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193 results on '"Eline A"'

8. Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment

Author

Bhattacharjee, Rudrarup, Jolly, Lachlan A., Corbett, Mark A., Wee, Ing Chee, Rao, Sushma R., Gardner, Alison E., Ritchie, Tarin, van Hugte, Eline J. H., Ciptasari, Ummi, Piltz, Sandra, Noll, Jacqueline E., Nazri, Nazzmer, van Eyk, Clare L., White, Melissa, Fornarino, Dani, Poulton, Cathryn, Baynam, Gareth, Collins-Praino, Lyndsey E., Snel, Marten F., Nadif Kasri, Nael, Hemsley, Kim M., Thomas, Paul Q., Kumar, Raman, and Gecz, Jozef

Published
2024
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9. Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications

Author

Sterenborg, Rosalie B. T. M., Steinbrenner, Inga, Li, Yong, Bujnis, Melissa N., Naito, Tatsuhiko, Marouli, Eirini, Galesloot, Tessel E., Babajide, Oladapo, Andreasen, Laura, Astrup, Arne, Åsvold, Bjørn Olav, Bandinelli, Stefania, Beekman, Marian, Beilby, John P., Bork-Jensen, Jette, Boutin, Thibaud, Brody, Jennifer A., Brown, Suzanne J., Brumpton, Ben, Campbell, Purdey J., Cappola, Anne R., Ceresini, Graziano, Chaker, Layal, Chasman, Daniel I., Concas, Maria Pina, Coutinho de Almeida, Rodrigo, Cross, Simone M., Cucca, Francesco, Deary, Ian J., Kjaergaard, Alisa Devedzic, Echouffo Tcheugui, Justin B., Ellervik, Christina, Eriksson, Johan G., Ferrucci, Luigi, Freudenberg, Jan, Fuchsberger, Christian, Gieger, Christian, Giulianini, Franco, Gögele, Martin, Graham, Sarah E., Grarup, Niels, Gunjača, Ivana, Hansen, Torben, Harding, Barbara N., Harris, Sarah E., Haunsø, Stig, Hayward, Caroline, Hui, Jennie, Ittermann, Till, Jukema, J. Wouter, Kajantie, Eero, Kanters, Jørgen K., Kårhus, Line L., Kiemeney, Lambertus A. L. M., Kloppenburg, Margreet, Kühnel, Brigitte, Lahti, Jari, Langenberg, Claudia, Lapauw, Bruno, Leese, Graham, Li, Shuo, Liewald, David C. M., Linneberg, Allan, Lominchar, Jesus V. T., Luan, Jian’an, Martin, Nicholas G., Matana, Antonela, Meima, Marcel E., Meitinger, Thomas, Meulenbelt, Ingrid, Mitchell, Braxton D., Møllehave, Line T., Mora, Samia, Naitza, Silvia, Nauck, Matthias, Netea-Maier, Romana T., Noordam, Raymond, Nursyifa, Casia, Okada, Yukinori, Onano, Stefano, Papadopoulou, Areti, Palmer, Colin N. A., Pattaro, Cristian, Pedersen, Oluf, Peters, Annette, Pietzner, Maik, Polašek, Ozren, Pramstaller, Peter P., Psaty, Bruce M., Punda, Ante, Ray, Debashree, Redmond, Paul, Richards, J. Brent, Ridker, Paul M., Russ, Tom C., Ryan, Kathleen A., Olesen, Morten Salling, Schultheiss, Ulla T., Selvin, Elizabeth, Siddiqui, Moneeza K., Sidore, Carlo, Slagboom, P. Eline, Sørensen, Thorkild I. A., Soto-Pedre, Enrique, Spector, Tim D., Spedicati, Beatrice, Srinivasan, Sundararajan, Starr, John M., Stott, David J., Tanaka, Toshiko, Torlak, Vesela, Trompet, Stella, Tuhkanen, Johanna, Uitterlinden, André G., van den Akker, Erik B., van den Eynde, Tibbert, van der Klauw, Melanie M., van Heemst, Diana, Verroken, Charlotte, Visser, W. Edward, Vojinovic, Dina, Völzke, Henry, Waldenberger, Melanie, Walsh, John P., Wareham, Nicholas J., Weiss, Stefan, Willer, Cristen J., Wilson, Scott G., Wolffenbuttel, Bruce H. R., Wouters, Hanneke J. C. M., Wright, Margaret J., Yang, Qiong, Zemunik, Tatijana, Zhou, Wei, Zhu, Gu, Zöllner, Sebastian, Smit, Johannes W. A., Peeters, Robin P., Köttgen, Anna, Teumer, Alexander, and Medici, Marco

Published
2024
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11. Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Author

Louis, Marie, Korlević, Petra, Nykänen, Milaja, Archer, Frederick, Berrow, Simon, Brownlow, Andrew, Lorenzen, Eline D., O’Brien, Joanne, Post, Klaas, Racimo, Fernando, Rogan, Emer, Rosel, Patricia E., Sinding, Mikkel-Holger S., van der Es, Henry, Wales, Nathan, Fontaine, Michael C., Gaggiotti, Oscar E., and Foote, Andrew D.

Published
2023
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12. Genes associated with cognitive ability and HAR show overlapping expression patterns in human cortical neuron types

Author

Driessens, Stan L. W., Galakhova, Anna A., Heyer, Djai B., Pieterse, Isabel J., Wilbers, René, Mertens, Eline J., Waleboer, Femke, Heistek, Tim S., Coenen, Loet, Meijer, Julia R., Idema, Sander, de Witt Hamer, Philip C., Noske, David P., de Kock, Christiaan P. J., Lee, Brian R., Smith, Kimberly, Ting, Jonathan T., Lein, Ed S., Mansvelder, Huibert D., and Goriounova, Natalia A.

Published
2023
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13. CD26-negative and CD26-positive tissue-resident fibroblasts contribute to functionally distinct CAF subpopulations in breast cancer

Author

Houthuijzen, Julia M., de Bruijn, Roebi, van der Burg, Eline, Drenth, Anne Paulien, Wientjens, Ellen, Filipovic, Tamara, Bullock, Esme, Brambillasca, Chiara S., Pulver, Emilia M., Nieuwland, Marja, de Rink, Iris, van Diepen, Frank, Klarenbeek, Sjoerd, Kerkhoven, Ron, Brunton, Valerie G., Scheele, Colinda L.G.J., Boelens, Mirjam C., and Jonkers, Jos

Published
2023
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14. Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers

Author

ter Brugge, Petra, Moser, Sarah C., Bièche, Ivan, Kristel, Petra, Ibadioune, Sabrina, Eeckhoutte, Alexandre, de Bruijn, Roebi, van der Burg, Eline, Lutz, Catrin, Annunziato, Stefano, de Ruiter, Julian, Masliah Planchon, Julien, Vacher, Sophie, Courtois, Laura, El-Botty, Rania, Dahmani, Ahmed, Montaudon, Elodie, Morisset, Ludivine, Sourd, Laura, Huguet, Léa, Derrien, Heloise, Nemati, Fariba, Chateau-Joubert, Sophie, Larcher, Thibaut, Salomon, Anne, Decaudin, Didier, Reyal, Fabien, Coussy, Florence, Popova, Tatiana, Wesseling, Jelle, Stern, Marc-Henri, Jonkers, Jos, and Marangoni, Elisabetta

Published
2023
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16. Cerebral small vessel disease genomics and its implications across the lifespan.

