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Abstract:

Spatial transcriptomics promises to reveal where genes are expressed within intact tissue, transforming how we study development, disease, and tumor biology. But how accurate are these spatial gene expression maps? Focusing on the widely used 10x Genomics Xenium technology, we uncovered evidence that off‑target probe binding can distort gene-specific expression patterns and alter biological conclusions. By comparing Xenium breast cancer data (an imaging-based technology) with matched Visium CytAssist (a sequencing-based technology) and single‑cell RNA‑seq data from the same breast tumor, we identified cases where spatial gene expression reflects contributions from unintended off-target transcripts rather than the intended target gene alone. In this talk, I will introduce the core ideas of spatial transcriptomics and highlight a subtle but consequential technical artifact that can affect imaging‑based technologies.