312 results on '"Yousefi, Paul"'
Search Results
2. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude.
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Rzehak, Peter, Grote, Veit, Langhendries, Jean-Paul, Verduci, Elvira, Ferre, Natalia, Gruszfeld, Darek, Gao, Lu, Guan, Weihua, Zeng, Xuehuo, Schisterman, Enrique, Dou, John, Bakulski, Kelly, Feinberg, Jason, Soomro, Munawar, Pesce, Giancarlo, Baiz, Nour, Isaevska, Elena, Plusquin, Michelle, Vafeiadi, Marina, Roumeliotaki, Theano, Langie, Sabine, Standaert, Arnout, Allard, Catherine, Perron, Patrice, Bouchard, Luigi, van Meel, Evelien, Felix, Janine, Jaddoe, Vincent, Yousefi, Paul, Ramlau-Hansen, Cecilia, Relton, Caroline, Tobi, Elmar, Starling, Anne, Yang, Ivana, Llambrich, Maria, Santorelli, Gillian, Lepeule, Johanna, Salas, Lucas, Bustamante, Mariona, Ewart, Susan, Zhang, Hongmei, Karmaus, Wilfried, Röder, Stefan, Zenclussen, Ana, Jin, Jianping, Nystad, Wenche, Page, Christian, Magnus, Maria, Jima, Dereje, Hoyo, Cathrine, Maguire, Rachel, Kvist, Tuomas, Czamara, Darina, Räikkönen, Katri, Gong, Tong, Ullemar, Vilhelmina, Rifas-Shiman, Sheryl, Oken, Emily, Almqvist, Catarina, Karlsson, Robert, Lahti, Jari, Murphy, Susan, Håberg, Siri, London, Stephanie, Herberth, Gunda, Kadalayil, Latha, Alam, Md, White, Cory, Ghantous, Akram, Walton, Esther, Gruzieva, Olena, Merid, Simon, Kumar, Ashish, Roy, Ritu, Solomon, Olivia, Huen, Karen, Arshad, Hasan, Sunyer, Jordi, Grazuleviciene, Regina, Dabelea, Dana, Steegers-Theunissen, Régine, Nohr, Ellen, Sørensen, Thorkild, Duijts, Liesbeth, Hivert, Marie-France, Nelen, Vera, Popovic, Maja, Kogevinas, Manolis, Nawrot, Tim, Herceg, Zdenko, Annesi-Maesano, Isabella, Fallin, M, Yeung, Edwina, Breton, Carrie, Koletzko, Berthold, Wiemels, Joseph, Melén, Erik, Sharp, Gemma, Silver, Matt, and Rezwan, Faisal
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Birth season ,DNA methylation ,Differentially methylated regions (DMR) ,Latitude ,Meta-analysis ,PACE ,Child ,Child ,Preschool ,Humans ,Infant ,Infant ,Newborn ,Asthma ,Carcinogenesis ,DNA Methylation ,Inflammation ,Seasons - Abstract
BACKGROUND: Seasonal variations in environmental exposures at birth or during gestation are associated with numerous adult traits and health outcomes later in life. Whether DNA methylation (DNAm) plays a role in the molecular mechanisms underlying the associations between birth season and lifelong phenotypes remains unclear. METHODS: We carried out epigenome-wide meta-analyses within the Pregnancy And Childhood Epigenetic Consortium to identify associations of DNAm with birth season, both at differentially methylated probes (DMPs) and regions (DMRs). Associations were examined at two time points: at birth (21 cohorts, N = 9358) and in children aged 1-11 years (12 cohorts, N = 3610). We conducted meta-analyses to assess the impact of latitude on birth season-specific associations at both time points. RESULTS: We identified associations between birth season and DNAm (False Discovery Rate-adjusted p values
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- 2023
3. Association of exposure to second-hand smoke during childhood with blood DNA methylation
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Cosin-Tomas, Marta, Hoang, Thanh, Qi, Cancan, Monasso, Giulietta S., Langdon, Ryan, Kebede Merid, Simon, Calas, Lucinda, de Prado-Bert, Paula, Richmond, Rebecca, Jaddoe, Vincent VW, Duijts, Liesbeth, Wright, John, Annesi-Maesano, Isabella, Grazuleviciene, Regina, Karachaliou, Marianna, Koppelman, Gerard H., Melén, Erik, Gruzieva, Olena, Vrijheid, Martine, Yousefi, Paul, Felix, Janine F., London, Stephanie J., and Bustamante, Mariona
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- 2025
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4. Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation.
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Solomon, Olivia, Huen, Karen, Yousefi, Paul, Küpers, Leanne K, González, Juan R, Suderman, Matthew, Reese, Sarah E, Page, Christian M, Gruzieva, Olena, Rzehak, Peter, Gao, Lu, Bakulski, Kelly M, Novoloaca, Alexei, Allard, Catherine, Pappa, Irene, Llambrich, Maria, Vives, Marta, Jima, Dereje D, Kvist, Tuomas, Baccarelli, Andrea, White, Cory, Rezwan, Faisal I, Sharp, Gemma C, Tindula, Gwen, Bergström, Anna, Grote, Veit, Dou, John F, Isaevska, Elena, Magnus, Maria C, Corpeleijn, Eva, Perron, Patrice, Jaddoe, Vincent WV, Nohr, Ellen A, Maitre, Lea, Foraster, Maria, Hoyo, Cathrine, Håberg, Siri E, Lahti, Jari, DeMeo, Dawn L, Zhang, Hongmei, Karmaus, Wilfried, Kull, Inger, Koletzko, Berthold, Feinberg, Jason I, Gagliardi, Luigi, Bouchard, Luigi, Ramlau-Hansen, Cecilia Høst, Tiemeier, Henning, Santorelli, Gillian, Maguire, Rachel L, Czamara, Darina, Litonjua, Augusto A, Langhendries, Jean-Paul, Plusquin, Michelle, Lepeule, Johanna, Binder, Elisabeth B, Verduci, Elvira, Dwyer, Terence, Carracedo, Ángel, Ferre, Natalia, Eskenazi, Brenda, Kogevinas, Manolis, Nawrot, Tim S, Munthe-Kaas, Monica C, Herceg, Zdenko, Relton, Caroline, Melén, Erik, Gruszfeld, Dariusz, Breton, Carrie, Fallin, MD, Ghantous, Akram, Nystad, Wenche, Heude, Barbara, Snieder, Harold, Hivert, Marie-France, Felix, Janine F, Sørensen, Thorkild IA, Bustamante, Mariona, Murphy, Susan K, Raikkönen, Katri, Oken, Emily, Holloway, John W, Arshad, Syed Hasan, London, Stephanie J, and Holland, Nina
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Humans ,DNA Methylation ,Epigenesis ,Genetic ,Pregnancy ,Sex Characteristics ,Adolescent ,Child ,Infant ,Newborn ,Female ,Male ,Epigenomics ,Epigenome ,Children ,Cord blood ,DNA methylation ,EWAS ,Sex ,Digestive Diseases ,Human Genome ,Genetics ,Prevention ,Pediatric ,Aetiology ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Toxicology - Abstract
BackgroundAmong children, sex-specific differences in disease prevalence, age of onset, and susceptibility have been observed in health conditions including asthma, immune response, metabolic health, some pediatric and adult cancers, and psychiatric disorders. Epigenetic modifications such as DNA methylation may play a role in the sexual differences observed in diseases and other physiological traits.MethodsWe performed a meta-analysis of the association of sex and cord blood DNA methylation at over 450,000 CpG sites in 8438 newborns from 17 cohorts participating in the Pregnancy And Childhood Epigenetics (PACE) Consortium. We also examined associations of child sex with DNA methylation in older children ages 5.5-10 years from 8 cohorts (n = 4268).ResultsIn newborn blood, sex was associated at Bonferroni level significance with differences in DNA methylation at 46,979 autosomal CpG sites (p
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- 2022
5. Blood-based epigenome-wide analyses of chronic low-grade inflammation across diverse population cohorts
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Hillary, Robert F., Ng, Hong Kiat, McCartney, Daniel L., Elliott, Hannah R., Walker, Rosie M., Campbell, Archie, Huang, Felicia, Direk, Kenan, Welsh, Paul, Sattar, Naveed, Corley, Janie, Hayward, Caroline, McIntosh, Andrew M., Sudlow, Cathie, Evans, Kathryn L., Cox, Simon R., Chambers, John C., Loh, Marie, Relton, Caroline L., Marioni, Riccardo E., Yousefi, Paul D., and Suderman, Matthew
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- 2024
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6. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude
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Kadalayil, Latha, Alam, Md. Zahangir, White, Cory Haley, Ghantous, Akram, Walton, Esther, Gruzieva, Olena, Merid, Simon Kebede, Kumar, Ashish, Roy, Ritu P., Solomon, Olivia, Huen, Karen, Eskenazi, Brenda, Rzehak, Peter, Grote, Veit, Langhendries, Jean-Paul, Verduci, Elvira, Ferre, Natalia, Gruszfeld, Darek, Gao, Lu, Guan, Weihua, Zeng, Xuehuo, Schisterman, Enrique F., Dou, John F., Bakulski, Kelly M., Feinberg, Jason I., Soomro, Munawar Hussain, Pesce, Giancarlo, Baiz, Nour, Isaevska, Elena, Plusquin, Michelle, Vafeiadi, Marina, Roumeliotaki, Theano, Langie, Sabine A. S., Standaert, Arnout, Allard, Catherine, Perron, Patrice, Bouchard, Luigi, van Meel, Evelien R., Felix, Janine F., Jaddoe, Vincent W. V., Yousefi, Paul D., Ramlau-Hansen, Cecilia H., Relton, Caroline L., Tobi, Elmar W., Starling, Anne P., Yang, Ivana V., Llambrich, Maria, Santorelli, Gillian, Lepeule, Johanna, Salas, Lucas A., Bustamante, Mariona, Ewart, Susan L., Zhang, Hongmei, Karmaus, Wilfried, Röder, Stefan, Zenclussen, Ana Claudia, Jin, Jianping, Nystad, Wenche, Page, Christian M., Magnus, Maria, Jima, Dereje D., Hoyo, Cathrine, Maguire, Rachel L., Kvist, Tuomas, Czamara, Darina, Räikkönen, Katri, Gong, Tong, Ullemar, Vilhelmina, Rifas-Shiman, Sheryl L., Oken, Emily, Almqvist, Catarina, Karlsson, Robert, Lahti, Jari, Murphy, Susan K., Håberg, Siri E., London, Stephanie, Herberth, Gunda, Arshad, Hasan, Sunyer, Jordi, Grazuleviciene, Regina, Dabelea, Dana, Steegers-Theunissen, Régine P. M., Nohr, Ellen A., Sørensen, Thorkild I. A., Duijts, Liesbeth, Hivert, Marie-France, Nelen, Vera, Popovic, Maja, Kogevinas, Manolis, Nawrot, Tim S., Herceg, Zdenko, Annesi-Maesano, Isabella, Fallin, M. Daniele, Yeung, Edwina, Breton, Carrie V., Koletzko, Berthold, Holland, Nina, Wiemels, Joseph L., Melén, Erik, Sharp, Gemma C., Silver, Matt J., Rezwan, Faisal I., and Holloway, John W.
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- 2023
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7. DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies
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Vehmeijer, Florianne OL, Küpers, Leanne K, Sharp, Gemma C, Salas, Lucas A, Lent, Samantha, Jima, Dereje D, Tindula, Gwen, Reese, Sarah, Qi, Cancan, Gruzieva, Olena, Page, Christian, Rezwan, Faisal I, Melton, Philip E, Nohr, Ellen, Escaramís, Geòrgia, Rzehak, Peter, Heiskala, Anni, Gong, Tong, Tuominen, Samuli T, Gao, Lu, Ross, Jason P, Starling, Anne P, Holloway, John W, Yousefi, Paul, Aasvang, Gunn Marit, Beilin, Lawrence J, Bergström, Anna, Binder, Elisabeth, Chatzi, Leda, Corpeleijn, Eva, Czamara, Darina, Eskenazi, Brenda, Ewart, Susan, Ferre, Natalia, Grote, Veit, Gruszfeld, Dariusz, Håberg, Siri E, Hoyo, Cathrine, Huen, Karen, Karlsson, Robert, Kull, Inger, Langhendries, Jean-Paul, Lepeule, Johanna, Magnus, Maria C, Maguire, Rachel L, Molloy, Peter L, Monnereau, Claire, Mori, Trevor A, Oken, Emily, Räikkönen, Katri, Rifas-Shiman, Sheryl, Ruiz-Arenas, Carlos, Sebert, Sylvain, Ullemar, Vilhelmina, Verduci, Elvira, Vonk, Judith M, Xu, Cheng-jian, Yang, Ivana V, Zhang, Hongmei, Zhang, Weiming, Karmaus, Wilfried, Dabelea, Dana, Muhlhausler, Beverly S, Breton, Carrie V, Lahti, Jari, Almqvist, Catarina, Jarvelin, Marjo-Riitta, Koletzko, Berthold, Vrijheid, Martine, Sørensen, Thorkild IA, Huang, Rae-Chi, Arshad, Syed Hasan, Nystad, Wenche, Melén, Erik, Koppelman, Gerard H, London, Stephanie J, Holland, Nina, Bustamante, Mariona, Murphy, Susan K, Hivert, Marie-France, Baccarelli, Andrea, Relton, Caroline L, Snieder, Harold, Jaddoe, Vincent WV, and Felix, Janine F
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Biological Sciences ,Genetics ,Prevention ,Clinical Research ,Human Genome ,Nutrition ,Childhood Obesity ,Obesity ,Pediatric ,2.1 Biological and endogenous factors ,Metabolic and endocrine ,Cardiovascular ,Cancer ,Stroke ,Oral and gastrointestinal ,Adolescent ,Body Mass Index ,Child ,Child ,Preschool ,CpG Islands ,Cross-Sectional Studies ,DNA Methylation ,Epigenesis ,Genetic ,Epigenome ,Female ,Fetal Blood ,Humans ,Male ,Parturition ,Pediatric Obesity ,Pregnancy ,Body mass index ,Childhood obesity ,DNA methylation ,Epigenetics ,Clinical Sciences - Abstract
BackgroundDNA methylation has been shown to be associated with adiposity in adulthood. However, whether similar DNA methylation patterns are associated with childhood and adolescent body mass index (BMI) is largely unknown. More insight into this relationship at younger ages may have implications for future prevention of obesity and its related traits.MethodsWe examined whether DNA methylation in cord blood and whole blood in childhood and adolescence was associated with BMI in the age range from 2 to 18 years using both cross-sectional and longitudinal models. We performed meta-analyses of epigenome-wide association studies including up to 4133 children from 23 studies. We examined the overlap of findings reported in previous studies in children and adults with those in our analyses and calculated enrichment.ResultsDNA methylation at three CpGs (cg05937453, cg25212453, and cg10040131), each in a different age range, was associated with BMI at Bonferroni significance, P
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- 2020
8. Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight.
