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Next-Generation Sequencing Firms Present Tech, Business Updates at ASHG


NEW YORK – Next-generation sequencing platform makers offered updates on their recent commercial activities and provided an outlook on their product development pipelines at the American Society of Human Genetics annual meeting in Washington, D.C., last week.

Ultima Genomics, which kept a low profile at this year’s Advances in Genome Biology and Technology (AGBT) annual meeting in February, resurfaced at ASHG with a new benchmarking dataset that represents what management called "fairly major improvements" to the company’s sequencing platform.

In addition, early-access customers at Stanford University and Baylor College of Medicine demonstrated the Ultima platform’s utility for assaying transposase-accessible chromatin with sequencing (ATAC-Seq) and deep-RNA sequencing, respectively.

"We have been in early-access mode for the last year or so," Ultima CSO Doron Lipson told GenomeWeb. "It was a learning curve for us to see how the system performs in the wild."

According to Lipson, the company has so far shipped "mid-teens" systems to customers and has undergone "a few rounds of updates, both in terms of stability and in terms of capacity," in preparation for its formal commercial launch.

While the company declined to provide a launch date for its platform, Ultima CEO Gilad Almogy told GenomeWeb, "you can look at AGBT to see that we are a sponsor [next] year; you can make your guesses."

Element Biosciences’ presentations at ASHG, meanwhile, focused on the strength of the company’s Aviti platform for rare-disease diagnosis applications.

"We have illustrated the efficiency of using our platform for trio [whole-genome] sequencing, where it is a trio per flow cell run in 38 hours. Even at very low volume use, that trio is sequenced for under $1,680 in consumable costs," Element CSO Shawn Levy told GenomeWeb.

For labs with a higher sample volume, meaning a few thousand genomes a year, that price can even go down further to under $1,000 per trio, he added.

Having shipped more than 100 instruments to date, Levy said the company has "a very full pipeline for next year" with "clear" launch dates for many upcoming products. However, he declined to provide more details, other than saying that the upcoming announcements "will only enhance the capabilities of the existing instrument — they won't require a significant hardware change."

Returning to the US market at the beginning of the year after ending its patent litigation on multiple fronts with Illumina, Complete Genomics, a subsidiary of Chinese NGS instrument maker MGI Tech, appears to charge ahead at full steam.

Rob Tarbox, Complete Genomics’ VP of product and marketing, told GenomeWeb that the company, which is now in charge of MGI’s business in the US and Canada, went on "a hiring spree" earlier this year to build up its commercial team.

Among the new hires this year — including Tarbox himself, who joined the company earlier this year after serving as the head of product management at Ultima — field application scientists and field support engineers make up the "largest share," he said.

Complete Genomics has not disclosed the number of instruments it has sold so far, but according to Tarbox, among the platforms that are currently available in North America, namely DNBSeq-G99, G400, and T7, orders for T7 are taking up "a pretty large fraction."

Mike Snyder, chair of the genetics department at Stanford University who presented at a Complete Genomics-sponsored workshop, told GenomeWeb after the session that his lab currently has a G400 for single-cell applications and is considering purchasing a T7 "mainly because of the price."

"It should be a lot cheaper," he said. "So it could become our workhorse." According to Tarbox, the list price for the T7 is $600,000.

Additionally, Tarbox said Complete Genomics is working with the city of San Jose, California, to obtain permits for its manufacturing facility. "The idea is to have more flexibility in our manufacturing," he said, since Complete Genomics instruments are currently mostly built in China.

Commenting on the product pipeline, Tarbox said DNBSeq-T20, MGI’s highest-throughput sequencer that is already available in China and some other countries, is "around the corner" for US customers. "That’s the one that we will launch [in the US] in the very near future," he said.

As the NGS newcomers continue to carve out their space in the sequencing industry, market leader Illumina also showcased its R&D efforts during the meeting, while announcing first shipments of the new 25B flow cell for the NovaSeq X.

Calling the 25B flow cell "the greatest leap" in scale across various different applications, Gary Schroth, VP and distinguished scientist at Illumina, said in a company-sponsored workshop that the new flow cell can generate 26 billion reads per run at a cost of about $.64 per million reads.

