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A technical comparison of spatial transcriptomics platforms across six cancer types.

Sergi Cervilla1, Daniela Grases1, Elena Perez1

  • 1Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.

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|January 12, 2026
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This study benchmarks five spatial transcriptomics platforms using FFPE tumor samples, revealing platform strengths and limitations for spatial multi-omics and informing future FFPE tumor profiling strategies.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Spatial transcriptomics (ST) technologies offer novel insights into tissue organization and cellular context.
  • Limited technical benchmarking exists for ST platforms, especially in formalin-fixed, paraffin-embedded (FFPE) clinical samples.

Purpose of the Study:

  • To systematically benchmark five commercial ST platforms using matched FFPE human tumor sections.
  • To enable direct technical comparisons across sequencing-based and imaging-based spatial capture modalities.
  • To evaluate platform performance for spatial multi-omics integration.

Main Methods:

  • Benchmarking of five ST platforms (Visium v1, v2/CytAssist, HD; Xenium; CosMx) on matched FFPE human tumor sections from six cancer types.
  • Evaluation of transcript and UMI detection, gene-histology concordance, and cell type recovery.
  • Integration with targeted protein panels and analysis of sampling strategies and area coverage.

Main Results:

  • Direct comparison of sequencing-based and imaging-based ST platforms on identical FFPE samples.
  • First same-sample comparison of Xenium Multi-Tissue and Xenium Prime platforms.
  • Demonstration of spatial multi-omics capabilities and quantification of RNA-protein decoupling in FFPE tumors.

Conclusions:

  • Provides a harmonized dataset and technical reference for the spatial transcriptomics community.
  • Offers insights into the relative strengths and limitations of ST platforms for FFPE tumor profiling.
  • Guides design considerations for high-throughput spatial profiling of FFPE tissues.