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Küpers, Leanne K, Monnereau, Claire, Sharp, Gemma C, Yousefi, Paul, Salas, Lucas A, Ghantous, Akram, Page, Christian M, Reese, Sarah E, Wilcox, Allen J, Czamara, Darina, Starling, Anne P, Novoloaca, Alexei, Lent, Samantha, Roy, Ritu, Hoyo, Cathrine, Breton, Carrie V, Allard, Catherine, Just, Allan C, Bakulski, Kelly M, Holloway, John W, Everson, Todd M, Xu, Cheng-Jian, Huang, Rae-Chi, van der Plaat, Diana A, Wielscher, Matthias, Merid, Simon Kebede, Ullemar, Vilhelmina, Rezwan, Faisal I, Lahti, Jari, van Dongen, Jenny, Langie, Sabine AS, Richardson, Tom G, Magnus, Maria C, Nohr, Ellen A, Xu, Zongli, Duijts, Liesbeth, Zhao, Shanshan, Zhang, Weiming, Plusquin, Michelle, DeMeo, Dawn L, Solomon, Olivia, Heimovaara, Joosje H, Jima, Dereje D, Gao, Lu, Bustamante, Mariona, Perron, Patrice, Wright, Robert O, Hertz-Picciotto, Irva, Zhang, Hongmei, Karagas, Margaret R, Gehring, Ulrike, Marsit, Carmen J, Beilin, Lawrence J, Vonk, Judith M, Jarvelin, Marjo-Riitta, Bergström, Anna, Örtqvist, Anne K, Ewart, Susan, Villa, Pia M, Moore, Sophie E, Willemsen, Gonneke, Standaert, Arnout RL, Håberg, Siri E, Sørensen, Thorkild IA, Taylor, Jack A, Räikkönen, Katri, Yang, Ivana V, Kechris, Katerina, Nawrot, Tim S, Silver, Matt J, Gong, Yun Yun, Richiardi, Lorenzo, Kogevinas, Manolis, Litonjua, Augusto A, Eskenazi, Brenda, Huen, Karen, Mbarek, Hamdi, Maguire, Rachel L, Dwyer, Terence, Vrijheid, Martine, Bouchard, Luigi, Baccarelli, Andrea A, Croen, Lisa A, Karmaus, Wilfried, Anderson, Denise, de Vries, Maaike, Sebert, Sylvain, Kere, Juha, Karlsson, Robert, Arshad, Syed Hasan, Hämäläinen, Esa, Routledge, Michael N, Boomsma, Dorret I, Feinberg, Andrew P, Newschaffer, Craig J, Govarts, Eva, Moisse, Matthieu, Fallin, M Daniele, Melén, Erik, and Prentice, Andrew M
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Fetus ,Humans ,Prenatal Exposure Delayed Effects ,Birth Weight ,Folic Acid ,DNA ,Body Mass Index ,Smoking ,DNA Methylation ,Epigenesis ,Genetic ,CpG Islands ,Fetal Development ,Pregnancy ,Genome ,Human ,Adolescent ,Adult ,Child ,Infant ,Newborn ,Female ,Male ,Genome-Wide Association Study ,Epigenesis ,Genetic ,Genome ,Human ,Infant ,Newborn - Abstract
Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from -183 to 178 grams per 10% increase in methylation (PBonferroni
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- 2019
9. Blood-based epigenome-wide association study and prediction of alcohol consumption.
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Bernabeu, Elena, Chybowska, Aleksandra D., Kresovich, Jacob K., Suderman, Matthew, McCartney, Daniel L., Hillary, Robert F., Corley, Janie, Valdés-Hernández, Maria Del C., Maniega, Susana Muñoz, Bastin, Mark E., Wardlaw, Joanna M., Xu, Zongli, Sandler, Dale P., Campbell, Archie, Harris, Sarah E., McIntosh, Andrew M., Taylor, Jack A., Yousefi, Paul, Cox, Simon R., and Evans, Kathryn L.
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- 2025
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10. Epigenome-wide association study of objectively measured physical activity in peripheral blood leukocytes.
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Fragoso-Bargas, Nicolas, Mcbride, Nancy S., Lee-Ødegård, Sindre, Lawlor, Deborah A., Yousefi, Paul D., Moen, Gunn-Helen, Opsahl, Julia O., Jenum, Anne Karen, Franks, Paul W., Prasad, Rashmi B., Qvigstad, Elisabeth, Birkeland, Kåre I., Richardsen, Kåre R., and Sommer, Christine
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MEDICAL sciences ,DNA methylation ,SEDENTARY behavior ,FALSE discovery rate ,MEDICAL genetics ,PREGNANCY - Abstract
Background: Few studies have explored the association between DNA methylation and physical activity. The aim of this study was to evaluate the association of objectively measured hours of sedentary behavior (SB) and moderate physical activity (MPA) with DNA methylation. We further aimed to explore the association between SB or MPA related CpG sites and cardiometabolic traits, gene expression, and genetic variation. Results: For discovery, we performed cross sectional analyses in pregnant women from the Epigenetics in pregnancy (EPIPREG) sample with both DNA methylation (Illumina MethylationEPIC BeadChip) and objectively measured physical activity data (SenseWear™ Pro 3 armband) (European = 244, South Asian = 109). For EWAS of SB and MPA, two main models were designed: model (1) a linear mixed model adjusted for age, smoking, blood cell composition, including ancestry as random intercept, and model (2) which was additionally adjusted for the total number of steps per day. In model 1, we did not identify any CpG sites associated with neither SB nor MPA. In model 2, SB was positively associated (false discovery rate, FDR < 0.05) with two CpG sites within the VSX1 gene. Both CpG sites were positively associated with BMI and were associated with several genetic variants in cis. MPA was associated with 122 significant CpG sites at FDR < 0.05 (model 2). We further analyzed the ten most statistically significant MPA related CpG sites and found that they presented opposite associations with sedentary behavior and BMI. We were not able to replicate the SB and MPA-related CpG sites in the Avon Longitudinal Study of Parents and Children (ALSPAC). ALSPAC had available objectively measured physical activity data from Actigraph (without steps/day available) and leucocyte DNA methylation data collected during adolescence (n = 408, European). Conclusion: This study suggests associations of objectively measured SB and MPA with maternal DNA methylation in peripheral blood leukocytes, that needs to be confirmed in larger samples of similar study design. [ABSTRACT FROM AUTHOR]
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- 2025
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11. DNA methylation-based predictors of health: applications and statistical considerations
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Yousefi, Paul D., Suderman, Matthew, Langdon, Ryan, Whitehurst, Oliver, Davey Smith, George, and Relton, Caroline L.
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- 2022
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12. CpG Methylation across the adipogenic PPARγ gene and its relationship with birthweight and child BMI at 9 years
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Volberg, Vitaly, Yousefi, Paul, Huen, Karen, Harley, Kim, Eskenazi, Brenda, and Holland, Nina
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Pediatric ,Birth Weight ,Body Mass Index ,Child ,CpG Islands ,DNA Methylation ,Humans ,Infant ,Newborn ,Longitudinal Studies ,PPAR gamma ,Epigenetics ,Birth cohort study ,PPAR. ,Obesity ,Newborns ,Children ,Whole blood ,DNA methylation ,PPARγ ,Clinical Sciences ,Genetics & Heredity ,Clinical sciences - Abstract
BackgroundTo examine methylation of the peroxisome proliferator-activated receptor γ (PPARγ) gene and its relationship with child weight status, at birth and 9 years.MethodsWe measured PPARγ methylation across 23 CpG sites using the Infinium Illumina 450 k array for children from the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort at birth (N = 373) and 9 years (N = 245).ResultsMethylation level correlation patterns across the 23 PPARγ CpG sites were conserved between birth and 9-year ages. We found high inter-CpG correlations between sites 1-3 (methylation block 1) and also between sites 18-23 (methylation block 2) for both time points, although these patterns were less pronounced at 9 years. Additionally, sites 1-3 (north shore) had the highest intra-CpG correlations over time (r = 0.24, 0.42, and 0.3; P = 0.002, P
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- 2017
13. Genome-wide methylation data mirror ancestry information
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Rahmani, Elior, Shenhav, Liat, Schweiger, Regev, Yousefi, Paul, Huen, Karen, Eskenazi, Brenda, Eng, Celeste, Huntsman, Scott, Hu, Donglei, Galanter, Joshua, Oh, Sam S, Waldenberger, Melanie, Strauch, Konstantin, Grallert, Harald, Meitinger, Thomas, Gieger, Christian, Holland, Nina, Burchard, Esteban G, Zaitlen, Noah, and Halperin, Eran
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Biological Sciences ,Genetics ,Cancer Genomics ,Human Genome ,Cancer ,Generic health relevance ,Algorithms ,CpG Islands ,DNA Methylation ,Databases ,Genetic ,Epigenomics ,Genome ,Human ,Genome-Wide Association Study ,Genotype ,Humans ,Internet ,Polymorphism ,Single Nucleotide ,Principal Component Analysis ,User-Computer Interface ,DNA methylation ,Population structure ,Ancestry ,Epigenetics ,Epigenome-wide association study ,Illumina 450K - Abstract
BackgroundGenetic data are known to harbor information about human demographics, and genotyping data are commonly used for capturing ancestry information by leveraging genome-wide differences between populations. In contrast, it is not clear to what extent population structure is captured by whole-genome DNA methylation data.ResultsWe demonstrate, using three large-cohort 450K methylation array data sets, that ancestry information signal is mirrored in genome-wide DNA methylation data and that it can be further isolated more effectively by leveraging the correlation structure of CpGs with cis-located SNPs. Based on these insights, we propose a method, EPISTRUCTURE, for the inference of ancestry from methylation data, without the need for genotype data.ConclusionsEPISTRUCTURE can be used to infer ancestry information of individuals based on their methylation data in the absence of corresponding genetic data. Although genetic data are often collected in epigenetic studies of large cohorts, these are typically not made publicly available, making the application of EPISTRUCTURE especially useful for anyone working on public data. Implementation of EPISTRUCTURE is available in GLINT, our recently released toolset for DNA methylation analysis at: http://glint-epigenetics.readthedocs.io.
