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July 5th, 2025
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Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Institute of Computational Biology, Computation
bioinformatics
biorxiv

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

Jensen, A. E. V.Open in Google Scholar•Crowell, H.Open in Google Scholar•Pascual Reguant, A.Open in Google Scholar•Ruano, I.Open in Google Scholar•Tejpar, S.Open in Google Scholar•Heyn, H.Open in Google Scholar•Nilsson, M.Open in Google Scholar•Marco Salas, S.Open in Google Scholar

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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