Allele-specific expression reveals interactions between genetic variation and environment

Nature Methods
David A KnowlesAlexis Battle

Abstract

Identifying interactions between genetics and the environment (GxE) remains challenging. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on associations between environmental variables and allele-specific expression. Combining whole-blood RNA-seq with extensive environmental annotations collected from 922 human individuals, we identified 35 GxE interactions, compared with only four using standard GxE interaction testing. EAGLE provides new opportunities for researchers to identify GxE interactions using functional genomic data.

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Methods Mentioned

BETA
RNA-seq
PCR
blood draw
genotyping

Software Mentioned

R
Ensembl
EAGLE
EAGLE Environment - ASE
R package MatrixEQTL
custom Perl script
Tophat2
Samtools 28 mpileup
RcppEigen

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