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Swedish Startup Aims to Increase Throughput of Imaging-Based Sequencing

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NEW YORK – Swedish startup Single Technologies believes it can increase the throughput of sequencing platforms that rely on imaging by using a faster scanning system and smaller flow cells, all without making changes to the sequencing chemistry.

The Stockholm-based company, which has about 20 employees, is working on a new sequencing system that it believes will rival and possibly exceed Illumina's NovaSeq in throughput while further lowering the cost of sequencing.

Last month, the company obtained SEK 15 million ($1.6 million) from Swedish investment firm JovB Holding and others. It plans to raise another $5 million by this summer to be able to develop a platform for human whole-genome sequencing.

CEO Johan Strömqvist said the company resulted from work he conducted at the Royal Institute of Technology using confocal imaging technology to study protein interactions in live cells. At that time, he said, such technology was very slow. Together with Bengt Sahlgren, who had founded Swedish fiber optics company Proximion, he started working on a new confocal scanning system that can do imaging in parallel.

"That was kind of the start," he said. "We realized quite soon that this tech could be used for genomics instead of proteomics and single-cell application, so we shifted more and more towards genomics with this platform." As a result, he and Sahlgren, together with Annika Bolind Bågenholm and Raoul Stubbe, founded Single Technologies in 2014.

One aspect of the company's technology is the highly parallel confocal scanning system, which is much faster than existing scanners and can speed up the sequencing imaging process. Currently about 100 times faster than a commercial confocal scanner, by this summer, the system is expected to be 800 times faster, he said.

The scanner also has very high sensitivity, making it in principle possible to use it for single-molecule sequencing, although the company is currently not striving for that. "We’re interested in that space but we think that it has not been robust enough," Strömqvist said.

The other aspect of the technology is the company's flow cells, which use nanofluidics instead of microfluidics, resulting in smaller reagent volumes and shorter distances. They also allow for nanopatterning. The flow cells do not use microchannels, though, and liquids can be exchanged quickly over large areas. "It doesn't have the limits you typically have with channels," Strömqvist said. "You can insert cells, tissues, even parts of organs into this flow cell, so it's different." Sequencing reactions on the new flow cell will likely be more efficient, he said, though the company needs to generate more data to show this.

Single Technologies has several patents and patent applications globally around its scanning technology and flow cells, he said.

The company does not intend to develop its own sequencing chemistry. Instead, it plans to partner with firms that already have a working sequencing chemistry, whether it’s sequencing by synthesis, hybridization, ligation, or another type of approach.

"We're teaming up with sequencing chemistry companies and we’re testing and validating their chemistries," Strömqvist said, adding that the company has already completed pilot studies with several unnamed firms and is involved in additional informal collaborations. Those chemistries should allow for read lengths on the order of 300 base pairs, placing Single Technologies' platform squarely into the short-read sequencing camp.

Partnerships around the sequencing chemistry could be a win-win for both companies, he believes. "The sequencing chemistry companies out there would still make money with us on the market," he said. "It's just that the market would grow with our system."

Single Technologies is undeterred by the fact that Illumina has asserted its sequencing chemistry patents against competitors such as Qiagen and BGI in recent years. "A lot of [patents for sequencing] chemistries are going to expire in coming years," Strömqvist said, "so I think the landscape will change."

Longer term, Single Technologies plans to sell high-throughput sequencing systems to core facilities or others in need of large amounts of sequencing data at low cost. This could be especially useful for single-cell sequencing projects that are currently constrained by the cost of sequencing, he said. The goal is to provide not only the sequencing platform but also the infrastructure and software for base calling and data storage, he added.

For now, the firm is demonstrating its technology by generating sequencing data. "Our focus area now is to generate NGS data and take this instrument to a level where we can start sequencing whole genomes," he said, which the firm hopes to achieve within 12 to 15 months.

In addition, Single Technologies' platform could be useful for in situ RNA sequencing, an application the firm has already explored in a multi-year collaboration with Mats Nilsson at Sweden's SciLifeLab. "Previously, we have generated a lot of data in the in situ sequencing space," Strömqvist said. "However, right now, our focus is on NGS."

Cartana, another Swedish startup, recently spun out of Nilsson's laboratory to commercialize in situ RNA-seq, while Spatial Transcriptomics, an in situ transcriptomics company spun out of another SciLifeLab group, was acquired by 10x Genomics in 2018.

"We think we have an excellent platform for that field," Strömqvist said, adding that Single Technologies maintains collaborations with several groups that have developed in situ RNA-seq chemistries that could be used for projects such as the Human Cell Atlas. "But as we see it now from a business perspective, we think it's in a very early phase, so we are currently focusing on NGS," he said.

Still, longer term, Single Technologies' platform "could be a very nice complement to 10x [Genomics]" for both sequencing and in situ RNA-seq, he added.

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