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Shifting Focus to Sample Prep, Circulomics Anticipates Launching First DNA Extraction Product


NEW YORK (GenomeWeb) – After several years of development supported by almost $8 million in NIH grants, nanoscale molecular technology firm Circulomics said this week that it is close to launching its first product, a DNA/RNA extraction approach the company calls Nanobind.

Though the company has also spent significant time developing molecular detection tools — specifically a technology for multiplex miRNA profiling, which it initially intended to launch as its first product, the firm's central focus is now on sample prep for DNA sequencing.

Kelvin Liu, who founded Circulomics to advance technology he developed at Johns Hopkins University, said this week that with much of the molecular analysis market moving to sequencing, he and his collaborators realized that the most appropriate niche for Circulomics as a commercial entity was going to be in the "up-front area — optimizing the processing of samples before they go into the sequencer."

"We did some informal stuff with [the] miRNA [technology]," he said. "But our first formal product launch will be DNA extraction … hopefully in the next few months.

Liu added that there are already a few pilot projects working with the company's Nanobind technology, which operates similarly to magnetic bead approaches, but with less damage to DNA molecules. This translates to faster, more efficient extraction of longer, higher-quality fragments.

The process is very similar to existing technologies, Liu said. "You bind, wash, elute … use a magnet to pull aside, and you can do it on a benchtop or an automated instrument."

"But instead of having a million little beads, you have one solid disk — usually about one-to-five millimeters in diameter — with a nanostructured silica surface," Liu explained. "DNA binds to the surface and pulls off … and there are no shear forces like there would be with millions of individual beads in solution."

The plan for Circulomics will be to focus its first commercial launch on the core Nanobind material with an affiliated set of chemistries for a particular group of sample types, and then develop a series of additional solutions focused on other specific areas.

"We want to provide plug-and-play solutions for traditional benchtop processes that don't work great right now," Liu said. "One of the first is long-read sequencing, or genome mapping, where you need large amounts of very high-quality DNA."

"Long term, we want to build a whole product portfolio, like you see with a company like Qiagen or Thermo Fisher, where we take the same core material and then develop chemistries to work in a range of different sample types.

The company's first kit that it is moving into beta now, Liu said, is for cultured cells, bacteria, and blood.

After that, Circulomics will work on solutions specific to human tissue samples, FFPE, and also for analysis of plant materials.

In 2017 the company won two new grants totaling about $1.7 million for its work on Nanobind — one a Phase I award to apply the technology to tunable size selection and purification in NGS library prep —and the other a Phase II grant to optimize Nanobind-based extraction of high-quality DNA from FFPE tissue samples.

In addition to Nanobind, Circulomics has developed a technology for single-molecule analysis it calls PicoSep.

As the company moves forward, Liu said that it will work on assays that can serve unmet needs in DNA quality control — also an integral part of the NGS process — for which PicoSep will be especially applicable.

"Current tools don't [do enough] to tell you how good the DNA is until you run it and look at the sequencing results," Liu said. "So, we are working on assays for that, and then that can either be done at the benchtop or could be run on our single-molecule instrument."

According to Liu, although the firm hopes to launch a first product in the next few months, Circulomics' commercial path is somewhat up in the air and depends on the market area in question. For some applications it might make sense to work with a larger industrial partner, but for others that might not be necessary.

"We are pretty small still, and trying to stay lean," he said. "So, right now our main business development and sales is me and our scientists who work with collaborators on the pilot projects we have going on."