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bioRxiv · 10.1101/2024.02.25.581931

Comparative Analysis of Gene Expression Analysis Methods for RNA In Situ Hybridization Images

Ariotta, V.·Azzalini, E.·Canzonieri, V.·Hautaniemi, S.·BONIN, S.
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Abstract

Gene expression analysis is pivotal in cancer research and clinical practice. While traditional methods lack spatial context, RNA in situ hybridization (RNA-ISH) is a powerful technique that retains spatial tissue information. Here, we investigated RNAscope score, RT-droplet digital PCR (RT-ddPCR), and automated QuantISH and QuPath in quantifying RNA-ISH expression values from formalin-fixed paraffin-embedded samples. We compared the methods using high-grade serous ovarian carcinoma samples, focusing on CCNE1, WFDC2, and PPIB genes. Our findings demonstrate good concordance between automated methods and RNAscope, with RT-ddPCR showing less concordance. We conclude that QuantISH exhibits robust performance, even for low-expressed genes like CCNE1, showcasing its modular design and enhancing accessibility as a viable alternative for gene expression analysis.

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Ariotta, V., Azzalini, E., Canzonieri, V., Hautaniemi, S., BONIN, S.. 2024-02-28. Comparative Analysis of Gene Expression Analysis Methods for RNA In Situ Hybridization Images. https://doi.org/10.1101/2024.02.25.581931

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