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).
Contacts
Investors: investors@10xgenomics.com
Media: media@10xgenomics.com
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SOURCE 10x Genomics, Inc