Literature DB >> 35103960

Data Analysis of DNA Methylation Epigenome-Wide Association Studies (EWAS): A Guide to the Principles of Best Practice.

Basharat Bhat1, Gregory T Jones2.   

Abstract

Array-based EWAS have become an increasingly popular technique to identify population epigenetic effects, particularly in humans. With the arrival of nonhuman species arrays, such as the mouse, this is likely to become an even more widely used technology. This chapter provides the less experienced researcher a guide to the analysis of data from the most widely used platform, the Illumina Infinium Methylation assay. This includes an overview of quality filtering, data normalization, analysis options, and techniques to improve the interpretation of results.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  DNA methylation; Epigenome-wide association studies; Methylation quantitative trait loci (meQTL)

Mesh：

Year:  2022        PMID： 35103960     DOI： 10.1007/978-1-0716-2140-0_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  26 in total

1.  Methylation of ELOVL2 gene as a new epigenetic marker of age.

Authors:  Paolo Garagnani; Maria G Bacalini; Chiara Pirazzini; Davide Gori; Cristina Giuliani; Daniela Mari; Anna M Di Blasio; Davide Gentilini; Giovanni Vitale; Sebastiano Collino; Serge Rezzi; Gastone Castellani; Miriam Capri; Stefano Salvioli; Claudio Franceschi
Journal:  Aging Cell       Date:  2012-10-14       Impact factor: 9.304

2.  Type 2 diabetes and leucocyte DNA methylation: an epigenome-wide association study in over 1,500 older adults.

Authors:  Ines Florath; Katja Butterbach; Jonathan Heiss; Melanie Bewerunge-Hudler; Yan Zhang; Ben Schöttker; Hermann Brenner
Journal:  Diabetologia       Date:  2015-10-03       Impact factor: 10.122

Review 3.  Epigenome-wide association studies for common human diseases.

Authors:  Vardhman K Rakyan; Thomas A Down; David J Balding; Stephan Beck
Journal:  Nat Rev Genet       Date:  2011-07-12       Impact factor: 53.242

4.  Epigenome-wide association study identifies TXNIP gene associated with type 2 diabetes mellitus and sustained hyperglycemia.

Authors:  Carolina Soriano-Tárraga; Jordi Jiménez-Conde; Eva Giralt-Steinhauer; Marina Mola-Caminal; Rosa M Vivanco-Hidalgo; Angel Ois; Ana Rodríguez-Campello; Elisa Cuadrado-Godia; Sergi Sayols-Baixeras; Roberto Elosua; Jaume Roquer
Journal:  Hum Mol Genet       Date:  2015-12-07       Impact factor: 6.150

Review 5.  DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies.

Authors:  Xu Gao; Min Jia; Yan Zhang; Lutz Philipp Breitling; Hermann Brenner
Journal:  Clin Epigenetics       Date:  2015-10-16       Impact factor: 6.551

6.  Epigenome-wide association study (EWAS) on lipids: the Rotterdam Study.

Authors:  Kim V E Braun; Klodian Dhana; Paul S de Vries; Trudy Voortman; Joyce B J van Meurs; Andre G Uitterlinden; Albert Hofman; Frank B Hu; Oscar H Franco; Abbas Dehghan
Journal:  Clin Epigenetics       Date:  2017-02-07       Impact factor: 6.551

7.  Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.

Authors:  Simone Wahl; Alexander Drong; Benjamin Lehne; Marie Loh; William R Scott; Sonja Kunze; Pei-Chien Tsai; Janina S Ried; Weihua Zhang; Youwen Yang; Sili Tan; Giovanni Fiorito; Lude Franke; Simonetta Guarrera; Silva Kasela; Jennifer Kriebel; Rebecca C Richmond; Marco Adamo; Uzma Afzal; Mika Ala-Korpela; Benedetta Albetti; Ole Ammerpohl; Jane F Apperley; Marian Beekman; Pier Alberto Bertazzi; S Lucas Black; Christine Blancher; Marc-Jan Bonder; Mario Brosch; Maren Carstensen-Kirberg; Anton J M de Craen; Simon de Lusignan; Abbas Dehghan; Mohamed Elkalaawy; Krista Fischer; Oscar H Franco; Tom R Gaunt; Jochen Hampe; Majid Hashemi; Aaron Isaacs; Andrew Jenkinson; Sujeet Jha; Norihiro Kato; Vittorio Krogh; Michael Laffan; Christa Meisinger; Thomas Meitinger; Zuan Yu Mok; Valeria Motta; Hong Kiat Ng; Zacharoula Nikolakopoulou; Georgios Nteliopoulos; Salvatore Panico; Natalia Pervjakova; Holger Prokisch; Wolfgang Rathmann; Michael Roden; Federica Rota; Michelle Ann Rozario; Johanna K Sandling; Clemens Schafmayer; Katharina Schramm; Reiner Siebert; P Eline Slagboom; Pasi Soininen; Lisette Stolk; Konstantin Strauch; E-Shyong Tai; Letizia Tarantini; Barbara Thorand; Ettje F Tigchelaar; Rosario Tumino; Andre G Uitterlinden; Cornelia van Duijn; Joyce B J van Meurs; Paolo Vineis; Ananda Rajitha Wickremasinghe; Cisca Wijmenga; Tsun-Po Yang; Wei Yuan; Alexandra Zhernakova; Rachel L Batterham; George Davey Smith; Panos Deloukas; Bastiaan T Heijmans; Christian Herder; Albert Hofman; Cecilia M Lindgren; Lili Milani; Pim van der Harst; Annette Peters; Thomas Illig; Caroline L Relton; Melanie Waldenberger; Marjo-Riitta Järvelin; Valentina Bollati; Richie Soong; Tim D Spector; James Scott; Mark I McCarthy; Paul Elliott; Jordana T Bell; Giuseppe Matullo; Christian Gieger; Jaspal S Kooner; Harald Grallert; John C Chambers
Journal:  Nature       Date:  2016-12-21       Impact factor: 49.962

