Andrew Spaventa, chairman, CEO, and founder, Singular Genomics

There are signs that the next-generation sequencing (NGS) field is about to get a little more crowded—and a lot more interesting. La Jolla-based Singular Genomics Systems says its recently launched G4 platform will mount a serious challenge to the longtime NGS leader Illumina, competing with two of Illumina’s top systems and appealing to customers looking for an alternative.

Singular asserts that the G4 lives up to the company’s name in several ways, starting with its power output ranging from of 15 to 400 gigabases (Gb)—delivering at the high end up to three times more data output per hour than other benchtop instruments—with run times for typical NGS applications starting at about five hours, up to between 16 and 19 hours for four complete human genomes.

That makes G4, Singular says, the world’s most powerful benchtop sequencer, delivering more data per day than competing products. Singular expects that will help G4 to effectively position itself between Illumina’s NextSeq and NovaSeq sequencing systems. It could also compete to some extent with the MiSeq as well, when the first G4 units get shipped to customers during the first half of 2022.

Illumina’s NextSeq™ 1000 and NextSeq 2000 Sequencing Systems, unveiled in 2020, are designed for higher intensity, high-throughput applications, including single-cell gene expression, whole-exome sequencing, shotgun metagenomics, and RNA sequencing. NovaSeq 6000 is Illumina’s most powerful instrument for whole-genome sequencing, with an output of up to 6 terabases (Tb) and 20 billion reads in under two days, and the flexibility to sequence a trio of genomes in one day or up to 48 genomes in about two days.

“Population scale genomics is very well served by a NovaSeq. That’s not really where this system (G4) is meant to be,” Andrew Spaventa, Singular’s chairman, CEO, and founder, told GEN Edge.

Instead, he said, G4 is designed to address institutions across academic, government and commercial spaces—including academic labs, children’s hospitals, commercial labs, CROs, government research labs, medical center labs, and regional clinical labs.

G4’s competitive advantages begin with a sequencing engine built from the ground up, starting with a proprietary four-color sequencing-by-synthesis (SBS) chemistry. That chemistry involves a process by which a DNA polymerase copies the target strand of DNA by adding a single nucleotide base one-by-one. The nucleotides can be modified with a marker that creates a signal when the nucleotide is incorporated along the strand. This marker can be a fluorophore which emits a color, or a change in ionic concentration that can identify the incorporation of a nucleotide into the elongating strand. The signal is read by a detector within the sequencer.

Throughout this process, Singular says, chemically modified nucleotides are used to ensure that only one base at a time can be incorporated by the DNA polymerase during each sequencing cycle. Once the identity of the new incorporated base has been read, the process of nucleotide addition is restarted and the next subsequent base is incorporated and read and so forth until the desired read length has been completed.

“We designed the chemistry and system from the ground up incorporating many novel and unique design decisions and approaches,” Spaventa said. “The fact that we designed and control the entire systems and technology provides a significant advantage for us long term.

Singular’s SBS chemistry includes its own polymers, enzymes, and nucleotides, designed to provide highly accurate paired-read sequencing, and fast sequencing cycle times that reduce run times from days to hours. Singular has also designed and synthesized its own dyes designed to optimize performance.

“When we talk about core chemistry, what we are usually referring to is the nucleotide; modifying the reversible terminator, attaching the linker and a dye, and then a polymerase that incorporates that modified nucleotide with the dye. That’s really the heart of what we created,” Spaventa said.

“One of our inherent advantages is that we’ve created a very fast core chemistry, meaning we can incorporate very fast, and we can cleave very fast, and we can have a very fast cycle time. So, once we started there with the chemistry, we began evolving it over time.”

“Faster, more flexible”

“Holistically we’ve provided a faster, more flexible offering that sits in the middle of the range between a NextSeq and a NovaSeq, and can provide a more flexible benchtop sequencer,” Spaventa said.

The reduced run times should attract academic core labs that serve sizeable numbers of PIs, he said, while startups and early-stage businesses should be drawn to the lower cost of G4. “This provides a really nice, attractive solution since you’re at a price point similar to a NextSeq but your data output rate is three to four times the NextSeq, and you can scale up into the low end of the NovaSeq range.” Singular says the maximum daily output for G4 is about 600 Gb.

