Author: "Prokisch, H. (Holger)" - Searchworks@Jio Institute Digital Library Search Results

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1. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Author: Vosa, U. (Urmo), Claringbould, A. (Annique), Westra, H.-J. (Harm-Jan), Bonder, M. J. (Marc Jan), Deelen, P. (Patrick), Zeng, B. (Biao), Kirsten, H. (Holger), Saha, A. (Ashis), Kreuzhuber, R. (Roman), Yazar, S. (Seyhan), Brugge, H. (Harm), Oelen, R. (Roy), de Vries, D. H. (Dylan H.), van der Wijst, M. G. (Monique G. P.), Kasela, S. (Silva), Pervjakova, N. (Natalia), Alves, I. (Isabel), Fave, M.-J. (Marie-Julie), Agbessi, M. (Mawusse), Christiansen, M. W. (Mark W.), Jansen, R. (Rick), Seppala, I. (Ilkka), Tong, L. (Lin), Teumer, A. (Alexander), Schramm, K. (Katharina), Hemani, G. (Gibran), Verlouw, J. (Joost), Yaghootkar, H. (Hanieh), Flitman, R. S. (Reyhan Sonmez), Brown, A. (Andrew), Kukushkina, V. (Viktorija), Kalnapenkis, A. (Anette), Rueger, S. (Sina), Porcu, E. (Eleonora), Kronberg, J. (Jaanika), Kettunen, J. (Johannes), Lee, B. (Bernett), Zhang, F. (Futao), Qi, T. (Ting), Hernandez, J. A. (Jose Alquicira), Arindrarto, W. (Wibowo), Beutner, F. (Frank), Dmitrieva, J. (Julia), Elansary, M. (Mahmoud), Fairfax, B. P. (Benjamin P.), Georges, M. (Michel), Heijmans, B. T. (Bastiaan T.), Hewitt, A. W. (Alex W.), Kahonen, M. (Mika), Kim, Y. (Yungil), Knight, J. C. (Julian C.), Kovacs, P. (Peter), Krohn, K. (Knut), Li, S. (Shuang), Loeffler, M. (Markus), Marigorta, U. M. (Urko M.), Mei, H. (Hailang), Momozawa, Y. (Yukihide), Mueller-Nurasyid, M. (Martina), Nauck, M. (Matthias), Nivard, M. G. (Michel G.), Penninx, B. W. (Brenda W. J. H.), Pritchard, J. K. (Jonathan K.), Raitakari, O. T. (Olli T.), Rotzschke, O. (Olaf), Slagboom, E. P. (Eline P.), Stehouwer, C. D. (Coen D. A.), Stumvoll, M. (Michael), Sullivan, P. (Patrick), Thiery, J. (Joachim), Tonjes, A. (Anke), van Dongen, J. (Jenny), van Iterson, M. (Maarten), Veldink, J. H. (Jan H.), Voelker, U. (Uwe), Warmerdam, R. (Robert), Wijmenga, C. (Cisca), Swertz, M. (Morris), Andiappan, A. (Anand), Montgomery, G. W. (Grant W.), Ripatti, S. (Samuli), Perola, M. (Markus), Kutalik, Z. (Zoltan), Dermitzakis, E. (Emmanouil), Bergmann, S. (Sven), Frayling, T. (Timothy), van Meurs, J. (Joyce), Prokisch, H. (Holger), Ahsan, H. (Habibul), Pierce, B. L. (Brandon L.), Lehtimaki, T. (Terho), Boomsma, D. I. (Dorret, I), Psaty, B. M. (Bruce M.), Gharib, S. A. (Sina A.), Awadalla, P. (Philip), Milani, L. (Lili), Ouwehand, W. H. (Willem H.), Downes, K. (Kate), Stegle, O. (Oliver), Battle, A. (Alexis), Visscher, P. M. (Peter M.), Yang, J. (Jian), Scholz, M. (Markus), Powell, J. (Joseph), Gibson, G. (Greg), Esko, T. (Tonu), and Franke, L. (Lude)
Abstract: Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium. We detected cis-eQTL for 88% of genes, and these were replicable in numerous tissues. Distal trans-eQTL (detected for 37% of 10,317 trait-associated variants tested) showed lower replication rates, partially due to low replication power and confounding by cell type composition. However, replication analyses in single-cell RNA-seq data prioritized intracellular trans-eQTL. Trans-eQTL exerted their effects via several mechanisms, primarily through regulation by transcription factors. Expression of 13% of the genes correlated with polygenic scores for 1,263 phenotypes, pinpointing potential drivers for those traits. In summary, this work represents a large eQTL resource, and its results serve as a starting point for in-depth interpretation of complex phenotypes.
Published: 2021

2. Meta-analyses identify DNA methylation associated with kidney function and damage

Author: Schlosser, P. (Pascal), Tin, A. (Adrienne), Matias-Garcia, P. R. (Pamela R.), Thio, C. H. (Chris H. L.), Joehanes, R. (Roby), Liu, H. (Hongbo), Weihs, A. (Antoine), Yu, Z. (Zhi), Hoppmann, A. (Anselm), Grundner-Culemann, F. (Franziska), Min, J. L. (Josine L.), Adeyemo, A. A. (Adebowale A.), Agyemang, C. (Charles), Arnlov, J. (Johan), Aziz, N. A. (Nasir A.), Baccarelli, A. (Andrea), Bochud, M. (Murielle), Brenner, H. (Hermann), Breteler, M. M. (Monique M. B.), Carmeli, C. (Cristian), Chaker, L. (Layal), Chambers, J. C. (John C.), Cole, S. A. (Shelley A.), Coresh, J. (Josef), Corre, T. (Tanguy), Correa, A. (Adolfo), Cox, S. R. (Simon R.), de Klein, N. (Niek), Delgado, G. E. (Graciela E.), Domingo-Relloso, A. (Arce), Eckardt, K.-U. (Kai-Uwe), Ekici, A. B. (Arif B.), Endlich, K. (Karlhans), Evans, K. L. (Kathryn L.), Floyd, J. S. (James S.), Fornage, M. (Myriam), Franke, L. (Lude), Fraszczyk, E. (Eliza), Gao, X. (Xu), Gao, X. (Xin), Ghanbari, M. (Mohsen), Ghasemi, S. (Sahar), Gieger, C. (Christian), Greenland, P. (Philip), Grove, M. L. (Megan L.), Harris, S. E. (Sarah E.), Hemani, G. (Gibran), Henneman, P. (Peter), Herder, C. (Christian), Horvath, S. (Steve), Hou, L. (Lifang), Hurme, M. A. (Mikko A.), Hwang, S.-J. (Shih-Jen), Järvelin, M.-R. (Marjo-Riitta), Kardia, S. L. (Sharon L. R.), Kasela, S. (Silva), Kleber, M. E. (Marcus E.), Koenig, W. (Wolfgang), Kooner, J. S. (Jaspal S.), Kramer, H. (Holly), Kronenberg, F. (Florian), Kuhnel, B. (Brigitte), Lehtimaki, T. (Terho), Lind, L. (Lars), Liu, D. (Dan), Liu, Y. (Yongmei), Lloyd-Jones, D. M. (Donald M.), Lohman, K. (Kurt), Lorkowski, S. (Stefan), Lu, A. T. (Ake T.), Marioni, R. E. (Riccardo E.), Marz, W. (Winfried), McCartney, D. L. (Daniel L.), Meeks, K. A. (Karlijn A. C.), Milani, L. (Lili), Mishra, P. P. (Pashupati P.), Nauck, M. (Matthias), Navas-Acien, A. (Ana), Nowak, C. (Christoph), Peters, A. (Annette), Prokisch, H. (Holger), Psaty, B. M. (Bruce M.), Raitakari, O. T. (Olli T.), Ratliff, S. M. (Scott M.), Reiner, A. P. (Alex P.), Rosas, S. E. (Sylvia E.), Schottker, B. (Ben), Schwartz, J. (Joel), Sedaghat, S. (Sanaz), Smith, J. A. (Jennifer A.), Sotoodehnia, N. (Nona), Stocker, H. R. (Hannah R.), Stringhini, S. (Silvia), Sundstrom, J. (Johan), Swenson, B. R. (Brenton R.), Tellez-Plaza, M. (Maria), van Meurs, J. B. (Joyce B. J.), van Vliet-Ostaptchouk, J. V. (Jana V.), Venema, A. (Andrea), Verweij, N. (Niek), Walker, R. M. (Rosie M.), Wielscher, M. (Matthias), Winkelmann, J. (Juliane), Wolffenbuttel, B. H. (Bruce H. R.), Zhao, W. (Wei), Zheng, Y. (Yinan), Loh, M. (Marie), Snieder, H. (Harold), Levy, D. (Daniel), Waldenberger, M. (Melanie), Susztak, K. (Katalin), Kottgen, A. (Anna), Teumer, A. (Alexander), Schlosser, P. (Pascal), Tin, A. (Adrienne), Matias-Garcia, P. R. (Pamela R.), Thio, C. H. (Chris H. L.), Joehanes, R. (Roby), Liu, H. (Hongbo), Weihs, A. (Antoine), Yu, Z. (Zhi), Hoppmann, A. (Anselm), Grundner-Culemann, F. (Franziska), Min, J. L. (Josine L.), Adeyemo, A. A. (Adebowale A.), Agyemang, C. (Charles), Arnlov, J. (Johan), Aziz, N. A. (Nasir A.), Baccarelli, A. (Andrea), Bochud, M. (Murielle), Brenner, H. (Hermann), Breteler, M. M. (Monique M. B.), Carmeli, C. (Cristian), Chaker, L. (Layal), Chambers, J. C. (John C.), Cole, S. A. (Shelley A.), Coresh, J. (Josef), Corre, T. (Tanguy), Correa, A. (Adolfo), Cox, S. R. (Simon R.), de Klein, N. (Niek), Delgado, G. E. (Graciela E.), Domingo-Relloso, A. (Arce), Eckardt, K.-U. (Kai-Uwe), Ekici, A. B. (Arif B.), Endlich, K. (Karlhans), Evans, K. L. (Kathryn L.), Floyd, J. S. (James S.), Fornage, M. (Myriam), Franke, L. (Lude), Fraszczyk, E. (Eliza), Gao, X. (Xu), Gao, X. (Xin), Ghanbari, M. (Mohsen), Ghasemi, S. (Sahar), Gieger, C. (Christian), Greenland, P. (Philip), Grove, M. L. (Megan L.), Harris, S. E. (Sarah E.), Hemani, G. (Gibran), Henneman, P. (Peter), Herder, C. (Christian), Horvath, S. (Steve), Hou, L. (Lifang), Hurme, M. A. (Mikko A.), Hwang, S.-J. (Shih-Jen), Järvelin, M.-R. (Marjo-Riitta), Kardia, S. L. (Sharon L. R.), Kasela, S. (Silva), Kleber, M. E. (Marcus E.), Koenig, W. (Wolfgang), Kooner, J. S. (Jaspal S.), Kramer, H. (Holly), Kronenberg, F. (Florian), Kuhnel, B. (Brigitte), Lehtimaki, T. (Terho), Lind, L. (Lars), Liu, D. (Dan), Liu, Y. (Yongmei), Lloyd-Jones, D. M. (Donald M.), Lohman, K. (Kurt), Lorkowski, S. (Stefan), Lu, A. T. (Ake T.), Marioni, R. E. (Riccardo E.), Marz, W. (Winfried), McCartney, D. L. (Daniel L.), Meeks, K. A. (Karlijn A. C.), Milani, L. (Lili), Mishra, P. P. (Pashupati P.), Nauck, M. (Matthias), Navas-Acien, A. (Ana), Nowak, C. (Christoph), Peters, A. (Annette), Prokisch, H. (Holger), Psaty, B. M. (Bruce M.), Raitakari, O. T. (Olli T.), Ratliff, S. M. (Scott M.), Reiner, A. P. (Alex P.), Rosas, S. E. (Sylvia E.), Schottker, B. (Ben), Schwartz, J. (Joel), Sedaghat, S. (Sanaz), Smith, J. A. (Jennifer A.), Sotoodehnia, N. (Nona), Stocker, H. R. (Hannah R.), Stringhini, S. (Silvia), Sundstrom, J. (Johan), Swenson, B. R. (Brenton R.), Tellez-Plaza, M. (Maria), van Meurs, J. B. (Joyce B. J.), van Vliet-Ostaptchouk, J. V. (Jana V.), Venema, A. (Andrea), Verweij, N. (Niek), Walker, R. M. (Rosie M.), Wielscher, M. (Matthias), Winkelmann, J. (Juliane), Wolffenbuttel, B. H. (Bruce H. R.), Zhao, W. (Wei), Zheng, Y. (Yinan), Loh, M. (Marie), Snieder, H. (Harold), Levy, D. (Daniel), Waldenberger, M. (Melanie), Susztak, K. (Katalin), Kottgen, A. (Anna), and Teumer, A. (Alexander)
Abstract: Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. Associations of DNA methylation with kidney function, such as CpGs at JAZF1, PELI1 and CHD2 were validated in kidney tissue. Methylation at PHRF1, LDB2, CSRNP1 and IRF5 indicated causal effects on kidney function. Enrichment analyses revealed pathways related to hemostasis and blood cell migration for estimated glomerular filtration rate, and immune cell activation and response for urinary albumin-to-creatinineratio-associated CpGs.
Published: 2021

3. DNA methylation and lipid metabolism:an EWAS of 226 metabolic measures

Author: Gomez-Alonso, M. d. (Monica del C.), Kretschmer, A. (Anja), Wilson, R. (Rory), Pfeiffer, L. (Liliane), Karhunen, V. (Ville), Seppala, I. (Ilkka), Zhang, W. (Weihua), Mittelstrass, K. (Kirstin), Wahl, S. (Simone), Matias-Garcia, P. R. (Pamela R.), Prokisch, H. (Holger), Horn, S. (Sacha), Meitinger, T. (Thomas), Serrano-Garcia, L. R. (Luis R.), Sebert, S. (Sylvain), Raitakari, O. (Olli), Loh, M. (Marie), Rathmann, W. (Wolfgang), Mueller-Nurasyid, M. (Martina), Herder, C. (Christian), Roden, M. (Michael), Hurme, M. (Mikko), Jarvelin, M.-R. (Marjo-Riitta), Ala-Korpela, M. (Mika), Kooner, J. S. (Jaspal S.), Peters, A. (Annette), Lehtimaki, T. (Terho), Chambers, J. C. (John C.), Gieger, C. (Christian), Kettunen, J. (Johannes), Waldenberger, M. (Melanie), Gomez-Alonso, M. d. (Monica del C.), Kretschmer, A. (Anja), Wilson, R. (Rory), Pfeiffer, L. (Liliane), Karhunen, V. (Ville), Seppala, I. (Ilkka), Zhang, W. (Weihua), Mittelstrass, K. (Kirstin), Wahl, S. (Simone), Matias-Garcia, P. R. (Pamela R.), Prokisch, H. (Holger), Horn, S. (Sacha), Meitinger, T. (Thomas), Serrano-Garcia, L. R. (Luis R.), Sebert, S. (Sylvain), Raitakari, O. (Olli), Loh, M. (Marie), Rathmann, W. (Wolfgang), Mueller-Nurasyid, M. (Martina), Herder, C. (Christian), Roden, M. (Michael), Hurme, M. (Mikko), Jarvelin, M.-R. (Marjo-Riitta), Ala-Korpela, M. (Mika), Kooner, J. S. (Jaspal S.), Peters, A. (Annette), Lehtimaki, T. (Terho), Chambers, J. C. (John C.), Gieger, C. (Christian), Kettunen, J. (Johannes), and Waldenberger, M. (Melanie)
Abstract: Background: The discovery of robust and trans-ethnically replicated DNA methylation markers of metabolic phenotypes, has hinted at a potential role of epigenetic mechanisms in lipid metabolism. However, DNA methylation and the lipid compositions and lipid concentrations of lipoprotein sizes have been scarcely studied. Here, we present an epigenome-wide association study (EWAS) (N = 5414 total) of mostly lipid-related metabolic measures, including a fine profiling of lipoproteins. As lipoproteins are the main players in the different stages of lipid metabolism, examination of epigenetic markers of detailed lipoprotein features might improve the diagnosis, prognosis, and treatment of metabolic disturbances. Results: We conducted an EWAS of leukocyte DNA methylation and 226 metabolic measurements determined by nuclear magnetic resonance spectroscopy in the population-based KORA F4 study (N = 1662) and replicated the results in the LOLIPOP, NFBC1966, and YFS cohorts (N = 3752). Follow-up analyses in the discovery cohort included investigations into gene transcripts, metabolic-measure ratios for pathway analysis, and disease endpoints. We identified 161 associations (p value < 4.7 × 10⁻¹⁰), covering 16 CpG sites at 11 loci and 57 metabolic measures. Identified metabolic measures were primarily medium and small lipoproteins, and fatty acids. For apolipoprotein B-containing lipoproteins, the associations mainly involved triglyceride composition and concentrations of cholesterol esters, triglycerides, free cholesterol, and phospholipids. All associations for HDL lipoproteins involved triglyceride measures only. Associated metabolic measure ratios, proxies of enzymatic activity, highlight amino acid, glucose, and lipid pathways as being potentially epigenetically implicated. Five CpG sites in four genes were associated with differential expression of transcripts in blood or adipose tissue. CpG sites in ABCG1 and PHGDH showed associations with metabolic measures
Published: 2021

4. Smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic traits

Author: Maas, S.C.E., Mens, M.M.J., Kuhnel, B. (Brigitte), Meurs, J.B.J. (Joyce) van, Uitterlinden, A.G. (André), Peters, A. (Annette), Prokisch, H. (Holger), Herder, C. (Christian), Grallert, H. (Harald), Kunze, S., Waldenberger, M. (Melanie), Kavousi, M. (Maryam), Kayser, M.H. (Manfred), Ghanbari, M. (Mohsen), Maas, S.C.E., Mens, M.M.J., Kuhnel, B. (Brigitte), Meurs, J.B.J. (Joyce) van, Uitterlinden, A.G. (André), Peters, A. (Annette), Prokisch, H. (Holger), Herder, C. (Christian), Grallert, H. (Harald), Kunze, S., Waldenberger, M. (Melanie), Kavousi, M. (Maryam), Kayser, M.H. (Manfred), and Ghanbari, M. (Mohsen)
Abstract: Background: Tobacco smoking is a well-known modifable risk factor for many chronic diseases, including cardiovascular disease (CVD). One of the proposed underlying mechanism linking smoking to disease is via epigenetic modifcations, which could afect the expression of disease-associated genes. Here, we conducted a three-way association study to identify the relationship between smoking-related changes in DNA methylation and gene expression and their associations with cardio-metabolic traits. Results: We selected 2549 CpG sites and 443 gene expression probes associated with current versus never smokers, from the largest epigenome-wide association study and transcriptome-wide association study to date. We examined three-way associations, including CpG versus gene expression, cardio-metabolic trait versus CpG, and cardio-metabolic trait versus gene expression, in the Rotterdam study. Subsequently, we replicated our fndings in The Cooperative Health Research in the Region of Augsburg (KORA) study. After correction for multiple testing, we identifed both cis- and trans-expression quantitative trait methylation (eQTM) associations in blood. Specifcally, we found 1224 smoking-related CpGs associated with at least one of the 443 gene expression probes, and 200 smoking-related gene expression probes to be associated with at least one of the 2549 CpGs. Out of these, 109 CpGs and 27 genes were associated with at least one cardio-metabolic trait in the Rotterdam Study. We were able to replicate the associations with cardio-metabolic traits of 26 CpGs and 19 genes in the KORA study. Furthermore, we identifed a three-way association of triglycerides with two CpGs and two genes (GZMA; CLDND1), and BMI with six CpGs and two genes (PID1; LRRN3). Finally, our results revealed the mediation efect of cg03636183 (F2RL3), cg06096336 (PSMD1), cg13708645 (KDM2B), and cg17287155 (AHRR) within the association between smoking and LRRN3 expression. Conclusions: Our study indicates that smoking
Published: 2020
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5. Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

Author: Porcu, E. (Eleonora), Rueger, S. (Sina), Lepik, K. (Kaido), Agbessi, M. (Mawusse), Ahsan, H. (Habibul), Alves, I. (Isabel), Andiappan, A. (Anand), Arindrarto, W. (Wibowo), Awadalla, P. (Philip), Battle, A. (Alexis), Beutner, F. (Frank), Bonder, M. J. (Marc Jan), Boomsma, D. (Dorret), Christiansen, M. (Mark), Claringbould, A. (Annique), Deelen, P. (Patrick), Esko, T. (Tonu), Fave, M.-J. (Marie-Julie), Franke, L. (Lude), Frayling, T. (Timothy), Gharib, S. A. (Sina A.), Gibson, G. (Gregory), Heijmans, B. T. (Bastiaan T.), Hemani, G. (Gibran), Jansen, R. (Rick), Kahonen, M. (Mika), Kalnapenkis, A. (Anette), Kasela, S. (Silva), Kettunen, J. (Johannes), Kim, Y. (Yungil), Kirsten, H. (Holger), Kovacs, P. (Peter), Krohn, K. (Knut), Kronberg-Guzman, J. (Jaanika), Kukushkina, V. (Viktorija), Lee, B. (Bernett), Lehtimaki, T. (Terho), Loeffler, M. (Markus), Marigorta, U. M. (Urko M.), Mei, H. (Hailang), Milani, L. (Lili), Montgomery, G. W. (Grant W.), Mueler-Nurasyid, M. (Martina), Nauck, M. (Matthias), Nivard, M. (Michel), Penninx, B. (Brenda), Perola, M. (Markus), Pervjakova, N. (Natalia), Pierce, B. L. (Brandon L.), Powell, J. (Joseph), Prokisch, H. (Holger), Psaty, B. M. (Bruce M.), Raitakari, O. T. (Olli T.), Ripatti, S. (Samuli), Rotzschke, O. (Olaf), Saha, A. (Ashis), Scholz, M. (Markus), Schramm, K. (Katharina), Seppala, I. (Ilkka), Slagboom, E. P. (Eline P.), Stehouwer, C. D. (Coen D. A.), Stumvoll, M. (Michael), Sullivan, P. (Patrick), Teumer, A. (Alexander), Thiery, J. (Joachim), Tong, L. (Lin), Tonjes, A. (Anke), van Dongen, J. (Jenny), van Iterson, M. (Maarten), van Meurs, J. (Joyce), Veldink, J. H. (Jan H.), Verlouw, J. (Joost), Visscher, P. M. (Peter M.), Volker, U. (Uwe), Vosa, U. (Urmo), Westra, H.-J. (Harm-Jan), Wijmenga, C. (Cisca), Yaghootkar, H. (Hanieh), Yang, J. (Jian), Zeng, B. (Biao), Zhang, F. (Futao), Beekman, M. (Marian), Boomsma, D. I. (Dorret I.), Bot, J. (Jan), Deelen, J. (Joris), Hofman, B. A. (Bert A.), Hottenga, J. J. (Jouke J.), Isaacs, A. (Aaron), Jhamai, P. M. (P. Mila), Kielbasa, S. M. (Szymon M.), Lakenberg, N. (Nico), Luijk, R. (Rene), Mei, H. (Hailiang), Moed, M. (Matthijs), Nooren, I. (Irene), Pool, R. (Rene), Schalkwijk, C. G. (Casper G.), Slagboom, P. E. (P. Eline), Suchiman, H. E. (H. Eka D.), Swertz, M. A. (Morris A.), Tigchelaar, E. F. (Ettje F.), Uitterlinden, A. G. (Andre G.), van den Berg, L. H. (Leonard H.), van der Breggen, R. (Ruud), van der Kallen, C. J. (Carla J. H.), van Dijk, F. (Freerk), van Duijn, C. M. (Cornelia M.), van Galen, M. (Michiel), van Greevenbroek, M. M. (Marleen M. J.), van Heemst, D. (Diana), van Rooij, J. (Jeroen), Van't Hof, P. (Peter), van Zwet, E. W. (Erik. W.), Vermaat, M. (Martijn), Verbiest, M. (Michael), Verkerk, M. (Marijn), Zhernakova, D. V. (Dasha V.), Zhernakova, S. (Sasha), Santoni, F. A. (Federico A.), Reymond, A. (Alexandre), and Kutalik, Z. (Zoltan)
Abstract: Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, but their biological interpretation often remains unclear. Most of these variants overlap with expression QTLs, indicating their potential involvement in regulation of gene expression. Here, we propose a transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) that uses multiple SNPs as instruments and multiple gene expression traits as exposures, simultaneously. Applied to 43 human phenotypes, it uncovers 3,913 putatively causal gene–trait associations, 36% of which have no genome-wide significant SNP nearby in previous GWAS. Using independent association summary statistics, we find that the majority of these loci were missed by GWAS due to power issues. Noteworthy among these links is educational attainment-associated BSCL2, known to carry mutations leading to a Mendelian form of encephalopathy. We also find pleiotropic causal effects suggestive of mechanistic connections. TWMR better accounts for pleiotropy and has the potential to identify biological mechanisms underlying complex traits.
Published: 2019

6. GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI

Author: Alves, A. C. (Alexessander Couto), De Silva, N. M. (N. Maneka G.), Karhunen, V. (Ville), Sovio, U. (Ulla), Das, S. (Shikta), Taal, H. R. (H. Rob), Warrington, N. M. (Nicole M.), Lewin, A. M. (Alexandra M.), Kaakinen, M. (Marika), Cousminer, D. L. (Diana L.), Thiering, E. (Elisabeth), Timpson, N. J. (Nicholas J.), Bond, T. A. (Tom A.), Lowry, E. (Estelle), Brown, C. D. (Christopher D.), Estivill, X. (Xavier), Lindi, V. (Virpi), Bradfield, J. P. (Jonathan P.), Geller, F. (Frank), Speed, D. (Doug), Coin, L. J. (Lachlan J. M.), Loh, M. (Marie), Barton, S. J. (Sheila J.), Beilin, L. J. (Lawrence J.), Bisgaard, H. (Hans), Bonnelykke, K. (Klaus), Alili, R. (Rohia), Hatoum, I. J. (Ida J.), Schramm, K. (Katharina), Cartwright, R. (Rufus), Charles, M.-A. (Marie-Aline), Salerno, V. (Vincenzo), Clement, K. (Karine), Claringbould, A. A. (Annique A. J.), van Duijn, C. M. (Cornelia M.), Moltchanova, E. (Elena), Eriksson, J. G. (Johan G.), Elks, C. (Cathy), Feenstra, B. (Bjarke), Flexeder, C. (Claudia), Franks, S. (Stephen), Frayling, T. M. (Timothy M.), Freathy, R. M. (Rachel M.), Elliott, P. (Paul), Widen, E. (Elisabeth), Hakonarson, H. (Hakon), Hattersley, A. T. (Andrew T.), Rodriguez, A. (Alina), Banterle, M. (Marco), Heinrich, J. (Joachim), Heude, B. (Barbara), Holloway, J. W. (John W.), Hofman, A. (Albert), Hypponen, E. (Elina), Inskip, H. (Hazel), Kaplan, L. M. (Lee M.), Hedman, A. K. (Asa K.), Läärä, E. (Esa), Prokisch, H. (Holger), Grallert, H. (Harald), Lakka, T. A. (Timo A.), Lawlor, D. A. (Debbie A.), Melbye, M. (Mads), Ahluwalia, T. S. (Tarunveer S.), Marinelli, M. (Marcella), Millwood, I. Y. (Iona Y.), Palmer, L. J. (Lyle J.), Pennell, C. E. (Craig E.), Perry, J. R. (John R.), Ring, S. M. (Susan M.), Savolainen, M. J. (Markku J.), Rivadeneira, F. (Fernando), Standl, M. (Marie), Sunyer, J. (Jordi), Tiesler, C. M. (Carla M. T.), Uitterlinden, A. G. (Andre G.), Schierding, W. (William), O'Sullivan, J. M. (Justin M.), Prokopenko, I. (Inga), Herzig, K.-H. (Karl-Heinz), Smith, G. D. (George Davey), O'Reilly, P. (Paul), Felix, J. F. (Janine F.), Buxton, J. L. (Jessica L.), Blakemore, A. I. (Alexandra I. F.), Ong, K. K. (Ken K.), Jaddoe, V. W. (Vincent W. V.), Grant, S. F. (Struan F. A.), Sebert, S. (Sylvain), McCarthy, M. I. (Mark I.), Jarvelin, M.-R. (Marjo-Riitta), Alves, A. C. (Alexessander Couto), De Silva, N. M. (N. Maneka G.), Karhunen, V. (Ville), Sovio, U. (Ulla), Das, S. (Shikta), Taal, H. R. (H. Rob), Warrington, N. M. (Nicole M.), Lewin, A. M. (Alexandra M.), Kaakinen, M. (Marika), Cousminer, D. L. (Diana L.), Thiering, E. (Elisabeth), Timpson, N. J. (Nicholas J.), Bond, T. A. (Tom A.), Lowry, E. (Estelle), Brown, C. D. (Christopher D.), Estivill, X. (Xavier), Lindi, V. (Virpi), Bradfield, J. P. (Jonathan P.), Geller, F. (Frank), Speed, D. (Doug), Coin, L. J. (Lachlan J. M.), Loh, M. (Marie), Barton, S. J. (Sheila J.), Beilin, L. J. (Lawrence J.), Bisgaard, H. (Hans), Bonnelykke, K. (Klaus), Alili, R. (Rohia), Hatoum, I. J. (Ida J.), Schramm, K. (Katharina), Cartwright, R. (Rufus), Charles, M.-A. (Marie-Aline), Salerno, V. (Vincenzo), Clement, K. (Karine), Claringbould, A. A. (Annique A. J.), van Duijn, C. M. (Cornelia M.), Moltchanova, E. (Elena), Eriksson, J. G. (Johan G.), Elks, C. (Cathy), Feenstra, B. (Bjarke), Flexeder, C. (Claudia), Franks, S. (Stephen), Frayling, T. M. (Timothy M.), Freathy, R. M. (Rachel M.), Elliott, P. (Paul), Widen, E. (Elisabeth), Hakonarson, H. (Hakon), Hattersley, A. T. (Andrew T.), Rodriguez, A. (Alina), Banterle, M. (Marco), Heinrich, J. (Joachim), Heude, B. (Barbara), Holloway, J. W. (John W.), Hofman, A. (Albert), Hypponen, E. (Elina), Inskip, H. (Hazel), Kaplan, L. M. (Lee M.), Hedman, A. K. (Asa K.), Läärä, E. (Esa), Prokisch, H. (Holger), Grallert, H. (Harald), Lakka, T. A. (Timo A.), Lawlor, D. A. (Debbie A.), Melbye, M. (Mads), Ahluwalia, T. S. (Tarunveer S.), Marinelli, M. (Marcella), Millwood, I. Y. (Iona Y.), Palmer, L. J. (Lyle J.), Pennell, C. E. (Craig E.), Perry, J. R. (John R.), Ring, S. M. (Susan M.), Savolainen, M. J. (Markku J.), Rivadeneira, F. (Fernando), Standl, M. (Marie), Sunyer, J. (Jordi), Tiesler, C. M. (Carla M. T.), Uitterlinden, A. G. (Andre G.), Schierding, W. (William), O'Sullivan, J. M. (Justin M.), Prokopenko, I. (Inga), Herzig, K.-H. (Karl-Heinz), Smith, G. D. (George Davey), O'Reilly, P. (Paul), Felix, J. F. (Janine F.), Buxton, J. L. (Jessica L.), Blakemore, A. I. (Alexandra I. F.), Ong, K. K. (Ken K.), Jaddoe, V. W. (Vincent W. V.), Grant, S. F. (Struan F. A.), Sebert, S. (Sylvain), McCarthy, M. I. (Mark I.), and Jarvelin, M.-R. (Marjo-Riitta)
Abstract: Early childhood growth patterns are associated with adult health, yet the genetic factors and the developmental stages involved are not fully understood. Here, we combine genome-wide association studies with modeling of longitudinal growth traits to study the genetics of infant and child growth, followed by functional, pathway, genetic correlation, risk score, and colocalization analyses to determine how developmental timings, molecular pathways, and genetic determinants of these traits overlap with those of adult health. We found a robust overlap between the genetics of child and adult body mass index (BMI), with variants associated with adult BMI acting as early as 4 to 6 years old. However, we demonstrated a completely distinct genetic makeup for peak BMI during infancy, influenced by variation at the LEPR/LEPROT locus. These findings suggest that different genetic factors control infant and child BMI. In light of the obesity epidemic, these findings are important to inform the timing and targets of prevention strategies.
Published: 2019

