Literature DB >> 28119308

QCEWAS: automated quality control of results of epigenome-wide association studies.

Peter J Van der Most, Leanne K Küpers, Harold Snieder, Ilja Nolte.   

Abstract

Summary: The increasing popularity of epigenome-wide association studies (EWAS) has led to the establishment of several large international meta-analysis consortia. However, when using data originating from multiple sources, a thorough and centralized quality control is essential. To facilitate this, we developed the QCEWAS R package. QCEWAS enables automated quality control of results files of EWAS. QCEWAS produces cohort-specific statistics and graphs to interpret the quality of the results files, graphs comparing results of multiple cohorts, as well as cleaned input files ready for meta-analysis. Availability and Implementation: https://cran.r-project.org/web/packages/QCEWAS. Contact: i.m.nolte@umcg.nl.
© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Mesh：

Year:  2017        PMID： 28119308     DOI： 10.1093/bioinformatics/btw766

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  9 in total

1.  Pregnancy exposure to phthalates and DNA methylation in male placenta - An epigenome-wide association study.

Authors:  Paulina Jedynak; Jörg Tost; Antonia M Calafat; Ekaterina Bourova-Flin; Lucile Broséus; Florence Busato; Anne Forhan; Barbara Heude; Milan Jakobi; Joel Schwartz; Rémy Slama; Daniel Vaiman; Johanna Lepeule; Claire Philippat
Journal:  Environ Int       Date:  2022-01-13       Impact factor: 9.621

2.  Genomic-environmental associations in wild cranberry (Vaccinium macrocarpon Ait.).

Authors:  Jeffrey L Neyhart; Michael B Kantar; Juan Zalapa; Nicholi Vorsa
Journal:  G3 (Bethesda)       Date:  2022-09-30       Impact factor: 3.542

3.  Maternal Dietary Glycemic Index and Glycemic Load in Pregnancy and Offspring Cord Blood DNA Methylation.

Authors:  Leanne K Küpers; Sílvia Fernández-Barrés; Giulia Mancano; Laura Johnson; Raffael Ott; Jesus Vioque; Marco Colombo; Kathrin Landgraf; Elmar W Tobi; Antje Körner; Romy Gaillard; Jeanne H M de Vries; Vincent W V Jaddoe; Martine Vrijheid; Gemma C Sharp; Janine F Felix
Journal:  Diabetes Care       Date:  2022-08-01       Impact factor: 17.152

4.  Maternal Mediterranean diet in pregnancy and newborn DNA methylation: a meta-analysis in the PACE Consortium.

Authors:  Leanne K Küpers; Sílvia Fernández-Barrés; Aayah Nounu; Chloe Friedman; Ruby Fore; Giulia Mancano; Dana Dabelea; Sheryl L Rifas-Shiman; Rosa H Mulder; Emily Oken; Laura Johnson; Mariona Bustamante; Vincent W V Jaddoe; Marie-France Hivert; Anne P Starling; Jeanne H M de Vries; Gemma C Sharp; Martine Vrijheid; Janine F Felix
Journal:  Epigenetics       Date:  2022-03-02       Impact factor: 4.861

5.  Epigenome-wide association meta-analysis of DNA methylation with coffee and tea consumption.

Authors:  Irma Karabegović; Eliana Portilla-Fernandez; Yang Li; Jiantao Ma; Silvana C E Maas; Daokun Sun; Emily A Hu; Brigitte Kühnel; Yan Zhang; Srikant Ambatipudi; Giovanni Fiorito; Jian Huang; Juan E Castillo-Fernandez; Kerri L Wiggins; Niek de Klein; Sara Grioni; Brenton R Swenson; Silvia Polidoro; Jorien L Treur; Cyrille Cuenin; Pei-Chien Tsai; Ricardo Costeira; Veronique Chajes; Kim Braun; Niek Verweij; Anja Kretschmer; Lude Franke; Joyce B J van Meurs; André G Uitterlinden; Robert J de Knegt; M Arfan Ikram; Abbas Dehghan; Annette Peters; Ben Schöttker; Sina A Gharib; Nona Sotoodehnia; Jordana T Bell; Paul Elliott; Paolo Vineis; Caroline Relton; Zdenko Herceg; Hermann Brenner; Melanie Waldenberger; Casey M Rebholz; Trudy Voortman; Qiuwei Pan; Myriam Fornage; Daniel Levy; Manfred Kayser; Mohsen Ghanbari
Journal:  Nat Commun       Date:  2021-05-14       Impact factor: 14.919

