eQTL Mapping Using RNA-seq Data.

Department of Biostatistics, Department of Genetics, Carolina Center of Genome Science, UNC Chapel Hill, Chapel Hill, NC 27599, USA.
Statistics in Biosciences 05/2013; 5(1):198-219. DOI: 10.1007/s12561-012-9068-3
Source: PubMed

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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