7. Association of methylation signals with incident coronary heart disease in an epigenome-wide assessment of circulating tumor necrosis factor α

Author: Aslibekyan, S. (Stella), Agha, G. (Golareh), Colicino, E. (Elena), Do, A. N. (Anh N.), Lahti, J. (Jari), Ligthart, S. (Symen), Marioni, R. E. (Riccardo E.), Marzi, C. (Carola), Mendelson, M. M. (Michael M.), Tanaka, T. (Toshiko), Wielscher, M. (Matthias), Absher, D. M. (Devin M.), Ferrucci, L. (Luigi), Franco, O. H. (Oscar H.), Gieger, C. (Christian), Grallert, H. (Harald), Hernandez, D. (Dena), Huan, T. (Tianxiao), Iurato, S. (Stella), Joehanes, R. (Roby), Just, A. C. (Allan C.), Kunze, S. (Sonja), Lin, H. (Honghuang), Liu, C. (Chunyu), Meigs, J. B. (James B.), van Meurs, J. B. (Joyce B.J.), Moore, A. Z. (Ann Zenobia), Peters, A. (Annette), Prokisch, H. (Holger), Räikkönen, K. (Katri), Rathmann, W. (Wolfgang), Roden, M. (Michael), Schramm, K. (Katharina), Schwartz, J. D. (Joel D.), Starr, J. M. (John M.), Uitterlinden, A. G. (André G.), Vokonas, P. (Pantel), Waldenberger, M. (Melanie), Yao, C. (Chen), Zhi, D. (Degui), Baccarelli, A. A. (Andrea A.), Bandinelli, S. (Stefania), Deary, I. J. (Ian J.), Dehghan, A. (Abbas), Eriksson, J. (Johan), Herder, C. (Christian), Järvelin, M.-R. (Marjo-Riitta), Levy, D. (Daniel), Arnett, D. K. (Donna K.), Aslibekyan, S. (Stella), Agha, G. (Golareh), Colicino, E. (Elena), Do, A. N. (Anh N.), Lahti, J. (Jari), Ligthart, S. (Symen), Marioni, R. E. (Riccardo E.), Marzi, C. (Carola), Mendelson, M. M. (Michael M.), Tanaka, T. (Toshiko), Wielscher, M. (Matthias), Absher, D. M. (Devin M.), Ferrucci, L. (Luigi), Franco, O. H. (Oscar H.), Gieger, C. (Christian), Grallert, H. (Harald), Hernandez, D. (Dena), Huan, T. (Tianxiao), Iurato, S. (Stella), Joehanes, R. (Roby), Just, A. C. (Allan C.), Kunze, S. (Sonja), Lin, H. (Honghuang), Liu, C. (Chunyu), Meigs, J. B. (James B.), van Meurs, J. B. (Joyce B.J.), Moore, A. Z. (Ann Zenobia), Peters, A. (Annette), Prokisch, H. (Holger), Räikkönen, K. (Katri), Rathmann, W. (Wolfgang), Roden, M. (Michael), Schramm, K. (Katharina), Schwartz, J. D. (Joel D.), Starr, J. M. (John M.), Uitterlinden, A. G. (André G.), Vokonas, P. (Pantel), Waldenberger, M. (Melanie), Yao, C. (Chen), Zhi, D. (Degui), Baccarelli, A. A. (Andrea A.), Bandinelli, S. (Stefania), Deary, I. J. (Ian J.), Dehghan, A. (Abbas), Eriksson, J. (Johan), Herder, C. (Christian), Järvelin, M.-R. (Marjo-Riitta), Levy, D. (Daniel), and Arnett, D. K. (Donna K.)
Abstract: Importance: Tumor necrosis factor α (TNF-α) is a proinflammatory cytokine with manifold consequences for mammalian pathophysiology, including cardiovascular disease. A deeper understanding of TNF-α biology may enhance treatment precision. Objective: To conduct an epigenome-wide analysis of blood-derived DNA methylation and TNF-α levels and to assess the clinical relevance of findings. Design, Setting, and Participants: This meta-analysis assessed epigenome-wide associations in circulating TNF-α concentrations from 5 cohort studies and 1 interventional trial, with replication in 3 additional cohort studies. Follow-up analyses investigated associations of identified methylation loci with gene expression and incident coronary heart disease; this meta-analysis included 11 461 participants who experienced 1895 coronary events. Exposures: Circulating TNF-α concentration. Main Outcomes and Measures: DNA methylation at approximately 450 000 loci, neighboring DNA sequence variation, gene expression, and incident coronary heart disease. Results: The discovery cohort included 4794 participants, and the replication study included 816 participants (overall mean [SD] age, 60.7 [8.5] years). In the discovery stage, circulating TNF-α levels were associated with methylation of 7 cytosine-phosphate-guanine (CpG) sites, 3 of which were located in or near DTX3L-PARP9 at cg00959259 (β [SE] = −0.01 [0.003]; P = 7.36×10⁻⁸), cg08122652 (β [SE] = −0.008 [0.002]; P = 2.24×10⁻⁷), and cg22930808(β [SE] = −0.01 [0.002]; P = 6.92×10⁻⁸); NLRC5 at cg16411857 (β [SE] = −0.01 [0.002]; P = 2.14×10⁻¹³) and cg07839457 (β [SE] = −0.02 [0.003]; P = 6.31×10⁻¹⁰); or ABO, at cg13683939 (β [SE] = 0.04 [0.008]; P = 1.42×10⁻⁷) and cg24267699 (β [SE] = −0.009 [0.002]; P = 1.67 × 10⁻⁷), after accounting for multiple testing. Of these, negative associations between TNF-α concentration and methylation of 2 loci in NLRC5 and 1 in DTX3L-14 PARP9 were replicated. Replicated TNF-α–linked CpG sites were associ
Published: 2018

8. A DNA methylation biomarker of alcohol consumption

Author: Liu, C. (C.), Marioni, R.E. (Riccardo), Hedman, A.K. (Asa), Pfeiffer, L. (L.), Tsai, P.-C. (P. C.), Reynolds, L.M. (Lindsay), Just, A.C. (A. C.), Duan, Q. (Qing), Boer, C.G. (Cindy), Tanaka, T. (T.), Elks, C.E. (Cathy), Aslibekyan, S. (S.), Brody, J.A. (Jennifer A.), Kuhnel, B. (Brigitte), Herder, C. (Christian), Almli, L.M. (L. M.), Zhi, D. (D.), Wang, Y. (Y.), Huan, T. (T.), Yao, C. (C.), Mendelson, M.M. (M. M.), Joehanes, R. (Roby), Liang, L. (Liming), Love, S.-A. (S. A.), Guan, W. (Weihua), Shah, S. (S.), McRae, A.F. (A. F.), Kretschmer, A. (A.), Prokisch, H. (Holger), Strauch, K. (K.), Peters, A. (Annette), Visscher, P.M. (Peter), Wray, N.R. (Naomi), Guo, X. (Xiuqing), Wiggins, K.L. (Kerri), Smith, A.K. (A. K.), Binder, E.B. (Elisabeth), Ressler, K.J. (Kerry), Irvin, M.R. (M. R.), Absher, D.M. (D. M.), Hernandez, D.G. (Dena), Ferrucci, L. (Luigi), Bandinelli, S. (Stefania), Lohman, K. (K.), Ding, J. (J.), Trevisi, L. (L.), Gustafsson, S. (Stefan), Sandling, J.K. (Johanna), Stolk, L. (Lisette), Uitterlinden, A.G. (André), Yet, I. (Idil), Castillo-Fernandez, J.E. (J. E.), Spector, T.D. (Timothy), Schwartz, J.D. (J. D.), Vokonas, P. (P.), Kao, W.H.L. (Wen), Li, Y. (Y.), Fornage, M. (Myriam), Arnett, D.K. (Donna), Wareham, N.J. (Nick), Sotoodehnia, N. (Nona), Ong, K.K. (Ken), Meurs, J.B.J. (Joyce) van, Conneely, K.N. (Karen N.), Baccarelli, A.A. (A. A.), Deary, I.J. (Ian), Bell, J.T. (J. T.), North, K.E. (Kari), Liu, Y. (YongMei), Waldenberger, M. (M.), London, S.J. (S. J.), Ingelsson, E. (Erik), Levy, D. (D.), Liu, C. (C.), Marioni, R.E. (Riccardo), Hedman, A.K. (Asa), Pfeiffer, L. (L.), Tsai, P.-C. (P. C.), Reynolds, L.M. (Lindsay), Just, A.C. (A. C.), Duan, Q. (Qing), Boer, C.G. (Cindy), Tanaka, T. (T.), Elks, C.E. (Cathy), Aslibekyan, S. (S.), Brody, J.A. (Jennifer A.), Kuhnel, B. (Brigitte), Herder, C. (Christian), Almli, L.M. (L. M.), Zhi, D. (D.), Wang, Y. (Y.), Huan, T. (T.), Yao, C. (C.), Mendelson, M.M. (M. M.), Joehanes, R. (Roby), Liang, L. (Liming), Love, S.-A. (S. A.), Guan, W. (Weihua), Shah, S. (S.), McRae, A.F. (A. F.), Kretschmer, A. (A.), Prokisch, H. (Holger), Strauch, K. (K.), Peters, A. (Annette), Visscher, P.M. (Peter), Wray, N.R. (Naomi), Guo, X. (Xiuqing), Wiggins, K.L. (Kerri), Smith, A.K. (A. K.), Binder, E.B. (Elisabeth), Ressler, K.J. (Kerry), Irvin, M.R. (M. R.), Absher, D.M. (D. M.), Hernandez, D.G. (Dena), Ferrucci, L. (Luigi), Bandinelli, S. (Stefania), Lohman, K. (K.), Ding, J. (J.), Trevisi, L. (L.), Gustafsson, S. (Stefan), Sandling, J.K. (Johanna), Stolk, L. (Lisette), Uitterlinden, A.G. (André), Yet, I. (Idil), Castillo-Fernandez, J.E. (J. E.), Spector, T.D. (Timothy), Schwartz, J.D. (J. D.), Vokonas, P. (P.), Kao, W.H.L. (Wen), Li, Y. (Y.), Fornage, M. (Myriam), Arnett, D.K. (Donna), Wareham, N.J. (Nick), Sotoodehnia, N. (Nona), Ong, K.K. (Ken), Meurs, J.B.J. (Joyce) van, Conneely, K.N. (Karen N.), Baccarelli, A.A. (A. A.), Deary, I.J. (Ian), Bell, J.T. (J. T.), North, K.E. (Kari), Liu, Y. (YongMei), Waldenberger, M. (M.), London, S.J. (S. J.), Ingelsson, E. (Erik), and Levy, D. (D.)
Abstract: The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal = 13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples. We performed meta-analysis and variable selection in whole-blood samples of people of European ancestry (n = 6926) and identified 144 CpGs that provided substantial discrimination (area under the curve = 0.90-0.99) for current heavy alcohol intake (≥42 g per day in men and ≥28 g per day in women) in four replication cohorts. The ancestry-stratified meta-analysis in whole blood identified 328 (9643 European ancestry samples) and 165 (2423 African ancestry samples) alcohol-related CpGs at Bonferroni-adjusted P<1×10-7. Analysis of the monocyte-derived DNA (n = 1251) identified 62 alcohol-related CpGs at P<1×10-7. In whole-blood samples of people of European ancestry, we detected differen
Published: 2018
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9. Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

Author: Xue, A. (Angli), Wu, Y. (Yang), Zhu, Z. (Zhihong), Zhang, F. (Futao), Kemper, K.E. (Kathryn E.), Zheng, Z. (Zhili), Yengo, L. (Loic), Lloyd-Jones, L.R. (Luke R.), Sidorenko, J. (Julia), Wu, Y. (Yeda), Agbessi, M. (Mawussé), Ahsan, H. (Habibul), Alves, I. (Isabel), Andiappan, A.K. (Anand Kumar), Awadalla, P. (Philip), Battle, A. (Alexis), Beutner, F. (Frank), Bonder, M.J. (Marc), Boomsma, D. (Dorret), Christiansen, M. (Mark), Claringbould, A. (Annique), Deelen, P. (Patrick), Esko, T. (Tõnu), Favé, M.-J. (Marie-Julie), Franke, L. (Lude), Frayling, T.M. (Timothy), Gharib, S.A. (Sina), Gibson, G. (Gregory), Hemani, G., Jansen, R. (Rick), Kähönen, M. (Mika), Kalnapenkis, A. (Anette), Kasela, S. (Silva), Kettunen, J. (Johannes), Kim, Y. (Yungil), Kirsten, H. (Holger), Kovacs, P. (Peter), Krohn, K. (Knut), Kronberg-Guzman, J. (Jaanika), Kukushkina, V. (Viktorija), Kutalik, Z. (Zoltán), Lee, B. (Bernett), Lehtimäki, T. (Terho), Loeffler, M. (Markus), Marigorta, U.M. (Urko), Metspalu, A. (Andres), Milani, L. (Lili), Müller-Nurasyid, M. (Martina), Nauck, M. (Matthias), Nivard, M. (Michel), Penninx, B.W.J.H. (Brenda), Perola, M. (Markus), Pervjakova, N. (Natalia), Pierce, A. (Andrew), Powell, J. (Joseph), Prokisch, H. (Holger), Psaty, B. (Bruce), Raitakari, O. (Olli), Ring, S.M. (Susan), Ripatti, S. (Samuli), Rotzschke, O. (Olaf), Ruëger, S. (Sina), Saha, A. (Ashis), Scholz, M. (Markus), Schramm, K. (Katharina), Seppälä, I. (Ilkka), Stumvoll, M. (Michael), Sullivan, P.F. (Patrick), Teumer, A. (Alexander), Thiery, J.P. (Joachim), Tong, L. (Lin), Tönjes, A. (Anke), Dongen, J. (Jenny) van, Meurs, J.B.J. (Joyce) van, Verlouw, J.A.M. (Joost), Völker, U. (Uwe), Võsa, U. (Urmo), Yaghootkar, H. (Hanieh), Zeng, B. (Biao), McRae, A.F. (Allan F.), Visscher, P.M. (Peter), Zeng, J. (Jian), Yang, J. (Jian), Xue, A. (Angli), Wu, Y. (Yang), Zhu, Z. (Zhihong), Zhang, F. (Futao), Kemper, K.E. (Kathryn E.), Zheng, Z. (Zhili), Yengo, L. (Loic), Lloyd-Jones, L.R. (Luke R.), Sidorenko, J. (Julia), Wu, Y. (Yeda), Agbessi, M. (Mawussé), Ahsan, H. (Habibul), Alves, I. (Isabel), Andiappan, A.K. (Anand Kumar), Awadalla, P. (Philip), Battle, A. (Alexis), Beutner, F. (Frank), Bonder, M.J. (Marc), Boomsma, D. (Dorret), Christiansen, M. (Mark), Claringbould, A. (Annique), Deelen, P. (Patrick), Esko, T. (Tõnu), Favé, M.-J. (Marie-Julie), Franke, L. (Lude), Frayling, T.M. (Timothy), Gharib, S.A. (Sina), Gibson, G. (Gregory), Hemani, G., Jansen, R. (Rick), Kähönen, M. (Mika), Kalnapenkis, A. (Anette), Kasela, S. (Silva), Kettunen, J. (Johannes), Kim, Y. (Yungil), Kirsten, H. (Holger), Kovacs, P. (Peter), Krohn, K. (Knut), Kronberg-Guzman, J. (Jaanika), Kukushkina, V. (Viktorija), Kutalik, Z. (Zoltán), Lee, B. (Bernett), Lehtimäki, T. (Terho), Loeffler, M. (Markus), Marigorta, U.M. (Urko), Metspalu, A. (Andres), Milani, L. (Lili), Müller-Nurasyid, M. (Martina), Nauck, M. (Matthias), Nivard, M. (Michel), Penninx, B.W.J.H. (Brenda), Perola, M. (Markus), Pervjakova, N. (Natalia), Pierce, A. (Andrew), Powell, J. (Joseph), Prokisch, H. (Holger), Psaty, B. (Bruce), Raitakari, O. (Olli), Ring, S.M. (Susan), Ripatti, S. (Samuli), Rotzschke, O. (Olaf), Ruëger, S. (Sina), Saha, A. (Ashis), Scholz, M. (Markus), Schramm, K. (Katharina), Seppälä, I. (Ilkka), Stumvoll, M. (Michael), Sullivan, P.F. (Patrick), Teumer, A. (Alexander), Thiery, J.P. (Joachim), Tong, L. (Lin), Tönjes, A. (Anke), Dongen, J. (Jenny) van, Meurs, J.B.J. (Joyce) van, Verlouw, J.A.M. (Joost), Völker, U. (Uwe), Võsa, U. (Urmo), Yaghootkar, H. (Hanieh), Zeng, B. (Biao), McRae, A.F. (Allan F.), Visscher, P.M. (Peter), Zeng, J. (Jian), and Yang, J. (Jian)
Abstract: Type 2 diabetes (T2D) is a very common disease in humans. Here we conduct a meta-analysis of genome-wide association studies (GWAS) with ~16 million genetic variants in 62,892 T2D cases and 596,424 controls of European ancestry. We identify 139 common and 4 rare variants associated with T2D, 42 of which (39 common and 3 rare variants) are independent of the known variants. Integration of the gene expression data from blood (n = 14,115 and 2765) with the GWAS results identifies 33 putative functional genes for T2D, 3 of which were targeted by approved drugs. A further integration of DNA methylation (n = 1980) and epigenomic annotation data highlight 3 genes (CAMK1D, TP53INP1, and ATP5G1) with plausible regulatory mechanisms, whereby a genetic variant exerts an effect on T2D through epigenetic regulation of gene expression. Our study uncovers additional loci, proposes putative genetic regulatory mechanisms for T2D, and provides evidence of purifying selection for T2D-associated variants.
Published: 2018
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10. Clinical, biochemical and genetic spectrum of 70 patients with ACAD9 deficiency: Is riboflavin supplementation effective?