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- 2017
14. Maternal BMI at the start of pregnancy and offspring epigenome-wide DNA methylation: findings from the pregnancy and childhood epigenetics (PACE) consortium
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Sharp, Gemma C, Salas, Lucas A, Monnereau, Claire, Allard, Catherine, Yousefi, Paul, Everson, Todd M, Bohlin, Jon, Xu, Zongli, Huang, Rae-Chi, Reese, Sarah E, Xu, Cheng-Jian, Baïz, Nour, Hoyo, Cathrine, Agha, Golareh, Roy, Ritu, Holloway, John W, Ghantous, Akram, Merid, Simon K, Bakulski, Kelly M, Küpers, Leanne K, Zhang, Hongmei, Richmond, Rebecca C, Page, Christian M, Duijts, Liesbeth, Lie, Rolv T, Melton, Phillip E, Vonk, Judith M, Nohr, Ellen A, Williams-DeVane, ClarLynda, Huen, Karen, Rifas-Shiman, Sheryl L, Ruiz-Arenas, Carlos, Gonseth, Semira, Rezwan, Faisal I, Herceg, Zdenko, Ekström, Sandra, Croen, Lisa, Falahi, Fahimeh, Perron, Patrice, Karagas, Margaret R, Quraishi, Bilal M, Suderman, Matthew, Magnus, Maria C, Jaddoe, Vincent WV, Taylor, Jack A, Anderson, Denise, Zhao, Shanshan, Smit, Henriette A, Josey, Michele J, Bradman, Asa, Baccarelli, Andrea A, Bustamante, Mariona, Håberg, Siri E, Pershagen, Göran, Hertz-Picciotto, Irva, Newschaffer, Craig, Corpeleijn, Eva, Bouchard, Luigi, Lawlor, Debbie A, Maguire, Rachel L, Barcellos, Lisa F, Smith, George Davey, Eskenazi, Brenda, Karmaus, Wilfried, Marsit, Carmen J, Hivert, Marie-France, Snieder, Harold, Fallin, M Daniele, Melén, Erik, Munthe-Kaas, Monica C, Arshad, Hasan, Wiemels, Joseph L, Annesi-Maesano, Isabella, Vrijheid, Martine, Oken, Emily, Holland, Nina, Murphy, Susan K, Sørensen, Thorkild IA, Koppelman, Gerard H, Newnham, John P, Wilcox, Allen J, Nystad, Wenche, London, Stephanie J, Felix, Janine F, and Relton, Caroline L
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Biological Sciences ,Genetics ,Pediatric ,Human Genome ,Perinatal Period - Conditions Originating in Perinatal Period ,Pregnancy ,Prevention ,Women's Health ,Obesity ,Nutrition ,Maternal Health ,2.1 Biological and endogenous factors ,Reproductive health and childbirth ,Adult ,Body Mass Index ,Cohort Studies ,DNA Methylation ,Epigenesis ,Genetic ,Epigenomics ,Female ,Humans ,Infant ,Newborn ,Male ,Maternal Inheritance ,Mothers ,Pregnancy Outcome ,Prenatal Exposure Delayed Effects ,Medical and Health Sciences ,Genetics & Heredity - Abstract
Pre-pregnancy maternal obesity is associated with adverse offspring outcomes at birth and later in life. Individual studies have shown that epigenetic modifications such as DNA methylation could contribute. Within the Pregnancy and Childhood Epigenetics (PACE) Consortium, we meta-analysed the association between pre-pregnancy maternal BMI and methylation at over 450,000 sites in newborn blood DNA, across 19 cohorts (9,340 mother-newborn pairs). We attempted to infer causality by comparing the effects of maternal versus paternal BMI and incorporating genetic variation. In four additional cohorts (1,817 mother-child pairs), we meta-analysed the association between maternal BMI at the start of pregnancy and blood methylation in adolescents. In newborns, maternal BMI was associated with small (
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- 2017
15. Prenatal phthalate exposure and altered patterns of DNA methylation in cord blood
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Solomon, Olivia, Yousefi, Paul, Huen, Karen, Gunier, Robert B, Escudero‐Fung, Maria, Barcellos, Lisa F, Eskenazi, Brenda, and Holland, Nina
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Reproductive Medicine ,Biomedical and Clinical Sciences ,Genetics ,Biological Sciences ,Pediatric ,Conditions Affecting the Embryonic and Fetal Periods ,Pregnancy ,Perinatal Period - Conditions Originating in Perinatal Period ,Human Genome ,Women's Health ,Endocrine Disruptors ,Prevention ,2.1 Biological and endogenous factors ,Reproductive health and childbirth ,CpG Islands ,DNA Methylation ,Demography ,Female ,Fetal Blood ,Humans ,Infant ,Newborn ,Male ,Maternal Exposure ,Metabolome ,Phthalic Acids ,Prenatal Exposure Delayed Effects ,in utero exposure ,phthalates ,children ,epigenetics ,450K ,Environmental Sciences ,Medical and Health Sciences ,Toxicology ,Medical biotechnology ,Public health - Abstract
Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Phthalates are known endocrine disruptors with ubiquitous exposures in the general population including pregnant women, and they have been linked with a number of adverse health outcomes. We examined the association between in utero phthalate exposure and altered patterns of cord blood DNA methylation in 336 Mexican-American newborns. Concentrations of 11 phthalate metabolites were analyzed in maternal urine samples collected at 13 and 26 weeks gestation as a measure of fetal exposure. DNA methylation was assessed using the Infinium HumanMethylation 450K BeadChip adjusting for cord blood cell composition. To identify differentially methylated regions (DMRs) that may be more informative than individual CpG sites, we used two different approaches, DMRcate and comb-p. Regional assessment by both methods identified 27 distinct DMRs, the majority of which were in relation to multiple phthalate metabolites. Most of the significant DMRs (67%) were observed for later pregnancy (26 weeks gestation). Further, 51% of the significant DMRs were associated with the di-(2-ethylhexyl) phthalate metabolites. Five individual CpG sites were associated with phthalate metabolite concentrations after multiple comparisons adjustment (FDR), all showing hypermethylation. Genes with DMRs were involved in inflammatory response (IRAK4 and ESM1), cancer (BRCA1 and LASP1), endocrine function (CNPY1), and male fertility (IFT140, TESC, and PRDM8). These results on differential DNA methylation in newborns with prenatal phthalate exposure provide new insights and targets to explore mechanism of adverse effects of phthalates on human health. Environ. Mol. Mutagen. 58:398-410, 2017. © 2017 Wiley Periodicals, Inc.
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- 2017
16. Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children’s Environmental Health Studies: The Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group
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Breton, Carrie V, Marsit, Carmen J, Faustman, Elaine, Nadeau, Kari, Goodrich, Jaclyn M, Dolinoy, Dana C, Herbstman, Julie, Holland, Nina, LaSalle, Janine M, Schmidt, Rebecca, Yousefi, Paul, Perera, Frederica, Joubert, Bonnie R, Wiemels, Joseph, Taylor, Michele, Yang, Ivana V, Chen, Rui, Hew, Kinjal M, Freeland, Deborah M Hussey, Miller, Rachel, and Murphy, Susan K
- Subjects
Public Health ,Health Sciences ,Genetics ,Prevention ,Human Genome ,Pediatric ,2.1 Biological and endogenous factors ,2.2 Factors relating to the physical environment ,Good Health and Well Being ,Child ,Child Health ,Child Welfare ,DNA Methylation ,Environmental Exposure ,Environmental Health ,Epigenesis ,Genetic ,Epigenomics ,Female ,Group Processes ,Humans ,Longitudinal Studies ,Pregnancy ,Research ,Environmental Sciences ,Medical and Health Sciences ,Toxicology ,Biomedical and clinical sciences ,Environmental sciences ,Health sciences - Abstract
BackgroundCharacterization of the epigenome is a primary interest for children's environmental health researchers studying the environmental influences on human populations, particularly those studying the role of pregnancy and early-life exposures on later-in-life health outcomes.ObjectivesOur objective was to consider the state of the science in environmental epigenetics research and to focus on DNA methylation and the collective observations of many studies being conducted within the Children's Environmental Health and Disease Prevention Research Centers, as they relate to the Developmental Origins of Health and Disease (DOHaD) hypothesis.MethodsWe address the current laboratory and statistical tools available for epigenetic analyses, discuss methods for validation and interpretation of findings, particularly when magnitudes of effect are small, question the functional relevance of findings, and discuss the future for environmental epigenetics research.DiscussionA common finding in environmental epigenetic studies is the small-magnitude epigenetic effect sizes that result from such exposures. Although it is reasonable and necessary that we question the relevance of such small effects, we present examples in which small effects persist and have been replicated across populations and across time. We encourage a critical discourse on the interpretation of such small changes and further research on their functional relevance for children's health.ConclusionThe dynamic nature of the epigenome will require an emphasis on future longitudinal studies in which the epigenome is profiled over time, over changing environmental exposures, and over generations to better understand the multiple ways in which the epigenome may respond to environmental stimuli.
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- 2017
17. Blood- and brain-based genome-wide association studies of smoking
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Chybowska, Aleksandra D., primary, Bernabeu, Elena, additional, Yousefi, Paul, additional, Suderman, Matthew, additional, Hillary, Robert F., additional, MacGillivray, Louise, additional, Murphy, Lee, additional, Harris, Sarah E., additional, Corley, Janie, additional, Campbell, Archie, additional, Spires-Jones, Tara L., additional, McCartney, Daniel L., additional, Cox, Simon R., additional, Price, Jackie F., additional, Evans, Kathryn L., additional, and Marioni, Riccardo E., additional
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- 2024
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18. Maternal anxiety during pregnancy and newborn epigenome-wide DNA methylation
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Sammallahti, Sara, Cortes Hidalgo, Andrea P., Tuominen, Samuli, Malmberg, Anni, Mulder, Rosa H., Brunst, Kelly J., Alemany, Silvia, McBride, Nancy S., Yousefi, Paul, Heiss, Jonathan A., McRae, Nia, Page, Christian M., Jin, Jianping, Pesce, Giancarlo, Caramaschi, Doretta, Rifas-Shiman, Sheryl L., Koen, Nastassja, Adams, Charleen D., Magnus, Maria C., Baïz, Nour, Ratanatharathorn, Andrew, Czamara, Darina, Håberg, Siri E., Colicino, Elena, Baccarelli, Andrea A., Cardenas, Andres, DeMeo, Dawn L., Lawlor, Deborah A., Relton, Caroline L., Felix, Janine F., van IJzendoorn, Marinus H., Bakermans-Kranenburg, Marian J., Kajantie, Eero, Räikkönen, Katri, Sunyer, Jordi, Sharp, Gemma C., Houtepen, Lotte C., Nohr, Ellen A., Sørensen, Thorkild I. A., Téllez-Rojo, Martha M., Wright, Robert O., Annesi-Maesano, Isabella, Wright, John, Hivert, Marie-France, Wright, Rosalind J., Zar, Heather J., Stein, Dan J., London, Stephanie J., Cecil, Charlotte A. M., Tiemeier, Henning, and Lahti, Jari
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- 2021
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19. Maternal phthalate exposure during pregnancy is associated with DNA methylation of LINE-1 and Alu repetitive elements in Mexican-American children
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Huen, Karen, Calafat, Antonia M, Bradman, Asa, Yousefi, Paul, Eskenazi, Brenda, and Holland, Nina
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Biological Sciences ,Environmental Sciences ,Chemical Sciences ,Pregnancy ,Genetics ,Women's Health ,Endocrine Disruptors ,Human Genome ,Pediatric ,Prevention ,Clinical Research ,Perinatal Period - Conditions Originating in Perinatal Period ,Conditions Affecting the Embryonic and Fetal Periods ,2.1 Biological and endogenous factors ,Reproductive health and childbirth ,Adolescent ,Adult ,Alu Elements ,Biomarkers ,Child ,DNA Methylation ,Environmental Pollutants ,Epigenesis ,Genetic ,Female ,Fetal Blood ,Humans ,Infant ,Newborn ,Long Interspersed Nucleotide Elements ,Male ,Maternal Exposure ,Maternal-Fetal Exchange ,Mexican Americans ,Middle Aged ,Phthalic Acids ,Prenatal Exposure Delayed Effects ,Young Adult ,DNA methylation ,Phthalate ,In Utero exposure ,Alu repeats ,LINE-1 repeats ,Toxicology ,Biological sciences ,Chemical sciences ,Environmental sciences - Abstract
Phthalates are frequently used in personal care products and plasticizers and phthalate exposure is ubiquitous in the US population. Exposure to phthalates during critical periods in utero has been associated with a variety of adverse health outcomes but the biological mechanisms linking these exposures with disease are not well characterized. In this study, we examined the relationship of in utero phthalate exposure with repetitive element DNA methylation, an epigenetic marker of genome instability, in children from the longitudinal birth cohort CHAMACOS. Methylation of Alu and long interspersed nucleotide elements (LINE-1) was determined using pyrosequencing of bisulfite-treated DNA isolated from whole blood samples collected from newborns and 9 year old children (n=355). Concentrations of eleven phthalate metabolites were measured in urine collected from pregnant mothers at 13 and 26 weeks gestation. We found a consistent inverse association between prenatal concentrations of monoethyl phthalate, the most frequently detected urinary metabolite, with cord blood methylation of Alu repeats (β(95%CI): -0.14 (-0.28,0.00) and -0.16 (-0.31, -0.02)) for early and late pregnancy, respectively, and a similar but weaker association with LINE-1 methylation. Additionally, increases in urinary concentrations of di-(2-ethylhexyl) phthalate metabolites during late pregnancy were associated with lower levels of methylation of Alu repeats in 9 year old blood (significant p-values ranged from 0.003 to 0.03). Our findings suggest that prenatal exposure to some phthalates may influence differences in repetitive element methylation, highlighting epigenetics as a plausible biological mechanism through which phthalates may affect health.
