STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer

Limin Chen; Darwin Chang; Bishal Tandukar; Delahny Deivendran; Joanna Pozniak; Noel Cruz-Pacheco; Raymond J. Cho; Jeffrey Cheng; Iwei Yeh; Chris Marine; Boris C. Bastian; Andrew L. Ji; A. Hunter Shain

doi:10.1186/s13059-023-03121-6

STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer

Limin Chen, Darwin Chang, Bishal Tandukar, Delahny Deivendran, Joanna Pozniak, Noel Cruz-Pacheco, Raymond J. Cho, Jeffrey Cheng, Iwei Yeh, Chris Marine, Boris C. Bastian, Andrew L. Ji, A. Hunter Shain

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.

Original language	English
Article number	273
Journal	Genome Biology
Volume	24
Issue number	1
DOIs	https://doi.org/10.1186/s13059-023-03121-6
State	Published - Dec 2023

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abstract = "Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.",

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doi = "10.1186/s13059-023-03121-6",

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T2 - a framework for visualizing somatic alterations in spatial transcriptomics data of cancer

AU - Chen, Limin

AU - Chang, Darwin

AU - Tandukar, Bishal

AU - Deivendran, Delahny

AU - Pozniak, Joanna

AU - Cruz-Pacheco, Noel

AU - Cho, Raymond J.

AU - Cheng, Jeffrey

AU - Yeh, Iwei

AU - Marine, Chris

AU - Bastian, Boris C.

AU - Ji, Andrew L.

AU - Shain, A. Hunter

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AB - Spatial transcriptomic technologies, such as the Visium platform, measure gene expression in different regions of tissues. Here, we describe new software, STmut, to visualize somatic point mutations, allelic imbalance, and copy number alterations in Visium data. STmut is tested on fresh-frozen Visium data, formalin-fixed paraffin-embedded (FFPE) Visium data, and tumors with and without matching DNA sequencing data. Copy number is inferred on all conditions, but the chemistry of the FFPE platform does not permit analyses of single nucleotide variants. Taken together, we propose solutions to add the genetic dimension to spatial transcriptomic data and describe the limitations of different datatypes.

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STmut: a framework for visualizing somatic alterations in spatial transcriptomics data of cancer

Abstract

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