Literature DB >> 27018579

Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies.

Elior Rahmani1, Noah Zaitlen2, Yael Baran1, Celeste Eng2, Donglei Hu2, Joshua Galanter2,3, Sam Oh2, Esteban G Burchard2,3, Eleazar Eskin4,5, James Zou6, Eran Halperin1,7,8.   

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.

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Mesh：

Year:  2016        PMID： 27018579      PMCID： PMC5548182          DOI： 10.1038/nmeth.3809

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  18 in total

1.  Epigenome-wide association studies without the need for cell-type composition.

Authors:  James Zou; Christoph Lippert; David Heckerman; Martin Aryee; Jennifer Listgarten
Journal:  Nat Methods       Date:  2014-01-26       Impact factor: 28.547

2.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

Authors:  Martin J Aryee; Andrew E Jaffe; Hector Corrada-Bravo; Christine Ladd-Acosta; Andrew P Feinberg; Kasper D Hansen; Rafael A Irizarry
Journal:  Bioinformatics       Date:  2014-01-28       Impact factor: 6.937

3.  Dominant clonotypes in the repertoire of peripheral CD4+ T cells in rheumatoid arthritis.

Authors:  J J Goronzy; P Bartz-Bazzanella; W Hu; M C Jendro; D R Walser-Kuntz; C M Weyand
Journal:  J Clin Invest       Date:  1994-11       Impact factor: 14.808

4.  Genetic ancestry influences asthma susceptibility and lung function among Latinos.

Authors:  Maria Pino-Yanes; Neeta Thakur; Christopher R Gignoux; Joshua M Galanter; Lindsey A Roth; Celeste Eng; Katherine K Nishimura; Sam S Oh; Hita Vora; Scott Huntsman; Elizabeth A Nguyen; Donglei Hu; Katherine A Drake; David V Conti; Andres Moreno-Estrada; Karla Sandoval; Cheryl A Winkler; Luisa N Borrell; Fred Lurmann; Talat S Islam; Adam Davis; Harold J Farber; Kelley Meade; Pedro C Avila; Denise Serebrisky; Kirsten Bibbins-Domingo; Michael A Lenoir; Jean G Ford; Emerita Brigino-Buenaventura; William Rodriguez-Cintron; Shannon M Thyne; Saunak Sen; Jose R Rodriguez-Santana; Carlos D Bustamante; L Keoki Williams; Frank D Gilliland; W James Gauderman; Rajesh Kumar; Dara G Torgerson; Esteban G Burchard
Journal:  J Allergy Clin Immunol       Date:  2014-10-06       Impact factor: 10.793

5.  SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips.

Authors:  Jovana Maksimovic; Lavinia Gordon; Alicia Oshlack
Journal:  Genome Biol       Date:  2012-06-15       Impact factor: 13.583

6.  Tobacco smoking leads to extensive genome-wide changes in DNA methylation.

Authors:  Sonja Zeilinger; Brigitte Kühnel; Norman Klopp; Hansjörg Baurecht; Anja Kleinschmidt; Christian Gieger; Stephan Weidinger; Eva Lattka; Jerzy Adamski; Annette Peters; Konstantin Strauch; Melanie Waldenberger; Thomas Illig
Journal:  PLoS One       Date:  2013-05-17       Impact factor: 3.240

7.  Accounting for cellular heterogeneity is critical in epigenome-wide association studies.

Authors:  Andrew E Jaffe; Rafael A Irizarry
Journal:  Genome Biol       Date:  2014-02-04       Impact factor: 13.583

8.  DNA methylation age of human tissues and cell types.

Authors:  Steve Horvath
Journal:  Genome Biol       Date:  2013       Impact factor: 13.583

9.  The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts.

Authors:  James R Wagner; Stephan Busche; Bing Ge; Tony Kwan; Tomi Pastinen; Mathieu Blanchette
Journal:  Genome Biol       Date:  2014-02-20       Impact factor: 13.583

