527 results on '"van Dongen, Jenny"'
Search Results
2. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use
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Fang, Fang, Quach, Bryan, Lawrence, Kaitlyn G., van Dongen, Jenny, Marks, Jesse A., Lundgren, Sara, Lin, Mingkuan, Odintsova, Veronika V., Costeira, Ricardo, Xu, Zongli, Zhou, Linran, Mandal, Meisha, Xia, Yujing, Vink, Jacqueline M., Bierut, Laura J., Ollikainen, Miina, Taylor, Jack A., Bell, Jordana T., Kaprio, Jaakko, Boomsma, Dorret I., Xu, Ke, Sandler, Dale P., Hancock, Dana B., and Johnson, Eric O.
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- 2024
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3. NMR metabolomics-guided DNA methylation mortality predictors
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Geleijnse, J.M., Boersma, E., van Spil, W.E., van Greevenbroek, M.M.J., Stehouwer, C.D.A., van der Kallen, C.J.H., Arts, I.C.W., Rutters, F., Beulens, J.W.J., Muilwijk, M., Elders, P.J.M., 't Hart, L.M., Ghanbari, M., Ikram, M.A., Netea, M.G., Kloppenburg, M., Ramos, Y.F.M., Bomer, N., Meulenbelt, I., Stronks, K., Snijder, M.B., Zwinderman, A.H., Heijmans, B.T., Lumey, L.H., Wijmenga, C., Fu, J., Zhernakova, A., Deelen, J., Mooijaart, S.P., Beekman, M., Slagboom, P.E., Onderwater, G.L.J., van den Maagdenberg, A.M.J.M., Terwindt, G.M., Thesing, C., Bot, M., Penninx, B.W.J.H., Trompet, S., Jukema, J.W., Sattar, N., van der Horst, I.C.C., van der Harst, P., So-Osman, C., van Hilten, J.A., Nelissen, R.G.H.H., Höfer, I.E., Asselbergs, F.W., Scheltens, P., Teunissen, C.E., van der Flier, W.M., van Dongen, J., Pool, R., Willemsen, A.H.M., Boomsma, D.I., Suchiman, H.E.D., Barkey Wolf, J.J.H., Cats, D., Mei, H., Slofstra, M., Swertz, M., Reinders, M.J.T., van den Akker, E.B., Bizzarri, Daniele, Reinders, Marcel J.T., Kuiper, Lieke, Beekman, Marian, Deelen, Joris, van Meurs, Joyce B.J., van Dongen, Jenny, Pool, René, Boomsma, Dorret I., Ghanbari, Mohsen, Franke, Lude, Slagboom, Pieternella E., and van den Akker, Erik B.
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- 2024
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4. Enhanced resolution profiling in twins reveals differential methylation signatures of type 2 diabetes with links to its complications
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Christiansen, Colette, Potier, Louis, Martin, Tiphaine C., Villicaña, Sergio, Castillo-Fernandez, Juan E., Mangino, Massimo, Menni, Cristina, Tsai, Pei-Chien, Campbell, Purdey J., Mullin, Shelby, Ordoñana, Juan R., Monteagudo, Olga, Sachdev, Perminder S., Mather, Karen A., Trollor, Julian N., Pietilainen, Kirsi H., Ollikainen, Miina, Dalgård, Christine, Kyvik, Kirsten, Christensen, Kaare, van Dongen, Jenny, Willemsen, Gonneke, Boomsma, Dorret I., Magnusson, Patrik K.E., Pedersen, Nancy L., Wilson, Scott G., Grundberg, Elin, Spector, Tim D., and Bell, Jordana T.
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- 2024
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5. Longitudinal multi-omics study reveals common etiology underlying association between plasma proteome and BMI trajectories in adolescent and young adult twins
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Drouard, Gabin, Hagenbeek, Fiona A., Whipp, Alyce M., Pool, René, Hottenga, Jouke Jan, Jansen, Rick, Hubers, Nikki, Afonin, Aleksei, Willemsen, Gonneke, de Geus, Eco J. C., Ripatti, Samuli, Pirinen, Matti, Kanninen, Katja M., Boomsma, Dorret I., van Dongen, Jenny, and Kaprio, Jaakko
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- 2023
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6. Comprehensive evaluation of smoking exposures and their interactions on DNA methylation
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Heijmans, Bastiaan, ’t Hoen, Peter, van Meurs, Joyce, Jansen, Rick, Franke, Lude, Boomsma, Dorret, Pool, René, van Dongen, Jenny, Hottenga, Jouke, van Greevenbroek, Marleen, Stehouwer, Coen, van der Kallen, Carla, Schalkwijk, Casper, Wijmenga, Cisca, Zhernakova, Sasha, Tigchelaar, Ettje, Slagboom, P. Eline, Beekman, Marian, Deelen, Joris, Van Heemst, Diana, Veldink, Jan, van den Berg, Leonard, van Duijn, Cornelia, Hofman, Bert, Isaacs, Aaron, Uitterlinden, André, Jhamai, P. Mila, Verbiest, Michael, Suchiman, H. Eka, Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, Zhernakova, Dasha, van ‘t Hof, Peter, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Luijk, René, Bonder, Marc, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon, Swertz, Morris, van Zwet, Erik, Hoang, Thanh T., Lee, Yunsung, McCartney, Daniel L., Kersten, Elin T.G., Page, Christian M., Hulls, Paige M., Lee, Mikyeong, Walker, Rosie M., Breeze, Charles E., Bennett, Brian D., Burkholder, Adam B., Ward, James, Brantsæter, Anne Lise, Caspersen, Ida H., Motsinger-Reif, Alison A., Richards, Marie, White, Julie D., Zhao, Shanshan, Richmond, Rebecca C., Magnus, Maria C., Koppelman, Gerard H., Evans, Kathryn L., Marioni, Riccardo E., Håberg, Siri E., and London, Stephanie J.
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- 2024
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7. Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging
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McCartney, Daniel L, Min, Josine L, Richmond, Rebecca C, Lu, Ake T, Sobczyk, Maria K, Davies, Gail, Broer, Linda, Guo, Xiuqing, Jeong, Ayoung, Jung, Jeesun, Kasela, Silva, Katrinli, Seyma, Kuo, Pei-Lun, Matias-Garcia, Pamela R, Mishra, Pashupati P, Nygaard, Marianne, Palviainen, Teemu, Patki, Amit, Raffield, Laura M, Ratliff, Scott M, Richardson, Tom G, Robinson, Oliver, Soerensen, Mette, Sun, Dianjianyi, Tsai, Pei-Chien, van der Zee, Matthijs D, Walker, Rosie M, Wang, Xiaochuan, Wang, Yunzhang, Xia, Rui, Xu, Zongli, Yao, Jie, Zhao, Wei, Correa, Adolfo, Boerwinkle, Eric, Dugué, Pierre-Antoine, Durda, Peter, Elliott, Hannah R, Gieger, Christian, de Geus, Eco JC, Harris, Sarah E, Hemani, Gibran, Imboden, Medea, Kähönen, Mika, Kardia, Sharon LR, Kresovich, Jacob K, Li, Shengxu, Lunetta, Kathryn L, Mangino, Massimo, Mason, Dan, McIntosh, Andrew M, Mengel-From, Jonas, Moore, Ann Zenobia, Murabito, Joanne M, Ollikainen, Miina, Pankow, James S, Pedersen, Nancy L, Peters, Annette, Polidoro, Silvia, Porteous, David J, Raitakari, Olli, Rich, Stephen S, Sandler, Dale P, Sillanpää, Elina, Smith, Alicia K, Southey, Melissa C, Strauch, Konstantin, Tiwari, Hemant, Tanaka, Toshiko, Tillin, Therese, Uitterlinden, Andre G, Van Den Berg, David J, van Dongen, Jenny, Wilson, James G, Wright, John, Yet, Idil, Arnett, Donna, Bandinelli, Stefania, Bell, Jordana T, Binder, Alexandra M, Boomsma, Dorret I, Chen, Wei, Christensen, Kaare, Conneely, Karen N, Elliott, Paul, Ferrucci, Luigi, Fornage, Myriam, Hägg, Sara, Hayward, Caroline, Irvin, Marguerite, Kaprio, Jaakko, Lawlor, Deborah A, Lehtimäki, Terho, Lohoff, Falk W, Milani, Lili, Milne, Roger L, Probst-Hensch, Nicole, Reiner, Alex P, Ritz, Beate, and Rotter, Jerome I
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Prevention ,Nutrition ,Aging ,Human Genome ,Genetics ,Generic health relevance ,Inflammatory and immune system ,Good Health and Well Being ,Adiposity ,Biomarkers ,C-Reactive Protein ,CpG Islands ,DNA Methylation ,Educational Status ,Epigenesis ,Genetic ,Genetic Loci ,Genetic Markers ,Genome ,Human ,Genome-Wide Association Study ,Granulocytes ,Humans ,Immunity ,Innate ,Lipid Metabolism ,Multifactorial Inheritance ,Plasminogen Activator Inhibitor 1 ,DNA methylation ,GWAS ,Epigenetic clock ,Genetics of DNA Methylation Consortium ,NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundBiological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation in these measures in populations has become a major goal in the field.ResultsLeveraging DNA methylation and SNP data from more than 40,000 individuals, we identify 137 genome-wide significant loci, of which 113 are novel, from genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and epigenetic surrogate markers for granulocyte proportions and plasminogen activator inhibitor 1 levels, respectively. We find evidence for shared genetic loci associated with the Horvath clock and expression of transcripts encoding genes linked to lipid metabolism and immune function. Notably, these loci are independent of those reported to regulate DNA methylation levels at constituent clock CpGs. A polygenic score for GrimAge acceleration showed strong associations with adiposity-related traits, educational attainment, parental longevity, and C-reactive protein levels.ConclusionThis study illuminates the genetic architecture underlying epigenetic aging and its shared genetic contributions with lifestyle factors and longevity.
