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New Chip for 10x Chromium X Promises Lower Cost, Higher Throughput for Single-Cell Studies


ORLANDO, FLORIDA – 10x Genomics is launching a new microfluidic chip design for its Chromium X line of single-cell isolation instruments, which could double the number of cells per run while also lowering cost per sample and cell.

The new chips were one of several technology updates provided by 10x here at the Advances in Genome Biology and Technology annual meeting, which included more information on previously teased product improvements.

10x CSO and Cofounder Ben Hindson introduced the new GEM-X products during a company-sponsored workshop on Wednesday. The firm's flagship single-cell 3' gene expression and 5' immune profiling assays will be the first to get the update, he said, and will begin shipping this quarter. The technology carries several other benefits, including higher sensitivity, reduced multiplet rate, and better cell recovery.

The new assays can detect up to twice as many genes compared to on-market Chromium assays. Multiplet rate is halved — improving data quality — and fewer droplets will be left empty, Hindson said. Cell recovery is raised to approximately 80 percent of cells, up from about 65 percent, CEO and Cofounder Serge Saxonov told GenomeWeb ahead of the presentation.

Hindson noted that the GEM-X assays would be "delivered at lower cost than [our] existing on-market products," and that the company is "going to drive the cost of single-cell analysis down to about $100 per sample."

10x is now accepting preorders for the GEM-X kits and plans to ship them this quarter.

"Researchers are always keen on identifying more genes per cell, as this significantly enhances our understanding of cellular mechanisms and offers unprecedented insights into the complexity of biological systems," said Luciano Martelotto, an expert in single-cell and spatial technologies at Australia's University of Adelaide. Better transcript capture of GEM-X over existing assays "has the potential to vastly improve the resolution of cellular heterogeneity, enable the clear distinction between different cell types and states, boost the detection of rare cell types, and foster a deeper understanding of regulatory networks. Coupled with improvements in transcriptome data quality, this will facilitate the integration of single-cell data across diverse studies and platforms," he added.

GEM-X is the first major update to single-cell chip design since 2019 when 10x introduced the Next-GEM chips, partly in response to a jury verdict that its original GEM chips infringed patents held by Bio-Rad Laboratories.

The new design is the "convergence of a number of different technologies" in chemistry, molecular biology, and microfluidics, Saxonov said. 10x had to develop high-precision milling techniques to create molds for the plastic microfluidic channels, he explained.

"The underlying architecture is much more robust," he said, noting that it should help lead to fewer failed runs. This issue is "not a big problem" for the firm, he said, but newer or less experienced customers are more likely to experience them, he suggested.

Saxonov predicted that the new chips would help drive placements of the Chromium X series instruments. "I think it will be hard to resist the up-conversion," he said. A year ago, 10x had said it would discontinue its legacy Chromium controllers in favor of the X series.

Other updates the company is making include the ability for 10x's single-cell Flex kits to do large-scale CRISPR guide RNA detection. The firm is also planning to launch workflow for fixation of whole blood at the point of collection.

In spatial biology, 10x CTO and Cofounder Michael Schnall-Levin provided some more detail on the new Visium HD kits that will launch this quarter. While the existing Visium product offers capture areas with about 5,000 spots approximately 55 microns across with 100 microns center-to-center distance, HD will have 11 million features 2 microns across with no gaps. "Almost any tissue is going to work with almost no optimization," he said. Visium HD will also enable H&E staining from the same tissue section, he noted.

10x is also launching a new add-on kit to help with cell segmentation on Xenium, its high-resolution RNA and, soon, protein detection platform.