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bioRxiv · 10.1101/2025.07.02.662761

In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics

Jensen, A. E. V.·Crowell, H.·Pascual Reguant, A.·Ruano, I.·Tejpar, S.·Heyn, H.·Nilsson, M.·Marco Salas, S.
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Abstract

Copy number variations (CNVs) drive cancer progression. So far, spatial CNV inference has relied on whole transcriptome-based sequencing technologies. However, advances in image-based spatial transcriptomics (iST) now enable high-plex gene measurement in situ. Here, we introduce an approach that adapts CNV inference to iST data, enabling spatial mapping of malignant clones and the tumor microenvironment, at single-cell resolution. Additionally, we assess how panel size and detection efficiency influence CNV inference.

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Jensen, A. E. V., Crowell, H., Pascual Reguant, A., Ruano, I., Tejpar, S., Heyn, H., Nilsson, M., Marco Salas, S.. 2025-07-05. In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics. https://doi.org/10.1101/2025.07.02.662761

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