High Sensitivity and Specificity of the Xenium Platform from 10x Genomics Outperforms NanoString's CosMx and Vizgen's Merscope in Benchmarking Preprint

Xenium In Situ demonstrates higher transcript counts per gene in new comparison study of three spatial imaging platforms

PLEASANTON, Calif., Dec. 13, 2023 /PRNewswire/ -- 10x Genomics, Inc. (Nasdaq: TXG), a leader in single cell and spatial biology, announced today that a new non-peer-reviewed study has independently evaluated the technical performance of three spatial imaging platforms and found the Xenium In Situ platform demonstrated higher quality transcript counts per gene at higher specificity for 22 formalin-fixed paraffin-embedded (FFPE) tissues compared to NanoString's CosMx and Vizgen's MERSCOPE. This comparison, presented in a preprint posted to bioRxiv, marks one of the first benchmarking studies of commercially available spatial imaging platforms using data independently generated in the customer's own lab.

In the study, "Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues," researchers from the Spatial Technology Platform at the Broad Institute along with collaborators at other institutions sought to compare the technical and biological performance of the 10x Xenium, NanoString CosMx, and Vizgen MERSCOPE on matched, archival FFPE tissue microarrays consisting of 22 healthy and diseased samples. FFPE was chosen specifically given the widespread use of FFPE preservation for clinical samples, which is one of the most exciting potential applications of spatial analysis. Furthermore, since the FFPE process is often associated with the degradation of RNA, the use of FFPE samples allowed for testing of technical performance under challenging conditions.

Xenium consistently demonstrated higher sensitivity than both CosMx (more than 12x the sensitivity) and MERSCOPE (over 2x more sensitive) when it came to comparing the expression levels of shared genes. Furthermore, Xenium was found to have both higher on-target calls and the lowest false discovery rate, both measures of specificity, reflecting the platform's ability to accurately measure genes of interest while minimizing false positives. In a second evaluation of the sensitivity of each platform, assessed by the number of genes reliably detected in each tissue type, Xenium was again on top, detecting the highest fraction of genes for both shared and total genes in the majority of tissues.

The researchers next compared the data from each platform to reference RNA sequencing data and found similar correlation coefficients overall, indicating agreement with the reference datasets. Importantly, the Xenium platform accurately measured low-expressing genes unlike CosMx and showed better correlations with healthy tissue than MERSCOPE. Xenium data also exhibited a distinct expression pattern of tissue markers in all tissues, whereas CosMx and MERSCOPE were less capable of distinguishing tissue-specific markers in most tissues.

Beyond comparisons of the technical metrics, the authors looked to understand how well the platforms could identify the representative biology of the various tissue types. Xenium performed well at distinguishing cells of distinct lineage and identifying all known cell types from breast and lung tissues. In healthy breast samples, Xenium identified all nine expected cell types, but CosMx only resolved six of these cell types. Cell-type identification data for MERSCOPE was only provided for breast cancer tissue and, much like CosMx, MERSCOPE did not recognize all the expected cell types. Of particular importance, Xenium's robust and accurate detection of lowly expressed genes enabled confident identification of immune cell types, like T and B cells, which are critical for studies in translational medicine and other key applications.

"These types of independent, customer-led comparisons help the industry move beyond rhetoric and focus on the metrics that matter -- helping researchers see what data quality they can expect in their own labs," said Michael-Schnall Levin, Founding Scientist and Chief Technology Officer at 10x Genomics. "These results also validate our product development strategy: We think deeply about the customer—their research questions, workflow and results—and strive to build best-in-class tools that create a best-in-class experience and deliver best-in-class data. As these findings show, this is precisely what we've done with Xenium. It's awesome to have this independent verification to give customers even more confidence that Xenium is the best performing platform for in situ analysis."

This is the second independent study conducted by researchers to compare In Situ platform performance using customer-generated data. The first study, led by Luciano Martelotto, Associate Professor at the University of Adelaide, in collaboration with David Cook, Postdoctoral Fellow at Lunenfeld-Tanenbaum Research Institute, and Simon Knott, Assistant Professor at Cedars-Sinai, compared the performance of Xenium and CosMx in adjacent prostate adenocarcinoma sections and similarly found that Xenium showed higher specificity and sensitivity than CosMx and more closely matched single cell reference data. The study also demonstrated that Xenium data has a broader dynamic range, which gives the platform a greater ability to more accurately quantify low versus highly expressed genes.

To learn more about the Broad Institute study, read the full article.

About 10x Genomics

10x Genomics is a life science technology company building products to accelerate the mastery of biology and advance human health. Our integrated solutions include instruments, consumables, and software for single cell and spatial biology, which help academic and translational researchers and biopharmaceutical companies understand biological systems at a resolution and scale that matches the complexity of biology. Our products are behind breakthroughs in oncology, immunology, neuroscience, and more, fueling powerful discoveries that are transforming the world's understanding of health and disease. To learn more, visit 10xgenomics.com or connect with us on LinkedIn or X (Twitter).

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