6.  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

7.  DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies.

Authors:  Florianne O L Vehmeijer; Leanne K Küpers; Gemma C Sharp; Lucas A Salas; Samantha Lent; Dereje D Jima; Gwen Tindula; Sarah Reese; Cancan Qi; Olena Gruzieva; Christian Page; Faisal I Rezwan; Philip E Melton; Ellen Nohr; Geòrgia Escaramís; Peter Rzehak; Anni Heiskala; Tong Gong; Samuli T Tuominen; Lu Gao; Jason P Ross; Anne P Starling; John W Holloway; Paul Yousefi; Gunn Marit Aasvang; Lawrence J Beilin; Anna Bergström; Elisabeth Binder; Leda Chatzi; Eva Corpeleijn; Darina Czamara; Brenda Eskenazi; Susan Ewart; Natalia Ferre; Veit Grote; Dariusz Gruszfeld; Siri E Håberg; Cathrine Hoyo; Karen Huen; Robert Karlsson; Inger Kull; Jean-Paul Langhendries; Johanna Lepeule; Maria C Magnus; Rachel L Maguire; Peter L Molloy; Claire Monnereau; Trevor A Mori; Emily Oken; Katri Räikkönen; Sheryl Rifas-Shiman; Carlos Ruiz-Arenas; Sylvain Sebert; Vilhelmina Ullemar; Elvira Verduci; Judith M Vonk; Cheng-Jian Xu; Ivana V Yang; Hongmei Zhang; Weiming Zhang; Wilfried Karmaus; Dana Dabelea; Beverly S Muhlhausler; Carrie V Breton; Jari Lahti; Catarina Almqvist; Marjo-Riitta Jarvelin; Berthold Koletzko; Martine Vrijheid; Thorkild I A Sørensen; Rae-Chi Huang; Syed Hasan Arshad; Wenche Nystad; Erik Melén; Gerard H Koppelman; Stephanie J London; Nina Holland; Mariona Bustamante; Susan K Murphy; Marie-France Hivert; Andrea Baccarelli; Caroline L Relton; Harold Snieder; Vincent W V Jaddoe; Janine F Felix
Journal:  Genome Med       Date:  2020-11-25       Impact factor: 11.117

8.  Meta-analysis of epigenome-wide associations between DNA methylation at birth and childhood cognitive skills.

Authors:  Doretta Caramaschi; Alexander Neumann; Andres Cardenas; Gwen Tindula; Silvia Alemany; Lea Zillich; Giancarlo Pesce; Jari M T Lahti; Alexandra Havdahl; Rosa Mulder; Janine F Felix; Henning Tiemeier; Lea Sirignano; Josef Frank; Stephanie H Witt; Marcella Rietschel; Michael Deuschle; Karen Huen; Brenda Eskenazi; Tabea Sarah Send; Muriel Ferrer; Maria Gilles; Maria de Agostini; Nour Baïz; Sheryl L Rifas-Shiman; Tuomas Kvist; Darina Czamara; Samuli T Tuominen; Caroline L Relton; Dheeraj Rai; Stephanie J London; Katri Räikkönen; Nina Holland; Isabella Annesi-Maesano; Fabian Streit; Marie-France Hivert; Emily Oken; Jordi Sunyer; Charlotte A M Cecil; Gemma Sharp
Journal:  Mol Psychiatry       Date:  2022-02-10       Impact factor: 13.437

9.  Maternal Glycemic Dysregulation During Pregnancy and Neonatal Blood DNA Methylation: Meta-analyses of Epigenome-Wide Association Studies.

Authors:  Elmar W Tobi; Diana L Juvinao-Quintero; Justiina Ronkainen; Raffael Ott; Rossella Alfano; Mickaël Canouil; Madelon L Geurtsen; Amna Khamis; Leanne K Küpers; Ives Y Lim; Patrice Perron; Giancarlo Pesce; Johanna Tuhkanen; Anne P Starling; Toby Andrew; Elisabeth Binder; Robert Caiazzo; Jerry K Y Chan; Romy Gaillard; Peter D Gluckman; Elina Keikkala; Neerja Karnani; Sanna Mustaniemi; Tim S Nawrot; François Pattou; Michelle Plusquin; Violeta Raverdy; Kok Hian Tan; Evangelia Tzala; Katri Raikkonen; Christiane Winkler; Anette-G Ziegler; Isabella Annesi-Maesano; Luigi Bouchard; Yap Seng Chong; Dana Dabelea; Janine F Felix; Barbara Heude; Vincent W V Jaddoe; Jari Lahti; Brigitte Reimann; Marja Vääräsmäki; Amélie Bonnefond; Philippe Froguel; Sandra Hummel; Eero Kajantie; Marjo-Riita Jarvelin; Regine P M Steegers-Theunissen; Caitlin G Howe; Marie-France Hivert; Sylvain Sebert
Journal:  Diabetes Care       Date:  2022-03-01       Impact factor: 19.112
  9 in total

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