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Comparison Between Expression Microarrays and RNA-Sequencing Using UKBEC Dataset Identified a trans-eQTL Associated
Letitia M F Sng1, Peter C Thomson1, Daniah Trabzuni2,3
1The University of Sydney, School of Life and Environmental Sciences, Australia.
Frontiers in Neurology and Neuroscience Research
|July 29, 2021
Summary
RNA-sequencing (RNA-Seq) and microarrays show high agreement for gene expression and differential expression analysis. However, RNA-Seq is superior for expression quantitative trait loci (eQTL) mapping in the human brain.
Area of Science:
- Genomics
- Neuroscience
- Bioinformatics
Background:
- RNA-sequencing (RNA-Seq) offers greater transcriptomic depth than microarrays but incurs higher computational costs.
- Choosing between RNA-Seq and microarrays involves balancing data richness with computational resources.
Purpose of the Study:
- To compare RNA-Seq and microarrays for gene expression analysis in the human brain.
- To evaluate the utility of each platform for identifying absolute expression levels, differentially expressed genes, and expression quantitative trait loci (eQTLs).
Main Methods:
- Utilized the United Kingdom Brain Expression Consortium (UKBEC) dataset.
- Compared gene expression levels, differential expression, and eQTL mapping between microarray and RNA-Seq data.
- Focused analysis on human brain regions.
Main Results:
- High agreement observed between microarrays and RNA-Seq for absolute expression levels and differential gene expression.
- Low agreement found when mapping expression quantitative trait loci (eQTLs) between the two platforms.
- Identified significant eQTLs, including a trans-eQTL for the MPZ gene in the substantia nigra, using both methods.
Conclusions:
- Microarray data may be sufficient and more cost-effective for studies focused solely on gene expression levels or differential expression.
- RNA-Seq provides superior resolution for expression quantitative trait loci (eQTL) mapping in the human brain.
- The identified eQTLs warrant further investigation for their roles in brain function and disease.
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