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- 2021
8. Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group
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Jia, Tianye, Chu, Congying, Liu, Yun, van Dongen, Jenny, Papastergios, Evangelos, Armstrong, Nicola J, Bastin, Mark E, Carrillo-Roa, Tania, den Braber, Anouk, Harris, Mathew, Jansen, Rick, Liu, Jingyu, Luciano, Michelle, Ori, Anil PS, Roiz Santiañez, Roberto, Ruggeri, Barbara, Sarkisyan, Daniil, Shin, Jean, Sungeun, Kim, Tordesillas Gutiérrez, Diana, van’t Ent, Dennis, Ames, David, Artiges, Eric, Bakalkin, Georgy, Banaschewski, Tobias, Bokde, Arun LW, Brodaty, Henry, Bromberg, Uli, Brouwer, Rachel, Büchel, Christian, Burke Quinlan, Erin, Cahn, Wiepke, de Zubicaray, Greig I, Ehrlich, Stefan, Ekström, Tomas J, Flor, Herta, Fröhner, Juliane H, Frouin, Vincent, Garavan, Hugh, Gowland, Penny, Heinz, Andreas, Hoare, Jacqueline, Ittermann, Bernd, Jahanshad, Neda, Jiang, Jiyang, Kwok, John B, Martin, Nicholas G, Martinot, Jean-Luc, Mather, Karen A, McMahon, Katie L, McRae, Allan F, Nees, Frauke, Papadopoulos Orfanos, Dimitri, Paus, Tomáš, Poustka, Luise, Sämann, Philipp G, Schofield, Peter R, Smolka, Michael N, Stein, Dan J, Strike, Lachlan T, Teeuw, Jalmar, Thalamuthu, Anbupalam, Trollor, Julian, Walter, Henrik, Wardlaw, Joanna M, Wen, Wei, Whelan, Robert, Apostolova, Liana G, Binder, Elisabeth B, Boomsma, Dorret I, Calhoun, Vince, Crespo-Facorro, Benedicto, Deary, Ian J, Hulshoff Pol, Hilleke, Ophoff, Roel A, Pausova, Zdenka, Sachdev, Perminder S, Saykin, Andrew, Wright, Margaret J, Thompson, Paul M, Schumann, Gunter, and Desrivières, Sylvane
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Biological Psychology ,Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Psychology ,Mental Health ,Neurosciences ,Genetics ,Human Genome ,Diabetes ,Neurodegenerative ,2.1 Biological and endogenous factors ,Aetiology ,Neurological ,Mental health ,CpG Islands ,DNA Methylation ,Epigenesis ,Genetic ,Epigenome ,Genome-Wide Association Study ,Humans ,Biological Sciences ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Psychiatry ,Clinical sciences ,Biological psychology ,Clinical and health psychology - Abstract
DNA methylation, which is modulated by both genetic factors and environmental exposures, may offer a unique opportunity to discover novel biomarkers of disease-related brain phenotypes, even when measured in other tissues than brain, such as blood. A few studies of small sample sizes have revealed associations between blood DNA methylation and neuropsychopathology, however, large-scale epigenome-wide association studies (EWAS) are needed to investigate the utility of DNA methylation profiling as a peripheral marker for the brain. Here, in an analysis of eleven international cohorts, totalling 3337 individuals, we report epigenome-wide meta-analyses of blood DNA methylation with volumes of the hippocampus, thalamus and nucleus accumbens (NAcc)-three subcortical regions selected for their associations with disease and heritability and volumetric variability. Analyses of individual CpGs revealed genome-wide significant associations with hippocampal volume at two loci. No significant associations were found for analyses of thalamus and nucleus accumbens volumes. Cluster-based analyses revealed additional differentially methylated regions (DMRs) associated with hippocampal volume. DNA methylation at these loci affected expression of proximal genes involved in learning and memory, stem cell maintenance and differentiation, fatty acid metabolism and type-2 diabetes. These DNA methylation marks, their interaction with genetic variants and their impact on gene expression offer new insights into the relationship between epigenetic variation and brain structure and may provide the basis for biomarker discovery in neurodegeneration and neuropsychiatric conditions.
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- 2021
9. Integrative Multi-omics Analysis of Childhood Aggressive Behavior
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Hagenbeek, Fiona A., van Dongen, Jenny, Pool, René, Roetman, Peter J., Harms, Amy C., Hottenga, Jouke Jan, Kluft, Cornelis, Colins, Olivier F., van Beijsterveldt, Catharina E. M., Fanos, Vassilios, Ehli, Erik A., Hankemeier, Thomas, Vermeiren, Robert R. J. M., Bartels, Meike, Déjean, Sébastien, and Boomsma, Dorret I.
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- 2023
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10. DNA methylation analysis is used to identify novel genetic loci associated with circulating fibrinogen levels in blood
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Hahn, Julie, Bressler, Jan, Domingo-Relloso, Arce, Chen, Ming-Huei, McCartney, Daniel L., Teumer, Alexander, van Dongen, Jenny, Kleber, Marcus E., Aïssi, Dylan, Swenson, Brenton R., Yao, Jie, Zhao, Wei, Huang, Jian, Xia, Yujing, Brown, Michael R., Costeira, Ricardo, de Geus, Eco J.C., Delgado, Graciela E., Dobson, Dre'Von A., Elliott, Paul, Grabe, Hans J., Guo, Xiuqing, Harris, Sarah E., Huffman, Jennifer E., Kardia, Sharon L.R., Liu, Yongmei, Lorkowski, Stefan, Marioni, Riccardo E., Nauck, Matthias, Ratliff, Scott M., Sabater-Lleal, Maria, Spector, Tim D., Suchon, Pierre, Taylor, Kent D., Thibord, Florian, Trégouët, David-Alexandre, Wiggins, Kerri L., Willemsen, Gonneke, Bell, Jordana T., Boomsma, Dorret I., Cole, Shelley A., Cox, Simon R., Dehghan, Abbas, Greinacher, Andreas, Haack, Karin, März, Winfried, Morange, Pierre-Emmanuel, Rotter, Jerome I., Sotoodehnia, Nona, Tellez-Plaza, Maria, Navas-Acien, Ana, Smith, Jennifer A., Johnson, Andrew D., Fornage, Myriam, Smith, Nicholas L., Wolberg, Alisa S., Morrison, Alanna C., and de Vries, Paul S.
