Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels.

ABSTRACT:

Background

RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through allele-specific expression (ASE) analysis. Given increasing numbers of RNA-seq samples in the public domain, we here studied to what extent eQTLs and ASE effects can be identified when using public RNA-seq data while deriving the genotypes from the RNA-sequencing reads themselves.

Methods

We downloaded the raw reads for all available human RNA-seq datasets. Using these reads we performed gene expression quantification. All samples were jointly normalized and subjected to a strict quality control. We also derived genotypes using the RNA-seq reads and used imputati

SUBMITTER: Deelen P 

PROVIDER: S-EPMC4423486 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature