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

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

in allelic imbalance / Animal Genetics and Genomics / Bioinformatics / Biomedical and Life Sciences / Cancer / chemistry / Cloning / computer software / Copy number / DNA / DNA sequencing / Evolutionary Biology / Formaldehyde / Gene expression / Gene Expression Profiling / genome / Genomics / High-Throughput Nucleotide Sequencing / Human Genetics / Humans / Hyperplasia / Life Sciences / Method / Microbial Genetics and Genomics / Mutation / Neoplasms - genetics / Paraffin Embedding / Plant Genetics and Genomics / Software / Transcriptome / Transcriptomics / Tumors

2023

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

2023

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

2023

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Journal Article

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

Bastian, Boris C.,

Cho, Raymond J.,

Cruz-Pacheco, Noel,

Yeh, Iwei,

Shain, A. Hunter,

Chen, Limin,

Tandukar, Bishal,

Pozniak, Joanna,

Cheng, Jeffrey,

Chang, Darwin,

Deivendran, Delahny,

Ji, Andrew L.,

Marine, Chris

2023

Overview

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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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

allelic imbalance

/ Animal Genetics and Genomics

/ Bioinformatics

/ Biomedical and Life Sciences

/ Cancer

/ chemistry

/ Cloning