STmut: A Framework for Visualizing Somatic Alterations in Spatial Transcriptomics Data of Cancer

Authors

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

Language

English

Publication Date

11-30-2023

Journal

Genome Biology

DOI

10.1186/s13059-023-03121-6

PMID

38037084

PMCID

PMC10688493

PubMedCentral® Posted Date

11-30-2023

PubMedCentral® Full Text Version

Post-print

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.

Keywords

Humans, Formaldehyde, Transcriptome, Paraffin Embedding, Neoplasms, Gene Expression Profiling, High-Throughput Nucleotide Sequencing

Published Open-Access

yes

Recommended Citation

Chen, Limin; Chang, Darwin; Tandukar, Bishal; et al., "STmut: A Framework for Visualizing Somatic Alterations in Spatial Transcriptomics Data of Cancer" (2023). Staff and Researcher Publications. 24.
https://digitalcommons.library.tmc.edu/clinic_pub/24