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

By Matti Pirinen, Tuuli Lappalainen, Noah A Zaitlen, GTEx Consortium, Emmanouil T Dermitzakis, Peter Donnelly, Mark I McCarthy, Manuel A. Rivas

Posted 17 Jul 2014
bioRxiv DOI: 10.1101/007211 (published DOI: 10.1093/bioinformatics/btv074)

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@helsinki.fi rivas@well.ox.ac.uk

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