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- 2016
20. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis
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Joubert, Bonnie R, Felix, Janine F, Yousefi, Paul, Bakulski, Kelly M, Just, Allan C, Breton, Carrie, Reese, Sarah E, Markunas, Christina A, Richmond, Rebecca C, Xu, Cheng-Jian, Küpers, Leanne K, Oh, Sam S, Hoyo, Cathrine, Gruzieva, Olena, Söderhäll, Cilla, Salas, Lucas A, Baïz, Nour, Zhang, Hongmei, Lepeule, Johanna, Ruiz, Carlos, Ligthart, Symen, Wang, Tianyuan, Taylor, Jack A, Duijts, Liesbeth, Sharp, Gemma C, Jankipersadsing, Soesma A, Nilsen, Roy M, Vaez, Ahmad, Fallin, M Daniele, Hu, Donglei, Litonjua, Augusto A, Fuemmeler, Bernard F, Huen, Karen, Kere, Juha, Kull, Inger, Munthe-Kaas, Monica Cheng, Gehring, Ulrike, Bustamante, Mariona, Saurel-Coubizolles, Marie José, Quraishi, Bilal M, Ren, Jie, Tost, Jörg, Gonzalez, Juan R, Peters, Marjolein J, Håberg, Siri E, Xu, Zongli, van Meurs, Joyce B, Gaunt, Tom R, Kerkhof, Marjan, Corpeleijn, Eva, Feinberg, Andrew P, Eng, Celeste, Baccarelli, Andrea A, Neelon, Sara E Benjamin, Bradman, Asa, Merid, Simon Kebede, Bergström, Anna, Herceg, Zdenko, Hernandez-Vargas, Hector, Brunekreef, Bert, Pinart, Mariona, Heude, Barbara, Ewart, Susan, Yao, Jin, Lemonnier, Nathanaël, Franco, Oscar H, Wu, Michael C, Hofman, Albert, McArdle, Wendy, Van der Vlies, Pieter, Falahi, Fahimeh, Gillman, Matthew W, Barcellos, Lisa F, Kumar, Ashish, Wickman, Magnus, Guerra, Stefano, Charles, Marie-Aline, Holloway, John, Auffray, Charles, Tiemeier, Henning W, Smith, George Davey, Postma, Dirkje, Hivert, Marie-France, Eskenazi, Brenda, Vrijheid, Martine, Arshad, Hasan, Antó, Josep M, Dehghan, Abbas, Karmaus, Wilfried, Annesi-Maesano, Isabella, Sunyer, Jordi, Ghantous, Akram, Pershagen, Göran, Holland, Nina, Murphy, Susan K, DeMeo, Dawn L, Burchard, Esteban G, Ladd-Acosta, Christine, Snieder, Harold, and Nystad, Wenche
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Biological Sciences ,Biomedical and Clinical Sciences ,Health Sciences ,Genetics ,Human Genome ,Prevention ,Tobacco Smoke and Health ,Tobacco ,Perinatal Period - Conditions Originating in Perinatal Period ,Pediatric ,Clinical Research ,2.1 Biological and endogenous factors ,Reproductive health and childbirth ,Respiratory ,Good Health and Well Being ,Asthma ,Child ,Child ,Preschool ,Chromosome Mapping ,Cleft Lip ,Cleft Palate ,DNA Methylation ,Epigenesis ,Genetic ,Female ,Genetic Association Studies ,Humans ,Infant ,Infant ,Newborn ,Pregnancy ,Smoking ,White People ,Medical and Health Sciences ,Genetics & Heredity ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - 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.
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- 2016
21. Estimation of blood cellular heterogeneity in newborns and children for epigenome‐wide association studies
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Yousefi, Paul, Huen, Karen, Quach, Hong, Motwani, Girish, Hubbard, Alan, Eskenazi, Brenda, and Holland, Nina
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Epidemiology ,Biomedical and Clinical Sciences ,Health Sciences ,Pediatric ,Clinical Research ,2.1 Biological and endogenous factors ,Age Factors ,Blood Cell Count ,Blood Cells ,Child ,Cohort Studies ,DNA Methylation ,Epigenesis ,Genetic ,Female ,Genome-Wide Association Study ,Humans ,Infant ,Newborn ,Leukocyte Count ,Longitudinal Studies ,Male ,Reference Values ,epigenetics ,minfi ,differential cell count ,birth cohort ,450K ,Environmental Sciences ,Biological Sciences ,Medical and Health Sciences ,Toxicology ,Genetics ,Medical biotechnology ,Public health - Abstract
Confounding by cellular heterogeneity has become a major concern for epigenome-wide association studies (EWAS) in peripheral blood samples from population and clinical studies. Adjusting for white blood cell percentage estimates produced by the minfi implementation of the Houseman algorithm (minfi) during statistical analysis is now an established method to account for this bias in adults. However, minfi has not been benchmarked against white blood cell counts in children that may differ substantially from the reference dataset used in its estimation. We compared estimates of white blood cell type percentages produced by two methods, minfi and differential cell count (DCC), in a birth cohort at two time points (birth and 12 years of age). We found that both minfi and DCC had similar trends as children aged, and neither count method differed by sex among newborns (P > 0.10). However, minfi estimates did not correlate well with DCC in samples from newborns (ρ = -0.05 for granulocytes; ρ = -0.03 for lymphocytes). In older children, correlation improved substantially (ρ = 0.77 for granulocytes; ρ = 0.75 for lymphocytes), likely due to increasing similarity with minfi's adult reference data as children aged. Our findings suggest that the minfi method may provide suitable estimates of white blood cell composition for samples from adults and older children, but may not currently be appropriate for EWAS involving newborns or young children.
- Published
- 2015
22. Sex differences in DNA methylation assessed by 450 K BeadChip in newborns
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Yousefi, Paul, Huen, Karen, Davé, Veronica, Barcellos, Lisa, Eskenazi, Brenda, and Holland, Nina
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Minority Health ,Clinical Research ,Pediatric ,Women's Health ,Human Genome ,2.1 Biological and endogenous factors ,Reproductive health and childbirth ,CpG Islands ,DNA Methylation ,Epigenesis ,Genetic ,Epigenomics ,Female ,Genome-Wide Association Study ,Humans ,Infant ,Newborn ,Male ,Epigenetics ,Gene ontology ,Birth cohort ,EWAS ,Gender ,Cord blood ,Information and Computing Sciences ,Medical and Health Sciences ,Bioinformatics ,Biological sciences ,Biomedical and clinical sciences - Abstract
BackgroundDNA methylation is an important epigenetic mark that can potentially link early life exposures to adverse health outcomes later in life. Host factors like sex and age strongly influence biological variation of DNA methylation, but characterization of these relationships is still limited, particularly in young children.MethodsIn a sample of 111 Mexican-American subjects (58 girls , 53 boys), we interrogated DNA methylation differences by sex at birth using the 450 K BeadChip in umbilical cord blood specimens, adjusting for cell composition.ResultsWe observed that ~3% of CpG sites were differentially methylated between girls and boys at birth (FDR P
- Published
- 2015
23. PON1 as a model for integration of genetic, epigenetic, and expression data on candidate susceptibility genes
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Huen, Karen, Yousefi, Paul, Street, Kelly, Eskenazi, Brenda, and Holland, Nina
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Biological Sciences ,Genetics ,Pediatric ,Health Disparities ,Human Genome ,2.1 Biological and endogenous factors ,methylation ,arylesterase ,paraoxonase ,mediation - Abstract
Recent genome- and epigenome-wide studies demonstrate that the DNA methylation is controlled in part by genetics, highlighting the importance of integrating genetic and epigenetic data. To better understand molecular mechanisms affecting gene expression, we used the candidate susceptibility gene paraoxonase 1 (PON1) as a model to assess associations of PON1 genetic polymorphisms with DNA methylation and arylesterase activity, a marker of PON1 expression. PON1 has been associated with susceptibility to obesity, cardiovascular disease, and pesticide exposure. In this study, we assessed DNA methylation in 18 CpG sites located along PON1 shores, shelves, and its CpG island in blood specimens collected from newborns and 9-year-old children participating (n = 449) in the CHAMACOS birth cohort study. The promoter polymorphism, PON1-108 , was strongly associated with methylation, particularly for CpG sites located near the CpG island (P << 0.0005). Among newborns, these relationships were even more pronounced after adjusting for blood cell composition. We also observed significant decreases in arylesterase activity with increased methylation at the same nine CpG sites at both ages. Using causal mediation analysis, we found statistically significant indirect effects of methylation (β(95% confidence interval): 6.9(1.5, 12.4)) providing evidence that DNA methylation mediates the relationship between PON1-108 genotype and PON1 expression. Our findings show that integration of genetic, epigenetic, and expression data can shed light on the functional mechanisms involving genetic and epigenetic regulation of candidate susceptibility genes like PON1.
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- 2015
24. Relationship between expression and methylation of obesity-related genes in children
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Davé, Veronica, Yousefi, Paul, Huen, Karen, Volberg, Vitaly, and Holland, Nina
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Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Genetics ,Pediatric ,Biotechnology ,Obesity ,2.1 Biological and endogenous factors ,Cancer ,Child ,CpG Islands ,DNA Methylation ,Epigenesis ,Genetic ,Female ,Gene Expression ,Glutathione Transferase ,Humans ,Male ,PPAR gamma ,Receptors ,Adiponectin ,Toxicology ,Pharmacology and pharmaceutical sciences - Abstract
Epigenetic control of gene expression in children remains poorly understood, but new technologies can help elucidate the relationship between expression and DNA methylation. Here, we utilized the nCounter Analysis System to characterise the expression of 60 genes in 69 9-year-old children from a cohort with a high prevalence of obesity. nCounter expression levels ranged broadly (from 3 to over 10000 messenger RNA counts) and were divided into four categories: high (>2000 counts), moderate (200-1000 counts), low (100-200 counts) and marginal (
- Published
- 2015
25. Epigenetic timing effects on child developmental outcomes: A longitudinal meta-regression of findings from the Pregnancy And Childhood Epigenetics Consortium
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Neumann, Alexander, primary, Sammallahti, Sara, additional, Cosin-Tomas, Marta, additional, Reese, Sarah E, additional, Suderman, Matthew, additional, Alemany, Silvia, additional, Almqvist, Catarina, additional, Andrusaityte, Sandra, additional, Arshad, Syed H, additional, Bakermans-Kranenburg, Marian J, additional, Beilin, Lawrence, additional, Breton, Carrie, additional, Bustamante, Mariona, additional, Czamara, Darina, additional, Dabelea, Dana, additional, Eng, Celeste, additional, Eskenazi, Brenda, additional, Fuemmeler, Bernard F, additional, Gilliland, Frank D, additional, Grazuleviciene, Regina, additional, Håberg, Siri E, additional, Herberth, Gunda, additional, Holland, Nina, additional, Hough, Amy, additional, Hu, Donglei, additional, Huen, Karen, additional, Hüls, Anke, additional, Jin, Jianping, additional, Julvez, Jordi, additional, Koletzko, Berthold V, additional, Koppelman, Gerard H, additional, Kull, Inger, additional, Lu, Xueling, additional, Maitre, Léa, additional, Mason, Dan, additional, Mélen, Erik, additional, Merid, Simon K, additional, Molloy, Peter L, additional, Mori, Trevor A, additional, Mulder, Rosa H, additional, Page, Christian M, additional, Richmond, Rebecca C, additional, Roder, Stefan, additional, Ross, Jason P, additional, Schellhas, Laura, additional, Sebert, Sylvain, additional, Sheppard, Dean, additional, Snieder, Harold, additional, Starling, Anne P, additional, Stein, Dan J, additional, Tindula, Gwen, additional, van IJzendoorn, Marinus H, additional, Vonk, Judith, additional, Walton, Esther, additional, Witonsky, Jonathan, additional, Xu, Cheng-Jian, additional, Yang, Ivana V, additional, Yousefi, Paul D, additional, Zar, Heather J, additional, Zenclussen, Ana C, additional, Zhang, Hongmei, additional, Tiemeier, Henning, additional, London, Stephanie J, additional, Felix, Janine F, additional, and Cecil, Charlotte, additional
- Published
- 2024
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26. Blood-based DNA methylation study of alcohol consumption
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Bernabeu, Elena, primary, Chybowska, Aleksandra, additional, Kresovich, Jacob K, additional, Suderman, Matthew, additional, McCartney, Daniel L., additional, Hillary, Robert F, additional, Corley, Janie, additional, Valdes Hernandez, Maria Del Carmen, additional, Munoz Maniega, Susana, additional, Bastin, Mark E, additional, Wardlaw, Joanna M, additional, Xu, Zongli, additional, Sandler, Dale P., additional, Campbell, Archie, additional, Harris, Sarah E, additional, McIntosh, Andrew M, additional, Taylor, Jack, additional, Yousefi, Paul Darius, additional, Cox, Simon R, additional, Evans, Kathryn L, additional, Robinson, Matthew Richard, additional, Vallejos, Catalina A, additional, and Marioni, Riccardo, additional
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- 2024
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27. Epigenetic modelling of former, current and never smokers
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Langdon, Ryan J., Yousefi, Paul, Relton, Caroline L., and Suderman, Matthew J.