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- 2023
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11. 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
12. An integrative cross-omics analysis of DNA methylation sites of glucose and insulin homeostasis
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Liu, Jun, Carnero-Montoro, Elena, van Dongen, Jenny, Lent, Samantha, Nedeljkovic, Ivana, Ligthart, Symen, Tsai, Pei-Chien, Martin, Tiphaine C, Mandaviya, Pooja R, Jansen, Rick, Peters, Marjolein J, Duijts, Liesbeth, Jaddoe, Vincent WV, Tiemeier, Henning, Felix, Janine F, Willemsen, Gonneke, de Geus, Eco JC, Chu, Audrey Y, Levy, Daniel, Hwang, Shih-Jen, Bressler, Jan, Gondalia, Rahul, Salfati, Elias L, Herder, Christian, Hidalgo, Bertha A, Tanaka, Toshiko, Moore, Ann Zenobia, Lemaitre, Rozenn N, Jhun, Min A, Smith, Jennifer A, Sotoodehnia, Nona, Bandinelli, Stefania, Ferrucci, Luigi, Arnett, Donna K, Grallert, Harald, Assimes, Themistocles L, Hou, Lifang, Baccarelli, Andrea, Whitsel, Eric A, van Dijk, Ko Willems, Amin, Najaf, Uitterlinden, André G, Sijbrands, Eric JG, Franco, Oscar H, Dehghan, Abbas, Spector, Tim D, Dupuis, Josée, Hivert, Marie-France, Rotter, Jerome I, Meigs, James B, Pankow, James S, van Meurs, Joyce BJ, Isaacs, Aaron, Boomsma, Dorret I, Bell, Jordana T, Demirkan, Ayşe, and van Duijn, Cornelia M
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Biological Sciences ,Genetics ,Nutrition ,Diabetes ,Human Genome ,Obesity ,2.1 Biological and endogenous factors ,Aetiology ,Metabolic and endocrine ,Adult ,Aged ,Aged ,80 and over ,Computer Simulation ,CpG Islands ,DNA Methylation ,Diabetes Mellitus ,Type 2 ,Epigenesis ,Genetic ,Epigenomics ,Female ,Gene Expression Profiling ,Gene Expression Regulation ,Genome-Wide Association Study ,Glucose ,Homeostasis ,Humans ,Insulin ,Male ,Metabolic Networks and Pathways ,Middle Aged ,Polymorphism ,Single Nucleotide ,Young Adult - Abstract
Despite existing reports on differential DNA methylation in type 2 diabetes (T2D) and obesity, our understanding of its functional relevance remains limited. Here we show the effect of differential methylation in the early phases of T2D pathology by a blood-based epigenome-wide association study of 4808 non-diabetic Europeans in the discovery phase and 11,750 individuals in the replication. We identify CpGs in LETM1, RBM20, IRS2, MAN2A2 and the 1q25.3 region associated with fasting insulin, and in FCRL6, SLAMF1, APOBEC3H and the 15q26.1 region with fasting glucose. In silico cross-omics analyses highlight the role of differential methylation in the crosstalk between the adaptive immune system and glucose homeostasis. The differential methylation explains at least 16.9% of the association between obesity and insulin. Our study sheds light on the biological interactions between genetic variants driving differential methylation and gene expression in the early pathogenesis of T2D.
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- 2019
13. Methylome-wide association study of antidepressant use in Generation Scotland and the Netherlands Twin Register implicates the innate immune system
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Barbu, Miruna C., Huider, Floris, Campbell, Archie, Amador, Carmen, Adams, Mark J., Lynall, Mary-Ellen, Howard, David M., Walker, Rosie M., Morris, Stewart W., Van Dongen, Jenny, Porteous, David J., Evans, Kathryn L., Bullmore, Edward, Willemsen, Gonneke, Boomsma, Dorret I., Whalley, Heather C., and McIntosh, Andrew M.
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- 2022
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14. DNA methylation in peripheral tissues and left-handedness
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Odintsova, Veronika V., Suderman, Matthew, Hagenbeek, Fiona A., Caramaschi, Doretta, Hottenga, Jouke-Jan, Pool, René, Dolan, Conor V., Ligthart, Lannie, van Beijsterveldt, Catharina E. M., Willemsen, Gonneke, de Geus, Eco J. C., Beck, Jeffrey J., Ehli, Erik A., Cuellar-Partida, Gabriel, Evans, David M., Medland, Sarah E., Relton, Caroline L., Boomsma, Dorret I., and van Dongen, Jenny
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- 2022
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15. Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations
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Breeze, Charles E., Haugen, Eric, Reynolds, Alex, Teschendorff, Andrew, van Dongen, Jenny, Lan, Qing, Rothman, Nathaniel, Bourque, Guillaume, Dunham, Ian, Beck, Stephan, Stamatoyannopoulos, John, Franceschini, Nora, and Berndt, Sonja I.
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- 2022
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16. Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data.
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van Hilten, Arno, van Rooij, Jeroen, Heijmans, Bastiaan T., 't Hoen, Peter A. C., Meurs, Joyce van, Jansen, Rick, Franke, Lude, Boomsma, Dorret I., Pool, René, van Dongen, Jenny, Hottenga, Jouke J., van Greevenbroek, Marleen M. J., Stehouwer, Coen D. A., van der Kallen, Carla J. H., Schalkwijk, Casper G., Wijmenga, Cisca, Zhernakova, Sasha, Tigchelaar, Ettje F., Slagboom, P. Eline, and Beekman, Marian
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GENE expression ,MULTIOMICS ,PREDICTION models ,NETWORK performance ,INDIVIDUALIZED medicine - Abstract
Integrating multi-omics data into predictive models has the potential to enhance accuracy, which is essential for precision medicine. In this study, we developed interpretable predictive models for multi-omics data by employing neural networks informed by prior biological knowledge, referred to as visible networks. These neural networks offer insights into the decision-making process and can unveil novel perspectives on the underlying biological mechanisms associated with traits and complex diseases. We tested the performance, interpretability and generalizability for inferring smoking status, subject age and LDL levels using genome-wide RNA expression and CpG methylation data from the blood of the BIOS consortium (four population cohorts, N
total = 2940). In a cohort-wise cross-validation setting, the consistency of the diagnostic performance and interpretation was assessed. Performance was consistently high for predicting smoking status with an overall mean AUC of 0.95 (95% CI: 0.90–1.00) and interpretation revealed the involvement of well-replicated genes such as AHRR, GPR15 and LRRN3. LDL-level predictions were only generalized in a single cohort with an R2 of 0.07 (95% CI: 0.05–0.08). Age was inferred with a mean error of 5.16 (95% CI: 3.97–6.35) years with the genes COL11A2, AFAP1, OTUD7A, PTPRN2, ADARB2 and CD34 consistently predictive. For both regression tasks, we found that using multi-omics networks improved performance, stability and generalizability compared to interpretable single omic networks. We believe that visible neural networks have great potential for multi-omics analysis; they combine multi-omic data elegantly, are interpretable, and generalize well to data from different cohorts. [ABSTRACT FROM AUTHOR]- Published
- 2024
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17. Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology
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Ferreira, Manuel A, Vonk, Judith M, Baurecht, Hansjörg, Marenholz, Ingo, Tian, Chao, Hoffman, Joshua D, Helmer, Quinta, Tillander, Annika, Ullemar, Vilhelmina, van Dongen, Jenny, Lu, Yi, Rüschendorf, Franz, Esparza-Gordillo, Jorge, Medway, Chris W, Mountjoy, Edward, Burrows, Kimberley, Hummel, Oliver, Grosche, Sarah, Brumpton, Ben M, Witte, John S, Hottenga, Jouke-Jan, Willemsen, Gonneke, Zheng, Jie, Rodríguez, Elke, Hotze, Melanie, Franke, Andre, Revez, Joana A, Beesley, Jonathan, Matheson, Melanie C, Dharmage, Shyamali C, Bain, Lisa M, Fritsche, Lars G, Gabrielsen, Maiken E, Balliu, Brunilda, Nielsen, Jonas B, Zhou, Wei, Hveem, Kristian, Langhammer, Arnulf, Holmen, Oddgeir L, Løset, Mari, Abecasis, Gonçalo R, Willer, Cristen J, Arnold, Andreas, Homuth, Georg, Schmidt, Carsten O, Thompson, Philip J, Martin, Nicholas G, Duffy, David L, Novak, Natalija, Schulz, Holger, Karrasch, Stefan, Gieger, Christian, Strauch, Konstantin, Melles, Ronald B, Hinds, David A, Hübner, Norbert, Weidinger, Stephan, Magnusson, Patrik KE, Jansen, Rick, Jorgenson, Eric, Lee, Young-Ae, Boomsma, Dorret I, Almqvist, Catarina, Karlsson, Robert, Koppelman, Gerard H, and Paternoster, Lavinia
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Biological Sciences ,Genetics ,Emerging Infectious Diseases ,Lung ,Prevention ,Asthma ,Human Genome ,Aetiology ,2.1 Biological and endogenous factors ,Inflammatory and immune system ,Good Health and Well Being ,Eczema ,Genetic Predisposition to Disease ,Genome-Wide Association Study ,Humans ,Hypersensitivity ,Phenotype ,Polymorphism ,Single Nucleotide ,Rhinitis ,Allergic ,Seasonal ,Risk Factors ,23andMe Research Team ,AAGC collaborators ,BIOS consortium ,LifeLines Cohort Study ,Medical and Health Sciences ,Developmental Biology ,Agricultural biotechnology ,Bioinformatics and computational biology - Abstract
Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 × 10-8), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes.
