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eQTL Mapping Using RNA-seq Data

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Abstract

As RNA-seq is replacing gene expression microarrays to assess genome-wide transcription abundance, gene expression Quantitative Trait Locus (eQTL) studies using RNA-seq have emerged. RNA-seq delivers two novel features that are important for eQTL studies. First, it provides information on allele-specific expression (ASE), which is not available from gene expression microarrays. Second, it generates unprecedentedly rich data to study RNA-isoform expression. In this paper, we review current methods for eQTL mapping using ASE and discuss some future directions. We also review existing works that use RNA-seq data to study RNA-isoform expression and we discuss the gaps between these works and isoform-specific eQTL mapping.

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Acknowledgements

We appreciate constructive comments and suggestions from an associate editor and an anonymous reviewer.

Wei Sun’s research is supported in part by the NIH Grant R01MH090936 and EPA Grant for Carolina Center for Computational Toxicology (RD-83382501). Dr. Hu’s research is supported in part by an internal grant from Emory University.

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  1. Department of Biostatistics, Department of Genetics, Carolina Center of Genome Science, UNC Chapel Hill, Chapel Hill, NC, 27599, USA

    Wei Sun

  2. Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA, 30322, USA

    Yijuan Hu

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Sun, W., Hu, Y. eQTL Mapping Using RNA-seq Data. Stat Biosci 5, 198–219 (2013). https://doi.org/10.1007/s12561-012-9068-3

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