SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data Article Swipe

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Diane Zhang , Åsa Segerstolpe , Michal Slyper , Julia Waldman , Evan Murray , Ralf Strasser , Jan Watter , Ofir Cohen , Orr Ashenberg , Daniel L. Abravanel , Judit Jané‐Valbuena , Simon Mages , Ana Lako , Karla Helvie , Orit Rozenblatt–Rosen , Scott J. Rodig , Fei Chen , Nikhil Wagle , Aviv Regev , Johanna Klughammer ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1186/s13059-025-03573-y

Solid tumors are spatially heterogeneous in their genetic, molecular, and cellular composition, but recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to identify copy number alterations (CNAs), we develop SlideCNA, a computational tool to extract CNA signals from sparse spatial transcriptomics data with near single cellular resolution. SlideCNA uses expression-aware spatial binning to overcome sparsity limitations while maintaining spatial signal to recover CNA patterns. We test SlideCNA on simulated and real Slide-seq data of (metastatic) breast cancer and demonstrate its potential for spatial subclone detection.

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Biology

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Biology Computational biology Transcriptome Leverage (statistics) Spatial analysis RNA-Seq RNA Copy-number variation Bioinformatics Genetics Computer science Gene expression Gene Genome Artificial intelligence Geology Remote sensing

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Type: article
Language: en
Landing Page: https://doi.org/10.1186/s13059-025-03573-y
PDF: https://genomebiology.biomedcentral.com/counter/pdf/10.1186/s13059-025-03573-y
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References: 33
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DOI: https://doi.org/10.1186/s13059-025-03573-y

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Title: SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data

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Language: en

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Publication year: 2025

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Publication date: 2025-05-02

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Authors: Diane Zhang, Åsa Segerstolpe, Michal Slyper, Julia Waldman, Evan Murray, Ralf Strasser, Jan Watter, Ofir Cohen, Orr Ashenberg, Daniel L. Abravanel, Judit Jané‐Valbuena, Simon Mages, Ana Lako, Karla Helvie, Orit Rozenblatt–Rosen, Scott J. Rodig, Fei Chen, Nikhil Wagle, Aviv Regev, Johanna Klughammer

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Landing page: https://doi.org/10.1186/s13059-025-03573-y

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Concepts: Biology, Computational biology, Transcriptome, Leverage (statistics), Spatial analysis, RNA-Seq, RNA, Copy-number variation, Bioinformatics, Genetics, Computer science, Gene expression, Gene, Genome, Artificial intelligence, Geology, Remote sensing

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