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- 2017
18. DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation
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Richard, Melissa A, Huan, Tianxiao, Ligthart, Symen, Gondalia, Rahul, Jhun, Min A, Brody, Jennifer A, Irvin, Marguerite R, Marioni, Riccardo, Shen, Jincheng, Tsai, Pei-Chien, Montasser, May E, Jia, Yucheng, Syme, Catriona, Salfati, Elias L, Boerwinkle, Eric, Guan, Weihua, Mosley, Thomas H, Bressler, Jan, Morrison, Alanna C, Liu, Chunyu, Mendelson, Michael M, Uitterlinden, André G, van Meurs, Joyce B, Consortium, BIOS, Heijmans, Bastiaan T, Hoen, Peter AC ’t, van Meurs, Joyce, Isaacs, Aaron, Jansen, Rick, Franke, Lude, Boomsma, Dorret I, Pool, René, van Dongen, Jenny, Hottenga, Jouke J, van Greevenbroek, Marleen MJ, Stehouwer, Coen DA, van der Kallen, Carla JH, Schalkwijk, Casper G, Wijmenga, Cisca, Zhernakova, Alexandra, Tigchelaar, Ettje F, Slagboom, P Eline, Beekman, Marian, Deelen, Joris, van Heemst, Diana, Veldink, Jan H, van den Berg, Leonard H, van Duijn, Cornelia M, Hofman, Albert, Jhamai, P Mila, Verbiest, Michael, Suchiman, H Eka D, Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, van ’t Hof, Peter, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Zhernakova, Dasha V, Luijk, René, Bonder, Marc Jan, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon M, Swertz, Morris A, van Zwet, Erik W, Franco, Oscar H, Zhang, Guosheng, Li, Yun, Stewart, James D, Bis, Joshua C, Psaty, Bruce M, Chen, Yii-Der Ida, Kardia, Sharon LR, Zhao, Wei, Turner, Stephen T, Absher, Devin, Aslibekyan, Stella, Starr, John M, McRae, Allan F, Hou, Lifang, Just, Allan C, Schwartz, Joel D, Vokonas, Pantel S, Menni, Cristina, Spector, Tim D, Shuldiner, Alan, Damcott, Coleen M, Rotter, Jerome I, Palmas, Walter, Liu, Yongmei, and Paus, Tomáš
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Epidemiology ,Biological Sciences ,Health Sciences ,Genetics ,Human Genome ,Biotechnology ,Aetiology ,2.1 Biological and endogenous factors ,Aged ,Blood Pressure ,CpG Islands ,Cross-Sectional Studies ,DNA Methylation ,Epigenesis ,Genetic ,Genetic Variation ,Genome-Wide Association Study ,Humans ,Mendelian Randomization Analysis ,Middle Aged ,Nerve Tissue Proteins ,Quantitative Trait Loci ,Tetraspanins ,BIOS Consortium ,DNA methylation ,Mendelian randomization ,blood pressure ,epigenome-wide association study ,gene expression ,sequence variation ,Medical and Health Sciences ,Genetics & Heredity ,Biological sciences ,Biomedical and clinical sciences ,Health sciences - Abstract
Genome-wide association studies have identified hundreds of genetic variants associated with blood pressure (BP), but sequence variation accounts for a small fraction of the phenotypic variance. Epigenetic changes may alter the expression of genes involved in BP regulation and explain part of the missing heritability. We therefore conducted a two-stage meta-analysis of the cross-sectional associations of systolic and diastolic BP with blood-derived genome-wide DNA methylation measured on the Infinium HumanMethylation450 BeadChip in 17,010 individuals of European, African American, and Hispanic ancestry. Of 31 discovery-stage cytosine-phosphate-guanine (CpG) dinucleotides, 13 replicated after Bonferroni correction (discovery: N = 9,828, p < 1.0 × 10-7; replication: N = 7,182, p 30%) and independent of known BP genetic variants, explaining an additional 1.4% and 2.0% of the interindividual variation in systolic and diastolic BP, respectively. Bidirectional Mendelian randomization among up to 4,513 individuals of European ancestry from 4 cohorts suggested that methylation at cg08035323 (TAF1B-YWHAQ) influences BP, while BP influences methylation at cg00533891 (ZMIZ1), cg00574958 (CPT1A), and cg02711608 (SLC1A5). Gene expression analyses further identified six genes (TSPAN2, SLC7A11, UNC93B1, CPT1A, PTMS, and LPCAT3) with evidence of triangular associations between methylation, gene expression, and BP. Additional integrative Mendelian randomization analyses of gene expression and DNA methylation suggested that the expression of TSPAN2 is a putative mediator of association between DNA methylation at cg23999170 and BP. These findings suggest that heritable DNA methylation plays a role in regulating BP independently of previously known genetic variants.
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- 2017
19. Intergenerational transmission of complex traits and the offspring methylome
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Hagenbeek, Fiona A., primary, Pool, René, additional, Van Asselt, Austin J., additional, Ehli, Erik A., additional, Bartels, Meike, additional, Hottenga, Jouke Jan, additional, Dolan, Conor V., additional, van Dongen, Jenny, additional, and Boomsma, Dorret I., additional
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- 2024
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20. A bivariate twin study of cannabis use and regular tobacco smoking across three different countries
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Zellers, Stephanie, primary, van Dongen, Jenny, additional, Maes, Hermine H M J L, additional, Ollikainen, Miina, additional, Fang, Fang, additional, VRIEZE, SCOTT, additional, Kaprio, Jaakko, additional, and Boomsma, Dorret, additional
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- 2024
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21. Comprehensive evaluation of smoking exposures and their interactions on DNA methylation
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Hoang, Thanh T., primary, Lee, Yunsung, additional, McCartney, Daniel L., additional, Kersten, Elin T.G., additional, Page, Christian M., additional, Hulls, Paige M., additional, Lee, Mikyeong, additional, Walker, Rosie M., additional, Breeze, Charles E., additional, Bennett, Brian D., additional, Burkholder, Adam B., additional, Ward, James, additional, Brantsæter, Anne Lise, additional, Caspersen, Ida H., additional, Motsinger-Reif, Alison A., additional, Richards, Marie, additional, White, Julie D., additional, Zhao, Shanshan, additional, Richmond, Rebecca C., additional, Magnus, Maria C., additional, Koppelman, Gerard H., additional, Evans, Kathryn L., additional, Marioni, Riccardo E., additional, Håberg, Siri E., additional, London, Stephanie J., additional, Heijmans, Bastiaan, additional, ’t Hoen, Peter, additional, van Meurs, Joyce, additional, Jansen, Rick, additional, Franke, Lude, additional, Boomsma, Dorret, additional, Pool, René, additional, van Dongen, Jenny, additional, Hottenga, Jouke, additional, van