Allele-specific expression reveals interactions between genetic variation and environment


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.

DOI: 10.1038/nmeth.4298

Cite this paper

@article{Knowles2017AllelespecificER, title={Allele-specific expression reveals interactions between genetic variation and environment}, author={David A. Knowles and Joe Davis and Hilary A Edgington and Anil Raj and M H Fave and Xiaowei Zhu and James B. Potash and Myrna M. Weissman and Jianxin Shi and Douglas F. Levinson and Philip Awadalla and Sara Mostafavi and Stephen B. Montgomery and Alexis Battle}, journal={Nature Methods}, year={2017}, volume={14}, pages={699-702} }