Assessing allele-specific expression across multiple tissues from RNA-Seq read data

rna-seqRNA 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 project (GTEx) 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.

A team led by researchers at the University of Helsinki have developed 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. They focus on strong ASE effects that they are expecting to see for protein-truncating variants, but this method can also be adjusted for other types of ASE effects. The researchers 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.

Availability –  http://www.well.ox.ac.uk/~rivas/mamba/  R-sources and data examples http://www.iki.fi/~mpirinen/

Contactmatti.pirinen@helsinki.fi ,  rivas@well.ox.ac.uk

Pirinen M, Lappalainen T, Zaitlen NA; GTEx Consortium, Dermitzakis ET, Donnelly P, McCarthy MI, Rivas MA. (2015) Assessing allele-specific expression across multiple tissues from RNA-seq read data. Bioinformatics [Epub ahead of print]. [abstract]

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