Author

Sargurupremraj, Muralidharan, Suzuki, Hideaki, Jian, Xueqiu, Sarnowski, Chloé, Evans, Tavia E, Bis, Joshua C, Eiriksdottir, Gudny, Sakaue, Saori, Terzikhan, Natalie, Habes, Mohamad, Zhao, Wei, Armstrong, Nicola J, Hofer, Edith, Yanek, Lisa R, Hagenaars, Saskia P, Kumar, Rajan B, van den Akker, Erik B, McWhirter, Rebekah E, Trompet, Stella, Mishra, Aniket, Saba, Yasaman, Satizabal, Claudia L, Beaudet, Gregory, Petit, Laurent, Tsuchida, Ami, Zago, Laure, Schilling, Sabrina, Sigurdsson, Sigurdur, Gottesman, Rebecca F, Lewis, Cora E, Aggarwal, Neelum T, Lopez, Oscar L, Smith, Jennifer A, Valdés Hernández, Maria C, van der Grond, Jeroen, Wright, Margaret J, Knol, Maria J, Dörr, Marcus, Thomson, Russell J, Bordes, Constance, Le Grand, Quentin, Duperron, Marie-Gabrielle, Smith, Albert V, Knopman, David S, Schreiner, Pamela J, Evans, Denis A, Rotter, Jerome I, Beiser, Alexa S, Maniega, Susana Muñoz, Beekman, Marian, Trollor, Julian, Stott, David J, Vernooij, Meike W, Wittfeld, Katharina, Niessen, Wiro J, Soumaré, Aicha, Boerwinkle, Eric, Sidney, Stephen, Turner, Stephen T, Davies, Gail, Thalamuthu, Anbupalam, Völker, Uwe, van Buchem, Mark A, Bryan, R Nick, Dupuis, Josée, Bastin, Mark E, Ames, David, Teumer, Alexander, Amouyel, Philippe, Kwok, John B, Bülow, Robin, Deary, Ian J, Schofield, Peter R, Brodaty, Henry, Jiang, Jiyang, Tabara, Yasuharu, Setoh, Kazuya, Miyamoto, Susumu, Yoshida, Kazumichi, Nagata, Manabu, Kamatani, Yoichiro, Matsuda, Fumihiko, Psaty, Bruce M, Bennett, David A, De Jager, Philip L, Mosley, Thomas H, Sachdev, Perminder S, Schmidt, Reinhold, Warren, Helen R, Evangelou, Evangelos, Trégouët, David-Alexandre, International Network against Thrombosis (INVENT) Consortium, International Headache Genomics Consortium (IHGC), Ikram, Mohammad A, Wen, Wei, DeCarli, Charles, Srikanth, Velandai K, Jukema, J Wouter, Slagboom, Eline P, and Kardia, Sharon LR

Subjects
International Network against Thrombosis (INVENT) Consortium, International Headache Genomics Consortium, Humans, Alzheimer Disease, Hypertension, Medical History Taking, Risk Assessment, Risk Factors, Adult, Aged, Aged, 80 and over, Middle Aged, Female, Male, Stroke, Genome-Wide Association Study, Young Adult, Diffusion Tensor Imaging, Genetic Loci, Mendelian Randomization Analysis, Cerebral Small Vessel Diseases, White Matter, and over
Abstract

White matter hyperintensities (WMH) are the most common brain-imaging feature of cerebral small vessel disease (SVD), hypertension being the main known risk factor. Here, we identify 27 genome-wide loci for WMH-volume in a cohort of 50,970 older individuals, accounting for modification/confounding by hypertension. Aggregated WMH risk variants were associated with altered white matter integrity (p = 2.5×10-7) in brain images from 1,738 young healthy adults, providing insight into the lifetime impact of SVD genetic risk. Mendelian randomization suggested causal association of increasing WMH-volume with stroke, Alzheimer-type dementia, and of increasing blood pressure (BP) with larger WMH-volume, notably also in persons without clinical hypertension. Transcriptome-wide colocalization analyses showed association of WMH-volume with expression of 39 genes, of which four encode known drug targets. Finally, we provide insight into BP-independent biological pathways underlying SVD and suggest potential for genetic stratification of high-risk individuals and for genetically-informed prioritization of drug targets for prevention trials.

Published
2020

17. A meta-analysis of genome-wide association studies identifies multiple longevity genes.

Author

Deelen, Joris, Evans, Daniel S, Arking, Dan E, Tesi, Niccolò, Nygaard, Marianne, Liu, Xiaomin, Wojczynski, Mary K, Biggs, Mary L, van der Spek, Ashley, Atzmon, Gil, Ware, Erin B, Sarnowski, Chloé, Smith, Albert V, Seppälä, Ilkka, Cordell, Heather J, Dose, Janina, Amin, Najaf, Arnold, Alice M, Ayers, Kristin L, Barzilai, Nir, Becker, Elizabeth J, Beekman, Marian, Blanché, Hélène, Christensen, Kaare, Christiansen, Lene, Collerton, Joanna C, Cubaynes, Sarah, Cummings, Steven R, Davies, Karen, Debrabant, Birgit, Deleuze, Jean-François, Duncan, Rachel, Faul, Jessica D, Franceschi, Claudio, Galan, Pilar, Gudnason, Vilmundur, Harris, Tamara B, Huisman, Martijn, Hurme, Mikko A, Jagger, Carol, Jansen, Iris, Jylhä, Marja, Kähönen, Mika, Karasik, David, Kardia, Sharon LR, Kingston, Andrew, Kirkwood, Thomas BL, Launer, Lenore J, Lehtimäki, Terho, Lieb, Wolfgang, Lyytikäinen, Leo-Pekka, Martin-Ruiz, Carmen, Min, Junxia, Nebel, Almut, Newman, Anne B, Nie, Chao, Nohr, Ellen A, Orwoll, Eric S, Perls, Thomas T, Province, Michael A, Psaty, Bruce M, Raitakari, Olli T, Reinders, Marcel JT, Robine, Jean-Marie, Rotter, Jerome I, Sebastiani, Paola, Smith, Jennifer, Sørensen, Thorkild IA, Taylor, Kent D, Uitterlinden, André G, van der Flier, Wiesje, van der Lee, Sven J, van Duijn, Cornelia M, van Heemst, Diana, Vaupel, James W, Weir, David, Ye, Kenny, Zeng, Yi, Zheng, Wanlin, Holstege, Henne, Kiel, Douglas P, Lunetta, Kathryn L, Slagboom, P Eline, and Murabito, Joanne M

Subjects
Humans, Heat-Shock Proteins, Longevity, Apolipoprotein E2, Apolipoprotein E4, Genome-Wide Association Study
Abstract

Human longevity is heritable, but genome-wide association (GWA) studies have had limited success. Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at death or at last contact was at or below the age corresponding to the 60th survival percentile. Consistent with previous reports, rs429358 (apolipoprotein E (ApoE) ε4) is associated with lower odds of surviving to the 90th and 99th percentile age, while rs7412 (ApoE ε2) shows the opposite. Moreover, rs7676745, located near GPR78, associates with lower odds of surviving to the 90th percentile age. Gene-level association analysis reveals a role for tissue-specific expression of multiple genes in longevity. Finally, genetic correlation of the longevity GWA results with that of several disease-related phenotypes points to a shared genetic architecture between health and longevity.

Published
2019

18. Hand2 delineates mesothelium progenitors and is reactivated in mesothelioma

Author

Prummel, Karin D., Crowell, Helena L., Nieuwenhuize, Susan, Brombacher, Eline C., Daetwyler, Stephan, Soneson, Charlotte, Kresoja-Rakic, Jelena, Kocere, Agnese, Ronner, Manuel, Ernst, Alexander, Labbaf, Zahra, Clouthier, David E., Firulli, Anthony B., Sánchez-Iranzo, Héctor, Naganathan, Sundar R., O’Rourke, Rebecca, Raz, Erez, Mercader, Nadia, Burger, Alexa, Felley-Bosco, Emanuela, Huisken, Jan, Robinson, Mark D., and Mosimann, Christian

Published
2022
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19. MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling

Author

Zimmerli, Dario, Brambillasca, Chiara S., Talens, Francien, Bhin, Jinhyuk, Linstra, Renske, Romanens, Lou, Bhattacharya, Arkajyoti, Joosten, Stacey E. P., Da Silva, Ana Moises, Padrao, Nuno, Wellenstein, Max D., Kersten, Kelly, de Boo, Mart, Roorda, Maurits, Henneman, Linda, de Bruijn, Roebi, Annunziato, Stefano, van der Burg, Eline, Drenth, Anne Paulien, Lutz, Catrin, Endres, Theresa, van de Ven, Marieke, Eilers, Martin, Wessels, Lodewyk, de Visser, Karin E., Zwart, Wilbert, Fehrmann, Rudolf S. N., van Vugt, Marcel A. T. M., and Jonkers, Jos

Published
2022
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20. Modification of BRCA1-associated breast cancer risk by HMMR overexpression

Author

Mateo, Francesca, He, Zhengcheng, Mei, Lin, de Garibay, Gorka Ruiz, Herranz, Carmen, García, Nadia, Lorentzian, Amanda, Baiges, Alexandra, Blommaert, Eline, Gómez, Antonio, Mirallas, Oriol, Garrido-Utrilla, Anna, Palomero, Luis, Espín, Roderic, Extremera, Ana I., Soler-Monsó, M. Teresa, Petit, Anna, Li, Rong, Brunet, Joan, Chen, Ke, Tan, Susanna, Eaves, Connie J., McCloskey, Curtis, Hakem, Razq, Khokha, Rama, Lange, Philipp F., Lázaro, Conxi, Maxwell, Christopher A., and Pujana, Miquel Angel

Published
2022
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21. Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels

Author

Jiang, Xia, O’Reilly, Paul F, Aschard, Hugues, Hsu, Yi-Hsiang, Richards, J Brent, Dupuis, Josée, Ingelsson, Erik, Karasik, David, Pilz, Stefan, Berry, Diane, Kestenbaum, Bryan, Zheng, Jusheng, Luan, Jianan, Sofianopoulou, Eleni, Streeten, Elizabeth A, Albanes, Demetrius, Lutsey, Pamela L, Yao, Lu, Tang, Weihong, Econs, Michael J, Wallaschofski, Henri, Völzke, Henry, Zhou, Ang, Power, Chris, McCarthy, Mark I, Michos, Erin D, Boerwinkle, Eric, Weinstein, Stephanie J, Freedman, Neal D, Huang, Wen-Yi, Van Schoor, Natasja M, van der Velde, Nathalie, Groot, Lisette CPGM de, Enneman, Anke, Cupples, L Adrienne, Booth, Sarah L, Vasan, Ramachandran S, Liu, Ching-Ti, Zhou, Yanhua, Ripatti, Samuli, Ohlsson, Claes, Vandenput, Liesbeth, Lorentzon, Mattias, Eriksson, Johan G, Shea, M Kyla, Houston, Denise K, Kritchevsky, Stephen B, Liu, Yongmei, Lohman, Kurt K, Ferrucci, Luigi, Peacock, Munro, Gieger, Christian, Beekman, Marian, Slagboom, Eline, Deelen, Joris, Heemst, Diana van, Kleber, Marcus E, März, Winfried, de Boer, Ian H, Wood, Alexis C, Rotter, Jerome I, Rich, Stephen S, Robinson-Cohen, Cassianne, den Heijer, Martin, Jarvelin, Marjo-Riitta, Cavadino, Alana, Joshi, Peter K, Wilson, James F, Hayward, Caroline, Lind, Lars, Michaëlsson, Karl, Trompet, Stella, Zillikens, M Carola, Uitterlinden, Andre G, Rivadeneira, Fernando, Broer, Linda, Zgaga, Lina, Campbell, Harry, Theodoratou, Evropi, Farrington, Susan M, Timofeeva, Maria, Dunlop, Malcolm G, Valdes, Ana M, Tikkanen, Emmi, Lehtimäki, Terho, Lyytikäinen, Leo-Pekka, Kähönen, Mika, Raitakari, Olli T, Mikkilä, Vera, Ikram, M Arfan, Sattar, Naveed, Jukema, J Wouter, Wareham, Nicholas J, Langenberg, Claudia, Forouhi, Nita G, Gundersen, Thomas E, Khaw, Kay-Tee, Butterworth, Adam S, Danesh, John, and Spector, Timothy

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, Clinical Research, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Amidohydrolases, Autoimmune Diseases, Cohort Studies, Female, Genome-Wide Association Study, Humans, Male, Polymorphism, Single Nucleotide, Vesicular Transport Proteins, Vitamin D, White People
Abstract

Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7×10-9 at rs8018720 in SEC23A, and P = 1.9×10-14 at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene-gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.

Published
2018

22. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

Author

Hehir-Kwa, Jayne Y, Marschall, Tobias, Kloosterman, Wigard P, Francioli, Laurent C, Baaijens, Jasmijn A, Dijkstra, Louis J, Abdellaoui, Abdel, Koval, Vyacheslav, Thung, Djie Tjwan, Wardenaar, René, Renkens, Ivo, Coe, Bradley P, Deelen, Patrick, de Ligt, Joep, Lameijer, Eric-Wubbo, van Dijk, Freerk, Hormozdiari, Fereydoun, Genome of the Netherlands Consortium, Uitterlinden, André G, van Duijn, Cornelia M, Eichler, Evan E, de Bakker, Paul IW, Swertz, Morris A, Wijmenga, Cisca, van Ommen, Gert-Jan B, Slagboom, P Eline, Boomsma, Dorret I, Schönhuth, Alexander, Ye, Kai, and Guryev, Victor

Subjects
Genome of the Netherlands Consortium, Chromosomes, Humans, RNA, Polymerase Chain Reaction, Sequence Analysis, DNA, Sequence Analysis, RNA, Computational Biology, Genomics, Gene Deletion, Genotype, Haplotypes, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome, Human, Algorithms, Software, Netherlands, INDEL Mutation, Genomic Structural Variation, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, Genome, Human
Abstract

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Published
2016

23. Identical twins carry a persistent epigenetic signature of early genome programming

Author

van Dongen, Jenny, Gordon, Scott D., McRae, Allan F., Odintsova, Veronika V., Mbarek, Hamdi, Breeze, Charles E., Sugden, Karen, Lundgren, Sara, Castillo-Fernandez, Juan E., Hannon, Eilis, Moffitt, Terrie E., Hagenbeek, Fiona A., van Beijsterveldt, Catharina E. M., Jan Hottenga, Jouke, Tsai, Pei-Chien, Min, Josine L., Hemani, Gibran, Ehli, Erik A., Paul, Franziska, Stern, Claudio D., Heijmans, Bastiaan T., Slagboom, P. Eline, Daxinger, Lucia, van der Maarel, Silvère M., de Geus, Eco J. C., Willemsen, Gonneke, Montgomery, Grant W., Reversade, Bruno, Ollikainen, Miina, Kaprio, Jaakko, Spector, Tim D., Bell, Jordana T., Mill, Jonathan, Caspi, Avshalom, Martin, Nicholas G., and Boomsma, Dorret I.

Published
2021
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25. Publisher Correction: A meta-analysis of genome-wide association studies identifies multiple longevity genes

Author

Deelen, Joris, Evans, Daniel S., Arking, Dan E., Tesi, Niccolò, Nygaard, Marianne, Liu, Xiaomin, Wojczynski, Mary K., Biggs, Mary L., van der Spek, Ashley, Atzmon, Gil, Ware, Erin B., Sarnowski, Chloé, Smith, Albert V., Seppälä, Ilkka, Cordell, Heather J., Dose, Janina, Amin, Najaf, Arnold, Alice M., Ayers, Kristin L., Barzilai, Nir, Becker, Elizabeth J., Beekman, Marian, Blanché, Hélène, Christensen, Kaare, Christiansen, Lene, Collerton, Joanna C., Cubaynes, Sarah, Cummings, Steven R., Davies, Karen, Debrabant, Birgit, Deleuze, Jean-François, Duncan, Rachel, Faul, Jessica D., Franceschi, Claudio, Galan, Pilar, Gudnason, Vilmundur, Harris, Tamara B., Huisman, Martijn, Hurme, Mikko A., Jagger, Carol, Jansen, Iris, Jylhä, Marja, Kähönen, Mika, Karasik, David, Kardia, Sharon L. R., Kingston, Andrew, Kirkwood, Thomas B. L., Launer, Lenore J., Lehtimäki, Terho, Lieb, Wolfgang, Lyytikäinen, Leo-Pekka, Martin-Ruiz, Carmen, Min, Junxia, Nebel, Almut, Newman, Anne B., Nie, Chao, Nohr, Ellen A., Orwoll, Eric S., Perls, Thomas T., Province, Michael A., Psaty, Bruce M., Raitakari, Olli T., Reinders, Marcel J. T., Robine, Jean-Marie, Rotter, Jerome I., Sebastiani, Paola, Smith, Jennifer, Sørensen, Thorkild I. A., Taylor, Kent D., Uitterlinden, André G., van der Flier, Wiesje, van der Lee, Sven J., van Duijn, Cornelia M., van Heemst, Diana, Vaupel, James W., Weir, David, Ye, Kenny, Zeng, Yi, Zheng, Wanlin, Holstege, Henne, Kiel, Douglas P., Lunetta, Kathryn L., Slagboom, P. Eline, and Murabito, Joanne M.

Published
2021
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26. Publisher Correction: Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology

Author

Stangherlin, Alessandra, Watson, Joseph L., Wong, David C. S., Barbiero, Silvia, Zeng, Aiwei, Seinkmane, Estere, Chew, Sew Peak, Beale, Andrew D., Hayter, Edward A., Guna, Alina, Inglis, Alison J., Putker, Marrit, Bartolami, Eline, Matile, Stefan, Lequeux, Nicolas, Pons, Thomas, Day, Jason, van Ooijen, Gerben, Voorhees, Rebecca M., Bechtold, David A., Derivery, Emmanuel, Edgar, Rachel S., Newham, Peter, and O’Neill, John S.

Published
2021
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28. Compensatory ion transport buffers daily protein rhythms to regulate osmotic balance and cellular physiology

Author

Stangherlin, Alessandra, Watson, Joseph L., Wong, David C. S., Barbiero, Silvia, Zeng, Aiwei, Seinkmane, Estere, Chew, Sew Peak, Beale, Andrew D., Hayter, Edward A., Guna, Alina, Inglis, Alison J., Putker, Marrit, Bartolami, Eline, Matile, Stefan, Lequeux, Nicolas, Pons, Thomas, Day, Jason, van Ooijen, Gerben, Voorhees, Rebecca M., Bechtold, David A., Derivery, Emmanuel, Edgar, Rachel S., Newham, Peter, and O’Neill, John S.