Author: Repp, B.M. (Birgit M.), Mastantuono, E. (Elisa), Alston, C.L. (Charlotte L.), Schiff, M. (Manuel), Haack, T.B. (Tobias B.), Rötig, A. (Agns), Ardissone, A. (Anna), Lombès, A. (Anne), Catarino, C.F.B.S., Diodato, D. (Daria), Schottmann, G. (Gudrun), Poulton, J. (Joanna), Burlina, A.B. (Alberto), Jonckheere, A. (An), Munnich, A. (Arnold), Rolinski, B. (Boris), Ghezzi, D. (Daniele), Rokicki, D. (Dariusz), Wellesley, D. (Diana), Martinelli, D. (Diego), Wenhong, D. (Ding), Lamantea, E. (Eleonora), Østergaard, E. (Elsebet), Pronicka, E. (Ewa), Pierre, G. (Germaine), Smeets, H.J.M. (Hubert), Wittig, I. (Ilka), Scurr, I. (Ingrid), Coo, I.F.M. (René) de, Moroni, I. (Isabella), Smet, J. (Joél), Mayr, J.A. (Johannes A.), Dai, L. (Lifang), Meirleir, L. (Linda) de, Schuelke, M. (Markus), Zeviani, M. (Massimo), Morscher, R.J. (Raphael J.), McFarland, R. (Robert), Seneca, S. (S.), Klopstock, T. (Thomas), Meitinger, T. (Thomas), Wieland, T. (Thomas), Strom, T.M. (Tim), Herberg, U. (Ulrike), Ahting, U. (Uwe), Sperl, W. (Wolfgang), Nassogne, M.C. (M.), Ling, H. (Han), Fang, F. (Fang), Freisinger, P. (Peter), Coster, R.N.A. (R. N A) van, Strecker, V. (Valentina), Taylor, R.W. (Robert William), Häberle, J. (Johannes), Vockley, J. (Jerry), Prokisch, H. (Holger), Wortmann, S.B. (S.), Repp, B.M. (Birgit M.), Mastantuono, E. (Elisa), Alston, C.L. (Charlotte L.), Schiff, M. (Manuel), Haack, T.B. (Tobias B.), Rötig, A. (Agns), Ardissone, A. (Anna), Lombès, A. (Anne), Catarino, C.F.B.S., Diodato, D. (Daria), Schottmann, G. (Gudrun), Poulton, J. (Joanna), Burlina, A.B. (Alberto), Jonckheere, A. (An), Munnich, A. (Arnold), Rolinski, B. (Boris), Ghezzi, D. (Daniele), Rokicki, D. (Dariusz), Wellesley, D. (Diana), Martinelli, D. (Diego), Wenhong, D. (Ding), Lamantea, E. (Eleonora), Østergaard, E. (Elsebet), Pronicka, E. (Ewa), Pierre, G. (Germaine), Smeets, H.J.M. (Hubert), Wittig, I. (Ilka), Scurr, I. (Ingrid), Coo, I.F.M. (René) de, Moroni, I. (Isabella), Smet, J. (Joél), Mayr, J.A. (Johannes A.), Dai, L. (Lifang), Meirleir, L. (Linda) de, Schuelke, M. (Markus), Zeviani, M. (Massimo), Morscher, R.J. (Raphael J.), McFarland, R. (Robert), Seneca, S. (S.), Klopstock, T. (Thomas), Meitinger, T. (Thomas), Wieland, T. (Thomas), Strom, T.M. (Tim), Herberg, U. (Ulrike), Ahting, U. (Uwe), Sperl, W. (Wolfgang), Nassogne, M.C. (M.), Ling, H. (Han), Fang, F. (Fang), Freisinger, P. (Peter), Coster, R.N.A. (R. N A) van, Strecker, V. (Valentina), Taylor, R.W. (Robert William), Häberle, J. (Johannes), Vockley, J. (Jerry), Prokisch, H. (Holger), and Wortmann, S.B. (S.)
Abstract: Background: Mitochondrial acyl-CoA dehydrogenase family member 9 (ACAD9) is essential for the assembly of mitochondrial respiratory chain complex I. Disease causing biallelic variants in ACAD9 have been reported in individuals presenting with lactic acidosis and cardiomyopathy. Results: We describe the genetic, clinical and biochemical findings in a cohort of 70 patients, of whom 29 previously unpublished. We found 34 known and 18 previously unreported variants in ACAD9. No patients harbored biallelic loss of function mutations, indicating that this combination is unlikely to be compatible with life. Causal pathogenic variants were distributed throughout the entire gene, and there was no obvious genotype-phenotype correlation. Most of the patients presented in the first year of life. For this subgroup the survival was poor (50% not surviving the first 2 years) comparing to patients with a later presentation (more than 90% surviving 10 years). The most common clinical findings were cardiomyopathy (85%), muscular weakness (75%) and exercise intolerance (72%). Interestingly, severe intellectual deficits were only reported in one patient and s
Published: 2018
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11. Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

Author: Qi, T. (Ting), Wu, Y. (Yang), Zeng, J. (Jian), Zhang, F. (Futao), Xue, A. (Angli), Jiang, L. (Longda), Zhu, Z. (Zhihong), Kemper, K. (Kathryn), Yengo, L. (Loic), Zheng, Z. (Zhili), Agbessi, M. (Mawussé), Ahsan, H. (Habibul), Alves, I. (Isabel), Andiappan, A.K. (Anand Kumar), Awadalla, P. (Philip), Battle, A. (Alexis), Beutner, F. (Frank), Jan Bonder, M. (Marc), Boomsma, D.I. (Dorret), Christiansen, M. (Mark), Claringbould, A. (Annique), Deelen, P. (Patrick), Esko, T. (Tõnu), Favé, M.-J. (Marie-Julie), Franke, L. (Lude), Frayling, T.M. (Timothy), Gharib, S.A. (Sina), Gibson, G. (Gregory), Hemani, G., Jansen, R. (Rick), Kähönen, M. (Mika), Kalnapenkis, A. (Anette), Kasela, S. (Silva), Kettunen, J. (Johannes), Kim, Y. (Yungil), Kirsten, H. (Holger), Kovacs, P. (Peter), Krohn, K. (Knut), Kronberg-Guzman, J. (Jaanika), Kukushkina, V. (Viktorija), Kutalik, Z. (Zoltán), Lee, B. (Bernett), Lehtimäki, T. (Terho), Loeffler, M. (Markus), Marigorta, U.M. (Urko), Metspalu, A. (Andres), Milani, L. (Lili), Müller-Nurasyid, M. (Martina), Nauck, M. (Matthias), Nivard, M. (Michel), Penninx, B.W.J.H. (Brenda), Perola, M. (Markus), Pervjakova, N. (Natalia), Pierce, A. (Andrew), Powell, J. (Joseph), Prokisch, H. (Holger), Psaty, B. (Bruce), Raitakari, O. (Olli), Ring, S.M. (Susan), Ripatti, S. (Samuli), Rotzschke, O. (Olaf), Ruëger, S. (Sina), Saha, A. (Ashis), Scholz, M. (Markus), Schramm, K. (Katharina), Seppälä, I. (Ilkka), Stumvoll, M. (Michael), Sullivan, P.F. (Patrick), Teumer, A. (Alexander), Thiery, J.P. (Joachim), Tong, L. (Lin), Tönjes, A. (Anke), Dongen, J. (Jenny) van, Meurs, J.B.J. (Joyce) van, Verlouw, J.A.M. (Joost), Völker, U. (Uwe), Võsa, U. (Urmo), Yaghootkar, H. (Hanieh), Zeng, B. (Biao), Marioni, R.E. (Riccardo), Montgomery, G.W. (Grant W.), Deary, I.J. (Ian), Wray, N.R. (Naomi R.), Visscher, P.M. (Peter), McRae, A.F. (Allan F.), Yang, J. (Jian), Qi, T. (Ting), Wu, Y. (Yang), Zeng, J. (Jian), Zhang, F. (Futao), Xue, A. (Angli), Jiang, L. (Longda), Zhu, Z. (Zhihong), Kemper, K. (Kathryn), Yengo, L. (Loic), Zheng, Z. (Zhili), Agbessi, M. (Mawussé), Ahsan, H. (Habibul), Alves, I. (Isabel), Andiappan, A.K. (Anand Kumar), Awadalla, P. (Philip), Battle, A. (Alexis), Beutner, F. (Frank), Jan Bonder, M. (Marc), Boomsma, D.I. (Dorret), Christiansen, M. (Mark), Claringbould, A. (Annique), Deelen, P. (Patrick), Esko, T. (Tõnu), Favé, M.-J. (Marie-Julie), Franke, L. (Lude), Frayling, T.M. (Timothy), Gharib, S.A. (Sina), Gibson, G. (Gregory), Hemani, G., Jansen, R. (Rick), Kähönen, M. (Mika), Kalnapenkis, A. (Anette), Kasela, S. (Silva), Kettunen, J. (Johannes), Kim, Y. (Yungil), Kirsten, H. (Holger), Kovacs, P. (Peter), Krohn, K. (Knut), Kronberg-Guzman, J. (Jaanika), Kukushkina, V. (Viktorija), Kutalik, Z. (Zoltán), Lee, B. (Bernett), Lehtimäki, T. (Terho), Loeffler, M. (Markus), Marigorta, U.M. (Urko), Metspalu, A. (Andres), Milani, L. (Lili), Müller-Nurasyid, M. (Martina), Nauck, M. (Matthias), Nivard, M. (Michel), Penninx, B.W.J.H. (Brenda), Perola, M. (Markus), Pervjakova, N. (Natalia), Pierce, A. (Andrew), Powell, J. (Joseph), Prokisch, H. (Holger), Psaty, B. (Bruce), Raitakari, O. (Olli), Ring, S.M. (Susan), Ripatti, S. (Samuli), Rotzschke, O. (Olaf), Ruëger, S. (Sina), Saha, A. (Ashis), Scholz, M. (Markus), Schramm, K. (Katharina), Seppälä, I. (Ilkka), Stumvoll, M. (Michael), Sullivan, P.F. (Patrick), Teumer, A. (Alexander), Thiery, J.P. (Joachim), Tong, L. (Lin), Tönjes, A. (Anke), Dongen, J. (Jenny) van, Meurs, J.B.J. (Joyce) van, Verlouw, J.A.M. (Joost), Völker, U. (Uwe), Võsa, U. (Urmo), Yaghootkar, H. (Hanieh), Zeng, B. (Biao), Marioni, R.E. (Riccardo), Montgomery, G.W. (Grant W.), Deary, I.J. (Ian), Wray, N.R. (Naomi R.), Visscher, P.M. (Peter), McRae, A.F. (Allan F.), and Yang, J. (Jian)
Abstract: Understanding the difference in genetic regulation of gene expression between brain and blood is important for discovering genes for brain-related traits and disorders. Here, we estimate the correlation of genetic effects at the top-associated cis-expression or -DNA methylation (DNAm) quantitative trait loci (cis-eQTLs or cis-mQTLs) between brain and blood (r b ). Using publicly available data, we find that genetic effects at the top cis-eQTLs or mQTLs are highly correlated between independent brain and blood samples (r b = 0.70 for cis-eQTLs and r ^ b = 0.78 for cis-mQTLs). Using meta-analyzed brain cis-eQTL/mQTL data (n = 526 to 1194), we identify 61 genes and 167 DNAm sites associated with four brain-related phenotypes, most of which are a subset of the discoveries (97 genes and 295 DNAm sites) using data from blood with larger sample sizes (n = 1980 to 14,115). Our results demonstrate the gain of power in gene discovery for brain-related phenotypes using blood cis-eQTL/mQTL data with large sample sizes.
Published: 2018
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12. Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity

