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

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.

A team led by researchers at the University of Helsinki presents 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 their 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: 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