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NGS Firms Pursue Slice of Low-Throughput Market


NEW YORK – Sequencing technology firms not named Illumina are reaching down to grab a chunk of the low-throughput end of the market, offering new instruments and reagents that are changing calculations about how to spend research dollars.

Earlier this month, MGI Tech — which also does business as Complete Genomics — announced that it recently launched a paired-end 300 bp reagent kit for the low- to mid-throughput DNBSEQ-G99 and will soon launch a single-end 400 bp kit.

And on Thursday, Element Biosciences announced several new sequencing reagent kits, including a 250 million read kit for 2x150 bp sequencing and a 100 million-read kit for 2x300 bp sequencing, as well as a lower-priced version of its Aviti sequencer that is locked out of running the firm's highest-throughput flow cells, although it will be upgradeable.

Joined by the Singular Genomics G4 instrument running a single 150 million-read F2 flow cell with four individually addressable lanes, these options offer a challenge to Illumina's dominance at this lower end of the sequencing market, especially the MiSeq, a low-throughput workhorse that runs flow cells yielding between 2 million and 50 million reads.

The new options from Element are in response to customer feedback, according to Shawn Levy, the firm's chief scientific officer and SVP of applications. "They wished they had lower throughput at lower price points," he said. "They're more interested in the cost per run than the cost per gigabase. It's about how much it costs to turn on the machine."

With Element's 2x300 bp kit listed at $1,680, compared to $1,887 list price for the most similar MiSeq kit, "the question is, do I even need to bother running my MiSeq?" said Scott Tighe, technical director of the University of Vermont Advanced Genomics Lab, which recently purchased a G4.

While sequencing companies have focused intently on high- and mid-throughput instruments over the past few years, the low-throughput market continues to drive placements. In 2022, Illumina shipped about 1,670 low-throughput instruments with nearly 700 going to new customers. In the same year, Illumina shipped 1,215 mid-throughput instruments. Lower instrument prices and lower consumables pull through have made it perhaps less lucrative than the higher end of the short-read market, mostly served by Illumina's NovaSeq line. But for many academic labs, including core facilities, the ability to do small runs remains important.

"For pilot projects, preliminary studies, and quality control before deep sequencing, these [low-throughput] technologies are key," said Chris Mason, a sequencing expert at Weill Cornell Medicine. "They fill a need in the market and in the lab that enables better and faster science."

MGI Tech launched the G99 a year ago, touting a run time of only seven hours. The firm has already sold it in sixteen countries, a spokesperson said in an email. MGI's 2x300 bp kit, primarily used for 16s microbial sequencing, is available in China now and will be available in the US later this year. The 400 bp kit will also have at least 80 million reads.

Singular, which designed its G4 to reach up or down from the middle of the market, began shipping last year. At about $600, a single F2 flow cell offers one of the lowest costs per run around, although it does not enable 2x300 bp runs.

Element's Levy said that flexibility was the driving force behind the new products, rather than a desire to specifically dip into low-throughput.

Jacob Enk, R&D manager at Daicel Arbor Biosciences, said in a statement that "a more versatile mix of flow cell capacities on the Aviti means we can migrate almost all of our routine sequencing activities — NGS services, product QC, and R&D — to a single instrument and workflow without the logistics issues of complicated batch management."

Still, Element's new products sparked interest among potential customers interested in smaller runs. "We had already planned to buy [an Aviti] for my lab, and this accelerates the desire," Mason said.

Element is also dropping the list price of the so-called Aviti LT from $290,000 to $210,000. Those instruments will be upgradeable to run higher-throughput flow cells for $99,000.

"[The price] is almost the most essential part," said Shana McDevitt, director of genomics at Medio Labs, a startup pursuing NGS-based pathogen detection. Currently, Medio's technology uses the Illumina MiniSeq platform, an instrument with even lower throughput than the MiSeq. "I can be super excited about a tropical island vacation, but if I can't afford the plane I'm staying put," she said.

Some suggested, however, that sequencing firms may not be dipping down far enough. A 100 million read flow cell is "the sweet spot for us," Medio's McDevitt said, but that may be more than what other applications need. "Outside of another pandemic, I don't know of a pathogen detection panel where you could quickly prep or have enough samples to need more, at least on our technology."

Mason from Weill Cornell added that even smaller flow cells in the range of 25 million to 50 million would be useful for pilot projects, small genomes, and QC.

"It would be nice to have a small flow cell for QC," Tighe said. "I don't want to have to spend $600 to decide if a library is good or not."

Tighe noted that MiSeq should be able to retain a lot of the low-throughput market where validation is essential, such as clinical and forensic applications. Eating into that bulwark "would be a huge undertaking" for the newer entrants, he said.

How the new products will translate into sales — especially instrument placements — remains to be seen. If Illumina has a plan to lower its prices, the firm is keeping that to itself, for now, suggesting the competition could be allowed to linger.

"I think the assumption has been that [low-throughput sequencing] is going away," Element's Levy said. "That's not the feedback we've been seeing."

Singular CEO and Cofounder Drew Spaventa agreed. The firm recently released its larger, F3 flow cell. "We thought [two of our customers] would migrate to the F3 and they're still ordering F2s," he said.