Greevenbroek, Marleen, additional, Stehouwer, Coen, additional, van der Kallen, Carla, additional, Schalkwijk, Casper, additional, Wijmenga, Cisca, additional, Zhernakova, Sasha, additional, Tigchelaar, Ettje, additional, Slagboom, P. Eline, additional, Beekman, Marian, additional, Deelen, Joris, additional, Van Heemst, Diana, additional, Veldink, Jan, additional, van den Berg, Leonard, additional, van Duijn, Cornelia, additional, Hofman, Bert, additional, Isaacs, Aaron, additional, Uitterlinden, André, additional, Jhamai, P. Mila, additional, Verbiest, Michael, additional, Suchiman, H. Eka, additional, Verkerk, Marijn, additional, van der Breggen, Ruud, additional, van Rooij, Jeroen, additional, Lakenberg, Nico, additional, Mei, Hailiang, additional, van Iterson, Maarten, additional, van Galen, Michiel, additional, Bot, Jan, additional, Zhernakova, Dasha, additional, van ‘t Hof, Peter, additional, Deelen, Patrick, additional, Nooren, Irene, additional, Moed, Matthijs, additional, Vermaat, Martijn, additional, Luijk, René, additional, Bonder, Marc, additional, van Dijk, Freerk, additional, Arindrarto, Wibowo, additional, Kielbasa, Szymon, additional, Swertz, Morris, additional, and van Zwet, Erik, additional
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- 2024
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22. Contributors
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Almqvist, Catarina, primary, Ando, Juko, additional, Bartels, Meike, additional, Bayartai, Munkh-Erdene, additional, Beam, Christopher R., additional, Beltz, Adriene M., additional, Berenbaum, Sheri A., additional, Boomsma, Dorret I., additional, Brikell, Isabell, additional, Bui, Minh, additional, Calais-Ferreira, Lucas, additional, Christensen, Kaare, additional, Corley, Robin P., additional, Cortessis, Victoria K., additional, Cozen, Wendy, additional, Craig, Jeffrey M., additional, DiLalla, Lisabeth Fisher, additional, DiLalla, David L., additional, Dolan, Conor V., additional, Dowty, James G., additional, Elman, Jeremy A., additional, Esser, Vivienne F.C., additional, Ferreira, Paulo H., additional, Finkel, Deborah, additional, Giardina, Irene, additional, Hagenbeek, Fiona A., additional, Haltrich, Irén, additional, Heikkinen, Aino, additional, Hopper, John L., additional, Hottenga, Jouke-Jan, additional, Hur, Yoon-Mi, additional, Jamnik, Matthew R., additional, Jayaweera, Kaushalya, additional, Kaprio, Jaakko, additional, Kim, Alice J., additional, Lam, Esther, additional, Larsson, Henrik, additional, Lee, Soo Ji, additional, Lengyel, Anna, additional, Li, Shuai, additional, Lichtenstein, Paul, additional, Littvay, Levente, additional, Loehlin, John C., additional, Loke, Yuk Jing, additional, Lundgren, Sara, additional, Mack, Thomas M., additional, Malta, Sue, additional, Marshall, Riley L., additional, Martin, Nicholas G., additional, McGue, Matt, additional, Medland, Sarah E., additional, Mitchell, Brittany L., additional, Mitrea, Elena Cristina, additional, Mohandas, Namitha, additional, Morosoli, José J., additional, Métneki, Julia, additional, Nguyen, Tuong L., additional, Niculae, Francisca J., additional, Odintsova, Veronika, additional, Ollikainen, Miina, additional, Ordoñana, Juan R., additional, Pali, Emily, additional, Panizzon, Matthew S., additional, Park, Hang A., additional, Pedersen, Nancy L., additional, Pham, Holly T., additional, Polderman, Tinca J.C., additional, Pool, René, additional, Pári, András, additional, Rankin, Monica, additional, Renzo, Gian Carlo Di, additional, Reynolds, Chandra A., additional, Salehi, Maryam, additional, Segal, Nancy L., additional, Silventoinen, Karri, additional, Slagboom, P. Eline, additional, Steinman, Gary, additional, Stephenson, Garth, additional, Sumathipala, Athula, additional, Sung, Joohon, additional, Tafforin, Carole, additional, Tarnoki, Adam D., additional, Tarnoki, David L., additional, Tosto, Valentina, additional, Tsibizova, Valentina, additional, Varjassy, Peter, additional, Vuoksimaa, Eero, additional, Willemsen, Gonneke, additional, Wong, Yen Ting, additional, de Geus, Eco, additional, de Vries, Lianne P., additional, van Dongen, Jenny, additional, and van de Weijer, Margot P., additional
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- 2022
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23. Twins and omics: the role of twin studies in multi-omics
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Hagenbeek, Fiona A., primary, van Dongen, Jenny, additional, Pool, René, additional, and Boomsma, Dorret I., additional
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- 2022
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24. Erratum: Genetic loci associated with heart rate variability and their effects on cardiac disease risk.
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Nolte, Ilja, Munoz, M, Tragante, Vinicius, Amare, Azmeraw, Jansen, Rick, Vaez, Ahmad, von der Heyde, Benedikt, Avery, Christy, Bis, Joshua, Dierckx, Bram, van Dongen, Jenny, Gogarten, Stephanie, Goyette, Philippe, Hernesniemi, Jussi, Huikari, Ville, Hwang, Shih-Jen, Jaju, Deepali, Kerr, Kathleen, Kluttig, Alexander, Krijthe, Bouwe, Kumar, Jitender, van der Laan, Sander, Lyytikäinen, Leo-Pekka, Maihofer, Adam, Minassian, Arpi, van der Most, Peter, Müller-Nurasyid, Martina, Nivard, Michel, Salvi, Erika, Stewart, James, Thayer, Julian, Verweij, Niek, Wong, Andrew, Zabaneh, Delilah, Zafarmand, Mohammad, Abdellaoui, Abdel, Albarwani, Sulayma, Albert, Christine, Alonso, Alvaro, Ashar, Foram, Auvinen, Juha, Axelsson, Tomas, Baker, Dewleen, de Bakker, Paul, Barcella, Matteo, Bayoumi, Riad, Bieringa, Rob, Boomsma, Dorret, Boucher, Gabrielle, Britton, Annie, Christophersen, Ingrid, Dietrich, Andrea, Ehret, George, Ellinor, Patrick, Eskola, Markku, Felix, Janine, Floras, John, Franco, Oscar, Friberg, Peter, Gademan, Maaike, Geyer, Mark, Giedraitis, Vilmantas, Hartman, Catharina, Hemerich, Daiane, Hofman, Albert, Hottenga, Jouke-Jan, Huikuri, Heikki, Hutri-Kähönen, Nina, Jouven, Xavier, Junttila, Juhani, Juonala, Markus, Kiviniemi, Antti, Kors, Jan, Kumari, Meena, Kuznetsova, Tatiana, Laurie, Cathy, Lefrandt, Joop, Li, Yong, Li, Yun, Liao, Duanping, Limacher, Marian, Lin, Henry, Lindgren, Cecilia, Lubitz, Steven, Mahajan, Anubha, McKnight, Barbara, Zu Schwabedissen, Henriette, Milaneschi, Yuri, Mononen, Nina, Morris, Andrew, Nalls, Mike, Navis, Gerjan, Neijts, Melanie, Nikus, Kjell, North, Kari, OConnor, Daniel, Ormel, Johan, Perz, Siegfried, Peters, Annette, and Psaty, Bruce
- Abstract
This corrects the article DOI: 10.1038/ncomms15805.