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- 2021
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28. Genetic modification of the effect of maternal household air pollution exposure on birth weight in Guatemalan newborns
- Author
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Thompson, Lisa M, Yousefi, Paul, Peñaloza, Reneé, Balmes, John, and Holland, Nina
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Reproductive Medicine ,Biomedical and Clinical Sciences ,Clinical Research ,Perinatal Period - Conditions Originating in Perinatal Period ,Health Effects of Household Energy Combustion ,Preterm ,Low Birth Weight and Health of the Newborn ,Pediatric ,Clinical Trials and Supportive Activities ,Genetics ,Social Determinants of Health ,Women's Health ,Health Effects of Indoor Air Pollution ,Climate-Related Exposures and Conditions ,2.2 Factors relating to the physical environment ,Reproductive health and childbirth ,Good Health and Well Being ,Air Pollution ,Birth Weight ,Female ,Glutathione Transferase ,Humans ,Infant ,Newborn ,Maternal Exposure ,Pregnancy ,Genetic susceptibility ,Glutathione S-transferase ,Low birth weight ,Gene-environment interaction ,RESPIRE/GRECER studies ,Woodsmoke ,Gene–environment interaction ,RESPIRE/CRECER studies ,Paediatrics and Reproductive Medicine ,Pharmacology and Pharmaceutical Sciences ,Public Health and Health Services ,Toxicology ,Pharmacology and pharmaceutical sciences ,Reproductive medicine - Abstract
Low birth weight is associated with exposure to air pollution during pregnancy. The purpose of this study was to evaluate whether null polymorphisms of Glutathione S-transferases (GSTs), specifically GSTM1 and GSTT1 genes in infants or mothers, modify the association between high exposures to household air pollution (HAP) from cooking fires and birth weight. Pregnant women in rural Guatemala were randomized to receive a chimney stove or continue to use open fires for cooking. Newborns were measured within 48 h of birth. 132 mother-infant pairs provided infant genotypes (n=130) and/or maternal genotypes (n=116). Maternal null GSTM1 was associated with a 144 g (95% CI, -291, 1) and combined maternal/infant null GSTT1 was associated with a 155 g (95% CI, -303, -8) decrease in birth weight. Although there was a trend toward higher birth weights with increasing number of expressed GST genes, the effect modification by chimney stove use was not demonstrated.
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- 2014
29. Human urinary mutagenicity after wood smoke exposure during traditional temazcal use
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Long, Alexandra S, Lemieux, Christine L, Yousefi, Paul, Ruiz-Mercado, Ilse, Lam, Nicholas L, Orellana, Carolina Romero, White, Paul A, Smith, Kirk R, and Holland, Nina
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Medical Biochemistry and Metabolomics ,Biomedical and Clinical Sciences ,Prevention ,Adolescent ,Adult ,Aged ,Biomarkers ,Carbon Monoxide ,Child ,Child ,Preschool ,Environmental Exposure ,Female ,Guatemala ,Humans ,Linear Models ,Male ,Middle Aged ,Mutagenicity Tests ,Mutagens ,Smoke ,Surveys and Questionnaires ,Wood ,Young Adult ,Pharmacology and Pharmaceutical Sciences ,Toxicology ,Pharmacology and pharmaceutical sciences - Abstract
In Central America, the traditional temazcales or wood-fired steam baths, commonly used by many Native American populations, are often heated by wood fires with little ventilation, and this use results in high wood smoke exposure. Urinary mutagenicity has been previously employed as a non-invasive biomarker of human exposure to combustion emissions. This study examined the urinary mutagenicity in 19 indigenous Mayan families from the highlands of Guatemala who regularly use temazcales (N = 32), as well as control (unexposed) individuals from the same population (N = 9). Urine samples collected before and after temazcal exposure were enzymatically deconjugated and extracted using solid-phase extraction. The creatinine-adjusted mutagenic potency of urine extracts was assessed using the plate-incorporation version of the Salmonella mutagenicity assay with strain YG1041 in the presence of exogenous metabolic activation. The post-exposure mutagenic potency of urine extracts were, on average, 1.7-fold higher than pre-exposure samples (P < 0.005) and also significantly more mutagenic than the control samples (P < 0.05). Exhaled carbon monoxide (CO) was ~10 times higher following temazcal use (P < 0.0001), and both CO level and time spent in temazcal were positively associated with urinary mutagenic potency (i.e. P < 0.0001 and P = 0.01, respectively). Thus, the wood smoke exposure associated with temazcal use contributes to increased excretion of conjugated mutagenic metabolites. Moreover, urinary mutagenic potency is correlated with other metrics of exposure (i.e. exhaled CO, duration of exposure). Since urinary mutagenicity is a biomarker associated with genetic damage, temazcal use may therefore be expected to contribute to an increased risk of DNA damage and mutation, effects associated with the initiation of cancer.
- Published
- 2014
30. Effects of age, sex, and persistent organic pollutants on DNA methylation in children
- Author
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Huen, Karen, Yousefi, Paul, Bradman, Asa, Yan, Liying, Harley, Kim G, Kogut, Katherine, Eskenazi, Brenda, and Holland, Nina
- Subjects
Biological Sciences ,Biomedical and Clinical Sciences ,Health Sciences ,Genetics ,Human Genome ,Prevention ,Endocrine Disruptors ,Perinatal Period - Conditions Originating in Perinatal Period ,Clinical Research ,Pediatric ,Conditions Affecting the Embryonic and Fetal Periods ,2.1 Biological and endogenous factors ,Reproductive health and childbirth ,Age Factors ,Alu Elements ,Cell Count ,Child ,Cohort Studies ,DDT ,DNA Methylation ,Dichlorodiphenyl Dichloroethylene ,Environmental Pollutants ,Epigenesis ,Genetic ,Female ,Fetal Blood ,Halogenated Diphenyl Ethers ,Humans ,Infant ,Newborn ,Long Interspersed Nucleotide Elements ,Male ,Maternal Exposure ,Mexican Americans ,Organic Chemicals ,Pregnancy ,Sex Factors ,Alu ,LINE-1 ,co-exposure ,DDE ,epigenetics ,PBDE ,Environmental Sciences ,Medical and Health Sciences ,Toxicology ,Medical biotechnology ,Public health - Abstract
Epigenetic changes such as DNA methylation may be a molecular mechanism through which environmental exposures affect health. Methylation of Alu and long interspersed nucleotide elements (LINE-1) is a well-established measure of DNA methylation often used in epidemiologic studies. Yet, few studies have examined the effects of host factors on LINE-1 and Alu methylation in children. We characterized the relationship of age, sex, and prenatal exposure to persistent organic pollutants (POPs), dichlorodiphenyl trichloroethane (DDT), dichlorodiphenyldichloroethylene (DDE), and polybrominated diphenyl ethers (PBDEs), with DNA methylation in a birth cohort of Mexican-American children participating in the CHAMACOS study. We measured Alu and LINE-1 methylation by pyrosequencing bisulfite-treated DNA isolated from whole blood samples collected from newborns and nine-year old children (n = 358). POPs were measured in maternal serum during late pregnancy. Levels of DNA methylation were lower in nine-year olds compared to newborns and were higher in boys compared to girls. Higher prenatal DDT/E exposure was associated with lower Alu methylation at birth, particularly after adjusting for cell type composition (P = 0.02 for o,p' -DDT). Associations of POPs with LINE-1 methylation were only identified after examining the co-exposure of DDT/E with PBDEs simultaneously. Our data suggest that repeat element methylation can be an informative marker of epigenetic differences by age and sex and that prenatal exposure to POPs may be linked to hypomethylation in fetal blood. Accounting for co-exposure to different types of chemicals and adjusting for blood cell types may increase sensitivity of epigenetic analyses for epidemiological studies.
- Published
- 2014
31. Associations between perinatal factors and adiponectin and leptin in 9‐year‐old Mexican–American children
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Volberg, Vitaly, Harley, Kim G, Aguilar, Raul S, Rosas, Lisa G, Huen, Karen, Yousefi, Paul, Davé, Veronica, Phan, Nguyet, Lustig, Robert H, Eskenazi, Brenda, and Holland, Nina
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Reproductive Medicine ,Biomedical and Clinical Sciences ,Public Health ,Health Sciences ,Prevention ,Nutrition ,Pediatric ,Childhood Obesity ,Clinical Research ,Obesity ,2.1 Biological and endogenous factors ,Cancer ,Stroke ,Oral and gastrointestinal ,Metabolic and endocrine ,Adiponectin ,Body Mass Index ,Child ,Child Nutritional Physiological Phenomena ,Female ,Humans ,Leptin ,Longitudinal Studies ,Male ,Maternal Exposure ,Mexican Americans ,Mothers ,Nutrition Surveys ,Nutritional Status ,Pregnancy ,Prenatal Exposure Delayed Effects ,Surveys and Questionnaires ,United States ,Adipokines ,growth rate ,lipid profile ,obesity ,Biomedical and clinical sciences ,Health sciences - Abstract
What is already known about this subjectMexican-American children are at particularly high risk of obesity. Features of the perinatal environment, including maternal nutrition, anthropometry, glucose tolerance and growth rate during infancy are implicated in programming of obesity in the offspring.What this study addsGreater rate of weight or length gain in the first 6 months of life is associated with lower 9-year child adiponectin levels, adjusting for 9-year child BMI. Nine-year-old child adipokine levels are strongly related to those of their mothers'.ObjectivesTo (i) determine whether perinatal factors (including maternal anthropometry and nutrition and early life growth measures) are associated with adiponectin and leptin levels in 9-year-old children, and (ii) assess relationships between adiponectin, leptin and concurrent lipid profile in these children.MethodsWe measured plasma adiponectin and leptin for 146 mothers-9-year-old child pairs from the ongoing longitudinal birth cohort followed by the Center for the Health Assessment of Mothers and Children of Salinas. Data on perinatal factors, including sociodemographics, maternal anthropometry and nutrition, and early life child growth were collected during pregnancy, birth and 6-month visits.ResultsGreater rate of weight and length gain during the first 6 months of life were associated with lower adiponectin in 9-year-olds (β = -2.0, P = 0.04; β = -8.2, P = 0.02, respectively) adjusting for child body mass index (BMI). We found no associations between child adipokine levels and either maternal calorie, protein, total fat, saturated fat, fibre, sugar-sweetened beverage consumption during pregnancy or children's concurrent sugar-sweetened beverage and fast food intake. Lipid profile in 9-year-old children closely reflected adiponectin but not leptin levels after adjustment for child BMI. Additionally, we report that child adipokine levels were closely related to their mothers' levels at the 9-year visit.ConclusionOverall, our results support the hypothesis that early life factors may contribute to altered adipokine levels in children.
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- 2013
32. Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies
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Yousefi, Paul, Huen, Karen, Schall, Raul Aguilar, Decker, Anna, Elboudwarej, Emon, Quach, Hong, Barcellos, Lisa, and Holland, Nina
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Biological Sciences ,Genetics ,Human Genome ,Child ,CpG Islands ,DNA Methylation ,Epigenesis ,Genetic ,Genetics ,Population ,Humans ,Longitudinal Studies ,Oligonucleotide Array Sequence Analysis ,Quality Control ,Software ,epigenetics ,DNA methylome ,pipeline ,technical variability ,bias correction ,microarray ,ASMN ,Biochemistry and Cell Biology ,Medical Biochemistry and Metabolomics ,Developmental Biology ,Biochemistry and cell biology - Abstract
Analysis of epigenetic mechanisms, particularly DNA methylation, is of increasing interest for epidemiologic studies examining disease etiology and impacts of environmental exposures. The Infinium HumanMethylation450 BeadChip(®) (450K), which interrogates over 480,000 CpG sites and is relatively cost effective, has become a popular tool to characterize the DNA methylome. For large-scale studies, minimizing technical variability and potential bias is paramount. The goal of this paper was to evaluate the performance of several existing and novel color channel normalizations designed to reduce technical variability and batch effects in 450K analysis from a large population study. Comparative assessment of 10 normalization procedures included the GenomeStudio(®) Illumina procedure, the lumi smooth quantile approach, and the newly proposed All Sample Mean Normalization (ASMN). We also examined the performance of normalizations in combination with correction for the two types of Infinium chemistry utilized on the 450K array. We observed that the performance of the GenomeStudio(®) normalization procedure was highly variable and dependent on the quality of the first sample analyzed in an experiment, which is used as a reference in this procedure. While the lumi normalization was able to decrease batch variability, it increased variation among technical replicates, potentially reducing biologically meaningful findings. The proposed ASMN procedure performed consistently well, both at reducing batch effects and improving replicate comparability. In summary, the ASMN procedure can improve existing color channel normalization, especially for large epidemiologic studies, and can be successfully implemented to enhance a 450K DNA methylation data pipeline.
