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3. Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion.

Author

Cleynen, Isabelle, Engchuan, Worrawat, Hestand, Matthew S, Heung, Tracy, Holleman, Aaron M, Johnston, H Richard, Monfeuga, Thomas, McDonald-McGinn, Donna M, Gur, Raquel E, Morrow, Bernice E, Swillen, Ann, Vorstman, Jacob AS, Bearden, Carrie E, Chow, Eva WC, van den Bree, Marianne, Emanuel, Beverly S, Vermeesch, Joris R, Warren, Stephen T, Owen, Michael J, Chopra, Pankaj, Cutler, David J, Duncan, Richard, Kotlar, Alex V, Mulle, Jennifer G, Voss, Anna J, Zwick, Michael E, Diacou, Alexander, Golden, Aaron, Guo, Tingwei, Lin, Jhih-Rong, Wang, Tao, Zhang, Zhengdong, Zhao, Yingjie, Marshall, Christian, Merico, Daniele, Jin, Andrea, Lilley, Brenna, Salmons, Harold I, Tran, Oanh, Holmans, Peter, Pardinas, Antonio, Walters, James TR, Demaerel, Wolfram, Boot, Erik, Butcher, Nancy J, Costain, Gregory A, Lowther, Chelsea, Evers, Rens, van Amelsvoort, Therese AMJ, van Duin, Esther, Vingerhoets, Claudia, Breckpot, Jeroen, Devriendt, Koen, Vergaelen, Elfi, Vogels, Annick, Crowley, T Blaine, McGinn, Daniel E, Moss, Edward M, Sharkus, Robert J, Unolt, Marta, Zackai, Elaine H, Calkins, Monica E, Gallagher, Robert S, Gur, Ruben C, Tang, Sunny X, Fritsch, Rosemarie, Ornstein, Claudia, Repetto, Gabriela M, Breetvelt, Elemi, Duijff, Sasja N, Fiksinski, Ania, Moss, Hayley, Niarchou, Maria, Murphy, Kieran C, Prasad, Sarah E, Daly, Eileen M, Gudbrandsen, Maria, Murphy, Clodagh M, Murphy, Declan G, Buzzanca, Antonio, Fabio, Fabio Di, Digilio, Maria C, Pontillo, Maria, Marino, Bruno, Vicari, Stefano, Coleman, Karlene, Cubells, Joseph F, Ousley, Opal Y, Carmel, Miri, Gothelf, Doron, Mekori-Domachevsky, Ehud, Michaelovsky, Elena, Weinberger, Ronnie, Weizman, Abraham, Kushan, Leila, Jalbrzikowski, Maria, Armando, Marco, Eliez, Stéphan, Sandini, Corrado, and Schneider, Maude

Subjects
International 22q11.2DS Brain and Behavior Consortium, Prevention, Serious Mental Illness, Genetics, Human Genome, Schizophrenia, Neurosciences, Mental Health, Clinical Research, Pediatric, Brain Disorders, 2.1 Biological and endogenous factors, Mental health, Psychiatry, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences
Abstract

Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.