10.  Characterization of whole-genome autosomal differences of DNA methylation between men and women.

Authors:  Paula Singmann; Doron Shem-Tov; Simone Wahl; Harald Grallert; Giovanni Fiorito; So-Youn Shin; Katharina Schramm; Petra Wolf; Sonja Kunze; Yael Baran; Simonetta Guarrera; Paolo Vineis; Vittorio Krogh; Salvatore Panico; Rosario Tumino; Anja Kretschmer; Christian Gieger; Annette Peters; Holger Prokisch; Caroline L Relton; Giuseppe Matullo; Thomas Illig; Melanie Waldenberger; Eran Halperin
Journal:  Epigenetics Chromatin       Date:  2015-10-19       Impact factor: 4.954
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  101 in total

1.  Epigenome-wide association study reveals methylation pathways associated with childhood allergic sensitization.

Authors:  Cheng Peng; Evelien R Van Meel; Andres Cardenas; Sheryl L Rifas-Shiman; Abhijeet R Sonawane; Kimberly R Glass; Diane R Gold; Thomas A Platts-Mills; Xihong Lin; Emily Oken; Marie-France Hivert; Andrea A Baccarelli; Nicolette W De Jong; Janine F Felix; Vincent W Jaddoe; Liesbeth Duijts; Augusto A Litonjua; Dawn L DeMeo
Journal:  Epigenetics       Date:  2019-03-28       Impact factor: 4.528

2.  Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Authors:  Shijie C Zheng; Stephan Beck; Andrew E Jaffe; Devin C Koestler; Kasper D Hansen; Andres E Houseman; Rafael A Irizarry; Andrew E Teschendorff
Journal:  Nat Methods       Date:  2017-02-28       Impact factor: 28.547

3.  Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation.

Authors:  Elior Rahmani; Noah Zaitlen; Yael Baran; Celeste Eng; Donglei Hu; Joshua Galanter; Sam Oh; Esteban G Burchard; Eleazar Eskin; James Zou; Eran Halperin
Journal:  Nat Methods       Date:  2017-02-28       Impact factor: 28.547

4.  Cumulative lifetime maternal stress and epigenome-wide placental DNA methylation in the PRISM cohort.

Authors:  Kelly J Brunst; Nicole Tignor; Allan Just; Zhonghua Liu; Xihong Lin; Michele R Hacker; Michelle Bosquet Enlow; Robert O Wright; Pei Wang; Andrea A Baccarelli; Rosalind J Wright
Journal:  Epigenetics       Date:  2018-08-15       Impact factor: 4.528

5.  Variability in DNA methylation at the serotonin transporter gene promoter: epigenetic mechanism or cell-type artifact?

Authors:  Sarah R Moore; Michael S Kobor
Journal:  Mol Psychiatry       Date:  2018-08-06       Impact factor: 15.992

6.  Clinical epigenomics for cardiovascular disease: Diagnostics and therapies.

Authors:  Matthew A Fischer; Thomas M Vondriska
Journal:  J Mol Cell Cardiol       Date:  2021-02-06       Impact factor: 5.000

7.  A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets.

Authors:  Johannes Brägelmann; Justo Lorenzo Bermejo
Journal:  Brief Bioinform       Date:  2019-11-27       Impact factor: 11.622

8.  Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates.

Authors:  Semira Gonseth; Adam J de Smith; Ritu Roy; Mi Zhou; Seung-Tae Lee; Xiaorong Shao; Juhi Ohja; Margaret R Wrensch; Kyle M Walsh; Catherine Metayer; Joseph L Wiemels
Journal:  Epigenetics       Date:  2016-07-12       Impact factor: 4.528

9.  Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.

Authors:  Vitor Onuchic; Ryan J Hartmaier; David N Boone; Michael L Samuels; Ronak Y Patel; Wendy M White; Vesna D Garovic; Steffi Oesterreich; Matt E Roth; Adrian V Lee; Aleksandar Milosavljevic
Journal:  Cell Rep       Date:  2016-11-15       Impact factor: 9.423

10.  Mediation by Placental DNA Methylation of the Association of Prenatal Maternal Smoking and Birth Weight.

Authors:  Andres Cardenas; Sharon M Lutz; Todd M Everson; Patrice Perron; Luigi Bouchard; Marie-France Hivert
Journal:  Am J Epidemiol       Date:  2019-11-01       Impact factor: 4.897
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