Author: Wahl, S. (Simone), Drong, A. (Alexander), Lehne, B. (Benjamin), Loh, M. (Marie), Scott, W.R. (William R.), Kunze, S. (Sonja), Tsai, P.-C. (Pei-Chien), Ried, J.S. (Janina S.), Zhang, W. (Weihua), Yang, Y. (Youwen), Tan, S. (Sili), Fiorito, G. (Giovanni), Franke, L. (Lude), Guarrera, S. (Simonetta), Kasela, S. (Silva), Kriebel, J. (Jennifer), Richmond, R.C. (Rebecca C.), Adamo, M. (Marco), Afzal, U. (Uzma), Ala-Korpela, M. (Mika), Albetti, B. (Benedetta), Ammerpohl, O. (Ole), Apperley, J. (Jane), Beekman, M. (Marian), Bertazzi, P.A. (Pier Alberto), Black, S.L. (S. Lucas), Blancher, C. (Christine), Bonder, M.J. (Marc), Brosch, M. (Mario), Carstensen-Kirberg, M. (Maren), Craen, A.J. (Anton) de, Lusignan, S. (Simon) de, Dehghan, A. (Abbas), Elkalaawy, M. (Mohamed), Fischer, K. (Krista), Franco, O.H. (Oscar), Gaunt, T.R. (Tom), Hampe, J. (Jochen), Hashemi, M. (Majid), Isaacs, A.J. (Aaron), Jenkinson, A. (Andrew), Jha, S. (Sujeet), Kato, N. (Norihiro), Krogh, V. (Vittorio), Laffan, M. (Michael), Meisinger, C. (Christa), Meitinger, T. (Thomas), Mok, Z.Y. (Zuan Yu), Motta, V. (Valeria), Ng, H.K. (Hong Kiat), Nikolakopoulou, Z. (Zacharoula), Nteliopoulos, G. (Georgios), Panico, S. (Salvatore), Pervjakova, N. (Natalia), Prokisch, H. (Holger), Rathmann, W. (Wolfgang), Roden, M. (Michael), Rota, F. (Federica), Rozario, M.A. (Michelle Ann), Sandling, J.K. (Johanna), Schafmayer, C. (Clemens), Schramm, K. (Katharina), Siebert, R. (Reiner), Slagboom, P.E. (Eline), Soininen, P. (Pasi), Stolk, L. (Lisette), Strauch, K. (Konstantin), Tai, E.S. (Shyong), Tarantini, L. (Letizia), Thorand, B. (Barbara), Tigchelaar, E.F. (Ettje F.), Tumino, R. (Rosario), Uitterlinden, A.G. (André), Duijn, C.M. (Cornelia) van, Meurs, J.B.J. (Joyce) van, Vineis, P. (Paolo), Wickremasinghe, A.R. (Ananda), Wijmenga, C. (Cisca), Yang, T.-P. (Tsun-Po), Yuan, W. (Wei), Zhernakova, A. (Alexandra), Batterham, R.L., Smith, A.V. (Davey), Deloukas, P. (Panos), Heijmans, B.T. (Bastiaan T.), Herder, C. (Christian), Hofman, A. (Albert), Lindgren, C.M. (Cecilia M.), Milani, L. (Lili), Harst, P. (Pim) van der, Peters, A. (Annette), Illig, T. (Thomas), Relton, C.L. (Caroline), Waldenberger, M. (Melanie), Jarvelin, M.-R. (Marjo-Riitta), Bollati, V. (Valentina), Soong, R. (Richie), Spector, T.D. (Timothy), Scott, J. (James), McCarthy, M.I. (Mark), Elliott, P. (Paul), Bell, J.T. (Jordana T.), Matullo, G., Gieger, C. (Christian), Kooner, J.S. (Jaspal S.), Grallert, H. (Harald), Chambers, J.C. (John C.), Wahl, S. (Simone), Drong, A. (Alexander), Lehne, B. (Benjamin), Loh, M. (Marie), Scott, W.R. (William R.), Kunze, S. (Sonja), Tsai, P.-C. (Pei-Chien), Ried, J.S. (Janina S.), Zhang, W. (Weihua), Yang, Y. (Youwen), Tan, S. (Sili), Fiorito, G. (Giovanni), Franke, L. (Lude), Guarrera, S. (Simonetta), Kasela, S. (Silva), Kriebel, J. (Jennifer), Richmond, R.C. (Rebecca C.), Adamo, M. (Marco), Afzal, U. (Uzma), Ala-Korpela, M. (Mika), Albetti, B. (Benedetta), Ammerpohl, O. (Ole), Apperley, J. (Jane), Beekman, M. (Marian), Bertazzi, P.A. (Pier Alberto), Black, S.L. (S. Lucas), Blancher, C. (Christine), Bonder, M.J. (Marc), Brosch, M. (Mario), Carstensen-Kirberg, M. (Maren), Craen, A.J. (Anton) de, Lusignan, S. (Simon) de, Dehghan, A. (Abbas), Elkalaawy, M. (Mohamed), Fischer, K. (Krista), Franco, O.H. (Oscar), Gaunt, T.R. (Tom), Hampe, J. (Jochen), Hashemi, M. (Majid), Isaacs, A.J. (Aaron), Jenkinson, A. (Andrew), Jha, S. (Sujeet), Kato, N. (Norihiro), Krogh, V. (Vittorio), Laffan, M. (Michael), Meisinger, C. (Christa), Meitinger, T. (Thomas), Mok, Z.Y. (Zuan Yu), Motta, V. (Valeria), Ng, H.K. (Hong Kiat), Nikolakopoulou, Z. (Zacharoula), Nteliopoulos, G. (Georgios), Panico, S. (Salvatore), Pervjakova, N. (Natalia), Prokisch, H. (Holger), Rathmann, W. (Wolfgang), Roden, M. (Michael), Rota, F. (Federica), Rozario, M.A. (Michelle Ann), Sandling, J.K. (Johanna), Schafmayer, C. (Clemens), Schramm, K. (Katharina), Siebert, R. (Reiner), Slagboom, P.E. (Eline), Soininen, P. (Pasi), Stolk, L. (Lisette), Strauch, K. (Konstantin), Tai, E.S. (Shyong), Tarantini, L. (Letizia), Thorand, B. (Barbara), Tigchelaar, E.F. (Ettje F.), Tumino, R. (Rosario), Uitterlinden, A.G. (André), Duijn, C.M. (Cornelia) van, Meurs, J.B.J. (Joyce) van, Vineis, P. (Paolo), Wickremasinghe, A.R. (Ananda), Wijmenga, C. (Cisca), Yang, T.-P. (Tsun-Po), Yuan, W. (Wei), Zhernakova, A. (Alexandra), Batterham, R.L., Smith, A.V. (Davey), Deloukas, P. (Panos), Heijmans, B.T. (Bastiaan T.), Herder, C. (Christian), Hofman, A. (Albert), Lindgren, C.M. (Cecilia M.), Milani, L. (Lili), Harst, P. (Pim) van der, Peters, A. (Annette), Illig, T. (Thomas), Relton, C.L. (Caroline), Waldenberger, M. (Melanie), Jarvelin, M.-R. (Marjo-Riitta), Bollati, V. (Valentina), Soong, R. (Richie), Spector, T.D. (Timothy), Scott, J. (James), McCarthy, M.I. (Mark), Elliott, P. (Paul), Bell, J.T. (Jordana T.), Matullo, G., Gieger, C. (Christian), Kooner, J.S. (Jaspal S.), Grallert, H. (Harald), and Chambers, J.C. (John C.)
Abstract: Approximately 1.5 billion people worldwide are overweight or affected by obesity, and are at risk of developing type 2 diabetes, cardiovascular disease and related metabolic and inflammatory disturbances. Although the mechanisms linking adiposity to associated clinical conditions are poorly understood, recent studies suggest that adiposity may influence DNA methylation, a key regulator of gene expression and molecular phenotype. Here we use epigenome-wide association to show that body mass index (BMI; a key measure of adiposity) is associated with widespread changes in DNA methylation (187 genetic loci with P < 1 × 10 -7, range P = 9.2 × 10 -8 to 6.0 × 10 -46; n = 10,261 samples). Genetic association analyses demonstrate that the alterations in DNA methylation are predominantly the consequence of adiposity, rather than the cause. We find that methylation loci are enriched for functional genomic features in multiple tissues (P < 0.05), and show that sentinel methylation markers identify gene expression signatures at 38 loci (P < 9.0 × 10 -6, range P = 5.5 × 10 -6 to 6.1 × 10 -35, n = 1,785 samples). The methylation loci identify genes involved in lipid and lipoprotein metabolism, substrate transport and inflammatory pathways. Finally, we show that the disturbances in DNA methylation predict future development of type 2 diabetes (relative risk per 1 standard deviation increase in methylation risk score: 2.3 (2.07-2.56); P = 1.1 × 10 -54). Our results provide new insights into the biologic pathways influenc
Published: 2017
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13. DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

Author: Ligthart, S. (Symen), Marzi, C. (Carola), Aslibekyan, S. (Stella), Mendelson, M.M. (Michael M.), Conneely, K.N. (Karen N.), Tanaka, T. (Toshiko), Colicino, E. (Elena), Waite, L. (Lindsay), Joehanes, R. (Roby), Guan, W. (Weihua), Brody, J.A. (Jennifer A.), Elks, C.E. (Cathy), Marioni, R.E. (Riccardo), Jhun, M.A. (Min A.), Agha, G. (Golareh), Bressler, J. (Jan), Ward-Caviness, C.K. (Cavin K.), Chen, B.H. (Brian), Huan, T. (Tianxiao), Bakulski, K.M. (Kelly M.), Salfati, E. (Elias), Fiorito, G. (Giovanni), Wahl, S. (Simone), Schramm, K. (Katharina), Sha, J. (Jin), Hernandez, D.G. (Dena), Just, A.C. (Allan C.), Smith, J.A. (Jennifer A), Sotoodehnia, N. (Nona), Pilling, L.C. (Luke), Pankow, J.S. (James), Tsao, P.S. (Phil S.), Liu, C. (Chunyu), Zhao, W. (Wei), Guarrera, S. (Simonetta), Michopoulos, V.J. (Vasiliki J.), Smith, A.K. (Alicia K.), Peters, M.J. (Marjolein), Melzer, D. (David), Vokonas, P. (Pantel), Fornage, M. (Myriam), Prokisch, H. (Holger), Bis, J.C. (Joshua), Chu, A.Y. (Audrey), Herder, C. (Christian), Grallert, H. (Harald), Yao, C. (Chen), Shah, S. (Sonia), McRae, A.F. (Allan F.), Lin, H., Horvath, S. (Steve), Fallin, D. (Daniele), Hofman, A. (Albert), Wareham, N.J. (Nick), Wiggins, K.L. (Kerri), Feinberg, A.P. (Andrew P.), Starr, J.M. (John), Visscher, P.M. (Peter), Murabito, J. (Joanne), Kardia, S.L.R. (Sharon L.R.), Absher, D. (Devin), Binder, E.B. (Elisabeth), Singleton, A. (Andrew), Bandinelli, S. (Stefania), Peters, A. (Annette), Waldenberger, M. (Melanie), Matullo, G., Schwartz, J.D. (Joel D.), Demerath, E.W. (Ellen), Uitterlinden, A.G. (André), Meurs, J.B.J. (Joyce B.J.), Franco, O.H. (Oscar), Chen, Y.D. (Y.), Levy, D. (Daniel), Turner, S.T. (Stephen), Deary, I.J. (Ian), Ressler, K.J. (Kerry), Dupuis, J. (Josée), Ferrucci, L. (Luigi), Ong, K.K. (Ken K.), Assimes, T.L. (Themistocles), Boerwinkle, E.A. (Eric), Koenig, W. (Wolfgang), Arnett, D.K. (Donna), Baccarelli, A.A. (Andrea), Benjamin, E.J. (Emelia), Dehghan, A. (Abbas), Ligthart, S. (Symen), Marzi, C. (Carola), Aslibekyan, S. (Stella), Mendelson, M.M. (Michael M.), Conneely, K.N. (Karen N.), Tanaka, T. (Toshiko), Colicino, E. (Elena), Waite, L. (Lindsay), Joehanes, R. (Roby), Guan, W. (Weihua), Brody, J.A. (Jennifer A.), Elks, C.E. (Cathy), Marioni, R.E. (Riccardo), Jhun, M.A. (Min A.), Agha, G. (Golareh), Bressler, J. (Jan), Ward-Caviness, C.K. (Cavin K.), Chen, B.H. (Brian), Huan, T. (Tianxiao), Bakulski, K.M. (Kelly M.), Salfati, E. (Elias), Fiorito, G. (Giovanni), Wahl, S. (Simone), Schramm, K. (Katharina), Sha, J. (Jin), Hernandez, D.G. (Dena), Just, A.C. (Allan C.), Smith, J.A. (Jennifer A), Sotoodehnia, N. (Nona), Pilling, L.C. (Luke), Pankow, J.S. (James), Tsao, P.S. (Phil S.), Liu, C. (Chunyu), Zhao, W. (Wei), Guarrera, S. (Simonetta), Michopoulos, V.J. (Vasiliki J.), Smith, A.K. (Alicia K.), Peters, M.J. (Marjolein), Melzer, D. (David), Vokonas, P. (Pantel), Fornage, M. (Myriam), Prokisch, H. (Holger), Bis, J.C. (Joshua), Chu, A.Y. (Audrey), Herder, C. (Christian), Grallert, H. (Harald), Yao, C. (Chen), Shah, S. (Sonia), McRae, A.F. (Allan F.), Lin, H., Horvath, S. (Steve), Fallin, D. (Daniele), Hofman, A. (Albert), Wareham, N.J. (Nick), Wiggins, K.L. (Kerri), Feinberg, A.P. (Andrew P.), Starr, J.M. (John), Visscher, P.M. (Peter), Murabito, J. (Joanne), Kardia, S.L.R. (Sharon L.R.), Absher, D. (Devin), Binder, E.B. (Elisabeth), Singleton, A. (Andrew), Bandinelli, S. (Stefania), Peters, A. (Annette), Waldenberger, M. (Melanie), Matullo, G., Schwartz, J.D. (Joel D.), Demerath, E.W. (Ellen), Uitterlinden, A.G. (André), Meurs, J.B.J. (Joyce B.J.), Franco, O.H. (Oscar), Chen, Y.D. (Y.), Levy, D. (Daniel), Turner, S.T. (Stephen), Deary, I.J. (Ian), Ressler, K.J. (Kerry), Dupuis, J. (Josée), Ferrucci, L. (Luigi), Ong, K.K. (Ken K.), Assimes, T.L. (Themistocles), Boerwinkle, E.A. (Eric), Koenig, W. (Wolfgang), Arnett, D.K. (Donna), Baccarelli, A.A. (Andrea), Benjamin, E.J. (Emelia), and Dehghan, A. (Abbas)
Abstract: Background: Chronic low-grade inflammation reflects a subclinical immune response implicated in the pathogenesis of complex diseases. Identifying genetic loci where DNA methylation is as
Published: 2016
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14. A meta-analysis of gene expression signatures of blood pressure and hypertension

Author: Huan, T. (Tianxiao), Esko, T. (Tõnu), Peters, M.J. (Marjolein), Pilling, L.C. (Luke), Schramm, K. (Katharina), Schurmann, C. (Claudia), Chen, B.H. (Brian), Liu, C. (Chunyu), Joehanes, R. (Roby), Johnson, A.D. (Andrew), Yao, C. (Chen), Ying, S.-X. (Sai-Xia), Courchesne, P. (Paul), Milani, L. (Lili), Raghavachari, N. (Nalini), Wang, R. (Richard), Liu, P. (Poching), Reinmaa, E. (Eva), Dehghan, A. (Abbas), Hofman, A. (Albert), Uitterlinden, A.G. (André), Hernandez, D.G. (Dena), Bandinelli, S. (Stefania), Singleton, A. (Andrew), Melzer, D. (David), Metspalu, A. (Andres), Carstensen, M. (Maren), Grallert, H. (Harald), Herder, C. (Christian), Meitinger, T. (Thomas), Peters, A. (Annette), Roden, M. (Michael), Waldenberger, M. (Melanie), Dörr, M. (Marcus), Felix, S.B. (Stephan), Zeller, T. (Tanja), Vasan, R. (Ramachandran), O'Donnell, C.J. (Christopher), Munson, P.J. (Peter J.), Yang, X. (Xia), Prokisch, H. (Holger), Völker, U. (Uwe), Meurs, J.B.J. (Joyce) van, Ferrucci, L. (Luigi), Levy, D. (Daniel), Huan, T. (Tianxiao), Esko, T. (Tõnu), Peters, M.J. (Marjolein), Pilling, L.C. (Luke), Schramm, K. (Katharina), Schurmann, C. (Claudia), Chen, B.H. (Brian), Liu, C. (Chunyu), Joehanes, R. (Roby), Johnson, A.D. (Andrew), Yao, C. (Chen), Ying, S.-X. (Sai-Xia), Courchesne, P. (Paul), Milani, L. (Lili), Raghavachari, N. (Nalini), Wang, R. (Richard), Liu, P. (Poching), Reinmaa, E. (Eva), Dehghan, A. (Abbas), Hofman, A. (Albert), Uitterlinden, A.G. (André), Hernandez, D.G. (Dena), Bandinelli, S. (Stefania), Singleton, A. (Andrew), Melzer, D. (David), Metspalu, A. (Andres), Carstensen, M. (Maren), Grallert, H. (Harald), Herder, C. (Christian), Meitinger, T. (Thomas), Peters, A. (Annette), Roden, M. (Michael), Waldenberger, M. (Melanie), Dörr, M. (Marcus), Felix, S.B. (Stephan), Zeller, T. (Tanja), Vasan, R. (Ramachandran), O'Donnell, C.J. (Christopher), Munson, P.J. (Peter J.), Yang, X. (Xia), Prokisch, H. (Holger), Völker, U. (Uwe), Meurs, J.B.J. (Joyce) van, Ferrucci, L. (Luigi), and Levy, D. (Daniel)
Abstract: Genome-wide association studies (GWAS) have uncovered numerous genetic variants (SNPs) that are associated with blood pressure (BP). Genetic variants may lead to BP changes by acting on intermediate molecular phenotypes such as coded protein sequence or gene expression, which in turn affect BP variability. Therefore, characterizing genes whose expression is associated with BP may reveal cellular processes involved in BP regulation and uncover how transcripts mediate genetic and environmental effects on BP variability. A meta-analysis of results from six studies of global gene expression profiles of BP and hypertension in whole blood was performed in 7017 individuals who were not receiving antihypertensive drug treatment. We identified 34 genes that were differentially expressed in relation to BP (Bonferroni-corrected p<0.05). Among these genes, FOS and PTGS2 have been previously reported to be involved in BP-related processes; the others are novel. The top BP signature genes in aggregate explain 5%-9% of inter-individual variance in BP. Of note, rs3184504 in SH2B3, which was also reported in GWAS to be associated with BP, was found to be a trans regulator of the expression of 6 of the transcripts we found to be associated with BP (FOS, MYADM, PP1R15A, TAGAP, S100A10, and FGBP2). Gene set enrichment analysis suggested that the BP-related global gene expression changes include genes involved in inflammatory response and apoptosis pathways. Our study provides new insights into molecular mechanisms underlying BP regulation, and suggests novel transcriptomic markers for the treatment and prevention of hypertension.
Published: 2015
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15. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