Published
2021

4. HLA-DP on Epithelial Cells Enables Tissue Damage by NKp44+ Natural Killer Cells in Ulcerative Colitis

Author

Akar, Alaa, Flemming, Cornelius, Felix, Flomm, Flosbach, Markus, Jäger, Julia, Jeromin, Niklas, Jung, Johannes, Ohms, Mareike, Reinshagen, Konrad, Rische, Johann, Sagebiel, Adrian, Sandfort, Deborah, Steinert, Fenja, Tomuschat, Christian, Wesche, Jasmin, Shifteh Abedian, Abraham, Clara, Achkar, Jean-Paul, Ahmad, Tariq, Alberts, Rudi, Alizadeh, Behrooz, Amininejad, Leila, Ananthakrishnan, Ashwin N., Andersen, Vibeke, Anderson, Carl A., Andrews, Jane M., Annese, Vito, Aumais, Guy, Baidoo, Leonard, Baldassano, Robert N., Bampton, Peter A., Barclay, Murray, Barrett, Jeffrey C., Bethge, Johannes, Bewshea, Claire, Bis, Joshua C., Bitton, Alain, BK, Thelma, Boucher, Gabrielle, Brain, Oliver, Brand, Stephan, Brant, Steven R., Cheon, Jae Hee, Chew, Angela, Cho, Judy H., Cleynen, Isabelle, Cohain, Ariella, Cooney, Rachel, Croft, Anthony, Daly, Mark J., D'Amato, Mauro, Danese, Silvio, Daryani, Naser Ebrahim, Datta, Lisa Wu, Degenhardt, Frauke, Denapiene, Goda, Denson, Lee A., Devaney, Kathy L., Dewit, Olivier, D'Inca, Renata, Drummond, Hazel E., Dubinsky, Marla, Duerr, Richard H., Edwards, Cathryn, Ellinghaus, David, Ellul, Pierre, Esaki, Motohiro, Essers, Jonah, Ferguson, Lynnette R., Festen, Eleonora A., Fleshner, Philip, Florin, Tim, Franchimont, Denis, Franke, Andre, Fuyuno, Yuta, Gearry, Richard, Georges, Michel, Gieger, Christian, Glas, Jürgen, Goyette, Philippe, Green, Todd, Griffiths, Anne M., Guthery, Stephen L., Hakonarson, Hakon, Halfvarson, Jonas, Hanigan, Katherine, Haritunians, Talin, Hart, Ailsa, Hawkey, Chris, Hayward, Nicholas K., Hedl, Matija, Henderson, Paul, Hold, Georgina L., Hong, Myhunghee, Hu, Xinli, Huang, Hailiang, Hugot, Jean-Pierre, Hui, Ken Y., Imielinski, Marcin, Jazayeri, Omid, Jonaitis, Laimas, Jostins, Luke, Juyal, Garima, Chandra Juyal, Ramesh, Kalla, Rahul, Karlsen, Tom H., Kennedy, Nicholas A., Khan, Mohammed Azam, Kim, Won Ho, Kitazono, Takanari, Kiudelis, Gediminas, Kubo, Michiaki, Kugathasan, Subra, Kupcinskas, Limas, Lamb, Christopher A., de Lange, Katrina M., Latiano, Anna, Laukens, Debby, Lawrance, Ian C., Lee, James C., Lees, Charlie W., Leja, Marcis, Lewis, Nina, Van Limbergen, Johan, Lionetti, Paolo, Liu, Jimmy Z., Louis, Edouard, Luo, Yang, Mahy, Gillian, Malekzadeh, Masoud Mohammad, Malekzadeh, Reza, Mansfield, John, Marriott, Suzie, Massey, Dunecan, Mathew, Christopher G., Matsui, Toshiyuki, McGovern, Dermot P.B., van der Meulen, Andrea, Midha, Vandana, Milgrom, Raquel, Mirzaei, Samaneh, Mitrovic, Mitja, Montgomery, Grant W., Mowat, Craig, Müller, Christoph, Newman, William G., Ng, Aylwin, Ng, Siew C., Evelyn Ng, Sok Meng, Nikolaus, Susanna, Ning, Kaida, Nöthen, Markus, Oikonomou, Ioannis, Okou, David, Orchard, Timothy R., Palmieri, Orazio, Parkes, Miles, Phillips, Anne, Ponsioen, Cyriel Y., Potocnik, Urõs, Poustchi, Hossein, Prescott, Natalie J., Proctor, Deborah D., Radford-Smith, Graham, Rahier, Jean- Francois, Regueiro, Miguel, Reinisch, Walter, Rieder, Florian, Rioux, John D., Roberts, Rebecca, Rogler, Gerhard, Russell, Richard K., Sanderson, Jeremy D., Sans, Miquel, Satsangi, Jack, Schadt, Eric E., Scharl, Michael, Schembri, John, Schreiber, Stefan, Schumm, L. Philip, Scott, Regan, Seielstad, Mark, Shah, Tejas, Sharma, Yashoda, Silverberg, Mark S., Simmons, Alison, Simms, Lisa A., Singh, Abhey, Skieceviciene, Jurgita, van Sommeren, Suzanne, Song, Kyuyoung, Sood, Ajit, Spain, Sarah L., Steinhart, A. Hillary, Stempak, Joanne M., Stronati, Laura, Sung, Joseph J.Y., Targan, Stephan R., Taylor, Kirstin M., Theatre, Emilie, Torkvist, Leif, Torres, Esther A., Tremelling, Mark, Uhlig, Holm H., Umeno, Junji, Vahedi, Homayon, Vasiliauskas, Eric, Velde, Anje ter, Ventham, Nicholas T., Vermeire, Severine, Verspaget, Hein W., De Vos, Martine, Walters, Thomas, Wang, Kai, Wang, Ming-Hsi, Weersma, Rinse K., Wei, Zhi, Whiteman, David, Wijmenga, Cisca, Wilson, David C., Winkelmann, Juliane, Wong, Sunny H., Xavier, Ramnik J., Yamazaki, Keiko, Yang, Suk-Kyun, Ye, Byong Duk, Zeissig, Sebastian, Zhang, Bin, Zhang, Clarence K., Zhang, Hu, Zhang, Wei, Zhao, Hongyu, Zhao, Zhen Z., Baumdick, Martin E., Niehrs, Annika, Schwerk, Maria, Hinrichs, Ole, Jordan-Paiz, Ana, Padoan, Benedetta, Wegner, Lucy H.M., Schloer, Sebastian, Zecher, Britta F., Malsy, Jakob, Joshi, Vinita R., Illig, Christin, Schröder-Schwarz, Jennifer, Möller, Kimberly J., Martin, Maureen P., Yuki, Yuko, Ozawa, Mikki, Sauter, Jürgen, Schmidt, Alexander H., Perez, Daniel, Giannou, Anastasios D., Carrington, Mary, Davis, Randall S., Schumacher, Udo, Sauter, Guido, Huber, Samuel, Puelles, Victor G., Melling, Nathaniel, Altfeld, Marcus, and Bunders, Madeleine J.

Published
2023
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5. Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

Author

Zhao, Yingjie, Diacou, Alexander, Johnston, H Richard, Musfee, Fadi I, McDonald-McGinn, Donna M, McGinn, Daniel, Crowley, T Blaine, Repetto, Gabriela M, Swillen, Ann, Breckpot, Jeroen, Vermeesch, Joris R, Kates, Wendy R, Digilio, M Cristina, Unolt, Marta, Marino, Bruno, Pontillo, Maria, Armando, Marco, Di Fabio, Fabio, Vicari, Stefano, van den Bree, Marianne, Moss, Hayley, Owen, Michael J, Murphy, Kieran C, Murphy, Clodagh M, Murphy, Declan, Schoch, Kelly, Shashi, Vandana, Tassone, Flora, Simon, Tony J, Shprintzen, Robert J, Campbell, Linda, Philip, Nicole, Heine-Suñer, Damian, García-Miñaúr, Sixto, Fernández, Luis, Consortium, International 22q11 2 Brain and Behavior, Antonarakis, Stylianos E, Biondi, Massimo, Boot, Erik, Breetvelt, Elemi, Busa, Tiffany, Butcher, Nancy, Buzzanca, Antonino, Carmel, Miri, Cleynen, Isabelle, Cutler, David, Dallapiccola, Bruno, de la Fuente Sanches, María Angeles, Epstein, Michael P, Evers, Rens, Fernandez, Luis, Fritsch, Rosemarie, Algas, Fernando García, Guo, Tingwei, Gur, Raquel, Hestand, Matthew S, Heung, Tracy, Hooper, Stephen, Jin, Andrea, Kushan-Wells, Leila, Laorden-Nieto, Alejandra Teresa, Lattanzi, Guido, Marshall, Christian, McCabe, Kathryn, Michaelovsky, Elena, Ornstein, Claudia, Silversides, Candice, Tran, Oanh, van Duin, Esther DA, Vergaelen, Elfi, Warren, Steve T, Weinberger, Ronnie, Weizman, Abraham, Zhang, Zhengdong, Zwick, Michael, Bearden, Carrie E, Vingerhoets, Claudia, van Amelsvoort, Therese, Eliez, Stephan, Schneider, Maude, Vorstman, Jacob AS, Gothelf, Doron, Zackai, Elaine, Agopian, AJ, Gur, Raquel E, Bassett, Anne S, Emanuel, Beverly S, Goldmuntz, Elizabeth, Mitchell, Laura E, Wang, Tao, and Morrow, Bernice E