Published
2021
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29. New-onset IgG autoantibodies in hospitalized patients with COVID-19

Author

Chang, Sarah Esther, Feng, Allan, Meng, Wenzhao, Apostolidis, Sokratis A., Mack, Elisabeth, Artandi, Maja, Barman, Linda, Bennett, Kate, Chakraborty, Saborni, Chang, Iris, Cheung, Peggie, Chinthrajah, Sharon, Dhingra, Shaurya, Do, Evan, Finck, Amanda, Gaano, Andrew, Geßner, Reinhard, Giannini, Heather M., Gonzalez, Joyce, Greib, Sarah, Gündisch, Margrit, Hsu, Alex Ren, Kuo, Alex, Manohar, Monali, Mao, Rong, Neeli, Indira, Neubauer, Andreas, Oniyide, Oluwatosin, Powell, Abigail E., Puri, Rajan, Renz, Harald, Schapiro, Jeffrey, Weidenbacher, Payton A., Wittman, Richard, Ahuja, Neera, Chung, Ho-Ryun, Jagannathan, Prasanna, James, Judith A., Kim, Peter S., Meyer, Nuala J., Nadeau, Kari C., Radic, Marko, Robinson, William H., Singh, Upinder, Wang, Taia T., Wherry, E. John, Skevaki, Chrysanthi, Luning Prak, Eline T., and Utz, Paul J.

Published
2021
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30. The transcriptional landscape of age in human peripheral blood.

Author

Peters, Marjolein J, Joehanes, Roby, Pilling, Luke C, Schurmann, Claudia, Conneely, Karen N, Powell, Joseph, Reinmaa, Eva, Sutphin, George L, Zhernakova, Alexandra, Schramm, Katharina, Wilson, Yana A, Kobes, Sayuko, Tukiainen, Taru, NABEC/UKBEC Consortium, Ramos, Yolande F, Göring, Harald HH, Fornage, Myriam, Liu, Yongmei, Gharib, Sina A, Stranger, Barbara E, De Jager, Philip L, Aviv, Abraham, Levy, Daniel, Murabito, Joanne M, Munson, Peter J, Huan, Tianxiao, Hofman, Albert, Uitterlinden, André G, Rivadeneira, Fernando, van Rooij, Jeroen, Stolk, Lisette, Broer, Linda, Verbiest, Michael MPJ, Jhamai, Mila, Arp, Pascal, Metspalu, Andres, Tserel, Liina, Milani, Lili, Samani, Nilesh J, Peterson, Pärt, Kasela, Silva, Codd, Veryan, Peters, Annette, Ward-Caviness, Cavin K, Herder, Christian, Waldenberger, Melanie, Roden, Michael, Singmann, Paula, Zeilinger, Sonja, Illig, Thomas, Homuth, Georg, Grabe, Hans-Jörgen, Völzke, Henry, Steil, Leif, Kocher, Thomas, Murray, Anna, Melzer, David, Yaghootkar, Hanieh, Bandinelli, Stefania, Moses, Eric K, Kent, Jack W, Curran, Joanne E, Johnson, Matthew P, Williams-Blangero, Sarah, Westra, Harm-Jan, McRae, Allan F, Smith, Jennifer A, Kardia, Sharon LR, Hovatta, Iiris, Perola, Markus, Ripatti, Samuli, Salomaa, Veikko, Henders, Anjali K, Martin, Nicholas G, Smith, Alicia K, Mehta, Divya, Binder, Elisabeth B, Nylocks, K Maria, Kennedy, Elizabeth M, Klengel, Torsten, Ding, Jingzhong, Suchy-Dicey, Astrid M, Enquobahrie, Daniel A, Brody, Jennifer, Rotter, Jerome I, Chen, Yii-Der I, Houwing-Duistermaat, Jeanine, Kloppenburg, Margreet, Slagboom, P Eline, Helmer, Quinta, den Hollander, Wouter, Bean, Shannon, Raj, Towfique, Bakhshi, Noman, Wang, Qiao Ping, Oyston, Lisa J, Psaty, Bruce M, Tracy, Russell P, Montgomery, Grant W, and Turner, Stephen T

Subjects
NABEC/UKBEC Consortium, Humans, Gene Expression Profiling, DNA Methylation, Aging, European Continental Ancestry Group, Transcriptome, Biomarkers
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

31. Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.

Author

van Leeuwen, Elisabeth M, Karssen, Lennart C, Deelen, Joris, Isaacs, Aaron, Medina-Gomez, Carolina, Mbarek, Hamdi, Kanterakis, Alexandros, Trompet, Stella, Postmus, Iris, Verweij, Niek, van Enckevort, David J, Huffman, Jennifer E, White, Charles C, Feitosa, Mary F, Bartz, Traci M, Manichaikul, Ani, Joshi, Peter K, Peloso, Gina M, Deelen, Patrick, van Dijk, Freerk, Willemsen, Gonneke, de Geus, Eco J, Milaneschi, Yuri, Penninx, Brenda WJH, Francioli, Laurent C, Menelaou, Androniki, Pulit, Sara L, Rivadeneira, Fernando, Hofman, Albert, Oostra, Ben A, Franco, Oscar H, Mateo Leach, Irene, Beekman, Marian, de Craen, Anton JM, Uh, Hae-Won, Trochet, Holly, Hocking, Lynne J, Porteous, David J, Sattar, Naveed, Packard, Chris J, Buckley, Brendan M, Brody, Jennifer A, Bis, Joshua C, Rotter, Jerome I, Mychaleckyj, Josyf C, Campbell, Harry, Duan, Qing, Lange, Leslie A, Wilson, James F, Hayward, Caroline, Polasek, Ozren, Vitart, Veronique, Rudan, Igor, Wright, Alan F, Rich, Stephen S, Psaty, Bruce M, Borecki, Ingrid B, Kearney, Patricia M, Stott, David J, Adrienne Cupples, L, Genome of The Netherlands Consortium, Jukema, J Wouter, van der Harst, Pim, Sijbrands, Eric J, Hottenga, Jouke-Jan, Uitterlinden, Andre G, Swertz, Morris A, van Ommen, Gert-Jan B, de Bakker, Paul IW, Eline Slagboom, P, Boomsma, Dorret I, Wijmenga, Cisca, and van Duijn, Cornelia M

Subjects
Genome of The Netherlands Consortium, Humans, Cholesterol, ATP-Binding Cassette Transporters, Gene Frequency, Mutation, Missense, Netherlands, Genetic Association Studies, Mutation, Missense
Abstract

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of The Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value

Published
2015

32. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins.

Author

Postmus, Iris, Trompet, Stella, Deshmukh, Harshal A, Barnes, Michael R, Li, Xiaohui, Warren, Helen R, Chasman, Daniel I, Zhou, Kaixin, Arsenault, Benoit J, Donnelly, Louise A, Wiggins, Kerri L, Avery, Christy L, Griffin, Paula, Feng, QiPing, Taylor, Kent D, Li, Guo, Evans, Daniel S, Smith, Albert V, de Keyser, Catherine E, Johnson, Andrew D, de Craen, Anton JM, Stott, David J, Buckley, Brendan M, Ford, Ian, Westendorp, Rudi GJ, Slagboom, P Eline, Sattar, Naveed, Munroe, Patricia B, Sever, Peter, Poulter, Neil, Stanton, Alice, Shields, Denis C, O'Brien, Eoin, Shaw-Hawkins, Sue, Chen, Y-D Ida, Nickerson, Deborah A, Smith, Joshua D, Dubé, Marie Pierre, Boekholdt, S Matthijs, Hovingh, G Kees, Kastelein, John JP, McKeigue, Paul M, Betteridge, John, Neil, Andrew, Durrington, Paul N, Doney, Alex, Carr, Fiona, Morris, Andrew, McCarthy, Mark I, Groop, Leif, Ahlqvist, Emma, Welcome Trust Case Control Consortium, Bis, Joshua C, Rice, Kenneth, Smith, Nicholas L, Lumley, Thomas, Whitsel, Eric A, Stürmer, Til, Boerwinkle, Eric, Ngwa, Julius S, O'Donnell, Christopher J, Vasan, Ramachandran S, Wei, Wei-Qi, Wilke, Russell A, Liu, Ching-Ti, Sun, Fangui, Guo, Xiuqing, Heckbert, Susan R, Post, Wendy, Sotoodehnia, Nona, Arnold, Alice M, Stafford, Jeanette M, Ding, Jingzhong, Herrington, David M, Kritchevsky, Stephen B, Eiriksdottir, Gudny, Launer, Leonore J, Harris, Tamara B, Chu, Audrey Y, Giulianini, Franco, MacFadyen, Jean G, Barratt, Bryan J, Nyberg, Fredrik, Stricker, Bruno H, Uitterlinden, André G, Hofman, Albert, Rivadeneira, Fernando, Emilsson, Valur, Franco, Oscar H, Ridker, Paul M, Gudnason, Vilmundur, Liu, Yongmei, Denny, Joshua C, Ballantyne, Christie M, Rotter, Jerome I, Adrienne Cupples, L, Psaty, Bruce M, Palmer, Colin NA, Tardif, Jean-Claude, and Colhoun, Helen M

