Allele-specific expression reveals interactions between genetic variation and environment

David A. Knowles, Joe R. Davis, Hilary Edgington, Anil Raj, Marie Julie Favé, Xiaowei Zhu, James Bennett Potash, Myrna M. Weissman, Jianxin Shi, Douglas F. Levinson, Philip Awadalla, Sara Mostafavi, Stephen B. Montgomery, Alexis Battle

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)699-702
Number of pages4
JournalNature Methods
Volume14
Issue number7
DOIs
StatePublished - Jun 29 2017
Externally publishedYes

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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