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Epidemiology, Health Sciences, Clinical Research, Human Genome, Heart Disease, Cardiovascular, Pediatric, Aetiology, 2.1 Biological and endogenous factors, Case-Control Studies, Chromosome Deletion, Chromosomes, Human, Pair 22, Cohort Studies, Female, Genome-Wide Association Study, Heart Defects, Congenital, Humans, Linkage Disequilibrium, Male, Phenotype, Polymorphism, Single Nucleotide, Proto-Oncogene Mas, Segmental Duplications, Genomic, International 22q11.2 Brain and Behavior Consortium, CRKL, DiGeorge syndrome, TBX1, chromosome 22q11.2 deletion syndrome, complex trait, congenital heart disease, conotruncal heart defects, copy number variation, genetic association, genetic modifier, haploinsufficiency, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

The 22q11.2 deletion syndrome (22q11.2DS) results from non-allelic homologous recombination between low-copy repeats termed LCR22. About 60%-70% of individuals with the typical 3 megabase (Mb) deletion from LCR22A-D have congenital heart disease, mostly of the conotruncal type (CTD), whereas others have normal cardiac anatomy. In this study, we tested whether variants in the hemizygous LCR22A-D region are associated with risk for CTDs on the basis of the sequence of the 22q11.2 region from 1,053 22q11.2DS individuals. We found a significant association (FDR p < 0.05) of the CTD subset with 62 common variants in a single linkage disequilibrium (LD) block in a 350 kb interval harboring CRKL. A total of 45 of the 62 variants were associated with increased risk for CTDs (odds ratio [OR) ranges: 1.64-4.75). Associations of four variants were replicated in a meta-analysis of three genome-wide association studies of CTDs in affected individuals without 22q11.2DS. One of the replicated variants, rs178252, is located in an open chromatin region and resides in the double-elite enhancer, GH22J020947, that is predicted to regulate CRKL (CRK-like proto-oncogene, cytoplasmic adaptor) expression. Approximately 23% of patients with nested LCR22C-D deletions have CTDs, and inactivation of Crkl in mice causes CTDs, thus implicating this gene as a modifier. Rs178252 and rs6004160 are expression quantitative trait loci (eQTLs) of CRKL. Furthermore, set-based tests identified an enhancer that is predicted to target CRKL and is significantly associated with CTD risk (GH22J020946, sequence kernal association test (SKAT) p = 7.21 × 10-5) in the 22q11.2DS cohort. These findings suggest that variance in CTD penetrance in the 22q11.2DS population can be explained in part by variants affecting CRKL expression.

Published
2020

6. Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

Author

Sazonovs, Aleksejs, Stevens, Christine R., Venkataraman, Guhan R., Yuan, Kai, Avila, Brandon, Abreu, Maria T., Ahmad, Tariq, Allez, Matthieu, Ananthakrishnan, Ashwin N., Atzmon, Gil, Baras, Aris, Barrett, Jeffrey C., Barzilai, Nir, Beaugerie, Laurent, Beecham, Ashley, Bernstein, Charles N., Bitton, Alain, Bokemeyer, Bernd, Chan, Andrew, Chung, Daniel, Cleynen, Isabelle, Cosnes, Jacques, Cutler, David J., Daly, Allan, Damas, Oriana M., Datta, Lisa W., Dawany, Noor, Devoto, Marcella, Dodge, Sheila, Ellinghaus, Eva, Fachal, Laura, Farkkila, Martti, Faubion, William, Ferreira, Manuel, Franchimont, Denis, Gabriel, Stacey B., Ge, Tian, Georges, Michel, Gettler, Kyle, Giri, Mamta, Glaser, Benjamin, Goerg, Siegfried, Goyette, Philippe, Graham, Daniel, Hämäläinen, Eija, Haritunians, Talin, Heap, Graham A., Hiltunen, Mikko, Hoeppner, Marc, Horowitz, Julie E., Irving, Peter, Iyer, Vivek, Jalas, Chaim, Kelsen, Judith, Khalili, Hamed, Kirschner, Barbara S., Kontula, Kimmo, Koskela, Jukka T., Kugathasan, Subra, Kupcinskas, Juozas, Lamb, Christopher A., Laudes, Matthias, Lévesque, Chloé, Levine, Adam P., Lewis, James D., Liefferinckx, Claire, Loescher, Britt-Sabina, Louis, Edouard, Mansfield, John, May, Sandra, McCauley, Jacob L., Mengesha, Emebet, Mni, Myriam, Moayyedi, Paul, Moran, Christopher J., Newberry, Rodney D., O’Charoen, Sirimon, Okou, David T., Oldenburg, Bas, Ostrer, Harry, Palotie, Aarno, Paquette, Jean, Pekow, Joel, Peter, Inga, Pierik, Marieke J., Ponsioen, Cyriel Y., Pontikos, Nikolas, Prescott, Natalie, Pulver, Ann E., Rahmouni, Souad, Rice, Daniel L., Saavalainen, Päivi, Sands, Bruce, Sartor, R. Balfour, Schiff, Elena R., Schreiber, Stefan, Schumm, L. Philip, Segal, Anthony W., Seksik, Philippe, Shawky, Rasha, Sheikh, Shehzad Z., Silverberg, Mark S., Simmons, Alison, Skeiceviciene, Jurgita, Sokol, Harry, Solomonson, Matthew, Somineni, Hari, Sun, Dylan, Targan, Stephan, Turner, Dan, Uhlig, Holm H., van der Meulen, Andrea E., Vermeire, Séverine, Verstockt, Sare, Voskuil, Michiel D., Winter, Harland S., Young, Justine, Duerr, Richard H., Franke, Andre, Brant, Steven R., Cho, Judy, Weersma, Rinse K., Parkes, Miles, Xavier, Ramnik J., Rivas, Manuel A., Rioux, John D., McGovern, Dermot P. B., Huang, Hailiang, Anderson, Carl A., and Daly, Mark J.

