market."

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