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- 2017
25. Genetic loci associated with heart rate variability and their effects on cardiac disease risk.
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Nolte, Ilja M, Munoz, M Loretto, Tragante, Vinicius, Amare, Azmeraw T, Jansen, Rick, Vaez, Ahmad, von der Heyde, Benedikt, Avery, Christy L, Bis, Joshua C, Dierckx, Bram, van Dongen, Jenny, Gogarten, Stephanie M, Goyette, Philippe, Hernesniemi, Jussi, Huikari, Ville, Hwang, Shih-Jen, Jaju, Deepali, Kerr, Kathleen F, Kluttig, Alexander, Krijthe, Bouwe P, Kumar, Jitender, van der Laan, Sander W, Lyytikäinen, Leo-Pekka, Maihofer, Adam X, Minassian, Arpi, van der Most, Peter J, Müller-Nurasyid, Martina, Nivard, Michel, Salvi, Erika, Stewart, James D, Thayer, Julian F, Verweij, Niek, Wong, Andrew, Zabaneh, Delilah, Zafarmand, Mohammad H, Abdellaoui, Abdel, Albarwani, Sulayma, Albert, Christine, Alonso, Alvaro, Ashar, Foram, Auvinen, Juha, Axelsson, Tomas, Baker, Dewleen G, de Bakker, Paul IW, Barcella, Matteo, Bayoumi, Riad, Bieringa, Rob J, Boomsma, Dorret, Boucher, Gabrielle, Britton, Annie R, Christophersen, Ingrid, Dietrich, Andrea, Ehret, George B, Ellinor, Patrick T, Eskola, Markku, Felix, Janine F, Floras, John S, Franco, Oscar H, Friberg, Peter, Gademan, Maaike GJ, Geyer, Mark A, Giedraitis, Vilmantas, Hartman, Catharina A, Hemerich, Daiane, Hofman, Albert, Hottenga, Jouke-Jan, Huikuri, Heikki, Hutri-Kähönen, Nina, Jouven, Xavier, Junttila, Juhani, Juonala, Markus, Kiviniemi, Antti M, Kors, Jan A, Kumari, Meena, Kuznetsova, Tatiana, Laurie, Cathy C, Lefrandt, Joop D, Li, Yong, Li, Yun, Liao, Duanping, Limacher, Marian C, Lin, Henry J, Lindgren, Cecilia M, Lubitz, Steven A, Mahajan, Anubha, McKnight, Barbara, Zu Schwabedissen, Henriette Meyer, Milaneschi, Yuri, Mononen, Nina, Morris, Andrew P, Nalls, Mike A, Navis, Gerjan, Neijts, Melanie, Nikus, Kjell, North, Kari E, O'Connor, Daniel T, Ormel, Johan, Perz, Siegfried, Peters, Annette, and Psaty, Bruce M
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Humans ,Heart Diseases ,Genetic Predisposition to Disease ,RGS Proteins ,Potassium Channels ,Muscle Proteins ,Risk Factors ,Cohort Studies ,Blood Pressure ,Heart Rate ,Polymorphism ,Single Nucleotide ,Quantitative Trait Loci ,European Continental Ancestry Group ,Genome-Wide Association Study ,Hyperpolarization-Activated Cyclic Nucleotide-Gated Channels ,Cardiovascular ,Genetics ,Heart Disease - Abstract
Reduced cardiac vagal control reflected in low heart rate variability (HRV) is associated with greater risks for cardiac morbidity and mortality. In two-stage meta-analyses of genome-wide association studies for three HRV traits in up to 53,174 individuals of European ancestry, we detect 17 genome-wide significant SNPs in eight loci. HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression quantitative trait loci (eQTLs) (influencing GNG11, RGS6 and NEO1), or are located in genes preferentially expressed in the sinoatrial node (GNG11, RGS6 and HCN4). Genetic risk scores account for 0.9 to 2.6% of the HRV variance. Significant genetic correlation is found for HRV with heart rate (-0.74g
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- 2017
26. A multi-omics data analysis workflow packaged as a FAIR Digital Object
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Niehues, Anna, primary, de Visser, Casper, additional, Hagenbeek, Fiona A, additional, Kulkarni, Purva, additional, Pool, René, additional, Karu, Naama, additional, Kindt, Alida S D, additional, Singh, Gurnoor, additional, Vermeiren, Robert R J M, additional, Boomsma, Dorret I, additional, van Dongen, Jenny, additional, ’t Hoen, Peter A C, additional, and van Gool, Alain J, additional
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- 2024
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27. New insights into the (epi)genetics of twinning
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van Dongen, Jenny, primary, Hubers, Nikki, additional, and Boomsma, Dorret I, additional
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- 2023
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28. Genome-wide association study meta-analysis of dizygotic twinning illuminates genetic regulation of female fecundity
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Mbarek, Hamdi, primary, Gordon, Scott D, additional, Duffy, David L, additional, Hubers, Nikki, additional, Mortlock, Sally, additional, Beck, Jeffrey J, additional, Hottenga, Jouke-Jan, additional, Pool, René, additional, Dolan, Conor V, additional, Actkins, Ky’Era V, additional, Gerring, Zachary F, additional, Van Dongen, Jenny, additional, Ehli, Erik A, additional, Iacono, William G, additional, Mcgue, Matt, additional, Chasman, Daniel I, additional, Gallagher, C Scott, additional, Schilit, Samantha L P, additional, Morton, Cynthia C, additional, Paré, Guillaume, additional, Willemsen, Gonneke, additional, Whiteman, David C, additional, Olsen, Catherine M, additional, Derom, Catherine, additional, Vlietinck, Robert, additional, Gudbjartsson, Daniel, additional, Cannon-Albright, Lisa, additional, Krapohl, Eva, additional, Plomin, Robert, additional, Magnusson, Patrik K E, additional, Pedersen, Nancy L, additional, Hysi, Pirro, additional, Mangino, Massimo, additional, Spector, Timothy D, additional, Palviainen, Teemu, additional, Milaneschi, Yuri, additional, Penninnx, Brenda W, additional, Campos, Adrian I, additional, Ong, Ken K, additional, Perry, John R B, additional, Lambalk, Cornelis B, additional, Kaprio, Jaakko, additional, Ólafsson, Ísleifur, additional, Duroure, Karine, additional, Revenu, Céline, additional, Rentería, Miguel E, additional, Yengo, Loic, additional, Davis, Lea, additional, Derks, Eske M, additional, Medland, Sarah E, additional, Stefansson, Hreinn, additional, Stefansson, Kari, additional, Del Bene, Filippo, additional, Reversade, Bruno, additional, Montgomery, Grant W, additional, Boomsma, Dorret I, additional, and Martin, Nicholas G, additional
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- 2023
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29. Trans-ancestry epigenome-wide association meta-analysis of DNA methylation with lifetime cannabis use
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Fang, Fang, primary, Quach, Bryan, additional, Lawrence, Kaitlyn G., additional, van Dongen, Jenny, additional, Marks, Jesse A., additional, Lundgren, Sara, additional, Lin, Mingkuan, additional, Odintsova, Veronika V., additional, Costeira, Ricardo, additional, Xu, Zongli, additional, Zhou, Linran, additional, Mandal, Meisha, additional, Xia, Yujing, additional, Vink, Jacqueline M., additional, Bierut, Laura J., additional, Ollikainen, Miina, additional, Taylor, Jack A., additional, Bell, Jordana T., additional, Kaprio, Jaakko, additional, Boomsma, Dorret I., additional, Xu, Ke, additional, Sandler, Dale P., additional, Hancock, Dana B., additional, and Johnson, Eric O., additional
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- 2023
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30. Validated inference of smoking habits from blood with a finite DNA methylation marker set
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BIOS Consortium, Maas, Silvana C. E., Vidaki, Athina, Wilson, Rory, Teumer, Alexander, Liu, Fan, van Meurs, Joyce B. J., Uitterlinden, André G., Boomsma, Dorret I., de Geus, Eco J. C., Willemsen, Gonneke, van Dongen, Jenny, van der Kallen, Carla J. H., Slagboom, P. Eline, Beekman, Marian, van Heemst, Diana, van den Berg, Leonard H., Duijts, Liesbeth, Jaddoe, Vincent W. V., Ladwig, Karl-Heinz, Kunze, Sonja, Peters, Annette, Ikram, M. Arfan, Grabe, Hans J., Felix, Janine F., Waldenberger, Melanie, Franco, Oscar H., Ghanbari, Mohsen, and Kayser, Manfred
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- 2019
31. Identical twins carry a persistent epigenetic signature of early genome programming
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van Dongen, Jenny, Gordon, Scott D., McRae, Allan F., Odintsova, Veronika V., Mbarek, Hamdi, Breeze, Charles E., Sugden, Karen, Lundgren, Sara, Castillo-Fernandez, Juan E., Hannon, Eilis, Moffitt, Terrie E., Hagenbeek, Fiona A., van Beijsterveldt, Catharina E. M., Jan Hottenga, Jouke, Tsai, Pei-Chien, Min, Josine L., Hemani, Gibran, Ehli, Erik A., Paul, Franziska, Stern, Claudio D., Heijmans, Bastiaan T., Slagboom, P. Eline, Daxinger, Lucia, van der Maarel, Silvère M., de Geus, Eco J. C., Willemsen, Gonneke, Montgomery, Grant W., Reversade, Bruno, Ollikainen, Miina, Kaprio, Jaakko, Spector, Tim D., Bell, Jordana T., Mill, Jonathan, Caspi, Avshalom, Martin, Nicholas G., and Boomsma, Dorret I.