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- 2013
33. Adiponectin and leptin trajectories in Mexican-American children from birth to 9 years of age.
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Volberg, Vitaly, Heggeseth, Brianna, Harley, Kim, Huen, Karen, Yousefi, Paul, Davé, Veronica, Tyler, Kristin, Vedar, Michelle, Eskenazi, Brenda, and Holland, Nina
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Humans ,Obesity ,Leptin ,Body Mass Index ,Longitudinal Studies ,Follow-Up Studies ,Prospective Studies ,Pregnancy ,Adolescent ,Adult ,Middle Aged ,Child ,Child ,Preschool ,Infant ,Infant ,Newborn ,Mexican Americans ,Female ,Male ,Adiponectin ,Young Adult ,Surveys and Questionnaires ,Preschool ,Newborn ,General Science & Technology - Abstract
ObjectivesTo address molecular mechanisms underlying obesity development, we examined patterns of critical metabolism-related hormones, adiponectin and leptin (adipokines), over childhood.Subjects and designPlasma adiponectin and leptin were measured in 80 Mexican-American children at birth and again at 2, 5, and 9 years from the ongoing prospective cohort followed by the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS). We used a mixture modeling approach to identify patterns in adipokine trajectories from birth to 9 years.ResultsLeptin was positively related to child body size within all ages, however adiponectin had inverse and weaker associations with BMI at 2, 5, and 9 years. Correlations between adipokine levels over the 0-2, 2-5, and 5-9-year periods increased for both leptin (r = 0.06, 0.31 and 0.62) and adiponectin (r = 0.25, 0.41 and 0.46). Our mixture modeling approach identified three trajectory clusters for both leptin (1L [slowly-rising], 2L [rapidly-rising], and 3L [stable]) and adiponectin (1A [steep-dropping and rebounding], 2A [moderately-dropping], and 3A [stable]). While leptin groups were most separated over the 2-9-year period, adiponectin trajectories displayed greatest heterogeneity from birth to 2 years. Children in the rapidly-rising 2L group had highest BMI and waist circumference at 9 years. Further, children with greater birth weight had increased odds of belonging to this high risk group (OR = 1.21 95% CI 1.03, 1.43, compared to stable group 3L). Children whose mothers consumed more sugar-sweetened beverages during pregnancy were at risk of being in the steep-dropping 1A group (OR = 1.08, 95% CI 1.01, 1.17, compared to stable group 3A).ConclusionOur results highlight developmental differences in leptin and adiponectin over the childhood period. Leptin closely reflects child body size however factors affecting adiponectin and long-term consequences of its changes over infancy need to be further explored.
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- 2013
34. Genome-Wide Association Study of Blood Mercury in European Pregnant Women and Children
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Dack, Kyle, primary, Bustamante, Mariona, additional, Taylor, Caroline M., additional, Llop, Sabrina, additional, Lozano, Manuel, additional, Yousefi, Paul, additional, Gražulevičienė, Regina, additional, Gutzkow, Kristine Bjerve, additional, Brantsæter, Anne Lise, additional, Mason, Dan, additional, Escaramís, Georgia, additional, and Lewis, Sarah J., additional
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- 2023
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35. Do nuclear magnetic resonance (NMR)-based metabolomics improve the prediction of pregnancy-related disorders? Findings from a UK birth cohort with independent validation
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McBride, Nancy, Yousefi, Paul, White, Sara L., Poston, Lucilla, Farrar, Diane, Sattar, Naveed, Nelson, Scott M., Wright, John, Mason, Dan, Suderman, Matthew, Relton, Caroline, and Lawlor, Deborah A.
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- 2020
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36. Validation and characterisation of a DNA methylation alcohol biomarker across the life course
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Yousefi, Paul Darius, Richmond, Rebecca, Langdon, Ryan, Ness, Andrew, Liu, Chunyu, Levy, Daniel, Relton, Caroline, Suderman, Matthew, and Zuccolo, Luisa
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- 2019
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37. Correction: Epigenome-wide association study of objectively measured physical activity in peripheral blood leukocytes.
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Fragoso-Bargas, Nicolas, Mcbride, Nancy S., Lee-Ødegård, Sindre, Lawlor, Deborah A., Yousefi, Paul D., Moen, Gunn-Helen, Opsahl, Julia O., Jenum, Anne Karen, Franks, Paul W., Prasad, Rashmi B., Qvigstad, Elisabeth, Birkeland, Kåre I., Richardsen, Kåre R., and Sommer, Christine
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PUBLIC health nursing ,GENETIC epidemiology ,MORBID obesity ,MEDICAL schools ,MEDICAL technology - Abstract
The correction notice for the article "Epigenome-wide association study of objectively measured physical activity in peripheral blood leukocytes" in BMC Genomics addresses an error in the affiliations section, specifically the addition of a missing affiliation for "Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK." The correction includes updating the affiliations list to reflect this addition and correct the numbering. The original article has been updated accordingly, and the authors involved in the study are listed in the notice. [Extracted from the article]
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- 2025
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38. Chromosome 18 Loss of Heterozygosity in Small Intestinal Neuroendocrine Tumours: Multi-Omic and Tumour Composition Analyses
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Waterfield, Scott, primary, Yousefi, Paul, additional, Webster, Amy, additional, Relton, Caroline, additional, Thirlwell, Chrissie, additional, and Suderman, Matt, additional
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- 2023
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39. Genetic modification of the effect of maternal household air pollution exposure on birth weight in Guatemalan newborns
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Thompson, Lisa M., Yousefi, Paul, Peñaloza, Reneé, Balmes, John, and Holland, Nina
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- 2014
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40. Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium
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Felix, Janine F, Joubert, Bonnie R, Baccarelli, Andrea A, Sharp, Gemma C, Almqvist, Catarina, Annesi-Maesano, Isabella, Arshad, Hasan, Baïz, Nour, Bakermans-Kranenburg, Marian J, Bakulski, Kelly M, Binder, Elisabeth B, Bouchard, Luigi, Breton, Carrie V, Brunekreef, Bert, Brunst, Kelly J, Burchard, Esteban G, Bustamante, Mariona, Chatzi, Leda, Cheng Munthe-Kaas, Monica, Corpeleijn, Eva, Czamara, Darina, Dabelea, Dana, Davey Smith, George, De Boever, Patrick, Duijts, Liesbeth, Dwyer, Terence, Eng, Celeste, Eskenazi, Brenda, Everson, Todd M, Falahi, Fahimeh, Fallin, M Daniele, Farchi, Sara, Fernandez, Mariana F, Gao, Lu, Gaunt, Tom R, Ghantous, Akram, Gillman, Matthew W, Gonseth, Semira, Grote, Veit, Gruzieva, Olena, Håberg, Siri E, Herceg, Zdenko, Hivert, Marie-France, Holland, Nina, Holloway, John W, Hoyo, Cathrine, Hu, Donglei, Huang, Rae-Chi, Huen, Karen, Järvelin, Marjo-Riitta, Jima, Dereje D, Just, Allan C, Karagas, Margaret R, Karlsson, Robert, Karmaus, Wilfried, Kechris, Katerina J, Kere, Juha, Kogevinas, Manolis, Koletzko, Berthold, Koppelman, Gerard H, Küpers, Leanne K, Ladd-Acosta, Christine, Lahti, Jari, Lambrechts, Nathalie, Langie, Sabine AS, Lie, Rolv T, Liu, Andrew H, Magnus, Maria C, Magnus, Per, Maguire, Rachel L, Marsit, Carmen J, McArdle, Wendy, Melén, Erik, Melton, Phillip, Murphy, Susan K, Nawrot, Tim S, Nisticò, Lorenza, Nohr, Ellen A, Nordlund, Björn, Nystad, Wenche, Oh, Sam S, Oken, Emily, Page, Christian M, Perron, Patrice, Pershagen, Göran, Pizzi, Costanza, Plusquin, Michelle, Raikkonen, Katri, Reese, Sarah E, Reischl, Eva, Richiardi, Lorenzo, Ring, Susan, Roy, Ritu P, Rzehak, Peter, Schoeters, Greet, Schwartz, David A, Sebert, Sylvain, Snieder, Harold, Sørensen, Thorkild IA, Starling, Anne P, Sunyer, Jordi, Taylor, Jack A, Tiemeier, Henning, Ullemar, Vilhelmina, Vafeiadi, Marina, Van Ijzendoorn, Marinus H, Vonk, Judith M, Vriens, Annette, Vrijheid, Martine, Wang, Pei, Wiemels, Joseph L, Wilcox, Allen J, Wright, Rosalind J, Xu, Cheng-Jian, Xu, Zongli, Yang, Ivana V, Yousefi, Paul, Zhang, Hongmei, Zhang, Weiming, Zhao, Shanshan, Agha, Golareh, Relton, Caroline L, Jaddoe, Vincent WV, and London, Stephanie J
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- 2018
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41. Organophosphate pesticide levels in blood and urine of women and newborns living in an agricultural community
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Huen, Karen, Bradman, Asa, Harley, Kim, Yousefi, Paul, Boyd Barr, Dana, Eskenazi, Brenda, and Holland, Nina
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- 2012
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42. The EWAS Catalog: a database of epigenome-wide association studies
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Battram, Thomas, primary, Yousefi, Paul, additional, Crawford, Gemma, additional, Prince, Claire, additional, Sheikhali Babaei, Mahsa, additional, Sharp, Gemma, additional, Hatcher, Charlie, additional, Vega-Salas, María Jesús, additional, Khodabakhsh, Sahar, additional, Whitehurst, Oliver, additional, Langdon, Ryan, additional, Mahoney, Luke, additional, Elliott, Hannah R., additional, Mancano, Giulia, additional, Lee, Matthew A., additional, Watkins, Sarah H., additional, Lay, Abigail C., additional, Hemani, Gibran, additional, Gaunt, Tom R., additional, Relton, Caroline L., additional, Staley, James R., additional, and Suderman, Matthew, additional
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- 2022
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43. DNA methylation changes associated with prenatal mercury exposure
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Lozano, Manuel, Yousefi, Paul, Broberg, Karin, Soler-Blasco, Raquel, Miyashita, Chihiro, Pesce, Giancarlo, Kim, Woo Jin, Rahman, Mohammad, Bakulski, Kelly, Haug, Line, Ikeda-Araki, Atsuko, Huel, Guy, Park, Jaehyun, Relton, Caroline, Vrijheid, Martine, Rifas-Shiman, Sheryl, Oken, Emily, Dou, John, Kishi, Reiko, Gutzkow, Kristine, Annesi-Maesano, Isabella, Won, Sungho, Hivert, Marie-France, Fallin, M. Daniele, Vafeiadi, Marina, Ballester, Ferran, Bustamante, Mariona, Llop, Sabrina, Universitat de València (UV), University of Bristol [Bristol], Karolinska Institutet [Stockholm], Lund University [Lund], Hokkaido Information University, Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Kangwon National University, Harvard Medical School [Boston] (HMS), University of Michigan [Dearborn], University of Michigan System, Norwegian Institute of Public Health [Oslo] (NIPH), Seoul National University [Seoul] (SNU), Instituto de Salud Global - Institute For Global Health [Barcelona] (ISGlobal), Spanish Consortium for Research on Epidemiology and Public Health, CIBER de Epidemiología y Salud Pública (CIBERESP), Universitat Pompeu Fabra [Barcelona] (UPF), Institut Desbrest de santé publique (IDESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), Johns Hopkins University (JHU), University of Crete [Heraklion] (UOC), 1999SGR 00241, 15/0025, 17/00260, 20/0006, FIS-FEDER PI16/1288, FIS-FEDER PI19/1338, FIS-FEDER-PI03–1615, FIS-FEDER-PI06/0867, FIS-PI04/1436, FIS-PI08/1151, FIS-PI11/00610, MC_UU_00011/5, National Institutes of Health, NIH: R37 HD034568, National Institute of Diabetes and Digestive and Kidney Diseases, NIDDK: R01 DK10324, National Institute of Neurological Disorders and Stroke, NINDS: 06A1, 1 UO1 NS 047537–01, National Institute of Environmental Health Sciences, NIEHS: N01-ES-75558, Z01-ES-49019, Centre International de Recherche sur le Cancer, CIRC, Japan Agency for Medical Research and Development, AMED: JPMH18950314, JPMH19188595, Wellcome Trust, WT: 102215/2/13/2, Horizon 2020 Framework Programme, H2020: 874583, Medical Research Council, MRC: MC_UU_12013_1, MC_UU_12013_2, MC_UU_12013_5, MC_UU_12013_8, WT088806, Biotechnology and Biological Sciences Research Council, BBSRC: BB/I025263/1, BB/I025751/1, European Commission, EC: 261357, European Research Council, ERC: 268479, University of Bristol, Japan Society for the Promotion of Science, KAKEN, Ministry of Education, Culture, Sports, Science and Technology, Monbusho: JP15H04780, JP16H02645, JP18H03035, JP18K10022, JP18K10042, JP19H01071, JP19K10576, JP19K10636, JP19K20457, JP19K22730, JPMEERF20145054, JPMEERF20175053, JPMEERF20205002, Bundesministerium für Bildung und Forschung, BMBF, Generalitat Valenciana, GVA: 090,430, BEST/2020/059, Ministry of Health, Labour and Welfare, MHLW: JPMH14427175, JPMH17932352, JPMH19189425, Helse- og Omsorgsdepartementet, Ministry of Environment, MOE: 2017001360005, Korea Environmental Industry and Technology Institute, KEITI, Instituto de Salud Carlos III, ISCIII: CB06/02/0041, INMA G03/176, Ministerio de Ciencia e Innovación, MICINN: MTM2015-68140-R, Seventh Framework Programme, FP7: R01HL111108, R01NR013945, Norges Forskningsråd: 221097, Institut National Du Cancer, INCa, Horizon 2020: 733206, Ministry of Internal Affairs and Communications, MIC: JPMI10001, Consejería de Educación e Investigación, The Norwegian Mother, Father and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research , NIH/NIEHS (contract no N01-ES-75558 ), NIH/NINDS (grant no. 1 UO1 NS 047537–01 and grant no.2 UO1 NS 047537–06A1 ). MoBa1 and MoBa 2 are supported by the Intramural Research Program of the NIH , National Institute of Environmental Health Sciences ( Z01-ES-49019 ) and Norwegian Research Council /BIOBANK (grant no 221097 ). The work in MoBa3 was supported in part by a Postdoctoral Fellowship grant from the Ulleval Hospitals Research Council (now under Oslo University Hospital) and travel grants from the