Subjects
Welcome Trust Case Control Consortium, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Pharmacogenetics, Polymorphism, Single Nucleotide, Cholesterol, LDL, Genome-Wide Association Study, Cholesterol, LDL, Polymorphism, Single Nucleotide
Abstract

Statins effectively lower LDL cholesterol levels in large studies and the observed interindividual response variability may be partially explained by genetic variation. Here we perform a pharmacogenetic meta-analysis of genome-wide association studies (GWAS) in studies addressing the LDL cholesterol response to statins, including up to 18,596 statin-treated subjects. We validate the most promising signals in a further 22,318 statin recipients and identify two loci, SORT1/CELSR2/PSRC1 and SLCO1B1, not previously identified in GWAS. Moreover, we confirm the previously described associations with APOE and LPA. Our findings advance the understanding of the pharmacogenetic architecture of statin response.

Published
2014

35. Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer

Author

Annunziato, Stefano, de Ruiter, Julian R., Henneman, Linda, Brambillasca, Chiara S., Lutz, Catrin, Vaillant, François, Ferrante, Federica, Drenth, Anne Paulien, van der Burg, Eline, Siteur, Bjørn, van Gerwen, Bas, de Bruijn, Roebi, van Miltenburg, Martine H., Huijbers, Ivo J., van de Ven, Marieke, Visvader, Jane E., Lindeman, Geoffrey J., Wessels, Lodewyk F. A., and Jonkers, Jos

Published
2019
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36. Homologous recombination deficiency derived from whole-genome sequencing predicts platinum response in triple-negative breast cancers

Author

Petra ter Brugge, Sarah C. Moser, Ivan Bièche, Petra Kristel, Sabrina Ibadioune, Alexandre Eeckhoutte, Roebi de Bruijn, Eline van der Burg, Catrin Lutz, Stefano Annunziato, Julian de Ruiter, Julien Masliah Planchon, Sophie Vacher, Laura Courtois, Rania El-Botty, Ahmed Dahmani, Elodie Montaudon, Ludivine Morisset, Laura Sourd, Léa Huguet, Heloise Derrien, Fariba Nemati, Sophie Chateau-Joubert, Thibaut Larcher, Anne Salomon, Didier Decaudin, Fabien Reyal, Florence Coussy, Tatiana Popova, Jelle Wesseling, Marc-Henri Stern, Jos Jonkers, and Elisabetta Marangoni

Subjects
Multidisciplinary, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract

The high frequency of homologous recombination deficiency (HRD) is the main rationale of testing platinum-based chemotherapy in triple-negative breast cancer (TNBC), however, the existing methods to identify HRD are controversial and there is a medical need for predictive biomarkers. We assess the in vivo response to platinum agents in 55 patient-derived xenografts (PDX) of TNBC to identify determinants of response. The HRD status, determined from whole genome sequencing, is highly predictive of platinum response. BRCA1 promoter methylation is not associated with response, in part due to residual BRCA1 gene expression and homologous recombination proficiency in different tumours showing mono-allelic methylation. Finally, in 2 cisplatin sensitive tumours we identify mutations in XRCC3 and ORC1 genes that are functionally validated in vitro. In conclusion, our results demonstrate that the genomic HRD is predictive of platinum response in a large cohort of TNBC PDX and identify alterations in XRCC3 and ORC1 genes driving cisplatin response.

Published
2023

37. A conserved regulatory program initiates lateral plate mesoderm emergence across chordates

Author

Prummel, Karin D., Hess, Christopher, Nieuwenhuize, Susan, Parker, Hugo J., Rogers, Katherine W., Kozmikova, Iryna, Racioppi, Claudia, Brombacher, Eline C., Czarkwiani, Anna, Knapp, Dunja, Burger, Sibylle, Chiavacci, Elena, Shah, Gopi, Burger, Alexa, Huisken, Jan, Yun, Maximina H., Christiaen, Lionel, Kozmik, Zbynek, Müller, Patrick, Bronner, Marianne, Krumlauf, Robb, and Mosimann, Christian

Published
2019
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38. A metabolic profile of all-cause mortality risk identified in an observational study of 44,168 individuals

Author

Deelen, Joris, Kettunen, Johannes, Fischer, Krista, van der Spek, Ashley, Trompet, Stella, Kastenmüller, Gabi, Boyd, Andy, Zierer, Jonas, van den Akker, Erik B., Ala-Korpela, Mika, Amin, Najaf, Demirkan, Ayse, Ghanbari, Mohsen, van Heemst, Diana, Ikram, M. Arfan, van Klinken, Jan Bert, Mooijaart, Simon P., Peters, Annette, Salomaa, Veikko, Sattar, Naveed, Spector, Tim D., Tiemeier, Henning, Verhoeven, Aswin, Waldenberger, Melanie, Würtz, Peter, Davey Smith, George, Metspalu, Andres, Perola, Markus, Menni, Cristina, Geleijnse, Johanna M., Drenos, Fotios, Beekman, Marian, Jukema, J. Wouter, van Duijn, Cornelia M., and Slagboom, P. Eline

Published
2019
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39. Author Correction: Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

Author

Davies, Gail, Lam, Max, Harris, Sarah E., Trampush, Joey W., Luciano, Michelle, Hill, W. David, Hagenaars, Saskia P., Ritchie, Stuart J., Marioni, Riccardo E., Fawns-Ritchie, Chloe, Liewald, David C. M., Okely, Judith A., Ahola-Olli, Ari V., Barnes, Catriona L. K., Bertram, Lars, Bis, Joshua C., Burdick, Katherine E., Christoforou, Andrea, DeRosse, Pamela, Djurovic, Srdjan, Espeseth, Thomas, Giakoumaki, Stella, Giddaluru, Sudheer, Gustavson, Daniel E., Hayward, Caroline, Hofer, Edith, Ikram, M. Arfan, Karlsson, Robert, Knowles, Emma, Lahti, Jari, Leber, Markus, Li, Shuo, Mather, Karen A., Melle, Ingrid, Morris, Derek, Oldmeadow, Christopher, Palviainen, Teemu, Payton, Antony, Pazoki, Raha, Petrovic, Katja, Reynolds, Chandra A., Sargurupremraj, Muralidharan, Scholz, Markus, Smith, Jennifer A., Smith, Albert V., Terzikhan, Natalie, Thalamuthu, Anbupalam, Trompet, Stella, van der Lee, Sven J., Ware, Erin B., Windham, B. Gwen, Wright, Margaret J., Yang, Jingyun, Yu, Jin, Ames, David, Amin, Najaf, Amouyel, Philippe, Andreassen, Ole A., Armstrong, Nicola J., Assareh, Amelia A., Attia, John R., Attix, Deborah, Avramopoulos, Dimitrios, Bennett, David A., Böhmer, Anne C., Boyle, Patricia A., Brodaty, Henry, Campbell, Harry, Cannon, Tyrone D., Cirulli, Elizabeth T., Congdon, Eliza, Conley, Emily Drabant, Corley, Janie, Cox, Simon R., Dale, Anders M., Dehghan, Abbas, Dick, Danielle, Dickinson, Dwight, Eriksson, Johan G., Evangelou, Evangelos, Faul, Jessica D., Ford, Ian, Freimer, Nelson A., Gao, He, Giegling, Ina, Gillespie, Nathan A., Gordon, Scott D., Gottesman, Rebecca F., Griswold, Michael E., Gudnason, Vilmundur, Harris, Tamara B., Hartmann, Annette M., Hatzimanolis, Alex, Heiss, Gerardo, Holliday, Elizabeth G., Joshi, Peter K., Kähönen, Mika, Kardia, Sharon L. R., Karlsson, Ida, Kleineidam, Luca, Knopman, David S., Kochan, Nicole A., Konte, Bettina, Kwok, John B., Le Hellard, Stephanie, Lee, Teresa, Lehtimäki, Terho, Li, Shu-Chen, Lill, Christina M., Liu, Tian, Koini, Marisa, London, Edythe, Longstreth, Jr, Will T., Lopez, Oscar L., Loukola, Anu, Luck, Tobias, Lundervold, Astri J., Lundquist, Anders, Lyytikäinen, Leo-Pekka, Martin, Nicholas G., Montgomery, Grant W., Murray, Alison D., Need, Anna C., Noordam, Raymond, Nyberg, Lars, Ollier, William, Papenberg, Goran, Pattie, Alison, Polasek, Ozren, Poldrack, Russell A., Psaty, Bruce M., Reppermund, Simone, Riedel-Heller, Steffi G., Rose, Richard J., Rotter, Jerome I., Roussos, Panos, Rovio, Suvi P., Saba, Yasaman, Sabb, Fred W., Sachdev, Perminder S., Satizabal, Claudia L., Schmid, Matthias, Scott, Rodney J., Scult, Matthew A., Simino, Jeannette, Slagboom, P. Eline, Smyrnis, Nikolaos, Soumaré, Aïcha, Stefanis, Nikos C., Stott, David J., Straub, Richard E., Sundet, Kjetil, Taylor, Adele M., Taylor, Kent D., Tzoulaki, Ioanna, Tzourio, Christophe, Uitterlinden, André, Vitart, Veronique, Voineskos, Aristotle N., Kaprio, Jaakko, Wagner, Michael, Wagner, Holger, Weinhold, Leonie, Wen, K. Hoyan, Widen, Elisabeth, Yang, Qiong, Zhao, Wei, Adams, Hieab H. H., Arking, Dan E., Bilder, Robert M., Bitsios, Panos, Boerwinkle, Eric, Chiba-Falek, Ornit, Corvin, Aiden, De Jager, Philip L., Debette, Stéphanie, Donohoe, Gary, Elliott, Paul, Fitzpatrick, Annette L., Gill, Michael, Glahn, David C., Hägg, Sara, Hansell, Narelle K., Hariri, Ahmad R., Ikram, M. Kamran, Jukema, J. Wouter, Vuoksimaa, Eero, Keller, Matthew C., Kremen, William S., Launer, Lenore, Lindenberger, Ulman, Palotie, Aarno, Pedersen, Nancy L., Pendleton, Neil, Porteous, David J., Räikkönen, Katri, Raitakari, Olli T., Ramirez, Alfredo, Reinvang, Ivar, Rudan, Igor, Dan Rujescu, Schmidt, Reinhold, Schmidt, Helena, Schofield, Peter W., Schofield, Peter R., Starr, John M., Steen, Vidar M., Trollor, Julian N., Turner, Steven T., Van Duijn, Cornelia M., Villringer, Arno, Weinberger, Daniel R., Weir, David R., Wilson, James F., Malhotra, Anil, McIntosh, Andrew M., Gale, Catharine R., Seshadri, Sudha, Mosley, Jr, Thomas H., Bressler, Jan, Lencz, Todd, and Deary, Ian J.

