Skip to main content
Premium Trial:

Request an Annual Quote

China's Direct Genomics Demonstrates Single-Molecule Sequencing of E. Coli


SAN FRANCISCO (GenomeWeb) – Direct Genomics has demonstrated that its single-molecule sequencing platform, GenoCare, can sequence Escherichia coli, and the firm is gearing up to commercialize its platform for clinical use.

The company also plans to deliver 50 instruments this year to SinoTech Genomics, a startup based in Shanghai that offers both clinical and research sequencing services. Direct Genomics CEO Jiankui He said that SinoTech Genomics committed to ultimately purchasing 700 GenoCare platforms from Direct Genomics and has also licensed the right to offer noninvasive prenatal testing on GenoCare.

In addition, Direct Genomics recently moved into a new manufacturing space in Shenzhen, China, which has the capacity of producing around 1,000 GenoCare instruments per year, and it has raised an undisclosed amount of funding from the investor Harvest Glory, He said.

Direct Genomics also aims to launch GenoCare in the US in September. The company first unveiled the platform, which is based on Helicos' underlying technology, in 2015, describing a prototype of it in a publication posted to the BioRxiv server. The platform is being designed specifically for clinically focused targeted sequencing applications such as NIPT and cancer gene sequencing.

He said that the firm had delayed its early-access program because it was still working on developing its reagent kits, but said that problem had now been resolved. In addition, He said the firm is preparing to start a clinical trial in collaboration with three Chinese hospitals for NIPT. The hospitals are sending samples to Direct Genomics and He said that the firm has now tested "dozens of NIPT samples."

In the most recent BioRxiv publication, the firm demonstrated its technology for sequencing the E. coli genome, comparing it to sequencing on the MiSeq.

As previously noted, a key feature of the GenoCare technology, which was also part of Helicos' core technology is the use of total internal fluorescence (TIRF) microscopy to increase the signal-to-noise ratio. In addition, the instrument does not require any sample prep instrumentation or PCR amplification. This helps reduce cost and time of sample prep and also reduces biases and error, He said.

The firm is also working on a number of changes, however, including implementing four differently colored dyes. Currently, it is using a two-color chemistry. It also offers both a 16-channel and 32-channel microfluidic chip, as opposed to the 25-channel flow cell for the Heliscope.

Bill Efcavitch, who previously served as chief technology officer of Helicos and is cofounder and chief scientific officer of Molecular Assemblies, said that the main difference between the former Helicos technology and the GenoCare platform is in the hardware. "It's completely different engineering," he said. "It's still single-molecule sequencing, but they're pretty much taking a fresh approach on the hardware." One facet that is the same is the use of Helicos' virtual terminator chemistry, which the Direct Genomics team has managed to reproduce, he said. Those molecules aren't commercially available and the reproduction of them was a pretty big accomplishment, he said. 

In the BioRxiv paper, the researchers showed that both the GenoCare and the MiSeq covered around 91 percent of the E. coli genome. In addition, for both platforms, just under 99 percent of consensus sequences matched the reference sequences, on average. 

As expected, where the platforms differed was in their read lengths and coverage. Whereas GenoCare only generated around 15x coverage of the genome with mean mapped read lengths of just under 29 bases, the MiSeq generated nearly 85-fold coverage with mean mapped read lengths of 146 bases.

In addition, the error rates for GenoCare were higher, although He noted that compared to error rates of other single-molecule sequencing systems the GenoCare's error rate is low. The highest errors were seen in the rate of deletions, at 1.25 percent, followed by a mismatch rate of 1.10 percent and an insertion rate of .46 percent. By contrast, the error rates for the MiSeq were 1.30 percent for mismatches, .01 percent for deletions, and .00 percent for insertions.

He said that Direct Genomics has developed a targeted strategy to compensate for GenoCare's short read lengths, where a gene-specific probe is immobilized onto the flow cell, and only that targeted region of interest is sequenced. That makes the system "capable to do NIPT, preimplantation genetic screening, cancer gene panels, genetic disease panels, and infectious disease detection," He said.

In the paper, the researchers reported that sample prep took three hours and that sequencing time was 20 hours.

Efcavitch noted that the firm's plan to pursue NIPT would be a good use of the technology. "Single-molecule sequencing excels at counting applications" like NIPT, he said. He added that an advantage of such a system in the clinical market would be its overall ease of use, particularly with regards to sample prep. That could be especially important for clinical markets like China, he said, where many hospitals may not have the expertise to run complex sequencers. 

Michael Schatz, associate professor of computer science and biology at Johns Hopkins University, said that while the paper is an "important milestone for Direct Genomics to reestablish the previous Helicos capabilities, it seems unlikely that the GenoCare will see significant adoption without substantial improvements." In particular, he noted the very short read lengths of the system, which would impose a "ceiling" on the technology's applications. When Helicos first launched its instrument, Schatz said the technology was interesting because it was the first commercially available single-molecule instrument and hit the market at a time when competing next-generation sequencing technology also had short read lengths of 25 to 30 bases. But, since then, the field has progressed. Now, companies like Pacific Biosciences and Oxford Nanopore routinely produce read lengths greater than 10,000 bases.

"That being said, sequencing-by-synthesis is a very powerful technology, and if they can drive up the throughput, decrease the costs, and increase the read lengths, it could become an interesting technology to create Illumina-like reads but with single-molecule resolution," Schatz added.