DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis
Bonnie R. Joubert,Janine F. Felix,Paul Yousefi,Kelly M. Bakulski,Allan C. Just,Carrie V. Breton,Sarah E. Reese,Christina A. Markunas,Christina A. Markunas,Rebecca C Richmond,Cheng-Jian Xu,Leanne K. Küpers,Sam S. Oh,Cathrine Hoyo,Olena Gruzieva,Cilla Söderhäll,Lucas A. Salas,Nour Baïz,Hongmei Zhang,Johanna Lepeule,Carlos Ruiz,Symen Ligthart,Tianyuan Wang,Jack A. Taylor,Liesbeth Duijts,Gemma C Sharp,Soesma A Jankipersadsing,Roy Miodini Nilsen,Ahmad Vaez,Ahmad Vaez,M. Daniele Fallin,Donglei Hu,Augusto A. Litonjua,Bernard F. Fuemmeler,Karen Huen,Juha Kere,Inger Kull,Monica Cheng Munthe-Kaas,Ulrike Gehring,Mariona Bustamante,Marie José Saurel-Coubizolles,Bilal M. Quraishi,Jie Ren,Jörg Tost,Juan R. González,Marjolein J. Peters,Siri E. Håberg,Zongli Xu,Joyce B. J. van Meurs,Tom R. Gaunt,Marjan Kerkhof,Eva Corpeleijn,Andrew P. Feinberg,Celeste Eng,Andrea A. Baccarelli,Sara E. Benjamin Neelon,Asa Bradman,Simon Kebede Merid,Anna Bergström,Zdenko Herceg,Hector Hernandez-Vargas,Bert Brunekreef,Mariona Pinart,Barbara Heude,Susan Ewart,Jin Yao,Nathanaël Lemonnier,Oscar H. Franco,Michael C. Wu,Albert Hofman,Albert Hofman,Wendy L. McArdle,Pieter van der Vlies,Fahimeh Falahi,Matthew W. Gillman,Lisa F. Barcellos,Ashok Kumar,Ashok Kumar,Ashok Kumar,Magnus Wickman,Magnus Wickman,Stefano Guerra,Marie-Aline Charles,John W. Holloway,Charles Auffray,Henning Tiemeier,George Davey Smith,Dirkje S. Postma,Marie-France Hivert,Brenda Eskenazi,Martine Vrijheid,Hasan Arshad,Josep M. Antó,Abbas Dehghan,Wilfried Karmaus,Isabella Annesi-Maesano,Jordi Sunyer,Akram Ghantous,Göran Pershagen,Nina Holland,Susan K. Murphy,Dawn L. DeMeo,Esteban G. Burchard,Christine Ladd-Acosta,Harold Snieder,Wenche Nystad,Gerard H. Koppelman,Caroline L Relton,Vincent W. V. Jaddoe,Allen J. Wilcox,Erik Melén,Erik Melén,Stephanie J. London +112 more
TLDR
This large scale meta-analysis of methylation data identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.Abstract:
Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.read more
Citations
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The Changing Epidemiology of Autism Spectrum Disorders
Kristen Lyall,Lisa A. Croen,Julie L. Daniels,M. Daniele Fallin,Christine Ladd-Acosta,Brian K. Lee,Brian K. Lee,Bo Y. Park,Nathaniel W. Snyder,Diana Schendel,Diana Schendel,Heather E. Volk,Gayle C. Windham,Craig J. Newschaffer +13 more
TL;DR: Eviologic investigations focused on nongenetic factors have established advanced parental age and preterm birth as ASD risk factors, indicated that prenatal exposure to air pollution and short interpregnancy interval are potentialrisk factors, and suggested the need for further exploration of certain prenatal nutrients, metabolic conditions, and exposure to endocrine-disrupting chemicals.
Journal ArticleDOI
Epigenetic Signatures of Cigarette Smoking
Roby Joehanes,Allan C. Just,Riccardo E. Marioni,Luke C. Pilling,Lindsay M. Reynolds,Pooja R. Mandaviya,Weihua Guan,Tao Xu,Cathy E. Elks,Stella Aslibekyan,Hortensia Moreno-Macías,Jennifer A. Smith,Jennifer A. Brody,Radhika Dhingra,Paul Yousefi,James S. Pankow,Sonja Kunze,Sonia Shah,Allan F. McRae,Kurt Lohman,Jin Sha,Jin Sha,Devin Absher,Luigi Ferrucci,Wei Zhao,Ellen W. Demerath,Jan Bressler,Megan L. Grove,Tianxiao Huan,Tianxiao Huan,Chunyu Liu,Chunyu Liu,Chunyu Liu,Michael M. Mendelson,Chen Yao,Douglas P. Kiel,Annette Peters,Rui Wang-Sattler,Peter M. Visscher,Naomi R. Wray,John M. Starr,Jingzhong Ding,Carlos J. Rodriguez,Nicholas J. Wareham,Marguerite R. Irvin,Degui Zhi,Myrto Barrdahl,Paolo Vineis,Srikant Ambatipudi,André G. Uitterlinden,Albert Hofman,Joel Schwartz,Elena Colicino,Lifang Hou,Pantel S. Vokonas,D. Hernandez,Andrew B. Singleton,Stefania Bandinelli,Stephen Turner,Erin B. Ware,Alicia K. Smith,Torsten Klengel,Elisabeth B. Binder,Bruce M. Psaty,Kent D. Taylor,Sina A. Gharib,Brenton R. Swenson,Liming Liang,Dawn L. DeMeo,George T. O'Connor,Zdenko Herceg,Kerry J. Ressler,Karen N. Conneely,N. Sotoodehnia,Sharon L.R. Kardia,David Melzer,Andrea A. Baccarelli,Joyce B. J. van Meurs,Isabelle Romieu,Donna K. Arnett,Ken K. Ong,Yongmei Liu,M. Waldenberger,Ian J. Deary,Myriam Fornage,Daniel Levy,Stephanie J. London +86 more
TL;DR: Cigarette smoking has a broad impact on genome-wide methylation that, at many loci, persists many years aftersmoking cessation, indicating a pattern of persistent altered methylation, with attenuation, after smoking cessation.