Author: Falk, M.J. (Marni J.), Shen, L. (Lishuang), Gonzalez, M. (Michael), Leipzig, J. (Jeremy), Lott, M.T. (Marie T.), Stassen, A.P.M. (Alphons P.M.), Diroma, M.A. (Maria Angela), Navarro-Gomez, D. (Daniel), Yeske, P. (Philip), Bai, R. (Renkui), Boles, R.G. (Richard G.), Brilhante, V. (Virginia), Ralph, D. (David), DaRe, J.T. (Jeana T.), Shelton, R. (Robert), Terry, S.F. (Sharon), Zhang, Z. (Zhe), Copeland, W.C. (William C.), Oven, M. (Mannis) van, Prokisch, H. (Holger), Wallace, D.C., Attimonelli, M. (Marcella), Krotoski, D. (Danuta), Zuchner, S. (Stephan), Gai, X. (Xiaowu), Bale, S. (Sherri), Bedoyan, J. (Jirair), Behar, D.M. (Doron), Bonnen, P. (Penelope), Brooks, L. (Lisa), Calabrese, C. (Claudia), Calvo, S. (Sarah), Chinnery, P.F. (Patrick), Christodoulou, J. (John), Church, D. (Deanna), Clima, R. (Rosanna), Cohen, B.H. (Bruce H.), Cotton, R.G.H. (Richard), Coo, I.F.M. (René) de, Derbenevoa, O. (Olga), Dunnen, J.T. (Johan) den, Dimmock, D. (David), Enns, G. (Gregory), Gasparre, G. (Giuseppe), Goldstein, A. (Amy), Gonzalez, I. (Iris), Gwinn, K. (Katrina), Hahn, S. (Sihoun), Haas, R.H. (Richard H.), Hakonarson, H. (Hakon), Hirano, M. (Michio), Kerr, D. (Douglas), Li, D. (Dong), Lvova, M. (Maria), Macrae, F. (Finley), Maglott, D. (Donna), McCormick, E. (Elizabeth), Mitchell, G. (Grant), Mootha, V.K. (Vamsi K.), Okazaki, Y. (Yasushi), Pujol, A. (Aurora), Parisi, M. (Melissa), Perin, J.C. (Juan Carlos), Pierce, E.A. (Eric A.), Procaccio, V. (Vincent), Rahman, S. (Shamima), Reddi, H. (Honey), Rehm, H. (Heidi), Riggs, E. (Erin), Rodenburg, R.J.T. (Richard), Rubinstein, Y. (Yaffa), Saneto, R. (Russell), Santorsola, M. (Mariangela), Scharfe, C. (Curt), Sheldon, C. (Claire), Shoubridge, E.A. (Eric), Simone, D. (Domenico), Smeets, B. (Bert), Smeitink, J.A.M. (Jan), Stanley, C. (Christine), Suomalainen, A. (Anu), Tarnopolsky, M.A. (Mark), Thiffault, I. (Isabelle), Thorburn, D.R. (David R.), Hove, J.V. (Johan Van), Wolfe, L. (Lynne), Wong, L.-J. (Lee-Jun), Falk, M.J. (Marni J.), Shen, L. (Lishuang), Gonzalez, M. (Michael), Leipzig, J. (Jeremy), Lott, M.T. (Marie T.), Stassen, A.P.M. (Alphons P.M.), Diroma, M.A. (Maria Angela), Navarro-Gomez, D. (Daniel), Yeske, P. (Philip), Bai, R. (Renkui), Boles, R.G. (Richard G.), Brilhante, V. (Virginia), Ralph, D. (David), DaRe, J.T. (Jeana T.), Shelton, R. (Robert), Terry, S.F. (Sharon), Zhang, Z. (Zhe), Copeland, W.C. (William C.), Oven, M. (Mannis) van, Prokisch, H. (Holger), Wallace, D.C., Attimonelli, M. (Marcella), Krotoski, D. (Danuta), Zuchner, S. (Stephan), Gai, X. (Xiaowu), Bale, S. (Sherri), Bedoyan, J. (Jirair), Behar, D.M. (Doron), Bonnen, P. (Penelope), Brooks, L. (Lisa), Calabrese, C. (Claudia), Calvo, S. (Sarah), Chinnery, P.F. (Patrick), Christodoulou, J. (John), Church, D. (Deanna), Clima, R. (Rosanna), Cohen, B.H. (Bruce H.), Cotton, R.G.H. (Richard), Coo, I.F.M. (René) de, Derbenevoa, O. (Olga), Dunnen, J.T. (Johan) den, Dimmock, D. (David), Enns, G. (Gregory), Gasparre, G. (Giuseppe), Goldstein, A. (Amy), Gonzalez, I. (Iris), Gwinn, K. (Katrina), Hahn, S. (Sihoun), Haas, R.H. (Richard H.), Hakonarson, H. (Hakon), Hirano, M. (Michio), Kerr, D. (Douglas), Li, D. (Dong), Lvova, M. (Maria), Macrae, F. (Finley), Maglott, D. (Donna), McCormick, E. (Elizabeth), Mitchell, G. (Grant), Mootha, V.K. (Vamsi K.), Okazaki, Y. (Yasushi), Pujol, A. (Aurora), Parisi, M. (Melissa), Perin, J.C. (Juan Carlos), Pierce, E.A. (Eric A.), Procaccio, V. (Vincent), Rahman, S. (Shamima), Reddi, H. (Honey), Rehm, H. (Heidi), Riggs, E. (Erin), Rodenburg, R.J.T. (Richard), Rubinstein, Y. (Yaffa), Saneto, R. (Russell), Santorsola, M. (Mariangela), Scharfe, C. (Curt), Sheldon, C. (Claire), Shoubridge, E.A. (Eric), Simone, D. (Domenico), Smeets, B. (Bert), Smeitink, J.A.M. (Jan), Stanley, C. (Christine), Suomalainen, A. (Anu), Tarnopolsky, M.A. (Mark), Thiffault, I. (Isabelle), Thorburn, D.R. (David R.), Hove, J.V. (Johan Van), Wolfe, L. (Lynne), and Wong, L.-J. (Lee-Jun)
Abstract: Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (. https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integr
Published: 2015
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16. Cell Specific eQTL Analysis without Sorting Cells

Author: Westra, H.J. (Harm-Jan), Arends, D. (Danny), Esko, T. (Tõnu), Peters, M.J. (Marjolein), Schurmann, C. (Claudia), Schramm, K. (Katharina), Kettunen, J. (Johannes), Yaghootkar, H. (Hanieh), Fairfax, B.P. (Benjamin), Andiappan, A.K. (Anand Kumar), Li, Y. (Yang), Fu, J. (Jingyuan), Karjalainen, J. (Juha), Platteel, I. (Inge), Visschedijk, M. (Marijn), Weersma, R.K. (Rinse K.), Kasela, S. (Silva), Milani, L. (Lili), Tserel, L. (Liina), Peterson, P. (Pärt), Reinmaa, E. (Eva), Hofman, A. (Albert), Uitterlinden, A.G. (André), Rivadeneira Ramirez, F. (Fernando), Homuth, G. (Georg), Petersmann, A. (Astrid), Lorbeer, R. (Roberto), Prokisch, H. (Holger), Meitinger, T. (Thomas), Herder, C. (Christian), Roden, M. (Michael), Grallert, H. (Harald), Ripatti, S. (Samuli), Perola, M. (Markus), Wood, A.R. (Andrew), Melzer, D. (David), Ferrucci, L. (Luigi), Singleton, A. (Andrew), Hernandez, D.G. (Dena), Knight, J.C. (Julian), Melchiotti, R. (Rossella), Lee, B. (Bernett), Poidinger, M. (Michael), Zolezzi, F. (Francesca), Larbi, A. (Anis), Wang, D.Y. (De Yun), Berg, L.H. (Leonard) van den, Veldink, J.H. (Jan), Rotzschke, O. (Olaf), Makino, S. (Seiko), Salomaa, V. (Veikko), Strauch, K. (Konstantin), Völker, U. (Uwe), Meurs, J.B.J. (Joyce) van, Metspalu, A. (Andres), Wijmenga, C. (Cisca), Jansen, R.C. (Ritsert), Franke, L. (Lude), Westra, H.J. (Harm-Jan), Arends, D. (Danny), Esko, T. (Tõnu), Peters, M.J. (Marjolein), Schurmann, C. (Claudia), Schramm, K. (Katharina), Kettunen, J. (Johannes), Yaghootkar, H. (Hanieh), Fairfax, B.P. (Benjamin), Andiappan, A.K. (Anand Kumar), Li, Y. (Yang), Fu, J. (Jingyuan), Karjalainen, J. (Juha), Platteel, I. (Inge), Visschedijk, M. (Marijn), Weersma, R.K. (Rinse K.), Kasela, S. (Silva), Milani, L. (Lili), Tserel, L. (Liina), Peterson, P. (Pärt), Reinmaa, E. (Eva), Hofman, A. (Albert), Uitterlinden, A.G. (André), Rivadeneira Ramirez, F. (Fernando), Homuth, G. (Georg), Petersmann, A. (Astrid), Lorbeer, R. (Roberto), Prokisch, H. (Holger), Meitinger, T. (Thomas), Herder, C. (Christian), Roden, M. (Michael), Grallert, H. (Harald), Ripatti, S. (Samuli), Perola, M. (Markus), Wood, A.R. (Andrew), Melzer, D. (David), Ferrucci, L. (Luigi), Singleton, A. (Andrew), Hernandez, D.G. (Dena), Knight, J.C. (Julian), Melchiotti, R. (Rossella), Lee, B. (Bernett), Poidinger, M. (Michael), Zolezzi, F. (Francesca), Larbi, A. (Anis), Wang, D.Y. (De Yun), Berg, L.H. (Leonard) van den, Veldink, J.H. (Jan), Rotzschke, O. (Olaf), Makino, S. (Seiko), Salomaa, V. (Veikko), Strauch, K. (Konstantin), Völker, U. (Uwe), Meurs, J.B.J. (Joyce) van, Metspalu, A. (Andres), Wijmenga, C. (Cisca), Jansen, R.C. (Ritsert), and Franke, L. (Lude)
Abstract: The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus.
Published: 2015
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17. The transcriptional landscape of age in human peripheral blood

Author: Peters, M.J. (Marjolein), Joehanes, R. (Roby), Pilling, L.C. (Luke), Schurmann, C. (Claudia), Conneely, K.N. (Karen N.), Powell, J.E. (Joseph), Reinmaa, E. (Eva), Sutphin, G.L. (George L.), Zhernakova, A. (Alexandra), Schramm, K. (Katharina), Wilson, Y.A. (Yana A.), Kobes, S. (Sayuko), Tukiainen, T. (Taru), Ramos, Y.F.M. (Yolande), Göring, H.H.H. (Harald H.), Fornage, M. (Myriam), Liu, Y. (YongMei), Gharib, S.A. (Sina), Stranger, B.E. (Barbara), Jager, P.L. (Philip) de, Aviv, A. (Abraham), Levy, D. (Daniel), Murabito, J. (Joanne), Munson, P.J. (Peter J.), Huan, T. (Tianxiao), Hofman, A. (Albert), Uitterlinden, A.G. (André), Rivadeneira Ramirez, F. (Fernando), Rooij, J.G.J. (Jeroen) van, Stolk, L. (Lisette), Broer, L. (Linda), Verbiest, M.M.P.J. (Michael), Jhamai, M. (Mila), Arp, P.P. (Pascal), Metspalu, A. (Andres), Tserel, L. (Liina), Milani, L. (Lili), Samani, N.J. (Nilesh), Peterson, P. (Pärt), Kasela, S. (Silva), Codd, V. (Veryan), Peters, A. (Annette), Ward-Caviness, C.K. (Cavin K.), Herder, C. (Christian), Waldenberger, M. (Melanie), Roden, M. (Michael), Singmann, P. (Paula), Zeilinger, S. (Sonja), Illig, T. (Thomas), Homuth, G. (Georg), Grabe, H.J. (Hans Jörgen), Völzke, H. (Henry), Steil, L. (Leif), Kocher, T. (Thomas), Murray, A. (Anna), Melzer, D. (David), Yaghootkar, H. (Hanieh), Bandinelli, S., Moses, E.K. (Eric), Kent, J.W. (Jack), Curran, J.E. (Joanne), Johnson, M.P. (Matthew), Williams-Blangero, S. (Sarah), Westra, H.J. (Harm-Jan), McRae, A.F. (Allan F.), Smith, J.A. (Jennifer A), Kardia, S.L.R. (Sharon), Hovatta, I. (Iiris), Perola, M. (Markus), Ripatti, S. (Samuli), Salomaa, V. (Veikko), Henders, A.K. (Anjali), Martin, N.G. (Nicholas), Smith, A.K. (Alicia K.), Mehta, D. (Divya), Binder, E.B. (Elisabeth B.), Nylocks, K.M. (K. Maria), Kennedy, E.M. (Elizabeth M.), Klengel, T. (Torsten), Ding, J. (Jingzhong), Suchy-Dicey, A. (Astrid), Enquobahrie, D., Brody, J.A. (Jennifer A.), Rotter, J.I. (Jerome I.), Chen, Y.-D.I. (Yii-Der I.), Houwing-Duistermaat, J.J. (Jeanine), Kloppenburg, M. (Margreet), Slagboom, P.E. (Eline), Helmer, Q. (Quinta), Hollander, W. (Wouter) den, Bean, S. (Shannon), Raj, T. (Towfique), Bakhshi, N. (Noman), Wang, Q.P. (Qiao Ping), Oyston, L.J. (Lisa J.), Psaty, B.M. (Bruce), Tracy, R.P. (Russell), Montgomery, G.W. (Grant), Turner, S.T. (Stephen), Blangero, J. (John), Meulenbelt, I. (Ingrid), Ressler, K.J. (Kerry), Yang, J. (Jian), Franke, L. (Lude), Kettunen, J. (Johannes), Visscher, P.M. (Peter), Neely, G.G. (G. Gregory), Korstanje, R. (Ron), Hanson, R.L. (Robert L.), Prokisch, H. (Holger), Ferrucci, L. (Luigi), Esko, T. (Tõnu), Teumer, A. (Alexander), Meurs, J.B.J. (Joyce) van, Johnson, A.D. (Andrew D.), Nalls, M.A. (Michael), Hernandez, D.G. (Dena), Cookson, M.R. (Mark), Gibbs, R.J. (Raphael J.), Hardy, J. (John), Ramasamy, A. (Adaikalavan), Zonderman, A.B. (Alan B.), Dillman, A. (Allissa), Traynor, B. (Bryan), Smith, C. (Colin), Longo, D.L. (Dan L.), Trabzuni, D. (Danyah), Troncoso, J.C. (Juan), Brug, M.P. (Marcel) van der, Weale, M.E. (Michael), O'Brien, R. (Richard), Johnson, R. (Robert), Walker, R. (Robert), Zielke, R.H. (Ronald H.), Arepalli, S. (Sampath), Ryten, M. (Mina), Singleton, A., Peters, M.J. (Marjolein), Joehanes, R. (Roby), Pilling, L.C. (Luke), Schurmann, C. (Claudia), Conneely, K.N. (Karen N.), Powell, J.E. (Joseph), Reinmaa, E. (Eva), Sutphin, G.L. (George L.), Zhernakova, A. (Alexandra), Schramm, K. (Katharina), Wilson, Y.A. (Yana A.), Kobes, S. (Sayuko), Tukiainen, T. (Taru), Ramos, Y.F.M. (Yolande), Göring, H.H.H. (Harald H.), Fornage, M. (Myriam), Liu, Y. (YongMei), Gharib, S.A. (Sina), Stranger, B.E. (Barbara), Jager, P.L. (Philip) de, Aviv, A. (Abraham), Levy, D. (Daniel), Murabito, J. (Joanne), Munson, P.J. (Peter J.), Huan, T. (Tianxiao), Hofman, A. (Albert), Uitterlinden, A.G. (André), Rivadeneira Ramirez, F. (Fernando), Rooij, J.G.J. (Jeroen) van, Stolk, L. (Lisette), Broer, L. (Linda), Verbiest, M.M.P.J. (Michael), Jhamai, M. (Mila), Arp, P.P. (Pascal), Metspalu, A. (Andres), Tserel, L. (Liina), Milani, L. (Lili), Samani, N.J. (Nilesh), Peterson, P. (Pärt), Kasela, S. (Silva), Codd, V. (Veryan), Peters, A. (Annette), Ward-Caviness, C.K. (Cavin K.), Herder, C. (Christian), Waldenberger, M. (Melanie), Roden, M. (Michael), Singmann, P. (Paula), Zeilinger, S. (Sonja), Illig, T. (Thomas), Homuth, G. (Georg), Grabe, H.J. (Hans Jörgen), Völzke, H. (Henry), Steil, L. (Leif), Kocher, T. (Thomas), Murray, A. (Anna), Melzer, D. (David), Yaghootkar, H. (Hanieh), Bandinelli, S., Moses, E.K. (Eric), Kent, J.W. (Jack), Curran, J.E. (Joanne), Johnson, M.P. (Matthew), Williams-Blangero, S. (Sarah), Westra, H.J. (Harm-Jan), McRae, A.F. (Allan F.), Smith, J.A. (Jennifer A), Kardia, S.L.R. (Sharon), Hovatta, I. (Iiris), Perola, M. (Markus), Ripatti, S. (Samuli), Salomaa, V. (Veikko), Henders, A.K. (Anjali), Martin, N.G. (Nicholas), Smith, A.K. (Alicia K.), Mehta, D. (Divya), Binder, E.B. (Elisabeth B.), Nylocks, K.M. (K. Maria), Kennedy, E.M. (Elizabeth M.), Klengel, T. (Torsten), Ding, J. (Jingzhong), Suchy-Dicey, A. (Astrid), Enquobahrie, D., Brody, J.A. (Jennifer A.), Rotter, J.I. (Jerome I.), Chen, Y.-D.I. (Yii-Der I.), Houwing-Duistermaat, J.J. (Jeanine), Kloppenburg, M. (Margreet), Slagboom, P.E. (Eline), Helmer, Q. (Quinta), Hollander, W. (Wouter) den, Bean, S. (Shannon), Raj, T. (Towfique), Bakhshi, N. (Noman), Wang, Q.P. (Qiao Ping), Oyston, L.J. (Lisa J.), Psaty, B.M. (Bruce), Tracy, R.P. (Russell), Montgomery, G.W. (Grant), Turner, S.T. (Stephen), Blangero, J. (John), Meulenbelt, I. (Ingrid), Ressler, K.J. (Kerry), Yang, J. (Jian), Franke, L. (Lude), Kettunen, J. (Johannes), Visscher, P.M. (Peter), Neely, G.G. (G. Gregory), Korstanje, R. (Ron), Hanson, R.L. (Robert L.), Prokisch, H. (Holger), Ferrucci, L. (Luigi), Esko, T. (Tõnu), Teumer, A. (Alexander), Meurs, J.B.J. (Joyce) van, Johnson, A.D. (Andrew D.), Nalls, M.A. (Michael), Hernandez, D.G. (Dena), Cookson, M.R. (Mark), Gibbs, R.J. (Raphael J.), Hardy, J. (John), Ramasamy, A. (Adaikalavan), Zonderman, A.B. (Alan B.), Dillman, A. (Allissa), Traynor, B. (Bryan), Smith, C. (Colin), Longo, D.L. (Dan L.), Trabzuni, D. (Danyah), Troncoso, J.C. (Juan), Brug, M.P. (Marcel) van der, Weale, M.E. (Michael), O'Brien, R. (Richard), Johnson, R. (Robert), Walker, R. (Robert), Zielke, R.H. (Ronald H.), Arepalli, S. (Sampath), Ryten, M. (Mina), and Singleton, A.
Abstract: Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the 'transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts.
Published: 2015
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18. Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease

Author: Medici, M. (Marco), Porcu, E. (Eleonora), Pistis, G. (Giorgio), Teumer, A. (Alexander), Brown, S.J. (Stephen), Jensen, R.A. (Richard), Rawal, R. (Rajesh), Roef, G.L. (Greet), Plantinga, T.S. (Theo S.), Vermeulen, S.H.H.M. (Sita), Lahti, J. (Jari), Simmonds, M.C. (Mark), Husemoen, L.L.N. (Lise Lotte), Freathy, R.M. (Rachel), Shields, B.M. (Beverley), Pietzner, D. (Diana), Nagy, R. (Rebecca), Broer, L. (Linda), Chaker, L. (Layal), Korevaar, T.I.M. (Tim), Plia, M.G. (Maria Grazia), Sala, C. (Cinzia), Völker, U. (Uwe), Richards, J.B. (Brent), Sweep, F.C. (Fred), Gieger, C. (Christian), Corre, T. (Tanguy), Kajantie, E. (Eero), Thuesen, L. (Leif), Taes, Y.E. (Youri), Visser, W.E. (Edward), Hattersley, A.T. (Andrew), Kratzsch, J. (Jürgen), Hamilton, A. (Amy), Li, W. (Wei), Homuth, G. (Georg), Lobina, M. (Monia), Mariotti, S. (Stefano), Soranzo, N. (Nicole), Cocca, M. (Massimiliano), Nauck, M. (Matthias), Spielhagen, C. (Christin), Ross, H.A. (Alec), Arnold, A.M. (Alice), Bunt, M. (Martijn) van de, Liyanarachchi, S. (Sandya), Heier, M. (Margit), Grabe, H.J. (Hans Jörgen), Masciullo, C. (Corrado), Galesloot, T.E. (Tessel), Lim, E.M. (Ee Mun), Reischl, G. (Gunilla), Leedman, P.J. (Peter), Lai, S. (Sandra), Delitala, A. (Alessandro), Bremner, A. (Alexandra), Philips, D.I.W. (David I.), Beilby, J.P. (John), Mulas, A. (Antonella), Vocale, M. (Matteo), Abecasis, G.R. (Gonçalo), Forsen, T. (Tom), James, A. (Alan), Widen, E. (Elisabeth), Hui, J. (Jennie), Prokisch, H. (Holger), Rietzschel, E.E. (Ernst), Palotie, A. (Aarno), Feddema, W. (Wouter), Fletcher, S.J. (Stephen), Schramm, K. (Katharina), Rotter, J.I. (Jerome), Kluttig, A. (Alexander), Radke, D. (Dörte), Traglia, M. (Michela), Surdulescu, G. (Gabriela), He, H. (Hao), Franklyn, J.A. (Jayne), Tiller, D. (Daniel), Vaidya, B. (Bijay), Meyer, T. (Thorsten), Jorgensen, T. (Torben), Hagen, K. (Knut), O'Leary, P.C. (Peter), Wichmann, E. (Eric), Hermus, A.R.M.M. (Ad), Psaty, B.M. (Bruce), Ittermann, T. (Till), Hofman, A. (Albert), Bosi, E. (Emanuele), Schlessinger, D. (David), Wallaschofski, H. (Henri), Pirastu, N. (Nicola), Aulchenko, Y.S. (Yurii), de la Chapelle, A. (Albert), Netea-Maier, R.T. (Romana), Gough, J.E. (Julie), Meyer zu Schwabedissen, H. (Henriette), Frayling, T.M. (Timothy), Kaufman, J.-M. (Jean-Marc), Linneberg, A. (Allan), Räikkönen, K. (Katri), Smit, J.W.A. (Jan), Kiemeney, L.A.L.M. (Bart), Rivadeneira Ramirez, F. (Fernando), Uitterlinden, A.G. (André), Walsh, J.P. (John), Meisinger, C. (Christa), Heijer, M. (Martin) den, Visser, T.J. (Theo), Spector, T.D. (Timothy), Wilson, S.G. (Scott), Völzke, H. (Henry), Cappola, A.R. (Anne), Toniolo, D. (Daniela), Sanna, S. (Serena), Naitza, S. (Silvia), Peeters, R.P. (Robin), Medici, M. (Marco), Porcu, E. (Eleonora), Pistis, G. (Giorgio), Teumer, A. (Alexander), Brown, S.J. (Stephen), Jensen, R.A. (Richard), Rawal, R. (Rajesh), Roef, G.L. (Greet), Plantinga, T.S. (Theo S.), Vermeulen, S.H.H.M. (Sita), Lahti, J. (Jari), Simmonds, M.C. (Mark), Husemoen, L.L.N. (Lise Lotte), Freathy, R.M. (Rachel), Shields, B.M. (Beverley), Pietzner, D. (Diana), Nagy, R. (Rebecca), Broer, L. (Linda), Chaker, L. (Layal), Korevaar, T.I.M. (Tim), Plia, M.G. (Maria Grazia), Sala, C. (Cinzia), Völker, U. (Uwe), Richards, J.B. (Brent), Sweep, F.C. (Fred), Gieger, C. (Christian), Corre, T. (Tanguy), Kajantie, E. (Eero), Thuesen, L. (Leif), Taes, Y.E. (Youri), Visser, W.E. (Edward), Hattersley, A.T. (Andrew), Kratzsch, J. (Jürgen), Hamilton, A. (Amy), Li, W. (Wei), Homuth, G. (Georg), Lobina, M. (Monia), Mariotti, S. (Stefano), Soranzo, N. (Nicole), Cocca, M. (Massimiliano), Nauck, M. (Matthias), Spielhagen, C. (Christin), Ross, H.A. (Alec), Arnold, A.M. (Alice), Bunt, M. (Martijn) van de, Liyanarachchi, S. (Sandya), Heier, M. (Margit), Grabe, H.J. (Hans Jörgen), Masciullo, C. (Corrado), Galesloot, T.E. (Tessel), Lim, E.M. (Ee Mun), Reischl, G. (Gunilla), Leedman, P.J. (Peter), Lai, S. (Sandra), Delitala, A. (Alessandro), Bremner, A. (Alexandra), Philips, D.I.W. (David I.), Beilby, J.P. (John), Mulas, A. (Antonella), Vocale, M. (Matteo), Abecasis, G.R. (Gonçalo), Forsen, T. (Tom), James, A. (Alan), Widen, E. (Elisabeth), Hui, J. (Jennie), Prokisch, H. (Holger), Rietzschel, E.E. (Ernst), Palotie, A. (Aarno), Feddema, W. (Wouter), Fletcher, S.J. (Stephen), Schramm, K. (Katharina), Rotter, J.I. (Jerome), Kluttig, A. (Alexander), Radke, D. (Dörte), Traglia, M. (Michela), Surdulescu, G. (Gabriela), He, H. (Hao), Franklyn, J.A. (Jayne), Tiller, D. (Daniel), Vaidya, B. (Bijay), Meyer, T. (Thorsten), Jorgensen, T. (Torben), Hagen, K. (Knut), O'Leary, P.C. (Peter), Wichmann, E. (Eric), Hermus, A.R.M.M. (Ad), Psaty, B.M. (Bruce), Ittermann, T. (Till), Hofman, A. (Albert), Bosi, E. (Emanuele), Schlessinger, D. (David), Wallaschofski, H. (Henri), Pirastu, N. (Nicola), Aulchenko, Y.S. (Yurii), de la Chapelle, A. (Albert), Netea-Maier, R.T. (Romana), Gough, J.E. (Julie), Meyer zu Schwabedissen, H. (Henriette), Frayling, T.M. (Timothy), Kaufman, J.-M. (Jean-Marc), Linneberg, A. (Allan), Räikkönen, K. (Katri), Smit, J.W.A. (Jan), Kiemeney, L.A.L.M. (Bart), Rivadeneira Ramirez, F. (Fernando), Uitterlinden, A.G. (André), Walsh, J.P. (John), Meisinger, C. (Christa), Heijer, M. (Martin) den, Visser, T.J. (Theo), Spector, T.D. (Timothy), Wilson, S.G. (Scott), Völzke, H. (Henry), Cappola, A.R. (Anne), Toniolo, D. (Daniela), Sanna, S. (Serena), Naitza, S. (Silvia), and Peeters, R.P. (Robin)
Abstract: Autoimmune thyroid diseases (AITD) are common, affecting 2-5% of the general population. Individuals with positive thyroid peroxidase antibodies (TPOAbs) have an increased risk of autoimmune hypothyroidism (Hashimoto's thyroiditis), as well as autoimmune hyperthyroidism (Graves' disease). As the possible causative genes of TPOAbs and AITD remain largely unknown, we performed GWAS meta-analyses in 18,297 individuals for TPOAb-positivity (1769 TPOAb-positives and 16,528 TPOAb-negatives) and in 12,353 individuals for TPOAb serum levels, with replication in 8,990 individuals. Significant associations (P<5×10-8) were detected at T
Published: 2014
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19. Systematic identification of trans eQTLs as putative drivers of known disease associations

Author: Westra, H.J. (Harm-Jan), Peters, M.J. (Marjolein), Esko, T. (Tõnu), Yaghootkar, H. (Hanieh), Schurmann, C. (Claudia), Kettunen, J. (Johannes), Christiansen, M.W. (Mark), Fairfax, B.P. (Benjamin), Schramm, K. (Katharina), Powell, J.E. (Joseph), Zhernakova, A. (Alexandra), Veldink, J.H. (Jan), Berg, L.H. (Leonard) van den, Karjalainen, J. (Juha), Withoff, S. (Sebo), Uitterlinden, A.G. (André), Hofman, B., Rivadeneira Ramirez, F. (Fernando), Hoen, P.A.C. (Peter) 't, Reinmaa, E. (Eva), Fischer, K. (Kathelijn), Nelis, M. (Mari), Milani, A.L. (Alfredo), Melzer, D. (David), Ferrucci, L. (Luigi), Singleton, A.B. (Andrew), Hernandez, D.G. (Dena), Nalls, M.A. (Michael), Homuth, G. (Georg), Nauck, M.A. (Matthias), Radke, D. (Dörte), Vol̈ker, U. (Uwe), Perola, M. (Markus), Salomaa, V. (Veikko), Brody, J.A. (Jennifer A.), Suchy-Dicey, A. (Astrid), Gharib, S.A. (Sina), Enquobahrie, D., Lumley, T. (Thomas), Montgomery, G.W., Makino, S. (Seiko), Prokisch, H. (Holger), Herder, C. (Christian), Roden, M. (Michael), Grallert, H. (Harald), Meitinger, T. (Thomas), Strauch, K. (Konstantin), Li, Y. (Yunmin), Jansen, J.R.C. (Jos), Visscher, P.M. (Peter M.), Knight, J.C. (Julian), Psaty, B.M. (Bruce), Ripatti, S. (Samuli), Teumer, A. (Alexander), Frayling, T.M. (Timothy), Metspalu, A. (Andres), Meurs, J.B.J. (Joyce) van, Franke, L. (Lude), Westra, H.J. (Harm-Jan), Peters, M.J. (Marjolein), Esko, T. (Tõnu), Yaghootkar, H. (Hanieh), Schurmann, C. (Claudia), Kettunen, J. (Johannes), Christiansen, M.W. (Mark), Fairfax, B.P. (Benjamin), Schramm, K. (Katharina), Powell, J.E. (Joseph), Zhernakova, A. (Alexandra), Veldink, J.H. (Jan), Berg, L.H. (Leonard) van den, Karjalainen, J. (Juha), Withoff, S. (Sebo), Uitterlinden, A.G. (André), Hofman, B., Rivadeneira Ramirez, F. (Fernando), Hoen, P.A.C. (Peter) 't, Reinmaa, E. (Eva), Fischer, K. (Kathelijn), Nelis, M. (Mari), Milani, A.L. (Alfredo), Melzer, D. (David), Ferrucci, L. (Luigi), Singleton, A.B. (Andrew), Hernandez, D.G. (Dena), Nalls, M.A. (Michael), Homuth, G. (Georg), Nauck, M.A. (Matthias), Radke, D. (Dörte), Vol̈ker, U. (Uwe), Perola, M. (Markus), Salomaa, V. (Veikko), Brody, J.A. (Jennifer A.), Suchy-Dicey, A. (Astrid), Gharib, S.A. (Sina), Enquobahrie, D., Lumley, T. (Thomas), Montgomery, G.W., Makino, S. (Seiko), Prokisch, H. (Holger), Herder, C. (Christian), Roden, M. (Michael), Grallert, H. (Harald), Meitinger, T. (Thomas), Strauch, K. (Konstantin), Li, Y. (Yunmin), Jansen, J.R.C. (Jos), Visscher, P.M. (Peter M.), Knight, J.C. (Julian), Psaty, B.M. (Bruce), Ripatti, S. (Samuli), Teumer, A. (Alexander), Frayling, T.M. (Timothy), Metspalu, A. (Andres), Meurs, J.B.J. (Joyce) van, and Franke, L. (Lude)
Abstract: Identifying the downstream effects of disease-associated SNPs is challenging. To help overcome this problem, we performed expression quantitative trait locus (eQTL) meta-analysis in non-transformed peripheral blood samples from 5,311 individuals with replication in 2,775 individuals. We identified and replicated trans eQTLs for 233 SNPs (reflecting 103 independent loci) that were previously associated with complex traits at genome-wide significance. Some of these SNPs affect multiple genes in trans that are known to be altered in individuals with disease: rs4917014, previously associated with systemic lupus erythematosus (SLE), altered gene expression of C1QB and five type I interferon response genes, both hallmarks of SLE. DeepSAGE RNA sequencing showed that rs4917014 strongly alters the 3′ UTR levels of IKZF1 in cis, and chromatin immunoprecipitation and sequencing analysis of the trans-regulated genes implicated IKZF1 as the causal gene. Variants associated with cholesterol metabolism and type 1 diabetes showed similar phenomena, indicating that large-scale eQTL mapping provides insight into the downstream effects of many trait-associated variants.
Published: 2013
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20. Multiple loci are associated with white blood cell phenotypes

