NEW YORK (GenomeWeb) – UK firm GeneFirst is gearing up to launch a next-generation sequencing library preparation kit that promises to help detect rare mutations in circulating tumor DNA from blood.
The research-use product, called ATOM-seq (Adaptor Template Oligonucleotide Mediated-sequencing), is the first NGS offering of the firm, which has previously focused on multiplex PCR assays.
The company has not yet published data on the technical details or performance of the method but claims that internal research has shown the technology improves the efficiency and sensitivity of mutation detection.
The firm believes that the approach will have particular relevance to liquid biopsy testing, where target DNA molecules may be present at very low frequencies compared to background. Winnie Wu, GeneFirst's chief operations officer, said the company is applying for several UK government grants to support clinical validation studies where it will create ATOM-seq-based mutation detection assays for applications like noninvasive cancer screening and disease monitoring.
According to Wu, GeneFirst filed for a patent on the ATOM-seq technology about two years ago and then sought funding to advance the method. A grant from Innovate UK, a government organization, allowed the company to shift focus from PCR and expand its team with five new employees. "We spent the best part of the last … two years looking at optimizing our protocol," Wu said. "And that's where we are now."
GeneFirst describes the ATOM-seq method as involving molecular barcodes bound directly to target DNA in a sample. A description in a patent application filed by the firm's founder and CEO, Guoliang Fu, further states that it is a method for extending a population of target sequences by incubating the target molecules with "adaptor template oligonucleotides" also called "removable template oligonucleotides."
Because the firm has not released detailed information on its approach, its unclear how it compares to some of the other barcoding methods that have already found favor in liquid biopsy testing.
Other techniques include methods like the Johns Hopkins-developed Safe-SeqS — which involves the assignation of unique barcodes to each DNA template molecule to help resolve true mutations from variants introduced through a technical error — and CAPP-seq, now marketed by Roche, among others.
Although various techniques have shown that they can achieve high sensitivity, detecting mutations in the minute quantity of circulating tumor DNA that might be in a cancer patient's blood sample, Wu said that GeneFirst believes its method can achieve similar sensitivities but with even lower quantities of DNA.
According to Wu, GeneFirst plans to be ready to launch ATOM-seq as a research tool, hopefully later this year. "We are probably going to be freezing our design in the next month or so. And once that's done, we're pretty much ready to go if people come to us and say [they] want to try this," she said.
Users can apply the kit itself to whatever their research question is, but GeneFirst is also planning to develop targeted panels for use in validation studies aimed at specific liquid biopsy applications.
With funding from the UK government, for example, the company plans to develop hotspot panels for lung and colorectal cancer, Wu said. It is also seeking new grants to support collaborative studies in different medical contexts.
"We have a couple of collaborations which have started, and this is dependent on whether we get the funding or not, [but] bowel screening is one of the bigger validation studies we are hoping to do," she said. Another area of interest is testing patient samples pre- and post-surgery to evaluate the technology for monitoring levels of cancer DNA in the blood.
Both applications have certainly become areas of interest for others, with groups advancing screening tests — both for colorectal cancer and across tumor types — and applying sequencing or multiplex PCR to monitoring circulating tumor DNA post-surgery or as a surrogate marker of drug response.
Because the use of these various platforms in the clinic is still in its infancy, uptake of existing products and those from new competitors, like GeneFirst, will likely continue to evolve. Wu agreed that clear data from the company's planned external validation work will be necessary for it to make a case for ATOM-seq against other available tools.