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Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.
Rahmani, Elior; Zaitlen, Noah; Baran, Yael; Eng, Celeste; Hu, Donglei; Galanter, Joshua; Oh, Sam; Burchard, Esteban G; Eskin, Eleazar; Zou, James; Halperin, Eran.
Afiliación
  • Rahmani E; Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.
  • Zaitlen N; Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
  • Baran Y; Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.
  • Eng C; Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
  • Hu D; Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
  • Galanter J; Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
  • Oh S; Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California, USA.
  • Burchard EG; Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
  • Eskin E; Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
  • Zou J; Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California, USA.
  • Halperin E; Department of Computer Science, University of California, Los Angeles, Los Angeles, California, USA.
Nat Methods ; 13(5): 443-5, 2016 05.
Article en En | MEDLINE | ID: mdl-27018579
In epigenome-wide association studies (EWAS), different methylation profiles of distinct cell types may lead to false discoveries. We introduce ReFACTor, a method based on principal component analysis (PCA) and designed for the correction of cell type heterogeneity in EWAS. ReFACTor does not require knowledge of cell counts, and it provides improved estimates of cell type composition, resulting in improved power and control for false positives in EWAS. Corresponding software is available at http://www.cs.tau.ac.il/~heran/cozygene/software/refactor.html.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Heterogeneidad Genética / Metilación de ADN / Análisis de Componente Principal / Estudio de Asociación del Genoma Completo / Epigenómica Tipo de estudio: Risk_factors_studies Límite: Humans Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2016 Tipo del documento: Article País de afiliación: Israel Pais de publicación: Estados Unidos
Texto completo
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PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Heterogeneidad Genética / Metilación de ADN / Análisis de Componente Principal / Estudio de Asociación del Genoma Completo / Epigenómica Tipo de estudio: Risk_factors_studies Límite: Humans Idioma: En Revista: Nat Methods Asunto de la revista: TECNICAS E PROCEDIMENTOS DE LABORATORIO Año: 2016 Tipo del documento: Article País de afiliación: Israel Pais de publicación: Estados Unidos