Published
2019
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42. Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation

Author

Teumer, Alexander, Chaker, Layal, Groeneweg, Stefan, Li, Yong, Di Munno, Celia, Barbieri, Caterina, Schultheiss, Ulla T., Traglia, Michela, Ahluwalia, Tarunveer S., Akiyama, Masato, Appel, Emil Vincent R., Arking, Dan E., Arnold, Alice, Astrup, Arne, Beekman, Marian, Beilby, John P., Bekaert, Sofie, Boerwinkle, Eric, Brown, Suzanne J., De Buyzere, Marc, Campbell, Purdey J., Ceresini, Graziano, Cerqueira, Charlotte, Cucca, Francesco, Deary, Ian J., Deelen, Joris, Eckardt, Kai-Uwe, Ekici, Arif B., Eriksson, Johan G., Ferrrucci, Luigi, Fiers, Tom, Fiorillo, Edoardo, Ford, Ian, Fox, Caroline S., Fuchsberger, Christian, Galesloot, Tessel E., Gieger, Christian, Gögele, Martin, De Grandi, Alessandro, Grarup, Niels, Greiser, Karin Halina, Haljas, Kadri, Hansen, Torben, Harris, Sarah E., van Heemst, Diana, den Heijer, Martin, Hicks, Andrew A., den Hollander, Wouter, Homuth, Georg, Hui, Jennie, Ikram, M. Arfan, Ittermann, Till, Jensen, Richard A., Jing, Jiaojiao, Jukema, J. Wouter, Kajantie, Eero, Kamatani, Yoichiro, Kasbohm, Elisa, Kaufman, Jean-Marc, Kiemeney, Lambertus A., Kloppenburg, Margreet, Kronenberg, Florian, Kubo, Michiaki, Lahti, Jari, Lapauw, Bruno, Li, Shuo, Liewald, David C. M., Lifelines Cohort Study, Lim, Ee Mun, Linneberg, Allan, Marina, Michela, Mascalzoni, Deborah, Matsuda, Koichi, Medenwald, Daniel, Meisinger, Christa, Meulenbelt, Ingrid, De Meyer, Tim, Meyer zu Schwabedissen, Henriette E., Mikolajczyk, Rafael, Moed, Matthijs, Netea-Maier, Romana T., Nolte, Ilja M., Okada, Yukinori, Pala, Mauro, Pattaro, Cristian, Pedersen, Oluf, Petersmann, Astrid, Porcu, Eleonora, Postmus, Iris, Pramstaller, Peter P., Psaty, Bruce M., Ramos, Yolande F. M., Rawal, Rajesh, Redmond, Paul, Richards, J. Brent, Rietzschel, Ernst R., Rivadeneira, Fernando, Roef, Greet, Rotter, Jerome I., Sala, Cinzia F., Schlessinger, David, Selvin, Elizabeth, Slagboom, P. Eline, Soranzo, Nicole, Sørensen, Thorkild I. A., Spector, Timothy D., Starr, John M., Stott, David J., Taes, Youri, Taliun, Daniel, Tanaka, Toshiko, Thuesen, Betina, Tiller, Daniel, Toniolo, Daniela, Uitterlinden, Andre G., Visser, W. Edward, Walsh, John P., Wilson, Scott G., Wolffenbuttel, Bruce H. R., Yang, Qiong, Zheng, Hou-Feng, Cappola, Anne, Peeters, Robin P., Naitza, Silvia, Völzke, Henry, Sanna, Serena, Köttgen, Anna, Visser, Theo J., and Medici, Marco

Published
2018
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43. Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

Author

Luijk, René, Wu, Haoyu, Ward-Caviness, Cavin K, Hannon, Eilis, Carnero-Montoro, Elena, Min, Josine L., Mandaviya, Pooja, Müller-Nurasyid, Martina, Mei, Hailiang, van der Maarel, Silvere M., BIOS Consortium, Relton, Caroline, Mill, Jonathan, Waldenberger, Melanie, Bell, Jordana T., Jansen, Rick, Zhernakova, Alexandra, Franke, Lude, ‘t Hoen, Peter A. C., Boomsma, Dorret I., van Duijn, Cornelia M., van Greevenbroek, Marleen M. J., Veldink, Jan H., Wijmenga, Cisca, van Meurs, Joyce, Daxinger, Lucia, Slagboom, P. Eline, van Zwet, Erik W., and Heijmans, Bastiaan T.

Published
2018
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44. Genome-wide identification of directed gene networks using large-scale population genomics data

Author

Luijk, René, Dekkers, Koen F., van Iterson, Maarten, Arindrarto, Wibowo, Claringbould, Annique, Hop, Paul, Boomsma, Dorret I., van Duijn, Cornelia M., van Greevenbroek, Marleen M. J., Veldink, Jan H., Wijmenga, Cisca, Franke, Lude, ’t Hoen, Peter A. C., Jansen, Rick, van Meurs, Joyce, Mei, Hailiang, Slagboom, P. Eline, Heijmans, Bastiaan T., van Zwet, Erik W., and BIOS (Biobank-based Integrative Omics Study) Consortium

Published
2018
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45. Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