Journal ArticleDOI
International Consensus Statement on Allergy and Rhinology: Allergic Rhinitis.
Sarah K. Wise,Sandra Y. Lin,Elina Toskala,Richard R. Orlandi,Cezmi A. Akdis,Jeremiah A. Alt,Antoine Azar,Fuad M. Baroody,Claus Bachert,G. Walter Canonica,Thomas Chacko,Cemal Cingi,Giorgio Ciprandi,Jacquelynne P. Corey,Linda Cox,Peter S. Creticos,Adnan Custovic,Cecelia Damask,Adam S. DeConde,John M. DelGaudio,Charles S. Ebert,Jean Anderson Eloy,Carrie E. Flanagan,Wytske Fokkens,Christine B. Franzese,Jan Gosepath,Ashleigh A. Halderman,Robert G. Hamilton,Hans Jürgen Hoffman,Jens M. Hohlfeld,Steven M. Houser,Peter H. Hwang,Cristoforo Incorvaia,Deborah Jarvis,Ayesha N. Khalid,Maritta Kilpeläinen,Todd T. Kingdom,Helene J. Krouse,Désirée Larenas-Linnemann,Adrienne M. Laury,Stella E. Lee,Joshua M. Levy,Amber U Luong,Bradley F. Marple,Edward D. McCoul,K. Christopher McMains,Erik Melén,James W. Mims,Gianna Moscato,Joaquim Mullol,Harold S. Nelson,Monica O. Patadia,Ruby Pawankar,Oliver Pfaar,Michael P. Platt,William R. Reisacher,Carmen Rondon,Luke Rudmik,Matthew W. Ryan,Joaquín Sastre,Rodney J. Schlosser,Russell A Settipane,Hemant Sharma,Aziz Sheikh,Timothy L. Smith,Pongsakorn Tantilipikorn,Jody R. Tversky,Maria C Veling,De Yun Wang,Marit Westman,Magnus Wickman,Mark A. Zacharek +71 more
TL;DR: To evaluate the existing AR literature, international multidisciplinary experts with an interest in AR have produced the International Consensus statement on Allergy and Rhinology: Allergic Rhinitis (ICAR:AR).
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DNA methylation in human diseases.
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TL;DR: Those promises and unique challenges of epigenetic epidemiological studies are described and some potential solutions are proposed to solve these challenges.
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Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution.
Maarten van Iterson,Erik W. van Zwet,Bastiaan T. Heijmans,Peter A C 't Hoen,Joyce B. J. van Meurs,Rick Jansen,Lude Franke,Dorret I. Boomsma,René Pool,Jenny van Dongen,Jouke J. Hottenga,Marleen J. van Greevenbroek,Coen D.A. Stehouwer,Carla J.H. van der Kallen,Casper G. Schalkwijk,Cisca Wijmenga,Sasha Zhernakova,Ettje F. Tigchelaar,P. Eline Slagboom,Marian Beekman,Joris Deelen,Diana van Heemst,Jan H. Veldink,Leonard H. van den Berg,Cornelia M. van Duijn,Bert A. Hofman,Aaron Isaacs,André G. Uitterlinden,P. Mila Jhamai,Michael M. P. J. Verbiest,H. Eka D. Suchiman,Marijn Verkerk,Ruud van der Breggen,Jeroen van Rooij,Nico Lakenberg,Hailiang Mei,Michiel van Galen,Jan Bot,Dasha V. Zhernakova,Peter Van ‘t Hof,Patrick Deelen,Irene Nooren,Matthijs Moed,Martijn Vermaat,René Luijk,Marc Jan Bonder,Freerk van Dijk,Wibowo Arindrarto,Szymon M. Kielbasa,Morris A. Swertz,Peter Bram 't Hoen +50 more
TL;DR: A Bayesian method to control bias and inflation in EWAS and TWAS based on estimation of the empirical null distribution is proposed and it is demonstrated that the method maximizes power while properly controlling the false positive rate.
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