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

doi:10.1038/nmeth.4298

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 journal › Article › peer-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 language	English (US)
Pages (from-to)	699-702
Number of pages	4
Journal	Nature Methods
Volume	14
Issue number	7
DOIs	https://doi.org/10.1038/nmeth.4298
State	Published - Jun 29 2017
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Allele-specific expression reveals interactions between genetic variation and environment. / Knowles, David A.; Davis, Joe R.; Edgington, Hilary; Raj, Anil; Favé, Marie Julie; Zhu, Xiaowei; Potash, James Bennett; Weissman, Myrna M.; Shi, Jianxin; Levinson, Douglas F.; Awadalla, Philip; Mostafavi, Sara; Montgomery, Stephen B.; Battle, Alexis.

In: Nature Methods, Vol. 14, No. 7, 29.06.2017, p. 699-702.

Research output: Contribution to journal › Article › peer-review

Knowles, David A. ; Davis, Joe R. ; Edgington, Hilary ; Raj, Anil ; Favé, Marie Julie ; Zhu, Xiaowei ; Potash, James Bennett ; Weissman, Myrna M. ; Shi, Jianxin ; Levinson, Douglas F. ; Awadalla, Philip ; Mostafavi, Sara ; Montgomery, Stephen B. ; Battle, Alexis. / Allele-specific expression reveals interactions between genetic variation and environment. In: Nature Methods. 2017 ; Vol. 14, No. 7. pp. 699-702.

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