Unger-Vetlesens foundation and the Norwegian American Womens Club , all to M.C.M.K. MoBa3 epigenomics data analyses were funded by INCA/Plan Cancer-EVA-INSERM, France, and the International Childhood Cancer Cohort Consortium (I4C), and performed by the Epigenetics Group at the International Agency for Research on Cancer (IARC, Lyon, France), A.G. was supported by the grant from INCA /Plan Cancer-EVA-INSERM (France, 2015) to Z.H. and also by the IARC Postdoctoral Fellowship, partially supported by the EC FP7 Marie Curie Actions-People-Co-funding of regional, national and international programmes (COFUND)., ALSPAC study was funded by the UK Medical Research Council and the Wellcome Trust (grant ref: 102215/2/13/2 ) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors, PY and CR, who will serve as guarantors for the contents of this paper. A comprehensive list of grants funding is available on the ALSPAC website ( http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf ). The Accessible Resource for Integrated Epigenomics Studies (ARIES), was funded by the UK Biotechnology and Biological Sciences Research Council ( BB/I025751/1 and BB/I025263/1 ). Additional epigenetic profiling of ALSPAC was supported by the UK Medical Research Council (MRC) Integrative Epidemiology Unit and the University of Bristol ( MC_UU_12013_1 , MC_UU_12013_2 , MC_UU_12013_5 and MC_UU_12013_8 ), the Wellcome Trust ( WT088806 ) and the United States National Institute of Diabetes and Digestive and Kidney Diseases ( R01 DK10324 ). PY and CR are supported by the UK MRC Integrative Epidemiology Unit ( MC_UU_00011/5 )., The Project Viva cohort is funded by NIH grants R01HL111108 , R01NR013945 , and R37 HD034568 ., The Hokkaido-Sapporo Study is supported by Grant-in-Aid for Scientific Research from the Japanese Ministry of Health , Labour and Welfare ( JPMH14427175 , JPMH19189425 , JPMH17932352 ), the Japan Society for the Promotion of Science, the Ministry of Education, Culture, Sports, Science and Technology ( JP16H02645 , JP19H01071 , JP18H03035 , JP15H04780 , JP19K10576 , JP19K10636 , JP18K10042 , JP18K10022 , JP19K22730 , JP19K20457 ), and an Environment Research and Technology Development fund ( JPMEERF20145054 , JPMEERF20175053 , JPMEERF20205002 ), AMED ( JPMH19188595 , JPMH18950314 ), and Ministry of Internal Affairs and Communications ( JPMI10001 )., Main funding of the epigenetic studies in INMA were grants from Instituto de Salud Carlos III ( Red INMA G03/176 , CB06/02/0041 ), Spanish Ministry of Health ( FIS-PI04/1436 , FIS-PI08/1151 including FEDER funds, FIS-PI11/00610 , FIS-FEDER-PI06/0867 , FIS-FEDER-PI03–1615 , FIS-FEDER PI16/1288 , FIS-FEDER PI19/1338, Miguel Servet FEDER 15/0025 and 20/0006, FIS-FSE : 17/00260 ), Generalitat de Catalunya-CIRIT 1999SGR 00241 , Generalitat Valenciana BEST/2020/059 , Fundacio ́ La Marato ́ de TV3 ( 090,430 ), EU Commission ( 261357 -MeDALL: Mechanisms of the Development of ALLergy), and European Research Council ( 268479 -BREATHE: Brain dEvelopment and Air polluTion ultrafine particles in school childrEn)., The authors would also like to thank Ingvild Essen for thorough field work, Heidi Marie Nordheim for biological sample management and the MoBa administrative unit (MoBa). The MoBa Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research . We are grateful to all the participating families in Norway who take part in this on-going cohort study., The Rhea project was financially supported by European projects , and the Greek Ministry of Health (Program of Prevention of Obesity and Neurodevelopmental Disorders in Preschool Children, in Heraklion district, Crete, Greece: 2011–2014, ‘Rhea Plus': Primary Prevention Program of Environmental Risk Factors for Reproductive Health, and Child Health: 2012–2015). The work was also supported by MICINN ( MTM2015-68140-R ), Centro Nacional de Genotipado - CEGEN-PRB2-ISCIII, the H2020 -EU.3.1.2. - Preventing Disease Programme (grant agreement no 874583 ) (ATHLETE project), and from the European Union's Horizon 2020 research and innovation programme (grant Agreement number: 733206 ) (Early Life stressors and Lifecycle Health (LIFECYCLE))., This study was supported by the Korean Environment Industry & Technology Institute ( KEITI ) through 'the Environmental Health Action Program', funded by Korea Ministry of Environment ( 2017001360005 )., ALSPAC. ALSPAC study is extremely grateful to all the families who took part in this study, the midwives for their help in recruiting them, and the whole ALSPAC team, which includes interviewers, computer and laboratory technicians, clerical workers, research scientists, volunteers, managers, receptionists and nurses. We would like to acknowledge Oliver Lyttleton, Hashem Shihab, Nabila Kazmi and Geoff Woodward for their earlier contribution to the generation of ARIES data (ALSPAC methylation data). INMA, The authors would like to thank all the participants for their generous collaboration. full roster of the INMA project investigators can be found at http://www.proyectoinma.org/presentacion-inma/listado-investigadores/en_listado-investigadores.html. MoBa, The authors would also like to thank Ingvild Essen for thorough field work, Heidi Marie Nordheim for biological sample management and the MoBa administrative unit (MoBa). The MoBa Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research. We are grateful to all the participating families in Norway who take part in this on-going cohort study. Project Viva, Project Viva researchers would like to thank all mothers, children and families for their ongoing participation. RHEA, The authors would like to thank Georgia Chalkiadaki and Danai Feida for biological sample management, to Eirini Michalaki, Mariza Kampouri, Anny Kyriklaki and Minas Iakovidis for field study performance and to Maria Fasoulaki for administrative assistance. SAPPORO-HOKKAIDO, We would like to express our appreciation to all of the study participants of the Hokkaido Study on Environment and Children? Health. We also express our profound gratitude to all personnel in the hospitals and clinics that collaborated with the study, including Sapporo Toho Hospital, Keiai Hospital, Endo Kikyo Maternity Clinic, Shiroishi Hospital, Memuro Municipal Hospital, Aoba Ladies Clinic, Obihiro-Kyokai Hospital, Akiyama Memorial Hospital, Sapporo Medical University Hospital, Hokkaido University Hospital, Kitami Red Cross Hospital, Hoyukai Sapporo Hospital, Gorinbashi Hospital, Hashimoto Clinic, Asahikawa Medical College Hospital, Hakodate Central General Hospital, Ohji General Hospital, Nakashibetsu Municipal Hospital, Sapporo Tokushukai Hospital, Asahikawa Red Cross Hospital, Wakkanai City Hospital, Kushiro Rosai Hospital, Sapporo-Kosei General Hospital, Shibetsu City General Hospital, Nikko Memorial Hospital, Sapporo City General Hospital, Kohnan Hospital, Hakodate City Hospital, Hokkaido Monbetsu Hospital, Tenshi Hospital, Hakodate Goryoukaku Hospital, Nakamura Hospital, Kin-ikyo Sapporo Hospital, Kitami Lady's Clinic, Engaru-Kosei General Hospital, Kushiro Red Cross Hospital, Nayoro City General Hospital, and Obihiro-Kosei General Hospital. We also deeply express our gratitude to the staff of The Hokkaido Study on Environment and Children's Health for their considerable efforts to support our study, including N. Goto, O. Hayashi, T. Hikichi, N. Kanda, K. Kunita, K. Miura, Y. Shibasaki, K. Sugawara, K. Tanaka, E. Toyama, and T. Yoshikawa. Special thanks to Ms. Mimi Takahashi on her effort to support writing this manuscript.ALSPAC study was funded by the UK Medical Research Council and the Wellcome Trust (grant ref: 102215/2/13/2) and the University of Bristol provide core support for ALSPAC. This publication is the work of the authors, PY and CR, who will serve as guarantors for the contents of this paper. A comprehensive list of grants funding is available on the ALSPAC website (http://www.bristol.ac.uk/alspac/external/documents/grant-acknowledgements.pdf). The Accessible Resource for Integrated Epigenomics Studies (ARIES), was funded by the UK Biotechnology and Biological Sciences Research Council (BB/I025751/1 and BB/I025263/1). Additional epigenetic profiling of ALSPAC was supported by the UK Medical Research Council (MRC) Integrative Epidemiology Unit and the University of Bristol (MC_UU_12013_1, MC_UU_12013_2, MC_UU_12013_5 and MC_UU_12013_8), the Wellcome Trust (WT088806) and the United States National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK10324). PY and CR are supported by the UK MRC Integrative Epidemiology Unit (MC_UU_00011/5).Main funding of the epigenetic studies in INMA were grants from Instituto de Salud Carlos III (Red INMA G03/176, CB06/02/0041), Spanish Ministry of Health (FIS-PI04/1436, FIS-PI08/1151 including FEDER funds, FIS-PI11/00610, FIS-FEDER-PI06/0867, FIS-FEDER-PI03?1615, FIS-FEDER PI16/1288, FIS-FEDER PI19/1338, FIS-FSE: 17/00260), Generalitat de Catalunya-CIRIT 1999SGR 00241, Generalitat Valenciana BEST/2020/059, Fundacio ? La Marato ? de TV3 (090,430), EU Commission (261357-MeDALL: Mechanisms of the Development of ALLergy), and European Research Council (268479-BREATHE: Brain dEvelopment and Air polluTion ultrafine particles in school childrEn).This study was supported by the Korean Environment Industry & Technology Institute (KEITI) through ?the Environmental Health Action Program?, funded by Korea Ministry of Environment (2017001360005).The Norwegian Mother, Father and Child Cohort Study is supported by the Norwegian Ministry of Health and Care Services and the Ministry of Education and Research, NIH/NIEHS (contract no N01-ES-75558), NIH/NINDS (grant no.1 UO1 NS 047537?01 and grant no.2 UO1 NS 047537?06A1). MoBa1 and MoBa 2 are supported by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences (Z01-ES-49019) and Norwegian Research Council/BIOBANK (grant no 221097). The work in MoBa3 was supported in part by a Postdoctoral Fellowship grant from the Ulleval Hospitals Research Council (now under Oslo University Hospital) and travel grants from the Unger-Vetlesens foundation and the Norwegian American Womens Club, all to M.C.M.K. MoBa3 epigenomics data analyses were funded by INCA/Plan Cancer-EVA-INSERM, France, and the International Childhood Cancer Cohort Consortium (I4C), and performed by the Epigenetics Group at the International Agency for Research on Cancer (IARC, Lyon, France), A.G. was supported by the grant from INCA/Plan Cancer-EVA-INSERM (France, 2015) to Z.H. and also by the IARC Postdoctoral Fellowship, partially supported by the EC FP7 Marie Curie Actions-People-Co-funding of regional, national and international programmes (COFUND).The Project Viva cohort is funded by NIH grants R01HL111108, R01NR013945, and R37 HD034568.The Rhea project was financially supported by European projects, and the Greek Ministry of Health (Program of Prevention of Obesity and Neurodevelopmental Disorders in Preschool Children, in Heraklion district, Crete, Greece: 2011?2014, Rhea Plus': Primary Prevention Program of Environmental Risk Factors for Reproductive Health, and Child Health: 2012?2015). The work was also supported by MICINN (MTM2015-68140-R), Centro Nacional de Genotipado-CEGEN-PRB2-ISCIII, the H2020-EU.3.1.2. - Preventing Disease Programme (grant agreement no 874583) (ATHLETE project), and from the European Union's Horizon 2020 research and innovation programme (grant Agreement number: 733206) (Early Life stressors and Lifecycle Health (LIFECYCLE)).The Hokkaido-Sapporo Study is supported by Grant-in-Aid for Scientific Research from the Japanese Ministry of Health, Labour and Welfare (JPMH14427175, JPMH19189425, JPMH17932352), the Ministry of Education, Culture, Sports, Science and Technology (JP16H02645, JP19H01071, JP18H03035, JP15H04780, JP19K10576, JP19K10636, JP18K10042, JP18K10022, JP19K22730, JP19K20457), and an Environment Research and Technology Development fund (JPMEERF20145054, JPMEERF20175053, JPMEERF20205002), AMED (JPMH19188595, JPMH18950314), and Ministry of Internal Affairs and Communications (JPMI10001)., European Project: 261357,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,MEDALL(2010), HAL UVSQ, Équipe, and Mechanisms of the Development of ALLergy - MEDALL - - EC:FP7:HEALTH2010-12-01 - 2015-05-31 - 261357 - VALID
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[SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health ,[SDV.TOX] Life Sciences [q-bio]/Toxicology ,DNA methylation ,[SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie ,Prenatal exposure ,[SDV.TOX]Life Sciences [q-bio]/Toxicology ,[SDV.EE.SANT] Life Sciences [q-bio]/Ecology, environment/Health ,Methylmercury ,[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie ,Mercury ,ALSPAC ,HELIX study ,PACE - Abstract
International audience; Mercury (Hg) is a ubiquitous heavy metal that originates from both natural and anthropogenic sources and is transformed in the environment to its most toxicant form, methylmercury (MeHg). Recent studies suggest that MeHg exposure can alter epigenetic modifications during embryogenesis. In this study, we examined associations between prenatal MeHg exposure and levels of cord blood DNA methylation (DNAm) by meta-analysis in up to seven independent studies (n = 1462) as well as persistence of those relationships in blood from 7 to 8 year-old children (n = 794). In cord blood, we found limited evidence of differential DNAm at cg24184221 in MED31 (β = 2.28 × 10−4, p-value = 5.87 × 10−5) in relation to prenatal MeHg exposure. In child blood, we identified differential DNAm at cg15288800 (β = 0.004, p-value = 4.97 × 10−5), also located in MED31. This repeated link to MED31, a gene involved in lipid metabolism and RNA Polymerase II transcription function, may suggest a DNAm perturbation related to MeHg exposure that persists into early childhood. Further, we found evidence for association between prenatal MeHg exposure and child blood DNAm levels at two additional CpGs: cg12204245 (β = 0.002, p-value = 4.81 × 10−7) in GRK1 and cg02212000 (β = −0.001, p-value = 8.13 × 10−7) in GGH. Prenatal MeHg exposure was associated with DNAm modifications that may influence health outcomes, such as cognitive or anthropometric development, in different populations.
