10x Genomics’ Million Cell Platform, High Def Spatial Transcriptomics, More

January 14, 2021

By Allison Proffitt

January 14, 2021 | Serge Saxonov, CEO and co-founder of 10x Genomics, painted a rosy picture of the future of single-cell technologies earlier this week at the 39th Annual J.P. Morgan Healthcare Conference in San Francisco.

“It is unambiguously clear to us that in the future the vast majority of biological tissue samples will need to be analyzed at large scale and at high resolution,” Saxonov said. And 10x has the product suite to enable that future, he continued, including a new version of the Chromium platform, a higher resolution version of the Visium platform, a coming In Situ platform, a wider rollout of the 10x Cloud, and new tools to address sample prep and cost.


Chromium: One Million Cell Experiments

The Chromium single-cell sequencing technology is 10x Genomics’ oldest product, and Saxonov quoted an install base of over 2,000 labs. “Single cell approaches will become the standard for many types of biological experiments across tens of thousands of labs around the world,” he said. 10x is investing heavily in the platform Saxonov said. He announced new kits to improve affordability and ease of use for Chromium users: a cell multiplexing kit, CellPlex, that should reduce per-sample costs by 60%; the Low-Throughput (LT) Single Cell Gene Expression solution, which will lower costs for initial adoption as well as piloting new projects; and a fixed RNA profiling kit.

Chromium X, the newest version of the platform, is expected in the second half of 2021 and Saxonov quoted a list price of “around $100,000”. The Chromium X will make 1 million cell experiments routine, he said. “Many of our customers have been intensely interested in larger and larger experiments,” he said. “We agree. We strongly believe that a greater scale of experimentation will accelerate new discoveries and drive further market expansion.”

At launch, the Chromium X will be targeted to the “most forward looking customers,” Saxonov said, listing larger single-cell census projects, combinatorial screens for drug development,  large-scale CRISPR-based knockout campaigns, and immune profiling as likely early applications. Population studies would be “a bit longer term,” he added.  


Visium: High Resolution Spatial Transcriptomics

While Saxonov describes the Chromium platform as 10x’s most discovery-focused tool, Visium Spatial Genomics shines in more translational research. “Chromium can tell you what is happening in your sample in individual cells—the fundamental unit of biology,” he said. “With our second platform, Visium, you can tell where things are happening.”

Saxonov announced Visium HD, a single-cell resolution spatial transcriptomics product expected in the first half of 2022 that he says offers visibility 400 times higher than the current Visium solution.

“Visium HD is based on big, fundamental advances in the underlying microarray technology,” Saxonov said. “We believe that this—together with all the other investments we’re making—will establish Visium as the single best platform for scientific discovery and translational research.”

He also announced updates for the Visium platform to facilitate ease of use. Visium for FFPE addresses the challenges of RNA degradation during formalin fixed paraffin embedding. The Gene Expression for FFPE Accessory Kit will be available in the second quarter of 2021. Visium CytAssist (expected the first half of 2022) is a benchtop device that will let users stain and pre-screen tissue sections mounted on standard microscopy slides prior to beginning gene or protein expression analysis with Visium assays.


Informatics and What’s Next

Finally, Saxonov shared the broad rollout of the 10x Cloud, a software-as-a-service informatics platform giving a limited release last year.

“Single cell experiments generate large amounts of data. To make use of those experiments, one needs to become adept at processing that data, storing it, analyzing, and visualizing it,” Saxonov said. “Many sophisticated labs have a resources and capabilities to address their own bioinformatics needs, but as we move out to more and more labs around the world to biologists and translational researchers, the informatics challenges become an increasing barrier to single-cell adoption.”

10x Cloud lets customers store their data and run analyses on it at no extra cost, and Saxonov emphasized that 10x Cloud is a long-term investment for the company that will see new features in coming years.

Finally, Saxonov touched on the coming In Situ Analysis platform born from internal development as well as 10x’s 2020 acquisitions of Readcoor and Cartana.

“Through these acquisitions, we obtained great technologies, great teams, and a strong intellectual property portfolio, including over 100 enabling patents covering multiple technical approaches,” he said. “We intend to invest extensively in this platform and build many great products for our customers.”