The sequencing chemistry is among four key innovations Singular has incorporated into G4. The other three are:

  • Cluster amplification for high accuracy sequencing regardless of the type of genetic input material.
  • Paired end equivalent sequencing designed for efficient mapping and detection of gene rearrangements, by.allowing the instrument to sequence from both ends of the DNA fragment, doubling the number of reads of a sequencing run for the same amount of genetic input material.
  • Detection technology consisting of a proprietary high-speed and high-resolution imaging system intended to optimize throughput, cycle time, accuracy and efficiency.

Spaventa said Singular does not foresee its innovations triggering IP challenges from Illumina or other rivals. As of the third quarter of 2021, those innovations were protected by 93 issued patents and patent applications, the company disclosed in a November 2021 presentation.

Upon its inception in 2016, Singular signed an exclusive license agreement with Columbia University covering two pending U.S. utility patent applications, a pending European patent application and certain materials and technical information. The applications covered compositions and methods for sequencing using nucleotides containing disulfide linkers.

According to Singular, the patents do not cover G4’s current chemistry, so the company does not expect to have to pay Columbia milestone payments (up to $3.9 million), plus royalties on sales due Columbia for use of the patents—though in the future, the system may include features that require such payments. To date, Singular has paid Columbia $100,000.

“OMIC has an encouraging prospect of driving attractive revenue growth and margin expansion, and we believe solid commercial progress will drive multiple expansion over time,” Tycho W. Peterson, a managing director at J.P. Morgan focused on life science tools, diagnostics, and medical devices, and three colleagues wrote December 21 in a research note.

G4 is one of two integrated platforms that Singular is counting on for future growth. The G4 platform includes G4x4, now under development and targeting high volume customers with specific batching needs, such as genome centers, commercial labs, and academic core labs.

Also under development is the PX Integrated Solution, a multi-omics, single-cell analysis, and spatial analysis platform targeting high-throughput analysis. According to Singular, PX is in an advanced prototype development stage, with an early access program expected to begin in 2022, followed by full commercial launch in 2023.

“Going up against Illumina will be hard. They aren’t the entrenched monopoly for no reason,” said Keith Robison, PhD, who monitors developments in genomics through his blog Omics! Omics! “There’s always a danger that many potential customers will use Singular as a bargaining chip to get better terms from Illumina. To rewrite the old saying: nobody got fired for buying Illumina!”

Illumina isn’t the only competitor Singular needs to concern itself with. Robison cited plans by MGI, the instrument subsidiary of China’s BGI Group, to possibly start selling products in the U.S. based on the CoolMPS™ High-throughput Sequencing Set platform by August. A jury recently invalidated Illumina’s U.S. Patent No. 7,541,444, titled “Modified nucleotides,” and claim 1 of U.S. Patent No. 10,480,025, titled “Labelled nucleotides”—while upholding four other Illumina patents. CoolMPS is a massively parallel sequencing (MPS) chemistry that incorporates bases by labeled antibodies.

Robison also cited the anticipated launch by Genapsys of its next electrical microfluidic sequencing chip with a scalable number of detectors, allowing for a wide range of applications. Compared to G4, he said the new chip “would deliver very similar performance for a much lower instrument purchase price.”

Library prep challenge

Another challenge for Singular will be library preparation, a market also dominated by kits for Illumina.

“It isn’t clear what will be required or if it will be possible for Singular customers to use kits designed for Illumina,” Robison observed. “For some methods, it is easy enough to reformat them and I’m sure Singular will make sure you can do basic DNA and RNA sequencing. But some of the more complex stuff—like 10x Genomics’ single-cell methods—may not be very accessible and not every kit maker in the world is likely to reformat their kits for new platforms.”

“That will be another wedge that Illumina marketing can drive: Buy brand X and you might be blocked out of applications Y and Z,” Robison added.

Singular says part of the offering is prep kits that focus on two fast growing research areas, oncology and Immunology.