Published
2022
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8. Plasma pTau181 and pTau217 predict asymptomatic amyloid accumulation equally well as amyloid-PET

Author

De Meyer, Steffi, primary, Schaeverbeke, Jolien M, additional, Luckett, Emma S, additional, Reinartz, Mariska, additional, Blujdea, Elena R, additional, Cleynen, Isabelle, additional, Dupont, Patrick, additional, Van Laere, Koen, additional, Vanbrabant, Jeroen, additional, Stoops, Erik, additional, Vanmechelen, Eugeen, additional, di Molfetta, Guglielmo, additional, Zetterberg, Henrik, additional, Ashton, Nicholas J, additional, Teunissen, Charlotte E, additional, Poesen, Koen, additional, and Vandenberghe, Rik, additional

Published
2024
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11. Clinical and genetic determinants of vitamin D receptor expression in cutaneous melanoma patients

Author

De Smedt, Julie, primary, Aura, Claudia, additional, Van Kelst, Sofie, additional, Janssen, Laudine, additional, Marasigan, Vivien, additional, Boecxstaens, Veerle, additional, Stas, Marguerite, additional, Bogaerts, Kris, additional, Belmans, Ann, additional, Cleynen, Isabelle, additional, Vanderschueren, Dirk, additional, Vandenberghe, Katleen, additional, Bechter, Oliver, additional, Nikkels, Arjen, additional, Strobbe, Tinne, additional, Emri, Gabriella, additional, Lambrechts, Dieter, additional, and Garmyn, Marjan, additional

Published
2024
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14. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis.

Author

Liu, Jimmy Z, Hov, Johannes Roksund, Folseraas, Trine, Ellinghaus, Eva, Rushbrook, Simon M, Doncheva, Nadezhda T, Andreassen, Ole A, Weersma, Rinse K, Weismüller, Tobias J, Eksteen, Bertus, Invernizzi, Pietro, Hirschfield, Gideon M, Gotthardt, Daniel Nils, Pares, Albert, Ellinghaus, David, Shah, Tejas, Juran, Brian D, Milkiewicz, Piotr, Rust, Christian, Schramm, Christoph, Müller, Tobias, Srivastava, Brijesh, Dalekos, Georgios, Nöthen, Markus M, Herms, Stefan, Winkelmann, Juliane, Mitrovic, Mitja, Braun, Felix, Ponsioen, Cyriel Y, Croucher, Peter JP, Sterneck, Martina, Teufel, Andreas, Mason, Andrew L, Saarela, Janna, Leppa, Virpi, Dorfman, Ruslan, Alvaro, Domenico, Floreani, Annarosa, Onengut-Gumuscu, Suna, Rich, Stephen S, Thompson, Wesley K, Schork, Andrew J, Næss, Sigrid, Thomsen, Ingo, Mayr, Gabriele, König, Inke R, Hveem, Kristian, Cleynen, Isabelle, Gutierrez-Achury, Javier, Ricaño-Ponce, Isis, van Heel, David, Björnsson, Einar, Sandford, Richard N, Durie, Peter R, Melum, Espen, Vatn, Morten H, Silverberg, Mark S, Duerr, Richard H, Padyukov, Leonid, Brand, Stephan, Sans, Miquel, Annese, Vito, Achkar, Jean-Paul, Boberg, Kirsten Muri, Marschall, Hanns-Ulrich, Chazouillères, Olivier, Bowlus, Christopher L, Wijmenga, Cisca, Schrumpf, Erik, Vermeire, Severine, Albrecht, Mario, UK-PSCSC Consortium, Rioux, John D, Alexander, Graeme, Bergquist, Annika, Cho, Judy, Schreiber, Stefan, Manns, Michael P, Färkkilä, Martti, Dale, Anders M, Chapman, Roger W, Lazaridis, Konstantinos N, International PSC Study Group, Franke, Andre, Anderson, Carl A, Karlsen, Tom H, and International IBD Genetics Consortium

Subjects
UK-PSCSC Consortium, International PSC Study Group, International IBD Genetics Consortium, Humans, Cholangitis, Sclerosing, Oligonucleotide Array Sequence Analysis, Risk Factors, Case-Control Studies, Gene Frequency, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic Loci, Genetic Pleiotropy, Genotyping Techniques, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

Primary sclerosing cholangitis (PSC) is a severe liver disease of unknown etiology leading to fibrotic destruction of the bile ducts and ultimately to the need for liver transplantation. We compared 3,789 PSC cases of European ancestry to 25,079 population controls across 130,422 SNPs genotyped using the Immunochip. We identified 12 genome-wide significant associations outside the human leukocyte antigen (HLA) complex, 9 of which were new, increasing the number of known PSC risk loci to 16. Despite comorbidity with inflammatory bowel disease (IBD) in 72% of the cases, 6 of the 12 loci showed significantly stronger association with PSC than with IBD, suggesting overlapping yet distinct genetic architectures for these two diseases. We incorporated association statistics from 7 diseases clinically occurring with PSC in the analysis and found suggestive evidence for 33 additional pleiotropic PSC risk loci. Together with network analyses, these findings add to the genetic risk map of PSC and expand on the relationship between PSC and other immune-mediated diseases.

Published
2013

16. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Author

Jostins, Luke, Ripke, Stephan, Weersma, Rinse K, Duerr, Richard H, McGovern, Dermot P, Hui, Ken Y, Lee, James C, Philip Schumm, L, Sharma, Yashoda, Anderson, Carl A, Essers, Jonah, Mitrovic, Mitja, Ning, Kaida, Cleynen, Isabelle, Theatre, Emilie, Spain, Sarah L, Raychaudhuri, Soumya, Goyette, Philippe, Wei, Zhi, Abraham, Clara, Achkar, Jean-Paul, Ahmad, Tariq, Amininejad, Leila, Ananthakrishnan, Ashwin N, Andersen, Vibeke, Andrews, Jane M, Baidoo, Leonard, Balschun, Tobias, Bampton, Peter A, Bitton, Alain, Boucher, Gabrielle, Brand, Stephan, Büning, Carsten, Cohain, Ariella, Cichon, Sven, D’Amato, Mauro, De Jong, Dirk, Devaney, Kathy L, Dubinsky, Marla, Edwards, Cathryn, Ellinghaus, David, Ferguson, Lynnette R, Franchimont, Denis, Fransen, Karin, Gearry, Richard, Georges, Michel, Gieger, Christian, Glas, Jürgen, Haritunians, Talin, Hart, Ailsa, Hawkey, Chris, Hedl, Matija, Hu, Xinli, Karlsen, Tom H, Kupcinskas, Limas, Kugathasan, Subra, Latiano, Anna, Laukens, Debby, Lawrance, Ian C, Lees, Charlie W, Louis, Edouard, Mahy, Gillian, Mansfield, John, Morgan, Angharad R, Mowat, Craig, Newman, William, Palmieri, Orazio, Ponsioen, Cyriel Y, Potocnik, Uros, Prescott, Natalie J, Regueiro, Miguel, Rotter, Jerome I, Russell, Richard K, Sanderson, Jeremy D, Sans, Miquel, Satsangi, Jack, Schreiber, Stefan, Simms, Lisa A, Sventoraityte, Jurgita, Targan, Stephan R, Taylor, Kent D, Tremelling, Mark, Verspaget, Hein W, De Vos, Martine, Wijmenga, Cisca, Wilson, David C, Winkelmann, Juliane, Xavier, Ramnik J, Zeissig, Sebastian, Zhang, Bin, Zhang, Clarence K, Zhao, Hongyu, Silverberg, Mark S, Annese, Vito, Hakonarson, Hakon, Brant, Steven R, Radford-Smith, Graham, Mathew, Christopher G, Rioux, John D, and Schadt, Eric E