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- 2022
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44. Determinants of Cord Blood DNA Methylation Variability in a Mexican-American Birth Cohort
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Yousefi, Paul Darius
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Environmental health ,Developmental biology ,450K ,Birth cohort ,Differentially methylated regions ,Environmental chemicals ,Epigenetics ,EWAS - Abstract
Epigenetic mechanisms, particularly DNA methylation, are a possible link between environmental and biological determinants of health. As the DNA methylome undergoes rearrangement in utero and is susceptible to environmental insults, it may be a mechanism explaining the developmental origins of human disease with public health importance. However, the epidemiologic studies needed to identify the role DNA methylation plays mediating environmental exposure disease risk still face several obstacles. This dissertation addresses knowledge gaps impeding the rigorous adoption of genome-scale measures of site-specific DNA methylation, like the Illumina Infinium HumanMethylation450 (450K) BeadChip®, into epidemiologic study designs. We then investigate the impact of prenatal exposure to polybrominated diphenyl ethers (PBDEs) on DNA methylation of children at birth. PBDEs are a class of flame retardant chemicals widely used in U.S. consumer products over the last 40 years that have previously been associated with adverse neurobehavioral outcomes, obesity, and other effects.Specifically, we aimed to:1)Identify and minimize sources of technical variation for site-specific DNA methylation measured by 450K BeadChip assay in epidemiologic studies2)Characterize sources of biological variation due to host factors (e.g. blood cell composition and sex) in measures of whole blood DNA methylation at birth3)Determine whether prenatal exposure to PBDEs is associated with differential methylation patterns of CpG sites in umbilical cord bloodOur results identified that the newly proposed All Sample Mean Normalization (ASMN) procedure performed consistently well, both at reducing batch effects and improving replicate comparability compared to several other leading normalization methods. It can be successfully implemented in epidemiologic studies to enhance 450K DNA methylation data preprocessing.In our examination biological variation, we found that a standard approach in epigenome-wide analysis – minfi white blood cell composition estimation – did not correlate well with white cell counts from newborns (ρ = -0.05 for granulocytes; ρ = -0.03 for lymphocytes), but improved substantially (ρ = 0.77 for granulocytes; ρ = 0.75 for lymphocytes) in older children likely due to increasing similarity with minfi’s adult reference data as children aged. This suggests that minfi may not currently be appropriate for analysis involving newborns or young children. Additionally, results on DNA methylation differences by sex identified 3,031 differentially methylated positions (DMPs) and 3,604 sex-associated differentially methylated regions (DMRs) on autosomes that were mostly hypermethylated in girls compared to boys. Our hits were significantly enriched for gene ontology terms related to nervous system development and behavior.Finally, we investigated the impact of exposure to PBDEs during the highly susceptible prenatal period on DNA methylation of Mexican-American children enrolled in the Center for Health Assessment of Mothers and Children of Salinas (CHAMACOS) at birth. We identified between 6 and 48 DMRs in umbilical cord blood associated with different measures of prenatal PBDE exposure. BDE’s-47, -99 and Σ4BDE had fewer (from 6 to 9), mostly hypomethylated DMRs. Prenatal BDE-100 and -153 levels were associated with more DMRs (11 and 48 respectively) and the majority hypermethylated. The PBDE-DMRs we found were located in genes (e.g. NRBP1, CDH9, NTN1, S100A13) involved in biologically relevant functions (including axon guidance and tumor suppression) given the health effects observed in association with BDE exposure to date.
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- 2016
45. Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation
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Solomon, Olivia, primary, Huen, Karen, additional, Yousefi, Paul, additional, Küpers, Leanne K., additional, González, Juan R., additional, Suderman, Matthew, additional, Reese, Sarah E., additional, Page, Christian M., additional, Gruzieva, Olena, additional, Rzehak, Peter, additional, Gao, Lu, additional, Bakulski, Kelly M., additional, Novoloaca, Alexei, additional, Allard, Catherine, additional, Pappa, Irene, additional, Llambrich, Maria, additional, Vives, Marta, additional, Jima, Dereje D., additional, Kvist, Tuomas, additional, Baccarelli, Andrea, additional, White, Cory, additional, Rezwan, Faisal I., additional, Sharp, Gemma C., additional, Tindula, Gwen, additional, Bergström, Anna, additional, Grote, Veit, additional, Dou, John F., additional, Isaevska, Elena, additional, Magnus, Maria C., additional, Corpeleijn, Eva, additional, Perron, Patrice, additional, Jaddoe, Vincent W.V., additional, Nohr, Ellen A., additional, Maitre, Lea, additional, Foraster, Maria, additional, Hoyo, Cathrine, additional, Håberg, Siri E., additional, Lahti, Jari, additional, DeMeo, Dawn L., additional, Zhang, Hongmei, additional, Karmaus, Wilfried, additional, Kull, Inger, additional, Koletzko, Berthold, additional, Feinberg, Jason I., additional, Gagliardi, Luigi, additional, Bouchard, Luigi, additional, Ramlau-Hansen, Cecilia Høst, additional, Tiemeier, Henning, additional, Santorelli, Gillian, additional, Maguire, Rachel L., additional, Czamara, Darina, additional, Litonjua, Augusto A., additional, Langhendries, Jean-Paul, additional, Plusquin, Michelle, additional, Lepeule, Johanna, additional, Binder, Elisabeth B., additional, Verduci, Elvira, additional, Dwyer, Terence, additional, Carracedo, Ángel, additional, Ferre, Natalia, additional, Eskenazi, Brenda, additional, Kogevinas, Manolis, additional, Nawrot, Tim S., additional, Munthe-Kaas, Monica C., additional, Herceg, Zdenko, additional, Relton, Caroline, additional, Melén, Erik, additional, Gruszfeld, Dariusz, additional, Breton, Carrie, additional, Fallin, M.D., additional, Ghantous, Akram, additional, Nystad, Wenche, additional, Heude, Barbara, additional, Snieder, Harold, additional, Hivert, Marie-France, additional, Felix, Janine F., additional, Sørensen, Thorkild I.A., additional, Bustamante, Mariona, additional, Murphy, Susan K., additional, Raikkönen, Katri, additional, Oken, Emily, additional, Holloway, John W., additional, Arshad, Syed Hasan, additional, London, Stephanie J., additional, and Holland, Nina, additional
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- 2022
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46. Paternal body mass index and offspring DNA methylation:findings from the PACE consortium
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Sharp, Gemma C, Alfano, Rossella, Ghantous, Akram, Urquiza, Jose, Rifas-Shiman, Sheryl L, Page, Christian M, Jin, Jianping, Fernández-Barrés, Silvia, Santorelli, Gillian, Tindula, Gwen, Yousefi, Paul, Kupers, Leanne, Ruiz-Arenas, Carlos, Jaddoe, Vincent WV, Demeo, Dawn, Fossati, Serena, Wright, John, Huen, Karen, Popovic, Maja, Nohr, Ellen A, Davey Smith, George, Lepeule, Johanna, Baccarelli, Andrea, Magnus, Maria C, Nystad, Wenche, Casas, Maribel, Oken, Emily, Håberg, Siri E, Vafeiadi, Marina, Roumeliotaki, Theano, Vrijheid, Martine, Munthe-Kaas, Monica C, Eskenazi, Brenda, Ronfani, Luca, Holland, Nina, Chatzi, Leda, Meltzer, Helle Margrete, Herceg, Zdenko, Plusquin, Michelle, Bustamante, Mariona, Hivert, Marie-France, Lawlor, Deborah A, Sørensen, Thorkild IA, London, Stephanie J, Felix, Janine F, Relton Caroline, L, Sharp, Gemma C, ALFANO, Rossella, Ghantous, Akram, Urquiza, Jose, Rifas-Shiman, Sheryl L, Page, Christian M, Jin, Jianping, Fernández-Barrés, Silvia, Santorelli, Gillian, and Tindula, Gwen
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0301 basic medicine ,Male ,Epigenomics ,Candidate gene ,Offspring ,Epidemiology ,Physiology ,fathers ,body mass index ,Reproductive health and childbirth ,Biology ,DNA methylation ,DOHaD ,Paternal ,epigenetics ,pregnancy ,Epigenesis, Genetic ,03 medical and health sciences ,0302 clinical medicine ,Genetic ,Clinical Research ,medicine ,Genetics ,Humans ,AcademicSubjects/MED00860 ,030212 general & internal medicine ,Epigenetics ,Obesity ,Genetic association ,Pediatric ,Pregnancy ,Contraception/Reproduction ,Human Genome ,Statistics ,General Medicine ,medicine.disease ,030104 developmental biology ,Public Health and Health Services ,other members of the Pregnancy and Childhood Epigenetics (PACE) consortium ,Female ,paternal ,Genomic imprinting ,Body mass index ,Epigenesis ,Systematic Reviews as Topic - Abstract
Background Accumulating evidence links paternal adiposity in the periconceptional period to offspring health outcomes. DNA methylation has been proposed as a mediating mechanism, but very few studies have explored this possibility in humans. Methods In the Pregnancy And Childhood Epigenetics (PACE) consortium, we conducted a meta-analysis of coordinated epigenome-wide association studies (EWAS) of paternal prenatal body mass index (BMI) (with and without adjustment for maternal BMI) in relation to DNA methylation in offspring blood at birth (13 data sets; total n = 4894) and in childhood (6 data sets; total n = 1982). Results We found little evidence of an association at either time point: at all CpGs, the false-discovery-rate-adjusted P-values were >0.05. In secondary sex-stratified analyses, we found just four CpGs for which there was robust evidence of an association in female offspring. To compare our findings to those of other studies, we conducted a systematic review, which identified seven studies, including five candidate gene studies showing associations between paternal BMI/obesity and offspring or sperm DNA methylation at imprinted regions. However, in our own study, we found very little evidence of enrichment for imprinted genes. Conclusion Our findings do not support the hypothesis that paternal BMI around the time of pregnancy is associated with offspring-blood DNA methylation, even at imprinted regions.
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- 2021
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47. Additional file 2 of Epigenetic modelling of former, current and never smokers
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Langdon, Ryan J., Yousefi, Paul, Relton, Caroline L., and Suderman, Matthew J.
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Additional file 2. Supplementary Tables 2A-2H - Supplementary Tables displaying results from enrichment analyses of genes mapped to CpGs from the smoking models presented in this paper. Supplementary Figures 1-4 - Network graphs of Human Phenotype Ontologies associated with CpGs from the smoking models presented in this paper.
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- 2021
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48. Additional file 3 of Epigenetic modelling of former, current and never smokers
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Langdon, Ryan J., Yousefi, Paul, Relton, Caroline L., and Suderman, Matthew J.
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Additional file 3. Supplementary Figure 5 - Comparison of the discriminative ability of cotinine and DNA methylation when distinguishing former from never smokers.
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- 2021
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49. Do Mass Spectrometry-Derived Metabolomics Improve the Prediction of Pregnancy-Related Disorders? Findings from a UK Birth Cohort with Independent Validation
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McBride, Nancy, primary, Yousefi, Paul, additional, Sovio, Ulla, additional, Taylor, Kurt, additional, Vafai, Yassaman, additional, Yang, Tiffany, additional, Hou, Bo, additional, Suderman, Matthew, additional, Relton, Caroline, additional, Smith, Gordon C. S., additional, and Lawlor, Deborah A., additional
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- 2021
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50. Do mass-spectrometry-derived metabolomics improve prediction of pregnancy-related disorders? Findings from a UK birth cohort with independent validation
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McBride, Nancy, primary, Yousefi, Paul, additional, Sovio, Ulla, additional, Taylor, Kurt, additional, Vafai, Yassaman, additional, Yang, Tiffany, additional, Hou, Bo, additional, Suderman, Matthew, additional, Relton, Caroline, additional, Smith, Gordon C., additional, and Lawlor, Deborah A., additional
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- 2021
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