Author

Davies, Gail, Lam, Max, Harris, Sarah E., Trampush, Joey W., Luciano, Michelle, Hill, W. David, Hagenaars, Saskia P., Ritchie, Stuart J., Marioni, Riccardo E., Fawns-Ritchie, Chloe, Liewald, David C. M., Okely, Judith A., Ahola-Olli, Ari V., Barnes, Catriona L. K., Bertram, Lars, Bis, Joshua C., Burdick, Katherine E., Christoforou, Andrea, DeRosse, Pamela, Djurovic, Srdjan, Espeseth, Thomas, Giakoumaki, Stella, Giddaluru, Sudheer, Gustavson, Daniel E., Hayward, Caroline, Hofer, Edith, Ikram, M. Arfan, Karlsson, Robert, Knowles, Emma, Lahti, Jari, Leber, Markus, Li, Shuo, Mather, Karen A., Melle, Ingrid, Morris, Derek, Oldmeadow, Christopher, Palviainen, Teemu, Payton, Antony, Pazoki, Raha, Petrovic, Katja, Reynolds, Chandra A., Sargurupremraj, Muralidharan, Scholz, Markus, Smith, Jennifer A., Smith, Albert V., Terzikhan, Natalie, Thalamuthu, Anbupalam, Trompet, Stella, van der Lee, Sven J., Ware, Erin B., Windham, B. Gwen, Wright, Margaret J., Yang, Jingyun, Yu, Jin, Ames, David, Amin, Najaf, Amouyel, Philippe, Andreassen, Ole A., Armstrong, Nicola J., Assareh, Amelia A., Attia, John R., Attix, Deborah, Avramopoulos, Dimitrios, Bennett, David A., Böhmer, Anne C., Boyle, Patricia A., Brodaty, Henry, Campbell, Harry, Cannon, Tyrone D., Cirulli, Elizabeth T., Congdon, Eliza, Conley, Emily Drabant, Corley, Janie, Cox, Simon R., Dale, Anders M., Dehghan, Abbas, Dick, Danielle, Dickinson, Dwight, Eriksson, Johan G., Evangelou, Evangelos, Faul, Jessica D., Ford, Ian, Freimer, Nelson A., Gao, He, Giegling, Ina, Gillespie, Nathan A., Gordon, Scott D., Gottesman, Rebecca F., Griswold, Michael E., Gudnason, Vilmundur, Harris, Tamara B., Hartmann, Annette M., Hatzimanolis, Alex, Heiss, Gerardo, Holliday, Elizabeth G., Joshi, Peter K., Kähönen, Mika, Kardia, Sharon L. R., Karlsson, Ida, Kleineidam, Luca, Knopman, David S., Kochan, Nicole A., Konte, Bettina, Kwok, John B., Le Hellard, Stephanie, Lee, Teresa, Lehtimäki, Terho, Li, Shu-Chen, Lill, Christina M., Liu, Tian, Koini, Marisa, London, Edythe, Longstreth, Jr, Will T., Lopez, Oscar L., Loukola, Anu, Luck, Tobias, Lundervold, Astri J., Lundquist, Anders, Lyytikäinen, Leo-Pekka, Martin, Nicholas G., Montgomery, Grant W., Murray, Alison D., Need, Anna C., Noordam, Raymond, Nyberg, Lars, Ollier, William, Papenberg, Goran, Pattie, Alison, Polasek, Ozren, Poldrack, Russell A., Psaty, Bruce M., Reppermund, Simone, Riedel-Heller, Steffi G., Rose, Richard J., Rotter, Jerome I., Roussos, Panos, Rovio, Suvi P., Saba, Yasaman, Sabb, Fred W., Sachdev, Perminder S., Satizabal, Claudia L., Schmid, Matthias, Scott, Rodney J., Scult, Matthew A., Simino, Jeannette, Slagboom, P. Eline, Smyrnis, Nikolaos, Soumaré, Aïcha, Stefanis, Nikos C., Stott, David J., Straub, Richard E., Sundet, Kjetil, Taylor, Adele M., Taylor, Kent D., Tzoulaki, Ioanna, Tzourio, Christophe, Uitterlinden, André, Vitart, Veronique, Voineskos, Aristotle N., Kaprio, Jaakko, Wagner, Michael, Wagner, Holger, Weinhold, Leonie, Wen, K. Hoyan, Widen, Elisabeth, Yang, Qiong, Zhao, Wei, Adams, Hieab H. H., Arking, Dan E., Bilder, Robert M., Bitsios, Panos, Boerwinkle, Eric, Chiba-Falek, Ornit, Corvin, Aiden, De Jager, Philip L., Debette, Stéphanie, Donohoe, Gary, Elliott, Paul, Fitzpatrick, Annette L., Gill, Michael, Glahn, David C., Hägg, Sara, Hansell, Narelle K., Hariri, Ahmad R., Ikram, M. Kamran, Jukema, J. Wouter, Vuoksimaa, Eero, Keller, Matthew C., Kremen, William S., Launer, Lenore, Lindenberger, Ulman, Palotie, Aarno, Pedersen, Nancy L., Pendleton, Neil, Porteous, David J., Räikkönen, Katri, Raitakari, Olli T., Ramirez, Alfredo, Reinvang, Ivar, Rudan, Igor, Dan Rujescu, Schmidt, Reinhold, Schmidt, Helena, Schofield, Peter W., Schofield, Peter R., Starr, John M., Steen, Vidar M., Trollor, Julian N., Turner, Steven T., Van Duijn, Cornelia M., Villringer, Arno, Weinberger, Daniel R., Weir, David R., Wilson, James F., Malhotra, Anil, McIntosh, Andrew M., Gale, Catharine R., Seshadri, Sudha, Mosley, Jr, Thomas H., Bressler, Jan, Lencz, Todd, and Deary, Ian J.

Published
2018
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46. Structure-based evolution of a promiscuous inhibitor to a selective stabilizer of protein–protein interactions

Author

Markus Kaiser, Kathrin Plitzko, Lech-Gustav Milroy, Christian Ottmann, Eline Sijbesma, Philipp Thiel, Emira Visser, Luc Brunsveld, Chemical Biology, and ICMS Core

Subjects
Virtual screening, 0301 basic medicine, Science, Chemie, General Physics and Astronomy, 02 engineering and technology, Computational biology, Mechanism of action, Crystallography, X-Ray, Molecular Docking Simulation, Article, General Biochemistry, Genetics and Molecular Biology, Protein–protein interaction, Small Molecule Libraries, Structure-Activity Relationship, 03 medical and health sciences, Drug Discovery, lcsh:Science, X-ray crystallography, Multidisciplinary, Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Drug discovery, Chemistry, Rational design, General Chemistry, 021001 nanoscience & nanotechnology, Small molecule, 030104 developmental biology, 14-3-3 Proteins, Drug Design, lcsh:Q, Structure-based drug design, 0210 nano-technology, Biologie, Protein Binding, Stabilizer (chemistry)
Abstract

The systematic stabilization of protein–protein interactions (PPI) has great potential as innovative drug discovery strategy to target novel and hard-to-drug protein classes. The current lack of chemical starting points and focused screening opportunities limits the identification of small molecule stabilizers that engage two proteins simultaneously. Starting from our previously described virtual screening strategy to identify inhibitors of 14-3-3 proteins, we report a conceptual molecular docking approach providing concrete entries for discovery and rational optimization of stabilizers for the interaction of 14-3-3 with the carbohydrate-response element-binding protein (ChREBP). X-ray crystallography reveals a distinct difference in the binding modes between weak and general inhibitors of 14-3-3 complexes and a specific, potent stabilizer of the 14-3-3/ChREBP complex. Structure-guided stabilizer optimization results in selective, up to 26-fold enhancement of the 14-3-3/ChREBP interaction. This study demonstrates the potential of rational design approaches for the development of selective PPI stabilizers starting from weak, promiscuous PPI inhibitors., Small molecule stabilizers of protein–protein interactions hold great therapeutic potential. Based on virtual screening and molecular docking, the authors here develop a strategy to evolve weak, promiscuous inhibitors of 14-3-3 interactions into selective stabilizers of the 14-3-3/ChREBP complex.

Published
2020

47. Altered function and differentiation of age-associated B cells contribute to the female bias in lupus mice

Author

Michela Manni, Juan Rivera-Correa, Daniel Jenkins, Tania Pannellini, Eline T. Luning Prak, Sanjay Gupta, Yurii Chinenov, Peter K. Sculco, Aaron M. Rosenfeld, Rolf Jessberger, Alessandra B. Pernis, Danny Flores-Castro, Edd Ricker, Wenzhao Meng, and Mahesh Bachu

Subjects
Male, Aging, Science, Population, General Physics and Astronomy, CD11c, Autoimmunity, Kaplan-Meier Estimate, Biology, medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, Article, Minor Histocompatibility Antigens, Immune system, Systemic lupus erythematosus, Sex Factors, Downregulation and upregulation, medicine, Animals, Guanine Nucleotide Exchange Factors, Lupus Erythematosus, Systemic, education, Cells, Cultured, Mice, Knockout, education.field_of_study, B cells, B-Lymphocytes, Multidisciplinary, Lupus erythematosus, fungi, Age Factors, Nuclear Proteins, Cell Differentiation, General Chemistry, TLR7, medicine.disease, CD11c Antigen, DNA-Binding Proteins, Mice, Inbred C57BL, Immunology, Female, T-Box Domain Proteins
Abstract

Differences in immune responses to viruses and autoimmune diseases such as systemic lupus erythematosus (SLE) can show sexual dimorphism. Age-associated B cells (ABC) are a population of CD11c+T-bet+ B cells critical for antiviral responses and autoimmune disorders. Absence of DEF6 and SWAP-70, two homologous guanine exchange factors, in double-knock-out (DKO) mice leads to a lupus-like syndrome in females marked by accumulation of ABCs. Here we demonstrate that DKO ABCs show sex-specific differences in cell number, upregulation of an ISG signature, and further differentiation. DKO ABCs undergo oligoclonal expansion and differentiate into both CD11c+ and CD11c− effector B cell populations with pathogenic and pro-inflammatory function as demonstrated by BCR sequencing and fate-mapping experiments. Tlr7 duplication in DKO males overrides the sex-bias and further augments the dissemination and pathogenicity of ABCs, resulting in severe pulmonary inflammation and early mortality. Thus, sexual dimorphism shapes the expansion, function and differentiation of ABCs that accompanies TLR7-driven immunopathogenesis., Autoimmunity mediated by age-associated B cells (ABC) can affect males and females differently. Here, using a lupus-like mouse model that affects females more severely, the authors observe an ABC mediated and guanine nucleotide exchange factor (GEF) restrained pathogenic process involving TLR7.