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Digestive Diseases, Human Genome, Inflammatory Bowel Disease, Biotechnology, Autoimmune Disease, Crohn's Disease, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Oral and gastrointestinal, Colitis, Ulcerative, Crohn Disease, Genetic Predisposition to Disease, Genome, Human, Genome-Wide Association Study, Haplotypes, Host-Pathogen Interactions, Humans, Inflammatory Bowel Diseases, Mycobacterium, Mycobacterium Infections, Mycobacterium tuberculosis, Phenotype, Polymorphism, Single Nucleotide, Reproducibility of Results, International IBD Genetics Consortium, General Science & Technology
Abstract

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Published
2012

18. Genetic Variants of the MGAT5 Gene Are Functionally Implicated in the Modulation of T Cells Glycosylation and Plasma IgG Glycome Composition in Ulcerative Colitis

Author

Pereira, Márcia S., Durães, Cecília, Catarino, Telmo A., Costa, José L., Cleynen, Isabelle, Novokmet, Mislav, Krištić, Jasminka, Štambuk, Jerko, Conceição-Neto, Nádia, Machado, José C., Marcos-Pinto, Ricardo, Magro, Fernando, Vermeire, Séverine, Lauc, Gordan, Lago, Paula, and Pinho, Salomé S.

Published
2020
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19. Genomic analyses of hair from Ludwig van Beethoven

Author

Begg, Tristan James Alexander, primary, Schmidt, Axel, additional, Kocher, Arthur, additional, Larmuseau, Maarten H.D., additional, Runfeldt, Göran, additional, Maier, Paul Andrew, additional, Wilson, John D., additional, Barquera, Rodrigo, additional, Maj, Carlo, additional, Szolek, András, additional, Sager, Michael, additional, Clayton, Stephen, additional, Peltzer, Alexander, additional, Hui, Ruoyun, additional, Ronge, Julia, additional, Reiter, Ella, additional, Freund, Cäcilia, additional, Burri, Marta, additional, Aron, Franziska, additional, Tiliakou, Anthi, additional, Osborn, Joanna, additional, Behar, Doron M., additional, Boecker, Malte, additional, Brandt, Guido, additional, Cleynen, Isabelle, additional, Strassburg, Christian, additional, Prüfer, Kay, additional, Kühnert, Denise, additional, Meredith, William Rhea, additional, Nöthen, Markus M., additional, Attenborough, Robert David, additional, Kivisild, Toomas, additional, and Krause, Johannes, additional

Published
2023
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20. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study

Author

Cleynen, Isabelle, Boucher, Gabrielle, Jostins, Luke, Schumm, L Philip, Zeissig, Sebastian, Ahmad, Tariq, Andersen, Vibeke, Andrews, Jane M, Annese, Vito, Brand, Stephan, Brant, Steven R, Cho, Judy H, Daly, Mark J, Dubinsky, Marla, Duerr, Richard H, Ferguson, Lynnette R, Franke, Andre, Gearry, Richard B, Goyette, Philippe, Hakonarson, Hakon, Halfvarson, Jonas, Hov, Johannes R, Huang, Hailang, Kennedy, Nicholas A, Kupcinskas, Limas, Lawrance, Ian C, Lee, James C, Satsangi, Jack, Schreiber, Stephan, Théâtre, Emilie, van der Meulen-de Jong, Andrea E, Weersma, Rinse K, Wilson, David C, Parkes, Miles, Vermeire, Severine, Rioux, John D, Mansfield, John, Silverberg, Mark S, Radford-Smith, Graham, McGovern, Dermot P B, Barrett, Jeffrey C, and Lees, Charlie W

Published
2016
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23. Additional file 1 of Longitudinal APOE4- and amyloid-dependent changes in the blood transcriptome in cognitively intact older adults

Author

Luckett, Emma S., Zielonka, Magdalena, Kordjani, Amine, Schaeverbeke, Jolien, Adamczuk, Katarzyna, De Meyer, Steffi, Van Laere, Koen, Dupont, Patrick, Cleynen, Isabelle, and Vandenberghe, Rik