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- 2021
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32. Validating biomarkers and models for epigenetic inference of alcohol consumption from blood
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Maas, Silvana C. E., Vidaki, Athina, Teumer, Alexander, Costeira, Ricardo, Wilson, Rory, van Dongen, Jenny, Beekman, Marian, Völker, Uwe, Grabe, Hans J., Kunze, Sonja, Ladwig, Karl-Heinz, van Meurs, Joyce B. J., Uitterlinden, André G., Voortman, Trudy, Boomsma, Dorret I., Slagboom, P. Eline, van Heemst, Diana, van der Kallen, Carla J. H., van den Berg, Leonard H., Waldenberger, Melanie, Völzke, Henry, Peters, Annette, Bell, Jordana T., Ikram, M. Arfan, Ghanbari, Mohsen, and Kayser, Manfred
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- 2021
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33. Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults
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Heijmans, Bastiaan T., ’t Hoen, Peter A.C., van Meurs, Joyce, Isaacs, Aaron, Jansen, Rick, Franke, Lude, Boomsma, Dorret I., Pool, René, van Dongen, Jenny, Hottenga, Jouke J., van Greevenbroek, Marleen M.J., Stehouwer, Coen D.A., van der Kallen, Carla J.H., Schalkwijk, Casper G., Wijmenga, Cisca, Zhernakova, Sasha, Tigchelaar, Ettje F., Slagboom, P. Eline, Beekman, Marian, Deelen, Joris, van Heemst, Diana, Veldink, Jan H., van den Berg, Leonard H., van Duijn, Cornelia M., Hofman, Bert A., Uitterlinden, André G., Jhamai, P. Mila, Verbiest, Michael, Suchiman, H. Eka D., Verkerk, Marijn, van der Breggen, Ruud, van Rooij, Jeroen, Lakenberg, Nico, Mei, Hailiang, van Iterson, Maarten, van Galen, Michiel, Bot, Jan, Zhernakova, Dasha V., Hof, Peter van ’t, Deelen, Patrick, Nooren, Irene, Moed, Matthijs, Vermaat, Martijn, Luijk, René, Bonder, Marc Jan, van Dijk, Freerk, Arindrarto, Wibowo, Kielbasa, Szymon M., Swertz, Morris A., van Zwet, Erik. W., Hoen, Peter-Bram ’t, Zilhão, Nuno R., Sugden, Karen, Hannon, Eilis J., Mill, Jonathan, Caspi, Avshalom, Agnew-Blais, Jessica, Arseneault, Louise, Corcoran, David L., Moffitt, Terrie E., Poulton, Richie, and Franke, Barbara
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- 2019
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34. Discordant monozygotic twin studies of epigenetic mechanisms in mental health
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van Dongen, Jenny, primary, Odintsova, Veronika V., additional, and Boomsma, Dorret I., additional
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- 2021
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35. Combining twin-family designs with measured genetic variants to study the causes of epigenetic variation
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Minică, Camelia C., primary, Neale, Michael C., additional, Boomsma, Dorret I., additional, and van Dongen, Jenny, additional
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- 2021
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36. Contributors
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Abramson, Michael J., primary, Armstrong, Nicola J., additional, Barrès, Romain, additional, Bell, Jordana T., additional, Boomsma, Dorret I., additional, Calais-Ferreira, Lucas, additional, Candler, T., additional, Cao, Weihua, additional, Christiansen, Colette, additional, Cortessis, Victoria K., additional, Cozen, Wendy, additional, van Dongen, Jenny, additional, Forgo, Bianka, additional, Gao, Wenjing, additional, Guo, Yuming, additional, Hernyes, Anita, additional, Hopper, John L., additional, Investigators, kConFab, additional, Jokkel, Zsofia, additional, Kim, Eunae, additional, Kim, Hakyung, additional, Kühnen, P., additional, Kurushima, Yuko, additional, Lam, Esther, additional, Lee, Soo Ji, additional, Li, Liming, additional, Li, Shuai, additional, Minică, Camelia C., additional, Neale, Michael C., additional, Odintsova, Veronika V., additional, Persely, Aliz, additional, Piroska, Marton, additional, Potier, Louis, additional, Prentice, A.M., additional, Scurrah, Katrina, additional, Silva, Mihiri J., additional, Silver, M.J., additional, Sørensen, Thorkild I.A., additional, Southey, Melissa C., additional, Stirzaker, Clare, additional, Sung, Joohon, additional, Szabo, Helga, additional, Szalontai, Laszlo, additional, Tarnoki, Adam Domonkos, additional, Tarnoki, David Laszlo, additional, Wu, Zhentian, additional, Xu, Rongbin, additional, and Ye, Zhoufeng, additional
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- 2021
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37. OTTERS:a powerful TWAS framework leveraging summary-level reference data
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Dai, Qile, Zhou, Geyu, Zhao, Hongyu, Võsa, Urmo, Franke, Lude, Battle, Alexis, Teumer, Alexander, Lehtimäki, Terho, Raitakari, Olli T., Esko, Tõnu, Agbessi, Mawussé, Ahsan, Habibul, Alves, Isabel, Andiappan, Anand Kumar, Arindrarto, Wibowo, Awadalla, Philip, Beutner, Frank, Jan Bonder, Marc, Boomsma, Dorret I., Christiansen, Mark W., Claringbould, Annique, Deelen, Patrick, Favé, Marie-Julie, Frayling, Timothy, Gharib, Sina A., Gibson, Greg, Heijmans, Bastiaan T., Hemani, Gibran, Jansen, Rick, Kähönen, Mika, Kalnapenkis, Anette, Kasela, Silva, Kettunen, Johannes, Kim, Yungil, Kirsten, Holger, Kovacs, Peter, Krohn, Knut, Kronberg, Jaanika, Kukushkina, Viktorija, Kutalik, Zoltan, Lee, Bernett, Loeffler, Markus, Marigorta, Urko M., Mei, Hailang, Milani, Lili, Montgomery, Grant W., Müller-Nurasyid, Martina, Nauck, Matthias, Nivard, Michel G., Penninx, Brenda, Perola, Markus, Pervjakova, Natalia, Pierce, Brandon L., Powell, Joseph, Prokisch, Holger, Psaty, Bruce M., Ripatti, Samuli, Rotzschke, Olaf, Rüeger, Sina, Saha, Ashis, Scholz, Markus, Schramm, Katharina, Seppälä, Ilkka, Slagboom, Eline P., Stehouwer, Coen D. A., Stumvoll, Michael, Sullivan, Patrick, ‘t Hoen, Peter A. C., Thiery, Joachim, Tong, Lin, Tönjes, Anke, van Dongen, Jenny, van Iterson, Maarten, van Meurs, Joyce, Veldink, Jan H., Verlouw, Joost, Visscher, Peter M., Völker, Uwe, Westra, Harm-Jan, Wijmenga, Cisca, Yaghootkar, Hanieh, Yang, Jian, Zeng, Biao, Zhang, Futao, Epstein, Michael P., Yang, Jingjing, Psychiatry, APH - Mental Health, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, APH - Digital Health, Biological Psychology, Amsterdam Reproduction & Development, APH - Methodology, APH - Personalized Medicine, Internal Medicine, Tampere University, Department of Clinical Chemistry, and Clinical Medicine
- Subjects
Multidisciplinary ,1182 Biochemistry, cell and molecular biology ,General Physics and Astronomy ,3111 Biomedicine ,General Chemistry ,Medical Genetics ,General Biochemistry, Genetics and Molecular Biology ,Medicinsk genetik - Abstract
Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies. Godkänd;2023;Nivå 0;2023-04-06 (hanlid);Funder: for more funders see the article https://doi.org/10.1038/s41467-023-36862-w
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- 2023
38. Integrative multi‐omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention‐Deficit/Hyperactivity Disorder.
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Hubers, Nikki, Hagenbeek, Fiona A., Pool, René, Déjean, Sébastien, Harms, Amy C., Roetman, Peter J., van Beijsterveldt, Catharina E. M., Fanos, Vassilios, Ehli, Erik A., Vermeiren, Robert R. J. M., Bartels, Meike, Hottenga, Jouke Jan, Hankemeier, Thomas, van Dongen, Jenny, and Boomsma, Dorret I.
