AI Article Synopsis
- Spatial transcriptomic technologies like the Visium platform allow researchers to analyze gene expression across various tissue regions.
- The article introduces a new software called STmut, which helps visualize genetic changes such as point mutations and copy number alterations in Visium data.
- While STmut can analyze copy number across different tissue sample types, it cannot evaluate single nucleotide variants in FFPE samples, highlighting the strengths and limitations of different data types.
Article 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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Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688493 | PMC |
| http://dx.doi.org/10.1186/s13059-023-03121-6 | DOI Listing |
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