Abstract

Additional file 1: Supplementary Figure 1. Differentially expressed genes at follow-up compared to baseline in amyloid non-accumulators. Data points are based coloured on significance: grey = non-significant, blue = non-significant but with FDR p-value < 0.05, red = significant with FDR p-value < 0.05 and log2FoldChange ± 1. N = 53. Pval on y-axis represents the uncorrected p-value < 0.05 threshold for visualisation. Supplementary Figure 2. Detection of modules using baseline expression data. (A) Scale independence and (B) mean connectivity used to derive the soft power threshold. (C) Clustering of module eigengenes, where similar clusters were merged using a cutHeight =0.25 (red line). (D) Cluster dendrogram of co-expression modules shown, both with the 28 dynamic modules (top row) and final merged 17 modules (bottom row). Supplementary Figure 3. Top 20 general cell types derived from cell-specific enrichment of the highly interconnected genes from the baseline blue WGCNA module. The genes are displayed from left to right ranked by the most significant human tissue-cell-type. The red dotted line is the Bonferronicorrected significance (p = 3.69 × 10 × 10−5) by 1355 tissue-cell types. The grey line is the nominal significance (p = 1 × 10 × 10−3). The Y-axis indicates the tissue-cell-type specificity (–log10 (combined p value)) for each tissue-cell-type from the cell-specific enrichment. Supplementary Figure 4. Detection of modules using follow-up expression data. (A) Scale independence and (B) mean connectivity used to derive the soft power threshold. (C) Clustering of module eigengenes, where similar clusters were merged using a cutHeight =0.25 (red line). (D) Cluster dendrogram of co-expression modules shown, both with the 32 dynamic modules (top row) and final merged 35 modules (bottom row). Supplementary Figure 5. Top 20 general cell types derived from cell-specific enrichment of the highly interconnected genes from the follow-up blue WGCNA module. The genes are displayed from left to right ranked by the most significant human tissue-cell-type. The red dotted line is the Bonferronicorrected significance (p = 3.69 × 10 × 10−5) by 1355 tissue-cell types. The grey line is the nominal significance (p = 1 × 10 × 10−3). The Y-axis indicates the tissue-cell-type specificity (–log10 (combined p value)) for each tissue-cell-type from the cell-specific enrichment. Supplementary Figure 6. Top 20 general cell types derived from cell-specific enrichment of the highly interconnected genes from the follow-up turquoise WCGNA module. The genes are displayed from left to right ranked by the most significant human tissue-cell-type. The red dotted line is the Bonferroni-corrected significance (p = 3.69 × 10 × 10−5) by 1355 tissue-cell types. The grey line is the nominal significance (p = 1 × 10 × 10−3). The Y-axis indicates the tissue-cell-type specificity (–log10 (combined p-value)) for each tissue-cell-type from the cell-specific enrichment. Supplementary Figure 7. Detection of modules using follow-up expression data. (A) Scale independence and mean connectivity used to derive the soft power threshold. (B) Cluster dendrogram of consensus modules.

Published
2023
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24. Additional file 2 of Longitudinal APOE4- and amyloid-dependent changes in the blood transcriptome in cognitively intact older adults

Author

Luckett, Emma S., Zielonka, Magdalena, Kordjani, Amine, Schaeverbeke, Jolien, Adamczuk, Katarzyna, De Meyer, Steffi, Van Laere, Koen, Dupont, Patrick, Cleynen, Isabelle, and Vandenberghe, Rik

Abstract

Additional file 2: Supplementary Table 1. APOE4 follow-up versus baseline significant differentially expressed genes. Supplementary Table 2. APOE4 non-carriers follow-up versus baseline significant differentially expressed genes. Supplementary Table 3. Cell deconvolution contributions generated using CIBERSORT. Supplementary Table 4. Amyloid non-accumulators follow-up versus baseline significant differentially expressed genes. Supplementary Table 5. Follow-up versus baseline significant differentially expressed genes in amyloid negative-positive and amyloid positive-positive individuals. Supplementary Table 6. Follow-up versus baseline significant differentially expressed genes in amyloid negative individuals. Supplementary Table 7. Direct association scores of significant differentially expressed genes at follow-up versus baseline in APOE4 carriers. Supplementary Table 8. Direct association scores of significant differentially expressed genes at follow-up versus baseline in amyloid negativepositive and amyloid positive-positive individuals. Supplementary Table 9. APOE4 carriers gene set enrichment analysis gene ontology upregulated. Supplementary Table 10. APOE4 non-carriers gene set enrichment analysis gene ontology upregulated. Supplementary Table 11. APOE4 carriers gene set enrichment analysis gene ontology downregulated. Supplementary Table 12. APOE4 non-carriers gene set enrichment analysis gene ontology downregulated. Supplementary Table 13. Amyloid non-accumulators gene set enrichment analysis gene ontology upregulated. Supplementary Table 14. Amyloid non-accumulators gene set enrichment analysis gene ontology downregulated. Supplementary Table 15. Amyloid negative-positive/positive-positive gene set enrichment analysis gene ontology upregulated. Supplementary Table 16. Amyloid negative-negative gene set enrichment analysis gene ontology upregulated. Supplementary Table 17. Amyloid negative-positive/positive-positive gene set enrichment analysis gene ontology downregulated. Supplementary Table 18. Amyloid negative-negative gene set enrichment analysis gene ontology downregulated. Supplementary Table 19. Baseline Blue module enrichment. Supplementary Table 20. Follow-up Blue module enrichment. Supplementary Table 21. Follow-up Turquoise module enrichment.

Published
2023
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33. Association of Plasma p-tau181 and p-tau231 Concentrations with Cognitive Decline in Patients with Probable Dementia with Lewy Bodies

Author

Gonzalez, Maria C., Ashton, Nicholas J., Gomes, Bárbara Fernandes, Tovar-Rios, Diego Alejandro, Blanc, Frédéric, Karikari, Thomas K., Mollenhauer, Brit, Pilotto, Andrea, Lemstra, Afina W., Paquet, Claire, Abdelnour, Carla, Kramberger, Milica G., Bonanni, Laura, Vandenberghe, Rik, Hye, Abdul, Blennow, Kaj, Zetterberg, Henrik, Aarsland, Dag, Carrarini, Claudia, Russo, Mirella, Vrillon, Agathe, Cognat, Emmanuel, Dumurgier, Julien, Hourregue, Claire, Gaubert, Sinead, Porché, Maximilien, Lilamand, Matthieu, Teunissen, Charlotte E., Bolsewig, Katharina, Anthony, Pierre, Cretin, Benjamin, Demunyck, Catherine, Martin, Catherine, Muller, Candice, Philippi, Nathalie, Ravier, Alix, Botzung, Anne, Albasser, Timothée, Epp-Ehrhard, Emmanuelle, Jung, Guillaume, Merignac, Jeanne, Monjoin, Laetitia, Poesen, Koen, Cleynen, Isabelle, Boada, Mercè, Orellana, Adela, Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie (ICube), École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES)-Université de Strasbourg (UNISTRA)-Institut National des Sciences Appliquées - Strasbourg (INSA Strasbourg), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Les Hôpitaux Universitaires de Strasbourg (HUS)-Centre National de la Recherche Scientifique (CNRS)-Matériaux et Nanosciences Grand-Est (MNGE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Neuropsychologie Cognitive et Physiopathologie de la Schizophrénie (NCPS), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Civil de Strasbourg, Neurology, and Amsterdam Neuroscience - Neurodegeneration

