SAN FRANCISCO (GenomeWeb) – Loop Genomics, a startup based in San Jose, California, has developed a synthetic long-read sequencing technology and is now commercializing a product for 16S and 18S rRNA sequencing.
Loop CEO Tuval Ben Yehezkel said that the company's core technology combines research from Stanford University, Michigan State University, A*STAR in Singapore, and the Weizmann Institute of Science in Israel. Research groups at those institutions were all working on synthetic long-read sequencing technologies, and the company founders "consolidated all those different lines of research and IP" to launch Loop in 2015, Yehezkel said. The company has filed for several patents for its barcoding chemistry, he added.
Loop's technology uses unique molecular identifiers, attaching the same barcode at multiple positions within a long single molecule. The company developed proprietary enzymes that "copy and paste" the original barcode at multiple positions throughout the molecule, Yehezkel said.
After barcoding, molecules are PCR amplified and then standard library prep and sequencing can proceed, Yehezkel explained. After sequencing, reads with the same barcodes are grouped together and assembled back into the longer molecules.
"An important part is that all amplification is always done post barcoding," Yehezkel said. "So, you get long-read sequencing, but also molecule counting."
He said that the concept is similar to techniques that use transposases to introduce adaptors into DNA fragments, except that the company uses a different enzyme and chemistry. The company is also working on two different forms of the chemistry, one that uses a random distribution model, distributing the barcodes randomly throughout the molecules, and another that uses a sequence-specific distribution.
A sequence-specific distribution will enable researchers to phase only certain parts of a molecule. For instance, he said, the firm is collaborating with a pharmaceutical company that is developing a targeted drug. There is a specific set of mutations around 9 kilobases apart from each other and the drug is effective only in patients that carry those mutations on the same chromosome. With the sequence-specific barcode distribution, just that targeted area needs to be phased. "That's a huge reduction in the amount of sequencing you need to do," he said.
Loop's first product, LoopSeq Complete, is for 16S and 18S rRNA sequencing and includes the sample prep as well as cloud-based analysis. The LoopSeq Complete kit also enables multiplexing of 24 or 96 samples, he said.
In addition, it plans to launch a second product for shotgun metagenomic sequencing in the next several months. Loop also plans to develop sequencing and phasing applications for HLA, transcriptome, and targeted amplicons.
The company has not yet described its technology in peer-reviewed studies, but Yehezkel said that several were in the works with the firm's collaborators.
In a technical note published on its website, Loop described using its technology to measure the relative abundance of eight microbial species from the ZymoBIOMICS Community Standard, a mock microbial community that can be used to assess and quality control next-generation sequencing workflows. Loop's technology demonstrated high concordance with the known species abundance. In addition, the firm measured microbial abundance in a complex environmental sample, demonstrating that its technology could better quantify low abundance species than standard Illumina sequencing.
Yehezkel said that the technology enables an error rate that is almost forty-fold lower than standard Illumina sequencing due to error correction steps post sequencing. After sequencing, the synthetic long reads are reconstructed by consensus, with overlapping short reads enabling error correction, Yehezkel said.
Currently, Yehezkel said the firm is collaborating with several unnamed ag-bio companies using its microbial sequencing product. It is also working with an unnamed company on developing an HLA phasing product.
Yehezkel said that Loop is targeting applications where read lengths of up to 10 kilobases will be the most useful. Thus far, the firm has not seen any technical limitations to read lengths aside from simply the size of the single molecule itself. In general, DNA extraction methods end up fragmenting the molecule to 10 kb or less, he said.
Yehezkel said that one advantage of Loop Genomics' technology is that it can take advantage of the existing Illumina user base. Labs that already have Illumina sequencing instruments do not need to purchase any additional equipment.
He said that would help set it apart from single-molecule sequencing companies like Pacific Biosciences and Oxford Nanopore Technologies. It will also help distinguish it from 10x Genomics, whose Chromium system can be used for phasing and generating long-range information, and Bionano Genomics, which markets a genome mapping system.
The company will likely compete with these technologies as well an Illumina's own long-read product — the TruSeq Synthetic Long Read library prep kit, based on technology originally developed by startup Moleculo, which Illumina acquired in 2012.
Researchers have also turned to technologies like Hi-C sequencing to capture long-range information without requiring a separate instrument. Yehezkel said that Loop's technology is fundamentally different from Hi-C, however, in that Hi-C captures structural information about chromosomes but "is not really long-read sequencing." It's "very application-specific for studying chromosome structure through crosslinking," he said.
How Loop will fare in a competitive sequencing market remains to be seen, but researchers have been increasingly interested in long-read sequencing technologies, particularly as costs of sequencing have come down and the technologies have improved.
The company is backed by an undisclosed amount in venture capital funding and has 10 full-time employees, though it has plans to double in size over the next six months.