Published
2021

48. Rebalancing of actomyosin contractility enables mammary tumor formation upon loss of E-cadherin

Author

Jos Jonkers, Micha Nethe, Anne Paulien Drenth, Eline van der Burg, Koen Schipper, Veronika Ramovs, Arnoud Sonnenberg, Jacco van Rheenen, Danielle Seinstra, and Landsteiner Laboratory

Subjects
0301 basic medicine, Stromal cell, Cell Survival, Science, Primary Cell Culture, General Physics and Astronomy, Breast Neoplasms, Mice, Transgenic, 02 engineering and technology, General Biochemistry, Genetics and Molecular Biology, Fat pad, Article, CDH1, Contractility, 03 medical and health sciences, Mice, Mammary Glands, Animal, Breast cancer, Laminin, medicine, Cell Adhesion, Animals, lcsh:Science, Cells, Cultured, Mammary tumor, Multidisciplinary, biology, Chemistry, Cadherin, Mammary Neoplasms, Experimental, Epithelial Cells, General Chemistry, Actomyosin, 021001 nanoscience & nanotechnology, Cadherins, Cell biology, Carcinoma, Lobular, 030104 developmental biology, medicine.anatomical_structure, biology.protein, Basal lamina, Female, lcsh:Q, 0210 nano-technology
Abstract

E-cadherin (CDH1) is a master regulator of epithelial cell adherence junctions and a well-established tumor suppressor in Invasive Lobular Carcinoma (ILC). Intriguingly, somatic inactivation of E-cadherin alone in mouse mammary epithelial cells (MMECs) is insufficient to induce tumor formation. Here we show that E-cadherin loss induces extrusion of luminal MMECs to the basal lamina. Remarkably, E-cadherin-deficient MMECs can breach the basal lamina but do not disseminate into the surrounding fat pad. Basal lamina components laminin and collagen IV supported adhesion and survival of E-cadherin-deficient MMECs while collagen I, the principle component of the mammary stromal micro-environment did not. We uncovered that relaxation of actomyosin contractility mediates adhesion and survival of E-cadherin-deficient MMECs on collagen I, thereby allowing ILC development. Together, these findings unmask the direct consequences of E-cadherin inactivation in the mammary gland and identify aberrant actomyosin contractility as a critical barrier to ILC formation., E-cadherin is a well-known tumor suppressor albeit loss of E-cadherin alone is insufficient to induce mammary tumorigenesis. Here the authors report that epithelial cells that have lost E-cadherin can survive by extruding to the basal lamina but require rebalancing of actomyosin contractility to drive tumor development.

Published
2019

49. Publisher Correction: A meta-analysis of genome-wide association studies identifies multiple longevity genes

Author

Sarah Cubaynes, Joanne M. Murabito, Eric S. Orwoll, Iris E. Jansen, Joanna Collerton, Vilmundur Gudnason, Mikko Hurme, Paola Sebastiani, Carol Jagger, Carmen Martin-Ruiz, Douglas P. Kiel, Henne Holstege, Kenny Ye, Pilar Galan, Wolfgang Lieb, Diana van Heemst, Janina Dose, Wanlin Zheng, Ilkka Seppälä, Ashley van der Spek, Jessica D. Faul, Nir Barzilai, David R. Weir, James W. Vaupel, Wiesje M. van der Flier, Dan E. Arking, Terho Lehtimäki, Marja Jylhä, Thomas B. L. Kirkwood, Andrew Kingston, Marcel J. T. Reinders, Jean-François Deleuze, Cornelia M. van Duijn, Hélène Blanché, Anne B. Newman, Chao Nie, Elizabeth J. Becker, Daniel S. Evans, P. Eline Slagboom, Marianne Nygaard, Lene Christiansen, Jean Marie Robine, Junxia Min, Almut Nebel, Tamara B. Harris, Lenore J. Launer, Mary K. Wojczynski, Ellen A. Nohr, Alice M. Arnold, Olli T. Raitakari, Birgit Debrabant, Jerome I. Rotter, Thorkild I. A. Sørensen, André G. Uitterlinden, Steven R. Cummings, Kristin L. Ayers, Jennifer A. Smith, Joris Deelen, Yi Zeng, Chloé Sarnowski, Heather J. Cordell, Karen Davies, Kent D. Taylor, Mika Kähönen, Albert V. Smith, Najaf Amin, Rachel Duncan, Michael A. Province, Leo-Pekka Lyytikäinen, Kathryn L. Lunetta, Kaare Christensen, Sharon L.R. Kardia, Thomas T. Perls, Erin B. Ware, Martijn Huisman, Mary L. Biggs, Marian Beekman, Sven J. van der Lee, David Karasik, Niccolò Tesi, Xiaomin Liu, Gil Atzmon, Claudio Franceschi, and Bruce M. Psaty

Subjects
Apolipoprotein E2, Science, Apolipoprotein E4, Longevity, MEDLINE, General Physics and Astronomy, Genome-wide association study, Diseases, Computational biology, Biology, Longevity genes, Genome-wide association studies, GeneralLiterature_MISCELLANEOUS, General Biochemistry, Genetics and Molecular Biology, SNP, Humans, Endoplasmic Reticulum Chaperone BiP, Heat-Shock Proteins, Multidisciplinary, Published Erratum, General Chemistry, Publisher Correction, Ageing, ComputingMethodologies_PATTERNRECOGNITION, Risk factors, Meta-analysis, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Genome-Wide Association Study
Abstract

Human longevity is heritable, but genome-wide association (GWA) studies have had limited success. Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at death or at last contact was at or below the age corresponding to the 60th survival percentile. Consistent with previous reports, rs429358 (apolipoprotein E (ApoE) ε4) is associated with lower odds of surviving to the 90th and 99th percentile age, while rs7412 (ApoE ε2) shows the opposite. Moreover, rs7676745, located near GPR78, associates with lower odds of surviving to the 90th percentile age. Gene-level association analysis reveals a role for tissue-specific expression of multiple genes in longevity. Finally, genetic correlation of the longevity GWA results with that of several disease-related phenotypes points to a shared genetic architecture between health and longevity.

Published
2021

50. A full gap above the Fermi level: the charge density wave of monolayer VS

Author

Camiel, van Efferen, Jan, Berges, Joshua, Hall, Erik, van Loon, Stefan, Kraus, Arne, Schobert, Tobias, Wekking, Felix, Huttmann, Eline, Plaar, Nico, Rothenbach, Katharina, Ollefs, Lucas Machado, Arruda, Nick, Brookes, Gunnar, Schönhoff, Kurt, Kummer, Heiko, Wende, Tim, Wehling, and Thomas, Michely

Subjects
Condensed Matter::Materials Science, Electronic properties and materials, Magnetic properties and materials, Condensed Matter::Superconductivity, Condensed Matter::Strongly Correlated Electrons, Two-dimensional materials, Article
Abstract

In the standard model of charge density wave (CDW) transitions, the displacement along a single phonon mode lowers the total electronic energy by creating a gap at the Fermi level, making the CDW a metal–insulator transition. Here, using scanning tunneling microscopy and spectroscopy and ab initio calculations, we show that VS2 realizes a CDW which stands out of this standard model. There is a full CDW gap residing in the unoccupied states of monolayer VS2. At the Fermi level, the CDW induces a topological metal-metal (Lifshitz) transition. Non-linear coupling of transverse and longitudinal phonons is essential for the formation of the CDW and the full gap above the Fermi level. Additionally, x-ray magnetic circular dichroism reveals the absence of net magnetization in this phase, pointing to coexisting charge and spin density waves in the ground state., A charge density wave (CDW) normally creates a gap at the Fermi level, inducing a metal-insulator transition. Here, the authors report that a CDW gap resides in the unoccupied states but induces a topological metal-metal transition at the Fermi level in monolayer VS2.

Published
2020

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