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- 2024
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39. 75. PUTATIVE CAUSAL EFFECTS BETWEEN CIGARETTE SMOKING AND PERIPHERAL BLOOD DNA METHYLATION: A MENDELIAN RANDOMIZATION DIRECTION-OF-CAUSATION (MR-DOC) STUDY
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Singh, Madhurbain, primary, Dolan, Conor, additional, Lapato, Dana, additional, Hottenga, Jouke-Jan, additional, Pool, Rene, additional, Hemani, Gibran, additional, Min, Josine L., additional, Boomsma, Dorret, additional, de Geus, Eco J., additional, Maes, Hermine, additional, Verhulst, Brad, additional, van Dongen, Jenny, additional, and Neale, Michael, additional
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- 2023
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40. Integrative multi‐omics analysis of genomic, epigenomic, and metabolomics data leads to new insights for Attention‐Deficit/Hyperactivity Disorder
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Hubers, Nikki, primary, Hagenbeek, Fiona A., additional, Pool, René, additional, Déjean, Sébastien, additional, Harms, Amy C., additional, Roetman, Peter J., additional, van Beijsterveldt, Catharina E. M., additional, Fanos, Vassilios, additional, Ehli, Erik A., additional, Vermeiren, Robert R. J. M., additional, Bartels, Meike, additional, Hottenga, Jouke Jan, additional, Hankemeier, Thomas, additional, van Dongen, Jenny, additional, and Boomsma, Dorret I., additional
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- 2023
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41. The Co-Twin Control Design: Implementation and Methodological Considerations
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Gonggrijp, Bodine M. A., primary, van de Weijer, Steve G. A., additional, Bijleveld, Catrien C. J. H., additional, van Dongen, Jenny, additional, and Boomsma, Dorret I., additional
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- 2023
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42. DNA methylation age is associated with an altered hemostatic profile in a multiethnic meta-analysis
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Ward-Caviness, Cavin K., Huffman, Jennifer E., Everett, Karl, Germain, Marine, van Dongen, Jenny, Hill, W. David, Jhun, Min A., Brody, Jennifer A., Ghanbari, Mohsen, Du, Lei, Roetker, Nicholas S., de Vries, Paul S., Waldenberger, Melanie, Gieger, Christian, Wolf, Petra, Prokisch, Holger, Koenig, Wolfgang, O'Donnell, Christopher J., Levy, Daniel, Liu, Chunyu, Truong, Vinh, Wells, Philip S., Trégouët, David-Alexandre, Tang, Weihong, Morrison, Alanna C., Boerwinkle, Eric, Wiggins, Kerri L., McKnight, Barbara, Guo, Xiuqing, Psaty, Bruce M., Sotoodenia, Nona, Boomsma, Dorret I., Willemsen, Gonneke, Ligthart, Lannie, Deary, Ian J., Zhao, Wei, Ware, Erin B., Kardia, Sharon L.R., Van Meurs, Joyce B.J., Uitterlinden, Andre G., Franco, Oscar H., Eriksson, Per, Franco-Cereceda, Anders, Pankow, James S., Johnson, Andrew D., Gagnon, France, Morange, Pierre-Emmanuel, de Geus, Eco J.C., Starr, John M., Smith, Jennifer A., Dehghan, Abbas, Björck, Hanna M., Smith, Nicholas L., and Peters, Annette
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- 2018
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43. Circulating metabolites and general cognitive ability and dementia: Evidence from 11 cohort studies
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van der Lee, Sven J., Teunissen, Charlotte E., Pool, René, Shipley, Martin J., Teumer, Alexander, Chouraki, Vincent, Melo van Lent, Debora, Tynkkynen, Juho, Fischer, Krista, Hernesniemi, Jussi, Haller, Toomas, Singh-Manoux, Archana, Verhoeven, Aswin, Willemsen, Gonneke, de Leeuw, Francisca A., Wagner, Holger, van Dongen, Jenny, Hertel, Johannes, Budde, Kathrin, Willems van Dijk, Ko, Weinhold, Leonie, Ikram, M. Arfan, Pietzner, Maik, Perola, Markus, Wagner, Michael, Friedrich, Nele, Slagboom, P. Eline, Scheltens, Philip, Yang, Qiong, Gertzen, Robert E., Egert, Sarah, Li, Shuo, Hankemeier, Thomas, van Beijsterveldt, Catharina E.M., Vasan, Ramachandran S., Maier, Wolfgang, Peeters, Carel F.W., Jörgen Grabe, Hans, Ramirez, Alfredo, Seshadri, Sudha, Metspalu, Andres, Kivimäki, Mika, Salomaa, Veikko, Demirkan, Ayşe, Boomsma, Dorret I., van der Flier, Wiesje M., Amin, Najaf, and van Duijn, Cornelia M.
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- 2018
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44. A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object
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Niehues, Anna, primary, de Visser, Casper, additional, Hagenbeek, Fiona A., additional, Kulkarni, Purva, additional, Pool, Rene, additional, Karu, Naama, additional, Kindt, Alida S. D., additional, Singh, Gurnoor, additional, Vermeiren, Robert R. J. M., additional, Boomsma, Dorret I., additional, van Dongen, Jenny, additional, 't Hoen, Peter A. C., additional, and van Gool, Alain J., additional
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- 2023
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45. Handedness and 23 Early Life Characteristics in 37,495 Dutch Twins
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Odintsova, Veronika V., primary, van Dongen, Jenny, additional, van Beijsterveldt, Catharina E. M., additional, Ligthart, Lannie, additional, Willemsen, Gonneke, additional, de Geus, Eco J. C., additional, Dolan, Conor V., additional, and Boomsma, Dorret I., additional
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- 2023
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46. Polygenic Score for Dizygotic Twinning in Mothers of Spontaneously and Artificially Conceived Twins and Singletons
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Hubers, Nikki, primary, Page, Christian, additional, Mbarek, Hamdi, additional, Lambalk, Nils, additional, Ligthart, Lannie, additional, Pool, Rene, additional, Jan, Hottenga Jouke, additional, van, Dongen Jenny, additional, Haberg, Siri, additional, Ehli, Erik, additional, Harris, Jennifer, additional, Willemsen, Gonneke, additional, and Boomsma, Dorret, additional
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- 2023
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47. Epigenetics and twin studies
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van Dongen, Jenny, primary and Boomsma, Dorret I, additional
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- 2019
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48. Identification, Heritability, and Relation With Gene Expression of Novel DNA Methylation Loci for Blood Pressure
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Huang, Yisong, Ollikainen, Miina, Muniandy, Maheswary, Zhang, Tao, van Dongen, Jenny, Hao, Guang, van der Most, Peter J., Pan, Yue, Pervjakova, Natalia, Sun, Yan V., Hui, Qin, Lahti, Jari, Fraszczyk, Eliza, Lu, Xueling, Sun, Dianjianyi, Richard, Melissa A., Willemsen, Gonneke, Heikkila, Kauko, Mateo Leach, Irene, Mononen, Nina, Kähönen, Mika, Hurme, Mikko A., Raitakari, Olli T., Drake, Amanda J., Perola, Markus, Nuotio, Marja-Liisa, Huang, Yunfeng, Khulan, Batbayar, Räikkönen, Katri, Wolffenbuttel, Bruce H.R., Zhernakova, Alexandra, Fu, Jingyuan, Zhu, Haidong, Dong, Yanbin, van Vliet-Ostaptchouk, Jana V., Franke, Lude, Eriksson, Johan G., Fornage, Myriam, Milani, Lili, Lehtimäki, Terho, Vaccarino, Viola, Boomsma, Dorret I., van der Harst, Pim, de Geus, Eco J.C., Salomaa, Veikko, Li, Shengxu, Chen, Wei, Su, Shaoyong, Wilson, James, Snieder, Harold, Kaprio, Jaakko, and Wang, Xiaoling
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- 2020
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49. Childhood aggression and the co-occurrence of behavioural and emotional problems: results across ages 3–16 years from multiple raters in six cohorts in the EU-ACTION project
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Bartels, Meike, Hendriks, Anne, Mauri, Matteo, Krapohl, Eva, Whipp, Alyce, Bolhuis, Koen, Conde, Lucia Colodro, Luningham, Justin, Fung Ip, Hill, Hagenbeek, Fiona, Roetman, Peter, Gatej, Raluca, Lamers, Audri, Nivard, Michel, van Dongen, Jenny, Lu, Yi, Middeldorp, Christel, van Beijsterveldt, Toos, Vermeiren, Robert, Hankemeijer, Thomas, Kluft, Cees, Medland, Sarah, Lundström, Sebastian, Rose, Richard, Pulkkinen, Lea, Vuoksimaa, Eero, Korhonen, Tellervo, Martin, Nicholas G., Lubke, Gitta, Finkenauer, Catrin, Fanos, Vassilios, Tiemeier, Henning, Lichtenstein, Paul, Plomin, Robert, Kaprio, Jaakko, and Boomsma, Dorret I.
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- 2018
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50. Brain reward responses to food stimuli among female monozygotic twins discordant for BMI
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Doornweerd, Stieneke, De Geus, Eco J., Barkhof, Frederik, Van Bloemendaal, Liselotte, Boomsma, Dorret I., Van Dongen, Jenny, Drent, Madeleine L., Willemsen, Gonneke, Veltman, Dick J., and IJzerman, Richard G.
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- 2018
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