"NovaSeq X is a big deal, but the 25B flow cell is probably the biggest deal," he said. "That might be the most important consumables product that we have ever launched."

During the workshop, Eric Chow, a biochemistry and biophysics professor at the University of California, San Francisco, showcased early-access data on the 25B flow cell from his group. In their hands, the flow cell produced between 3.4 billion and 3.8 billion reads per lane depending on the library type, leading to roughly 30 billion reads per flow cell, he said.

As a result of the increased throughput, Chow said, his lab can now use Perturb-seq for drug screening, which typically requires 100 billion to 300 billion reads, running 10 25B flow cells on a NovaSeq X for five days. In contrast, the same amount of data would typically require 25 S4 flow cells on one NovaSeq 6000 platform for four weeks. 

Illumina is also planning to launch the new P4 flow cell for the NextSeq 1000 and 2000 platform early next year, Schroth said. That flow cell can produce 1.7 billion reads, or 500 Gb of data, per run and is powered by the XLeap-SBS chemistry, he added.

Beyond that, Illumina is gearing up to release an enrichment kit for its synthetic long-read technology, called Complete Long Read. Slated for Q1 2024, the kit will be pre-manufactured and optimized to enhance coverage of challenging regions of human protein-coding genes, he said.

Meanwhile, long-read sequencing companies also charted their progress at ASHG.

"The conference provided more evidence that long-read sequencing is starting to make an impact in the clinical sequencing world due to reduced cost and significant improvements in data quality and workflows," Toumy Guettouche, CSO of Mercy BioAnalytics and an NGS expert, told GenomeWeb at the sidelines of the meeting. "This makes long-read WGS even more feasible for clinical applications and could also lead to disruption in the cytogenetics space, where microarrays are still commonly used," he added.

"The topic of long-read technologies, both in the industry as well as academic talks, was striking," said Alexander Hoischen, a genomics researcher at Radboud University Medical Center in the Netherlands. "I see a general strong trend to upscaling — and only this enables the currently ongoing push towards clinical applications."

Pacific Biosciences, in addition to announcing a new rare disease clinical research consortium, which Hoischen is part of, at ASHG, also launched new products — such as the Kinnex RNA kits — and tertiary analysis partnerships with Geneyx and Golden Helix to expand its wet-lab and analysis workflows.

In an interview, PacBio Chief Commercial Officer Jeff Eidel also provided updates regarding Onso, the firm's new short-read sequencing-by-binding platform.

"We started shipping the first systems in August of this year," he said. "We're still ramping up manufacturing capabilities, and that probably won't be at full scale until sometime in the first half of next year."

In the meantime, he said the company will continue to carry out pilot projects in its application lab to generate Onso data for early-access customers "on a limited basis."

Also aiming at enhancing the scalability of its technology, Oxford Nanopore put its TurBot end-to-end platform on display for the first time at ASHG.

Roughly the size of a dishwasher, TurBot can process up to 48 samples in parallel including nucleic acid extraction, library preparation, and sequencing, promising to deliver a sample-to-answer solution in one device. In addition, the instrument can have up to three MinIons or one PromethIon2 on board.

"​​As we’ve come to better understand our customers and their needs across this continuum, it has become clear that a number of them are deploying nanopore sequencing in locked-down applications where speed and information richness have an enormous impact," Rosemary Sinclair Dokos, Oxford Nanopore's senior VP of product and program management told GenomeWeb. "To accelerate the rollout of these transformational assays, sample-to-answer solutions are highly valuable, with TurBot being our first offering in this space."

Dokos said the platform caters especially to applied and industrial customers, for applications such as microbial isolate sequencing, targeted, whole-genome, and shallow sequencing applications. The platform is yet to be placed in a customer's lab, with early beta testing expected later this year, and a formal early-access program and launch next year, she said.

"I was really pleased to see Oxford Nanopore introduce an end-to-end device that could handle extraction, library prep, loading, and analysis using their Epi2Me pipeline," Danny Miller, a pediatric geneticist at the University of Washington and a nanopore sequencing expert who attended ASHG, told GenomeWeb. "I think this addresses one of the biggest challenges with the clinical adoption of long-read sequencing — that the protocols can be time-consuming and were not previously reliably automatable."