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

Overview

Journal J Mol Diagn

Publisher Elsevier

Specialties Molecular Biology
Pathology

Date 2024 Jul 28

PMID 39068989

Authors

Valeria Ariotta

Eros Azzalini

Vincenzo Canzonieri

Sampsa Hautaniemi

Serena Bonin

Affiliations

Soon will be listed here.

Abstract

Gene expression analysis is pivotal in cancer research and clinical practice. Although traditional methods lack spatial context, RNA in situ hybridization (RNA-ISH) is a powerful technique that retains spatial tissue information. Here, RNAscope score, RT-droplet digital PCR, and automated QuantISH and QuPath were used for quantifying RNA-ISH expression values from formalin-fixed, paraffin-embedded samples. The methods were compared using high-grade serous ovarian carcinoma samples, focusing on CCNE1, WFDC2, and PPIB genes. The findings demonstrate good concordance between automated methods and RNAscope, with RT-droplet digital PCR showing less concordance. Additionally, 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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