scGIST: Gene Panel Design for Spatial Transcriptomics With Prioritized Gene Sets

Authors

Mashrur Ahmed Yafi
Md Hasibul Husain Hisham
Francisco Grisanti
James F Martin
Atif Rahman
Md Abul Hassan Samee

Publication Date

2-26-2024

Journal

Genome Biology

DOI

10.1186/s13059-024-03185-y

PMID

38408997

PMCID

PMC10895727

PubMedCentral® Posted Date

2-26-2024

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

In Situ Hybridization, Fluorescence, Gene Expression Profiling, Transcriptome

Abstract

A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluorescence in situ hybridization, they are typically limited to panels of about a thousand genes. This constrains researchers to build panels from only the marker genes of different cell types and forgo other genes of interest, e.g., genes encoding ligand-receptor complexes or those in specific pathways. We propose scGIST, a constrained feature selection tool that designs sc-ST panels prioritizing user-specified genes without compromising cell type detection accuracy. We demonstrate scGIST's efficacy in diverse use cases, highlighting it as a valuable addition to sc-ST's algorithmic toolbox.

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