8.  Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight.

Authors:  Leanne K Küpers; Claire Monnereau; Gemma C Sharp; Paul Yousefi; Lucas A Salas; Akram Ghantous; Christian M Page; Sarah E Reese; Allen J Wilcox; Darina Czamara; Anne P Starling; Alexei Novoloaca; Samantha Lent; Ritu Roy; Cathrine Hoyo; Carrie V Breton; Catherine Allard; Allan C Just; Kelly M Bakulski; John W Holloway; Todd M Everson; Cheng-Jian Xu; Rae-Chi Huang; Diana A van der Plaat; Matthias Wielscher; Simon Kebede Merid; Vilhelmina Ullemar; Faisal I Rezwan; Jari Lahti; Jenny van Dongen; Sabine A S Langie; Tom G Richardson; Maria C Magnus; Ellen A Nohr; Zongli Xu; Liesbeth Duijts; Shanshan Zhao; Weiming Zhang; Michelle Plusquin; Dawn L DeMeo; Olivia Solomon; Joosje H Heimovaara; Dereje D Jima; Lu Gao; Mariona Bustamante; Patrice Perron; Robert O Wright; Irva Hertz-Picciotto; Hongmei Zhang; Margaret R Karagas; Ulrike Gehring; Carmen J Marsit; Lawrence J Beilin; Judith M Vonk; Marjo-Riitta Jarvelin; Anna Bergström; Anne K Örtqvist; Susan Ewart; Pia M Villa; Sophie E Moore; Gonneke Willemsen; Arnout R L Standaert; Siri E Håberg; Thorkild I A Sørensen; Jack A Taylor; Katri Räikkönen; Ivana V Yang; Katerina Kechris; Tim S Nawrot; Matt J Silver; Yun Yun Gong; Lorenzo Richiardi; Manolis Kogevinas; Augusto A Litonjua; Brenda Eskenazi; Karen Huen; Hamdi Mbarek; Rachel L Maguire; Terence Dwyer; Martine Vrijheid; Luigi Bouchard; Andrea A Baccarelli; Lisa A Croen; Wilfried Karmaus; Denise Anderson; Maaike de Vries; Sylvain Sebert; Juha Kere; Robert Karlsson; Syed Hasan Arshad; Esa Hämäläinen; Michael N Routledge; Dorret I Boomsma; Andrew P Feinberg; Craig J Newschaffer; Eva Govarts; Matthieu Moisse; M Daniele Fallin; Erik Melén; Andrew M Prentice; Eero Kajantie; Catarina Almqvist; Emily Oken; Dana Dabelea; H Marike Boezen; Phillip E Melton; Rosalind J Wright; Gerard H Koppelman; Letizia Trevisi; Marie-France Hivert; Jordi Sunyer; Monica C Munthe-Kaas; Susan K Murphy; Eva Corpeleijn; Joseph Wiemels; Nina Holland; Zdenko Herceg; Elisabeth B Binder; George Davey Smith; Vincent W V Jaddoe; Rolv T Lie; Wenche Nystad; Stephanie J London; Debbie A Lawlor; Caroline L Relton; Harold Snieder; Janine F Felix
Journal:  Nat Commun       Date:  2019-04-23       Impact factor: 14.919

9.  DNA methylation of blood cells is associated with prevalent type 2 diabetes in a meta-analysis of four European cohorts.

Authors:  Diana L Juvinao-Quintero; Riccardo E Marioni; Carolina Ochoa-Rosales; Tom C Russ; Ian J Deary; Joyce B J van Meurs; Trudy Voortman; Marie-France Hivert; Gemma C Sharp; Caroline L Relton; Hannah R Elliott
Journal:  Clin Epigenetics       Date:  2021-02-23       Impact factor: 6.551

10.  Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.

Authors:  Ruth Pidsley; Elena Zotenko; Timothy J Peters; Mitchell G Lawrence; Gail P Risbridger; Peter Molloy; Susan Van Djik; Beverly Muhlhausler; Clare Stirzaker; Susan J Clark
Journal:  Genome Biol       Date:  2016-10-07       Impact factor: 13.583
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