Dataset Information
Assessing allele-specific expression across multiple tissues from RNA-seq read data.
Ontology highlight
ABSTRACT: Motivation
RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data.Results
We present a statistical method to compare different patterns of ASE across tissues and to classify genetic variants according to their impact on the tissue-wide expression profile. We focus on strong ASE effects that we are expecting to see for protein-truncating variants, but our method can also be adjusted for other types of ASE effects. We illustrate the method with a real data example on a tissue-wide expression profile of a variant causal for lipoid proteinosis, and with a simulation study to assess our method more generally.
SUBMITTER: Pirinen M
PROVIDER: S-EPMC4514921 | biostudies-literature | 2015 Aug
REPOSITORIES: biostudies-literature
Publications
Assessing allele-specific expression across multiple tissues from RNA-seq read data.
Bioinformatics (Oxford, England) 20150327 15
<h4>Motivation</h4>RNA sequencing enables allele-specific expression (ASE) studies that complement standard genotype expression studies for common variants and, importantly, also allow measuring the regulatory impact of rare variants. The Genotype-Tissue Expression (GTEx) project is collecting RNA-seq data on multiple tissues of a same set of individuals and novel methods are required for the analysis of these data.<h4>Results</h4>We present a statistical method to compare different patterns of ...[more]
