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Robust identification of regulatory variants (eQTLs) using a differential expression framework developed for RNA-sequencing

Authors :
Mackenzie A. Marrella
Fernando H. Biase
Source :
Journal of Animal Science and Biotechnology, Vol 14, Iss 1, Pp 1-11 (2023)
Publication Year :
2023
Publisher :
BMC, 2023.

Abstract

Abstract Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait, and expression quantitative trait loci (eQTL) studies provide important information to help close that gap. However, two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution. Multiple pipelines have been suggested to address this. For instance, the most recent analysis of the human and farm Genotype-Tissue Expression (GTEx) project proposes using trimmed means of M-values (TMM) to normalize the data followed by an inverse normal transformation. Results In this study, we reasoned that eQTL analysis could be carried out using the same framework used for differential gene expression (DGE), which uses a negative binomial model, a statistical test feasible for count data. Using the GTEx framework, we identified 35 significant eQTLs (P

Details

Language :
English
ISSN :
20491891
Volume :
14
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Journal of Animal Science and Biotechnology
Publication Type :
Academic Journal
Accession number :
edsdoj.1c8983c310a54156a33331a10af84d67
Document Type :
article
Full Text :
https://doi.org/10.1186/s40104-023-00861-0