title: Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.
abstract: 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.
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.
authors.forename: Elior
authors.initials: E
authors.lastname: Rahmani
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Noah
authors.initials: N
authors.lastname: Zaitlen
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.
authors.forename: Yael
authors.initials: Y
authors.lastname: Baran
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Celeste
authors.initials: C
authors.lastname: Eng
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Donglei
authors.initials: D
authors.lastname: Hu
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California, USA.|Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Joshua
authors.initials: J
authors.lastname: Galanter
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Sam
authors.initials: S
authors.lastname: Oh
authors.affiliation: Department of Medicine, University of California, San Francisco, San Francisco, California, USA.|Department of Bioengineering and Therapeutic Science, University of California, San Francisco, San Francisco, California, USA.
authors.forename: Esteban G
authors.initials: EG
authors.lastname: Burchard
authors.affiliation: Department of Computer Science, University of California, Los Angeles, Los Angeles, California, USA.|Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, USA.
authors.forename: Eleazar
authors.initials: E
authors.lastname: Eskin
authors.affiliation: Microsoft Research New England, Cambridge, Massachusetts, USA.
authors.forename: James
authors.initials: J
authors.lastname: Zou
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv, Israel.|International Computer Science Institute, Berkeley, California, USA.|The Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel Aviv, Israel.
authors.forename: Eran
authors.initials: E
authors.lastname: Halperin
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D057890:Epigenomics / Q000379:methods* / Q000706:statistics & numerical data; D018740:Genetic Heterogeneity; D055106:Genome-Wide Association Study / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D007962:Leukocytes / Q000166:cytology / Q000378:metabolism; D025341:Principal Component Analysis