{Reference Type}: Journal Article
{Title}: Comparative Analysis of Gene Expression Analysis Methods for RNA in Situ Hybridization Images.
{Author}: Ariotta V;Azzalini E;Canzonieri V;Hautaniemi S;Bonin S;
{Journal}: J Mol Diagn
{Volume}: 0
{Issue}: 0
{Year}: 2024 Jul 26
{Factor}: 5.341
{DOI}: 10.1016/j.jmoldx.2024.06.010
{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.