Subjects
Lewy Body Disease, Male, medicine.medical_specialty, tau Proteins, Disease, behavioral disciplines and activities, 03 medical and health sciences, 0302 clinical medicine, Cerebrospinal fluid, Internal medicine, mental disorders, medicine, Humans, Cognitive Dysfunction, Cognitive decline, Phosphorylation, 030304 developmental biology, Aged, 0303 health sciences, Mini–Mental State Examination, medicine.diagnostic_test, business.industry, Dementia with Lewy bodies, Correction, medicine.disease, 3. Good health, Cohort, Biomarker (medicine), Female, Lewy Bodies, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neurology (clinical), Alzheimer's disease, business, 030217 neurology & neurosurgery
Abstract

Importance: Plasma phosphorylated tau (p-tau) has proven to be an accurate biomarker for Alzheimer disease (AD) pathologic characteristics, offering a less expensive and less invasive alternative to cerebrospinal fluid (CSF) and positron emission tomography biomarkers for amyloid-β and tau. Alzheimer disease comorbid pathologic characteristics are common and are associated with more rapid cognitive decline in patients with dementia with Lewy bodies (DLB); therefore, it is anticipated that plasma p-tau concentrations may have utility in assessing cognitive impairment in individuals with this disorder. Objective: To measure the concentrations of plasma p-tau (p-tau181 and p-tau231) and evaluate their associations with cognitive decline in individuals with probable DLB. Design, Setting, and Participants: This multicenter longitudinal cohort study included participants from the European-DLB (E-DLB) Consortium cohort enrolled at 10 centers with harmonized diagnostic procedures from January 1, 2002, to December 31, 2020, with up to 5 years of follow-up. A total of 1122 participants with plasma samples were available. Participants with acute delirium or terminal illness and patients with other previous major psychiatric or neurologic disorders were excluded, leaving a cohort of 987 clinically diagnosed participants with probable DLB (n = 371), Parkinson disease (n = 204), AD (n = 207), as well as healthy controls (HCs) (n = 205). Main Outcomes and Measures: The main outcome was plasma p-tau181 and p-tau231 levels measured with in-house single molecule array assays. The Mini-Mental State Examination (MMSE) was used to measure cognition. Results: Among this cohort of 987 patients (512 men [51.9%]; mean [SD] age, 70.0 [8.8] years), patients with DLB did not differ significantly regarding age, sex, or years of education from those in the AD group, but the DLB group was older than the HC group and included more men than the AD and HC groups. Baseline concentrations of plasma p-tau181 and p-tau231 in patients with DLB were significantly higher than those in the HC group but lower than in the AD group and similar to the Parkinson disease group. Higher plasma concentrations of both p-tau markers were found in a subgroup of patients with DLB with abnormal CSF amyloid-β42 levels compared with those with normal levels (difference in the groups in p-tau181, -3.61 pg/mL; 95% CI, -5.43 to -1.79 pg/mL; P =.049; difference in the groups in p-tau231, -2.51 pg/mL; 95% CI, -3.63 to -1.39 pg/mL; P =.02). There was no difference between p-tau181 level and p-tau231 level across confirmed AD pathologic characteristcs based on reduced Aβ42 level in CSF in individuals with DLB. In DLB, a significant association was found between higher plasma p-tau181 and p-tau231 levels and lower MMSE scores at baseline (for p-tau181, -0.092 MMSE points; 95% CI, -0.12 to -0.06 MMSE points; P =.001; for p-tau231, -0.16 MMSE points; 95% CI, -0.21 to -0.12 MMSE points; P

Published
2022

34. Lack of association between bridging integrator 1 (BIN1) rs744373 polymorphism and tau-PET load in cognitively intact older adults

Author

Schaeverbeke, Jolien, Luckett, Emma S, Gabel, Silvy, Reinartz, Mariska, De Meyer, Steffi, Cleynen, Isabelle, Sleegers, Kristel, Van Broeckhoven, Christine, Bormans, Guy, Serdons, Kim, Van Laere, Koen, Dupont, Patrick, Vandenberghe, Rik, and Alzheimer’s Disease Neuroimaging Initiative (ADNI)

Subjects
Psychiatry and Mental health, PET, preclinical Alzheimer's disease, mental disorders, ADNI, [18F]AV1451, Neurology (clinical), Human medicine, BIN1 rs744373, F‐PACK, APOE, MCI
Abstract

INTRODUCTION: The bridging integrator 1(BIN1) rs744373 risk polymorphism has been linked to increased [18F]AV1451 signal in non-demented older adults (ie., mild cognitive impairment [MCI] plus cognitively normal [CN] individuals). However, the association of BIN1 with in vivo tau, amyloid beta (Aβ) burden, and cognitive impairment in the asymptomatic stage of Alzheimer's disease (AD) remains unknown. METHODS: The BIN1 effect on [18F]AV1451 binding was evaluated in 59 cognitively normal (CN) participants (39% apolipoprotein E [APOE ε4]) from the Flemish Prevent AD Cohort KU Leuven (F-PACK), as well as in 66 Alzheimer's Disease Neuroimaging Initiative (ADNI) CN participants, using voxelwise and regional statistics. For comparison, 52 MCI patients from ADNI were also studied. RESULTS: Forty-four percent of F-PACK participants were BIN1 rs744373 risk-allele carriers, 21% showed high amyloid burden, and 8% had elevated [18F]AV1451 binding. In ADNI, 53% and 50% of CNs and MCIs, respectively, carried the BIN1 rs744373 risk-allele. Amyloid positivity was present in 23% of CNs and 51% of MCIs, whereas 2% of CNs and 35% of MCIs showed elevated [18F]AV1451 binding. There was no significant effect of BIN1 on voxelwise or regional [18F]AV1451 in F-PACK or ADNI CNs, or in the pooled CN sample. No significant association between BIN1 and [18F]AV1451 was obtained in ADNI MCI patients. However, in the MCI group, numerically higher [18F]AV1451 binding was observed in the BIN1 risk-allele group compared to the BIN1 normal group in regions corresponding to more progressed tau pathology. DISCUSSION: We could not confirm the association between BIN1 rs744373 risk-allele and elevated [18F]AV1451 signal in CN older adults or MCI. Numerically higher [18F]AV1451 binding was observed, however, in the MCI BIN1 risk-allele group, indicating that the previously reported positive effect may be confounded by group. Therefore, when studying how the BIN1 risk polymorphism influences AD pathogenesis, a distinction should be made between asymptomatic, MCI, and dementia stages of AD. ispartof: ALZHEIMERS & DEMENTIA-TRANSLATIONAL RESEARCH & CLINICAL INTERVENTIONS vol:8 issue:1 ispartof: location:United States status: published