“If you’re thinking about rare variant detection in liquid biopsy or MRD, they require a lot of depth of sequencing, a lot of throughput for rare variants. And that’s really something well suited for the G4 as a base application,” Spaventa said.

Addressing rare variant detection is Singular’s HD-seq special application kit, which he said offers users Q 50 type accuracy for cell free DNA: “This should be a much more efficient, more accurate lower cost way to do so, so that’s an oncology beachhead for us.”

Cancer research is dominated by RNA-seq and enrichment panels, Robison noted: “The panels in cancer would seem to fit well—many samples per run on the Singular specs. That probably represents a good entry market, as opposed to something like human genetics where the focus is increasingly grinding out large numbers of complete genomes.”

Another specialty kit, XR-seq, offers extended range sequencing stretching from about 450 base reads with B cells for VDJ sequencing, up to 3000 base pairs—which according to Singular will enable research in immunology and other applications that require longer sequencing reads.

G4 enables sequencing to be performed independently on one, two, three, or four flow cells in parallel, with each containing four individually addressable lanes capable of running separate samples.

To maximize flexibility, flow cells with two different output levels will be available: The F2 flow cell available with initial launch can generate approximately 150 million reads, which supports RNA gene expression, single cell and total RNA-seq, exome, and target enrichment.

At a later date, Singular will make available the F3 flow cell, which can generate about 300 million reads, which will support all F2 applications, as well as the 16–19-hour whole human genome sequencing capability.

Addressing pain points

Spaventa revealed that Singular has visited many of its customers in their labs, who highlighted five pain points that G4 is designed to address.

“The first thing we heard was two things: cost and vendor option, meaning that a lot of customers want lower costs and an option in choosing a sequencing supplier, having something that’s so core to your business as sequencing,” Spaventa said. “A lot of these customers spending a tremendous amount of money every year on sequencing, so they really don’t want to be sole-vendor dependent.”

The G4 will cost users from the mid- teens ($16–$17) per gigabase up to the mid-$40s—less than half the expense, Spaventa said, of Illumina’s MiSeq instrument, designed for smaller applications than NextSeq and NovaSeq, such as targeted resequencing, 16S metagenomics, targeted RNA sequencing, and targeted gene expression profiling.

“For those people that are starting to have a buying decision: should I be buying several NexSeqs, or spending more money and stepping into a NovaSeq? Do I have enough pull through to justify that that capital expense? That’s where we provide a really interesting value proposition,” Spaventa said.

Customers also expressed interest in products that offer speed, faster turnaround times, and flexibility, he added.

As Singular ramps up commercial activity on G4, it expects to increase its headcount, which was around 200 people as of September 2021. Key growth areas will focus on manufacturing to support the launch of the system, as well sales, field application specialists, field service engineers, and customer service.

Singular will attend the Advances in Genome Biology and Technology (AGBT) general meeting in February, but has no formal presentation scheduled: “We may share information through other channels at that time; posters, press release, etcetera.”

G4 will enable Singular to generate revenue after years of operating in the red. The company had an accumulated deficit of $132 million as of September 30—but reported cash and short-term investments of $357 million.

“We have runway for much longer than 12 months,” Spaventa said, adding that the company’s current cash has the potential to get Singular to profitability, although it may consider raising additional money to accelerate growth.

The launch of G4 caps a transformative year for Singular, which was founded in 2016. In May, the company went public through an initial public offering (IPO) that generated net proceeds of approximately $237 million from the sale of 11.73 million shares at $22 a share.  Since then, Singular’s share price has fluctuated from a high of $31 in June 2021 to a low of $10.45 on December 20, four days after the launch of G4.

“I think we’re in a show-me type place right now with the investment community. In our opinion, the data we’re releasing with the early access program (EAP) partners should instill a lot of confidence that the technology is solid, and that the G4 will be well received,” Spaventa said.

“I think it’s hard to speculate on the stock right now. It’s just an interesting time in the market and there’s a lot of instability and fear given a number of external factors that have nothing to do with G4,” he added. “But as we continue to execute, we feel really good about where the stock will be in the long term.”

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