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 association between environment and allele-specific expression (ASE). Combining RNA-sequencing of whole blood and...

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Autores principales: Knowles, David A., Davis, Joe R., Edgington, Hilary, Raj, Anil, Favé, Marie-Julie, Zhu, Xiaowei, Potash, James B., Weissman, Myrna M., Shi, Jianxin, Levinson, Douglas F., Awadalla, Philip, Mostafavi, Sara, Montgomery, Stephen B., Battle, Alexis
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2017
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501199/
https://www.ncbi.nlm.nih.gov/pubmed/28530654
http://dx.doi.org/10.1038/nmeth.4298
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author Knowles, David A.
Davis, Joe R.
Edgington, Hilary
Raj, Anil
Favé, Marie-Julie
Zhu, Xiaowei
Potash, James B.
Weissman, Myrna M.
Shi, Jianxin
Levinson, Douglas F.
Awadalla, Philip
Mostafavi, Sara
Montgomery, Stephen B.
Battle, Alexis
author_facet Knowles, David A.
Davis, Joe R.
Edgington, Hilary
Raj, Anil
Favé, Marie-Julie
Zhu, Xiaowei
Potash, James B.
Weissman, Myrna M.
Shi, Jianxin
Levinson, Douglas F.
Awadalla, Philip
Mostafavi, Sara
Montgomery, Stephen B.
Battle, Alexis
author_sort Knowles, David A.
collection PubMed
description Identifying interactions between genetics and the environment (GxE) remains challenging. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on association between environment and allele-specific expression (ASE). Combining RNA-sequencing of whole blood and extensive environmental annotations collected from 922 human individuals, we identified 35 GxE interactions, compared to only four using standard GxE testing. EAGLE provides new opportunities to identify GxE interactions using functional genomic data.
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spelling pubmed-55011992017-11-22 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 B. Weissman, Myrna M. Shi, Jianxin Levinson, Douglas F. Awadalla, Philip Mostafavi, Sara Montgomery, Stephen B. Battle, Alexis Nat Methods Article Identifying interactions between genetics and the environment (GxE) remains challenging. We have developed EAGLE, a hierarchical Bayesian model for identifying GxE interactions based on association between environment and allele-specific expression (ASE). Combining RNA-sequencing of whole blood and extensive environmental annotations collected from 922 human individuals, we identified 35 GxE interactions, compared to only four using standard GxE testing. EAGLE provides new opportunities to identify GxE interactions using functional genomic data. 2017-05-22 2017-07 /pmc/articles/PMC5501199/ /pubmed/28530654 http://dx.doi.org/10.1038/nmeth.4298 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Knowles, David A.
Davis, Joe R.
Edgington, Hilary
Raj, Anil
Favé, Marie-Julie
Zhu, Xiaowei
Potash, James B.
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
title Allele-specific expression reveals interactions between genetic variation and environment
title_full Allele-specific expression reveals interactions between genetic variation and environment
title_fullStr Allele-specific expression reveals interactions between genetic variation and environment
title_full_unstemmed Allele-specific expression reveals interactions between genetic variation and environment
title_short Allele-specific expression reveals interactions between genetic variation and environment
title_sort allele-specific expression reveals interactions between genetic variation and environment
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501199/
https://www.ncbi.nlm.nih.gov/pubmed/28530654
http://dx.doi.org/10.1038/nmeth.4298
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