RT Journal Article SR Electronic T1 Assessing allele specific expression across multiple tissues from RNA-seq read data JF bioRxiv FD Cold Spring Harbor Laboratory SP 007211 DO 10.1101/007211 A1 Matti Pirinen A1 Tuuli Lappalainen A1 Noah A. Zaitlen A1 GTEx Consortium A1 Emmanouil T. Dermitzakis A1 Peter Donnelly A1 Mark I. McCarthy A1 Manuel A. Rivas YR 2014 UL http://biorxiv.org/content/early/2014/07/17/007211.abstract AB 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 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.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.Availability: MAMBA software: http://birch.well.ox.ac.uk/∼rivas/mamba/ R source code and data examples: http://www.iki.fi/mpirinen/Contact: matti.pirinen{at}helsinki.firivas{at}well.ox.ac.uk