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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 B; Weissman, Myrna M; Shi, Jianxin; Levinson, Douglas F; Awadalla, Philip; Mostafavi, Sara; Montgomery, Stephen B; Battle, Alexis.
Affiliation
  • Knowles DA; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
  • Davis JR; Department of Radiology, Stanford University School of Medicine, Stanford, California, USA.
  • Edgington H; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
  • Raj A; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Favé MJ; University of Toronto, Toronto, Ontario, Canada.
  • Zhu X; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.
  • Potash JB; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
  • Weissman MM; CHU Sainte Justine, Montréal, Quebec, Canada.
  • Shi J; Department of Psychiatry, Stanford University School of Medicine, Stanford, California, USA.
  • Levinson DF; Department of Psychiatry, University of Iowa Hospitals &Clinics, Iowa City, Iowa, USA.
  • Awadalla P; Department of Psychiatry, Columbia University and New York State Psychiatric Institute, New York, New York, USA.
  • Mostafavi S; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA.
  • Montgomery SB; Department of Psychiatry, Stanford University School of Medicine, Stanford, California, USA.
  • Battle A; Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
Nat Methods ; 14(7): 699-702, 2017 Jul.
Article in En | MEDLINE | ID: mdl-28530654
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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genetic Variation / Gene Expression Regulation / Epigenesis, Genetic / Alleles Type of study: Etiology_studies / Incidence_studies / Observational_studies / Prognostic_studies / Risk_factors_studies Limits: Adult / Female / Humans / Male Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2017 Type: Article Affiliation country: United States
Fulltext
Print
XML
PubMed Links
Search on Google

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Genetic Variation / Gene Expression Regulation / Epigenesis, Genetic / Alleles Type of study: Etiology_studies / Incidence_studies / Observational_studies / Prognostic_studies / Risk_factors_studies Limits: Adult / Female / Humans / Male Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2017 Type: Article Affiliation country: United States