Published
2022

40. Genetic variation in the lymphotoxin-α (LTA)/tumour necrosis factor-α (TNFα) locus as a risk factor for idiopathic achalasia

Author

Wouters, Mira M, Lambrechts, Diether, Becker, Jessica, Cleynen, Isabelle, Tack, Jan, Vigo, Ana G, Ruiz de León, Antonio, Urcelay, Elena, Pérez de la Serna, Julio, Rohof, Wout, Annese, Vito, Latiano, Anna, Palmieri, Orazio, Mattheisen, Manuel, Mueller, Michaela, Lang, Hauke, Fumagalli, Uberto, Laghi, Luigi, Zaninotto, Giovanni, Cuomo, Rosario, Sarnelli, Giovanni, Nöthen, Markus M, Vermeire, Séverine, Knapp, Michael, Gockel, Ines, Schumacher, Johannes, and Boeckxstaens, Guy E

Published
2014
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41. Genetic and microbial factors modulating the ubiquitin proteasome system in inflammatory bowel disease

Author

Cleynen, Isabelle, Vazeille, Emilie, Artieda, Marta, Verspaget, Hein W, Szczypiorska, Magdalena, Bringer, Marie-Agnès, Lakatos, Peter L, Seibold, Frank, Parnell, Kirstie, Weersma, Rinse K, Mahachie John, Jestinah M, Morgan-Walsh, Rebecca, Staelens, Dominiek, Arijs, Ingrid, De Hertogh, Gert, Müller, Stefan, Tordai, Atilla, Hommes, Daniel W, Ahmad, Tariq, Wijmenga, Cisca, Pender, Sylvia, Rutgeerts, Paul, Van Steen, Kristel, Lottaz, Daniel, Vermeire, Severine, and Darfeuille-Michaud, Arlette

Published
2014
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42. Genetic variants in CDC42 and NXPH1 as susceptibility factors for constipation and diarrhoea predominant irritable bowel syndrome

Author

Wouters, Mira M, Lambrechts, Diether, Knapp, Michael, Cleynen, Isabelle, Whorwell, Peter, Agréus, Lars, Dlugosz, Aldona, Schmidt, Peter Thelin, Halfvarson, Jonas, Simrén, Magnus, Ohlsson, Bodil, Karling, Pontus, Van Wanrooy, Sander, Mondelaers, Stéphanie, Vermeire, Severine, Lindberg, Greger, Spiller, Robin, Dukes, George, DʼAmato, Mauro, and Boeckxstaens, Guy

Published
2014
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44. Fine-mapping inflammatory bowel disease loci to single-variant resolution

Author

Huang, Hailiang, Fang, Ming, Jostins, Luke, Umievi Mirkov, Maa, Boucher, Gabrielle, Anderson, Carl A., Andersen, Vibeke, Cleynen, Isabelle, Cortes, Adrian, Crins, Franois, DAmato, Mauro, Deffontaine, Valrie, Dmitrieva, Julia, Docampo, Elisa, Elansary, Mahmoud, Farh, Kyle Kai-How, Franke, Andre, Gori, Ann-Stephan, Goyette, Philippe, Halfvarson, Jonas, Haritunians, Talin, Knight, Jo, Lawrance, Ian C., Lees, Charlie W., Louis, Edouard, Mariman, Rob, Meuwissen, Theo, Mni, Myriam, Momozawa, Yukihide, Parkes, Miles, Spain, Sarah L., Thtre, Emilie, Trynka, Gosia, Satsangi, Jack, van Sommeren, Suzanne, Vermeire, Severine, Xavier, Ramnik J., Weersma, Rinse K., Duerr, Richard H., Mathew, Christopher G., Rioux, John D., McGovern, Dermot P. B., Cho, Judy H., Georges, Michel, Daly, Mark J., and Barrett, Jeffrey C.

Subjects
Inflammatory bowel diseases -- Genetic aspects, Quantitative trait loci -- Health aspects, Genetic variation -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These 45 variants are significantly enriched for protein-coding changes (n=13), direct disruption of transcription-factor binding sites (n=3), and tissue-specific epigenetic marks (n=10), with the last category showing enrichment in specific immune cells among associations stronger in Crohns disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms., Author(s): Hailiang Huang (corresponding author) [1, 2]; Ming Fang [3, 4]; Luke Jostins [5, 6]; Maa Umievi Mirkov [7]; Gabrielle Boucher [8]; Carl A. Anderson [7]; Vibeke Andersen [9, 10]; [...]

Published
2017
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48. Prostaglandin E2 receptor PTGER4-expressing macrophages promote intestinal epithelial barrier regeneration upon inflammation

Author

Na, Yi Rang, primary, Jung, Daun, additional, Stakenborg, Michelle, additional, Jang, Hyeri, additional, Gu, Gyo Jeong, additional, Jeong, Mi Reu, additional, Suh, Soo Youn, additional, Kim, Hak Jae, additional, Kwon, Yoon Hey, additional, Sung, Tae Sik, additional, Ryoo, Seung Bum, additional, Park, Kyu Joo, additional, Im, Jong Pil, additional, Park, Ji Yong, additional, Lee, Yun Sang, additional, Han, Heonjong, additional, Park, Boyoun, additional, Lee, Sungwook, additional, Kim, Daesik, additional, Lee, Ho Su, additional, Cleynen, Isabelle, additional, Matteoli, Gianluca, additional, and Seok, Seung Hyeok, additional

Published
2021
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49. Genetic factors conferring an increased susceptibility to develop Crohnʼs disease also influence disease phenotype: results from the IBDchip European Project

Author

Cleynen, Isabelle, González, Juan R, Figueroa, Carolina, Franke, Andre, McGovern, Dermot, Bortlík, Martin, Crusius, Bart J A, Vecchi, Maurizio, Artieda, Marta, Szczypiorska, Magdalena, Bethge, Johannes, Arteta, David, Ayala, Edgar, Danese, Silvio, van Hogezand, Ruud A, Panés, Julian, Peña, Salvador Amado, Lukas, Milan, Jewell, Derek P, Schreiber, Stefan, Vermeire, Severine, and Sans, Miquel

Published
2013
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