# RNA-Seq Can Be Used to Quantify Gene Expression Levels for Use in the GARDskin Assay

## TL;DR

This paper shows that RNA-seq can replace the current method in the GARDskin assay for identifying skin sensitizers, with equally accurate results.

## Contribution

The study demonstrates RNA-seq as a viable alternative to NanoString nCounter for gene expression quantification in the GARDskin assay.

## Key findings

- RNA-seq and NanoString nCounter gene expression profiles were highly similar with a Spearman’s correlation of 0.95.
- RNA-seq correctly classified all 24 treatments using the GARDskin pipeline, matching reference classifications.
- RNA-seq data showed strong concordance with NanoString data (Lin’s concordance correlation coefficient of 0.87).

## Abstract

Non-animal methods for identification and characterization of skin sensitizers are continuously evolving, advancing towards more effective, accurate, and informational assays. The GARDskin assay is a scientifically and regulatory recognized assay for the assessment of skin sensitizers. It currently relies on targeted gene expression measurement to derive hazard classifications. With the progression of next generation sequencing technologies, whole transcriptome analysis provides an interesting alternative to the currently implemented targeted gene expression approach. RNA-seq was evaluated for its use in the GARDskin assay as a gene expression quantification method. Based on 24 paired samples acquired on both RNA-seq and the NanoString nCounter platform (the currently standard GARDskin acquisition method), gene expression profiles were found to be highly similar. Comparisons of treatment effects yielded a Spearman’s correlation coefficient of 0.95 and a Lin’s concordance correlation coefficient of 0.87. RNA-seq data was also used to classify the sensitizing hazard of 24 treatments using the standard GARDskin analysis pipeline. The classifications corresponded completely with references, rendering correct classifications for all treatments. In conclusion, it was found that the RNA-seq data strongly resembled NanoString nCounter data, and that it could be used to derive reliable hazard classifications in the GARDskin assay.