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

Autor: Chen L; Department of Dermatology, University of California, San Francisco, San Francisco, USA., Chang D; Department of Immunology, H. Lee Moffitt Cancer Center, Tampa, USA., Tandukar B; Department of Dermatology, University of California, San Francisco, San Francisco, USA., Deivendran D; Department of Dermatology, University of California, San Francisco, San Francisco, USA., Pozniak J; Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium.; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium., Cruz-Pacheco N; Department of Dermatology, University of California, San Francisco, San Francisco, USA., Cho RJ; Department of Dermatology, University of California, San Francisco, San Francisco, USA., Cheng J; Department of Dermatology, University of California, San Francisco, San Francisco, USA., Yeh I; Department of Dermatology, University of California, San Francisco, San Francisco, USA.; Department of Pathology, University of California, San Francisco, San Francisco, USA.; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA., Marine C; Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Louvain, Belgium.; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Louvain, Belgium., Bastian BC; Department of Dermatology, University of California, San Francisco, San Francisco, USA.; Department of Pathology, University of California, San Francisco, San Francisco, USA.; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA., Ji AL; Department of Dermatology, Department of Oncological Sciences, Black Family Stem Cell Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, USA., Shain AH; Department of Dermatology, University of California, San Francisco, San Francisco, USA. hunter.shain@ucsf.edu.; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, USA. hunter.shain@ucsf.edu.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2023 Nov 30; Vol. 24 (1), pp. 273. Date of Electronic Publication: 2023 Nov 30.
DOI: 10.1186/s13059-023-03121-6
Abstrakt: 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.
(© 2023. The Author(s).)
Databáze: MEDLINE
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