Author: Nalls, M.A. (Michael), Couper, D. (David), Tanaka, T. (Toshiko), Rooij, F.J.A. (Frank) van, Chen, M-H. (Ming-Huei), Smith, A.V. (Albert Vernon), Toniolo, D. (Daniela), Zakai, N.A. (Neil), Yang, Q. (Qiong Fang), Greinacher, A. (Andreas), Wood, A.R. (Andrew), Garcia, M. (Melissa), Gasparini, P. (Paolo), Liu, Y. (YongMei), Lumley, T. (Thomas), Folsom, A.R. (Aaron), Reiner, A.P. (Alex), Gieger, C. (Christian), Lagou, V. (Vasiliki), Felix, J.F. (Janine), Völzke, H. (Henry), Gouskova, N.A. (Natalia), Biffi, A. (Alessandro), Döring, A. (Angela), Völker, U. (Uwe), Chong, S. (Sean), Wiggins, K.L. (Kerri), Rendon, A. (Augusto), Dehghan, A. (Abbas), Moore, M. (Matt), Taylor, K.D. (Kent), Wilson, J.G. (James), Lettre, G. (Guillaume), Hofman, A. (Albert), Bis, J.C. (Joshua), Pirastu, N. (Nicola), Fox, C.S. (Caroline), Meisinger, C. (Christa), Sambrook, J.G. (Jennifer), Arepalli, S. (Sampath), Nauck, M. (Matthias), Prokisch, H. (Holger), Stephens, J. (Jonathan), Glazer, N.L. (Nicole), Cupples, L.A. (Adrienne), Okada, Y. (Yukinori), Takahashi, A. (Atsushi), Kamatani, Y. (Yoichiro), Matsuda, K. (Koichi), Tsunoda, T. (Tatsuhiko), Kubo, M. (Michiaki), Nakamura, Y. (Yusuke), Yamamoto, K. (Kazuhiko), Stumvoll, M. (Michael), Tönjes, A. (Anke), Prokopenko, I. (Inga), Illig, T. (Thomas), Patel, K.V. (Kushang), Garner, S.F. (Stephen), Kuhnel, B. (Brigitte), Mangino, M. (Massimo), Oostra, B.A. (Ben), Thein, S.L., Coresh, J. (Josef), Wichmann, H.E. (Heinz Erich), Menzel, S. (Stephan), Lin, J., Pistis, G. (Giorgio), Uitterlinden, A.G. (André), Spector, T.D. (Timothy), Teumer, A. (Alexander), Eiriksdottir, G. (Gudny), Gudnason, V. (Vilmundur), Bandinelli, S. (Stefania), Frayling, T.M. (Timothy), Chakravarti, A. (Aravinda), Tikka-Kleemola, P. (Päivi), Melzer, D. (David), Ouwehand, W.H. (Willem), Levy, D. (Daniel), Boerwinkle, E.A. (Eric), Singleton, A. (Andrew), Hernandez, D.G. (Dena), Longo, D.L. (Dan), Soranzo, N. (Nicole), Witteman, J.C.M. (Jacqueline), Psaty, B.M. (Bruce), Ferrucci, L. (Luigi), Harris, T.B. (Tamara), O'Donnell, C.J. (Christopher), Ganesh, S.K. (Santhi), Nalls, M.A. (Michael), Couper, D. (David), Tanaka, T. (Toshiko), Rooij, F.J.A. (Frank) van, Chen, M-H. (Ming-Huei), Smith, A.V. (Albert Vernon), Toniolo, D. (Daniela), Zakai, N.A. (Neil), Yang, Q. (Qiong Fang), Greinacher, A. (Andreas), Wood, A.R. (Andrew), Garcia, M. (Melissa), Gasparini, P. (Paolo), Liu, Y. (YongMei), Lumley, T. (Thomas), Folsom, A.R. (Aaron), Reiner, A.P. (Alex), Gieger, C. (Christian), Lagou, V. (Vasiliki), Felix, J.F. (Janine), Völzke, H. (Henry), Gouskova, N.A. (Natalia), Biffi, A. (Alessandro), Döring, A. (Angela), Völker, U. (Uwe), Chong, S. (Sean), Wiggins, K.L. (Kerri), Rendon, A. (Augusto), Dehghan, A. (Abbas), Moore, M. (Matt), Taylor, K.D. (Kent), Wilson, J.G. (James), Lettre, G. (Guillaume), Hofman, A. (Albert), Bis, J.C. (Joshua), Pirastu, N. (Nicola), Fox, C.S. (Caroline), Meisinger, C. (Christa), Sambrook, J.G. (Jennifer), Arepalli, S. (Sampath), Nauck, M. (Matthias), Prokisch, H. (Holger), Stephens, J. (Jonathan), Glazer, N.L. (Nicole), Cupples, L.A. (Adrienne), Okada, Y. (Yukinori), Takahashi, A. (Atsushi), Kamatani, Y. (Yoichiro), Matsuda, K. (Koichi), Tsunoda, T. (Tatsuhiko), Kubo, M. (Michiaki), Nakamura, Y. (Yusuke), Yamamoto, K. (Kazuhiko), Stumvoll, M. (Michael), Tönjes, A. (Anke), Prokopenko, I. (Inga), Illig, T. (Thomas), Patel, K.V. (Kushang), Garner, S.F. (Stephen), Kuhnel, B. (Brigitte), Mangino, M. (Massimo), Oostra, B.A. (Ben), Thein, S.L., Coresh, J. (Josef), Wichmann, H.E. (Heinz Erich), Menzel, S. (Stephan), Lin, J., Pistis, G. (Giorgio), Uitterlinden, A.G. (André), Spector, T.D. (Timothy), Teumer, A. (Alexander), Eiriksdottir, G. (Gudny), Gudnason, V. (Vilmundur), Bandinelli, S. (Stefania), Frayling, T.M. (Timothy), Chakravarti, A. (Aravinda), Tikka-Kleemola, P. (Päivi), Melzer, D. (David), Ouwehand, W.H. (Willem), Levy, D. (Daniel), Boerwinkle, E.A. (Eric), Singleton, A. (Andrew), Hernandez, D.G. (Dena), Longo, D.L. (Dan), Soranzo, N. (Nicole), Witteman, J.C.M. (Jacqueline), Psaty, B.M. (Bruce), Ferrucci, L. (Luigi), Harris, T.B. (Tamara), O'Donnell, C.J. (Christopher), and Ganesh, S.K. (Santhi)
Abstract: White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count-3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte count-2q31 at ITGA4, 3q21, 8q24 an intergenic region, 9q31 near EDG2), including three previously reported associations and seven novel associations. To investigate functional relationships among variants contributing to variability in the six WBC traits, we utilized gene expression- and pathways-based analyses. We implemented gene-clustering algorithms to evaluate functional connectivity among implicated loci and showed functional relationships across cell types. Gene expression data from whole blood was utilized to show that significant biological consequences can be extracted from our genome-wide analyses, with effect estimates for significant loci from the meta-analyses being highly corellated with the proximal gene expression. In addition, collaborative efforts between the groups contributing to this study and related studies conducted by the COGENT and RIKEN groups allowed for the examination of effect homogeneity for genome-wide significant associations across populations of diverse
Published: 2011
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21. Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations

Author: Kolz, M. (Melanie), Johnson, T. (Toby), Sanna, S. (Serena), Teumer, A. (Alexander), Vitart, V. (Veronique), Perola, M. (Markus), Mangino, M. (Massimo), Albrecht, E. (Eva), Wallace, C. (Chris), Farrall, M. (Martin), Johansson, A. (Åsa), Dimas, A.S. (Antigone), Aulchenko, Y.S. (Yurii), Beckmann, J.S. (Jacques), Bergmann, S.M. (Sven), Bochud, M. (Murielle), Brown, M.J. (Morris), Campbell, H. (Harry), Connell, J. (John), Dominiczak, A. (Anna), Homuth, G. (Georg), Lamina, C. (Claudia), McCarthy, M.I. (Mark), Meitinger, T. (Thomas), Mooser, V. (Vincent), Munroe, P. (Patricia), Nauck, M. (Matthias), Peden, J. (John), Prokisch, H. (Holger), Salo, P. (Perttu), Salomaa, V. (Veikko), Samani, N.J. (Nilesh), Schlessinger, D. (David), Uda, M. (Manuela), Waeber, G. (Gérard), Waterworth, D. (Dawn), Wang-Sattler, R. (Rui), Wright, A.F. (Alan), Adamski, J. (Jerzy), Whitfield, J.B. (John), Gyllensten, U. (Ulf), Wilson, J.F. (James), Rudan, I. (Igor), Pramstaller, P.P. (Peter Paul), Watkins, H. (Hugh), Doering, A. (Angela), Wichmann, H.E. (Erich), Spector, T.D. (Timothy), Peltonen, L. (Leena Johanna), Völzke, H. (Henry), Nagaraja, R. (Ramaiah), Vollenweider, P. (Peter), Caulfield, M. (Mark), Illig, T. (Thomas), Gieger, C. (Christian), Völker, U. (Uwe), Kolz, M. (Melanie), Johnson, T. (Toby), Sanna, S. (Serena), Teumer, A. (Alexander), Vitart, V. (Veronique), Perola, M. (Markus), Mangino, M. (Massimo), Albrecht, E. (Eva), Wallace, C. (Chris), Farrall, M. (Martin), Johansson, A. (Åsa), Dimas, A.S. (Antigone), Aulchenko, Y.S. (Yurii), Beckmann, J.S. (Jacques), Bergmann, S.M. (Sven), Bochud, M. (Murielle), Brown, M.J. (Morris), Campbell, H. (Harry), Connell, J. (John), Dominiczak, A. (Anna), Homuth, G. (Georg), Lamina, C. (Claudia), McCarthy, M.I. (Mark), Meitinger, T. (Thomas), Mooser, V. (Vincent), Munroe, P. (Patricia), Nauck, M. (Matthias), Peden, J. (John), Prokisch, H. (Holger), Salo, P. (Perttu), Salomaa, V. (Veikko), Samani, N.J. (Nilesh), Schlessinger, D. (David), Uda, M. (Manuela), Waeber, G. (Gérard), Waterworth, D. (Dawn), Wang-Sattler, R. (Rui), Wright, A.F. (Alan), Adamski, J. (Jerzy), Whitfield, J.B. (John), Gyllensten, U. (Ulf), Wilson, J.F. (James), Rudan, I. (Igor), Pramstaller, P.P. (Peter Paul), Watkins, H. (Hugh), Doering, A. (Angela), Wichmann, H.E. (Erich), Spector, T.D. (Timothy), Peltonen, L. (Leena Johanna), Völzke, H. (Henry), Nagaraja, R. (Ramaiah), Vollenweider, P. (Peter), Caulfield, M. (Mark), Illig, T. (Thomas), Gieger, C. (Christian), and Völker, U. (Uwe)
Abstract: Elevated serum uric acid levels cause gout and are a risk factor for cardiovascular disease and diabetes. To investigate the polygenetic basis of serum uric acid levels, we conducted a meta-analysis of genome-wide association scans from 14 studies totalling 28,141 participants of European descent, resulting in identification of 954 SNPs distributed across nine loci that exceeded the threshold of genome-wide significance, five of which are novel. Overall, the common variants associated with serum uric acid levels fall in the following nine regions: SLC2A9 (p = 5.2×10-201), ABCG2 (p = 3.1×10-26), SLC17A1 (p = 3.0×10-14), SLC22A11 (p = 6.7×10-14), SLC22A12 (p = 2.0×10-9), SLC16A9 (p = 1.1×10-8), GCKR (p = 1.4×10-9), LRRC16A (p = 8.5×10-9), and near PDZK1 (p = 2.7×10-9). Identified variants were analyzed for gender differences. We found that the minor allele for rs734553 in SLC2A9 has greater influence in lowering uric acid levels in women and the minor allele of rs2231142 in ABCG2 elevates uric acid levels more strongly in men compared to women. To further characterize the identified variants, we analyzed their association with a panel of metabolites. rs12356193 within SLC16A9 was associated with DL-carnitine (p = 4.0×10-26) and propionyl-L-carnitine (p = 5.0×10-8) concentrations, which in turn were associated with serum UA levels (p = 1.4×10-57and p = 8.1×10-54, respectively), forming a triangle between SNP, metabolites, and UA levels. Taken together, these associations highlight additional pathways that are important in the regulation of serum uric acid levels and point toward novel potential targets for pharmacological intervention to prevent or treat hyperuricemia. In addition, these findings strongly support the hypothesis that transport proteins are key in regulating serum uric acid levels.
Published: 2009
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21 results on '"Prokisch, H. (Holger)"'

1. Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

2. Meta-analyses identify DNA methylation associated with kidney function and damage

3. DNA methylation and lipid metabolism:an EWAS of 226 metabolic measures

4. Smoking-related changes in DNA methylation and gene expression are associated with cardio-metabolic traits

5. Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

6. GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI

7. Association of methylation signals with incident coronary heart disease in an epigenome-wide assessment of circulating tumor necrosis factor α

8. A DNA methylation biomarker of alcohol consumption

9. Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

10. Clinical, biochemical and genetic spectrum of 70 patients with ACAD9 deficiency: Is riboflavin supplementation effective?

11. Identifying gene targets for brain-related traits using transcriptomic and methylomic data from blood

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

13. DNA methylation signatures of chronic low-grade inflammation are associated with complex diseases

14. A meta-analysis of gene expression signatures of blood pressure and hypertension

15. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

16. Cell Specific eQTL Analysis without Sorting Cells

17. The transcriptional landscape of age in human peripheral blood

18. Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease

19. Systematic identification of trans eQTLs as putative drivers of known disease associations

20. Multiple loci are associated with white blood cell phenotypes

21. Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations

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