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Sweden's Single Technologies Progresses Towards 3D Sequencing, $10 Human Genome

Sequencing data

NEW YORK – Swedish startup Single Technologies is beginning to give shape to its high-throughput sequencing instrument, which it has been working on since 2019. 

The firm has come up with a design for a 3D "matrix" to replace the traditional 2D flow cell, which it says can maximize use of reagents, leading to lower costs. Pairing that with its imaging technology, which it claims could become thousands of times faster than confocal imaging, CEO Johan Strömqvist said the firm might one day sequence a human genome for approximately $10.  

"[It's the] first disruptive architecture I've seen since the HiSeq," said Bob Kain, a former leader in Illumina's R&D organization, who has linked up with Single Technologies as a paid advisor.

The technology literally adds a new dimension to lowering the cost of sequencing. "At Illumina, we looked at trying to add more surfaces to the flow cell, because those are free bases from a consumable-dollar standpoint," he said. "Single's technology allows you to basically add bases throughout the volume of the flow cell, so all of a sudden now you have a third dimension: as density goes up, your clusters per reagent dollar or per consumable dollar increase as the cube and not the square." 

Kain is not the only person who has taken an interest in the company's technology. A European consortium attempting to use epigenetic manipulation to reprogram glial cells in the brain into neurons has partnered with Single Technologies and for certain sequencing applications. The project, dubbed "Regenerar," has received €3 million ($3.2 million) from the European Commission's European Innovation Council Pathfinder program. 

Founded in 2014, Single Technologies began by commercializing an optical technology that would be faster than confocal imaging, mostly with applications in proteomics and spatial biology. However, in 2019 the firm began working on a sequencer, raising a total of $7.7 million in 2020. Since then, it has raised approximately $2 million in equity financing, bringing its total to over $13 million, as well as convertible debt of $2.6 million. 

Its instrument, the Theta sequencer, is smaller than an Illumina NovaSeq, Strömqvist said, but weighing in at nearly 300 kg and taking up space of around 1 cubic meter, it is designed to be used in production-scale labs. Single Technologies has at least one prototype and is building two more. As previously disclosed, it plans to use established sequencing-by-synthesis methods, taking advantage of the fact that the core Illumina patents covering this approach have expired over the last several years. 

Pushing the envelope on scanning speed has been critical for paving the path to sequencing a whole genome. In 2020, Single Technologies told GenomeWeb that it aimed to be 800 times faster than confocal imaging. Strömqvist claimed that the firm has achieved this and is now targeting a system that would be 3,000 times faster.  

The firm has applied for patents on several components of the sequencer, including the matrix layer which "may comprise a gel, such as a hydrogel," according to the application, and which may be applied to a rotatable surface. The application suggests a disk or cylinder, however, Strömqvist said the firm is currently using a toroid, or donut shape, for the polymerizable gel matrix.  "We are using a linear coordinate system and treat the sample as if it is a rectangular volume," he said. "The system is flexible in terms of matrix thickness, and there are different optimum matrix thicknesses depending on the application." 

One potential application is in situ spatial analysis, especially of cells, similar to how fellow sequencing startups Element Biosciences and Singular Genomics Systems are repurposing their instrumentation. However, the first applications are likely to be sequencing-based counting applications, Strömqvist said, though he declined to disclose read lengths.  

"As we start running commercially, we expect to sequence at Q30 reliably for the counting applications," he said. Run times depend on a combination of the number of reads and number of cycles. The firm is currently doing billions of reads "but we have a path towards one trillion in the not-so-distant future," he said. Thus, run times are on the order of days for the applications being pursued.

How Regenerar will use Single Technologies' capabilities is unclear. Investigators at Helmholtz Munich and Portugal's University of Coimbra did not respond to interview requests before deadline. Other partners on the project include contract research organizations Hovione and Fraunhofer-Gesellschaft, as well as consulting firm SPI (Sociedade Portuguesa de Inovação,)

"We're trying to raise capital now," Strömqvist said. "Once we have the funding, we will publish what we have. We'll have more data to present soon."